title: Chromatin Signatures in Multipotent Human HSCs Indicate the Fate of Bivalent Genes during Differentiation

status: Public on Jan 09 2009

city: Charlottesville

state: VA

institute: University of Virginia

summary: Histone modifications have been implicated in stem cell maintenance and differentiation. We have analyzed genome-wide changes in gene expression and histone modifications during differentiation of multipotent human primary hematopoietic stem cells/progenitor cells (HSCs/HPCs) into erythrocyte precursors. Our data indicate that H3K4me1, H3K9me1, and H3K27me1 associate with enhancers of differentiation genes prior to their activation and correlate with basal expression, suggesting that these monomethylations are involved in the maintenance of activation potential required for differentiation. In addition, although the majority of genes associated with both H3K4me3 and H3K27me3 in HSCs/HPCs become silent and lose H3K4me3 after differentiation, those that lose H3K27me3 and become activated after differentiation are associated with increased levels of H2A.Z, H3K4me1, H3K9me1, H4K20me1, and RNA polymerase II in HSCs/HPCs. Thus, our data suggest that gene expression changes during differentiation are programmed by chromatin modifications present at the HSC/HPC stage and provide a resource for enhancer and promoter identification.

overall_design: Genome-wide analysis of 8 histone methylations, H2AZ, and RNA Polymerase II in human CD133+ and CD36+ cells. (20 samples in total) and global change in gene expression in human CD133+ and CD36+ cells. (4 samples in total)

first: Kairong

last: Cui

first: Richard

last: Childs

first: Weiqun

first: Keji

last: Zhao


title: Exploring and dissecting genome-wide transcriptional responses of Penicillium chrysogenum to phenylacetic acid

status: Public on Feb 10 2009

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: In studies on beta-lactam production by Penicillium chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillin-G production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillin-G high-producing strain without a functional penicillin-biosynthesis gene cluster (pcbAB-pcbC-penDE) was constructed. The copy number of this cluster was first reduced to one via spontaneous recombination. The remaining copy was removed by targeted deletion, thereby completely abolishing beta-lactam biosynthesis. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. A low rate of penicillin-G-independent PAA consumption indicated activity of a PAA-degrading pathway. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillin-G producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies. This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on transcriptional regulation.

overall_design: Mutants of P. chrysogenum impaired in penicillin biosynthesis have been described. Most of these mutants were derived by random mutagenesis from the low-producing strain Wisconsin54-1255, which contains one copy of the penicillin biosynthesis cluster. Although these mutants were very useful for studying gene expression and gene/enzyme relationships, for identification of the factors important for penicillin-G production and PAA consumption a strain obtained from a high-producing strain background by targeted deletion is more beneficial. To this end we constructed a strain in which the tandem-repeated penicillin biosynthesis cluster was specifically deleted, whereas the strain background was retained. In such a way it is possible to identify, by a combinatorial approach, those genes affected by phenylacetic acid and those specifically important for penicillin-G biosynthesis.

first: Diana

middle: M

last: Harris

first: Jack

middle: T

last: Pronk


title: Mapping Novel Chromatin Regions Using Sono-Seq

status: Public on Dec 18 2008

city: New Haven

first: Raymond

middle: K

last: Auerbach

state: CT

address: 266 Whitney Ave

country: USA

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites.  Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments.

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: For this analysis, seven samples from HeLa S3 cells were included: RNA Polymerase II (GEO accession GSM320734), Sono-Seq/Input DNA (small fragments) that was size selected at 100-350 bp (GEO accession GSM320735), Sono-Seq/Input DNA (large fragments) size selected between 350-800 bp, naked DNA, normal mouse IgG, Sono-Seq/Input DNA stimulated with interferon-gamma (GEO accession GSM320737), and MNase-digested DNA.  Two replicates were used for MNase-digested DNA and Sono-Seq/Input DNA (large fragments) whereas three replicates were used for all other samples.  Naked DNA was used as a reference for scoring peaks.

first: Ghia

last: Euskirchen

first: Joel

last: Rozowsky

first: Nathan

last: Lamarre-Vincent

first: Zarmik

last: Moqtaderi

first: Kevin

last: Struhl

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: Chip-seq from MEF cells H3K27me3

status: Public on Dec 22 2008

city: Vienna

first: Florian

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

summary: Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons.

