title: Pharmacodynamic-induced changes in SLE Patients from the ILLUMINATE-2 phase III trial of B cell activating factor blockade with tabalumab

status: Public on Oct 25 2016

city: Indianapolis

first: Robert

last: Hoffman

address: Lilly Corporate Center

department: Lilly Bio-Medicines/Immunology

institute: Eli Lilly and Company

summary: Objective: Systemic lupus erythematosus (SLE) has substantial unmet medical need and its pathogenesis is incompletely understood. This study characterized baseline gene expression and pharmacodynamic (PD)-induced changes in whole blood gene expression from two phase III, 52-week (W), randomized, placebo-controlled, double-blind studies of 1,760 SLE patients treated with the B cell activating factor (BAFF)-blocking IgG4 monoclonal antibody, tabalumab. Methods: Patient samples were obtained from ILLUMINATE-1 and -2 while control samples were from healthy donors. Blood was collected in TempusTM tubes at baseline, W16 and W52. RNA was analyzed using the Affymetrix Human Transcriptome Array 2.0 and NanoStringTM. Results: At baseline there was elevation of interferon responsive genes (IRG) in patients compared to controls, with 75% positive for this IRG signature. There was, however, substantial heterogeneity of IRG expression and complex relationships among gene networks. The interferon signature was a predictor of future time to flare, independent of anti-double stranded DNA antibody (dsDNA), C3 and C4 levels, and overall disease activity. PD changes in gene expression following tabalumab treatment were extensive, occurring predominantly in B cell-related and immunoglobulin (Ig) genes, and were consistent with other PD-induced changes including dsDNA, C3, and Ig levels. Conclusions: SLE patients demonstrated elevated expression of an IRG signature, detected in 75% of the patients at baseline in ILLUMINATE-1 and -2. There was substantial heterogeneity of gene expression detected among individual patients and in gene networks. The interferon signature was an independent risk factor for future flares. PD changes in gene expression were consistent with the mechanism of BAFF blockade by tabalumab.

overall_design: Transcripts from 139 SLE patients at baseline not treated were compared with 135 (week 16) and 144 patients (week 52) treated with the BAFF/BLyS-blocking, fully-human IgG4 monoclonal antibody, tabalumab (120 mg Q2W or 120 mg Q4W) for pharmacodynamic changes.

first: Ernst

middle: R

last: Dow

first: Narayanan

last: Perumal


title: Primate-specific gene TMEM14B promotes cortical expansion and folding

status: Public on Dec 02 2016

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

country: China

institute: China Medical University

type: Expression profiling by high throughput sequencing

summary: A massively expanded outer subventricular zone (OSVZ) in the primate and human has been proposed for generating majority of neocortical neurons, which consists of basally located radial glia cells. Previous studies with various strategies have tried to recognize genes specifically expressed in those cells; however, the molecular and cellular features of these cells still remain uncertain.  By profiling gene expression across single cells isolated from cellular anatomy location and subtype sorting, we identified a primate-specific gene TMEM14B as a novel marker for basally located radial glia. Expression of TMEM14B induced dramatic increase in the number of radial glial and OSVZ region. Finally, we found that OSVZ progenitor’s extensive proliferative potential was up regulated through IQGAP1 phosphorylation and nuclear translocation, and remarkably, led to the gyrification in postnatal mouse.  These results highlight that evolutionary expansion promoted by primate-specific genes enabling the evolutionary expansion and folding of the human neocortex.

overall_design: Find specific markers from dataset of 4 different types of cells

first: Jing

first: Lu

last: Yang

first: Qian

last: Wu

first: Haofeng

last: Zhang

first: Ai

last: Fang

first: Long

last: Li

first: Xiaohui

last: Xu

first: Le

last: Sun

first: Jun

first: Fuchou

last: Tang

first: Xiaoqun

last: Wang


title: Transcriptomic analyses of Kras induced zebrafish liver cancer

status: Public on Jan 24 2017

city: Saint-Petersburg

first: Ekaterina

last: Matyunina

address: Pudogsakya str 7

country: Russia

institute: The Biomedical Center

summary: The krasV12-induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone-free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably, complete tumor regression with scarred fibrosis of the former tumor tissue was observed after 4 weeks of mifepristone withdrawal.

overall_design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma, livers of  transgenic fishes after mifepristone withdrawal and normal livers from non-induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.

first: E

first: A

last: Emelyanov

middle: P

last: Kozlov


title: Gene expression changes of o-nitroanisole-induced in renal cortex of rats

status: Public on Sep 27 2016

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-nitroanisole, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. o-nitroanisole treated group). Three biological replicates were performed for each group.

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: Gene expression changes of o-anthranilic acid-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-anthranilic acid, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. o-anthranilic acid treated group). Three biological replicates were performed for each group.


title: Gene expression changes of o-anisidine hydrochloride-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-anisidine hydrochloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. o-anisidine hydrochloride treated group). Three biological replicates were performed for each group.


title: Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme) [ChIP-Seq]

status: Public on Dec 14 2016

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fusion of active protein domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been widely used for epigenome editing, but the specificities of these engineered proteins have still not been fully investigated. Targeted methylation of specific gene loci offers a direct approach to perturb DNA methylation-associated biological processes. In this study, we generated and validated the global off-target characteristics of CRISPR-guided DNA methyltransferases (CRISPRme) by fusing the catalytic domain of DNMT3A or DNMT3B to the C terminus of the dCas9 protein from S. pyogenes. Using targeted quantitative bisulfite pyrosequencing and whole genome bisulfite sequencing (WGBS), we prove that CRISPRme can efficiently methylate the CpG dinucleotides flanking its target sites in genomic loci (uPA and TGFBR3) in human cells (HEK293T) with CpG-methylation levels exceeding 70% for some target sites. Using qPCR, fluorescent reporter cells, and RNA sequencing, we found that CRISPRme can mediate transient inhibition of gene expression which appears to result from Cas9-mediated interference with transcription rather than de novo DNA methylation. Analyses of whole genome methylation did not identify global methylation changes, however a substantial number of CRISPRme off-target differentially methylated regions (DMR, over 6000) were still identified. The majority of these DMRs were hypermethylated both in cells expressing CRISPRme alone and cells expressing CRISPRme together with gRNAs. These off-target hypermethylated sites were enriched in gene bodies, introns, 5’UTR, CGI shores, Alu sequences, open chromatin and PAM rich regions, but not correlated with off-target binding sites predicted by ChIP-seq. Our results prove that CRISPRme allows for efficient RNA-guided methylation of endogenous CpGs, however with high frequencies of off-target methylation indicating that further improvements of the specificity of CRISPR-dCas9 based DNA methylation modifiers are still required.

overall_design: For ChIP samples, there are one input sample and one treatment sample which are ChIP against HA-ta-Cas9.

first: Lin

last: Lin

first: Yong

first: Fengping

first: Jinrong

last: Huang

first: Tina

middle: F

last: Daugaard

first: Trine

middle: S

last: Petersen

first: Bettina

last: Hansen

first: Lingfei

last: Ye

first: Qing

last: Zhou

first: Fang

first: Shengting

first: Lasse

last: Fløe

first: Ellen

last: Shrock

first: Huanming

first: Jian

first: Xun

first: Lars

last: Bolund

first: Anders

middle: L

last: Nielse


title: Gene expression changes of cisplatin-induced in renal cortex of rats

first: Hiroshi

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with cisplatin, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. cisplatin treated group). Three biological replicates were performed for each group.

first: Fumiyo

first: Masahiro


title: Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases (CRISPRme)

first: Yonglun

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression changes of tris(2-chloroethyl)phosphate-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tris(2-chloroethyl)phosphate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. tris(2-chloroethyl)phosphate treated group). Three biological replicates were performed for each group.


title: Gene expression changes of tricresyl phosphate-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tricresyl phosphate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. tricresyl phosphate treated group). Three biological replicates were performed for each group.


title: Gene expression changes of 4,4'-thiobis(6-tert-butyl-m-cresol)-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 4,4'-thiobis(6-tert-butyl-m-cresol), and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 4,4'-thiobis(6-tert-butyl-m-cresol) treated group). Three biological replicates were performed for each group.


