title: Genetic modifiers of progression-free survival in never-smoking lung adenocarcinoma patients treated with first-line TKIs

status: Public on Apr 30 2016

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

institute: National Health Research Institutes

summary: Via a GWA study, several SNPs have been identified as markers capable of predicting prognosis of lung cancer patients receiving TKIs therapy as first-line treatment. In order to get insights into how these genetic variants are linked to traits of interest, we conducted a genome-wide eQTL study by integrated analyses of  SNP genotyping array data and gene expression array data of 115 subjects of lung adenocarcinoma. Our study successfully identified several SNPs as eQTLs, whose genotype were significantly associated with expression levels of several already known genes related  to lung cancer.

overall_design: From the  Lung Cancer Tissue Core, 115 non-smoking subjects of lung adenocarcinoma (ADC) were selected to obtain the gene expression profiles of both lung tumor and their adjacent normal lung tissues, using Illumina WG-DASL HumanRef8 v3 or HumanHT12 v4 BeadChip. Only shared probes of those two platforms were analyzed.

first: Chao

last: Hsiung

first: I-Shou

last: Chang


title: Transcript profiling of transgenic rice lines where the OsMADS26 gene is over-expressed or down growing cultivated in standard or osmotic stress condition

status: Public on Nov 20 2015

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

summary:
Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), in stress-related developmental processes such as abscission, fruit ripening and senescence and the role of some of them in stress response regulation was reported. The aim of this study was to decipher the genes that are under the control of the OsMADS26 transcription factor in rice in standard or osmotic stress condition.
Transcriptome analysis in over-expressor and down-regulated OsMADS26 rice transgenic lines revealed that several major regulators of biotic and abiotic stress responses are mis-regulated compared to control plants, suggesting that OsMADS26 acts as an upstream negative regulator of stress-associated genes.

overall_design: Transgenic plants over-expressing or down-regulated (by RNA interference) for OsMADS26 were obtained and used to study the impact of this transcription factor on gene regulation in plants cultivated in standard or osmotic stress (100 mM manitol) condition.

first: Giang

middle: N

last: Khong

first: Jean-Benoit

last: Morel

first: Emmanuel

last: Guiderdoni


title: CPC+AC0-Gene DNA Methylation Data from Illumina 450k

status: Public on Dec 31 2015

city: Toronto

first: Paul

middle: C

last: Boutros

state: ON

address: 661 University Avenue

department: Informatics and Bio-Computing

country: Canada

institute: Ontario Institute for Cancer Research

type: Methylation profiling by genome tiling array

summary: DNA methylation profile for the samples from 143 prostate cancer patients are provided.

overall_design: DNA methylation profiling of 143 prostate cancer patients.


title: Human B-1 and pre-plamablast like cells Gene Expression Array

status: Public on Feb 01 2016

city: Manhasset

first: Tam

middle: D

last: Quach

state: NY - New York

address: 350 Community Drive

country: USA

institute: The Feinstein Medical Research Institute

summary: Human B-1 cells (CD20+CD27+CD43+CD38lo/int) and pre-plasmablast like cells (CD20+CD27hiCD38hi) are new antibody secreting cells identified in circulation. We used microarray to compare and contrast expressed genes between these two cell population

overall_design: Cell subsets of interested were sort purified using BD Influx cell sorter and were subject for RNA extraction and hybridization on Human Gene 2.1 ST arrays.

first: Tâm

last: Quách

first: Thomas

middle: L

last: Rothstein


title: Differential expression for P and Fe

status: Public on Jan 01 2016

city: New Delhi

first: Vandna

last: Rai

state: Delhi

address: Pusa campus

department: Genomics

country: India

institute: NRCPB

summary:
Root samples were used
We exposed young seedlings to P and Fe deficiency

overall_design: Expression study after 7 days of treatment

first: Ajay

last: Jain

first: Raghavendrarao

last: Sanagala


title: The plasma membrane NADPH oxidase OsRbohA plays a crucial role in developmental regulation and drought-stress response in rice

city: Yangling

first: Kunming

last: Chen

state: Shaanxi

address: Xinong Road 22#

department: College of Life Sciences

country: China

institute: Northwest A&F University

summary:
Plasma membrane NADPH oxidases (NOXs) are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. Rice NOXs have multiple homologs but their functional mechanisms are largely unknown.
We used microarrays to detail the global gene expression profiles in rice wild-type (WT, Dongjin) and a mutant osnox2 which loss the functions of OsNOX2 protein under drought and identified distinct classes of genes between the two type rice plants under both normal growth and drought stressed conditions.

overall_design: The youngest fully expanded leaves from 2.5-month-old WT and osnox2 plants (three replicates each), grown under normal growth (soil moisture, 47.3%) and drought conditions (soil moisture, 8.5%), were used for RNA extraction and hybridization on Affymetrix microarrays. Control: normal growth condition; Drought: drought stress condition.

first: Xiang

last: Wang

first: Cong-Yi

last: Zhou

first: Kun-Ming


title: Identification of recurrent GBM patients that may benefit from Bevacizumab and CCNU:  A report from the BELOB trial by the Dutch Neurooncology Group

status: Public on Jan 19 2016

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: The results from the randomized phase II BELOB trial provided evidence for a potential benefit of bevacizumab (beva; a humanized monoclonal antibody against circulating VEGF-A) when added to CCNU chemotherapy in recurrent GBM patients. In this study, we have performed gene expression profiling (DASL and RNA-seq) on formalin fixed, paraffin embedded (FFPE) tumor material from patients treated within the BELOB trial to identify recurrent GBM patients who benefit most from combined beva/CCNU treatment. We first extensively validate the use of FFPE tissues for expression profiling on both DASL and RNA-seq. Our data show that tumors assigned to IGS-18 or ‘classical’ GBMs show a significant benefit in progression free survival (PFS) and a trend towards benefit in overall survival (OS) from beva+CCNU treatment; other subtypes do not show such benefit. In particular, expression of FMO4 and OSBPL3 were associated with treatment response. All molecular glioma subtypes are evenly distributed along the different study arms and the improved outcome in the beva/CCNU arm therefore is not explained by an uneven distribution of prognostically favorable subtypes. Analysis of RNA-seq data highlighted genetic changes, including mutations, gene fusions (and identification of the exact genomic breakpoint), and copy number changes (albeit with limited resolution) within this well-defined cohort of tumors. When validated in an independent dataset, the predictive markers identified in this study will allow selection of recurrent GBM patients that benefit from beva+CCNU treatment.

overall_design:
A total of 112 samples of patients included in the Belob trial were profiled. Profiling was done in three batches (3 raw data files; Belob1, Belob2 and Belob3*.txt).

Please note that several replicates were performed to demonstrate platform reproducibility on FFPE material (basically the entire first experiment, samples 1-10 described in the all_sample_description.txt). In addition, a few samples were scraped (macrodissection) as the original tissue block contained a too low tumor content (as indicated in the  sample description field).  These Samples omitted from the final analysis are marked with X at the end of the patient ID column (in the all_sample_description.txt). Also, Of the 117 individual patients, the following patient samples were excluded in the final analysis: B11, B57, B73, B91 and B59. These samples were outliers in the gene expression analysis and did not meet the quality criteria (their median overall expression was <7.5 (log2)).

The complete sample description and raw data (of 135 samples) are provided in the all_sample_description.txt and Belob*French.txt files, however only 112 samples (included in the final data analysis) are included in this record.

Tumor Subtype (in the sample 'characteriscts) is defined by Gravendeel et al, Cancer Res 2009 Dec 1;69(23):9065-72.
TCGA subtype (in the sample 'characteriscts) is defined by Verhaak et al, Cancer Cell. 2010 Jan 19;17(1):98-110.
The sample 'chracteristic:Sensor' values indicate whether the patient alive or dead at time of analysis.

first: Andrew

last: Stubbs

first: Martin

last: van den Bent


title: Systematic drug perturbations of cancer cells reveal diverse exit paths from the proliferative state

status: Public on Oct 23 2015

city: Seattle

first: Joseph

last: ZHOU

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: Analysis of the time courses of  gene expression profiles of breast cancer cell line MCF7 treated by 16 differentiation-inducing drugs at day 1, day 3 and day 5. The drugs are the screening results from the the JHCCL library (1,500 drugs). The hypothesis tested in the present study was that cancer cells exit the proliferative state via multiple paths. Results showed that cell state transition trajectories firstly diverged and later converged to a quiescient differentiated state

overall_design: MCF7 cells were cultured in 150mm dishes and treated 1/5/10 μM of each of the 16 drugs (see details in Table S1-2). 14 plates of cells were left untreated as control samples. Cells were collected after 1, 3 and 5 days of drug treatment in RNeasy (Qiagen) lysis buffer and RNA was isolated according to the manufacture’s protocol and sent to Vancouver Prostate Center for transcript profiling.

middle: X

first: Sui

last: Huang


title: Expression data from brown planthhoper (BPH) infested and non-infested rice

status: Public on Nov 06 2015

city: Hangzhou

first: Gongyin

last: Ye

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary:
KMD is genetically engenered to be highly resistant to lepidopteran pests through expressing a synthetic cry1Ab gene and its parent non-transgenic rice is Xiushui 11.The developmental duration of BPH feeding on  KMD2 was significantly delayed. And moreover, the fecundity of BPH was significantly lower when fed on Bt rice than on the non-Bt parental plants.To investigate unintended effects in KMD2 that causes changes in BPH performance, we performed microarray (GeneChip) analysis to compare the gene expression profiles between Bt rice and non-transgenic parental plants in response to BPH infestation.
We used microarrays to detect Bt-independent variation, which might render Bt rice more defensive or less nutritious to BPH.

