XTA系列晶片2014 – 2015的文獻列表(含Meeting摘要)

Human Transcriptome Array Publications

including meeting abstracts

2014 – 2015

current thru Sep 21, 2015




A phase II and pharmacodynamic study of sunitinib in relapsed/refractory oesophageal and gastro-oesophageal cancers

C Wu, S Mikhail, L Wei, C Timmers, S Tahiri, A Neal, J Walker, S El-Dika, M Blazer, J Rock, D J Clark, X Yang, J L Chen, J Liu, M V Knopp and T Bekaii-Saab

British Journal of Cancer 113, 220-225 (14 July 2015) | doi:10.1038/bjc.2015.197

... Whole-transcriptome profiling was performed using the SensationPlus FFPE kit and Affymetrix HTA 2.0 array.



Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer

Shuo Wei, Shingo Kozono, Lev Kats, Morris Nechama, Wenzong Li, Jlenia Guarnerio, Manli Luo, Mi-Hyeon You, Yandan Yao, Asami Kondo, Hai Hu, Gunes Bozkurt, Nathan J Moerke, Shugeng Cao, Markus Reschke, Chun-Hau Chen, Eduardo M Rego, Francesco Lo-Coco, Lewis C Cantley, Tae Ho Lee, Hao Wu, Yan Zhang, Pier Paolo Pandolfi, Xiao Zhen Zhou & Kun Ping Lu

Nature Medicine, May 2015, 21(5):457-466.

... Microarray expression profiles were collected using Affymetrix Human Transcriptome Array 2.0.



Activity of the Type II JAK2 Inhibitor CHZ868 in B Cell Acute Lymphoblastic Leukemia

Shuo-Chieh Wu, Loretta S. Li, Nadja Kopp, Joan Montero, Bjoern Chapuy, Akinori Yoda, Amanda L. Christie, Huiyun Liu, Alexandra Christodoulou, Diederik van Bodegom, Jordy van der Zwet, Jacob V. Layer, Trevor Tivey, Andrew A. Lane, Jeremy A. Ryan, Samuel Y. Ng, Daniel J. DeAngelo, Richard M. Stone, David Steensma, Martha Wadleigh, Marian Harris, Emeline Mandon, Nicolas Ebel, Rita Andraos, Vincent Romanet, Arno Dölemeyer, Dario Sterker, Michael Zender, Scott J. Rodig, Masato Murakami, Francesco Hofmann, Frank Kuo, Michael J. Eck, Lewis B. Silverman, Stephen E. Sallan, Anthony Letai, Fabienne Baffert, Eric Vangrevelinghe, Thomas Radimerski, Christoph Gaul, David M. Weinstock

Cancer Cell, 13 July 2015, 28(1): 29–41.

... RNA quality and concentration were confirmed by PicoGreen and profiling was performed on an Affymetrix human HTA-2_0 gene chip in the Dana-Farber Microarray Core ...



Adipose-derived Mesenchymal Stem Cells Are Phenotypically Superior for Regeneration in the Setting of Osteonecrosis of the Femoral Head

Cody C. Wyles, Matthew T. Houdek, Ruben J. Crespo-Diaz, German A. Norambuena, Paul G. Stalboerger,  Andre Terzic, Atta Behfar, Rafael J. Sierra

Clinical Orthopaedics and Related Research®, October 2015, 473(10): 3080-3090.

... RNA was isolated from aMSCs and bmMSCs in five patients to assess differentially expressed genetic pathways using the Affymetrix GeneChip® Human Transcriptome Array 2.0 platform.  ...


5-    Meeting abstract

Clinical translation pathway to Precision Medicine in GBM through simulation and repurposing.

Sandeep C. Pingle, Pengfei Jiang, Rajesh Mukthavaram, Natsuko Nomura, Prashant Nair, Ansu Kumar, Neeraj Singh, Taher Abbasi, Shireen Vali and Santosh Kesari

Journal of Clinical Oncology, 20 May 2015, 33(15 Sup):e13041 [ASCO Annual Mtg, May 29-Jun 2, 2015]

... Our predictive simulation-based approach for glioblastoma (GBM) incorporates comprehensive representation of disease pathophysiology. Here, we employ this model to design rational drug combinations for GBM. To create simulation avatars of patient-derived GBM tumors, we used copy number, expression, and mutation data (OncoScan, Human Transcriptome Array - Affymetrix). ...




Combination Therapy with Anti–CTLA-4 and Anti–PD-1 Leads to Distinct Immunologic Changes In Vivo

Rituparna Das, Rakesh Verma, Mario Sznol, Chandra Sekhar Boddupalli, Scott N. Gettinger, Harriet Kluger, Margaret Callahan, Jedd D. Wolchok, Ruth Halaban, Madhav V. Dhodapkar, Kavita M. Dhodapkar

Journal of Immunology, 1 February 2015, 194(3):950-959.  doi: 10.4049/​jimmunol.1401686

... employing RMA16 or PLIER16 (normalization) for analyzing the coding genes using the specific annotation support file for human transcriptome array 2.0 ... using the Exon workflow of the Partek GS 6.6 by taking into account exon probes from Affymetrix HTA 2.0 genechip ...


7-   Meeting abstract

Common long noncoding RNAs (lncRNA) with altered expression levels in colorectal adenoma and carcinoma

Alexandra Kalmar, Zsofia B. Nagy, Orsolya Galamb, Barnabas Wichmann, Barbara K. Bartak, Zsolt Tulassay, Bela Molnar

American Association for Cancer Research Annaul Meeting, 19 April 2015: Abstract #165.

...This study aimed to identify differentially expressed long non-coding RNAs (lncRNA) in colorectal adenoma and CRC cases. ...Expression levels of lncRNAs were analyzed with HGU133Plus2.0 microarrays (Affymetrix). ... total RNA including miRNAs was isolated from 20 independent biopsy samples (7 CRCs, 6 colonic adenomas, 7 normal donors without evidence of disease) ... and expression levels of 40.914 non-protein coding transcripts were analyzed by using Human Transcriptome Array 2.0 (Affymetrix).



Comparative Investigation of Human Amniotic Epithelial Cells and Mesenchymal Stem Cells for Application in Bone Tissue Engineering 

Jiawen Si, Jiewen Dai, Jianjun Zhang, Sha Liu, Jing Gu, Jun Shi, Steve G. F. Shen, Lihe Guo

Stem Cells International, 2015, 2015: Article ID 565732.   http://dx.doi.org/10.1155/2015/565732

... Samples were subjected to gene expression analysis using the Affymetrix human HTA2.0 microarray ...


9-   Meeting abstract

Comparing gene expression of matched FFPE colorectal cancer samples measured by Nanostring nCounter® platform and Affymetrix GeneChip® Human Transcriptome Array platform

Jing Zhu, Natasha G. Deane, Keeli B. Lewis, Mary K. Washington, Xi Chen, Robert D. Beauchamp.

American Association for Cancer Research Annual Meeting, 21 April 2015, Abstract #3421.

... Most available clinical samples are Formalin Fixed and Paraffin Embedded (FFPE). Nanostring nCounter® and Affymetrix GeneChip® Human Transcriptome Array (HTA) are two latest platforms that enable gene expression profiling of FFPE samples. In this study, we evaluated these two platforms for validating the prognostic gene expression signature based on FFPE-derived CRC samples. ...Overall, we found that the gene expression patterns visualized in the HTA dataset were more consistent within defined subtypes as compared to those of the nCounter dataset and the HTA-based assignments are better supported by the corresponding survival estimates. ... Discovery of CRC subtypes was more definitive using data from the HTA platform as compared to the nCounter® platform. ...



Crosstalk between the microbiome and cancer cells by quorum sensing peptides

Evelien Wynendaele, Frederick Verbeke, Matthias D’Hondt, An Hendrix, Christophe Van De Wiele, Christian Burvenich, Kathelijne Peremans, Olivier De Wever, Marc Bracke, Bart De Spiegeleer

Peptides, February 2015, 64:40–48.

... treated cells were analyzed in duplicate ... for whole transcriptome expression using Affymetrix GeneChip Human Transcriptome Array 2.0 by AROS Applied Biotechnology A/S (Aarhus, Denmark) ...



Cytomegalovirus Infection Drives Adaptive Epigenetic Diversification of NK Cells with Altered Signaling and Effector Function

Heinrich Schlums, Frank Cichocki, Bianca Tesi, Jakob Theorell, Vivien Beziat, Tim D. Holmes, Hongya Han, Samuel C.C. Chiang, Bree Foley, Kristin Mattsson, Stella Larsson, Marie Schaffer, Karl-Johan Malmberg, Hans-Gustaf Ljunggren, Jeffrey S. Miller, Yenan T. Bryceson

Immunity, 17 March 2015, 42(3):443–456.

... Samples were hybridized to GeneChip Human Transcriptome Array 2.0 cartridges (Affymetrix). ... transcription factors were stained with fluorochrome-conjugated antibodies to ... Eomes (WD1928, eBioscience), PLZF (Mags.21F7, eBioscience) ...