title: Expression data from Diffuse Large B Cell Lymphoma (DLBCL) patients

status: Public on Jan 30 2017

city: Rouen

first: Sydney

last: Dubois

address: Rue d'Amiens

country: France

institute: Centre Henri Becquerel

summary:
Diffuse large B-cell lymphoma (DLBCL) is currently divided into three main molecular subtypes, defined by gene expression profiling (GEP): Germinal Center B-cell like (GCB), Activated B-Cell like (ABC), and Primary Mediastinal B-cell Lymphoma (PMBL).
DLBCL subtypes were determined according to patients' gene expression profiles.

overall_design: 223 DLBCL patients enrolled in prospective and multicenter LYSA trials were selected and molecular subtype classification was obtained according to GeneChip HGU133+2.0 (Affymetrix)

first: Martin

last: Figeac

first: Pauline

last: Peyrouze

first: Bruno

last: Tesson

first: Jean-Philippe

last: Jais

first: Fabrice

last: Jardin


title: Gene expression changes of sulfone bis(p-chlorophenyl)-induced in renal cortex of rats

last: Matsumoto

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with sulfone bis(p-chlorophenyl), and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. sulfone bis(p-chlorophenyl) treated group). Three biological replicates were performed for each group.

last: Saito

last: Takeyoshi


title: Gene expression and pharmacodynamic-induced changes in 1760 SLE Patients from two phase III trials of B cell activating factor blockade with tabalumab

first: Robert

middle: W

last: Hoffman

state: IN

country: USA

first: Ernst

last: Dow

first: Narayanan

middle: B

last: Perumal


title: Pharmacodynamic-induced changes in SLE Patients from the ILLUMINATE-1 phase III trial of B cell activating factor blockade with tabalumab

overall_design: Transcripts from 302 SLE patients at baseline not treated were compared with 302 (week 16) and 304 patients (week 52) treated with the BAFF/BLyS-blocking, fully-human IgG4 monoclonal antibody, tabalumab (120 mg Q2W or 120 mg Q4W) for pharmacodynamic changes.


title: Gene expression changes of tert-butyl alchol-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tert-butyl alchol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. tert-butyl alchol treated group). Three biological replicates were performed for each group. Rats were humanely sacrified by bleeding under anesthesia with CO2-O2 (4:1) or isoflurane gas inhalation 24 hr after final administration.


title: Gene expression data from Duchenne muscular dystrophy patients versus controls

status: Public on Jul 01 2016

city: Baltimore

first: Susan

middle: G

last: Dorsey

address: 655 West Lombard Street

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

summary:
gene expression data is from RNA extracted from muscle biopsy samples taken from boys with Duchenne muscular dystrophy (DMD) or pathologically normal controls (CTRL). Each muscle biospy was examined in detail histologically by Dr. Eric P. Hoffman at Children's National Medical Center to determine stage of disease. In addition, the absence or presence of dystrophin was determined via western blot analyses.
We utilized Human U133 2.0 arrays to examine the transcriptome of each muscle, and then we compared differential gene expression between DMD patient muscles and CTRL muscules. We set the FDR p value for significance at 0.05 and at least a 1.5 fold difference in DMD/CTRL

overall_design: compared differential gene exrpression between DMD versus Control

first: Christopher

last: Ward


title: The dynamic translatome of retinal ganglion cell axons during assembly and maintenance of the mouse visual system

status: Public on Jun 16 2016

city: Cambridge

first: Christine

middle: E

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

country: United Kingdom

institute: University of Cambridge

summary: Local mRNA translation mediates the adaptive responses of axons to extrinsic signals but direct evidence that it occurs in mammalian CNS axons in vivo is scant. We developed an axon-TRAP-RiboTag approach in mouse that allows deep-sequencing analysis of ribosome-bound mRNAs in the retinal ganglion cell axons of the developing and adult retinotectal projection in vivo. The embryonic-to-postnatal axonal translatome comprises an evolving subset of enriched genes with axon-specific roles suggesting distinct steps in axon wiring, such as elongation, pruning and synaptogenesis. Adult axons, remarkably, have a complex translatome with strong links to axon survival, neurotransmission and neurodegenerative disease. Translationally co-regulated mRNA subsets share common upstream regulators, and novel sequence elements generated by alternative splicing that promote axonal mRNA translation. Our results indicate that intricate regulation of compartment-specific mRNA translation in mammalian CNS axons supports the formation and maintenance of neural circuits in vivo.

overall_design: The profiling of ribosome-bound mRNAs in mouse retinal ganglion cell axons at 4 different developmental stages

first: Toshiaki

last: Shigeoka

first: Jane

last: Jung

first: Benita

last: Turner-Bridger

first: Ji-Yeon

last: Ok

first: Julie

middle: Q

last: Lin

first: Paul

last: Amieux

first: Hosung


title: Eicosapentaenoic acid and docosahexaenoic acid - enriched high fat diet modulates immune genes in the spleen transcriptome of C57BL/6J mice

status: Public on Aug 31 2016

city: Gothenburg

first: Nikulkumar

middle: Kirtilal

last: Soni

state: Vastra Gotaland

address: Kemivagen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Effects of EPA/DHA enriched high fat diets (HFD) compared to HFD-Corn oil after 8 weeks intervention on spleen immune function

overall_design: Four mice representing each diet group on the basis of body weight, plasma triglyceride and plasma cholesterol levels were selected for RNA isolation and microarray analysis. Total RNA from skeletal muscle of these selected animals was purified using the RNeasy® Plus Universal Mini kit (Qiagen Nordic, Sollentuna, Sweden) by following the manufacturer's instruction carefully. The extracted RNA was quantified by NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific, USA) and the quality of the RNA was estimated by RNA 6000 Nano LabChip for Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).


title: Expression Profiling of human Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

status: Public on Jun 01 2016

city: Bethesda

first: Frederic

last: Barr

state: MD

address: 10 Center Drive, Rm 3B55

institute: National Cancer Institute

summary: Genome-wide gene expression in 33 fusion-positive and 25 fusion-negative rhabdomyosarcoma cases was studied using GeneChip Human Genome U133 Plus2 (Affymetrix)

overall_design: Fusion-positive versus fusion-negative rhabdomyosarcoma tumors

first: Wenyue

last: Sun


title: Inhibition of uPA expression by CRISPR-dCas9 DNA methyltransferases

first: Yonglun

last: Luo

summary: We report the generation of CRISPR-dCas9 DNA methyltransferases to mediate targeted DNA methylation. Using the dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B methyltransferases, we have demonstrated that these two methyltransferase can mediate targeted methylation in three human genes tested: uPA, TGFBR3, and CDKN2A in human HEK293T cells. We also showed that these methyltransferases could mediate gene inhibition.

overall_design: five samples co-transfected with five uPA sgRNAs and each of the four dCas9 fusions, or control transfection with pUC19 plasmid


title: DNA IP for 5hmC modified CpGs in the liver of control mice and a Tet1 -/- mouse liver [hmeDIP-seq]

status: Public on May 17 2016

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression.

overall_design: We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report on the genome-wide 5hmC patterns. Heterozygote pairs of Tet1 B6;129S4-Tet1tm1.1Jae/J mice were  bought from The Jackson Laboratory (Maine USA). Heterozygotes were interbred to produce homozygous knock out males with colony mate wild type controls. Genome-wide 5hmC patterns were generated by hydroxymethyl-DNA immuoprecipitation (hmeDIP) followed by genome wide sequencing on the Ion Proton P1 sequencer.

first: Marcus

middle: J

last: Lyall

first: Amanda

last: Drake

first: Richard

last: Meehan


title: Profiling of epigenetic and transcriptomic landscapes in normal mouse liver, phenobarbital exposed mouse livers and mouse liver tumours

type: Methylation profiling by genome tiling array


title: Chromatin IP for H3 K27me3 modified histone tails in the liver of control mice,  Phenobarbital exposed mice and a resulting Ctnnb1 mutated PB liver tumour [ChIP-seq]

overall_design: We carry out Chromatin immunoprecipitation (ChIP) prior to sequencing on Illumina Hiseq 2500 to report on the genome-wide H3K27me3 patterns in normal mouse liver, 12 week Phenobarbital exposed mouse livers and 35 week pehonbarbital exposed liver tumours.