overall_design: For BPH treatment, 10 second-instar nymphs were infested onto each 30-day-old seedling. After 72 h, the BPH nymphs were carefully removed and rice shoots of both BPH-infested and non-infested plants were sampled for microarray analysis. There were four treatments: Xiushui 11-non infested, Xiushui 11-BPH infested, KMD2-non infested, KMD2-BPH infested, three biological replications.

first: Fang


title: Gene expression profiling of Type II Enteropathy-associated T-cell lymphoma

status: Public on Mar 03 2016

city: Singapore

first: Sanjanaa

last: Nagarajan

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

summary: Type II Enteropathy-associated T-cell lymphoma (Type II EATL) is an aggressive intestinal T-cell lymphoma with poor prognosis and has not been molecularly profiled. Through targeted amplicon sequencing, we identified a large portion of Type II EATL samples that harbor mutations in the STAT5B, JAK3 and GNAI2 genes. Here we performed gene expression profiling on four Type II EATL samples in order to better characterize this disease. As Type II EATL is suggested to arise from CD8+ IELs, we integrated our data with publicly available profile of CD8αα and CD8αβ T-cells from healthy donors (GSE33374). Gene expression profiling independently demonstrated strong enrichment of several aspects of GPCR and JAK-STAT signaling pathways. Moreover, an significant association was identified with genes containing STAT5B binding sites in their promoters.

overall_design: Microarray gene expression profiling was performed on 4 Type II Enteropathy-associated T-cell lymphoma and a combination of unsupervised and supervised clustering was performed to determine any differentially activated pathways between samples with tumor and healthy human CD161++CD8aa and CD161++CD8ab T cells (found under accession number GSE33374)

first: Maarja-Liisa

last: Nairismägi

first: Choon

middle: K

last: Ong


title: Genome-wide Gene Expression Profiling of Salinity Responsiveness in Rice

status: Public on Nov 02 2015

city: Beijing

first: Wensheng

address: 12# Zhong-guan-cun south street

institute: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences

summary: Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.

overall_design: In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.

first: Binying

last: Fu


title: Gene expression profiling of primary HER2-positive breast cancers treated with adjuvant trastuzumab

status: Public on Oct 19 2015

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Trastuzumab, a humanized monoclonal antibody directed to the HER2 protein, is the standard-of-care treatment for patients with HER2 positive breast cancer, reducing the risk of relapse and death in patients. Nonetheless, some patients relapse after treatment, underscoring the need to identify patients for whom chemotherapy + trastuzumab is adequate versus patients requiring additional drugs. To search for genes predictive of relapse in HER2-positive breast carcinoma patients treated with adjuvant trastuzumab, we conducted gene expression profiling analysis in 53 cases treated in the clinic with doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF) and trastuzumab.

overall_design: Gene expression profiling was performed using RNA from formalin-fixed paraffin-embedded tissues from 53 patients with primary HER2-positive (HER2+) tumors. The series consists in 23 relapsed and 30 non-relapsed cases with similar clinical-pathological characteristics (size, pathological lymph node involvement and estrogen receptor positivity) (3-year median follow up).

first: L

first: T

last: Triulzi

first: E

last: Tagliabue


title: Circulating RNAs profile in non-small cell lung cancer patients

status: Public on Oct 06 2015

city: Taoyuan

first: Ji-Dung

last: Luo

address: No. 259, Wen-Hua 1st road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

summary: Circulating RNAs are a less invasive and easy accessed source of samples for biomedical research and clinical applications. However, circulating mRNA is mostly fragmented and less abundant. High throughput RNA sequencing (RSEQ) and DASL assay have been both applied to profile such fragmented RNA samples. In this study, we compared the ability of transcriptomic profiling of the two platforms. Circulating RNAs from three non-small cell lung cancer patients and three age-matched healthy controls were analyzed by RSEQ and DASL assay. The concordance of each gene analyzed by the two platforms were measured with Pearson's correlation coefficient. And gene expression level determined by both platforms were confirmed by RT-PCR. The two platforms showed modest to moderate correlation. Genes with higher expression level represented higher cross-platform concordance. Compare the results of RT-PCR and the two platforms, RSEQ was much higher correlated with RT-PCR. This data suggested that RSEQ could be more suitable for circulating RNA profiling. In conclusion, we have demonstrated that genes with higher expression levels showed cross-platform concordance. And, the RSEQ could be more suitable tool for profiling circulating RNAs.

overall_design: Whole blood samples were obtained from three NSCLC patients and three healthy volunteers. The plasma section were collected after 1,600 x g centrifugation. The plasma RNAs were extracted with TRIzol-LS reagents. Total cell-free RNAs were quantitized with NanoDrop-1000. The gene expression levels were determined by Illumina DASL-HT12-v4 array. Gene expression determined by Illumina data analysis pipeline with quantile normalization. The pathways activated in each groups were identified with gene set enrichment analysis.

first: Chung-Liang

last: Shih

first: John

middle: W

last: Chang

first: Chiuan-Chian

last: Chiou


title: Gene expression profiles of ovarian Sertoli-Leydig cell tumors

status: Public on Oct 01 2015

city: Vancouver

first: Yemin

last: Wang

state: BC

address: 2660 Oak Street

department: Pathology and Laboratory Medicine

institute: University of British Columbia

summary: Analysis of the global gene expression in ovarian Sertoli-Leydig cell tumor samples with or without DICER1 RNase IIIb domain mutation

overall_design: The global expression expression profiles of eight formalin-fixed paraffin-embeded (FFPE) ovarian Sertoli-Leydig cell tumors were determined by the Ilumina DASL whole transcriptome analysis.


title: Expression data of 8 rice accessions under cold stress in seedling stage

city: Wuhan

first: Hanyan

state: Hubei

address: No. 5, Shizishan street

institute: HuaZhong Agricultural University

summary:
Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1  intermediate type accession.
We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.

overall_design: In order to getting more understanding of gene expression after cold treatment in rice seedling stage, we applied 8 accessions by cold stress screening in this Affymetrix microarrays, and each accession include 3 time-points samples: (1) before the cold treatment; (2) 6 hours after the cold treatment; (3) 24 hours after the cold treatment.

first: Haiyan

first: Yan

last: Lv

first: Lizhong

last: Xiong


title: Gene-expression profiles of hepatocellular carcinoma beyond Milan criteria undergoing liver transplantation

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Introduction: Several attempts have been made to expand the indications of liver transplantation for hepatocellular carcinoma (HCC) beyond Milan criteria. We aimed to define genomic features that enable the identification of patients with HCC beyond Milan criteria who have acceptable transplant outcomes.    Methods: Among 770 consecutive HCC patients transplanted at Mount Sinai Hospital and Mayo Clinic between 1990 and 2013, 132 had tumors exceeding Milan criteria on pathology and were enrolled in the study. Explant tumors were analyzed to assess genomic signatures of poor prognosis and immunohistochemical markers associated with tumor recurrence and overall survival.     Results: Most of the patients were males (80%) and HCV positive (71%) with a median age of 56. HCC beyond Milan criteria was defined pre-operative in 67%. On pathology, 44% of the patients satisfied the ‘up-to-7 rule’. At a median follow-up of 88 months, 64 patients had died and 45 recurred; the 5-year overall survival (OS) and recurrence rates were 57% and 35%, respectively. CK19 gene signature was independently associated with recurrence (HR=2.95, p<0.001), along with tumor size >5 cm (HR=3.37, p=0.023) and presence of satellite lesions (HR=2.98, p=0.001). S2 subclass signature, which is known to be associated with progenitor cell markers, was independently associated with poor OS (HR=3.18, p=0.001), along with tumor size >5 cm (HR=5.06, p<0.001) and outside up-to-seven rule (HR=2.50, p=0.002). Using the presence of markers of progenitor cells (either CK19 or S2 subclass signatures) patients may be classified into poor-prognosis (n=58; 5-year recurrence 53%, survival 45%) and good-prognosis subgroups (n=74; 5-year recurrence 19%, survival 67%) (HR=3.16, p<0.001 for recurrence, and HR=1.72, p=0.04 for OS).      Conclusion: Gene signatures associated with progenitor cell markers (CK19 and S2 subclass signatures) define outcome of HCC patients beyond Milan criteria after transplantation. Patients without these signatures achieve survival rates similar as those patients within Milan criteria. Once prospectively validated, these markers may provide the rationale for a limited expansion of liver transplantation indications.

overall_design: Gene expression profiling of marcodissected formalin-fixed paraffin-embedded (FFPE) heaptocellular carcinoma tumor tissues obtained from explanted livers.

first: Oriana

last: Miltiadous

first: Isabel

last: Fiel

first: Daniela

last: Sia

first: Swan

last: Thung

first: Andrew

last: Harrington

first: Poh

middle: S

last: Tan

first: Hui

last: Dong

first: Monica

last: Higuera

first: Kate

last: Revill

first: Charissa

first: Sasan

last: Roayaie

first: Jorge

last: Rakela

first: Thomas

middle: J

last: Byrne

first: Sander

last: Florman

first: Myron

last: Schwartz

first: Josep

middle: M

last: Llovet


title: Deciphering the gene expression response of human immune cells to stimulation with RSV in the context of antibodies

city: Nijmegen

first: Marloes

last: Vissers

address: Geert Grooteplein Zuid 10

department: Department of Pediatrics

institute: Radboud university medical center

summary: RSV is an important pathogen in young infants, who are largely dependent on innate immunity and the presence of maternal antibodies. However, not much is known about the interaction between the immune system and antibodies. Here, we studied the gene expression of human immune cells (PBMCs) after RSV infection in the presence of antibodies.