overall_design: mapping of H3K27me3 histone modification in one MEF cell line (MEFF)

first: F

first: M

middle: A

last: Sloane

first: D

middle: P

last: Barlow


status: Public on Dec 04 2008

city: New York

first: Nicolas

last: Robine

state: NY

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

type: Non-coding RNA profiling by high throughput sequencing

summary:
High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells.
total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

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: Small RNAs were sequenced from D. melanogaster S2R+ cells. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt.

first: Eric

middle: C

last: Lai

first: Raquel

last: Martin

first: Lucy

last: Cherbas

first: Susan

last: Celniker


title: The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: Nucleosome organization is critical for gene regulation.  In living cells, this organization is determined by multiple factors, including the action of chromatin remodelers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves.  However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors.  Here, we determine the importance of DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA.  The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is remarkably similar to in vivo nucleosome maps generated in three different growth conditions.  In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, suggesting that nucleosome depletion at these sites in vivo is partially encoded in the genome.  We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for ~40,000 double-stranded 150bp oligonucleotides.  Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in C. elegans.  Our results indicate that the intrinsic DNA sequence preferences of nucleosomes play a central role in determining the organization of nucleosomes in vivo.

sample_organism:
Saccharomyces cerevisiae
synthetic construct

platform_organism:
Saccharomyces cerevisiae
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Solexa/Illumina sequencing of in vivo and in vitro mononucleosomes.  In vitro: 2 biological replicates; YPD: 6 biological replicates (4 non-crosslinked, 2 crosslinked); YPEthanol: 4 replicates (2 non-crosslinked, 2 crosslinked); YPGalactose: 3 replicates (2 non-crosslinked, 1 crosslinked).
Microarray hybridization (GPL7641)  of in vitro reconstitution on synthetic sequences:  Three technical replicates, pool 1 (DT sequences), pool 2 (ES sequences), pool 3 (DT and ES sequences combined).
Sequencing of in vitro reconstituted nucleosomes on synthetic sequences.  Input pool 1 (DT sequences, 3 technical replicates), Input pool 2 (ES sequences, 2 technical replicates), reconstituted pool 1 (3 technical replicates), reconstituted pool 2 (3 technical replicates)

first: Noam

last: Kaplan

first: Irene

last: Moore

first: Yvonne

last: Fondufe-Mittendorf

first: Andrea

last: Gossett

first: Yair

last: Field

first: Emily

last: LeProust

first: Timothy

middle: R

last: Hughes

first: Jason

middle: D

last: Lieb

first: Jonathan

last: Widom

first: Eran

last: Segal


status: Public on Dec 10 2008

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary:
Genome-wide profiling of PPARγ:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis.

Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activated receptor gamma (PPARg) and retinoid X receptor (RXR) binding sites, and RNA polymerase II (RNAPII) occupancy at high resolution throughout adipocyte differentiation of 3T3-L1 cells.  The data  provides the first positional and temporal map PPARγ and RXR occupancy during adipocyte differentiation at a global scale. The number of PPARγ:RXR shared binding sites is steadily increasing from D0 to D6. At Day6 there are over 5000 high confidence shared PPARy:RXR binding sites. We show that at the early days of differentiation several of these sites bind not only PPARγ:RXR but also other RXR dimers. The data also provides a comprehensive temporal map of RNAPII occupancy at genes throughout 3T3-L1 adipogenesis thereby uncovering groups of similarly regulated genes belonging to glucose and lipid metabolic pathways. The majority of the upregulated but very few downregulated genes have assigned PPARγ:RXR target sites, thereby underscoring the importance of PPARγ:RXR in gene activation during adipogenesis and indicating that a hitherto unrecognized high number of adipocyte genes are directly activated by PPARγ:RXR

overall_design: Examination of PPARg and RXR bindingsites during adipocyte differentiation (day 0 to 6) and association with transcription via RNAPII occupancy.

