title: Expression data from colorectal cancer and the adjacent normal tissues infected without F. nucleatum

institute: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University

summary:
Colorectal cancer and the adjacent normal tissues (CONTROL) infected with F. nucleatum. Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cDNA was generated using the PimeScript TMRT Reagent Kit (Takara).
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes between Colorectal cancer and the adjacent normal tissues (CONTROL) infected without F. nucleatum .

overall_design: Affymetrix’ new GeneChip® Human Transcriptome Array 2.0 chips were used to analysis 25 specimens (15  colorectal cancers, 10   controls).


title: Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers

status: Public on Dec 03 2018

city: Gothenburg

first: Martin

last: Boström

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

summary: Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions, in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor (TF) binding sites. While sometimes interpreted as functional driver events, these mutations are commonly believed to be due to locally inhibited DNA repair. Here, we first show that low-dose UV light induces mutations preferably at a known ETS promoter hotspot in cultured cells even in the absence of global or transcription-coupled nucleotide excision repair (NER). Further, by genome-wide mapping of cyclobutane pyrimidine dimers (CPDs) shortly after UV exposure and thus before DNA repair, we find that ETS-related mutation hotspots exhibit strong increases in CPD formation efficacy in a manner consistent with tumor mutation data at the single-base level. Analysis of a large whole genome cohort illustrates the widespread contribution of this effect to recurrent mutations in melanoma. While inhibited NER underlies a general increase in somatic mutation burden in regulatory elements including ETS sites, our data supports that elevated DNA damage formation at specific genomic bases is at the core of the prominent promoter mutation hotspots seen in skin cancers, thus explaining a key phenomenon in whole-genome cancer analyses.

overall_design: Mapping CPD formation in A375 melanoma cells in +UV cellular, +UV naked DNA and control treated cells with modified CPD-seq

first: Kerryn

last: Elliott

first: Stefan

last: Filges

first: Markus

last: Lindberg

first: Jimmy

last: Van den Eynden

first: Anders

last: Ståhlberg

last: Clausen

first: Erik

last: Larsson


title: Expression data (Hs695T) after treatment with MAPKi, HDACi or both

status: Public on Jan 25 2019

city: Boston

first: Ryan

middle: P

last: Kuzmickas

state: MA

address: 77 Avenue Louis Pasteur, NRB458B

department: Genetics

country: USA

institute: Brigham and Women's Hospital

summary: Transcriptional profiles were examined in Hs695T melanoma cells treated with vehicle (DMSO), dabrafenib+trametinib (DT, MAPKi), entinostat (E, HDACi) or all 3 agents (DTE) at 24 hours, prior to the commencement of cell death, to investigate the molecular mechamism by which these drugs and their combinations are functioning.

overall_design: RNA was isolated from Hs695T cells 24 hours after treatment with the indicated drugs (3 technical triplicates per treatment arm)

first: Ophélia

last: Maertens


title: Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq

status: Public on Aug 01 2018

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

summary: The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.

sample_organism:
Escherichia coli
Cereibacter sphaeroides
Arabidopsis thaliana
Saccharomyces cerevisiae
Leishmania major
Trypanosoma brucei
Plasmodium falciparum
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus

overall_design: 24 library samples, 150 base pairs custom protocol (G4-Seq2) sequenced as two-times single-end reads on HiSeq 2500: 12 samples from different species for Li+ (Read-1) and K+ (Read-2); 12 samples from different species for Li+ (Read-1) and PDS+K+ (Read-2).

first: Vicki

middle: S

last: Chambers

first: Aleksandr

last: Sahakyan

first: Jonathan

middle: M

last: Boutell

first: Marco

last: Di Antonio

first: Shanakr

last: Balasubramanian


title: Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

status: Public on Oct 01 2018

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

summary: The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of transcription factors. By studying Pitx1, a regulator of hindlimb development, we show that dynamic changes in chromatin conformation can restrict the activity of enhancers. Inconsistent with its hindlimb-restricted expression, Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. By Capture Hi-C and three-dimensional modeling of the locus, we demonstrate that forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs, causing partial arm-to-leg transformation in mice and humans. Thus, tissue-specific three-dimensional chromatin conformation can contribute to enhancer activity and specificity in vivo and its disturbance can result in gene misexpression and disease.

overall_design: We used capture Hi-C enriching a 3Mb region at the Pitx1 locus in Mus musculus. We analysed four biological replicates of wild type and two biological replicates of CRISPR-Cas9 genome engineered structural variants and indel mutant tissues. Micro-dissected embryonic E11.5 forelimb and hindlimb tissues as well as E10.5 midbrain tissue were used as starting material. In total nine mouse mutants were used.

first: Bjørt

middle: K

last: Kragesteen


title: Gene expression profiling of HNSCC cells derived from primary and matched metastatic  tumors

status: Public on Jul 27 2018

city: Toronto

first: Bradly

middle: G.

last: Wouters

state: ON

address: 101 College st West

country: Canada

institute: UHN

summary: To look at genes/pathways differentially expressed in metastatic and primary tumor cells we performed global gene expression profiling of the 3 sets of HNSCC lines derived from primary tumors and matched metastatic sites. Illumina HT-12 v4 BeadChip arrays were used. The data suggest that HNSCC lines derived from metastatic sites exhibit phenotypes distinct from those found in cells derived from the corresponding primary tumors. Metastatic cell lines upregulated several pathways involved in stem cell self-renewal, invasion and migration, which are well known characteristics of metastatic progression. We conclude that the cell lines derived from primary patient tumors and matched metastatic sites represent a reliable model to study HNSCC metastasis.