overall_design: After 24h of stimulation of human PBMCs (n=4) with RPMI medium, 10% human serum,10%  antibody depleted human serum in combination with RPMI medium, RSV (MOI 0.2) and inactivated RSV (MOI 0.2), total RNA was isolated and labeled cDNA was generated according to standard Nimblegen gene expression array protocols and hybridized to 12-plex 135K human gene expression arrays for read-out.

first: Gerben

last: Ferwerda


title: Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade

status: Public on Sep 11 2015

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: Phages have emerged as prime suspects in the adaptation of pathogens to new hosts and the emergence of new pathogens or epidemic clones. Here we describe the genomic features of two related prophages (Ab105-1Ø and Ab105-2Ø) present in the ST-2 epidemic clone of Acinetobacter baumannii clinical strain Ab105_GEIH-2010 and not present in genetically related Ab155_GEIH-2000 strain isolated 10 years before. The Quasicore genome of Ab105-1Ø and Ab105-2Ø prophages revealed genes that promote bacterial-host fitness. The results of microarray analysis under stress conditions, SOS response activation revealed 5% and 30% of genes expressed by Ab105-1Ø and Ab105-2Ø prophages (which produce bacterial lysis) in the first case and underexpression of these genes from prophages in the second case. Hence, the QS system plays a major role in the evolution of phages in their natural hosts and environments. Interestingly, in host-virus interactions, RT-PCR showed several mechanisms of overexpression of the SOS response in relation to phage defence mechanisms: i) SAM or AdoMet-MTase (methyltransferases) and MazG protein (pyrophosphohydrolase) associated with phage defence in response to bacterial attack; ii) eukaryotic-like protein kinase (glutamate 5-kinase) associated with prevention of secondary infection by the same or a closely related virus. Overexpression of secretory virulence factors such as oxidoreductase (DsbA-like), anfo-nitrogenase and chromosome segregation proteins were also observed. In conclusion, study of the co-evolution of phages (virus) and bacteria may be essential in the search for means of combatting multi-resistant epidemic clones.

overall_design: Three replicates from RNA of the Ab105_GEIH-2010 strain x1 condition (SOS response by Mitomycin).

first: M

last: López

first: A

last: Rueda

first: J

middle: P

last: Florido

first: L

last: Blasco

last: Fernández-García

first: Rocío

last: Trastoy

first: F

last: Fernández-Cuenca

last: Martínez-Martínez

last: Vila A Pascual

first: G

last: Bou

last: Tomás


title: Expression analysis of sk-hep-1(sk) cell and sk-hep-1-sh EZH2(sks) cell

status: Public on Aug 13 2015

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Investigation of EZH2 knocking down on whole genome gene expression level changes in  sk-hep-1 compared to sk-hep-1-sh EZH2.

overall_design: Examination of mRNA levels in sk-hep-1 cell and sk-hep-1-shEZH2. The endogenous EZH2 was knocked down in sk-hep-1-shEZH2.

first: Dan

last: Xie

first: MY

last: Cai


title: Gene Expression by array after Ferritin Knockdown in Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells

status: Public on Sep 30 2015

city: Cleveland

first: Tyler

middle: E

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

summary: Glioblastomas display hierarchies with self-renewing cancer stem-like cells (CSCs). RNA sequencing and enhancer mapping revealed regulatory programs unique to CSCs causing upregulation of the iron transporter transferrin, the top differentially expressed gene compared to tissue-specific progenitors. Direct interrogation of iron uptake demonstrated CSCs potently extract iron from the microenvironment more effectively than other tumor cells. Systematic interrogation of iron flux determined that CSCs preferentially require transferrin receptor and ferritin - two core iron regulators - to propagate and form tumors in vivo.  Depleting ferritin disrupted CSC mitotic progression, through the STAT3-FoxM1 regulatory axis, revealing an iron-regulated CSC pathway. Iron is a unique, primordial metal fundamental for earliest life forms, and on which CSCs have an epigenetically programmed, targetable dependence.

overall_design: Ferritin Light chain (FTL) or Ferritin Heavy Chain (FTH1) were knocked down by shRNA and compared to control shRNA treatment in 5 GBM stem cell lines. Affymetrix arrays were used to determine gene expression changes after ferritin knockdown.

first: David

last: Schonberg

first: Jeremy

last: Rich


title: Gene expression profiling of small bowel adenocarcinoma

status: Public on Sep 03 2015

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

country: United Kingdom

institute: University of Cambridge

summary:
The whole genome DASL HT assay was used in combination with the HumanHT-12 v4 BeadChip for screening  normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients.
Non-normalized and average normalized (background subtracted) data

overall_design: Comparing differences in gene expression in a matched normal tumour cohort of 28 small bowel adenocarcinoma patients.

middle: A

first: Manuel

last: Salto-Tellez


title: Induction of USP17 by combining BET and HDAC inhibitors in breast cancer cells.

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Members of bromodomain and extra-C terminal (BET) domain family and the histone deacetylase (HDAC) enzyme family efficiently regulate the expression of important oncogenes and tumor suppressors. HDACs induce histone hypoacetylation meanwhile BET proteins bind to acetylated lysines on histones to regulate gene transcription. Here we show that the BET inhibitor JQ1 inhibited proliferation and induced apoptosis of both triple negative and estrogen receptor positive breast cancer cells.  Consistent with the critical role of histone acetylation in the regulation of gene expression, microarray analysis revealed broad transcriptional changes after JQ1 or HDAC inhibitor treatment. By examining the molecular pathways affected by the epigenetic inhibitors we found that both BET and HDAC inhibitors are suppressing similar genes that were involved in cell cycle regulation.  Combining JQ1 with HDAC inhibitors, we found that the combination significantly decreased cell viability. This effect was partly mediated by the more efficient suppression of genes essential for cell-cycle progression.  Furthermore, we detected a dramatic increase in the expression of several members of the USP17 family of deubiquitinating enzymes in response to the single agent treatment, which further increased by the combination treatment. Since constitutive expression of USP17 has been reported to block the Ras/MAPK pathway, our data also suggest that the blockade of the Ras/MAPK pathway might also be involved in the synergistic effect of the combination treatment. In conclusion, this study suggests that co-treatment with BET inhibitors and HDAC inhibitors could be an effective treatment regime in future breast cancer therapy.

overall_design: MDA-MB-231 cells were treated with 1 µM JQ1 or 3.17 µM mocetinostat or with the combination of both for 48 hours. After treatment, total RNA was harvested, reverse transcribed and analyzed for gene expression by Affymetrix® Human Gene 2.1 ST Array.  Three biological replicates were used for each group.

first: Gabor

last: Borbely

first: Chunyan

last: Zhao

first: Lars-Arne

last: Haldosen


title: Expression data from early rice endosperm

status: Public on Sep 01 2015

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

summary: We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of regulated genes during this process.

overall_design: Rice endosperm at 2 days after pollination(DAP) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the endosperm expression profile at 2 DAP. To that end, we hand-selected endosperm according to morphological criteria at 2 DAP before cellularization.


title: Role of milk fat globule membrane (MFGM) in modulating gene expression in humans

status: Public on Aug 01 2015

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

summary:
The aim of this study was to investigate if milk fat globule membrane (MFGM) enclosing the dairy fat influence peripheral blood mononuclear cells (PBMC) gene expression. This study was a 8-week single-blind, randomized, controlled isocaloric trial with two parallel groups including overweight (mean BMI: 28) adult  women (n=30). All subjects consumed 40 g dairy fat per day either as cream (MFGM diet) or as butter oil (control diet).
MFGM diet and control diet showed differential responses in plasma cholesterol. Absolute differences in gene expression were calculated for each gene in each subject, comparing after with before the intervention. These absolute differences in gene expression were compared between intervention groups with T-test and with Significance Analysis of Microarrays (SAM). 19 genes were significantly different regulated by the two diets with a FDR of 23%. Most of thechanges in gene expression correlated with changes in blood lipids.

overall_design: Patients were examined in the morning after 12 h's fasting. Whole blood was obtained before (W0) and after completion (W8) of the dietary intervention for isolation of PBMCs and RNA extraction. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.). Signicance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.

first: Ulf

last: Riserus


title: Effect of DC-SCRIPT expression in MCF7 breast cancer cell line

city: Suita

first: Jonas

middle: Nørskov

last: Søndergaard

state: Osaka

address: IFReC Research Building, Osaka University 3-1 Yamadaoka

department: Center for Infectious Disease Education and Research (CIDER)

country: Japan

institute: Osaka University

summary: Breast cancer is one of the most common causes of cancer-related deaths in women. Nuclear receptors (NR) and their regulators are well known for their role in breast cancer. Especially ligands for the type I NRs, Estrogen Receptor (ER) and Progesterone Receptor have growth promoting effects in breast cancer cells. The NR coregulator DC-SCRIPT (ZNF366) has been found to be a strong and independent prognostic marker in ER positive (ESR1) breast cancer patients. DC-SCRIPT modulates the function of multiple NRs and has opposing effects on type I versus type II NRs. It represses the function of the growth promoting type I NRs, whereas it enhances the mainly anti-proliferative type II NRs. In this study we aimed to gain further insight into the functional role of DC-SCRIPT in breast cancer cells.  Therefore, the effect of DC-SCRIPT expression on breast cancer cell gene expression was investigated using a novel DC-SCRIPT-inducible MCF7 breast cancer cell line model. In the presence of DC-SCRIPT, multiple cell cycle related genes were differentially expressed, including the tumor suppressor gene CDKN2B.

overall_design: MCF7EV (empty vector control) and MCF7SC (DC-SCRIPT-inducible) breast cancer cell lines were treated with doxycyline for a total of 68h (to induce DC-SCRIPT expression in MCF7SC clones). After the first 24h, cells were serum starved for 24h to synchronize the cells. Subsequently, cells were released with 10 nM estradiol during the last 20 hours of culturing. Total RNA from two replicate experiments were obtained, and used to compare MCF7EV to MCF7SC clones.