DDB2 modulates TGF-β signal transduction in human ovarian cancer cells by downregulating NEDD4L  [open access]

Ran Zhao, Tiantian Cui, Chunhua Han, Xiaoli Zhang, Jinshan He, Amit Kumar Srivastava, Jianhua Yu, Altaf A. Wani, Qi-En Wang

Nucleic Acids Research, online 29 June 2015, doi: 10.1093/nar/gkv667

... Total RNA were extracted from CP70 and CP70-DDB2 cells using Trizol reagent (Life Technologies) and processed for Affymetrix transcriptsome assay using GeneChip Human transcriptome array 2.0 (Affymetrix, Santa Clara, CA, USA) at The Microarray Shared Resource of OSUCCC.


13-     Meeting abstract

Difference between the blood-brain barrier and blood-nerve barrier: Analyses using new human in vitro blood- brain and blood-nerve barrier models.

Abe Masaaki, Yasuteru Sano, Hideaki Nishihara, Hironori Sano, Yukio Takeshita, ToshihikoMaeda, Takashi Kanda

Neurology, April 6, 2015, 84(14, Supplement): Abstract # P2.106.

... In this study, we performed detailed comparative analyses for the barrier properties with both of new established endothelial cell lines derived from human BBB and BNB. ... Firstly, we measured transendothelial electrical resistance (TEER) values of TY10 cells and FH-BNBs. In addition, Affymetrix chips, Human Transcriptome Array 2.0, were used to elucidate the difference of the expression level of the tight junction molecules on the BBB and the BNB. ...


14-    Meeting abstract

Differential Effects of Fingolimod on Gene Expression of Helper and Cytotoxic T-Cells in the Blood of MS Patients

Michael Hecker, Brit Fitzner, Dirk Koczan, Jörg Friess, Luisa Roch, Ina Schröder, Kristin Flechtner, Hans-Jürgen Thiesen, Alexander Winkelmann, Uwe Zettl

Neurology, April 6, 2015, 84(14, Supplement): Abstract #P1.156.  

OBJECTIVE: To study the gene expression patterns of T-cells before and during fingolimod treatment in order to better understand the molecular mechanisms of the drug and to identify biomarkers of the individual biological response to therapy. ...The RNA from separated CD4+ and CD8+ T-cells was analyzed with Affymetrix Human Transcriptome Arrays (HTA) 2.0, which contain >6.0 million distinct probes covering the exons of >67.500 coding and non-coding transcripts. ... We present the first study that used high-resolution gene expression microarrays to analyze how the molecular properties of CD4+ and CD8+ T-cells are modulated during therapy. Except for T-cell activation, distinct biological processes were affected in these cells. Study Supported by: Novartis


15-   Meeting abstract

Differential transcription profile of epithelia in fimbria versus the ampulla of the fallopian tube

Sophia H. George, Anca Milea, Noor Hera Salman, and Patricia Ann Shaw

University Health Network, Toronto, Ontario, Canada.

Cancer Research, 2015, 75(15 Suppl): Abstract #2080. [AACR Annual Meeting, April 18-22, 2015; Philadelphia, PA]

Background: Recently described precursors of high-grade serous carcinoma (HGSC), the p53 signature, a latent precursor, and Serous Tubal Intraepithelial Carcinoma (STIC), a pre-malignant precursor, occur most frequently at the distal and fimbriated end of the fallopian tube (FTE). ...The objective of this study is to compare the transcriptome profiles of normal fimbria (high-risk epithelia prone to transformation) FTE and normal ampulla (low-risk epithelia) FTE which may lead to understanding the distal end of the fallopian tube as the preferential anatomic location of the fallopian to tube for cellular transformation. ... Total RNA was isolated, RNA extracted and cDNA amplified. The expression profiles were generated using Affymetrix Human Genome HTA-2.0 Array. ...



DNA-PKcs plays role in cancer metastasis through regulation of secreted proteins involved in migration and invasion

Ewa Kotula, Nathalie Berthault, Celine Agrario, Marie-Christine Lienafa, Anthony Simon, Florent Dingli, Damarys Loew, Vonick Sibut, Simon Saule & Marie Dutreix

Cell Cycle, posted online 27 May 2015, 14(12): 1961-1972.

... Human Transcriptome Array 2.0 ST arrays were hybridized according Affymetrix recommendations using the WT PLUS protocol and labelling and hybridization kits from Affymetrix. The assay was performed at the Institut Curie microarray core facility.



DNA methyltransferase 3A promotes cell proliferation by silencing CDK inhibitor p18INK4C in gastric carcinogenesis

He Cui, Chengcheng Zhao, Pihai Gong, Ling Wang, Huazhang Wu, Kun Zhang, Rongping Zhou, Li Wang, Ting Zhang, Sheng Zhong,  Hong Fan

Scientific Reports, 9 September 2015, 5: 13781.

... Affymetrix GeneChip Human Transcriptome Array 2.0 was used for microarray analysis. Microarray hybridization was performed by the Shanghai Biotechnology Corporation (Shanghai, China) ...



Dysregulation of the Transforming Growth Factor β Pathway in Induced Pluripotent Stem Cells Generated from Patients with Diamond Blackfan Anemia

Jingping Ge,  Marisa Apicella,  Jason A. Mills,  Loïc Garçon,  Deborah L. French,  Mitchell J. Weiss,  Monica Bessler,  Philip J. Mason 

PLOS ONE, 10 August 2015, 10(8): e0134878.

... The level of whole genome transcripts was measured by an Affymetrix GeneChip human transcriptome array or human Exon array (Affymetrix ...



Epigenome-wide and transcriptome-wide analyses reveal gestational diabetes is associated with alterations in the human leukocyte antigen complex

Alexandra M. Binder, Jessica LaRocca, Corina Lesseur, Carmen J. Marsit, and Karin B. Michels

Clinical Epigenetics, 5 August 2015, 7(1): 79.

... To assess the mechanistic aspects of fetal programming, we measured genome-wide methylation (Infinium HumanMethylation450 BeadChips) and expression ... in placental tissue ... Gene expression was assessed using the Human Transcriptome Array 2.0 (Affymetrix).


20-   Meeting abstract

Establishment and characterization of primary penile carcinoma cell culture versus xenograft by using transcriptome analysis

Juan José Augusto Moyano Muñoz, Sandra A. Drigo, Tiago Goss, Hellen Kuasne, Fabio Marchi, Gustavo Guimaraes, Ademar Lopes, Cristovam S. Neto, Silvia R. Rogatto

Cancer Research, 2015, 75(15 Suppl): Abstract #3248. [AACR Annual Meeting, April 18-22, 2015,  Philadelphia, PA]

...Total RNA was extracted from cell cultures and xenograft tissues in duplicate and evaluated for gene expression by using Human Transciptome Array (HTA) 2.0 (Affymetrix). Expression Console (Affymetrix), SAM, hierarchical clustering analysis, Ingenuity Pathway Analysis (IPA). ...


21-    Meeting abstract

Fimbria and Ampulla Tubal Epithelium Have Similar Transcriptome Profiles

Sophia George, Anca Milea, Noor Salman, Patricia Shaw.

Laboratory Investigation, February 2015, 95(S1): Abstract #1140. [U.S & Canadian Academy of Pathology, 104th Annual Meeting, March 21-27, 2015]

Total RNA was isolated, RNA extracted and cDNA amplified. The expression profiles were generated using Affymetrix Human Genome HTA-2.0 Array. ...



Functional Analysis of microRNA in Multiple Myeloma

Maria Teresa Di Martino, Nicola Amodio, Pierfrancesco Tassone, Pierosandro Tagliaferri

Methods in Molecular Biology, online 14 May 2015.  doi:10.1007/7651_2015_250

... We here describe a workflow based on the identification of dysregulated miRNAs in plasma cells from MM patients based on Affymetrix technology. ... Affymetrix® miRNA 2.0, 3.0, or 4.0 Array ... Affymetrix® GeneChip Human Transcriptome Array 2.0 ... unparalleled coverage of this array provides the deepest insight into all coding and noncoding transcripts available.


23-   Misidentified as an Agilent array

Gene Expression Profile of Persistent Postoperative Hypertension Patients with Aldosterone-producing Adenomas

Li-Fang Xie, Jin-Zhi Ouyang, An-Ping Wang, Wen-Bo Wang, Xin-Tao Li, Bao-Jun Wang, Yi-Ming Mu

Chinese Medical Journal, online 8 June 2015, 128(12): 1618-1626.

... Microarray analysis was performed by a commercial company (Oebiotech, PRC), using GeneChip® Human Transcriptome Array 2.0 (Agilent Technologies) designed to contain approximately 245349 array protein coding transcripts and 40914 array nonprotein coding transcripts derived from authoritative databases ...


