title: Long noncoding RNA expression in several hematopoietic progenitor and differentiated cell populations using a custom Agilent microarray

status: Public on Feb 20 2014

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

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

summary:
Mammals express thousands of long noncoding (lnc) RNAs, a few of which are shown to function in tissue development. However, the entire repertoire of lncRNAs and the extent to which they regulate biological processes in different tissues and species are not defined. Indeed, most lncRNAs are not conserved between species, raising questions about function. We used RNA-Seq to identify lncRNAs in primary murine fetal liver erythroblasts expressing the lineage marker TER119, megakaryocytes (CD41+) cultured from embryonic day (E) 14.5 murine fetal liver and megakaryocyte erythroid progenitors (MEPs) isolated from mouse bone marrow. We identified 683 and 594 polyadenylated lncRNAs expressed in red blood cell (erythroid) precursors of mice and humans, respectively. More than one half of erythroid lncRNAs are un-annotated, emphasizing the opportunity for new discovery through studies of specialized cell types. We analyzed the expression of these identified lncRNAs in several hematopoietic compartments using a custom microarray to identify erythroid-specific lncRNAs that were robustly expressed in both fetal liver and adult erythroid cells as targets for knockdown. Over 90% of fetal liver erythroid lncRNAs detected using RNA-seq were expressed in adult erythroblasts measured on the microarray. Analysis of the murine erythroid lncRNA transcriptome indicates that ~75% arise from promoters and 25% from enhancers, many of which are regulated by the key erythroid transcription factors GATA1 and SCL/TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatically greater species-specificity than coding genes. We investigated potential functions of 21 relatively abundant erythroid-specific murine lncRNAs (both conserved and non-conserved) by RNA interference in primary mouse erythroid precursors, and identified 7 whose knockdown inhibited features of terminal erythroid maturation including cell size reduction and enucleation. Strikingly, at least 6 of the 7 lncRNAs have no detectable expression in human erythroblasts, demonstrating that lack of conservation between mammalian species does not predict lack of function. These results reflect marked evolutionary differences between protein-coding genes and lncRNAs and indicate that the latter exert tissue- and species-specific roles in development.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: A custom Agilent microarray was designed to interrogate expression levels of long noncoding RNAs identified using RNA-seq in several different hematopoietic progenitor and differentiated cell populations. LncRNA gene definitions and RNA-seq data used to identify long noncoding RNAs are deposited in GEO with the accession numbers GSE51667 and GSE40522 respectively. The Agilent eArray platform was used to customize the SurePrint G3 Mouse GE 8x60K microarray to add 3 custom-designed probes (60nt length) each against several categories of genes, namely pseudogene, genes with small RNA overlap, low stringency lncRNAs and high stringency lncRNAs . We interrogated 7 types of hematopoietic cells, HSC, CMP, MEP, GMP, early and late erythroblasts and granulocytes. Expression measurements were determined at least in duplicate for all samples and in triplicate for most samples.

first: Vikram

last: Paralkar

first: Tejaswini

last: Mishra

first: Jing

last: Luan

first: Yu

last: Yao

first: Andrew

last: Kossenkov

first: Maxim

last: Pimkin

first: Meghneel

last: Gore

first: Diana

last: Sun

first: Neeraja

last: Konuthula

first: Xiuli

last: An

first: Narla

last: Mohandas

first: David

last: Bodine

first: Mitchell

middle: J

last: Weiss


title: Long noncoding RNA expression in several hematopoietic progenitor and differentiated cell populations

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Trophoblast giant cell underrepresentation (tiling)

status: Public on May 29 2014

city: Stanford

first: Roberta

middle: L

last: Hannibal

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

type: Genome variation profiling by genome tiling array

summary: We profiled trophoblast stem cell replication-timing in order to compare these data to our data on underrepresented (UR) domainss in trophoblast giant cells (polyploid cells derived from 2N trophoblast stem cells).  We found that UR domains are formed from late-replicating regions in tropoblast stem cells.

overall_design: Profile of early and late replicating regions in cultured trophoblast stem cells.

first: Edward

middle: B

last: Chuong

first: Julie

middle: C

last: Baker

first: Juan

last: Mulia

last: Gilbert


title: Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

status: Public on Nov 21 2013

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

summary: Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h.

overall_design: Samples were collected from 24 h in constant light to 68 h in constant light and were labelled accordingly. Two biological replicates of each time point were made, with a dye swap with the reference. The reference used was a equimolar solution of all samples.

first: Carlos

middle: T

last: Hotta

middle: Y

first: Glaucia

middle: M

last: Souza


title: Genistein Protects Hematopoietic Stem Cells against G-CSF-Induced DNA Damage

status: Public on Feb 07 2014

city: Atlanta

first: Liliana

state: GA

address: 1365 C Clifton RD, NE

department: Hematology/Oncology

institute: Emory University

summary:
Granulocyte colony-stimulating factor (G-CSF) has been utilized to treat neutropenia in various clinical settings. Although clearly beneficial, there are concerns that use of G-CSF in certain conditions increases the risk of myelodysplastic syndrome (MDS) and/or acute myeloid leukemia (AML). The most striking example is in severe congenital neutropenia (SCN). SCN patients develop MDS/AML at a high rate that is directly correlated to the cumulative lifetime dosage of G-CSF. MDS and AML that arise in these settings are commonly associated with chromosomal deletions. We demonstrate that chronic G-CSF treatment in mice results in expansion of the hematopoietic stem cell population. Furthermore, primitive hematopoietic progenitors from G-CSF–treated mice show evidence of DNA damage as demonstrated by an increase in double strand breaks and recurrent chromosomal deletions. Concurrent treatment with genistein, a natural soy isoflavone, limits DNA damage in this population.  The protective effect of genistein appears to be related to its preferential inhibition of G-CSF–induced proliferation of hematopoietic stem cells. Importantly, genistein does not impair G-CSF–induced proliferation of committed hematopoietic progenitors, nor diminish neutrophil production. The protective effect of genistein was accomplished with plasma levels that are easily attainable through dietary supplementation.
aCGH was performed using NimbleGen