first: Marleen

last: Ansems

first: Gosse

last: Adema


title: Expression analysis of gene expression changes in Homo sapiens SGC-7901 cells after knock down of MTA2 or overexpression of SNHG5

status: Public on Sep 09 2015

first: Shi

last: Juan

address: 5 Dong Dan San Tiao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Expression analysis of gene expression changes in Homo sapiens SGC-7901 cells after knock down of MTA2 (Metastasis-associated protein) or overexpression SNHG5 (snoRNA host gene 5)
Investigation of whole genome gene expression level changes in a Homo sapiens gastric carcinoma cells SGC-7901 after knock down MTA2 expression and upregulation of SNHG5

overall_design: A four chip study using total RNA extracted from  SGC-7901 cells transfected with siRNA negative control and SGC-7901 cells knock down of MTA2 with siRNA. Each chip measures the expression level of 45033 genes collected from the authoritative data source including NCBI

first: Dexian

last: Zheng

first: Juan

last: Shi

first: Lianmei


title: Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects

status: Public on Jul 15 2015

city: Ann Arbor

first: Matthew

middle: Gordon

last: Sampson

state: MI

address: 8220DMSRB3 1150 West Medical Center Drive

department: Pediatrics

institute: University of Michigan School of Medicine

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [GSK126]

status: Public on Aug 11 2015

first: Ilona

last: Kryczek

address: 1150 W. Medical Center Dr.

institute: University of Michigan

summary: To define the gene profile altered by EZH2 and H3K27me3 in response to IFNg, we performed several microarrays in primary ovarian cancer cells transfected with shEZH2 or treated with GSK126. We found that 155 and 124 genes were altered by shEZH2 and GSK126 treatment, respectively, and 20 genes were increased or decreased by both shEZH2 and GSK126 treatment.

overall_design: Primary ovarian cancer cells were pretreated with GSK126, or transduced with a shEZH2 lentivirus, and stimulated with IFNg for 24 hours. RNA were isolated by Rneasy kit according to the manufacturer's protocol, and applied for affymetrix microarray at University of Michigan DNA Sequencing Core

first: Dongjun

last: Peng

first: Nisha

last: Nagarsheth

first: Lili

first: Shuang

last: Wei

first: Weimin

last: Wang

first: Yuqing

last: Sun

first: Ende

first: Linda

last: Vatan

first: Wojciech

last: Szeliga

first: Jan

last: Kotarski

first: Rafał

last: Tarkowski

first: Yali

last: Dou

first: Kathleen

last: Cho

first: Sharon

last: Hensley-Alford

first: Adnan

last: Munkarah

first: Rebecca

last: Liu

first: Weiping

last: Zou


title: Transferring genomics to the clinic: distinguishing Burkitt and Diffuse large B-cell lymphoma

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

institute: University of Leeds


title: Effect of NDRG3 overexpression on cell response to hypoxia

status: Public on Jul 24 2015

city: Daejeon

first: Minho

last: Kang

address: 125 Gwahak-ro, Yuseong-gu

department: Medical Genomics Research Center

country: South Korea

institute: KRIBB

summary: Analysis of HeLa cells overexpressing NDRG3 or exposed to hypoxic condition.

overall_design: Gene expression profiles of HeLa cells stably expressing NDRG3 were compared to gene expression profiles of HeLa stable cells expressing mock or hypoxia-mediated gene expression profiles.

first: Dong

last: Lee

first: Ye

last: Jang

first: Young

middle: I

last: Yeom


title: Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome

first: Ilona

last: Kryczek


title: Transcriptome profiling for drought tolerant and susceptible cultivars of indica rice

status: Public on Jun 30 2015

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

summary: Traditional rice varieties found in India have many desirable characteristics. Amongst them, their differential responses to abiotic and biotic stresses are of great agricultural importance. Drought or osmotic stress is one of the major abiotic stresses afflicting crop plants in India. Indigenous varieties like Dagad deshi have been found to be drought resistant and, thereby, are being studied in great detail by plant breeders and biotechnologists alike. In this study, we have analyzed the transciptomes of two contrasting cultivars, i.e. Dagad deshi (tolerant) and IR20 (susceptible), under control and stress conditions to elucidate the differences in their responses to drought stress using Affymetrix microarray platform.

overall_design: Hydroponically grown seven-day-old seedlings of Dagad deshi and IR20 were subjected to drought stress by placing them on 3 mm Whatmann sheets under light for 3 h and 6 h at 28±1oC. For control samples, seedlings were kept in RGM (root growth medium) for 6 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, eighteen samples were analyzed representing control, 3 h and 6 h of dehydration stress for each cultivar (Dagad deshi and IR20).

first: Pratikshya

last: Borah

first: Sanjay

last: Kapoor


title: Expression data from -Pi treatment between WT, phr1, phr3 and phr1phr2phr3 triple mutant

status: Public on Jun 25 2015

city: Hangzhou

first: Guo

last: meina

address: 866 Yu Hang Tang Road

institute: Zhejiang University

summary: Fourteen days plants growth under hydroponic +P condition (200 μM) were treated under –P (no phosphate) condition for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis.  We used microarrays to detail the global programme of gene expression underlying -Pi condition among WT and mutants of phr1, phr3 and triple mutant of phr1phr2phr3.

first: M

last: Guo

first: W

last: Ruan

first: X

last: Mo


title: Whole genome expression profiling of rice leaves treated with Xanthomonas oryzae pv. oryzae secreted cell wall degrading lipase/esteraseA (LipA) at early time points, 30 min. and 120 min.

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

institute: Centre for cellular and molecular biology (CCMB)

summary:
Treatment of rice tissues with purified preparations of a Xanthomonas oryzae pv. oryzae (Xoo) secreted plant cell wall degrading enzyme, Lipase/Esterase (LipA), elicits cell wall damage induced innate immune responses. LipA activity is required for induction of defense responses.
In order to characterize the early events during elaboration of cell wall degrading enzyme, Lipase/Esterase (LipA) induced innate immune response in rice, we have performed global gene expression profiling of rice leaves treated with purified LipA at early time points, 30 minutes and 120min, after treatment. Whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips

overall_design:
Leaves of two weeks old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo  Lipase/Esterase (LipA)(500μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.0) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 30 min. and 120 min. after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo  Lipase/Esterase (LipA)and the buffer
Gene Expression profiling of rice leaves undergoing an innate immune respone induced by LipA (Lipase/Esterase A) enzyme

first: Ashish

last: Ranjan

first: Hitendra

last: Patel

first: Palaparthi

last: Ramesh

middle: V


title: Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [shEZH2]

first: Dongjun

last: Peng

first: Nisha

last: Nagarsheth

first: Lili

last: Zhao

first: Shuang

last: Wei

first: Weimin

last: Wang

first: Yuqing

last: Sun

first: Ende

first: Linda

last: Vatan

first: Wojciech

last: Szeliga

first: Jan

last: Kotarski

first: Rafał

last: Tarkowski

first: Yali

last: Dou

first: Kathleen

last: Cho

first: Sharon

last: Hensley-Alford

first: Adnan

last: Munkarah

first: Rebecca

last: Liu

first: Weiping

last: Zou


title: Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects [tubulointerstitium]

first: Matthew

last: Sampson

summary:
Tubulointersitial expression data from human kidney biopsy in African American subjects with glomerulopathies
We used microarrays to analyze the transcriptome of African American subjects with glomerulopathies and the association of expression with APOL1 risk alleles (G1 and G2)

overall_design: RNA from tubulointerstitial compartment was extracted and processed for hybridization on Affymetrix microarrays.

first: Catherine

last: Robertson

first: Sebastian

last: Martini

first: Laura

last: Mariani

first: Kevin

last: Lemley

first: Christopher

last: Gillies

first: Edgar

last: Otto

first: Jeffrey

last: Kopp

first: Anne

last: Randolph

first: Virginia

last: Vega-Warner

first: Felix

last: Eichinger

first: Viji

last: Nair

first: Debbie

last: Gipson

first: Daniel

last: Cattran

first: Duncan

last: Johnstone

first: John

last: O'Toole

first: Serena

last: Bagnasco

first: Peter

last: Song

last: Barisoni

first: Jonathan

last: Troost

first: Matthias

last: Kretzler

last: Sedor


title: Gene expression changes induced in Rice (Oryza sativa) leaves following treatment with any one of the following: wild type Xoo, lipopolysaccharide (LPS) and exopolysaccaride (EPS) deficient Xoo mutant;  LPS proficient but EPS deficient Xoo mutant

first: Ramesh

last: Sonti

summary:
Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. In rice we have shown that Xoo LPS induce callose deposition, reactive oxygen production and induced resistance response. The exopolysaccaride (EPS) secreted by Xoo might be involved in supressing these defense responses.
We have performed transcriptional profiling of rice leaf gene expression changes after treatment with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (LPS+ EPS-) and BXO43 (wild type) along with milliQ treated leaves to identify the genes that are differentially expressed.

overall_design: RNA was isolated from mid veins of rice leaves 15 hours after injecting them with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (EPS-), BXO43 (wild type)  or milli-Q water. The rice gene expression in each of the treatment was normalized based on the gene expression in the milli-Q treatment.

first: Anil

last: Girija


title: Gene expression changes induced in Rice (Oryza sativa) leaves by lipopolysaccharide (LPS) extracted from Xanthomonas oryzae pv. oryzae (Xoo) strain BXO43

summary:
Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. We have shown that treatment of rice leaves with Xoo LPS induces callose deposition, reactive oxygen production and enhances resistance against subsequent infection by the pathogen.
We have performed transcriptional profiling of rice leaves that are treated with Xoo LPS to identify differentially expressed genes.