title: Gene expression changes in baseline SLE patients vs. healthy controls from two phase III trials (ILLUMINATE-1 and ILLUMINATE-2) of B cell activating factor blockade with tabalumab

first: Robert

last: Hoffman

summary: Objective: Systemic lupus erythematosus (SLE) has substantial unmet medical need and its pathogenesis is incompletely understood. This study characterized baseline gene expression and pharmacodynamic (PD)-induced changes in whole blood gene expression from two phase III, 52-week (W), randomized, placebo-controlled, double-blind studies of 1,760 SLE patients treated with the B cell activating factor (BAFF)-blocking IgG4 monoclonal antibody, tabalumab. Methods: Patient samples were obtained from ILLUMINATE-1 and -2 while control samples were from healthy donors. Blood was collected in TempusTM tubes at baseline, W16 and W52. RNA was analyzed using the Affymetrix Human Transcriptome Array 2.0 and NanoStringTM. Results: At baseline there was elevation of interferon responsive genes (IRG) in patients compared to controls, with 75% positive for this IRG signature. There was, however, substantial heterogeneity of IRG expression and complex relationships among gene networks. The interferon signature was a predictor of future time to flare, independent of anti-double stranded DNA antibody (dsDNA), C3 and C4 levels, and overall disease activity. PD changes in gene expression following tabalumab treatment were extensive, occurring predominantly in B cell-related and immunoglobulin (Ig) genes, and were consistent with other PD-induced changes including dsDNA, C3, and Ig levels. Conclusions: SLE patients demonstrated elevated expression of an IRG signature, detected in 75% of the patients at baseline in ILLUMINATE-1 and -2. There was substantial heterogeneity of gene expression detected among individual patients and in gene networks. The interferon signature was an independent risk factor for future flares. PD changes in gene expression were consistent with the mechanism of BAFF blockade by tabalumab.

overall_design: 1760 SLE patients at baseline from ILLUMINATE 1 (n=879) and ILLUMINATE 2 (n=881) were compared to 60 healthy controls for differential gene expression.

first: Ernst

last: Dow

first: Narayanan

last: Perumal


title: Gene expression changes of potassium bromate-induced in renal cortex of rats

first: Hiroshi

last: Matsumoto

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with potassium bromate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. potassium bromate treated group). Three biological replicates were performed for each group.

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: IP of 5-methylcytosine (5-mc) enriched DNA fragments from control, PB treated mouse livers, resulting Ctnnb1 mutated PB liver tumours and PB minus Ha-Ras mutate liver tumour

overall_design: 5-mc is a well establisehd epigenetic mark typically related to gene silencing events. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in the livers of 12 week PB treated mice. We also profile 5mC in liver tumours arising in the presence of long term PB exposure (35 week: resulting in Ctnnb1 mutated tumours) to a Ha-Ras liver tumour which arose without PB.  Samples: 2 control and 2 PB exposed mouse livers, 3 liver tumours resulting from long term PB exposrue and 1 liver tumour arising without PB

first: Harri

last: Lempiäinen

first: Arne

last: Muller

first: Remi

last: Terranova

first: Jonathan

last: Moggs

first: Michael

last: Schwarz


title: IP of 5-hydroxymethylcytosine (5-hmC) enriched DNA fragments from control ,PB treated mouse livers , resulting Ctnnb1 mutated PB liver tumours and PB minus Ha-Ras mutate liver tumour

overall_design: 5-hmC is a novel epigenetic mark derived from oxidation of methylcytosine. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 12 week PB treated mice. We also profile 5hmC in liver tumours arising in the presence of long term PB exposure (35 week: resulting in Ctnnb1 mutated tumours) to a Ha-Ras liver tumour which arose without PB.  Samples: 5hmC profiles in 2 control and 2 PB exposed mouse livers, 3 liver tumours resulting from long term PB exposrue and 1 liver tumour arising without PB


title: IP of 5-methylcytosine (5-mc) enriched DNA fragments from control and mice with non-acoholic steatohepatitis (NASH) related hepatocellular carcinoma (HCC)

overall_design: 5-mc is a well establisehd epigenetic mark typically related to gene silencing events. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5mC in both control mouse livers as well as in liver tumours of high fat diet exposed mice who have progressed through NASH. Samples: 5mC profiles in livers of 2 control and 2 NASH driven HCC samples

first: Raffaele

last: Ottaviano


title: Gene expression data from ATRT tumor samples

status: Public on Mar 02 2016

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

summary: Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large series of human ATRTs. Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA and RNA sequencing found no recurrent mutations in addition to SMARCB1 that would explain the differences between subgroups. Whole-genome bisulfite sequencing and H3K27Ac chromatin-immunoprecipitation sequencing of primary tumors, however, revealed clear differences, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets.

overall_design:
49 ATRT samples were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays.
----------------------------------------
This submission consists of the expression data for 49 of 170 samples only

first: Stefan

last: Pfister


title: Genome-Wide Gene Expression Perturbation Induced by Loss of C2 Chromosome in Allotetraploid Brassica napus L.

status: Public on Dec 07 2015

city: Wuhan P.R. China

first: Bin

last: Zhu

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

summary: Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and nullisomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n=38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the nullisomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than nullisomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome

overall_design: The newly expanded third leaves without petioles from six plants of each genotype were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with two replicates were sequenced via  Illumina HiSeqTM 2000.

first: Yujiao

last: Shao

first: Qi

last: Pan

first: Xianhong

last: Ge

first: Zaiyun

last: Li


title: Genome-wide maps of nuclear lamina interactions (DamID on microarray; LaminB1, KBM7 cells, haploid)

status: Public on Sep 24 2015

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization.

overall_design: LaminB1-chromatin interactions were assayed in human KBM7 by viral transductions with Dam-Lamn B1 and Dam-only constructs. There were 2 biological replicates, hybridized in a dye-swap design

first: Jop

last: Kind

first: Ludo

last: Pagie

first: Sandra

last: de Vries

first: Mario

last: Amendola


title: Induced genomic rearrangements and chromothripsis by micronucleus-mediated chromosome transfer [850K]

status: Public on Aug 13 2015

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

institute: University Medical Center Utrecht

summary: Chromosome segregation errors have been linked to DNA damage and genomic rearrangements. Accumulating evidence has shown that catastrophic genomic rearrangements, like chromothripsis, can result from lagging chromosomes undergoing aberrant DNA replication and DNA damage in micronuclei. Detailed characterization of genomic rearrangements resulting from DNA damage in micronuclei has been hampered because of difficulties in culturing daughter cells with DNA damage.   Here, we employ a method by which a specific single chromosome is trapped in a micronucleus, followed by transfer to an acceptor cell. Next, stably propagating clonal cell lines with an extra chromosome were established and analyzed by copy number profiling and whole genome sequencing. While non-transformed, p53 proficient and telomerase-immortalized RPE1 cells showed a stable genome following addition of the transferred chromosome, we observed frequent de novo genomic rearrangements in cells derived from the HCT116 colorectal cancer cell line after chromosome transfer. The de novo rearrangements varied from simple deletions and duplications to complex rearrangements. Phase-informative SNPs revealed that the rearrangements specifically occurred on the transferred chromosome. We found that the complex rearrangements recapitulated all features of chromothripsis, including massive oscillation between two copy number states, localization to a single chromosome, random joining of chromosome fragments and non-homologous or micro-homologous repair.   We describe an approach that enables the isolation of clonal cell lines with genomic rearrangements and chromothripsis on a specific chromosome in p53 proficient cells. The procedure enables further investigation of the exact mechanism leading to chromothripsis and the analysis of its consequences for cell survival (viability) and cancer development.

overall_design: We analyzed 38 cell clones, originating from HCT116 or RPE1 cells respectively, with Illumina beadchip arrays to test for unique de novo copy number variants and to determine the chromosome affacted by the CNAs.