overall_design: DNA was extracted from bone marrow samples from mice treated with G-CSF or diluent for 4 months and analyzed using NimbleGen 3x720K mouse copy number arrays

middle: R

first: Morgan

last: McLemore


title: Genome-wide Polycomb localization in Drosophila whole testes and purified germline precursor cells.

status: Public on Oct 18 2013

city: Cambridge

first: Sherif

last: El-Sharnouby

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Drosophila spermatogenesis cell differentiation pathway involves the activation of a large set of genes in primary spermatocytes. Most of these genes are activated by testis-specific TATA-binding protein associated factors (tTAFs). In the current model for the activation mechanism, Polycomb plays a key role silencing these genes in the germline precursors, and tTAF-dependent activation in primary spermatocytes involves the displacement of Polycomb from gene promoters.

We investigated the genome-wide binding of Polycomb in wild type and tTAF mutant testes. According to the model we expected to see a clear enhancement in Polycomb binding at tTAF-dependent spermatogenesis genes in tTAF mutant testes. However, we find little evidence for such an enhancement in tTAF mutant testes compared to wild type. To avoid problems arising from cellular heterogeneity in whole testis analysis, we further tested the model by analysing Polycomb binding in purified germline precursors, representing cells before tTAF-dependent gene activation. Although we find Polycomb associated with its canonical targets, we find little or no evidence of Polycomb at spermatogenesis genes.

The lack of Polycomb at tTAF-dependent spermatogenesis genes in precursor cells argues against a model where Polycomb displacement is the mechanism of spermatogenesis gene activation.

overall_design: This genome-wide ChIP-array study investigates the binding of Polycomb in three biological samples: wild type (WT) whole testes, tTAF (can) mutant whole testes, and FACS-sorted germline precursor cells. We performed two biological replicates for each sample, except wild type whole testes where we performed three. For all ChIP-array experiments, input chromatin was used as the reference control to assay ChIP enrichment. We used Cy3/Cy5-labelled ChIP and input DNA for hybridisation onto Nimblegen arrays, and we performed a Cy3/Cy5 dye swap for one biological replicate of each sample (see supplementary file: GSE39935_README.txt).

first: Robert

middle: A

last: White


title: DamID data for Comr binding in drosophila testes

status: Public on Aug 13 2013

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

type: Genome binding/occupancy profiling by array

summary:
Comr protein was found to be a major regulator of gene activity in drosophila spermatocytes. We obtained Comr binding profile to determine targets of Comr.
Comr binding in drosophila male germ line cells was determined using DamID technique.

overall_design: Comparison of Dam-Comr binding to Dam-alone signal in duplicate for each sample type.

first: Stepan

last: Belyakin

first: Daniil

last: Maksimov


title: Su(H) bound regions in Su(H) induced wing-disc hyperplasia

status: Public on Dec 31 2013

first: Sarah

last: Bray

department: PDN

institute: University  of Cambridge

summary: The outcome of Notch activation on proliferation depends on cellular context. In Drosophila wing discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand the underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes directly activated during wing disc hyperplasia. These data are the results from ChIP-Chip experiments to identify genomic regions occupied by Su(H) in hyperplastic Su(H)-expressing Drosophila wing discs.

overall_design: 3 independent replicates. Immuno Precipitation perfomed with Su(H) antibody on chromatin isolated from wing discs overexpressing Su(H) (UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver) and compared to the total input DNA. Samples from replicate #1 and #2 were labelled with Cy5 and replicate #3 as dye-swap with Cy3.

first: Alexandre

last: Djiane

first: Alena

last: Krejci


title: Ethanol and benzyl alcohol induced H4Ac ChIP-chip in Drosophila heads

status: Public on Sep 05 2013

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

summary: Sustained or repeated exposure to sedating drugs such as alcohol triggers homeostatic adaptations in the brain that lead to the development of drug tolerance and dependence. These adaptations involve long-term changes in the transcription of drug-responsive genes as well as an epigenetic restructuring of chromosomal regions that is thought to signal and maintain the altered transcriptional state. Drug-induced epigenetic changes have been shown to be important in the long-term adaptation that leads to alcohol tolerance and dependence endophenotypes. A major constraint impeding progress is that alcohol produces a surfeit of changes in gene expression, most that may not make any meaningful contribution to the ethanol response under study. Here we used a novel genomic epigenetic approach to find genes relevant for functional alcohol tolerance by exploiting the commonalities of two chemically distinct drugs. In Drosophila melanogaster, ethanol and benzyl alcohol induce mutual cross-tolerance, indicating that they share a common mechanism for producing tolerance. We surveyed the genome-wide changes in histone acetylation that occur in response to these drugs. Each drug induces modifications in a large number of genes. The genes that respond similarly to either treatment, however, represent a subgroup enriched for genes important for the common tolerance response. Genes were functionally tested for behavioral tolerance to the sedative effects of ethanol and benzyl alcohol using mutant and inducible RNAi stocks. We identified a network of genes that are essential for the development of tolerance to sedation by alcohol.