overall_design:
Global gene expression profiling of the 3 sets of HNSCC lines derived from primary tumors and matched metastatic sites
Cell lines were received from Dr. R. Grenman from Turku University Hospital (Finland)


title: Widespread backtracking by RNA pol II is a major effector of gene activation, 5’ pause release, termination and transcription elongation rate

status: Public on Nov 30 2018

city: Aurora

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. We identified backtracking sites using mNET-seq in human cells expressing dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3’ flanking regions where termination is enhanced by TFIISDN. Inhibition of the rescue from backtracked pol II by TFIISDN impaired the escape from 5’ pause sites, the completion of long transcripts, and activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half as measured by sequencing nascent transcripts pulse labeled with Bromouridine (Bru-seq) and by anti-pol II ChIP-seq at time points after release of a DRB block. These results suggest that rescue of backtracked pol II by TFIIS is a major stimulus of elongation.

overall_design: 66 samples

first: David

last: Bentley


title: Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

status: Public on Jul 17 2018

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6,225 RGCs (average of 5,000 genes per cell) from right and left eyes by single cell RNA-seq and classify them into 40 subtypes using clustering algorithms. We identify additional subtypes and markers, as well as transcription factors predicted to cooperate in specifying RGC subtypes. Zic1, a marker of the right eye-enriched subtype, is validated by immunostaining in situ. Runx1 and Fst, the markers of other subtypes, are validated in purified RGCs by fluorescent in situ hybridization (FISH) and immunostaining. We show the extent of gene expression variability needed for subtype segregation, and we show a hierarchy in diversification from a cell type population to subtypes. Finally, we present a website for comparing the gene expression of RGC subtypes.

overall_design: Examination and comparison of single, P5 mouse retinal ganglion cells' transcriptional landscapes and clustering of similar profiles.

first: Bruce

last: Rheaume


title: Transcriptional change of THP-1 after HSV-1UL37WT or HSV-1UL37C819S

status: Public on May 29 2018

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

country: China

institute: Wuhan University

summary: we reporter the transcritional difference after THP-1 cells were infected with HSV-1UL37WT virus or HSV-1UL37C819S virus.

overall_design: RNA sequencing of 3 samples with 2 repeats

first: Pinghui

last: Feng


title: DNA methylation and inflammation marker profiles associated with a history of depression.

status: Public on Jun 01 2018

city: Exeter

first: Therese

last: Murphy

address: RILD building

department: University of Exeter Medical School

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n=100) and individuals without a history of depression (n=100) using the Illumina 450K microarray. Our analysis identified 6 significant (Sidak corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Sidak corrected P = 1.27 x 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.

overall_design: DNA from whole blood from 194 individuals

first: Bethany

last: Crawford

first: Zoe

last: Craig

first: Georgina

last: Mansell

first: Isobel

last: White

first: Adam

last: Smith

first: Steve

last: Spaull

first: Jennifer

last: Imm

first: Eilis

last: Hannon

first: Andrew

last: Wood

first: Hanieh

last: Yaghootkar

first: Yingjie

last: Ji

first: Niamh

last: Mullins

first: Cathryn

last: Lewis

last: Mill


title: Effects of Inhibition of CDK8/19 Mediator Kinase by Senexin B in HCT116 and HEK293 cells treated with or without TNF-alpha

status: Public on Aug 18 2017

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

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

overall_design: Refer to individual Series


title: NF-kB regulator Bcl3 modulates bone density and turnover

status: Public on Jan 17 2019

city: Glasgow

first: Hussain

last: Jaffery

state: Scotland

address: 120 University Place

department: Institute of Infection Immunity and Inflammation

institute: University of Glasgow

summary: B-cell lymphoma 3-encoded protein (Bcl3) is an intimate and context-specific regulator of the NF-kB family of transcription factors, a ubiquitous master regulator involved in many homeostatic and inflammatory processes. NF‑kB signalling determines the fates of bone-forming osteoblasts and bone-resorbing osteoclasts. Herein we show that Bcl3 is a negative regulator of NF‑kB via control of osteoblast and osteoclast function. Mice lacking Bcl3 (Bcl3−/−) have congenitally increased bone density, long bone dwarfism, increased biomechanical strength and altered bone turnover. Bcl3−/− osteoblasts and osteoclasts have accelerated differentiation and increased activity; whereas, rescue overexpression with a Bcl3 mimetic peptide inhibits differentiation. Early-differentiating Bcl3−/− osteoblasts have altered gene transcription favouring bone formation, including perturbation of the RANKL-OPG axis. In a model of osteoarthritic aberrant mineralisation Bcl3−/− mice exhibit decreased pathological osteophyte formation. Cumulatively, these findings identify Bcl3 as a viable target for controlling NF‑kB signalling in the treatment of skeletal pathologies.

overall_design: The study comprises a total of 12 tested samples - forming 4 groups with 3 biological replicates in each group. The experimental groups, namely Bcl3−/− (Bcl3 knockout), and the control groups, namely WT (wild-type), differ in genotype. Each genotype has two tested time-points - at Day 1 and Day 3 post-treatment. Thus, 3 replicates each for the following groups are submitted: Day 1 WT, Day 1 Bcl3−/−, Day 3 WT, and Day 3 Bcl3−/−.

first: Carl

last: Goodyear

first: Ruaidhrí

middle: J

last: Carmody


title: Expression data from Tnrc6a (GW182) mutant E18.5 lungs

status: Public on May 01 2017

city: New York

first: Jining

last: Lu

address: 630 West 168th Street, BB8-801c

department: Medicine

institute: Columbia University Medical Center

summary:
GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in airway multiciliated cells (MCCs), and that gene-trap disruption of GW182 leads to defective multicilia formation and downregulation of broad miRNA targets
To investigate roles of GW182 in  airway multiciliated cells (MCCc), we assessed changes in mRNA expression in E18.5 Tnrc6a mutant lungs using microarrays (Affymetrix).

overall_design: E18.5 lung of wild type littermates and GW182gt/gt embryos were collected for total RNA isolation using Trizol (Invitrogen). RNAs were purified according to the manufacturer’s protocol before subjected to  Mouse Gene 1.0 ST Whole Genome Array (Affymetrix) for  mRNA expression profiling. Experiments were performed in triplicate. Differentially expressed mRNAs were identified using a two-sample t-test (P<0.05 considered significant).