24-     Meeting abstract

Gene expression profiling after radiation in human breast cancer specimens and breast cancer cell lines

Sharareh Siamakpour-Reihani, Wei Chen, Chen-Ting Lee, Yingchun Zhou, Kouros Owzar, Jen-Tsan Chi, Janet K. Horton.

American Association for Cancer Research Annaul Meeting, 21 April 2015: Abstract #3331.

... Here we report on gene expression profiles associated with radiation response from: i) a rare clinico-genomic data in women treated with preoperative breast radiation and, ii) data from a pilot study of 16 biologically diverse breast tumor cell lines. Methods: Microarray analysis was done using the Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) and the Affymetrix HU133A2.0 arrays. RNA was harvested from paired pre- and post-radiation formalin-fixed paraffin-embedded breast cancer tissue in 26 patients ...


25-   Meeting abstract

Gene profiling in different stages of Alzheimer’s disease: a genome-wide study

F. Fernandez-Enright, J. Andrews, B. Grenyer, K. Lewis, M. Snelling, J. Potter1, H. Brodaty

Journal of Neurochemistry, August 2015, 134(Suppl 1): Abstract #MTU02-06.  [Special Issue: 25th Biennial Meeting of the International Society for Neurochemistry jointly with the 13th Meeting of the Asian-Pacific Society for Neurochemistry in conjunction with the 35th Meeting of the Australasian Neuroscience Society 23–27 August 2015, Cairns, Australia]

... Despite recent progress in genetic research, gene testing is currently not sufficiently reliable for most individuals and has limited utility for predictive purposes. We here examined gene expression profiles and microRNA patterns using the Affymetrix Human Transcriptome array 2.0 in saliva in patients across several stages of AD (mild, moderate and severe) compared to a healthy control group ... This is the first study examining a complete genetic profile specific at each stage of AD in saliva samples using a whole genome expression array. ...


26-     Meeting abstract

Genomic, transcriptome and epigenomic analysis reveal new genetic pathways in penile carcinoma

Hellen Kuasne1, Fabio A. Marchi1, Ariane F. Busso1, Mateus C. Barros-Filho1, Juan JAM Muñoz1, Hector Hernandez-Vargas2, Cristovam Scapulatempo-Neto3, Eliney F. Faria3, Ademar Lopes1, Gustavo C. Guimarães4, Jose C. Trindade-Filho5, Zdenko Herceg2, Silvia R. Rogatto6.

American Association for Cancer Research Annaul Meeting, 21 April 2015: Abstract #3828.

Background: Penile carcinoma (PeCa) is a rare and high morbidity disease. ... aim was to identify molecular drivers in PeCa. Patients and Methods: 37 PeCa samples, 16 surrounding normal tissues and 14 normal glands were used for evaluate DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies), large-scale expression (4x44K Whole Human Genome Microarray, Agilent Technologies and GeneChip® Human Transcriptome Array 2.0, Affymetrix), miRNA expression (TaqMan Human MicroRNA Array v2.0, Applied Biosystems) and genomic copy number alterations by array-CGH (Agilent Human 4x44K CGH Microarrays ...



Genomics of injury: The Glue Grant experience [invited editorial]

Ronald G. Tompkins

Journal of Trauma and Acute Care Surgery, April 2015, 78(4):671-686.

... led by Wenzhong Xiao and Michael Mindrinos, the program created new microarrays in collaboration with Affymetrix. These are currently marketed as GeneChip Human Transcriptome Array 2.0 (HTA 2.0) and GeneChip Mouse Transcriptome Assay 1.0 (MTA 1.0) ... Although not commercially available yet, the human array also has been annotated for macaque monkeys...



Human intracellular ISG15 prevents interferon-α/β over-amplification and auto-inflammation

Xianqin Zhang, Dusan Bogunovic, Béatrice Payelle-Brogard, Véronique Francois-Newton, Scott D. Speer, Chao Yuan, Stefano Volpi, Zhi Li, Ozden Sanal, Davood Mansouri, Ilhan Tezcan, Gillian I. Rice, Chunyuan Chen, Nahal Mansouri, Seyed Alireza Mahdaviani, Yuval Itan, Bertrand Boisson, Satoshi Okada, Lu Zeng, Xing Wang, Hui Jiang, Wenqiang Liu, Tiantian Han, Delin Liu, Tao Ma, Bo Wang, Mugen Liu, Jing-Yu Liu, Qing K. Wang, Dilek Yalnizoglu, Lilliana Radoshevich, Gilles Uzé, Philippe Gros, Flore Rozenberg, Shen-Ying Zhang, Emmanuelle Jouanguy, Jacinta Bustamante, Adolfo García-Sastre, Laurent Abel, Pierre Lebon, Luigi D. Notarangelo, Yanick J. Crow, Stéphanie Boisson-Dupuis, Jean-Laurent Casanova & Sandra Pellegrini

Nature, 1 January 2015, 517:89–93. 

... For PBMCs and hTert fibroblasts, total RNA was extracted with the RNeasy Mini kit (Qiagen) and the standard protocol for hybridization to Affymetrix HTA 2.0 chips was performed.



Identification of Histone Deacetylase Inhibitors with Benzoylhydrazide Scaffold that Selectively Inhibit Class I Histone Deacetylases

Yunfei Wang, Ryan L. Stowe, Christie E. Pinello, Guimei Tian, Franck Madoux, Dawei Li, Lisa Y. Zhao, Jian-Liang Li, Yuren Wang, Yuan Wang, Haiching Ma, Peter Hodder, William R. Roush, Daiqing Liao

Chemistry & Biology, 19 February 2015, 22(2): 273–284.

... UF010 activates tumor suppression mechanisms while inhibiting oncogenic pathways ... To assess cellular effects of UF010 comprehensively, we treated MDA-MB-231 cells with UF010 ... and analyzed its impact on global gene expression in comparison with DMSO control using the Affymetrix Human Transcriptome Array 2.0 ...



Identification of multi-target effects of Huaier aqueous extract via microarray profiling in triple-negative breast cancer cells

Xiangnan Kong, Xia Ding, Qifeng Yang

International Journal of Oncology, May 2015, 46(5): 2047-2056. 

... Based on microarray data, we studied several functions of Huaier extract and in return verified the results of microarray profiling. ... cDNA were hybridized in Hybridization Oven 645 for 16 h at 45˚C on GeneChip Human Transcriptome Array 2.0.



Impaired Telomere Maintenance and Decreased Canonical WNT Signaling but Normal Ribosome Biogenesis in Induced Pluripotent Stem Cells from X-Linked Dyskeratosis Congenita Patients

Bai-Wei Gu, Marisa Apicella, Jason Mills, Jian-Meng Fan, Dara A. Reeves, Deborah French, Gregory M. Podsakoff, Monica Bessler, Philip J. Mason

PLOS ONE, 18 May 2015, 10(5): e0127414.

... To gain insight into the pathways active in stem cells that are altered by mutant dyskerin we performed a high resolution microarray on the WT and mutant iPS cells using a GeneChip Human Transcriptome Array 2.0 ...



Innate immune activity correlates with CD4 T cell-associated HIV-1 DNA decline during latency-reversing treatment with panobinostat

Rikke Olesen, Selena Vigano, Thomas Rasmussen, Ole S. Søgaard, Zhengyu Ouyang, Maria Buzon, Arman Bashirova, Mary Carrington, Sarah Palmer, Christel R. Brinkmann, Xu G. Yu, Lars Østergaard, Martin Tolstrup, Mathias Lichterfeld

Journal of Virology, Accepted manuscript posted online 29 July 2015, doi: 10.1128/JVI.01484-15

... extracted using the PAXgene Blood RNA kit, (Qiagen) and subjected to whole-genome transcriptional profiling using Affymetrix Human Transcriptome Array 2.0 microarrays ...





Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns

Caitlyn Riedmann, Ye Ma, Manana Melikishvili, Steven Grason Godfrey, Zhou Zhang, Kuey Chu Chen, Eric C Rouchka and Yvonne N Fondufe-Mittendorf

BMC Genomics, 19 March 2015, 16:212 

... For this analysis, RNA from HeLa NT cells and iAs-T HeLa cells were analyzed using the Affymetrix GeneChip® Human Transcriptome Array 2.0.



Insights into the Distinguishing Stress-induced Cytotoxicity of Chiral Gold Nanoclusters and the Relationship with GSTP1 

Chunlei Zhang, Zhijun Zhou, Xiao Zhi,1Yue Ma, Kan Wang, Yuxia Wang, Yingge Zhang, Hualin Fu,Weilin Jin, Fei Pan, Daxiang Cui

Theranostics, 1 January 2015, 5(2):134–149. 

... Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the Affymetrix Human HTA 2.0 microarray.