overall_design: A total of six samples. Two H4Ac ChIP-chip biological replicates from heads of Drosophila (untreated, IP/input), two H4Ac ChIP-chip biological replicates from heads of Drosophila sedated with benzyl alcohol (IP_treated/IP_control), and two H4Ac ChIP-chip biological replicates from heads of Drosophila sedated with ethanol (IP_treated/IP_control) are included.

first: Harish

last: Krishnan

first: Linda

last: Lew

first: Francisco

last: Prado

first: Darryl

middle: S

last: Ong

first: Nigel

last: Atkinson


title: Su(H) bound regions in Nicd induced wing-disc hyperplasia

summary: The outcome of Notch activation on proliferation depends on cellular context. In Drosophila wing discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand the underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes directly activated during wing disc hyperplasia. These data are the results from ChIP-Chip experiments to identify genomic regions occupied by Su(H) in hyperplastic Nicd-expressing Drosophila wing discs.

overall_design: 2 independent replicates; Immunoprecipitation perfomed with Su(H) antibody on chromatin isolated from wing discs overexpressing Nicd (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B) and compared to the total input DNA.


title: Expression of circulating microRNAs in Influenza A patients.

status: Public on Aug 01 2013

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

country: Singapore

institute: National University of Singapore

summary: Altered expression of microRNAs in circulation, in H1N1 infected patients, were determined using expression profiling

overall_design: microRNA expression profiling of blood samples from H1N1 infected patients

first: Paul

last: Tambyah

first: Sugunavathi

last: Sepramaniam

first: Jaminah

last: Ali

first: Chai

last: Ching

first: Priyadharshini

last: Swaminathan

first: Arunmozhiarasi

last: Armugam


title: Notch-regulated genes in wing disc hyperplasia


title: DamID experiment looking at Dichaete-bound regions in 2-7h old Drosophila embryos

status: Public on Jul 22 2013

first: Steve

last: Russell

address: Tennis Court Road

summary: Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, by finding out where in the genome it's binding using the DamID technique.

overall_design: 3 independent biological replicates. Embryos between 2-7 h old were collected. The sample embryos contained a Dichaete-Dam methylase fusion, while the control embryos had a Dam methylase only to simulate the background level of methylation not specific to transcription factor binding.

first: Enrico

last: Ferrero

first: Jelena

last: Aleksic

first: Bettina

last: Fischer


title: Expression of novel long noncoding RNAs during erythro-megakaryopoiesis and GATA1-induced erythroid differentiation using RNA-seq

first: Ross

last: Hardison

summary:
Mammals express thousands of long noncoding (lnc) RNAs, a few of which are shown to function in tissue development. However, the entire repertoire of lncRNAs and the extent to which they regulate biological processes in different tissues and species are not defined. Indeed, most lncRNAs are not conserved between species, raising questions about function. We used RNA-Seq to identify lncRNAs in primary murine fetal liver erythroblasts expressing the lineage marker TER119, megakaryocytes (CD41+) cultured from embryonic day (E) 14.5 murine fetal liver and megakaryocyte erythroid progenitors (MEPs) isolated from mouse bone marrow. Strand-specific, paired-end, deep sequencing was performed on polyA+ mRNA from biological replicates of each sample. We assembled the transcriptomes using the Cufflinks package and generated a high-confidence transcriptome of 13,131 genes expressed in the three cell types. We identified 683 and 594 polyadenylated lncRNAs expressed in red blood cell (erythroid) precursors of mice and humans, respectively. More than one half of erythroid lncRNAs are un-annotated, emphasizing the opportunity for new discovery through studies of specialized cell types. Analysis of the murine erythroid lncRNA transcriptome indicates that ~75% arise from promoters and 25% from enhancers, many of which are regulated by the key erythroid transcription factors GATA1 and SCL/TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatically greater species-specificity than coding genes. We investigated potential functions of 21 relatively abundant erythroid-specific murine lncRNAs (both conserved and non-conserved) by RNA interference in primary mouse erythroid precursors, and identified 7 whose knockdown inhibited features of terminal erythroid maturation including cell size reduction and enucleation. Strikingly, at least 6 of the 7 lncRNAs have no detectable expression in human erythroblasts, demonstrating that lack of conservation between mammalian species does not predict lack of function. These results reflect marked evolutionary differences between protein-coding genes and lncRNAs and indicate that the latter exert tissue- and species-specific roles in development.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Strand-specific polyA+ RNA profiles from megakaryocyte erythroid progenitors (MEP), CD41+ megakaryocytes, TER119+ erythroblasts and estradiol-induced G1E-ER4 cells were generated in duplicate using deep sequencing on the Illumina HiSeq 2000. Long noncoding RNAs were identified from a high-confidence transcriptome assembled using MEP, megakaryocytes and erythroblasts. Transcripts that passed several filters for coding potential and lacked long open reading frames (>300 nt) were defined as long noncoding RNAs. Expression was estimated in MEP, megakaryocytes, erythroblasts and additionally in the estradiol-inducible GATA1 knockout and rescue system, G1E-ER4 cells over a 30-hour time-course after induction.  Expression levels of lncRNAs were estimated using Cufflinks. Raw sequence data have been deposited in GEO record GSE40522 as part of the Mouse ENCODE Project. From GSE40522, samples GSM995525, GSM995533 and GSM995537 were used to assemble transcripts and identify lncRNAs. Expression of lncRNAs in response to GATA1 restoration was also measured using GSE40522 samples GSM995527, GSM995531, GSM995532, GSM995538, GSM995539 & GSM995541.
Data processing details are provided in the 'README.txt'.