first: Mirjam

last: de Pagter

first: Markus

last: van Roosmalen

first: Verena

last: Passerini

first: Aline

last: Campos Sparr

first: Ivo

last: Renkens

first: Karen

last: Duran

first: Fenna

last: Kropveld

first: Zuzana

last: Storchová


title: Induced genomic rearrangements and chromothripsis by micronucleus-mediated chromosome transfer

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

overall_design: Refer to individual Series


title: Spatial reconstruction of single-cell gene expression

status: Public on Apr 13 2015

city: New York City

first: Rahul

last: Satija

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

overall_design: We generated single-cell RNA-seq profiles from dissociated cells from developing zebrafish embryos (late blastula stage  - 50% epiboly)


title: Mapping and dynamics of regulatory DNA in A. thaliana tissues and cell types across developmental transitions

status: Public on Sep 01 2015

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: We performed DNase-seq on root tissue, root epidermal cell types, seed coat epidermal cells at two developmental stages, and open and closed flowers.

overall_design:
Root: We performed chromatin profiling (DNase-seq) on whole root (all cell types), or root epidermal cell types (hair cell, non-hair cell). Seed coat: We performed chromatin profiling on seed coat epidermal cells from siliques at two developmental stages (4 days past anthesis, 7 days past anthesis). We preformed chromatin profiling (DNase-seq) on flowers at two developmental time points (open and closed flowers). All plants were grown on plates (roots only) or in soild in LD conditions (16hr light 22°C, 8hr dark 20°C).

The following processed data files are pooled short read data from 2 biological replicates (GSM1289379 [DS21306] and GSM1824051 [DS20134]):
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.peaks.bed

The following processed data files are pooled short read data from 2 biological replicates (GSM1824052 [DS20131] and GSM1824053 [DS20132]):
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.peaks.bed

The following processed data files are pooled  pooled short read data from 2 biological replicates (GSM1824054 [DS19056] and GSM1824055 [DS21512]):
Col-0.Root.Hair.DNase.pooled.6.8M.signal.bw
Col-0.Root.Hair.DNase.pooled.6.8M.peaks.bed

first: Alessandra

middle: M

last: Sullivan

first: Andrej

last: Arsovski

first: Kerry

last: Bubb

first: Peter

last: Sabo

first: Richard

last: Sandstrom

first: Robert

last: Thurman

first: Shane

last: Neph

first: Alex

last: Reynolds

first: Audra

middle: K

last: Johnson

first: Eric

last: Haugen

first: Agnieszka

last: Dargiel

first: Jun

last: Neri

first: Molly

last: Weaver

first: Morgan

last: Diegel

first: Jennifer

last: Nemhauser

first: Christine

last: Queitsch


title: MicroRNA profiling of cells isolated from human abdominal aortic aneurysms. Let-7f, a new potential circulating biomarker

status: Public on Oct 09 2014

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary:
This study aims to identify and characterize miRNA expression in aneurysmal smooth muscle cells (SMCs) and M1 and M2 macrophages isolated by laser microdissection from human AAA biopsy samples.
The aim of this study was to profile (with microarray technology) miRNAs in M1 and M2 macrophages and Smooth muscle cells (SMCs), isolated by laser capture microdissection (LCM). SMCs isolated from control non-aneurysmal aortas were the control group according to which data were normalized. Areas enriched in M1 macrophages, M2 macrophages and smooth muscle cells were microdissected (9.8 [4.7-16.2] mm2) from two different biopsy samples of human abdominal aortic aneurysm. An area enriched in smooth muscle cells was microdissected from two biopsy samples of non aneurysmal abdominal aortas. Each microdissected samples were analyzed independently on microarray.

overall_design: M1 and M2 macrophages and smooth muscle cells expressed in human abdominal aneurysmal aortas were each analyzed in duplicate (each isolated from different human donors of abdominal aortic aneurysm). Analysis of replicated samples of cells were performed on a second microarray. Data were normalized with smooth muscle cells isolated from human abdominal non aneurysmal aortas.

first: Rafaëlle

last: Spear

first: Renaud

last: Blervaque


title: MiR-221 mediated gene expression in human PCa cells

status: Public on Mar 27 2014

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: MiR-221 overexpression leads to activation of apoptosis, growth arrest and reduced invasivness in PCa cells. Interaction of miR-221 with potential target genes was analyzed by a genome wide expression profiling.. Regulation of selected genes and proteins identified in the gene array analysis was confirmed by Real Time RT-PCR assay (IRF1, IRF2 SOCS3, STAT1), and Western Blotting. In total, 282 genes were upregulated and 64 downregulated based on a more than 2-fold difference to untransfected PC-3 cells. Regulated genes are involved in apoptosis, hemostasis, oxidative stress response,  tumorigenesis and inflammation. We confirmed dysregulation of IRF-2 SOCS3, STAT1,IRF9. These results indicate that miR-221 overexpression might lead to activation of the JAK/STAT pathway and downregulation of miR-221 might contribute to tumorigenesis in PCa cells.

overall_design: pre-miR-221 transfected PC-3 cells vs unstimulated control cells - total samples analysed are 4.

first: Martin

last: Spahn

first: Markus

last: Krebs

first: Burkhard


title: Analysis of Blimp-1 and Irf-1 genomic binding in wild type and Prdm1/Blimp-1 mutant embryonic gut

status: Public on Jul 10 2015

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

summary: The goal of this study was to profile Blimp1 binding in E18.5 small intestine using a Blimp-1-eGFP knock-in allele, and to compare Blimp-1-eGFP genomic binding with Irf-1 genomic binding in normal small intestine.  Changes in Irf-1 binding between wild type and Prdm1/Blimp-1 mutant small intestine were also assessed.

overall_design: ChIP-seq was performed for Blimp-1-eGFP in duplicate in E18.5 small intestine expressing the fusion protein using anti-GFP antibody.  As a negative control a single anti-GFP ChIP was also performed in wild type small intestine.  ChIP-seq for Irf-1 was performed in duplicate in both wild type and Prdm1/Blimp-1 mutant E18.5 small intestine using an anti-Irf-1 antibody. Duplicate IgG ChIP control in wild types was performed as a negative control.  All samples had an associated input chromatin sample sequenced.

first: Marc

last: Morgan

first: Andrew

middle: C

last: Nelson

first: Elizabeth

last: Bikoff

last: Robertson


title: Toxicogenomic Assessment of Liver Responses following subchronic exposure to furan in Fischer F344 rats [cRNA]

status: Public on Oct 30 2014

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

country: Canada

institute: health canada

summary: Furan is a widely used industrial chemical and a common contaminant in heated foods. Chronic furan exposure has been shown to cause cholangiocarcinoma and hepatocellular tumors at doses of 2 mg/kg bw/day with gender differences in frequency and severity. The hepatic transcriptional alterations induced by low doses of furan (doses below those inducing liver tumors) and the potential mechanisms underlying gender differences are largely unexplored. We used DNA microarrays to examine the global hepatic mRNA and microRNA transcriptional profiles of male and female rats exposed to 0, 0.03, 0.12, 0.5 or 2 mg/kg bw/day furan over 90 days. Marked gender differences in gene expression responses to furan were observed, with many more altered genes in exposed males than females, confirming the increased sensitivity of males even at the low doses. Pathway analysis supported that key events in furan-induced hepatotoxicity in males included gene expression changes related to oxidative stress, apoptosis and inflammatory response, while pathway changes in females were consistent with primarily adaptive responses (regeneration). Pathway benchmark doses (BMDs) were estimated and compared to relevant apical endpoints. Transcriptional BMDs could be examined in males, they ranged from 0.08 – 1.43 mg/kg bw/day and approximated those derived from traditional histopathology. MiR-34a (a target of P53 signalling) was the only microRNA significantly increased at the 2 mg/kg bw/day, providing evidence in support of the importance of apoptosis and cell proliferation in furan hepatotoxicity. Overall, this study demonstrates the use of transcriptional profiling to discern mode of action and mechanisms involved in gender differences.