first: Zhihua

last: Jiang


title: Genome-wide small RNAs analysis of herpes simplex virus type 1 (HSV-1) infected cells

status: Public on Aug 10 2017

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

summary: The goal of this study was to compare small RNA profiles (sRNA-seq) of HSV-1 infected and mock infected human fibroblast KMB17 strain at 48 hours post infection.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: Small RNA profiles of  HSV-1 infected and mock infected human fibroblast KMB17 cells at 48 hours post infection were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

first: Yunzhang

last: Hu


title: Chromatin accessibility dynamics across C. elegans development and ageing [ChIP-seq]

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,918 protein-coding promoters and 17,918 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

overall_design: ChIP-seq was used to profile H3K4me3, H3K4me1, H3K36me3, and H3K27me3 across development

first: Przemysław

last: Stempor

first: Jürgen

last: Jänes


title: Gene Expression analysis of Oral Leukoplakia and Early Stage Oral Squamous Cell Carcinoma

status: Public on Apr 26 2017

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

country: India

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

summary: Gene Expression Profiling of Oral Leukoplakia (OPL) and Early Stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate gene/s clusters with potential to distinguish normal, OPL and tumor tissue from Gingivobuccal complex. All tissue samples were collected after obtaining written informed consent. The RNA profile of 15 OPL and 34 OSCC samples was compared with 1 independent controls Gingivobuccal complex tissue from healthy donors.

overall_design: Agilent one-color experiment,Organism: Human ,Agilent-014850 Whole Human Genome Microarray 4x44K G4112F  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Priyanka

middle: G

last: Bhosale

middle: B


title: 3dpf untreated zebrafish larvae vs. 3dpf zebrafish larvae treated with 20mM PTZ for 30 minutes and 90 minutes

status: Public on Feb 24 2017

city: Sheffield

first: Vincent

middle: Trevor

last: Cunliffe

state: South Yorkshire

address: Western Bank

department: School of Biosciences

institute: University of Sheffield

summary: Transcriptional profiling of 3dpf wild type zebrafish larvae treated with 20mM PTZ for 30 and 90 minutes compared with 3dpf wild type control untreated zebrafish larvae.

overall_design: Four-condition experiment: 3dpf untreated zebrafish larvae vs 3dpf zebrafish larvae treated with 20mM PTZ for 30 minutes; 3dpf untreated zebrafish larvae vs 3dpf zebrafish larvae treated with 20mM PTZ for 90 minutes. Biological replicates: 2 (separate mating) Technical replicates: 4 (2 of which are dye-swap)

first: Paola

middle: L

last: Meza Santoscoy

first: Harriet

last: Jackson


title: Networks of cultured iPSC-derived neurons reveal the human synaptic activity-regulated adaptive gene program

status: Public on Jan 03 2017

city: Heidelberg

first: Priit

last: Pruunsild

address: INF 364

department: Neurobiology

country: Germany

institute: University of Heidelberg

summary: We studied the synaptic activity-regulated gene expression response in the human genetic background using cultured human iPSC-derived (hiPSCd) neuronal networks and networks of hiPSCd neurons mixed with mouse primary neurons. Our results confirm that genetic changes affect the synaptic activity-regulated gene program, proposing a functional mechanism how they have driven evolution of human cognitive abilities.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We compared RNA profiles of untreated hiPSCd neurons and hiPSCd neurons treated with bicuculline and 4-aminopyridine for 1 or 4 hours. Samples were collected from hiPSCd neuron-only cultures and from co-cultures of hiPSCd neurons and mouse primary hippocampal neurons.

first: C

last: Bengtson

first: Hilmar

last: Bading


title: Gene Expression data from Mouse Balb/c Bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection [Balb/c]

status: Public on Nov 19 2012

city: Tunis

first: lamia

last: Guizani-Tabbane

address: 13, Place Pasteur BP74. Tunis-Belvedere

department: Immunopathology

country: Tunisia

institute: Insitut Pasteur de Tunis

summary:
We analyzed the transcriptional signatures of mouse bone marrow-derived macrophages (BMDM) at different times after infection with promastigotes of the protozoan parasite Leishmania major.
GeneChip Mouse Gene 1.0 ST arrays were used to analyse global changes in gene transcripts to generate a pool of genes that was statistically significant (p-value < 0.05) and a fold change cut-off of 1.5 in at least one of the five infected samples versus non-infected samples.

overall_design: Three independent biological replicates for each biological condition (Non infected "NI", infected with lived parasite "P" or "heat inactivated parasite "Kp") at 1h (T1), 3(T3), 6(T6), 12 (T12) and 24hours (T24) were performed. The Non infected (NI) at 0 hour (T0) biological condition were used as an additional control.

first: Imen

last: Rabhi

first: Sameh

first: Rym

last: Ben-Othman

first: Axel

last: Rasche

first: Andriani

last: Daskalaki

first: Béatrice

last: Regnault

first: Lamia


title: Gene Expression data from mouse bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection

status: Public on Dec 19 2012


title: Gene expression profile in mouse back skin after cyclophosphamide treatment

status: Public on Aug 29 2018

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Chemotherapy-induced hair loss (alopecia; CIA) is a highly distressing adverse effect that many cancer patients endure. Yet the molecular pathobiology of CIA remains largely unknown. We analysis the changes of mRNA profiles at different time points after cyclophosphamide treatment using Next-generation Sequencing in a mouse model of CIA. Our result revealed that Shh signaling is an evolutionarily conserved key target in CIA pathobiology.