overall_design: Xoo LPS was injected into mid-veins of rice leaves and RNA was isolated 15 hours later.


title: Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects [glomerulus]

first: Matthew

last: Sampson

summary:
Glomerular expression data from human kidney biopsy in African American subjects with glomerulopathies
We used microarrays to analyze the transcriptome of African American subjects with glomerulopathies and the association of expression with APOL1 risk alleles (G1 and G2)

overall_design: RNA from glomerular compartment was extracted and processed for hybridization on Affymetrix microarrays.

first: Catherine

last: Robertson

first: Sebastian

last: Martini

first: Laura

last: Mariani

first: Kevin

last: Lemley

first: Christopher

last: Gillies

last: Otto

last: Kopp


title: Expression analysis of Human pancreatic cancer cell line Panc1 pretreated with DMSO and Clofibrate.

status: Public on Jun 09 2015

city: suzhou

first: Shuyu

last: Zhang

state: jiangsu

address: No.199 Ren’ai Rd

department: Medical  College

institute: Soochow  University

summary: Investigation of whole genome gene expression level changes of Panc1 pretreated with Clofibrate, compared to Panc1 pretreated with DMSO.

overall_design: Compare differentially expressed genes by analyzing mRNA profilings between DMSO and Clofibrate pretreating Panc1 cell.


title: Expression data from Oryza sativa and Arabidopsis thaliana

status: Public on Jun 10 2015

city: Capital Federal

first: Mariana

last: Obertello

address: Vuelta de Obligado 2490

department: Department of Biology

country: Argentina

institute: INGEBI-CONICET

summary: In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: We also study the interspecies conservation, comparing rice with Arabidopsis thaliana nitrogen transcriptomes, to help identify conserved nitrogen regulation.

first: Stuti

last: Srivastava

first: Manpreet

last: Katari

first: Gloria

last: Coruzzi


title: An analysis of genomic structural alteration in three human ES cell lines.

status: Public on May 20 2015

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for three human ES cell lines, namely, SEES-1, SEES-2, and SEES-3. Samples were collected after 4 to 60 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher genomic stability of the ES cells compared to some well-known normal cell lines.

overall_design: Several samples were collected after 4 to 60 passages and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the ES cells.

first: Hidenori

last: Akutsu

first: Kazuhiro

last: Nakabayashi

first: Kohji

last: Okamura

first: Kenichiro

last: Hata


title: SNP data from human fibroblasts and induced Pluripotent Stem cells.

status: Public on May 28 2015

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Single cell RT-qPCR analysis of induced pluripotent stem cell-derived cortical neurons reveals frequent dual layer identity. Handel AE, Chintawar S, Lalic T, Whiteley E, Giustacchini A, Argoud K, Sopp P, Bowden R, Cowley SA, Newey S, Ackerman C, Ponting CP and Cader ZM. Submitted

overall_design: human iPSc lines were derived from human dermal fibroblasts from control donors. SNP and gene expression datasets from control lines. Note that iPS NHDF-1, also used in the current study, has been published previously [Van Wilgenburg B., Browne C., Vowles J. & Cowley S. A. Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions. PLoS One 8, e71098 (2013);  Physiological characterisation of human iPS-derived dopaminergic neurons.  Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA, Wade-Martins R.  PLoS One. 2014 9(2):e87388]

first: A

last: Handel

first: S

last: Chintawar

first: T

last: Lalic

first: E

last: Whiteley

last: Giustacchini

first: K

last: Argoud

first: P

last: Sopp

first: R

last: Bowden

last: Newey

first: C

last: Ackerman

last: Ponting

first: Z

last: Cader


title: Effect of As (V) 50µm in  transcription change of six rice genotypes (BRG-12, BRG-15, BRG-20, CN1646-5, NAYANMONI and CN1646-2)

status: Public on Feb 28 2015

city: Lucknow

first: Debasis

last: Chakarbarty

state: U.P, India

address: Rana Pratap Marg

institute: National Botanical Research Institute

summary: Affymetrix expression analysis was used to check transcipt expression in As (V) stress.

overall_design: The RNA from root of six rice genotypes (BRG-12, BRG-15, BRG-20, CN1646-5, NAYANMONI and CN1646-2) was isolated after 24 hrtreatment of As (V) 0µm and 50µm .The rice gene chip was used for expression analysis.

first: CHAKRABARTY

last: DEBASIS

first: RAI

last: ARTI

first: BHARDWAJ

last: ARCHANA

first: MISRA

last: PRASHANT

first: BAG

last: SUMIT

first: ADHIKARI

last: BIJAN

first: TRIPATHI

last: RD

first: TRIVEDI

last: PRABODH


title: KDM4A depletion by siRNA in HEK293T cells

status: Public on Mar 31 2015

city: Charlestown

first: Johnathan

last: Whestine

state: MA

address: RM7103 Bldg 149 13th Street

department: Cancer Center

institute: MGH

summary:
The goal of this study was to determine genes affected by depletion of KDM4A in HEK293T cells
This data was used in Van Rechem et. al. Cancer Discovery 2014 to demonstrate that depletion of KDM4A did not alter expression of genese associated with translation.

overall_design: The experiment uses two different shRNA constructs; shKDM4A.2 in a pSuper backbone and shKDM4A.6 in a pLKO backbone.  A corresponding empty vector control was conducted for each backbone.  Each shRNA was compared to its own control.

middle: R

last: Whetstine


title: Concurrent whole-genome haplotyping and copy number profiling of single cells

status: Public on May 15 2015

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: Genomic analysis of Fibrolammellar Hepatocellular Carcinoma reveals an unique molecular profile [Training set]

status: Public on Feb 12 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Background & Aims: Fibrolamellar hepatocellular carcinoma (FLC) is a rare primary  hepatic cancer usually developed in non-cirrhotic livers of children and young adults  with unknown etiology. Treatment is limited to surgical intervention. To date, molecular  pathogenesis of FLC has been poorly characterized. Herein, we aim to provide an  integrative genomic analysis from a large series of FLC patients.  Methods: A clinically annotated cohort of 77 FLCs was analyzed through whole transcriptome,  SNP-array and whole-exome sequencing. Non-negative matrix  factorization was performed for class discovery, and GSEA, NTP, IPA and  immunohistochemistry for functional annotation. GISTIC algorithm identified  chromosomal aberrations; Mutect and VarScan2, somatic mutations, and Random  survival forest the prognostic signature, validated in an independent cohort.  Results: Unsupervised gene expression clustering revealed 3 robust molecular  classes: Proliferation-51%, enriched with liver cancer proliferation signatures and  mTOR signaling activation, Inflammation-26%, with pro-inflammatory cytokines  signatures, and Unannotated-23%, with non-liver-related cancer signatures.  Neuroendocrine genes and cholangiocyte and hepatocyte histological markers were  present in all classes. FLC showed few copy number variations, being the most  frequent: focal amplification at 8q24.3(12.5%), and deletions at 19p13(28%) and  22q13.32(25%). DNAJB1-PRKACA fusion transcript was observed in 79% of cases.  FLC tumors had 32 damaging mutations on average, affecting uncommon genes in  liver neoplasms (BRCA2, U2AF1). An 8-gene prognostic signature predicted survival in  FLC patients.  Conclusions: FLC genomic analysis reveals a unique molecular portrait characterized  by uncommon damaging mutations and chromosomal aberrations, and a highly  prevalent fusion protein. Three molecular classes, including Proliferation and  Inflammation, define the biological behavior. Prognostic signature will allow better  patient stratification.

overall_design: Gene-expression profiles of formalin-fixed, paraffin-embedded human fibrolamellar hepatocellular carcinoma

first: H

last: Cornella

first: S

last: Sayols


title: Genomic analysis of Fibrolammellar Hepatocellular Carcinoma reveals an unique molecular profile [Test set]

summary: Background & Aims: Fibrolamellar hepatocellular carcinoma (FLC) is a rare primary  hepatic cancer usually developed in non-cirrhotic livers of children and young adults  with unknown etiology. Treatment is limited to surgical intervention. To date, molecular  pathogenesis of FLC has been poorly characterized. Herein, we aim to provide an  integrative genomic analysis from a large series of FLC patients.  Methods: A clinically annotated cohort of 77 FLCs was analyzed through wholetranscriptome,  SNP-array and whole-exome sequencing. Non-negative matrix  factorization was performed for class discovery, and GSEA, NTP, IPA and  immunohistochemistry for functional annotation. GISTIC algorithm identified  chromosomal aberrations; Mutect and VarScan2, somatic mutations, and Random  survival forest the prognostic signature, validated in an independent cohort.  Results: Unsupervised gene expression clustering revealed 3 robust molecular  classes: Proliferation-51%, enriched with liver cancer proliferation signatures and  mTOR signaling activation, Inflammation-26%, with pro-inflammatory cytokines  signatures, and Unannotated-23%, with non-liver-related cancer signatures.  Neuroendocrine genes and cholangiocyte and hepatocyte histological markers were  present in all classes. FLC showed few copy number variations, being the most  frequent: focal amplification at 8q24.3(12.5%), and deletions at 19p13(28%) and  22q13.32(25%). DNAJB1-PRKACA fusion transcript was observed in 79% of cases.  FLC tumors had 32 damaging mutations on average, affecting uncommon genes in  liver neoplasms (BRCA2, U2AF1). An 8-gene prognostic signature predicted survival in  FLC patients.  Conclusions: FLC genomic analysis reveals a unique molecular portrait characterized  by uncommon damaging mutations and chromosomal aberrations, and a highly  prevalent fusion protein. Three molecular classes, including Proliferation and  Inflammation, define the biological behavior. Prognostic signature will allow better  patient stratification.