first: Vikram

last: Paralkar

first: Tejaswini

last: Mishra

first: Belinda

last: Giardine

first: Cheryl

last: Keller

first: Jing

last: Luan

first: Yu

last: Yao

first: Andrew

last: Kossenkov

first: Maxim

last: Pimkin

first: Meghneel

last: Gore

first: Diana

last: Sun

first: Neeraja

last: Konuthula

first: Xiuli

last: An

first: Narla

last: Mohandas

first: David

last: Bodine

first: Mitchell

last: Weiss


title: CGH analysis of chemical induced pluripotent stem cells

city: beijing

first: chun

last: liu

state: beijing

address: beijing

country: China

institute: Peking University

summary:
Comparative genomic hybridization (CGH) analysis of CiPSCs (clone CiPS-57 and CiPS-58) and OSKM-iPSCs. C57BL/6 mouse embryonic fibroblasts (MEFs) genome DNA as a reference.
No consistent copy number variations (CNVs) among CiPSCs and OSKM-iPSCs.

overall_design: Genome DNA of CiPSCs and OSKM-iPSCs (both of them induced form C57BL/6 MEFs) was isolated and compared with C57BL/6 MEFs genomic DNA reference by the NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array.

first: Pingping

last: Hou

first: Yanqin

last: Li

first: Xu

last: Zhang

first: Chun

last: Liu

first: Jingyang

last: Guan

first: Honggang

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: The role of Dichaete in transcriptional regulation during Drosophila embryonic development

first: Steve

last: Russell


title: Response of Cupriavidus metallidurans CH34 to different Au-species

status: Public on Mar 15 2013

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

country: Germany

summary: Response of Cupriavidus metallidurans CH34 to NaAuCl4, Au(I)-thiomalate, Au(I)-thiosulfate, KAuCN, (KCN as control)

overall_design: In this study 10 different treatments were performed (first 7 as 3 replicates) to acquire expression profiles of the total genome of Cupriavidus metallidurans

last: Grosse

first: Dietrich

middle: H

last: Nies


title: ChIP-chip from Kc cells with Su(H) antibodies after 30 minutes Notch activation

status: Public on Mar 08 2013

first: Sarah

last: Bray

summary: During hematopoiesis, Notch regulates both the emergence of stem and progenitor cells and the subsequent cell fate choices and differentiation. To investigate how Notch drives cells to differentiate we have used a genome-wide approach to identify direct Notch targets in Drosophila Kc cells. These data are the results from Su(H) ChIP-Chip experiments to identify genomic regions occupied by Su(H) after Notch activation in Kc cells.

overall_design: 3 replicates of Su(H) ChIP after 30 min. Notch activation..

first: Alena

last: Krejci

first: Fred

last: Bernard


title: Gene expression profiling of lithium stimulated human mesenchymal stem cells

status: Public on Feb 02 2013

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

summary: Wnt signaling in essential for osteoblast differentiation and is activated by lithium via inhibition of glycogen synthase kinase 3beta. Although lithium has been shown to enhance osteoblast differentiation in mice models and accelerate bone repair, its effect in humans is not clear. Therefore, we performed gene expression profiling of human MSCs from 3 donors treated with lithium (5mM) for 7 days. Microarray profiling of lithium-stimulated hMSC revealed decreased expression of adipogenic genes (CEBPA, CMKLR1, HSD11B1) and genes involved in lipid biosynthesis. Interestingly, osteoclastogenic factors and immune responsive genes (IL7, IL8, CXCL1, CXCL12, CCL20) were also downregulated. Negative transcriptional regulators of the osteogenic program (TWIST1 and PBX1) were suppressed while genes involved in mineralization like CLEC3B and ATF4 were induced. These results suggest suppression of adipogenic program and induction of osteogenic genes.

overall_design: Agilent one-color experiment, Organism: Human, Agilent-Custom Whole Genome Human 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 025085), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Neeraj

middle: K

last: Satija


title: Replication timing profiling by Repli-chip in Mus musculus

status: Public on Apr 16 2013

city: Tallahassee

first: David

middle: M.

last: Gilbert

state: Florida

address: 319 Stadium Drive

institute: Florida State University

summary: The replication timing program, or the order in which DNA is duplicated during S-phase, is associated with various features of chromosome structure and function, including gene expression, histone modifications, and 3-D compartmentalization of chromatin.

overall_design: 3 cell types, with a total of 6 individual replicates

first: Tyrone

last: Ryba


title: CMV 2b immunoprecipitated small RNAs data set

status: Public on Jan 18 2013

first: sadia

last: hamera

address: state key lab of plant genomics

institute: chinese academy of sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: We report that CMV2b exist in a complex of sRNAs in arabidopsis, with significant preference to repeat-associated AGO4-related 24nt siRNAs. This differential selection of siRNAs in vivo helps CMV 2b to perturb host epigenetic defense in the form of transposons activation and severeal repeat associated loci hypomethylation.