overall_design: All mice used in this study were male C57BL/6 purchased from Shanghai SLAC animal facility center, and housed in Fuzhou University Animal Facility Center. Active hair growth (anagen) was induced in the back skin by wax-depilation in 7-8 weeks old male mice. Cyclophosphamide (CYP, Sigma) was dissolved in PBS and i.p. injected at day 9 post-depilation at a dose of 150mg/kg.Mouse back skin samples were taken before (T0) or at 6hr, 12hr, 24hr, and 48hr after CYP treatment. Total RNAs were isolated using Trizol reagent (Invitrogen). Total RNAs were quality monitored by Agilent 2100 analysis, and sequenced by Illumina Genome Analyzer in Novogene Corporation., Beijing, China.

first: Zhicao

last: Yue

first: Guixuan

last: Zhou

first: Xu

last: Teng


title: Exploration of the Chicken Pituitary Gland

status: Public on Feb 10 2017

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

institute: University of Delaware

summary: The pituitary gland is a neuroendocrine organ that is involved in several processes within the body such as metabolism, growth, immune function, and reproduction. Increased ambient temperatures are environmental stressor that leads to several welfare concerns in poultry production but also economic losses. Because of the involvement of the pituitary gland in several processes that are affected by heat stress, it is hypothesized this tissue's gene expression will be impacted by heat stress. The objectives of the project are to (a) identify genes that constitue the pituitary gland when compared to other collected chicken tissues (Insert tissues) and (b) identify genes that respond to heat stress via differential expression analysis to better understand the chicken's response to heat at the transcriptomic level.

overall_design: Ross 708 broiler chickens were raised from day of hatch to day 42, typical market age, on the University of Delaware farm. Birds were placed into two separate houses, one thermoneutral house and one experimental (heat stress) house. Both houses were kept at 23 hours of light and 1 hour of dark and birds were placed on litter and given feed (meeting all NRC requirements) and water with ad libitum access.  Both houses were kept at 35 degrees celsius for the first week and the temperature was decreased 5 degrees celsius each week until 25 degrees celsius. The thermoneutral hosue was maintained at 25 degrees celsius for the remainder of the study. Starting on day 21, the experimental house began a cyclical heat stress scheme with 8 hours per day of increased temperatures (35 - 37 degrees celsius) through completion of the trial at day 42. Necropsies were performed at several points throughout the trial (days 21, 22, 26, 32, and 42).

first: Elizabeth

last: Pritchett


title: Whole genome tomato transcriptional response to tomato-adapted and non-adapted Tetranychus urticae herbivory

status: Public on Jul 20 2015

city: London

first: Vladimir

last: Zhurov

address: 1151 Richmond Street

department: Biology

institute: University of Western Ontario

summary:
Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genome-wide transcriptional changes in both spider mite and tomato as a consequence of mite’s adaptation to tomato
We used microarray to assess global gene expression in Solanum lycopersicum cv. Moneymaker upon Tetranychus urticae attack by tomato-adapted and non-adapted spider mite lines.

overall_design: 1 month old tomato plants were subjected to Tetranychus urticae attack through application of 100 adult mites on a terminal leaflet of leaves 3 and 4 for 24 hours (200 mites per plant).

first: Catherine

last: Martel

first: Nicky

last: Wybouw

first: Thomas

last: Van Leeuwen

first: Vojislava

last: Grbic


title: Effect of PD-1 immune checkpoint in Alzheimer's disease transgenic mice

status: Public on Jan 01 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We examined the brain's choroid plexus and myeloid cell populations isolated from the brain of 5XFAD Alzheimer's disease transgenic mice following PD-1 blockade

overall_design: Choroid plexus samples and myeloid cell populations were isolated from the brain of 5XFAD mice following PD-1 blockade, and sequenced. For choroid plexus samples, 5 mice were treated with anti-PD-1, 5 with IgG control, and 4 were left untreated. For the myeloid cells samples,  myeloid cells sorted from the brains of 5XFAD mice according to a gating strategy that seperate microglia (CD11b+CD45-low) and monocytes-derived macrophages  (CD11b+CD45-high).

first: Kuti

last: Baruch

first: Eyal

last: David


title: Conditional deletion of miR-21 in sensory neurons is associated with gene changes in macrophages isolated from L4/L5 ipsilateral DRG

status: Public on Nov 01 2017

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

institute: King's College Londonn

summary: A microarray analysis (MA) on the F4/80+ CD11b+ macrophages (population P5) isolated from a pool of ipsilateral L4/L5 DRG in spared nerve injured WT and miR-21 cKO

overall_design: An Affymetrix Array analysis of the consequence of miR-21 loss in F4/80+ CD11b+ macrophages (population P5)  from a pool of ipsilateral L4/L5 DRG in spared nerve injured WT and miR-21 cKO

first: Marzia

last: Malcangio

first: Raffaele

last: Simeoli


title: Effects of Inhibition of CDK8/19 Mediator Kinase by Senexin B in HEK293 cells treated with or without TNF-alpha

first: Mengqian

last: Chen

summary: We have investigated the effects of CDK8/19 inhibitor Senexin B on NFκB-mediated transcription, induced by a canonical NFκB activator, TNFα.

overall_design: HEK293 cells were pre-treated with or without 1 μM Senexin B for 1 hour, followed by 2 hour treatment with 10 ng/ml TNFα. Each treatment condition was done in biological triplicate.

first: Jiaxin

last: Liang

first: Hao

last: Ji

first: Zhengguan

last: Yang

first: Serena

last: Altilia

first: Bing

last: Hu

first: Adam

last: Schronce

first: Martina

last: McDermott

first: Gary

last: Schools

first: Chang-uk

last: Lim

last: Oliver

first: Michael

last: Shtutman

first: Tao

last: Lu

first: George

middle: R

last: Stark

first: Donald

middle: C

last: Porter

first: Eugenia

middle: V

last: Broude

first: Igor

last: Roninson


title: Whole-genome gene expression profiles of non-tumorous human lung tissues: GRNG set

status: Public on Jun 11 2012

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

institute: Laval University

summary: We profiled genome-wide gene expression in non-tumorous human lung tissues. The overall goal of this project is to improve our molecular understanding of various lung diseases including lung cancer and chronic obstructive pulmonary disease (COPD).