overall_design: Gene-expression profiles of fresh frozen human fibrolamellar hepatocellular carcinoma


title: Concurrent whole-genome haplotyping and copy number profiling of single cells (Illumina)

summary: Methods for haplotyping and DNA copy number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required that substantially distorts the frequency and composition of the cell’s alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP-genotypes (AA, AB, BB), and DNA copy number profiling remains difficult as true DNA copy number aberrations have to be discriminated from WGA-artifacts. Here, we developed a single-cell genome analysis method that reconstructs genome-wide haplotype architectures as well as the copy-number and segregational origin of those haplotypes by deciphering WGA-distorted SNP B-allele fractions, using a process we coin haplarithmisis. We demonstrate clinical precision of the method on single cells biopsied from human embryos to diagnose disease alleles genome wide, we advance and facilitate the detection of numerical and structural chromosomal anomalies in single cells, and can distinguish meiotic from mitotic segregation errors in a single assay.

overall_design: Here we provide two sample sets, including (1) a reference family delivering samples applied for the development and optimization of single-cell genotyping, QC-metrics, haplarithmisis and the siCHILD algorithm. Specifically, the reference family delivers genomic DNA samples isolated from peripheral blood of two siblings 'S1' and 'S2', the mother and father of these siblings, as well as of the maternal grandmother and grandfather. Of individuals ‘S1’ and ‘S2’, six EBV-transformed lymphoblastoid single cells were also isolated, of which three were whole-genome amplified using MDA and three using PicoPlex. These multi-cell genomic DNA samples and single-cell WGA-products were hybridized to Illumina HumanCytoSNP12-v2.1 SNP-arrays following: (i) the protocol as recommended by the company and/or (ii) a modified rapid protocol as described below. Subsequently, the SNP-probe signals were interpreted by two different genotyping algorithms (GenCall and GenoSNP). Based on overall performance, we decided to use GenCall for interpreting Illumina SNP-probe signals of single-cell and multi-cell DNA samples. (2) A set of 12 families undergoing genetic diagnosis (for Mendelian disorders or translocation chromosomes) of preimplantation embryos following in vitro fertilization. In general, each family delivers genomic DNA samples isolated from peripheral blood of the two parents as well as a sibling and/or other close relatives; the specific kinships for each family are given in the 'description' column. In addition, of each family single blastomeres biopsied from preimplantation embryos obtained via in vitro fertilization of the parental gametes are also provided. All single-cell genomes were amplified by MDA. All the samples were hybridized to Illumina HumanCytoSNP12-v2.1 SNP-arrays following the rapid protocol. This data was used for clinical validation of the siCHILD algorithm.

first: Eftychia

last: Dimitriadou

first: Ligia

last: Mateiu

first: Cindy

last: Melotte

first: Niels

last: Van der Aa

first: Parveen

last: Kumar

first: Rakhi

last: Das

first: Koen

last: Theunis

first: Jiqiu

last: Cheng

first: Eric

last: Legius

first: Yves

last: Moreau

first: Sophie

last: Debrock

first: Thomas

last: D'Hooghe

first: Pieter

last: Verdyck

first: Martine

last: DeRycke

first: Karen

last: Sermon

first: Joris

last: Vermeesch

first: Thierry

last: Voet


title: Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus [miRNA]

status: Public on May 07 2015

city: Heidelberg

first: Tobias

last: Bauer

address: Im Neuenheimer Feld 280

department: Theoretical Bioinformatics

country: Germany

institute: German Cancer Research Center

summary: Short hairpin RNA (shRNA) expression strategies that allow safe and persistent target mRNA knockdown are key to the success of many in vitro or in vivo RNAi applications. Here, we propose a novel solution which is expression of a promoterless miRNA-adapted shRNA (shmiRNA) from an engineered genomic miRNA locus. For proof-of-concept, we genetically “vaccinated” liver cells against a human pathogen, by using TALEns or CRISPR to integrate an anti-hepatitis C virus (HCV) shmiRNA into the liver-specific miR-122/hcr gene. Reporter assays and qRT-PCR confirmed anti-HCV shmiRNA expression as well as miR-122 integrity and functionality. Specificity and safety of shmiRNA integration were validated via PCR, cDNA and miRNA profiling, and whole genome sequencing. A subgenomic HCV replicon and a full-length reporter virus, but not a Dengue virus control, were significantly impaired in the modified cells. Our original combination of DNA engineering and RNA expression technologies should benefit numerous applications, from basic miRNA research, to human cell and gene therapy

overall_design: Four Huh7 cells lines at 3 different passages were analyzed. The reference cell line was Huh7 wild type cells (WT). The other three cell lines had an integration of an anti-HCV shmiRNA in the hcr locus and miR-122 intact (T2 31.3) or mutated (TS 30.20 and U6 20.16). RNA was extracted from three different passages.

first: Elena

last: Senis

first: Dirk

last: Grimm


title: Expression data from rice meiosis-stage young inflorescences

status: Public on Apr 28 2015

city: Wuhan

first: Yufang

last: Pan

address: bayi road

institute: Wuhan university

summary:
Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). UGPase protein accumulates in TGMS-Co27 florets at low temperatures and temperature-sensitive splicing is involved in its sterility transitions.However, details of the molecular mechanisms involved are unknown.
we use microarrays to compare transcriptomic profiles during the meiosis-stage of flower development in TGMS-Co27 and wild-type (H1493) plants grown at high and low temperatures. The detected differences in expression profiles provide further understanding of the regulatory networks underlying flower development generally, identify genes involved in the TGMS process in TGMS-Co27 and may provide reference data for analyses of molecular mechanisms underlying sterility transitions in other PGMS/TGMS rice lines.

overall_design: Meiosis-stage inflorescences were used for this study because pollen mother cells (PMCs) of TGMS-Co27 plants begin to degenerate at this stage. Samples from H1493 grown at high temperature, TGMS-Co27 grown at high temperature, H1493 grown at low temperature and TGMS-Co27 grown at low temperature were harvested to compare the difference between fertile and sterile rice lines.

first: Rongzhi

last: Chen


title: Expression data in PD-L1 positive and PD-L1 negative human melanoma samples

status: Public on May 01 2015

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary:
Blocking the PD-1/PD-L1 immunosuppressive pathway has shown promise in the treatment of certain cancers including melanoma.
This study investigates differences in the gene expression profiles of human melanomas that do or do not display the immunosuppressive protein PD-L1.
Further understanding of genes expressed within the tumor microenvironment of PD-L1+ tumors may lead to improved rationally designed treatments.

overall_design:
Gene expression profiling was performed on total RNA extracted by laser capture microdissection from 11 archived formalin-fixed paraffin-embedded (FFPE) melanoma specimens,
5 of which were PD-L1 positive and 6 PD-L1 negative. Details of the design, and the gene signatures found are given in the paper associated with this GEO Series:
Janis M. Taube, Geoffrey D. Young, Tracee L. McMiller, Shuming Chen, January T. Salas, Theresa S. Pritchard, Haiying Xu, Alan K. Meeker, Jinshui Fan, Chris Cheadle,
Alan E. Berger, Drew M. Pardoll, and Suzanne L. Topalian, Differential expression of immune-regulatory genes associated
with PD-L1 display in melanoma:  implications for PD-1 pathway blockade,
Clin Cancer Res 2015, in press.

first: Janis

last: Taube

first: Geoffrey

middle: D

last: Young

first: Tracee

middle: L

last: McMiller

first: Shuming

first: January

middle: T

last: Salas

first: Theresa

last: Pritchard

first: Haiying

last: Xu

last: Meeker

first: Jinshui

last: Fan

first: Chris

last: Cheadle

first: Drew

last: Pardoll

first: Suzanne

last: Topalian


title: Time-course analysis of transcriptomes of human long-term (LT) and short-term (ST) hematopoietic stem cells (HSC) after xenotransplantation

status: Public on Feb 20 2015

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

summary: Here we tracked transcriptional changes in LT, ST-HSC and MLP after transplantation into immunocompromised mice. We show that LT- and ST-HSC activate similar pathways upon transplantation but they modulate distinct sets of genes.

overall_design: Total RNA was obtained from flow-sorted populations of human LT-, ST-HSC and MLP isolated from cord blood or immunocompromised mice transplanted with human at hematopoeitic progenitors at different time points after transplantation.

first: Jian-Bing

first: John

last: Dick


title: miRNA expression of extracellular vesicles

status: Public on Apr 02 2015

city: Tokyo

first: Naoomi

last: Tominaga

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research institute

summary: To further investigate the molecular mechanisms by which EVs mediated the abnormal localization of tight junction proteins and adherence junction protein, we performed miRNA microarray analysis of extracellular vesicles isolated from breast cancer cells.

overall_design: miRNA expression in extracellular vesicles was collected from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.

first: Nobuyoshi

last: Kosaka


title: SNP data from human fibroblasts and induced Pluripotent Stem cells from amyotrophic lateral sclerosis patients

status: Public on Dec 31 2014

first: Sally

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) from amyotrophic lateral sclerosis (ALS, motor neuron disease) patients, using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to motor neuron cultures and downstream functional assays.
Mutihac R., Scaber J., Lalic T., Ababneh N., Vowles, J., Fletcher-Jones A., Douglas A.G.L., Browne C., Nakanishi M., Turner M., Wade-Martins R., Cowley S.A. and Talbot K. Altered ER calcium homeostasis and stress granule formation in iPSC-derived motor neurons from ALS/FTD patients with C9orf72 expansions. Submitted

overall_design: human iPSc lines were derived from human dermal fibroblasts from 3 ALS patients with C9orf72 mutations (2 lines per patient) and control donors. SNP datasets for control fibroblasts HDF OX1 and NHDF, and SNP and gene expression datasets from control lines iPS OX1-19 and iPS NHDF-1, have been published previously: Van Wilgenburg B., Browne C., Vowles J. & Cowley S. A. Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions. PLoS One 8, e71098 (2013). GEO Superseries GSE45472  ;  Physiological characterisation of human iPS-derived dopaminergic neurons.  Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA, Wade-Martins R.PLoS One. 2014 9(2):e87388 GEO superseries GSE43904. SNP dataset for control fibroblasts HDF AH017 is in press, and is available in GEO Superseries GSE69302.