overall_design: Examination of CMV 2b presence in sRNAs complex in vivo

first: Sadia

last: Hamera

first: Wu

last: Jun


title: ChIP-chip time-course from DmD8 cells with Pol II (Ser 2 and Ser 5 phosphorylated) antibody after 0, 10, 20, 30 40, 60 and 100 minutes Notch activation

status: Public on Dec 31 2012

summary: Cellular responses to signalling pathways are often highly dynamic, however most analyses of developmental signalling pathways focus on a single endpoint. We have analyzed the temporal changes in transcription following a short Notch activation treatment and related these to the recruitment of the Notch pathway transcription factor, CSL [Suppressor of Hairless, Su(H), in Drosophila], and to the state of RNA Polymerase II (Pol II) binding. A total of 154 genes showed significant differential expression over time and their expression profiles stratified into 14 clusters based on temporal and quantitative differences in their responses. These differences were partially reflected in the profiles of Pol II and Su(H) binding. However, neither could fully account for the different response profiles. Furthermore, the timing of the different responses was unaffected by more prolonged Notch activation. Instead our data suggest that regulatory relationships between genes that segregate into different response clusters can partially account for the stratification. Thus, feed-forward repression, where products of early responding Enhancer of split bHLH genes (E(spl)bHLH) inhibit expression of endogenous repressors, is one mechanism that explains the profile of genes that exhibit delayed up-regulation. E(spl)bHLH genes may therefore be responsible for co-ordinating the Notch response of a wide spectrum of other targets, explaining their critical functions in many developmental and disease contexts.

overall_design: DmD8 cells were collected at 7 time points (0’, 10’, 20’, 30’, 40’, 60’ and 100’) after a 5 minute Notch stimulation as 3 independent replicates. Immunoprecipitation was performed with Pol II (Ser 2 and Ser 5 phosphorylated) antibody and compared to the total input DNA. Samples from replicates #1 and #3 were labelled with Cy5, and replicate #2 was labelled with Cy3 as a dye-swap.

first: Ben

middle: E

last: Housden

first: Audrey

middle: Q

last: Fu

first: Bettina

last: Fischer

first: Simon

last: Tavaré

first: Steven


title: ChIP-chip time-course from DmD8 cells with Su(H) antibody after 0, 10, 20, 30 40, 60 and 100 minutes Notch activation

overall_design: DmD8 cells were collected at 7 time points (0’, 10’, 20’, 30’, 40’, 60’ and 100’) after a 5 minute Notch stimulation as 3 independent replicates. Immunoprecipitation was performed with Su(H) antibody and compared to the total input DNA. Samples from replicates #1 and #2 were labelled with Cy5, and replicate #3 was labelled with Cy3 as a dye-swap. For time point 10’, only 2 biological replicates were obtained.

last: Russell

middle: J


title: Microarray gene expression profiles of adipose-derived mesenchymal stem cells from LEW and PVG rats upon 24h and 48h LPS stimulation

status: Public on Oct 02 2012

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: We have extended our investigation to differential immunogenicity between tolerogenic PVG rats and immunogenic LEW rats by analyzing gene expression in adipose-derived mesenchymal stem cells (ASCs) with LPS stimulation. Furthermore, to establish a direct link between gene expression and immunogenic functional annotation, ASCs from LEW and PVG rats were obtained, and the effects of inherent difference and LPS treatment on global gene expression were evaluated using microarray analyses.

overall_design: We analyzed microarray gene expression profiles of ASCs from 3 LEW and 3 PVG rats of 8-week age and separated ASCs from each individual into four conditions, 24h and 48h control, 24h and 48h with 1 μg/ml LPS stimulation. The total RNA samples of triplicate ASCs isolated from LEW and PVG with and without LPS treatment were pooled in each condition and the global gene expression profiles were analyzed using microarray.

first: Chao-Long


title: ChIP-chip time-course from DmD8 cells with Pol II (Ser 2 and Ser 5 phosphorylated) antibody or Su(H) antibody after Notch activation

first: Sarah

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

overall_design: Refer to individual Series


title: DamID-based chromatin profiling of UpSET in Kc cells and chromatic accesibility evaluation in UpSET knock down Kc cells

status: Public on Dec 07 2012

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

summary: Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domaincontaining protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.

overall_design: For determining DamID based UpSET chromatin profile, three biological replicates were used. For evaluating chromatin accessibility, two biological replicates were performed.

first: Ryan

last: Basom


title: UpSET Recruits HDAC Complexes and Restricts Chromatin Accessibility and Acetylation at Promoter Regions

type: Expression profiling by genome tiling array


title: CGH analysis of androgenetic haploid embryonic stem cells

status: Public on Aug 30 2012

city: Beijing

first: Wei

last: Li

address: Beichen West Road

department: State key lab of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Comparative genomic hybridization (CGH) analysis of  androgenetic haploid embryonic stem cells was done with 129/Sv male mouse kidney genomic DNA as reference. The results revealed no consistent copy number variations (CNVs) among the examined cell lines (AH129-5, AH129-N1 and AH129-NC1), except for the global difference on the X chromosome to the male control.

overall_design: Genomic DNA of FACS sorted G0/G1 stage ahES cells was compared with 129/Sv male mouse kidney genomic DNA reference by the NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9) [100718_MM9_WG_CGH_HX3]

first: Qi

last: Zhou

first: Xiaoyang

last: Zhao


title: Validation of an expression signature for lymph node metastasis detection in oral cavity squamous cell carcinoma

status: Public on Oct 10 2012

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

summary: Validation of a previously established gene expression profile for detection of lymph node metastasis (ArrayExpress E-UMCU-11).