overall_design: Lung specimens were obtained from patients with a variety of lung diseases. After resection, tissue samples of the lobes or lungs not relevant for the diagnostic work-up were frozen and stored at -80C. RNAs were extracted and then hybridized to a single custom-made whole-genome human Affymetrix array.

first: Wim

last: Timens

first: Dirkje

last: Postma


status: Public on Oct 30 2011

first: Manoj

last: Mahimkar

summary: Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent.

overall_design:
The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors.
Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

first: Srikant

last: Ambatipudi


title: Expression data for HT29 cells treated with 5-aza-deoxy-cytidine

status: Public on Sep 17 2013

city: Stony Brook

first: Xiao

last: Xu

state: NY

address: Stony Brook University

institute: Stony Brook University BME

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

overall_design: Refer to individual Series


title: Whole-genome gene expression profiles of non-tumorous human lung tissues


title: Array CGH analysis of Oral Leukoplakia and Early Stage Oral Squamous Cell Carcinoma

summary: Array Comparative Genomic Hybridization (CGH) profiling of Oral Leukoplakia (OPL) and early stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with disease progression and clinico-pathological parameters. The array CGH hybridizations were performed for 24 OPL and 38 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.

overall_design: Agilent two-color CGH experiment,Organism: Agilent-21764 Human Genome CGH Microarray 105A (G4412A), Labeling kit:  Agilent Sure tag DNA labeling kit (Agilent Technologies, 5190-3400).

first: Priyanka

last: Bhosale


title: Early emergence of cortical interneuron diversity in the mouse embryo

status: Public on Mar 06 2018

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

institute: Yale University School of Medicine

summary: GABAergic interneurons play crucial roles in the regulation of neural circuit activity in the cerebral cortex. A hallmark of cortical interneurons is their remarkable structural and functional diversity, yet the molecular determinants and the precise timing underlying their diversification remain largely unknown. Here we use single-cell transcriptomics to identify distinct types of progenitor cells and newborn neurons in the ganglionic eminences, the embryonic proliferative regions that give rise to cortical interneurons. These embryonic precursors define temporally and spatially restricted transcriptional trajectories that unambiguously relate to specific classes of interneurons in the adult cerebral cortex. Our findings therefore suggest that interneuron diversity is already patent shortly after neurons become postmitotic through the acquisition of specific transcriptional programs that unfold over several weeks in the developing cortex

overall_design: Mouse embryos were isolated at E12.5 and E14.5 from timed pregnant CD1 female mice. The dorsal MGE (dMGE), ventral MGE (vMGE) and caudal ganglionic eminence (CGE) regions were dissected. Cells were captured with small-sized (5-10 µm) RNA-seq IFCs using the Fluidigm C1 system. Libraries of single cells pooled from each C1 IFC were denatured and HiSeq flow cell was run for 100 cycles using a single-read recipe.

first: Da

last: Mi

first: Zhen

last: Li

first: Mingfeng


title: Genes expression profiles of postmenopausal osteoporosis with kidney Yin deficiency

status: Public on Mar 23 2014

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

institute: Fujian Academy of Traditional Chinese Medicine

summary: Investigate genes expression  profiles of postmenopausal osteoporosis with kidney Yin deficiency in peripheral blood

overall_design: By TCM syndrome, 10 patients with postmenopausal osteoporosis were divided into three groups: kidney Yin deficiency (n=4), kidney Yang deficiency (n=3), non-kidney deficiency (n=3), another 3 healthy postmenopausal women also were selected as control group. Whole human genome oligo microarray were applied to explore gene expression difference of the groups. Kidney Yin deficiency group was compared with other three groups respectively.

first: Jirong

last: Ge

first: Lihua

first: Shengqiang

first: Juan

last: Chen

first: Huijuan


title: Regulation of dendritic cell genes by alpha fetoprotein

status: Public on Dec 23 2014

city: Pittsburgh

first: Lisa

middle: Helene

last: Butterfield

state: PA

address: 5117 Centre Ave.

institute: University of Pittsburgh

summary: Human dendritic cells (DC) are suppressed by tumor-derived alpha fetoprotein (AFP), but less so by cord blood-derived normal AFP.

overall_design: We tested human DC from 5 healthy donors for transcriptional changes induced by tumor (tAFP) or cord blood (nAFP) AFP, vs. chicken ovalbumin (OVA) control.

middle: H

first: Angela

last: Pardee

first: Jian

last: Shi

first: William

last: LaFramboise


title: Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]

summary: The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. The results showed a strong correlation between the two platforms, yet it also confirmed the existence of fixed and proportional biases on the gene expression measurements between microarray and RNA-Seq. The DEG analysis indicated the relative superiority of DESeq method in terms of its performance; high consistency was confirmed between DESeq, baySeq methods from RNA-Seq and SAM/eBayes from microarray data.

overall_design: Experiment on human colon cancer HT29 cell line treated with 3 concentrations of 5-aza-deoxy-cytidine

first: Ellen

first: Jennie

last: Williams

first: Eric

last: Antoniou

first: W

last: McCombie

first: Paula

last: Denoya


title: Gene Expression data from Mouse C57bl6 Bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection [C57bl6]

status: Public on Oct 01 2014

first: lamia

last: Guizani-Tabbane

first: Imen

last: Rabhi

first: Sameh

first: Rym

last: Ben-Othman

first: Axel

last: Rasche

first: Andriani

last: Daskalaki

first: Béatrice

last: Regnault

first: Lamia


title: Gene expression data from healthy, adjacent normal and tumor colon cells

status: Public on Mar 14 2014

city: L'Hospitalet de Llobregat

first: Victor

last: Moreno

state: Barcelona

address: Granvia 199

department: Oncology Data Analytics Program

country: Spain

institute: Catalan Institute of Oncology

summary: Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae, were obtained through Affymetrix Human Genome U219 Arrays. This dataset is in the context of the COLONOMICS project and to query additional information you can visit the project website www.colonomics.org.