first: Henk

middle: G

first: D

last: Hagenbeek

first: P

last: Moulos

first: Kees-Jan

last: Françoijs

first: Sergei

last: Denissov

first: Eva

last: Megens

first: Susanne

last: Mandrup

first: Ronni

last: Nielsen

first: Thomas

last: Åskov Pedersen

first: Rasmus

last: Siersbæk

first: Michael

last: Børgesen


title: Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

city: Ithaca

first: Leighton

middle: James

last: Core

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

summary: RNA polymerases are highly regulated molecular machines.  We present a method (GRO-seq) that maps the position, amount, and orientation of transcriptionally-engaged RNA polymerases genome-wide. In this method, nuclear run-on RNAs are subjected to large-scale parallel sequencing and mapped to the genome.  Here, we show that peaks of promoter-proximal polymerase reside on ~30% of human genes, transcription extends beyond pre-mRNA 3’ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene.  This divergent polymerase is associated with active genes, but does not elongate effectively beyond the promoter.  These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.

overall_design: Two biological replicates of nascent RNA sequencing

middle: J

first: Joshua

last: Waterfall

first: John

last: Lis


title: ChIP-Seq of RNA Pol II with antibodies S2, 4H8 and 8WG16 during C. elegans L1 arrest and recovery

status: Public on Feb 27 2009

city: Durham

first: L.

middle: Ryan

last: Baugh

state: NC

address: 4314 French Family Science Center

department: Biology

institute: Duke University

summary: When C. elegans larvae hatch in the absence of food they persist in a stress resistant, developmentally arrested state (L1 arrest) for weeks or until food becomes available.  We characterized growth, mRNA expression, and RNA Polymerase II activity genome-wide during L1 arrest and recovery.  RNA Pol II binding data resulting from ChIP-Seq experiments using the Illumina Genome Analyzer are included in this GEO submission.  Complementary mRNA expression data from the Affymetrix microarray platform can be found at GEO accession# GSE11055.  The goals of the Pol II ChIP-Seq compononent of this project were to use Pol II antibodies 1) to investigate patterns of transcription in developmentally arrested larvae, when mRNA expression levels have reached steady state; 2) to investigate patterns of transcription in immediate response to feeding, when mRNA expression levels change dramatically; and 3) to investigate accumulation of Pol II at promoters during arrest and recovery.  We started our ChIP studies with the S2 antibody (Abcam ab5095) since it was raised against a Ser2 phosphorylated peptide from the C-terminal domain of Pol II and should therefore be relatively specific for active, elongating Pol II, and it worked well for the first two goals above.  In order to investigate accumulation of Pol II at promoters, we used the S2 antibody and complemeted it with antibody 4H8 (Abcam ab5408), which according to the manafacturer recognizes phosphorylated and non-phosphorylated Pol II, and antibody 8WG16 (Abcam ab817), which binds primarily to non-phosphorylated Pol II but also relatively weakly to phosphorylated Pol II.  We were somewhat surprised to find that the results obtained with each of these antibodies were very similar, though upon deeper analysis we discovered relatively subtle differences consistent with the relative specificities of each antibody and existing models regarding phosphorylation state of Pol II and its activity and location. In summary, we find that while Pol II continues transcribing starvation genes, it is ‘paused’ accumulates on the promoters of growth and development genes during L1 arrest.  Consistent with it poising arrested larvae for recovery, pausingpromoter accumulation  decreases in response to feeding, while elongation and mRNA levels increase.  These results demonstrate that Pol II pausing is widespread in C. elegans and that it is nutritionally controlled during development.These results demonstrate that accumulation of Pol II at promoters of growth and development genes is common in C. elegans and that promoter accumulation anticipates nutritionally controlled gene expression during development.

overall_design:
RNA Pol II binding was examined with three different antibodies (S2, 4H8, and 8WG16) during either L1 arrest (starvation) or after 1 hr recovery by feeding.  For the S2 antibody two different time points during L1 arrest were examined (6 and 12 hr).  14 total samples are included: 4 independent control samples (Input), a pair biological replicates with the S2 antibody at 6 hr L1 arrest, a pair of biological replicates with the 4H8 antibody at 12 hr L1 arrest and at 1 hr recovery, and singletons for the S2 and 8WG16 antibodies at 12 hr L1 arrest and at 1 hr recovery.