35-    Meeting abstract

Intrinsic subtypes and MRI patterns in brain metastasis associated with breast cancer

Nicole Williams, Vinay Varadan, Aditi Vadodkar, Kristy Miskimen, Stephanie Kim, Shaveta Vinayak, Paula Silverman, Jill Barnholtz-Sloan, Andrew Sloan, Cheryl Thompson, Lisa Rogers, Hannah Gilmore,

Lyndsay Harris

Cancer Research, 2015, 75(9 Suppl): Abstract #P6-16-03. [CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX]

... Gene expression profiling was performed using Affymetrix Human Transcriptome Array 2.0 microarray on BM samples for which sufficient RNA was available. ...



Microarray gene expression profiling reveals potential mechanisms of tumor suppression by the class I HDAC-selective benzoylhydrazide inhibitors  

Iqbal Mahmud, Daiqing Liao

Genomics Data, September 2015, 5:257–259.

... sense strand DNA was fragmented, biotinylated, and hybridized with rotation at 45 °C for 16 h to microarray chips (GeneChip® Human Transcriptome Array 2.0, Affymetrix).



Mineralocorticoid receptors are present in skeletal muscle and represent a potential therapeutic target

Jessica A. Chadwick, J. Spencer Hauck, Jeovanna Lowe, Jeremiah J. Shaw, Denis C. Guttridge, Celso E. Gomez-Sanchez, Elise P. Gomez-Sanchez, Jill A. Rafael-Fortney

The FASEB Journal, Published online before print July 15, 2015, doi:10.1096/fj.15-276782

... Labeled cDNA targets were hybridized to Affymetrix GeneChip Human Transcriptome Array 2.0 or Mouse Genome 430 Array for human and mouse gene expression, respectively ...



mTORC1 Upregulates GP73 to Promote Proliferation and Migration of Hepatocellular Carcinoma Cells and Growth of Xenograft Tumors in Mice

Xinxin Chen, Yanan Wang, Jun Tao, Yuzhuo Shi, Xiaochen Gai, Fuqiang Huang, Qian Ma, Zhenzhen Zhou, Hongyu Chen, Haihong Zhang, Zhibo Liu, Qian Sun, Haiyong Peng, Rongrong Chen, Yanling Jing, Huayu Yang, Yilei Mao, Hongbing Zhang1

Gastroenterology, September 2015, 149(3): 741–752.e14

... We used microarray analysis to compare expression patterns between GP73-knockdown and control MHCC97H cells.... using Affymetrix GeneChip® Human Transcriptome Array 2.0.




39-    Meeting poster

Novel biomarkers in chronic neuropathic pain

David Buckley, David Finn, Mark Johnson & Patrick McHugh

The Challenge of Chronic Pain, Cambridge, February 2015, poster abstract.  

... Transcriptomic analysis was performed using a GeneChip® Human Transcriptome Array 1.0 (Affymetrix) and 869 genes were found to be significantly differentially expressed. ...

NOTE: Further discussion available at Dr Patrick McHugh - Biomarkers and Stem Cell Research, ... The group also forms the basis of Dr McHugh spearheading an International project between the UK, Ireland and the US involving the development of clinical cohorts, in which the UK arm of the project has been adopted to the prestigious National Institute of Health Research Clinical Research Network Portfolio. A transcriptomic analysis using Affymetrix HTA 2.0 arrays, comparing PAX RNA blood samples from chronic pain patients and control samples (Fig 3), has identified a subset of RNA molecules that could potentially act as diagnostic pain biomarkers and/or provide clues into the condition, thus potentially enabling clinicians to improve diagnosis and treatment 3.



Oxytocin differentially effects 3β-hydroxysteroid dehydrogenase and 5α-reductase activities in prostate cancer cell lines

Stephen J. Assinder, Kathryn Davies, Jonathan Surija, Frank Liu-Fu

Peptides, September 2015, 71:149–155

... effects of oxytocin on expression of SRD5A1, SRD5A2, HSD3B1 and HSD3B2 were investigated by transcriptome analysis (Affymetrix HTA 2.0 transcriptome array) ... first report that oxytocin modulates activity of key steroidogenic enzymes in prostate cancer cells.



p54nrb/NONO Regulates Cyclic AMP-Dependent Glucocorticoid Production by Modulating Phosphodiesterase mRNA Splicing and Degradation

Jia Yang Lu and Marion B. Sewer

Molecular and Cellular Biology, April 2015, 35(7):1223-1237.

...  Affymetrix human transcriptome array 2.0 arrays were hybridized according to Affymetrix recommendations using the Ambion WT protocol (Life Technologies) and Affymetrix labeling and hybridization kits.


42-   Meeting abstract

Pharmacodynamic Changes in Gene Expression Observed in Two Phase 3 Trials of Baff Blockade with Tabalumab in SLE

R. Hoffman, J.T. Merrill, M.E. Alarcón-Riquelme, M. Petri, E.R. Dow, E. Nantz, L.K. Nisenbaum, K.M. Schroeder, W.J. Komocsar, N.B. Perumal, G.V. Rocha, and R.E. Higgs

Annals of the Rheumatic Diseases, Jun 2015; 74:98–99. Abstract #OP0079 

... RNA was extracted and analyzed using Affymetrix HTA 2.0 whole genome microarrays. ...



Phosphatase and tensin homolog deleted on chromosome 10 contributes to phenotype transformation of fibroblasts in idiopathic pulmonary fibrosis via multiple pathways.

Geng J, Huang X, Li Y, Xu X, Li S, Jiang D, Liu Z, Dai H

Experimental Biology and Medicine (Maywood), 11 August 2015.  doi: 10.1177/1535370215600100

... cDNA was hybridized to HTA 2.0 (GeneChip Human Transcriptome Array 2.0, Affymetrix, Santa Clara, CA) according to the User Manual.



Preoperative Single-Fraction Partial Breast Radiotherapy – A Novel Phase I Dose-Escalation Protocol with Radiation Response Biomarkers

Janet K. Horton, Rachel C. Blitzblau, Sua Yoo, Joseph Geradts, Zheng Chang, Jay A. Baker, Gregory S. Georgiade, Wei Chen, Sharareh Siamakpour-Reihani, Chunhao Wang, Gloria Broadwater, Jeff Groth,

Manisha Palta, Mark Dewhirst, William T. Barry, Eileen A. Duffy, Jen-Tsan A. Chi, E. Shelley Hwang

International Journal of Radiation Oncology*Biology*Physics,  15 July 2015, 92(4): 846–855.

... FFPE RNA extraction and labeling was performed using ... SensationPlus™ FFPE Amplification and Labeling Kit (Affymetrix, ... Whole transcriptome expression analysis was evaluated with HTA 2.0 arrays (Affymetrix, ...




RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays  [open access]

Junhee Seok, Weihong Xu, Ronald W. Davis,  Wenzhong Xiao 

Scientific Reports, 6 July 2015,  5: 11917

Human transcriptome arrays (HTA) have recently been developed for high-throughput alternative splicing analysis by measuring signals not only from exons but also from exon-exon junctions. ... we introduce a computational method, Robust Alternative Splicing Analysis (RASA), for the analysis of the new transcriptome arrays by effective integration of the exon and junction signals. ... RASA was demonstrated with Affymetrix HTAs and its performance was evaluated with mRNA-Seq and RT-PCR. ... the recently released Affymetrix HTA 2.021 covers ~560 k exons and ~340 k exon-exon junctions of the human genome. The HTAs have relatively low cost (about $250 per sample in the US including reagents) and short processing time, which makes the HTAs as a good complementary tool of mRNA-Seq for clinical studies that often require several hundreds or thousands of samples20. While a number of such studies are underway using HTA platforms22, computational challenges remain to effectively utilize the rich exon and junction signals in the data. ... muscle tissue samples were hybridized on Affymetrix HTA 1.0, previously high-density human exon junction array, HJAY24.



RhoC is an Unexpected Target of RhoGDI2 in Prevention of Lung Colonization of Bladder Cancer

Erin M. Griner, Garrett M. Dancik, James C. Costello, Charles Owens, Sunny Guin, Michael G. Edwards, David L. Brautigan, Dan Theodorescu

Molecular Cancer Research, version 2 published 28 April 2015.  doi: 10.1158/1541-7786.MCR-14-0420

...  RNA was hybridized to GeneChip Human Transcriptome Array 2.0 arrays (Affymetrix).