overall_design: Two cohorts of 94 and 222 primary HNSCC tumors were analyzed against the Universal human reference cell line (UHR)


title: Effect of live Mycobacterium leprae on primary human Schwann cell gene expression

status: Public on Jul 01 2012

city: Rio de Janeiro

first: Anna Beatriz

middle: Robottom

last: Ferreira

state: Rio de Janeiro

address: Rua Adolfo Lutz 55 apt 201

institute: Fundação Oswaldo Cruz

summary: In attempt to understand M.leprae interaction with the human host, Applied Biosystems microarrays containing 30,865 probles were used to identify modulated genes in primary human Schwann Cells (SC) infected with live M. leprae at two early time points, 24 and 48 hours.

overall_design: A total of 4 independent experimental samples were prepared which were hybridized to two replicate microarrays each.The four experimental samples included both uninfected and M. leprae infected Schwann cells at both 24 and 48 hours.

first: Anna

last: Robottom-Ferreira

first: Alejandra

middle: N

last: Martinez

first: Tana

last: Pitmann

first: Marcelo

last: Ribeiro-Alves

first: Diana

last: Wiliams

first: Milton

middle: O

last: Moraes


title: Sugarcane Expression Data from Stress Time Series

status: Public on Aug 01 2012

middle: Yutaka

last: Nishiyama Jr

summary: Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Regular watering was maintained for 90 days and suppressed after this period for the experimental group. Leaves were collected 24 h, 72 h and 120 h after exposure to drought conditions for the control and experimental groups. Samples were collected and immediately frozen in liquid nitrogen. Leaves from six plantlets were used for each time point. Extraction of total RNA was performed separately on each sample pool. Keywords: time course of stress response

overall_design: RNA from experimental sample and from its respective control sample (untreated plants) was used for hybridization to dual channel arrays. Two biological replicates were used for each experimental point. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).

first: Carolina

middle: G

last: Lembke

first: Paloma

last: Sato

first: Rodrigo

middle: F

last: de Andrade

first: Glaucia

last: Souza


title: Replication-Timing Boundaries Facilitate Cell-type and Species-specific Regulation of a Rearranged Human Chromosome in Mouse

status: Public on Jun 05 2012

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

summary: In multicellular organisms, developmental changes to replication timing occur in 400-  800 kb domains across half the genome. While clear examples of epigenetic control of  replication timing have been described, a role for DNA sequence in mammalian  replication timing has not been substantiated. To assess the role of DNA sequences in  directing these changes, we profiled replication timing in mice carrying a genetically  rearranged Human Chromosome 21 [Hsa21]. In two distinct mouse cell types, Hsa21  sequences maintained human-specific replication timing, except at points of Hsa21  rearrangement. Changes in replication timing at rearrangements extended up to 900 kb  and consistently reconciled with the wild-type replication pattern at developmental  boundaries of replication-timing domains. Our results demonstrate DNA sequencedriven  regulation of Hsa21 replication timing during development and provide evidence  that mammalian chromosomes consist of multiple independent units of replication timing  regulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profile comparison of fibroblast and T-cell cultures from trans-chromosomic mice and human and mouse controls.

middle: D

first: Tamir

last: Chandra


title: CGH analysis of AG-haESCs (androgenetic haploid embryonic stem cells)

status: Public on Apr 27 2012

city: Shanghai

first: Linyu

last: Shi

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

summary: The genomic DNA sample of AG-haESCs were compared to the C57BL/6J male mouse kidney by comparative genomic hybridization. The data confirmed that the haploid cells sustained genome integrity.

overall_design: The analysis was performed on a NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array to analyse the copy number variations in AG-haESCs, and the genomic DNA of C57BL/6J  male  mouse kidney was used as control, which had the same background with haploid ESCs.

first: Jinsong

last: Li

first: Guoliang

last: Xu


title: The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: ChIP-seq data

status: Public on Dec 07 2010

city: Lincoln

first: Jean-Jack

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels  in the Arabidopsis thaliana genome when plants are subjected to water deficit stress.

Keywords: stress response, histone modification

overall_design: Arabidopsis thaliana DNA histone modifications were immonuprecipitated from control (watered) and treatment (water-deficit) samples for Illumina 1G Solexa sequencing.

first: Karin

last: van Dijk

middle: M

first: Jingyi

last: Yang

first: Peter

last: Laczko

first: Han

last: Chen

first: Yuannan

last: Xia

first: Istvan

last: Ladunga

first: Michael

last: Fromm


title: Small RNAs from Arabidopsis plants infected with CMV-∆2b

status: Public on Mar 01 2012

city: Riverside

first: JUAN

last: JOVEL

address: 3401 Watkins Drive

department: Plant Pathology

institute: University of California Riverside

summary: We focused our analyses on the description of viral (CMV-∆2b) and, based on genetic and molecular evidence, classified them and discussed their relevance in antiviral defense.

overall_design: Small RNAs from Arabidopsis plants from different genetic backgrounds infected with (CMV-∆2b) were sequenced before or after immunoprecipitation with antibodies against key proteins involved in antiviral defense.