overall_design: A total of 50 RNA samples (5 female and 5 male rats per dose group, 5 dose groups total) were labelled with Cyanine 5-CTP using Low Input Quick Amp Labelling kits (Agilent Technologies Inc.) following the manufacturer’s instruction. Universal rat reference total RNA (Agilent Technologies Inc.) was labelled with Cyanine 3-CTP. Cy5-sample cRNA and Cy3-reference cRNA were hybridized to Agilent G4853A SurePrint G3 Rat GE 8 X 60K microarrays (Agilent Technologies Inc.). One microarray from the male group did not pass the quality control and was eliminated from further analyses

first: Hongyan

last: Dong

first: Santokh

last: Gill

first: Ivan

middle: H

last: Curran

last: Williams

first: Byron

last: Kuo

first: Michael

last: Wade

first: Carole

last: Yauk


title: Gene expression changes chemically-induced in renal cortex of rats

status: Public on Sep 27 2016

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan


title: Toxicogenomic Assessment of Liver Responses following subchronic exposure to furan in Fischer F344 rats [miRNA]

overall_design: Total RNAs from 16 liver samples (4 males and 4 females from control and 2 mg/kg bw/day dose groups) were processed using the miRNA Complete Labelling and Hybridization kit (Agilent Technologies Inc.). Labelled RNA was hybridized on 8 X 15K Agilent rat miRNA microarray slides. Arrays were scanned using an Agilent G2505B scanner (5 μM resolution). Feature extraction (version 10.7.3.1, Agilent Tech. Inc.) was used to acquire the fluorescence intensity of each probe.


title: Effect of estradiol on murine alveolar macrophages and RAW264.7 cells in vitro

status: Public on Jan 01 2014

city: Boston

first: Alexey

last: Fedulov

state: MA

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary: Mouse BAL alveolar macrophages from pregnant E14 and control dams are compared to RAW cells cultured with estradiol to determine shared gene expression change patterns induced by pregnancy and estrogen

overall_design: BAL cells from intact pregnant and control mice were directly processed for RNA extraction. RAW cells were cultured overnight with estradiol or vehicle, then RNA was exctracted.

first: Lester

last: Kobzik

middle: V


title: Comparison of metastatic derivatives of colon cancer cell line selected in vivo

status: Public on Apr 22 2014

city: Barcelona

first: Xabier

last: Garcia-Albeniz

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: Using a human colorectal cancer cell line we incremented its metastatic capacity in a mouse model of liver and lung metastasis. Afterwards, a comparison between the different metastatic derivatives is done.

overall_design: Metastatic derivatives were selected by the use of a balb/c nude mouse model. Once the metastasis appeared, the cells were extracted and expanded in culture. Thereafter RNA was extracted and hybridized

first: X

first: J

last: Urosevic


title: Toxicogenomic Assessment of Liver Responses following subchronic exposure to furan in Fischer F344 rats

type:
Expression profiling by array
Non-coding RNA profiling by array


title: RNA-seq of mouse ES cells depleted of MOF, MSL1, MSL2 or KANSL3

status: Public on Jun 03 2014

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

summary: We have studied the regulatory potential of MYST1-(MOF)-containing MSL and NSL complexes in mouse embryonic stem cells (ESCs) and neuronal progenitors. We find that both complexes influence transcription by binding to promoters as well as TSS-distal enhancer regions. In contrast to flies, the MSL complex is not enriched on the X chromosome yet it is crucial for mammalian X chromosome regulation as it specifically regulates Tsix ncRNA, the major repressor of Xist lncRNA. MSL depletion leads to severely decreased Tsix expression, reduced REX1 recruitment, and consequently accumulation of Xist RNA in ESCs. The NSL complex provides additional, Tsix-independent repression of Xist by maintaining pluripotency. MSL and NSL complexes therefore act synergistically by using distinct pathways to ensure a fail-safe mechanism for the repression of X inactivation in ESCs.

overall_design:
We have performed ChIP-seq of KANSL3, MCRS1, MOF, MSL1 and MSL2 in mouse ESCs, and KANSL3, MOF and MSL2 in NPCs, in duplicate and normalised against their inputs. We have also performed RNA-seq following knockdown of Kansl3, Mof, Msl1 and Msl2 mouse embryonic stem cells in triplicate. NB: Kansl3 and Mof knockdown-RNAseq are analyzed against their own scrambled controls, and Msl1 and Msl2 against another scrambled control triplicate.

siMCRS1 & siMOF were compared to scrambled1 (scr1)
siMsl1 and siMsl2 were compared to scr2
siNsl3 was compared to scr3

first: Tomek

last: Chelmicki

first: Matthew

last: Turley

first: Tasneem

last: Khanam

first: Tugce

last: Aktas

first: Patrick

last: Wright

first: Pavankumar

last: Videm

first: Rolf

last: Backofen

first: Thomas

last: Manke

first: Asifa

last: Akhtar


title: Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology

status: Public on Sep 30 2014

city: East Lansing

first: Frances

last: Trail

state: MI

address: 612 Wilson Road

department: Plant Biology; Plant, Soil and Microbial Sciences

institute: Michigan State University

summary: Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. To identify corresponding differences in the transcriptional program underlying fruiting body development in the two species, comparative expression was performed, analyzing six developmental stages. To accompany the transcriptional analysis, detailed morphological characterization of F. verticillioides development was performed and compared to a previous morphological analysis of F. graminearum. Morphological development was similar between the two species, except for the observation of possible trichogynes in F. verticillioides ascogonia, which have not been previously reported for any Fusarium species. Expression of over 9000 orthologous genes were measured for the two species. Functional assignments of highly expressed orthologous genes at each time-point revealed the majority of highly expressed genes fell into the ‘‘unclassified proteins’’ category, reflecting the lack of characterization of genes for sexual development in both species. Simultaneous examination of morphological development and stage-specific gene expression suggests that degeneration of the paraphyses during sexual development is an apoptotic process. Expression of mating type genes in the two species differed, possibly reflecting the divergent roles they play in sexual development. Overall, the differences in gene expression reflect the greater role of fruiting bodies in the life cycle and ecology of F. graminearum versus F. verticillioides.

sample_organism:
Fusarium graminearum
Fusarium verticillioides

overall_design: mRNA were sampled and compared from six time points across sexual reproduction in two Fusarium species

first: Usha

middle: R

last: Sikhakolli

first: Francesc

last: López-Giráldez

first: Ning

last: Li

first: Ralph

last: Common

first: Jeffrey

middle: P

last: Townsend


title: Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

status: Public on Dec 15 2013

first: John

last: Stamatoyannopoulos

summary: We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. Analysis of >700,000 TF footprints disclosed an extensive cis-regulatory lexicon, and enabled construction of large-scale TF cross-regulatory networks. Although the cis- and trans-regulatory repertoire is markedly distinct from mammals, the architecture of A. thaliana TF networks is strikingly similar to those of human. Analysis of the DHS landscape and TF network dynamics during heat shock and photomorphogenesis revealed thousands of conditionally-sensitive elements and enabled mapping of key regulatory circuits. Our results provide an extensive resource for understanding and enabling diverse aspects of A. thaliana biology.

overall_design: Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old dark-grown seedlings exposed to 0hr light, 30min light, 3hr light or 24hr LD conditions.  Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old LD-grown seedlings treated with a brief sever heat shock or kept under control conditions. Replicates are included when available; controls and read-normalized samples (samples that were subsampled to the same read-depth) are also included here.

first: Alessandra

last: Sullivan

first: Andrej

last: Arsovski

first: Kerry

middle: L

last: Bubb

first: Peter

last: Sabo

first: Richard

last: Sandstrom

first: Robert

last: Thurman

first: Shane

last: Neph

first: Alex

last: Reynolds

first: Andrew

last: Stergachis

first: Benjamin

last: Vernot

first: Audra

last: Johnson

first: Eric

last: Haugen

first: Agnieszka

last: Dargiel

first: Jun

last: Neri

first: Molly

last: Weaver

first: Morgan

last: Diegel

first: Timothy

last: Hughes

first: Jennifer

last: Nemhauser

first: Christine

last: Queitsch


title: RNAseq Expression data for mouse liver, Phenobarbital exposed livers and resulting liver tumours.

status: Public on May 17 2016

first: John

last: Thomson

summary: Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression.