Spatial genomic heterogeneity within localized, multifocal prostate cancer

Paul C Boutros, Michael Fraser, Nicholas J Harding, Richard de Borja, Dominique Trudel, Emilie Lalonde, Alice Meng, Pablo H Hennings-Yeomans, Andrew McPherson, Veronica Y Sabelnykova, Amin Zia, Natalie S Fox, Julie Livingstone, Yu-Jia Shiah, Jianxin Wang, Timothy A Beck, Cherry L Have, Taryne Chong, Michelle Sam, Jeremy Johns, Lee Timms, Nicholas Buchner, Ada Wong, John D Watson, Trent T Simmons, Christine P'ng, Gaetano Zafarana, Francis Nguyen, Xuemei Luo, Kenneth C Chu, Stephenie D Prokopec, Jenna Sykes, Alan Dal Pra, Alejandro Berlin, Andrew Brown, Michelle A Chan-Seng-Yue, Fouad Yousif, Robert E Denroche, Lauren C Chong, Gregory M Chen, Esther Jung, Clement Fung, Maud H W Starmans, Hanbo Chen, Shaylan K Govind, James Hawley, Alister D'Costa, Melania Pintilie, Daryl Waggott, Faraz Hach, Philippe Lambin, Lakshmi B Muthuswamy, Colin Cooper, Rosalind Eeles, David Neal, Bernard Tetu, Cenk Sahinalp, Lincoln D Stein, Neil Fleshner, Sohrab P Shah, Colin C Collins, Thomas J Hudson, John D McPherson, Theodorus van der Kwast & Robert G Bristow

Nature Genetics, online 25 May 2015, 47: 736–745.

... whole genome–amplified (IGRT biopsy) or genomic (radical prostatectomy) DNA on Affymetrix OncoScan FFPE Express 2.0 SNP arrays.... assayed using the HuGene 2.0 Affymetrix array ... (batch 2) were assayed using the Human Transcriptome Array (HTA) ...



The histone deacetylase inhibitor panobinostat lowers biomarkers of cardiovascular risk and inflammation in HIV patients.

Høgh Kølbæk Kjær AS, Brinkmann CR, Dinarello CA, Olesen R, Østergaard L, Søgaard OS, Tolstrup M, Rasmussen TA.

AIDS, 19 June 2015, 29(10):1195-200.

... Whole-genome expression in peripheral blood mononuclear cells was analyzed at baseline and on-panobinostat employing the Affymetrix Human Transcriptome Array 2.0 microarray assay.



The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes

Yuan Xie, Tobias Bergström, Yiwen Jiang, Patrik Johansson, Voichita Dana Marinescu, Nanna Lindberg, Anna Segerman, Grzegorz Wicher, Mia Niklasson, Sathishkumar Baskaran, Smitha Sreedharan, Isabelle Everlien, Marianne Kastemar, Annika Hermansson, Lioudmila Elfineh, Sylwia Libard, Eric Charles Holland, Göran Hesselager, Irina Alafuzoff, Bengt Westermark, Sven Nelander, Karin Forsberg-Nilsson, Lene Uhrbom

EbioMedicine, online 15 August 2015, In Press, Corrected Proof. doi:10.1016/j.ebiom.2015.08.026

... Total RNA extracted from 48 GC lines ... labeled and hybridized on Affymetrix GeneChip Human Exon 1.0 ST arrays. ... copy number aberration in all of our 48 GC lines employing Affymetrix Cytoscan HD arrays ... RNA was prepared from cells and tumor tissue and analyzed on the Affymetrix HTA 2.0 platform.


50-   Meeting abstract


R. Vassena,a J. Pons,b A. Ferrer,a A. Schweitzer,c J. Hubbard,c H. Auer,d A. Rodolosse,e M. Barragan.a aClinica EUGIN, Barcelona, Spain; bFGC, Institute for Research in Biomedicine Barcelona, Barcelona, Spain; cAffymetrix, Santa Clara, CA; dFunctional GenOmics Consulting, Barcelona, Spain; eIRB, Barcelona, Spain. Fertility and Sterility

Fertility and Sterility, Sep 2015,104(3, Sup): Abstract #e19.  [71st Annual Meeting Am Soc for Repro Med]

... Total RNAwas purified from individual MII and WTA2 cDNA libraries prepared; 10 mg cDNA was fragmented and biotinylated; 36 GeneChip Human Transcriptome Array 2.0 arrays were hybridized, washed, stained, and scanned. ...



The Quorum Sensing Peptides PhrG, CSP and EDF Promote Angiogenesis and Invasion of Breast Cancer Cells In Vitro

Bart De Spiegeleer, Frederick Verbeke, Matthias D’Hondt, An Hendrix, Christophe Van De Wiele, Christian Burvenich, Kathelijne Peremans, Olivier De Wever, Marc Bracke, Evelien Wynendaele

PLoS ONE, March 17, 2015, 10(3): e0119471.

...  Cells treated with either EDF, PhrG or CSP were analyzed in duplicate (independent treatment and analysis) for whole transcriptome expression using Affymetrix GeneChip Human Transcriptome Array 2.0. by AROS Applied Biotechnology A/S (Aarhus, Denmark) ...


52-   Meeting abstract

The Thailand initiative in genomics and expression research for liver cancer (TIGER-LC): Defining novel subtypes of hepatocellular carcinoma and cholangiocarcinoma

Jittiporn Chaisaingmongkol, Anuradha Budhu, Hien Dang, Siritida Rabibhadana, Benjarath Pupacdi, Marshonna Forgues, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Anon Chotirosniramit, Chawalit Pairojkul, Chirayu U. Auewarakul, Thaniya Sricharunrat, Kannika Phornphutkul, Suleeporn Sangrajrang, Maggie Cam, Ping He, Stephen M. Hewitt, Xiaolin Wu, Snorri S. Thorgeirsson, Paul S. Meltzer, Christopher A. Loffredo, Robert H. Wiltrout, Curtis C. Harris, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin W. Wang

Cancer Research, 2015, 75(15 Suppl): Abstract #LB-173.  [Proceedings AACR Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA]

... We performed genomic profiling of 398 surgical specimens derived from 199 liver cancer patients. We employed the Affymetrix Human Transcriptome Array 2.0 to examine transcriptome profiles. ...


53-    Meeting abstract

TransCONFIRM: The correlative analysis of breast tumors from patients with advanced hormone receptor positive disease identifies a genetic …

Rinath M Jeselsohn, William T Barry, Jin Zhao, Gilles Buchwalter, Cristina Guarducci, Ilenia Migliaccio, Chiara Biagioni, Martina Bonechi, Naomi Laing, Yuri Rukazenkov, Eric P Winer, Myles Brown, Angelo Di Leo and Luca Malorni

Cancer Research, 2015, 75(9 Suppl): Abstract #S1-01. [CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX]

... RNA was sufficient for gene expression profiling in 112 of the cases using the NuGEN Ovation FFPE WTA System and Affymetrix HTA 2.0 GeneChip. ...


54-   Meeting abstract

Tumor infiltrating lymphocytes associated with brain metastasis in breast cancer.

Nicole Olivia Williams, Cheryl L. Thompson, Shikha Parsai, Vinay Varadan, Kristy Miskimen, Jill Barnholtz-Sloan, Paula Silverman, Shaveta Vinayak, Lisa R. Rogers, Andrew E. Sloan, Lyndsay Harris and Hannah L. Gilmore

Journal of Clinical Oncology, 2015, 33(15, May 20 Sup): 2059.  [ASCO Annual Mtg, May 2-Jun 2, 2015]

... The aim of this study is to characterize the immune response to BM in breast cancer. Methods: The cohort included 75 initial and recurrent BM samples and 20 matched primary breast tumors. Stromal (sTILs) were evaluated on H&E sections and scored according to international TILs working group guidelines and categorized as having no, low (1-5%), moderate (6-20%) or high ( > 20%) TILs. Tumor DNA/RNA was extracted on corresponding archival FFPE material. Gene expression profiling was performed using Affymetrix Human Transcriptome Array 2.0 microarrays. ...



Vemurafenib resistance selects for highly malignant brain and lung-metastasizing melanoma cells

Inna Zubrilov, Orit Sagi-Assif, Sivan Izraely, Tsipi Meshel, Shlomit Ben-Menahem, Ravit Ginat, Metsada Pasmanik-Chor, Clara Nahmias, Pierre-Olivier Couraud, Dave S.B. Hoon, Isaac P. Witz

Cancer Letters, 28 May 2015, 361(1):86–96.

... to identify possible biomarkers associated with the emergence of drug resistant melanoma cells. ... mRNA of Vemurafenib-resistant and sensitive melanoma cells was hybridized to GeneChip® Human Transcriptome Array 2.0 (Affymetrix, ...




A Mitogen-activated Protein Kinase/Extracellular Signal-regulated Kinase Kinase (MEK)-dependent Transcriptional Program Controls Activation of the Early Growth Response 1 (EGR1) Gene during Amino Acid Limitation

Jixiu Shan, Mukundh N. Balasubramanian, William Donelan, Lingchen Fu, Jaclyn Hayner, Maria-Cecilia Lopez, Henry V. Baker, Michael S. Kilberg

Journal of Biological Chemistry, 29 Aug 2014, 289:24665-24679.

...  Labeled targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 for 16 h at 45 °C and washed according to Affymetrix standard protocols.


57-   Meeting abstract

Biologic pathways associated with breast cancer metastases to the brain.