first: R

last: Mutihac

first: J

last: Scaber

first: T

last: Lalic

first: N

last: Ababneh

last: Vowles

first: A

last: Fletcher-Jones

middle: G

last: Douglas

first: C

last: Browne

first: M

last: Nakanishi

last: Turner

last: Wade-Martins

first: S

first: K

last: Talbot


title: Transcript profiling in stem base of crown root less 1 mutant after ectopic expression induction by dexamethasome of CRL1

status: Public on Jan 01 2015

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

summary:
Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1.
Transcriptome analysis in crl1 mutant plants where the CRL1 gene expression was ectopically induced revealed a set of 277 up regulated genes including a large part of genes encoding transcription factors and genes encoding proteins associated to hormone homeostasis, to cell division, expansion and differentiation.

overall_design: We transformed crl1 mutant plants with a construction allowing the control of CRL1 expression by exogenous dexamethasone.  Three independents transgenic lines were used. Controls were untranformed or transformed with an empty plasmid crl1 mutant plants. Transcriptome profiling were conducted 4h and 8h after dexamethasone treatment to identify early CRL1-activated genes.

first: Yoan

last: Coudert


title: Serious leaf damage caused by Osslac7 mutation arouses self-protection mechanism in rice

first: Xiaolei

last: Fan

address: Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary:
OsSLAC7 in Oryza sativa L. is a homolog of Arabidopsis thaliana AtSLAC1, which contains conserved C4-Dicarboxylate transporter domain. Loss of its function caused cell membrane instability and serious leaf damage.
We used Affymetrix Rice Genome Array to detail the differences in global gene expression between widetype and the OsSLAC7 T-DNA insertion mutants, and to make clear the bioprocesses affected by the mutation.

overall_design: OsSLAC7(Os01g0385400) T-DNA insertion mutant and wildtype japonica rice cultivar Zhonghua11 were used for RNA extraction and hybridization on Affymetrix Rice Genome Array.

first: Weiwei

last: Tie

first: Jiemin

last: Wu

first: Taiyu

last: Chen

first: Liaoxun

last: Lu

first: Hao

first: Fei

last: Zhou

first: Yongjun

last: Lin


title: Genomic analysis of Fibrolammellar Hepatocellular Carcinoma reveals an unique molecular profile.

first: Manel

last: Esteller

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Affymetrix SNP array data for Healthy Individual Malay Sub-Ethnic Group

status: Public on Feb 11 2015

city: KOta Bharu

first: Bin Alwi

last: Zilfalil

address: School of Medical Sciences, Kubang Kerian

department: Department of Paediatrics

country: Malaysia

institute: Universiti Sains Malaysia

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: The Malaysian Node of the Human Variome Project Database (MyHVPDb) is a country specific database of human variant and gene mutation that was established in 2011. This ethnic specific mutation and variation databases are being continuously updated, recording extensive information over the genetic heterogeneity of the Malaysian ethnic groups. The database comprises of SNP Database and Mutation Database. The SNP database has stored 291718 SNPs that was obtained by genotyping the SNPs of 101 healthy individuals from six Malay sub-ethnic groups which consist of Malay Kelantan, Malay Banjar, Malay Kedah, Malay Jawa, Malay Bugis and Malay Champa.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.

first: Shafawati

last: Ab-Rajab

first: Hatin

last: Wan-isa

first: Halim-Fikri

last: Hashim


title: Expression data from Incidental vs. Surgical BPH samples

status: Public on Jan 27 2015

city: Dallas

first: douglas

middle: william

last: strand

address: 5323 Harry Hines Blvd, Urology Dept. JA5.150D

department: Urology

institute: UT Southwestern Medical Center

summary: used to identify differences between tissues from patients undergoing surgery for BPH with unresolved symptoms compared to incidental BPH from patients with prostate cancer

overall_design: cohorts are based on surgical distinction

first: Strand

last: Douglas

first: Hayward

last: Simon


title: Inoculation of rice with the non-host pathogen Puccinia triticina f. sp. tritici elicits an active transcriptional response

status: Public on Dec 01 2014

city: Manhattan

first: Jianfa

last: Bai

state: KS

address: 1800 Denison Ave

department: Diagnostic Medicine and Pathobiology

institute: Kansas State University

summary:
Japonica rice cultivar Nipponbare was inoculated with wheat leaf rust (Puccinia triticina f. sp. tritici, non-host pathogen to rice) to compare gene expression profiles with mock-inoculated
controls.  Although eventually failed in invasion, leaf rust induced a set of rice genes that were distinctally up-regulated, some of those were confirmed by quantitative real-time PCR assays.

overall_design: Rice leaves were heavily inoculated with a non-host pathogen, wheat leaf rust fungus, and compared with mock inoculation with 3 biological replications.

first: Hongbing

last: Li

first: Tariq

last: Mahmood

first: Ginny

last: Antony

first: Mike

last: Pumphreys

first: Robert

last: Bowden

first: Bikram

last: SGill

first: Zhensheng

last: Kang

first: Frank

middle: F

last: White


title: Rice Hybrid Weakness is Caused mainly by the Enhanced Stress-Response

status: Public on Feb 03 2015

city: Shang Hai

first: Li

last: Song

address: FengLin Road

institute: SIPPE

summary: Hybrid weakness is a type of reproductive barrier found in many plant species and is important to plant evolution. Compared with heterosis, hybrid weakness has received less attention in evolutionary genetics studies. In rice, the hybrid weakness of the F1 progenies between the Jamaica- and temperate Japonica-types has been intensively genetically surveyed, and it has been found to be controlled by two complementary genes, Hwc1 and Hwc2. The defective development of the hybrid F1 seedlings was found to be mainly due to abnormal root growth, resulting in non-continuous growth and the eventual lethality of the plants. Detailed genome-wide analyses using the hybrid F1 plant and parents showed that, in contrast to heterosis, in which photosynthesis- and starch metabolism-related genes are preferentially expressed, the abscisic acid (ABA)-response and abiotic-/biotic- and defense-related genes were significantly up-regulated in the roots of  the hybrid F1, resulting in suppressed growth of the whole plant. This indicates that the mechanisms of heterosis and hybrid weakness differ and provides informative clues to facilitate the understanding of the mechanisms controlling the reproductive isolation and hybrid weakness.

overall_design: Here we report the analysis of gene expression patterns between the rice hybrid and its parents, using a whole-genome microarray and 12 samples were analyzed. Our results indicate that the expressions of abscisic acid (ABA)-response genes as well as abiotic and biotic stress-response genes were also enriched in the hybrid F1 root, which may result in the poor growth of the hybrid roots.

first: Jiang

last: Hu

first: Liang-jiao

last: Xue

first: Qian

last: Qian

first: Hong-wei


title: Expression data from cynosure (cyn) mutant and its CYNOSURE (CYN) wild-type at before flowering and 5 days after pollination stage

status: Public on Nov 03 2014

city: Kunming

first: LI

last: JUAN

state: Yunnan

address: Black Dragon Pool

department: Rice Research Institute

institute: Yunnan Agricultural University

summary: To assess further the role of CYN in relation to integument morphogenesis, gametophytic cell fate specification, embryogenesis and endosperm development, we compared the expression profiles between the cyn mutant and wild-type at two different stages(before flowering and 5 days after pollination stage) of ovule development by microarray analysis. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as  auxin efflux & polarity & cell differentiation, flower and embryonic development, signal transduction.These results supported that MADS protein CYN could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes (including MADS or non-MADS transcription factors) involved in developmental and hormonal pathways.

overall_design: Three independent biological replicates of cyn mutant and wild-type panicle mRNA at two different stages of ovule development were used for microarray experiments. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at before flowering and 5 days after pollination stage.

first: D

middle: S

last: Lee

first: L

middle: J

last: Chen

first: C

middle: Y

first: Y

last: Liu

first: X

last: Tan

first: B

last: Lu

first: J

first: S

middle: X

last: Gan

first: H

middle: K

last: Snh

last: Zhu


title: Stromal contribution to expression signatures of colorectal cancer (rectal samples)

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: We noticed that a recently identified poor prognosis stem/serrated molecular subtype of colorectal cancer (CRC) is characterized by up-regulation of transcripts known to be also expressed by stromal cells. To better define the origin of such transcripts, we analyzed  RNAseq and microarray datasets from CRC mouse xenografts, where human cancer cells are supported by murine stroma. The analysis revealed that mRNA levels of stem/serrated subtype genes are mostly due to stromal expression, even when the stromal fraction is below 5%. Indeed, a classifier based on genes exclusively expressed by cancer-associated fibroblasts was significantly associated, in multiple datasets, to poor prognosis of CRC and to radioresistance of rectal cancer.

overall_design:
Molecular Characterization of 72 primary rectal cancer formalin-fixed, paraffin-embedded (FFPE) specimens including 58 pretreatment specimens, 14 surgical specimens.