overall_design: We carry out paired end , strand specific RNAseq prior to sequencing on Illumina Hiseq 2500 to report on the transcriptional landscape in replicate control mouse livers (n=2), 12 week Phenobarbital exposed livers (n=2)and resulting (35 week PB) liver tumours (n=3).

first: Michael

last: Schwarz

last: Meehan


title: RNA Seq analysis of Schmidtea mediterranea treated with RNAi against chd4, p53, or unc22 to identify factors involved in neoblast differentiation.

status: Public on Oct 21 2015

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Adult stem cells are tissue-specific cells with the capacity to self-renew and differentiate to continually replace cells lost to normal physiological turnover or injury. Neoblasts, the planarian stem cells, are widely distributed throughout the body mesenchyme, driving constitutive renewal of tissues during homeostasis and endowing planarians with the remarkable capacity to regenerate wholly from tiny tissue fragments. Neoblasts are the only dividing cells in planarians and are believed to be collectively comprised of both a heterogeneous population of pluripotent cells with broad differentiation potential and also lineage-committed progenitor cells that give rise to specific tissues. Recent work has identified a prominent class of neoblasts referred to as zeta-class, which express the zinc-finger gene zfp-1.  Zfp-1, along with the chromatin remodeling factor chd4, the tumor suppressor gene p53, and most recently an RNA-binding protein mex3-1, have all been shown to be required for maintenance of two related post-mitotic, sub-epidermal cell populations expressing the specific marker genes prog-1 and AGAT-1, which have been widely used to asses neoblast differentiation. Given that zeta-class neoblasts are required for the generation of prog-1 and AGAT-1 positive cells and other markers of epidermal cell types, prog-1 and AGAT-1 likely mark two major populations of epidermal progeny cells. To understand the molecular mechanisms underlying neoblast differentiation and how they give rise to multiple cell types, we devised a strategy to identify critical factors enriched in the AGAT-1 positive cell population required for epidermal lineage progression. We performed RNA-Seq analysis of chd4 and p53 RNAi animals and characterized additional markers enriched in AGAT-1 positive and related post-mitotic cells.

overall_design: Examine gene expression profiles of adult flatworms after 3, 6, 9, 12, 15, or 18 days of treatment with RNAi against either chd4, p53, or an unc22 non-targeting control. Experiments were performed in triplicate yielding a total of 50 samples after removal of an outlier. The chd4 time course extends to only 15 days due to lethality.

first: Kimberly

last: Tu

first: Li-Chun

last: Cheng

first: Hanh

middle: T

last: Vu

first: Jeffrey

last: Lange

first: Sean

last: McKinney

first: Alejandro

middle: S

last: Alvarado


title: A common set of DNA regulatory elements shapes Drosophila appendages

status: Public on Nov 07 2013

city: Chapel Hill

first: Daniel

last: McKay

state: NC

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

summary: We mapped open chromatin by FAIRE-seq and measured gene expression by RNA-seq in 3 types of Drosophila samples: staged whole embryos, imaginal discs, pharate appendages. We first demonstrate that regions of open chromatin precisely define regions of enhancer activity in developing embryos. In contrast to the dynamic changes in open chromatin observed between different stages of embryogenesis, we found that the open chromatin profiles in wing, leg, and haltere imaginal discs are nearly identical. This was also true again later in development, where the adult appendages also share nearly identical open chromatin profiles. Therefore, at a given developmental time point, different appendages are specified using a shared set of DNA regulatory elements. However, from one time point to the next, the set of accessible regulatory elements changes. Open chromatin profiles in appendage imaginal discs are almost entirely different than those of the adult appendages. We propose that master regulator transcription factors create morphologically distinct structures by differentially influencing the function of the same set of DNA regulatory modules.

overall_design: Open chromatin profiling during Drosophila development: 3 stages of embryogenesis (2-replicates each); wing, leg, and haltere 3rd instar imaginal discs (3-replicates each); 3rd larval central nervous system (2-replicates); eye-antennal imaginal discs (2-replicates); wing, leg, and haltere pharate appendages (2-replicates each); Genomic DNA Inputs. Sequencing performed on Illumina GAII and HiSeq.

first: Jason

middle: D

last: Lieb


title: Genomic signatures characterize leukocyte infiltration in myositis muscles

status: Public on Nov 01 2012

city: Gaithersburg

first: Wei

last: Zhu

state: Md

address: One MedImmune Way

department: Translational Sciences

institute: MedImmune

summary: Immune cell infiltration in myositis were by examining microarray expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls.

overall_design: Muscle samples from 36 subjects (5 normal controls, 5 NM, 8 DM, 8 PM and 10 IBM) were studied

last: Morehouse

first: Brandon

last: Higgs


title: Induced genomic rearrangements and chromothripsis by micronucleus-mediated chromosome transfer [CytoSNP12]

status: Public on Aug 13 2015

first: Wigard

last: Kloosterman

summary: Chromosome segregation errors have been linked to DNA damage and genomic rearrangements. Accumulating evidence has shown that catastrophic genomic rearrangements, like chromothripsis, can result from lagging chromosomes undergoing aberrant DNA replication and DNA damage in micronuclei. Detailed characterization of genomic rearrangements resulting from DNA damage in micronuclei has been hampered because of difficulties in culturing daughter cells with DNA damage.   Here, we employ a method by which a specific single chromosome is trapped in a micronucleus, followed by transfer to an acceptor cell. Next, stably propagating clonal cell lines with an extra chromosome were established and analyzed by copy number profiling and whole genome sequencing. While non-transformed, p53 proficient and telomerase-immortalized RPE1 cells showed a stable genome following addition of the transferred chromosome, we observed frequent de novo genomic rearrangements in cells derived from the HCT116 colorectal cancer cell line after chromosome transfer. The de novo rearrangements varied from simple deletions and duplications to complex rearrangements. Phase-informative SNPs revealed that the rearrangements specifically occurred on the transferred chromosome. We found that the complex rearrangements recapitulated all features of chromothripsis, including massive oscillation between two copy number states, localization to a single chromosome, random joining of chromosome fragments and non-homologous or micro-homologous repair.   We describe an approach that enables the isolation of clonal cell lines with genomic rearrangements and chromothripsis on a specific chromosome in p53 proficient cells. The procedure enables further investigation of the exact mechanism leading to chromothripsis and the analysis of its consequences for cell survival (viability) and cancer development.

overall_design: We analyzed 38 cell clones, originating from HCT116 or RPE1 cells respectively, with Illumina beadchip arrays to test for unique de novo copy number variants and to determine the chromosome affacted by the CNAs.

first: Mirjam

last: de Pagter

first: Markus

last: van Roosmalen

first: Verena

last: Passerini

first: Aline

last: Campos Sparr

first: Ivo

last: Renkens

first: Karen

last: Duran

first: Fenna

last: Kropveld

first: Zuzana

last: Storchová


title: Multidimensional regulation in transcriptome during sexual development in Neurospora crassa revealed with RNA sequencing