Vinay Varadan, Aditi Palkar, Kristy L. S. Miskimen, Nicole Olivia Williams, Matthew Morton, Steve Maximuk, Shaveta Vinayak, Lisa R. Rogers, Andrew E. Sloan, Jill Barnholtz-Sloan, Hannah L. Gilmore and Lyndsay Harris

Journal of Clinical Oncology, 2014, 32(15, May 20 Sup):Abstract#11038.  [ASCO Annual Meeting Abstracts; Also presented at 19th Annual Scientific Meeting of the Society for Neuro-Oncology, Miami, Florida, Nov 13-16, 2014]

... Tumor DNA/RNA was extracted from macrodissected 2 mm cores from FFPE. Gene expression profiling was performed using Affymetrix HTA 2.0 arrays on 96 FFPE samples for whom sufficient RNA was available. ...



Comparative Analysis of Gene Expression Profile between Keshan disease and dilated cardiomyopathy

Xiaohui Su,Shulan He,Wuhong Tan

Experimental & Clinical Cardiology, 2014, 20(7):1373-1384.

... Total RNA were isolated, amplified, labeled and hybridized to Affymetrix Human Transcriptome Array (HTA2.0) chips.


59-     Meeting abstract

Comparison of Illumina and Ion Torrent RNA-Sequencing and Microarray-based approaches for Profiling the Transcriptome

Rebecca Kusko, Ashley LeClerc, Samantha Swahn, Marc Lenburg, and Avrum Spira

Journal of BiomolecularTechniques, 2014 May; 25(Suppl): S14.

... Lastly, the same samples were interrogated using Agilent V2 Human Whole Genome arrays, Affymetrix Gene arrays ST (1.0 and 2.0) and newly commercialized Affymetrix Human Transcriptome Arrays. ...




60-     Meeting abstract

Concordance of Affymetrix GeneChip® Human Transcriptome Array 2.0 and USB® VeriQuest™ real-time PCR data  

Andrea Ujvari, Sangpen Chamnongpol, Olga Kourennaia, Kim Myers, Vincent Bressler, Jason Hubbard, Anthony Schweitzer, Chris Kubu

The FASEB Journal, April 2014, 28(1 Supp):Abstract LB207.

Global gene expression analysis using Affymetrix GeneChip Human Transcriptome Array (HTA) 2.0 combined with Affymetrix Transcriptome Analysis Console (TAC) Software empowers scientists not only to gain information about RNA expression at the gene-level, but also about RNA alternative splicing at the exon-level. Real-time PCR is routinely used to verify microarray results due to its high sensitivity and wide dynamic range, and was used in this study to validate Affymetrix GeneChip HTA 2.0 data. ... Excellent fold-change correlation of microarray and qPCR data were observed using USB VeriQuest Probe real-time PCR (R=0.96, slope=0.70). For alternative splicing validation of Affymetrix GeneChip HTA 2.0, total RNA from three different tissues (liver, muscle and brain) were used. Exon level information provided by TAC Software was utilized to design custom PCR primers for USB VeriQuest SYBR Green real-time PCR. All alternative splicing events selected for validation were confirmed by real-time PCR. We show excellent inter-platform concordance between Affymetrix microarray and VeriQuest real-time PCR data.



Concordance of Affymetrix GeneChip® Human Transcriptome Array 2.0 and real-time PCR results using USB® VeriQuest® qPCR master mixes [sponsored paper]

BioTechniques, 2014, 56(5) : 274-275.

 [First paragraph]  Global gene expression analysis using Affymetrix GeneChip Human Transcriptome Array (HTA) 2.0, combined with Affymetrix Transcriptome Analysis Console (TAC) software, empowers scientists not only to gain information about RNA expression at the genelevel, but also about RNA alternative splicing at the exon-level in different biological samples. …


62-     Meeting abstract

Correlation Between Gene Expression Profiles in Peripheral Blood Mononuclear Cells and Structural and Functional Brain Networks in Chronic Visceral Pain

Emeran Mayer*, Steve Cole, Arpana Gupta, Swapna Joshi, Trang Nguyen, Lisa Kilpatrick, Kirsten Tillisch, Lin Chang, Jennifer Labus

Neuropsychopharmacology, 10 December 2014, 39:Abstract #W260.

...  AIMS: To use different analytic approaches in order to test the following two complementary hypotheses: 1) IBS subjects show altered gene expression profiles in PBMCs, consistent with the CTRA pattern, which are correlated with structural changes in brain regions of the salience and emotional arousal networks. 2) Inflammatory gene expression profiles are correlated with functional changes in the salience network. Methods: The sample consisted of 40 individuals (20 IBS; 20 healthy controls [HCs]) completed structural and resting state MRI scans. Gene expression was assessed using human transcriptome array 2 (HTA-2, Affymetrix). ...



Evaluation of Cancer Stem Cell Markers CD133, CD44, CD24: Association with AKT Isoforms and Radiation Resistance in Colon Cancer Cells

Sara Häggblad Sahlberg, Diana Spiegelberg, Bengt Glimelius, Bo Stenerlöw, Marika Nestor

PLoS ONE, 23 April 2014, 9(4): e94621.

… total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip WT PLUS Reagent Kit User Manual (P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA). GeneChip HTA Arrays (GeneChip Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C incubator …


64-     Meeting abstract

Expression Profiling Smackdown: Human Transcriptome Array HTA 2.0 vs. RNA-Seq

Tim Hunter, Meghann Palermo, Heather Driscoll, Scott Tighe, Julie Dragon, Jeff Bond, Arti Shukla, Mahesh Vangala, James Vincent

Journal of Biomolecular Techniques, May 2014, 25(Suppl):S20–S21.  [Assoc of Biomolecular Resource Facilities (ABRF), March 22-25, 2014, New Mexico]  

... A new high-resolution array from Affymetrix, GeneChip Human Transcriptome Array 2.0 (HTA 2.0), has been designed to interrogate all transcript isoforms in the human transcriptome with >6 million probes targeting coding transcripts, exon-exon splice junctions, and non-coding transcripts. Here we compare expression results from GeneChip HTA 2.0 and RNA-Seq data using identical RNA extractions from three samples each of healthy human mesothelial cells in culture ...



Functional Analysis of the TRIB1 Associated Locus Linked to Plasma Triglycerides and Coronary Artery Disease

Adrianna Douvris, PhD; Sébastien Soubeyrand, PhD; Thet Naing, BSc; Amy Martinuk, MSc; Majid Nikpay, PhD; Andrew Williams, MSc; Julie Buick, MSc; Carole Yauk, PhD; Ruth McPherson, MD, PhD

Journal of the American Heart Association, 3 June 2014, 3:e000884

...  Labeled cRNAs were hybridized on GeneChip Human Transcriptome Arrays 2.0, and results were analyzed by using Expression Console and the Transcriptome Analysis Console from Affymetrix. The analyses are available at the Gene Expression Omnibus (accession number GSE54957).


66-   Meeting abstract

Gene Expression Profiling of CD34+/Lin- Cells of Patients with Chronic Myeloid Leukemia at Diagnosis and after 12 Months of Nilotinib

Alessandra Trojani, Milena Lodola, Barbara Di Camillo, Giuseppe Rossi, MD, Adele Capucci, Alessandra Perego, Enrico Maria Pogliani, MD, Ester Orlandi, MD, Alessandra Iurlo, MD PhD, Simona Malato, Paolo Corradini, MD, Roberto Cairoli, Marco Bregni, Salvatore Artale, Enrica Morra, Ester Pungolino, MD

Blood, 6 December 2014,124(21):Abstract# 5177.

Chronic myeloid leukemia (CML) is a disease of stemming from genetic damage to a hematopoietic stem cell. Despite nilotinib being a very effective drug for the treatment of CML, drug resistance can emerge.

... we performed an exploratory study aimed to identify the gene expression signature of bone marrow (BM) CD34+/lin- cells of CML patients at diagnosis as well as after 12 months of nilotinib to investigate the genes and pathways responsible for the response or resistance to nilotinib. Microarray experiments were performed using the latest generation Affymetrix GeneChip HTA 2.0 to further investigate genomic complexity. ...



Gene Expression Profiling of Hematopoietic Stem Cells (HSCs)

Nalini Raghavachari

Methods in Molecular Biology [Hematopoietic Stem Cell Protocols], 28 June 2014, 1185:91-119.

... This chapter describes detailed protocols for isolating RNA from purified population of hematopoietic cells and gene expression profiling of those purified cells using both microarrays (Affymetrix) and RNA-Seq technology (Illumina Platform).

Excerpt:   2.2 Microarrays. 1. Affymetrix Gene Chips—Exon 1.0 ST arrays or Human Transcriptome Array 2.0 or comparable arrays according to the cells from species other than humans.



Genome-wide analysis of the human ​p53 transcriptional network unveils a lncRNA tumour suppressor signature  

Yolanda Sánchez,Victor Segura,Oskar Marín-Béjar,Alejandro Athie,Francesco P. Marchese,Jovanna González,Luis Bujanda,Shuling Guo,Ander Matheu& Maite Huarte

Nature Communications, 19 December 2014, 5:5812

... by integrating RNA-seq with ​p53 ChIP-seq analyses ... we define a high-confidence set of 18 lncRNAs that are ​p53 transcriptional targets. ... total RNA was extracted and hybridized to Affymetrix Human Transcriptome Array 2.0.