The study was approved by the ethic institutional review board for "Biobanking and use of human tissues for experimental studies" of the Pathology Service of the Azienda Ospedaliera Città della Salute e della Scienza di Torino, Torino, Italy. The project provided a verbal  informed consent from the patients due to the retrospective approach of the study, which did not impact on their treatment. All the cases were anonymously recorded. The IRB approved this consent procedure.

first: Claudio

last: Isella

first: Guy

last: Strorme

first: Paola

last: Cassoni


title: Integrinated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact

status: Public on Oct 09 2014

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

summary: Cancer results from processes prone to selective pressure and dysregulation acting along the sequence-to-phenotype continuum DNA→RNA→Protein→Disease. However, the extent to which cancer is a manifestation of the proteome is unknown. Here we present an integrated omic map representing non-small cell lung carcinoma. Dysregulated proteins not previously implicated as cancer drivers are encoded throughout the genome including but not limited to regions of recurrent DNA amplification/deletion. Clustering reveals signatures composed of metabolism proteins particularly highly recapitulated between patient-matched primary and xenograft tumours. Interrogation of The Cancer Genome Atlas reveals cohorts of patients with lung and other cancers that have DNA alterations in genes encoding the signatures, and this was accompanied by differences in survival. The recognition of genome and proteome alterations as related products of selective pressure driving the disease phenotype may be a general approach to uncover and group together cryptic, polygenic disease drivers.

overall_design: Total RNAs from xenografts, primary tumor, and normal adjacent tissues were amplified by DASL kit and hybridized to Illumina HT12v4 chip

first: Ming-Sound

first: Chang-Qi


title: Differential Gene Expression between Active and Quiescent Stages of Ulcerative Colitis: Insights into a Distinctive Pathogenesis Profile

status: Public on Dec 12 2014

first: Xinmei

last: Zhao

address: 5200 Eastern Avenue

department: Division allergy and clinical immunology

institute: Johns Hopkins U

summary:
Our objective was to elucidate patterns of gene expression underlying the progression of UC disease.
Single endoscopic pinch biopsies (n=40) were assayed using the Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) microarray. Tissue was sampled in consecutive active and quiescent stages at the same site in individual UC patients, and these stages (active and inactive) were compared with each other as well as to non-inflammatory bowel disease (non-IBD) healthy controls.

overall_design: Gene expression of UC active and inactive is compared at a global level using total RNA from the same UC pateints using the Illumina microarray platform.

first: Chris

last: Cheadle


title: Gene Expression profiling of rice leaves undergoing an innate immune response induced by XOO secreted cell wall degrading enzyme LipA (Lipase/Esterase A)

city: Hyderabad

first: Ramesh

last: Sonti

address: Uppal Road

department: Plant Microbe Interactions

institute: Centre for cellular and molecular biology (CCMB)

summary:
The plant cell wall degrading enzyme LipA (Lipase/Esterase A) is a Type II secretion system secreted protein of Xanthomonas oryzae pv. oryzae (Xoo; the casual of bacterial leaf blight of rice). LipA is an Xoo virulence factor. However, LipA is a double edged sword for Xoo as it induces rice defense responses such as programmed cell death/hypersensitive response like reaction (HR) and callose deposition. Prior treatment with LipA enhances resistance against subseqent Xoo infection.
In order to understand the molecular events associated with  Esterase (LipA) induced innate immune responsein rice , whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips

overall_design: Leaves of two weeks old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo Lipase/Esterase A (LipA) (500μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.6) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12 h after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo  LipA and the buffer.

first: Ashish

last: Ranjan

first: Hitendra

last: Patel

first: Palaparthi

last: Ramesh


title: A Genome-wide Study of Cytogenetic Changes in Colorectal Cancer Using SNP Microarrays: Possibilities for Future Personalized Treatment

status: Public on Dec 19 2014

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

summary: In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh-frozen tissue from 86 CRC patients using Illumina’s Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF), which is a representation of allelic composition.  This data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (MSI, histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g., amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From the Therapeutic Target Database we found relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions harboring genes which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high-density SNP arrays for cytogenetic study in CRC  and its importance for personalized treatment.

overall_design:
DNA was extracted from colon tissue samples provided by 86 CRC patients. Each patient provided paired CRC tumor tissue and adjacent normal colon mucosa samples, which were fresh-frozen after resection. Samples were genotyped using Illumina's Infinium-based 610 Quad and CytoSNP 12 microarray chips. The genotype data from paired tumor and normal samples was used to detect tumor-specific chromosomal instabilities in copy number, including copy-neutral LOH, which cannot be assessed by many other cytogenetic methods.

Supplementary file "GSE34678_raw_GPL8887.txt" includes the raw data for Samples using GPL8887 (GSM853162-GSM853239); supplementary file "GSE34678_raw_GPL13829.txt" includes the raw data for Samples using GPL13829 (GSM853240-GSM853363).

first: Jasmine

last: Farzana

first: Ronald

last: Rahaman

first: Charlotte

last: Dodsworth

first: Roy

last: Shantanu

first: Paul

last: Rupash

first: Maruf

last: Raza

first: Rachelle

last: Paul-Brutus

first: Mohammed

last: Kamal

first: Habibul

last: Ahsan


title: Genome-wide analysis of gene expression in early stage non-small cell lung cancer (NSCLC)

city: Pittsburgh

first: Marjorie

last: Romkes

state: PA

address: 5117 Centre Avenue

department: Medicine - Hematology/Oncology

institute: University of Pittsburgh

summary: Analysis of disease free and overall survival at gene expression level. Specific hypothesis evaluated is that MMP19 functions through multiple mechanisms to promote the development and progression of NSCLC

overall_design: Total RNA obtained from snap frozen tumor tissue samples.

first: Jill

last: Siegfried


title: Microarray analysis of gene expression in rice lacking cytosolic glutamine synthetase 1;2

status: Public on Nov 28 2014

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

institute: RIKEN

summary:
Goal of the study is to characterize specific function(s) of the cytosolic glutamine synthetase (GS) 1;2 for apical meristem induction in rice plants. To address the issue, we conducted transcript profiling toward basal parts of the knockout mutant lacking GS1;2.
We used microarrays conduct transcript profiling of gs1;2 plants. Wild-type samples were used as control.

overall_design: 12 samples were analyzed; 3 biological replicates were used for each tissue.

first: Miwa

last: Ohashi

first: Miyako

last: Kusano

first: Tomoko

last: Nishizawa

first: Tomoyuki

last: Yamaya


title: Expression data in Arabidopsis Col-0 with cold acclimation (CA) treatment and subsequent cold deacclimation (DA) treatment.

status: Public on Oct 02 2014

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

summary: To understand mRNA expression pattern during cold acclimation and deacclimation, transcriptional profiling of cold acclimation and deacclimation-treated plants were analyzed using Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F.

overall_design: Arabidopsis Col-0 were grown on MS plate for 2 weeks (16 hours light / 8 hours dark). Two week-old Arabidopsis samples (NA, non acclimation) were treated with cold (2 ºC) for 7 days (CA7d) under 12h/12h light/dark conditions. Deacclimation-treated samples (DA6h, DA12h, DA24h) were grown at normal growth temperature under long day conditions after cold treatment for 7 days. Then total RNA was prepared from the whole seedling and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

first: Kentaro

last: Nakaminami

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Junko

last: Ishida


title: Ghd7 is a central regulator for growth, development, adaptation and responses to biotic and abiotic stresses

status: Public on Sep 01 2014

first: Xiaoyu

last: Weng

address: HZAU

institute: NCPGR

summary:
Ghd7 regulates a range of functions in growth and development in response to environmental cues to maximize the reproductive success of the rice plant.
We used microarrays to detail the regulated genes in OX-Ghd7HJ19 transgenic plants.

overall_design: To gain clues to downstream genes regulated by Ghd7, we performed a microarray analysis using Affimetrix rice gene chips. Young leaves in vegetative stage (35-days old) and developing panicles (0.1cm) from field-grown OX-Ghd7HJ19 transgenic and wild-type plants with two biological replicates were used to isolate RNA for chip analysis.

first: Lei

last: Wang

first: Jia

first: Yong

last: Hu

first: Caiguo

last: Xu

first: Yongzhong

last: Xing

first: Xianghua

last: Li

first: Jinghua

last: Xiao

first: Qifa

last: Zhang


title: Expression data from Rice leaves

status: Public on Sep 15 2014

first: Rajeshwari

last: Ramanan

department: Plant Science

institute: Centre for Cellular and molecular biology

summary:
Senescence is a developmental process and chlorophyll is an indicator of leaf senescene. In plants cytokinin plays a role in delaying leaf senescence. Chlorophyll degradation is tightly regulated during senescence and cytokinin might interplay in the chrorophyll degradation pathway to regulate leaf greening.
we used microarray to study the differential gene expression during leaf senescence and inpresence of a synthetic cytokinin (6-benzyl adenine).

overall_design: third leaf of 30-day-old rice plant were selected and incubated for 72 hours in solution containing 6-BA in darkness. Control condition leaves were incubated in solution without 6-BA. Three sets of control versus 6-BA treated leaves were used for RNA extraction and hybridation on Affymatrix rice gene chip.

first: Madhusmita

last: Panigrahy

first: Hitendra

last: Patel

first: Ramesh

last: Palaparthi


title: Expression analysis of Human esophagus cancer cell line TE-1 transfected with PCDNA3.1 and PCDNA3.1-Pax2

city: suzhou

first: Shuyu

address: No.199 Ren’ai Rd

department: Medical  College

institute: Soochow  University

summary: Investigation of whole genome gene expression level changes of  TE-1 transfected with PCDNA3.1-Pax2 ,compared to TE-1 transfected with PCDNA3.1.

overall_design: Compare PAX2 activated genes by analyzing mRNA profilings between pcDNA3.1 and pcDNA3.1-PAX2- transfected TE-1 cells.