"GSE13973_PolII_ChIP-Seq.xls.gz" contains 5 worksheets with the following contents:
"geneDensity" includes the number of reads per million mapping to each gene model normalized to gene length.  Units are reads per million per kilobase.
"TSSdensity" includes the number of reads per million mapping to a 200 bp window spanning the most upstream transcription start site for each gene and normalized by length (200 bp).  Units are reads per million per kilobase.
"geneEnrichment" includes the fold-enrichment of read density over each gene model relative to input.  Where input values were below the median of all input values then the median was used.  Units are fold-enrichment.
"TSSenrichment" includes the fold-enrichment of read density over the 200 bp TSS window relative to input.  Where input values were below the median of all input values then the median was used.  Units are fold-enrichment.
"5' bias" includes 5' bias calculation for each gene and each antibody in each condition.

"GSE13973_CelegansWS190_GeneCoordinates.xls.gz" contains the gene coordinates based on version WS190 of the C. elegans genome.

first: L

first: Paul

middle: W

last: Sternberg


title: HOX A13 Expression in Hepatocellular Carcinomas

status: Public on Dec 01 2008

city: Basel

first: Luigi

last: Terracciano

email: lterracciano@uhbs.ch, ccillo@uhbs.ch

state: Basel

address: Schönbeinstrasse 40

department: Molecular Pathology

country: Switzerland

institute: Pathology

summary:
HOX A13 over expression represents: i) a novel molecular marker of hepatocellular carcinomas; ii) a sign of epithelial-endothelial transition accounting for tumor independent angiogenesis and lymphangiogenesis.
Keywords: cancer; disease-state analysis

overall_design: Genomic analysis of high HOX A13 expressing pairs (HCC/non tumorous liver tissues) to investigate the molecular mechanisms responsible for the increased expression of HOX A13 in liver cancers and to identify potential HOX A13 targets.

first: Clemente

last: Cillo

first: Giulia

last: Schiavo

first: Monica

last: Cantile

first: Michel

last: Bihl

first: Paolo

last: Sorrentino

first: Maria

last: D’Armiento

first: Massimo

last: Roncalli

first: Raffaela

last: Vecchione

last: Tornillo


title: Divergent transcription from active promoters

city: Cambridge

first: Stuart

last: Levine

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute

summary: Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II.

overall_design: ChIP-seq in murine embryonic stem cells for RNA polymerase II

first: Richard

last: Young


title: Annotating Low Abundance and Transient RNAs in Yeast using Ultra High-throughput Sequencing

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary:
Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing Reveals New Transcripts that are not Conserved Across Closely Related Yeast Species

A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and may provide insights into the organism’s evolution.  Despite the status of Saccharomyces cerevisiae as arguably the most well studied model eukaryote, we still do not have a full catalog or understanding of all its genes.  In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts.  We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells.  We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study.  It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts.  Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae.  Such regions of the genome have typically been less well studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

Keywords: Saccharomyces cerevisiae, transcriptome, RNA-Seq, RNA degradation, XRN1, RRP6, LSM1, PAT1, Salt Shock, NaCl

overall_design: Four samples, a wild-type reference and three mutants (1 containing 4 deletions and the other two containing 3 each), were subjected to high salt shock, and total RNA was harvested.  PolyA RNA was purified, and  libraries were generated for the Solexa platform. Each library was run on 4 lanes of a Solexa flow cell.

first: Albert

last: Lee

first: Kasper

last: Hansen

first: James

last: Bullard

first: Sandrine

last: Dudoit


title: Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: High-throughput pyrosequencing of endogenous small RNAs associated to human Argonaute 1 & 2

status: Public on Nov 21 2008

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

country: Germany

institute: Max Planck Institute of Biochemistry

summary: Small non-coding RNAs function in concert with Argonaute (Ago) proteins to regulate gene  expression at the level of transcription, mRNA stability or translation. Ago proteins bind  small RNAs and form the core of silencing complexes. Here we report the analysis of small  RNAs associated with human Ago1 and Ago2 revealed by immunoprecipitation and deep  sequencing. Among the reads we find small RNAs originating from the small nucleolar RNA  (snoRNA) ACA45. Moreover, processing of ACA45 requires Dicer activity but is  independent of Drosha/DGCR8. Using bio-informatic prediction algorithms and luciferase  reporter assays, we uncover the mediator subunit CDC2L6 as one potential mRNA target of  ACA45 small RNAs suggesting a role for ACA45 processing products in post-transcriptional  gene silencing. We further identify a number of human snoRNAs with microRNA (miRNA)-  like processing signatures. We have therefore identified a novel class of small RNAs in  human cells that originate from snoRNAs and can function like miRNAs.