first: Juan

last: Jovel

first: Xianbing

last: Wang

first: Shou-Wei

last: Ding


title: Analysis of gene expression profiles on 38 days-old sea bass heads

status: Public on Oct 22 2010

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads. Statistical analysis with SAM (Significance Analysis of Microarray) didn’t identify any difference in expression patterns between the two groups. Samples were then employed as biological replicates to determine array-to-array reproducibility, the degree of mutual agreement among replicates was estimated using Pearson correlation coefficients on the entire set of expression values. For all pairs of experiments correlation coefficients were always significant (p-value <0.01) and never less than 0.99.

overall_design: In this study, we analyzed six (6) samples, three (3) pools of heads dissected from normal sea bass and three (3) dissected from individuals affected by prognathism. Gene expression profiling was performed using the Agilent-019810 Dicentrarchus labrax Oligo Microarray platform (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays  were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Massimo

last: Milan

first: Luca

last: Bargelloni


title: Expression data from Aspergillus nidulans grown under hypoxic condition.

status: Public on Aug 14 2010

city: tsukuba

first: masuo

last: shunsuke

address: 1-1-1 tennodai

country: Japan

institute: university of tsukuba

summary: Hypoxia imposes a challenge upon most of the filamentous fungi that require oxygen for proliferation. Here, we used whole genome DNA microarrays to investigate global transcriptional changes in Aspergillus nidulans gene expression after exposure to hypoxia followed by normoxia. Aeration affected the expression of 2,864 genes (27% of the total number of genes in the fungus), of which 50% were either induced or repressed under hypoxic conditions. Up-regulated genes included those for glycolysis, ethanol production, the tricarboxylic acid (TCA) cycle, and for the γ-aminobutyrate (GABA) shunt that bypasses two steps of the TCA cycle. Ethanol and lactate production under hypoxic conditions indicated that glucose was fermented to these compounds via the glycolytic pathway. Since the GABA shunt bypasses the NADH-generating reaction of the TCA cycle catalyzed by oxoglutarate dehydrogenase, hypoxic A. nidulans cells eliminated excess NADH. Hypoxia down-regulated some genes involved in transcription initiation by RNA polymerase II, and lowered the cellular mRNA content. These functions were resumed by reoxygenation, indicating that A. nidulans controls global transcription to adapt to a hypoxic environment. This study is the first to show that hypoxia elicits systematic transcriptional responses in A. nidulans.

overall_design: We transferred A. nidulans cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 3 and 6 h of exposure to hypoxia, followed by 3 and 6 h of reoxygenation.

first: Yasunobu

last: Terabayashi

first: Motoyuki

last: Shimizu

first: Tatsuya

last: Fujii

last: Kitazume

first: Naoki

last: Takaya


title: Small RNAs in four Argonaute complexes in Arabidopsis

status: Public on Apr 06 2008

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

summary:
The core components of RNA silencing effector complexes include small RNAs and members of the Argonaute (AGO) protein family. Arabidopsis encodes ten AGOs and complex population of small RNAs. It remains largely unknown how these small RNAs are recognized and recruited by each AGO complex. Here we purified four AGO complexes and identified small RNAs in each complex by deep sequencing.
Keywords: Small RNA sorting

overall_design: Small RNAs were prepared from Arabidopsis AGO1, AGO2, AGO4 and AGO5 complexes, ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing. For technical details, see Qi, Y., He, X., Wang, X.J., Kohany, O., Jurka, J., and Hannon, G.J. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443(7114): 1008-1012.

first: S

last: Mi

first: T

first: Y

last: Qi


title: Comparison of gene expression profile between 58 days-old prognatous sea bass jaws and control ones

summary: A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from four (4) independent biological replicates, each consisting of pools of five (5) jaws. Statistical analysis with SAM (Significance Analysis of Microarray) identified 333 probes (corresponding to 242 unique transcripts) significantly down-regulated in deformed individuals compared to normal ones.

overall_design: In this study, we analyzed eight(8) samples, four (4) pools of jaws dissected from normal sea bass and four (4) pools of jaws dissected from individuals affected by prognathism. Gene expression profiling was performed using the Agilent-019810 Dicentrarchus labrax Oligo Microarray platform (8 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Ferraresso

last: Serena

first: Milan

last: Massimo

first: Bargelloni

last: Luca


title: An Antifibrotic Regulatory Network Governed by the Transcription Factor EGR4

status: Public on Mar 05 2010

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

summary: Fibrotic diseases are a group of pathologies with high incidence and mortality. Despite extensive research efforts, efficient therapies are still not available. Understanding the molecular mechanisms driving the onset, progression and possible resolution of fibrosis is a prerequisite to the development of successful therapies. The central role of the TGF-beta pathway and myofibroblasts in the pathogenesis of fibrosis is now generally accepted. The possible mechanisms of myofibroblast elimination or dedifferentiation, on the other hand, are still almost uncharted territory. Basic fibroblast growth factor (bFGF) is able to suppress myofibroblastic differentiation of mesenchymal cells, but the underlying mechanism has not been studied in detail. Here, we show that sustained expression of the transcription factor EGR4, which is inducible by bFGF, in primary chicken embryo dermal myofibroblasts results in suppression of the myofibroblastic phenotype, characterized by the loss of smooth muscle actin fibers and a substantial reduction in the production of extracellular matrix. Detailed analysis of the possible molecular mechanisms revealed FOXG1, BAMBI, NAB1, NAB2 and DUSP5 genes forming an EGR4 regulated network counteracting autocrine TGF-beta signaling.