status: Public on Oct 10 2013

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Fungi exhibit a huge diversity in morphology and ecology, and genetic basis of morphological development in sexual reproduction of multi-cellular fungi has not been fully investigated with genome-wide approaches. Model organism Neurospora crassa is the very first sequenced genome for multi-cellular fungi, and well-annotated genome and gene markers characterized for key morphological traits make N. crassa an ideal platform to investigate transcriptome and its regulation during sexual development. RNA sequencing with different priming strategies have been efficient to provide fine-scale transcriptome landscapes for a multiple-staged development process. RNA were sampled for eight time points cross perithecial development, including two points right before and after crossing, for which mat A protoperithecia were fertilized with mat a conidia. Transcription profiles for 9717 genes were achieved for all eight time-points using multi-targeting priming and additional 14 genes for five time-points using random hexmas priming. Majority of the genome showed continually up- or down- regulated expression patterns during the later perithecial development stages after 72 or 96 h. Functionally unclassified proteins were counted for most up-regulated genes, while genes were enriched with different functions for different down-regulation patterns. We observed significant increase in transcription for mat a-1 and for mat A-1 specific pheromone precursor ccg-4 during the perithecial development, and expression of genetic markers for morphological traits in perithecium, ascus, and ascospore, and for development traits in meiosis often showed multiple peaks during the experiment. We also observed different expression patterns in transcription for other transcription factors and for genes involved in Meiotic Silencing and Repeat Induced Point Mutation, and expression of a gene encoding a protein similar to stc-1 in fission yeast, was increased after crossing and reached almost 1000 fold changes at 144h. Different expression patterns were also observed for genes involved in heterokaryotic and vegetative incompatibility and for genes functioning in the heterotrimmeric G protein signalling systems and in the MAP kinase signalling pathways. By sequencing RNAs from different development stages with two priming strategies, this study provided a large amount of data to quantifiably describe the sophisticated transcriptomic landscape in pre-mating, crossing and sexual reproduction of N. crassa.  As major expression patterns for genes in different function categories were recognized during this process, our results in general supported previous observation of expression patterns for genetic markers and regulatory genes/pathway. This study provided further evidence for functional correlation among genes involved in same function or pathways, which included mating type genes and pheromones, transcription factors, pigmentation, heterokaryotic incompatibility, singaling pathways, and RNA silencing. Besides, we also disclosed different expression patterns for the regulatory genes/pathways cross the whole sexual development, and functions of some of these genes were also suggested with phenotypic studies of knockouts. Understanding how these different regulatory elements and their function networks adjust genome-wide transcriptomic and proteomic expression will provide detailed insights about morphological development of tissue-differentiated perithecia in N. crassa.

overall_design: RNA were sampled for eight time points cross perithecial development, including two points right before and after crossing, for which mat A protoperithecia were fertilized with mat a conidia. Two priming MTP and N6 were used separately as technique replicates for the first strain synthesis during cDNA preparation of all samples. Total 16 cDNAs were sequenced

first: Zheng

last: Wang

last: Lopez-Giraldez

first: Nina

last: Lehr

first: Marta

last: Farré

first: Frances

last: Trail

last: Townsend


title: Global gene expression profiling using total RNA [BMM, MPI and SPG]

status: Public on Jun 08 2013

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

institute: Max-Planck-Institute for Immunobiology and Epigenetics

summary:
Differentiation of myeloid progenitor cells leads to distinct populations of mononuclear phagocytes.Various  macrophages exhibit distinct biological properties.
Here wanted to delineate and characterize gene expression patterns in bone marrow derived macrophages
Here wanted to delineate and characterize gene expression patterns in two newly established, self-renewing, in vitro grown non-transformed lines (MPI cells) and in the SP37A3 immature myeloid dendritic cell line.
We used microarrays to detail the global programme of gene expression in MPI cells and to compare them to other types of mononuclear phagocytes.

overall_design:
[BMM] Total cellular RNA from ex vitro differentiated bone marrow derived macrophages was extracted and hybridized to Affymetrix microarrays to carry out cluster analysis and overlap and gene set analysis for enriched pathways.
[MPI and SPG] Total cellular RNA from independently established MPI lines and a splenic immature dendritic cell line was extracted and hybridized to Affymetrix microarrays to carry out cluster analysis and overlap and gene set analysis for enriched pathways.

first: Gyorgy

last: Fejer

first: Marina

last: Freudenberg

first: Lars

last: Dolken


title: Hepatic transcriptome changes in testosterone-deficient pigs fed a high-fat diet

status: Public on Jan 08 2015

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

summary: To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels.

overall_design: Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.

first: Zhaowei

last: Cai


title: The differential expression pattern of human dental epithelial cells vs non-dental epithelial cells

status: Public on Feb 01 2016

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

summary:
In order to identify the genes that are specific to the ameloblast phenotype, we collected epithelial cells differentiated from HESCs (ES-EC), human fetal oral epithelia cells (OE), and presecretory ameloblasts (PAB) and SAB, and conducted the microarray to compare the overall transcription patterns of these four cell types.
Stage specific ameloblasts did exhibit distinctive gene expression patterns as comapred to non-dental epithelia cells ES-EC and OE. There were 908 genes in PAB and 1203 genes in SAB that were either down-regulated or upregulated more than 2.0-fold as comapred to the non-dental epthelial cells ( average of ES-EC and OE)

overall_design: Stage specific secretory ameloblasts (SAB) and maturation ameloblasts (MAB) were laser microdissected from mandibular incisors of control and 50 ppm F treated mice.

first: Liwei

last: Zheng


title: Inflammatory gene profiling of Ewing sarcoma family of tumors (set B)

status: Public on Dec 01 2011

city: Helsinki

first: Suvi

last: Savola

address: Haartmaninkatu 3

department: Pathology

country: Finland

institute: University of Helsinki

summary:
Purpose: Unlike in most adult-onset cancers, an association between typical paediatric neoplasms and inflammatory triggers is rare. We studied whether immune system related genes are activated and have prognostic significance in Ewing sarcoma family of tumours (ESFT). Experimental design: Data-analysis was performed on gene expression profiles of 44 ESFT patient, 11 ESFT cell line, and 18 normal muscle tissue samples. 238 inflammation related genes were selected based on literature and a macrophage gene expression signature was derived from SymAtlas. Differential expression of the genes was analysed by t-test and survival analysis was performed according to gene expression.

Results: Inflammatory genes are activated in ESFT patient samples, as 38 of 238 (16%) inflammatory genes were significantly upregulated (p<0.001) when compared to ESFT cell lines. This inflammatory gene activation was characterized by significant enrichment of macrophage related gene expression with 58 of 299 (19%) of these genes being upregulated (p<0.001). By combining expression data from ESFT patients, cell lines and muscle tissue samples we were able to identify a total of 32 presumptive inflammatory genes that characterize and distinguish tumour site in vivo from surrounding normal tissues. High expression of C5 correlated with better event free (p=0.01) and overall survival (p=0.004) in dose dependent manner. C5 and its receptor C5aR1 expression was verified at protein level by immunohistochemistry on tumor tissue microarray. Also, high expression of JAK1 correlated with favourable overall survival (p=0.04) and high expression of IL8, derived presumably from infiltrating immune cells, resulted in poor overall survival in Ewing sarcoma (p=0.04). Conclusions: Immune system related gene activation is observed in ESFT patient samples and several prognostically significant inflammatory genes (C5, JAK1 and IL8) for ESFT were identified.

overall_design: 44 Ewing sarcoma family of tumor patient and 18 normal muscle samples obtained from GSE6798 and GSE3526.

first: Arto

last: Klami

first: Samuel

last: Myllykangas

first: Cristina

last: Manara

first: Katia

last: Scotlandi

first: Piero

last: Picci

first: Sakari

last: Knuutila

first: Jukka

last: Vakkila


title: Inflammatory gene profiling of Ewing sarcoma family of tumors

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

overall_design: Refer to individual Series


title: The overexpression of microRNA 21 correlates with biochemical recurrence after radical prostatectomy

status: Public on May 09 2013

city: Campinas

first: Paulo

last: Viadanna JR

state: Sao Paulo

address: Rua Francisco Otaviano, 62

country: Brazil

institute: Scylla Bioinformatics

summary:
The objective of this study was to utilize a microarray platform to determine the microRNA (miRNA) expression profile in prostate cancer tissue from patients who underwent radical prostatectomy and were followed for an average of 47 months. The GeneChip® miRNA Array (Affymetrix) contains more than 46,000 probes, and more than 1,100 mature human miRNAs and transcripts. An expression level higher or lower than 1.1 with a p<0.05 were considered to be differentially expressed. When tumors with a GS<7 were compared with those with a GS≥7, five miRNAs were down-regulated and nine were up-regulated. In comparing tumors from patients with PSA <10 ng/mL vs. those with PSA ≥10 ng/mL, 21 miRNAs were down-regulated and 29 were overexpressed. There was decreased expression of 21 miRNAs and increased expression of 22 miRNAs when pT2 and pT3 tumors were compared.
The comparison of the expression profiles of men with vs. without recurrent disease (PSA>0.2 ng/mL) revealed that 14 miRNAs were down-regulated and 17 were up-regulated.  Considering the three prognostic factors and biochemical recurrence, miR-335 was overexpressed in pT3 tumors in patients with PSA>10 ng/mL, miR-1202 was overexpressed in recurrent tumors in which PSA >10 ng/mL, and miR-885 and miR-1226 were overexpressed in recurrent pT3 tumors. Six miRNAs (miR- 361, 378, 548, 574, 652 and 892) had decreased expression in pT3 tumors in patients with PSA >10 ng/mL. miR-16 was down-regulated in recurrent pT3 tumors. miR-92 and miR-450 exhibited decreased expression in recurrent tumors in patients with PSA > 10 ng/mL. miR-28 was down-regulated in pT3 adenocarcinomas with a GS ≥ 7. The differentially expressed miRNAs in recurrent tumors were validated using qRT-PCR in 74 additional specimens.  miR-21 was overexpressed in recurrent tumors, and in the Cox model, expression levels higher than 0.64 were indicative of biochemical recurrence with a risk of 2.4. These results, which were based on clinical specimens from patients treated in a standardized way and followed for an average of 47 months, provide an initial understanding of the role of miRNAs in prostatecancer progression; the foremost representative is miR-21, which has been implicated in the progression of various human cancers.