overall_design: Two samples examined. Small RNAs associated to human Argonaute 1 and human Argonaute 2

first: Christine

last: Ender

first: Azra

last: Krek

first: Marc

last: Friedländer

first: Michaela

last: Beitzinger

first: Nikolaus

last: Rajewsky


title: Changes in expression of microRNAs during C. elegans development

first: Frank

last: Slack

department: MCDB

summary:
Recent work has shown that small non-coding RNAs, including miRNAs, serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of C. elegans. Here we use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs, including miRNAs, changes dynamically during development and in the different sexes of C. elegans; approximately 16% of known miRNAs changed over 10 fold in expression during C. elegans development and about 12% of miRNAs showed major changes in expression between males and hermaphrodites of C. elegans. These results should lead to a better understanding of the expression and function of small RNAs in C. elegans 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: Examination of small RNA expression in six different developmental stages of hermaphrodites (Embryo, mid-L1, mid-L2, mid-L3, mid-L4, young adult), and young adult males (dpy-28;him-8) and spermatogenesis-defective young adult hermaphrodites (spe-9). The number of sequence reads for miRNA was assessed from the raw sequence data from Solexa sequencing using perfect sequence matching to known miRNAs (miRBase Release 11.0).

first: Masaomi

last: Kato

first: Alexandre

last: de Lencastre


title: Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq

status: Public on Mar 20 2009

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

type: Genome binding/occupancy profiling by genome tiling array

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila 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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE15422
SuperSeries of: GSE15423
SuperSeries of: GSE15424
SuperSeries of: GSE15425
SuperSeries of: GSE15426
SuperSeries of: GSE15427
SuperSeries of: GSE15430
SuperSeries of: GSE16013
SuperSeries of: GSE16702
SuperSeries of: GSE18068

overall_design:
ChIP-chip: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.

ChIP-seq: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure.

RNA-seq: For each time-point (E-0-4h, E-4-8h, E-8-12h, E-12-16h, E-16-20h, E20-24h, L1, L2, L3, Pupae, Adult Males and Adult Females) a total RNA extraction has been performed. After conversion into double stranded DNA, the samples have been sequenced in duplicate on Solexa Genome Analyzer following Solexa sequencing procedure.


title: Drosophila melanogaster short read RNA

status: Public on Nov 04 2008

city: St Louis

first: Marijke

middle: Jeltje

last: van Baren

state: MO

address: One Brookings Drive

department: CSE

institute: Washington University

summary:
Drosophila melanogaster RNA sequencing with Illumina Genome Analyzer.
High-throughput sequencing of Drosophila melanogaster RNAs.

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:
5 Samples:
Single Stranded cDNA, Oligo-DT Primed, run using a 1, 2 and 4 p-mol concentration, no replicates.
Double Stranded cDNA, Random Primed, run using a 2 p-mol concentration, 2 replicates.

first: Michael

last: Brent

last: J.van Baren

first: Laura

last: Langton

first: Charles

middle: L

last: Comstock

first: Randall

middle: H

last: Brown

first: Brian

last: Koebbe


title: AGO1-dependent Small RNA in Arabidopsis Identified by High-Throughput Sequencing

status: Public on Nov 17 2008

city: Saint Louis

first: James

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary:
The goal of this study was to identify AGO1-dependent miRNA and tasiRNA in Arabidopsis by sequencing small RNA from wild type (Col-0) and ago1-25 plants.