69-    Meeting abstract


I. Romero, J.A. Lopez Guerrero, J. Palacios, B. Ojeda, C. Illueca, A. Gutierrez Pecharromán, S. Blanch, E. Cristóbal, M.Z. Garcia Casado, B. Vieites, I. Ruiz Díaz, F.J. Vera Sempere, F. Pastor, E. Andrada, M. Culubret, D. Hardisson, E. Calvo, C. Churruca, A. Santaballa and A.M. Poveda

Annals of Oncology, 2014, 25(suppl 4): Abst# 1630P iv564.

Aim: Early-stage (FIGO stage I/IIB) ovarian carcinoma (ESOC) represents 15% of all ovarian cancers and the molecular characterization of their different histologies has not been clearly defined. The aim of this study is to measure genomic abnormalities on a series of ESOCs to identify molecular alterations that influence pathophysiology, prognosis and constitute therapeutic targets.  ... A series of 31 formalin-fixed and paraffin-embedded (FFPE) low-grade endometrioid (LGE) and 15 two-tier low-grade serous (LGS) ESOC were selected for analyses. Recurrence was reported in 6 of the 46 analyzed cases. Transcriptome analyses was performed in 36 cases (12 LGS and 24 LGE) using the GeneChip® Human Transcriptome Array 2.0 (Affymetrix). Whole genome copy number variations (CNV) was analyzed in the 46 cases with the OncoScan™ FFPE Assay Kit (Affymetrix).  ...


70-     Meeting abstract

Identification of Gene Expression Signatures to Predict the Response of Low-Grade Lymphomas to Very Low Dose Radiation Therapy

J.J. Cuaron, J. Yahalom, R. Sundaram, S. Katz, G. Wang, M. Sharma, P. Yau, R.S. Bindra

International Journal of Radiation Oncology*Biology*Physics, 1 September 2014, 90(1):Abstract #339.  [American Society for Radiation Oncology (ASTRO) 56th Annual Meeting]

... We performed a pilot study to identify gene expression patterns that predict the response of low grade, indolent lymphomas to very low dose RT (2 Gy x 2) in a cohort of patients treated at a single institution. ... As an initial test of feasibility, formalin-fixed paraffin-embedded (FFPE) samples from 4 patients with follicular lymphoma (2 with CRs and 2 with NRs) were used for RNA extraction and transcriptome labeling with the Affymetrix FFPE kit. Microarray profiling was performed with Affymetrix GeneChip HTA 2.0 chips. ... These data highlight the feasibility of whole transcriptome profiling using FFPE tissue specimens from retrospective studies, ...



Induced pluripotent stem cells from human revertant keratinocytes for the treatment of epidermolysis bullosa

Noriko Umegaki-Arao, Anna M. G. Pasmooij, Munenari Itoh, Jane E. Cerise, Zongyou Guo, Brynn Levy, Antoni Gostyński, Lisa R. Rothman, Marcel F. Jonkman, Angela M. Christiano*

Science Translational Medicine (AAAS), 26 November 2014; 6:264ra164.

... Global gene expression profiling was performed with the Affymetrix Human Transcriptome Array (HTA) 2.0 to compare revertant-iPSC KC (P1) to the original revertant keratinocytes ... DNA was prepared and hybridized to a CytoScan HD Array Kit (Affymetrix) ...


72-  Meeting abstract

Integrated Nuclear Proteomics and Transcriptomics Identifies New High Frequency Dysregulated Transcription Factors in AML

Chinmay R Munje, BSc PhD*, Andrew J. K. Williamson, BSc, PhD*, Samuel Taylor, BSc, PhD*, Robert K. Hills, MA, MSc, DPhil, Steven Knapper, DM BMBCh, Alan K. Burnett, MD, Andrew Pierce, BSc, PhD*, Anthony Whetton, BSc, PhD*, Richard L. Darley, BSc PhD*, Alex Tonks, BSc PhD

Blood, 6 December 2014,124(21): Abstract# 3554.

... In parallel mRNA from these samples were analysed using Human Transcriptome Array 2.0 (Affymetrix, USA). ...These data are the first analysis of the nuclear proteome in AML and have identified changes in transcription factor expression that would not have been seen at the mRNA level. ...


73-   Meeting abstract

Microarray of Bone Marrow CD34+/Lin- Cells from Patients with Chronic Myeloid Leukemia (CML)

Alessandra Trojani* , Milena Lodola*, Barbara Di Camillo*, Giuseppe Rossi, MD, Adele Capucci*, Alessandra Perego*, Enrico Maria Pogliani, MD, Ester Orlandi, MD*, Alessandra Iurlo, MD PhD*, Simona Malato*, Paolo Corradini, MD, Roberto Cairoli*, Marco Bregni*, Sergio Pauli*, Enrica Morra, Ester Pungolino, MD*

Blood, 6 December 2014,124(21): Abstract#5178.

This study aimed to determine the gene expression profiling (GEP) of bone marrow (BM) CD34+/lin- cells of CML patients at diagnosis and after nilotinib treatment.Microarray was performed on 30 CML patients at diagnosis as well as 8 patients after 12 months of nilotinib treatment using the latest generation Affymetrix GeneChip HTA 2.0 to further investigate genomic complexity. ... Microarray experiments were performed on CD34+/lin- cells of 30 CML patients at diagnosis with HTA 2.0. Moreover, we performed microarray experiments on CD34+/lin- cells of 8 CML patients at diagnosis vs. 8 CML patients after 12 months of nilotinib using HTA 2.0. ...



Nodal Pathway Genes Are Down-regulated in Facial Asymmetry

Nicot, Romain; Hottenstein, Molly; Raoul, Gwenael; Ferri, Joel; Horton, Michael; Tobias, John W.; Barton, Elisabeth; Gelé, Patrick; Sciote, James J.

Journal of Craniofacial Surgery, November 2014, 25(6): e548–e555.

... Patients were classified as class II or III and open or deep bite malocclusion with or without facial asymmetry. Muscle samples were analyzed for gene expression differences on Affymetrix HT2.0 microarray global expression chips. ...


75-   Meeting abstract

QTLs in breast tumor and breast normal adjacent FFPE specimens from the Nurses’ Health Study

Alejandro Quiroz-Zarate, Benjamin J. Harshfield, Rong Hu, Nick Knoblauch, Andrew H. Beck, Vincent Carey, Susan E. Hankinson, Rulla M. Tamimi, David J. Hunter, John Quackenbush, Aditi Hazra

Cancer Research, October 2014, 74(19 Suppl): Abstract# 3269.  [AACR Annual Mtg, April 5-9, 2014; San Diego, CA]

... We used a network medicine approach to associate breast cancer risk single nucleotide polymorphisms (SNPs) with transcript abundance in formalin fixed paraffin embedded (FFPE) breast tissue. ... We identified invasive postmenopausal breast cancer cases in the Nurses’ Health Study (NHS) diagnosed from 1990-2004 with GWAS data and sufficient RNA for expression profiling in breast tumor and normal adjacent breast tissue. RNA was extracted using the Qiagen AllPrep RNA isolation kit, amplified using the NuGen Ovation FFPE WTA kit, and profiled using the Affymetrix Human Transcriptome Array (HTA 3.0v1).  ...


76-   Meeting abstract

RV-infection modifies DNA-methylation in nasal airway epithelium cell line: Evaluation as a possible asthma trigger

Martin Pech, Brian G. Oliver, Andre Franke, Femke-Anouska Heinsen, Markus Weckmann, Matthias Kopp

European Respiratory Journal, 1 September 2014, 44(Sup 58): Abstract #3231.

During childhood recurrent rhino virus (RV) infections of the respiratory tract significantly increase the risk to develop asthma. To improve our knowledge about possible trigger mechanisms, a viral infected bronchial airway epithelium cell line was analyzed to detect modifications of the epigenetic gene regulatory mechanisms of DNA-methylation. ... Differential gene expression will be verified with the help of GeneChip Human Transcriptome Array 2.0 (Affymetrix).


77-      Meeting abstract

Search of biomarkers associated with disability progression by means of gene expression profiling in patients with progressive multiple sclerosis

R Nurtdinov, C Tur, S Malhotra, J Sastre-Garriga, X Montalban, M Comabella

Multiple Sclerosis Journal, September 2014, 20(1, suppl): Abstract #P269  [ACTRIMS-ECTRIMS MS, Boston 2014]

... We aimed to identify genes associated with disability progression in peripheral blood mononuclear cells (PBMC) from patients with primary progressive MS (PPMS).  ... gene expression profiles were determined in PBMC at baseline and after two years of follow-up by means of the Affymetrix GeneChip® Human Transcriptome Array 2.0.  ...