overall_design: Fifty-three patients underwent a radical prostatectomy performed by the same surgeon (MS) to treat localized PC between August 2000 and June 2002. The mean age was 65 years (SD: 7.5, range: 49 - 77). The mean Gleason score was 7 (SD: 1.1, range: 5 - 10); 15 tumors had a score of 5 or 6, and 38 had a score between 7 and 10. Twenty-four (45.3%) of the patients had pT2 tumors, and 29 (54.7%) had pT3 tumors.  The control group consisted of three patients with lower urinary tract symptoms, a mean age of 55.3 years and a diagnosis of benign prostatic hyperplasia (BPH) who consented to open surgery.

last: Leite

first: Sabrina

last: Reis

first: Nayara

last: Viana

first: Denis

last: Morais

first: Iran

last: Silva

first: José

last: Pontes Jr

first: Betina

last: Katz

first: Miguel

last: Srougi


title: Expression data from complex genetic sarcomas

status: Public on Jun 27 2010

city: Bordeaux

first: fred

last: chibon

address: 229 cours de l'argonne

institute: Institut Bergonie

summary:
For this study, we selected, from the French Sarcoma Group (FSG) database, soft tissue sarcomas with no recurrent chromosomal translocations and for which frozen tissue of the untreated primary tumor was available. One hundred and eighty-three cases were studied.

We used microarrays to detail the global program of gene expression underlying the tumor biology.

overall_design: Every case was histologically reviewed by pathologists and classified according to the 2002 WHO classification using histology, immunohistochemistry and molecular genetic and cytogenetic when needed.

first: Frederic

last: Chibon

first: Jean-Michel

last: Coindre

first: Alain

last: Aurias


title: atmyc2_cop1_mutant_light_ABA_treatment

status: Public on Dec 31 2009

city: New Delhi

first: Sudip

last: Chattopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute For Plant Genome Research

summary:
Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling
Keywords: Light and abscisic acid treatment

overall_design:
Expression data for wild-type, atmyc2, cop1-6, and atmyc2 cop1-6 seedlings under constant dark, blue-light and blue-light along with abscisic acid
Ten-day-old Arabidopsis (wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant) seedlings grown under constant dark, constant blue-light (35 µmol/sec/m2), and constant blue-light along with ABA (0.5 µm) were used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.

first: Mukesh

last: Jain

first: Sreeramaiah

middle: N

last: Gangappa

first: Jitendra

last: Khurana


title: Expression data of HCV-associated advance disease state

status: Public on Nov 01 2007

city: Riyadh

first: Saira

last: Khalid

address: Amr Ibn Alaas street

country: Saudi Arabia

institute: King Saud University

summary:
Introduction: Mechanisms that contribute to the pathogenesis of liver damage caused by hepatitis C virus (HCV) are not fully understood. Our previous work on liver biopsies from chronic HCV patients has shown modulation of the expression of certain cell cycle proteins indicating HCV-induced modifications of cell cycle events. We therefore hypothesize that HCV infection disrupts normal  regulation of cell cycle that contributes to disease progression. Objective: To identify molecular disruptions during the course of HCV-associated disease progression, using liver biopsy specimens of chronic hepatitis C patients. Methods:  Liver biopsy samples classified on histological basis as early (fibrosis stage 0-1) or advanced (fibrosis stage 3-4) disease stage were studied using oligonucleotide array ( HG U133 Plus 2.0, Affymetrix GeneChip™ System). For comparison, liver specimens from patients with non-viral hepatitis were also analyzed by microarray. Expression data was analyzed using Genespring (GX 7.2) and Ingenuity Pathway analysis (3.0). The differential expression of selected cell cycle genes (cyclin D2, KPNA2, HERC5 and Bcl-2) identified after microarray analysis was confirmed by quantitative real-time RT-PCR.  Results: Microarray analysis revealed two-fold or greater transcriptional change in 792 genes of the total 38,500 known human genes in HCV-advance disease stage (HCV-A) as compared to HCV-early disease stage (HCV-E). Most of the genes have a defined role in immune response, extracellular matrix and cell cycle and apoptosis.
Keywords: HCV-advance disease state

overall_design: Liver biopsy samples were collected from patients of (a) HCV-infected early disease stage (HCV-E, control 1) (b) non-HCV advance disease stage (control 2) and (c) HCV-infected advance disease stage (HCV-A) for RNA extraction. Equal amount of RNA was pooled from samples (n=4)within each group and hybridized to HG-U133 Plus 2.0 array.

last: Sarfraz

first: Saeed

last: Hamid

first: Anwar

last: Siddiqui

first: Christopher

last: Lee

first: Asaf

last: Qureshi

first: Nilofer


title: Early Dysregulation of Cell Adhesion and Extracellular Matrix Pathways in Breast Cancer Progression

status: Public on Sep 08 2009

first: Lyndsey

middle: A.

last: Emery

address: 650 Albany Street - EBRC 4th Floor

department: Medicine - Hematology/Oncology

institute: Boston University Medical Center

summary:
Proliferative breast lesions, such as simple ductal hyperplasia (SH) and atypical ductal hyperplasia (ADH), are candidate precursors to ductal carcinoma in situ (DCIS) and invasive cancer. To better understand their relationship to more advanced disease, we used microdissection and DNA microarrays to profile the gene expression of patient-matched histologically normal (HN), ADH, and DCIS from 12 patients with ER+ sporadic breast cancer. SH were profiled from a subset of cases. We found 837 differentially expressed genes between DCIS-HN and 447 between ADH-HN, with >90% of the ADH-HN genes also present among the DCIS-HN genes. Only 61 genes were identified between ADH-DCIS. Expression differences were reproduced in an independent cohort of patient-matched lesions by qRT-PCR. Many breast cancer-related genes and pathways were dysregulated in ADH and maintained in DCIS. Particularly, cell adhesion and extracellular matrix (ECM) interactions were overrepresented. Focal adhesion was the top pathway in each gene set. We conclude that ADH and DCIS share highly similar gene expression and are distinct from HN. In contrast, SH appear more similar to HN. These data provide genetic evidence that ADH (but not SH) are often precursors to cancer and suggest cancer-related genetic changes, particularly adhesion and ECM pathways, are dysregulated prior to invasion and even before malignancy is apparent. These findings could lead to novel risk stratification, prevention, and treatment approaches.
Patient-matched (HN, SH, ADH, DCIS) samples were isolated from within patients with ER+ sporadic breast cancers via laser capture microdissection.  Use of patient-matched samples decreases between patient variations.

overall_design: Forty total samples were analyzed via Affymetrix U133A. Patient age ranged from 48-92. Case numbers correspond to individual patients. Each sample is identified by case number, histologic lesion and corresponding microarray ID.

first: Carol

last: Rosenberg


title: Expression data from hyaline cartilages

status: Public on Sep 10 2012

city: Enschede

first: Jeroen

last: Leijten

address: Drienerlolaan 5

institute: University of Twente

summary: Comparison of human prepuberal articular and growth plate cartilage

overall_design: Total RNA was isolated from healthy human prepuberal tibiae and femurs donors

first: J

first: M

last: Karperien