Keywords: Small RNA

overall_design: Sequencing-by-synthesis technology was used to sequence small RNA from flower tissue (stages 1-12) from wild-type (Col-0) and ago1-25 Arabidopsis thaliana plants. Three biological replicates were sequenced for both Col-0 and ago1-25.

first: Taiowa

last: Montgomery


title: CTCF demarcates chromatin domains

status: Public on Oct 20 2008

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers.  CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates and has been shown to bind many enhancer-blocking elements. However, it is not clear whether it plays a role in chromatin domain barriers between active and repressive domains. Here, we used ChIP-Seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3. Although we find an extensive overlapping of CTCF binding sites across the three cell types, its association with the domain boundaries is cell type-specific. We further show that the nucleosomes flanking CTCF binding sites are well positioned and associated with histone H2AK5 acetylation (H2AK5ac). Interestingly, we found a complementary pattern between the repressive H3K27me3 and the active H2AK5ac regions, which are separated by CTCF. Our findings indicate that CTCF may play important roles in the barrier activity of insulators and provide a resource for further investigation of the CTCF function in organizing chromatin in the human genome.

overall_design:
Examination of the role of CTCF in chromatin domain barrier function
In addition to the ChIP-seq analysis, two replicates of HeLa expression data were studied.

first: Suresh

last: Cuddapah

first: Dustein

middle: E

last: Schones

first: Tae-Young

last: Roe

first: Kairong

last: Cui

first: Keji

last: Zhao


title: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

status: Public on Nov 19 2008

city: Toronto

first: Weijun

last: Gao

address: 10 King's College Rd.

country: Canada

institute: University of Toronto

summary:
We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.

Keywords: mRNA expression

overall_design: 32-nucleotide sequence reads from six human tissues including brain, cerebral cortex, heart, liver, lung and skeletal muscle.

first: Qun

last: Pan

first: Ofer

last: Shai

first: Leo

last: Lee

first: Brendan

last: Frey

first: Benjamin

last: Blencowe


title: Alternative Isoform Regulation in Human Tissue Transcriptomes

status: Public on Oct 01 2008

city: Hayward

first: Shujun

last: Luo

address: 25861 Industrial Blvd

institute: Illumina inc

summary: Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that ~94% of human genes undergo alternative splicing (AS), ~86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that a majority of AS and alternative cleavage and polyadenylation (APA) events exhibit variation between tissues. Variations in alternative mRNA isoform expression between 6 individuals were also detected in cerebellar cortex, with ~2- to 3-fold less isoform variation observed between individuals than between tissues. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation, and sequence conservation of known regulatory motifs in both regulated introns and 3' UTRs suggested common involvement of the same factors in regulation of tissue-specific splicing and polyadenylation.

overall_design: Exam mRNA expression in 15 human tissues and cell lines

first: Eric

middle: T

last: Wang

first: Rickard

last: Sandberg

first: Irina

last: Khrebtukova

first: Lu

last: Zhang

first: Christine

last: Mayr

first: Stephen

middle: F

last: Kingsmore

first: Gary

last: Schroth

first: Christopher

middle: B

last: Burge


title: Mapping polycomb complexes in human and mouse embryonic stem cells

status: Public on Nov 01 2008

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary:
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes: the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes.

Keywords: cell type comparison

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Suz12, Ezh2, Ring1b ChIP-Seq in singlicate from mouse embryonic stem (mES) cells. H3K4me3, H3K27me3, H3K36me3, Ezh2 and Ring1b ChIP-Seq in singlicate from human embyonic stem cells (hES; H9).

first: Manching

last: Ku

first: Richard

middle: P

last: Koche

first: Esther

last: Rheinbay

first: Chad

middle: A

last: Cowan

last: Lander

first: Bradley

last: Bernstein


title: A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice

city: Cold Spring Harbor

first: Alexei

last: Aravin

address: 1 Bungtown Rd

institute: Cold Soring Harbor Lab

summary: We examined the construction of the piRNA system in the restricted developmental window in which methylation patterns are set during mammalian embryogenesis. We find robust expression of two Piwi family proteins, MIWI2 and MILI. Their associated piRNA profiles reveal differences from Drosophila wherein large piRNA clusters act as master regulators of silencing. Instead, in mammals, dispersed transposon copies initiate the pathway, producing primary piRNAs, which predominantly join MILI in the cytoplasm. MIWI2, whose nuclear localization and association with piRNAs depend upon MILI, is enriched for secondary piRNAs antisense to the elements that it controls. The Piwi pathway lies upstream of known mediators of DNA methylation, since piRNAs are still produced in Dnmt3L mutants, which fail to methylate transposons.  This implicates piRNAs as specificity determinants of DNA methylation in germ cells.