overall_design: Comparison of expression profiles of chicken embryo dermal myofibroblasts infected with retroviral construct SFCVneo-EGR4 versus chicken embryo dermal myofibroblasts infected with empty retroviral vector SFCVneo. Three biological replicates were analyzed for each group.


title: Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis

status: Public on Nov 25 2009

first: David

last: Gilbert

overall_design:
GSE17980 (Expression): 8 cell lines, with a total of 14 individual replicates (i.e. 6 in duplicates, 2 in single replicates)
GSE17983 (WG_CGH; Replication Timing): 22 cell lines, with a total of 36 individual replicates (i.e. 14 in duplicates, 8 in single replicates)
GSE45716: 3 cell types, with a total of 6 individual replicates


title: Effects of Oxygen on Virulence Traits of Streptococcus mutans

status: Public on Oct 11 2007

city: Gainesville

first: Robert

middle: A

last: Burne

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

institute: University of Florida

summary:
To gain further insights into the molecular basis of the effects of oxygen on biofilm formation by S. mutans (Ahn and Burne, 2007), we used DNA microarrays to analyze gene expression profiles of cells cultured under aerobic or anaerobic conditions.
Keywords: Oxygen, Biofilm, Caries, Microarray

overall_design:
For aerobic growth, an overnight culture of S. mutans UA159 was diluted 1:50 into a 250-ml conical flask containing 50 ml of brain heart infusion (BHI, Difco) and cultures were grown on a rotary shaker (150 rpm) at 37°C until the absorbance at 600 nm reached 0.4 (mid-exponential phase).  For anaerobic growth, cultures were similarly diluted and incubated  without agitation in a BBL GasPak Plus anaerobic system (BD, Franklin Lakes, NJ) to the same optical density.

Total RNA was isolated from 10 ml of exponential phase (O.D.600 = 0.4) cultures, as described previously.  All RNA samples were DNase I-treated and purified using the RNeasy mini kit (Qiagen).  RNA concentration was estimated spectrophotometrically in triplicate.  Reverse transcription (RT) and microarray reactions were performed with 5.0 μg of total bacterial RNA, as described elsewhere.  S. mutans UA159 microarrays were provided by The Institute for Genomic Research (TIGR), and each slide contained four copies of 1960 corresponding to ORFs in the genome.  For each microarray slide, a separate RNA preparation from a separate culture was utilized, so a total of 8 slides (4 for each condition) were used in this study.  Hybridizations were performed in a Maui hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Additional details regarding array protocols are available at http://pfgrc.tigr.org/protocols/protocols.shtml.

After the slides were scanned, the resulting images were analyzed by TIGR 23
Spotfinder software (http://www.tigr.org/software/) and further normalized using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis using TIGR microarray data analysis system (MIDAS; http://www.tigr.org/software/).  Statistical analysis was carried out using BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html/) with a cutoff P value of 0.001.

first: Sang-Joon

last: Ahn

first: Zezhang

middle: T

last: Wen


title: Astrocyte proximity modulates the myelination gene fabric of oligodendrocytes

status: Public on Oct 27 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Extensive literature documented that astrocytes release neurotransmitters, cytokines and other signaling molecules that modulate migration, maturation and myelin synthesis of oligodendrocytes through mechanisms primarily converging on cytosolic [Ca2+] transients. Considering the long term effects, it is expected that astrocyte conditioned medium is a major regulator of gene expression in oligodendrocytes even in the absence of cytosol-to-cytosol communication via astrocyte-oligodendrocyte gap junction channels. Indeed, by comparing  the transcriptomes of immortalized precursor oligodendrocyte (Oli-neu) cells when cultured alone and cocultured with non-touching astrocytes we found profound changes in gene expression level, control and networking. Remarkably, the astrocyte proximity was more effective in remodeling the myelination (MYE) gene fabric and its control by cytokine receptor (CYR) modulated intercellular Ca2+-signaling (ICS) transcriptomic network than the db-cAMP treatment induced transformation into myelin-associated glycoprotein-positive oligodendrocyte-like cells. Moreover, astrocyte proximity up-regulated 37 MYE genes and switched on another 14 MYE, 23 ICS and 4 CYR genes, enhancing the roles of the leukemia inhibitory factor receptor and connexins Cx29 and Cx47. The novel Prominent Gene Analysis identified enhancer of zeste homolog 2 as the most relevant MYE gene in the astrocyte proximity, notch gene homolog1 in control and B-cell leukemia/lymphoma 2 in differentiated Oli-neu cells.

overall_design: Determine the modifications of the myelination transcriptome induced in Oli- neu control cells by differentiating treatment and proximity of cortical astrocytes. Four culture dishes of each of control, differentiated and in the astrocyte proximity Oli-neu cells were profiled using Duke mouse 30K and 36k oligonucleotide arrays in the "multiple yellow" hybrization design.

first: Sanda

middle: C

last: Spray


title: SNP array data from the Cancer Cell Line Encyclopedia (CCLE)

status: Public on Mar 20 2012

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

summary:
The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, the Novartis Institutes for Biomedical Research and the Genomics Novartis Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models
It consists of a compilation of gene expression, chromosomal copy number, and massively parallel sequencing data from nearly 1,000 human cancer cell lines. All raw and processed data are available through an integrated portal on www.broadinstitute.org/ccle

overall_design: The final cell line collection spans 36 cancer types. Representation of cell lines for each cancer type was mainly driven by cancer mortality in the United States, as a surrogate of unmet medical need, as well as availability.