overall_design: Colon tumor and adjacent paired normal mucosa tissues samples used in this study were selected from a series of cases with a new diagnosis of colorectal adenocarcinoma histologically confirmed. Included cases were from a homogenous series of patients with more than three years of follow up, early stage (II), without neoadjuvant chemotherapy and microsatellite stable colon cancer. Additionally, samples of colon mucosa from 50 healthy donors without colonic lesions were obtained during colonoscopy.

first: Xavi

last: Solé

first: Marta

last: Crous-Bou

first: Rebeca

last: Sanz-Pamplona

first: Laia

last: Paré

first: David

last: Cordero

first: Elisabet

last: Guinó

first: Antoni

last: Berenguer

first: Adrià

last: Closa

last: Olivares

first: Adriana

last: Lopez-Doriga


title: Depletion of PARP-2 in HepG2 cells

status: Public on Dec 31 2013

city: Debrecen

first: Peter

last: Bai

address: Nagyerdei krt. 98.

department: Department of Medical Chemistry

country: Hungary

institute: University of Debrecen, Medical and Health Science Center

summary: Poly(ADP-ribose) polymerase-2 (PARP-2) is acknowledged as a DNA repair enzyme; however, recently metabolic properties had been attributed to it. Hereby, we examined the metabolic consequences of PARP-2 ablation in liver. Microarray analysis of PARP-2 knockdown HepG2 cells revealed the dysregulation of lipid and cholesterol metabolism genes. Induction of cholesterol biosynthesis genes stemmed from the enhanced expression of sterol-regulatory element binding protein (SREBP)-1. We revealed that PARP-2 is a suppressor of the SREBP-1 promoter, therefore ablation of PARP-2 induces SREBP-1 expression and consequently cholesterol synthesis. PARP-2-/- mice had higher SREBP-1 expression that was translated into enhanced hepatic and serum cholesterol levels.

overall_design: PARP-2 silencing was performed employing shPARP-2 (small hairpin) and scPARP-2 (scrambled) shRNA by lentiviral delivery (Sigma) using 40 MOI lentiviruses coding shRNA sequence against PARP-2.


title: Whole genome tomato transcriptional response to Tetranychus urticae herbivory [Heinz1706]

status: Public on Jan 05 2015

first: Vladimir

last: Zhurov

summary:
The two-spotted spider mite, Tetranychus urticae, is one of the most significant mite pests in agriculture that can feed on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. Here, we described tomato transcriptional responses to spider mite feeding and compared them to Arabidopsis in order to determine conserved and divergent responses to this pest. 2,133 differentially expressed genes (DEGs) were detected at 1, 3, 6, 12 or 24 hours post spider mite infestation (hpi) relative to non-infested control plants. Based on Biological Process Gene Ontology annotations, improved in the course of our analysis, DEGs were grouped in 60 significantly enriched gene sets that highlighted perception of the spider mite attack (1 hpi), metabolic reprogramming (3-6 hpi), and establishment and maintenance of the defense responses (6-24 hpi).
We used microarray to assess global gene expression in Solanum lycopersicum cv. Heinz 1706 upon Tetranychus urticae attack.

overall_design: 1 month old tomato plants were subjected to Tetranychus urticae attack through application of 100 adult mites on a terminal leaflet of leaf 3 for various periods of time (timecourse scenario) or hundreds of mites for 1 hour (feeding site scenario).

first: Catherine

last: Martel

first: Marie

last: Navarro

first: Manuel

last: Martinez

first: Marc

last: Cazaux

first: Philippe

last: Auger

first: Alain

last: Migeon

first: M

middle: E

last: Santamaria

first: Nicky

last: Wybouw

first: Isabel

last: Diaz

first: Thomas

last: Van Leeuwen

first: Maria

last: Navajas

first: Miodrag

last: Grbic

first: Vojislava


title: Expression data from actomyosin contractility regulated genes

status: Public on Aug 24 2010

first: Chris

last: Marshall

address: 237 Fulham Road

department: Cell and Molecular Biology

institute: Institute of Cancer Research

summary: Actomyosin contractility regulates cell morphology and movement.  The objective of this study was to identify whether actomyosin contractility regulates gene expression in tumour cells and whether such genes are involved in cell morphology and movement.  Gene expression analysis was carried out on highly contractile melanoma cell line A375M2 plated on a deformable collagen matrix under conditions where actomyosin contractility could be altered following treatment with blebbistatin, a direct inhibitor of myosin II, or Rho-kinase inhibitors Y27632 or H1152 that interfere with signalling to myosin II.

overall_design: 18 samples (6 x 3 biological replicates).  Cells were plated on rigid or deformable matrices.  Rounded cells (A375M2 melanoma cells) plated on deformable matrices were left untreated or treated with Rho-kinase inhibitors Y27632, H1152 or blebbistatin an inhibitor of mysoin II.

first: Victoria

last: Sanz-Moreno


title: Whole-genome gene expression profiles of non-tumorous human lung tissues: UBC set

first: Yohan

last: Bossé

overall_design: The samples from the University of British Columbia (UBC) were derived from a long-standing tissue bank started by Drs. James C. Hogg and Peter D. Paré (Ding L, Quinlan KB, Elliott WM, Hamodat M, Paré PD, Hogg JC, Hayashi S. A Lung Tissue Bank for Gene Expression Studies in Chronic Obstructive Pulmonary Disease. COPD: Journal of Chronic Obstructive Pulmonary Disease 2004;1:191-204 (PMID 17136987)). Lung specimens were obtained from patients undergoing lung surgery. Primarily this was for resection of benign or malignant lesions. Some were the diseased lungs from transplant recipients. Patients are approached prior to surgery and asked if they would like to donate a portion of the lung tissue that is to be removed for research. It is explained that this would be done after the appropriate diagnostic specimens are taken and that only portions of lung that would be otherwise discarded will be used for research. A small number of lung samples were obtained at the time of autopsy. Immediately after resection, the lobes or lungs were inflated using a 50% mixture of Cryomatrix and saline. The specimens were then frozen in liquid nitrogen fumes and stored at -80C for later RNA extraction. RNAs were extracted and then hybridized to a single custom-made whole-genome human Affymetrix array.