overall_design: Examination of total small RNA and MILI associated piRNAs in embryonic and post-birth mouse testes, MIWI2-associated piRNAs in embryonic testes.

first: Ravi

last: Sachidanandam

first: Deborah

last: Bourc'his

last: Schaefer

first: Dubravka

last: Pezic

first: Katalin

last: Toth

first: Timothy

last: Bestor

first: Gregory

last: Hannon


status: Public on Sep 16 2008

city: New Haven

first: Flora

last: Vaccarino

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

summary:
We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor STAT1 in HeLa S3 cells. The STAT1 ChIP was performed using HeLa S3 cells that are stimulated using gamma-interferon. We have also generated a seqenced input DNA dataset for gamma-interferon stimulated HeLa S3 cells.

Raw data for this study is available for download from the Short Read Archive database at:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000703.

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: Examination of the STAT1 transcription factor in Human HeLa S3.

first: Joel

last: Rozowsky

first: Ghia

last: Euskirchen

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: STOX1 overexpression in choriocarcinoma cells mimicks transcriptional alterations observed in preeclamptic placentas

status: Public on Nov 07 2008

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

summary:
Background
Mutations in STOX1 were proposed as causal for predisposing to preeclampsia, a hypertensive disorder originating from placental defects, affecting up to 10% of human pregnancies. However, after the first study published in 2005 three other groups have dismissed the polymorphism described in the first paper as a causal mutation.

Methodology and Principal Findings
In the present study, we have developed a choriocarcinoma cell line overexpressing STOX1. This overexpression results in the transcriptional modification of 12.5% of the genes, some of them being direct targets as shown by chromatin immunoprecipitation. STOX1 overexpression correlates strongly and specifically with transcriptomic alterations in preeclamptic placentas (r=0.30, p=9.10-7). Numerous known key modulators of preeclampsia (such as Endoglin, Syncytin, human chrionic gonadotrophin-hCG-, and Glial Cell Missing Homolog -GCM1-) were modified in these transformed choriocarcinoma cells.

Conclusions
Our results contribute to reconcile contradictory data about the involvement of STOX1 in preeclampsia. In addition, they strongly suggest that anomalies in STOX1 expression are associated with the onset of preeclampsia, thus indicating that this gene should be the target of future studies. Furthermore, our cellular model could constitute an invaluable resource for studying specific aspects of this human disease.

overall_design: Microarrays expression

first: Virginie

last: Rigourd

first: Caroline

last: Chauvet

first: Sonia

last: Chelbi

first: Régis

last: Rebourcet

first: Françoise

last: Mondon

first: Franck

last: Letourneur

first: Thérèse-Marie

last: Mignot

first: Sandrine

last: Barbaux


title: Drosophila melanogaster late embryo, larval, pupal and adult head small RNA libraries

status: Public on Sep 30 2008

city: New York

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

institute: Memorial Sloan Kettering Cancer Center

summary:
High-throughput sequencing of Drosophila melanogaster small RNAs. Total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

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: Small RNAs were sequenced from D. melanogaster (Canton S) wandering late embryos, first instar larvae, third instar larvae or from 2-4 day old pupae and adult female heads or male heads. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt.

first: Eric

middle: C

last: Lai

first: Katsutomo

last: Okamura

first: Michelle

last: Rooks


title: TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the S. pombe siRNA pathway

status: Public on Sep 02 2008

first: Noah

last: Spies

address: 300 Pasteur Dr

department: Pathology

summary: In the fission yeast Schizosaccharomyces pombe, the RNAi machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the non-canonical Cid14 polyA polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5’-uracil, largely because these are loaded most efficiently into Argonaute. In wild-type cells, most sRNAs match to repeated regions of the genome, whereas in cid14 cells, the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.

overall_design: Ago1-associated RNA was isolated as in Bühler, et al, (Cell, 2007), and 20-30nt long RNAs were PAGE purified. The eluted small RNAs were cloned based upon the pre-activated, adenylated linkering method using a mutant T4 RNA ligase (Rnl2(1-249)). Single stranded DNA suitable to go directly into the emulsion PCR step of 454 pyrosequencing was generated as described in Margulies, et al (Nature, 2005).