78-     Link is to poster list

SEQC Evaluation of the Performance of Microarrays and RNA-seq

Weihong Xu, Anthony Schweitzer, Leming Shi, SEQC consortium, Wenzhong Xiao

International Conference Intelligent Systems for Molecular Biology (ISMB), July 11-15, 2014, Boston, MA, Poster #F48.

... Here we utilized a comprehensive RNA-Seq dataset of four titration pools from two human reference RNA samples generated by the SEQC consortium and systematically evaluated RNA-Seq and several commercially available microarrays (Affymetrix Hu133plus2, PrimeView, HuGene2.0), in terms of reproducibility, accuracy and detection power for both gene- and exon-level analyses. We found that different microarrays are comparable to RNA-Seq at different read depth, contingent on performance metrics. ... The new exon-junction array HTA2.0 shows competitive strength for exon-level analysis that matches to RNA-Seq at 1-2 HiSeq lane per sample.


79-   Meeting abstract

SIRPB1 Is a Strong Predictor Biomarker of Response to 5-Azacitidine Therapy in MDS and AML Patients

Viviana Guadagnuolo, Cristina Papayannidis, Ilaria Iacobucci, Antonella Padella, Giorgia Simonetti, Stefania Paolini, Mariachiara Abbenante, Sarah Parisi, Francesca Volpato, Chiara Sartor, Maria Chiara Fontana, Emanuela Ottaviani, Anna Ferrari, Nicoletta Testoni, Carmen Baldazzi, Massimo Delledonne, Carla Filì, Michele Malagola, Federica Cattina, Simona Bernardi, Domenico Russo, Giovanni Martinelli

Blood, 6 December 2014,124(21): Abstract#1030.

Myelodisplastic syndromes (MDS) and Acute Myeloid Leukemia (AML) are a group of diseases of the elderly that initiates in a hematopoietic stem cell ... In both diseases, 5-Azacitidine (5-Aza) has been successful, inducing prolonged survival and delayed AML evolution. To identify the genes mostly predictive of treatment response, we use high-throughput genomic analysis (SNP arrays and/or NGS-RNA-seq and/or NGS-WES and/or GEP) in azacitidine-sensitive and resistant MDS/AML patients. NGS-WES or RNA seq HiSeq 2000 (Illumina) was positively done in 35/214 AML samples (16%), GEP (GeneChip Human Transcriptome Array 2.0, Affymetrix Inc.) was performed in 65/214 AML samples (30%). SNPs arrays (CytoScan HD Array, Affymetrix Inc.) was done in 125/214 AML samples (58%) and 18/32 MDS samples (56%) at diagnosis, ...



The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation

Pin Wang, Yiquan Xue, Yanmei Han, Li Lin, Cong Wu, Sheng Xu, Zhengping Jiang, Junfang Xu, Qiuyan Liu1, Xuetao Cao

Science (AAAS), 18 April 2014, 344(6181):310-313

Long noncoding RNAs (lncRNAs) play important roles in diverse biological processes; however, few have been identified that regulate immune cell differentiation and function. Here, we identified lnc-DC, which was exclusively expressed in human conventional dendritic cells (DCs).  ... [from sup file] … cDNA were hybridized for 16 hr at 45 on GeneChip Human Transcriptome Array 2.0


81-    Meeting abstract

TNF-á and IL-17 can induce inflammatory changes in human aortic endothelial cells, potentially promoting early stages of atherogenesis in psoriasis

M Cannizzaro,1,3 H Mitsui,1 J Gonzalez,2 J Fuentes-Duculan,1 M Suarez-Farinas1 and J Krueger1 1 Laboratory for Investigative Dermatology, Rockefeller University, New York, NY, 2 Translational Technology Core Lab (CCTS), Rockefeller University, New York, NY and 3 Department of Dermatology, University of Rome “Tor Vergata”, Rome, Italy

Journal of Investigative Dermatology, May 2014, 134(S1) : Abstr #088.  [Society for Investigative Dermatology, New Mexico, May 7- 0, 2014]

... Since psoriasis is an independent risk factor for development of cardiovascular diseases, we hypothesized that a mechanistic link between skin inflammation and atherogenesis could be high-levels of psoriasis related cytokines (IL-17, TNF, IFN-γ) in the circulation with attendant effects on aortic endothelial cells. Expression of IL-17 receptor on human aortic endothelial cells was demonstrated using double immunofluorescence with CD31 and confirmed by RT-PCR. ... We studied effects on gene expression using the new Affymetrix HTA 2.0 arrays. ...


82-   Meeting abstract

Transcriptome analysis demonstrates differential mRNA splicing patterns in response to LPS

Shadley, Jeffery; Dahmer, Mary; Quasney, Michael

Critical Care Medicine, December 2014, 42(12):Abstract #973. 

...  We hypothesized that genome-wide differential splicing of mRNA occurs in THP-1 cells treated with LPS.  Mrthods: THP-1 cells were treated with LPS for 4 hours and total RNA was isolated. RNA samples were hybridized to the Affymetrix GeneChip® Human Transcriptome Array 2.0. ...


83-  Meeting abstract

Transcriptome-Wide Analysis of Bone Marrow CD19+ Cells As Well As Bone Marrow B Cell Clones of Waldenström's Macroglobulinemia (WM) Vs. IgM Monoclonal Gammopathy of Undetermined Significance (IgM-MGUS)

Alessandra Trojani, Antonino Greco, Alessandra Tedeschi, MD, Milena Lodola, Barbara Di Camillo, Anna Maria Frustaci, and Enrica Morra

Blood, 6 December 2014,124(21): Abstract# 5176.

We performed a transcriptome-wide analysis of bone marrow (BM) CD19+ cells of WM vs. IgM-MGUS to find the genes and key pathways mostly involved in the comparison between WM and IgM-MGUS. We isolated BM CD19+ and CD138+ cells of 36 WM and 13 IgM-MGUS using Miltenyi Microbeads and we performed expression analysis with Affymetrix GeneChip HG U133 Plus 2.0 Array. ... We performed gene expression profiling (GEP) of the isolated BM cell clones of WM vs. IgM-MGUS using Affymetrix next-generation GeneChip HTA 2.0 to further investigate genomic complexity. ...


84-   Meeting abstract

Treatment with the histone deacetylase inhibitor Panobinostat markedly reduces chronic inflammation in HIV-infected patients

Anne Sofie H. K. Kjaer ; Reported by Jules Levin

20th International AIDS Conference, July 20-25, 2014, Melbourne, Australia.

... Gene expression in PBMCs was analyzed on a HTA 2.0 chip (Affymetrix); fold changes and p-values were computed using TAC software. ...


85-     HTA 2.0 incorrectly identified as an ILMN array

Triple-negative breast cancer subtypes and pathologic complete-response rate to neoadjuvant chemotherapy: Results from the GEICAM/2006-2003 study.

Angela Santonja, Joan Albanell, Jose Ignacio Chacon, Ana Lluch, Alfonso Sanchez-Muñoz, Federico Rojo, Antonio Anton, Laura G. Estevez, Beatriz Cirauqui, V. de Luque, Lourdes Calvo, Miguel Angel Seguí-Palmer, Arrate Plazaola, Sonia Gonzalez, Ana Santaballa, Juan de la Haba-Rodriguez, Cesar Rodriguez, Rosalia Caballero, Eva Maria Carrasco and Emilio Alba

Journal of Clinical Oncology, 2014, 32(15, May 20 Sup): Abstr# 1024. [ASCO Annual Meeting Abstracts]

... We determined TNBC molecular subtypes in FFPE pre-treatment tumor biopsies from pts recruited in this study. Gene expression profile was determined using HTA 2.0 arrays (Illumina).



Upregulation of eIF5B controls cell-cycle arrest and specific developmental stages

Sooncheol Lee, Samuel S. Truesdell, Syed I. A. Bukhari, Ju Huck Lee, Olivier LeTonqueze, Shobha Vasudevan

Proceedings of the National Academy of Sciences USA, Octover 2014, 111:E4315-E4322.

... The synthesized cDNA probe (WT Expression Kit; Ambion) was hybridized to Gene Chip Human Transcriptome Array 2.0 (Affymetrix) by the Partners Healthcare Center for Personalized Genetic Medicine Microarray facility.



Zn-Driven Discovery of a Hydrothermal Vent Fungal Metabolite Clavatustide C, and an Experimental Study of the Anti-Cancer Mechanism of Clavatustide B

Panpan Ye, Ling Shen, Wei Jiang, Ying Ye, Chen-Tung Arthur Chen, Xiaodan Wu, Kuiwu Wang, Bin Wu

Marine Drugs, online 28 May 2014, 12(6):3203-3217

... To further explore the mechanism of anti-proliferation effect, particularly the G1-S phase inhibition, Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array was used to screen transcriptome differences between clavatustide B treated and untreated HepG2 cells. .. RNA (25 ng) was used to produce biotin-labeled cRNA, which was hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0.




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