first: James

last: Hogg

first: Peter

middle: D

last: Paré


title: Preclinical investigation of the novel histone deacetylase inhibitor AR-42 in the treatment of cancer-induced cachexia

status: Public on Mar 13 2015

city: Columbus

first: Ching-Shih

last: Chen

state: Ohio

address: 500 W 12th Ave

department: Internal Medicine and Urology

institute: The Ohio State University

summary:
Purpose: We assessed the anti-cachectic activity of the novel HDAC inhibitor AR-42 in murine models of cancer cachexia.
Methods: Effects on classic features of cachexia, including decreased body weight, skeletal muscle and adipose tissue mass, muscle fiber cross-sectional area, and muscle strength, and increased intramuscular mRNA expression of E3 ligases Atrogin-1/MAFbx and MuRF1 were examined. Metabolomic analysis, whole transcriptome shotgun sequencing (RNA-seq) analysis, and cytokine profiling were used to compare metabolic phenotype and mRNA expression profiles in muscle, and cytokine production in serum, respectively, in AR-42- and vehicle-treated tumor-bearing and tumor-free control mice.
Results: Orally administered AR-42 suppressed cancer cachexia in the C-26 colon adenocarcinoma model. This anti-cachectic effect, also confirmed in Lewis lung carcinoma-bearing mice, was not observed after treatment with other HDAC inhibitors (vorinostat, romidepsin).  Cytokine profiling and RNA-seq analyses revealed effects of AR-42 on tumor-induced changes in inflammatory cytokine production and multiple transcriptional programs in muscle, including the inhibition of multiple pro-cachexia drivers, such as IL-6 and its receptor IL-6ra, leukemia inhibitory factor, Foxo1, Atrogin-1, MuRF1, adipose triglyceride lipase, uncoupling protein 3, and myocyte enhancer factor 2c.  Metabolomic analysis indicated the reprogramming of skeletal muscle metabolism, including reduced glycolysis and glycogen synthesis and increased protein degradation, which was restored by AR-42 to a state characteristic of tumor-free mice.
Conclusions: These findings support further investigation of AR-42 as part of a comprehensive therapeutic strategy for cancer cachexia.

overall_design: Mice bearing subcutaneous C-26 tumors, as well as tumor-free mice, were randomized into groups that were treated with either AR-42 (50 mg/kg, p.o. by gavage, every other day) or vehicle (0.5% methylcellulose (w/v) and 0.1% Tween-80 (v/v) in sterile water) starting 6 days after cell injection.  Skeletal muscles (hind limb) were harvested at terminal sacrifice on day-15 after tumor cell injection, snap-frozen in liquid nitrogen, and stored at -80 degress F until analysis.  For RNA-seq, 3 muscle samples were analyzed from each of 4 groups: (a) tumor-bearing/vehicle treated (T/Veh); (b) tumor-bearing/AR-42-treated (T/AR); (c) tumor-free/vehicle-treated (TF/Veh); (d) tumor-free/Ar-42-treated (TF/AR).

first: Yu-Chou

last: Tseng

first: Samuel

last: Kulp

first: I-Lu

last: Lai

first: En-Chi

last: Hsu

first: Wei

middle: A

last: He

first: David

last: Frankhouser

first: Pearlly

middle: S

last: Yan

first: Xiaokui

last: Mo

first: Mark

last: Bloomston

first: Gregory

last: Lesinski

first: Guido

last: Marcucci

first: Denis

last: Guttridge

first: Tanios

last: Bekaii-Saab


title: Mapping of  disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes

status: Public on Jun 14 2010

city: Boston

first: Benjamin

last: Raby

state: MA

address: 181 Longwood Avenue

institute: Channing Laboratory

summary: Analysis of expression quantitative trait loci (eQTLs) using RNA derived from freshly harvested peripheral blood CD4+ lymphocytes from 200 asthmatics collected in clinical settings.

overall_design: RNA was obtained from peripheral blood CD4+ lymphocytes at four study centers. Peripheral blood (17 cc) was collected into BD Vacutainer CPT tubes (BD Diagnostics, Franklin Lakes, New Jersey) and placed on ice. Samples were centrifuged within 1 hour of collection for 20 minutes at 1700RCF, followed by mononuclear cell layer isolation and suspension in 10 ml of PBS. We isolated CD4+ lymphocytes using anti-CD4+ microbeads by column separation (Miltenyi Biotec, Auburn, CA) using 20 µl anti-CD4+ Micro beads per 106 total cells


title: Whole-genome gene expression profiles of non-tumorous human lung tissues: Laval set

first: Yohan

last: Bossé

overall_design: Lung specimens were obtained from patients undergoing lung cancer surgery at the Institut Universitaire de Cardiologie et de Pneumologie de Québec. All lung specimens were derived from a homogeneous piece of peripheral tissue free of tumour obtained at surgery performed between April 2004 and December 2008. These lung tissues were stored in the biobank of the Respiratory Health Network of the FRSQ, site Institut Universitaire de Cardiologie et de Pneumologie de Québec. The time from surgical removal to freezing was between 15 to 30 minutes. RNAs were extracted and then hybridized to a single custom-made whole-genome human Affymetrix array.

first: Michel

last: Laviolette


title: Expression data from Tnrc6a (GW182) mutant yolk sac

status: Public on Sep 01 2011

city: BoSTON

first: jining

last: lu

address: 715 Albany street R304

institute: Boston University

summary:
GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality.
To investigate roles of GW182 in the yolk sac endoderm, we assessed changes in mRNA expression in the yolk sac of E9.5 GW182gt/gt embryos using microarrays (Affymetrix).

overall_design: Yolk sac of wild type littermates and GW182gt/gt embryos at E9.5 was collected for total RNA isolation using Trizol (Invitrogen). RNAs were purified according to the manufacturer’s protocol before subjected to  Mouse Gene 1.0 ST Whole Genome Array (Affymetrix) for  mRNA expression profiling. Experiments were performed in triplicate. Differentially expressed mRNAs were identified using a two-sample t-test (P<0.05 considered significant).

first: Jining

last: Lu

first: Zhihua

last: Jiang


title: Array CGH analysis of Oral Squamous Cell Carcinoma

status: Public on Mar 11 2011

city: Navi Mumbai

first: Manoj

last: Mahimkar

address: Sector-22, Owe Village, Kharghar Node

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

type: Genome variation profiling by genome tiling array

summary: Array Comparative Genomic Hybridization (CGH) profiling of Oral Sqaumaous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with clinico-pathological parameters. The array CGH hybridizations were performed for 60 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.

overall_design: Agilent two-color CGH experiment,Organism: Human ,Agilent-014698 Agilent-21764 Human Genome CGH Microarray 105A (G4412A) , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453): 60 OCC patients/samples

first: Srikant

last: Ambatipudi


title: Primary and secondary ovarian tumors

status: Public on Apr 14 2010

city: PARIS

first: Jean-Philippe

last: MEYNIEL

address: 26, rue d'Ulm

department: Translational Research Dept

country: France

institute: Institut Curie

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

summary:
The distinction between primary and secondary ovarian tumors may be challenging for pathologists.
We performed transcriptomic analysis in order to discriminate between primary ovarian tumors and ovarian metastases after primary breast cancer.
We performed genomic analysis on tumor paired samples (breast/ovary) in order to know if genomic profiles could help for the discrimination of primary ovarian tumors and ovarian metastases after primary breast cancer.

overall_design:
1) Transcriptomic profiling: The transcriptomes of ovarian carcinomas from patients with previous history of breast cancer, and for which the primary or secondary status was uncertain, were analyzed using Affymetrix U133plus2 Arrays. A hierarchical clustering of these samples was performed, combined with a dataset of well-identified primary and secondary ovarian tumors.
2) Genomic profiling: Sixteen paired breast-ovary tumors from patients with a former dignosis of breast cancer were collected. The genomic profiles of paired tumors were analyzed using Affymetrix 50k_Xba or SNP6 arrays.

last: Meyniel

first: Paul

last: Cottu

first: Charles

last: Decraene

first: Marc-Henri

last: Stern

first: Jérôme

last: Couturier

first: Ingrid

last: Lebigot

first: André

last: Nicolas

first: Nina

last: Weber

first: Virginie

last: Fourchotte

first: Séverine

last: Alran

first: Audrey

last: Rapinat

last: Gentien

first: Sergio

last: Roman-Roman

first: Laurent

last: Mignot

first: Xavier

last: Sastre-Garau


title: Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age

status: Public on Oct 10 2008

city: Los Angeles

first: Stanley

last: Nelson

state: CA

address: 695 Charles E. Young Drive South, Bldg Gonda, Rm 5554

department: Human Genetics

summary:
Background: Glioblastomas are the most common primary brain tumour in adults.  While the prognosis for patients is poor, gene expression profiling has detected signatures that can sub-classify GBMs relative to histopathology and clinical variables.  One category of GBM defined by a gene expression signature is termed ProNeural (PN), and has substantially longer patient survival relative to other gene expression-based subtypes of GBMs.   Age of onset is a major predictor of the length of patient survival where younger patients survive longer than older patients. The reason for this survival advantage has not been clear.

We collected 267 GBM CEL files and normalized them relative to other microarrays of the same Affymetrix platform.  377 probesets on U133A and U133 Plus 2.0 arrays were used in a gene voting strategy with 177 probesets of matching genes on older U95Av2 arrays.  Kaplan-Meier curves and Cox proportional hazard analyses were applied in distinguishing survival differences between expression subtypes and age.

Results: Here we collected 267 glioblastomas and explore the relationship between gene expression subtype, age at diagnosis, and survival.  This meta-analysis of published data in addition to new data confirms the existence of four distinct GBM expression-signatures.  Further, patients with PN subtype GBMs had longer survival, as expected.  However, the age of the patient at diagnosis is not predictive of survival time when controlled for the PN subtype.
Conclusions: The survival benefit of younger age is nullified when patients are stratified by gene expression group. Thus, the main cause of the age effect in GBMs is the more frequent occurrence of PN GBMs in younger patients relative to older patients.

Keywords: Gene expression profiling, GBM, glioblastoma, survival, MGMT, VEGFA, EGFR, Temozolomide, Affymetrix

overall_design: Clinical data including histopathology, age, sex, and survival time from diagnosis were retrieved  from 181 glioblastomas which have been reported within previous studies between 2003 and 2006 and for which CEL files (Affymetrix, Santa Clara, CA) were available from the authors.  In addition, we collected 86 new patient-unique tumour biopsies from the UCLA Neuro-oncology Program (n = 55) and the Barrow Neurological Institute (n = 31) for a grand total of 267 glioblastomas.  Newly acquired tumours were collected through institutional review board approved protocols and assigned WHO grades at UCLA Neuropathology or Barrow Neuropathology by PSM.  Time of survival (days), sex, and, age were collected where available.  Patient age at the time of diagnosis was available for 239 patients and ranged from 18 to 86 years.  Sex of the individual was available for those 239 patients (151 males and 88 females). There were no technical replicates.  There were no control or reference samples.  No dye swap due to single channel array platforms.

first: Yohan

last: Lee

first: Adrienne

last: Scheck

first: Timothy

last: Cloughesy

first: Albert

last: Lai

first: Jun

last: Dong

first: Haumith

middle: K

last: Farooqi

first: Linda

middle: M

last: Liau

first: Steve

last: Horvath

last: Mischel