first: Marc

last: Bühler

first: David

last: Bartel

first: Danesh

last: Moazed


title: The Early Origins and Evolution of microRNAs and piRNAs in Animals

first: andrew

last: grimson

address: 9 Cambridge Center

summary: We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon

sample_organism:
Trichoplax adhaerens
Nematostella vectensis
Monosiga brevicollis
Amphimedon queenslandica

overall_design: Employ HTS of endogenous small RNAs

first: Andrew

last: Grimson

first: Mansi

last: Srivastava

first: Bryony

last: Fahey

first: Ben

last: Woodcroft

first: H

middle: R

last: Chiang

first: Nicole

last: King

first: Bernard

middle: M

last: Degnan

first: Daniel

last: Rokhsar


title: RBP40_arrays

status: Public on Oct 28 2008

last: Hogan

address: 279 Campus Dr B439

summary:
In this study, we systematically identified the RNAs associated with a selective sample of 40 of ~600 yeast RNA-binding proteins (RBPs). To identify RNAs associated with each putative RBP, C-terminal tandem affinity purification (TAP)-tagged proteins, expressed under control of their native promoters, were affinity purified from whole cell extracts of cultures grown to mid-log phase in rich medium [1-3]. Extracts were incubated with immunoglobulin G (IgG) agarose beads, washed, and ribonuclear protein complexes were eluted by tobacco etch virus (TEV) protease treatment (Text S2). We performed two to four independent isolations with each tagged strain. As controls, we performed 13 immunoaffinity purifications (IPs) of untagged strains to identify and exclude potential false-positive RNA targets. We purified total RNA from the whole-cell extracts and TEV-purified fractions, reverse transcribed with an amino-allyl-dUTP/dNTP mix, coupled the purified cDNA to Cy3 and Cy5 dyes, respectively, mixed the two differentially labeled cDNA pools, and then hybridized them to DNA microarrays (Datasets S1-S4).
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Genotype: strain expressing tagged version of RNA-BP

Keywords: all_pairs

overall_design: Computed

first: Andre

last: Gerber


title: Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

status: Public on Jul 30 2008

first: Whitehead

last: Institute

department: Genome Technology Core

summary:
MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established.  We describe here a new map of the transcriptional regulatory circuitry of ES cells that incorporates both protein-coding and miRNA genes, and which is based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types.  We find that the key ES cell transcription factors are associated with promoters for most miRNAs that are preferentially expressed in ES cells and with promoters for a set of silent miRNA genes.  This silent set of miRNA genes is co-occupied by Polycomb Group proteins in ES cells and expressed in a tissue-specific fashion in differentiated cells.  These data reveal how key ES cell transcription factors promote the miRNA expression program that contributes to self-renewal and cellular differentiation, and integrate miRNAs and their targets into an expanded model of the regulatory circuitry controlling ES cell identity.

Keywords: ChIP-seq analysis of ES cell transcriptional regulators and chromatin modifications. Cell-type comparison of short RNA transcritome.  Analysis of changes in short RNA transcritome upon Oct4 ablation.

overall_design: ChIP-seq in murine embryonic stem cells for Oct4, Sox2 (2 runs), Nanog (2 runs), Tcf3 (2 runs), Suz12 (2 runs), H3K4me3 (4 runs), H3k79me2 (2 runs), H3k36me3 (2 runs) and whole cell extract input DNA (WCE, 2 runs).  Short transcript sequencing from murine embryonic stem cells (mES, v6.5), mouse embryonic fibroblasts (MEF), murine neural precursor cells (NPC), and ZHBT-c4 cells (from Austin Smith) untreated (0h), with 12 hours of doxycyclin treatment (12h), and with 24 hours of doxycyclin treatment (24h).

first: Richard

last: Young


title: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

status: Public on Jul 25 2008

first: Tarjei

last: Mikkelsen

summary:
Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Histone H3 or H4 tri-methylation ChIP-Seq in singlicate from murine embryonic stem (ES) cells, ES-derived neural precursor cells, and embryonic fibroblasts.

first: Manching

last: Ku

first: Eric

last: Lander

first: Bradley

last: Bernstein


title: Properties of mammalian neural progenitor cells as revealed by genome-wide single cell gene expression profiles

status: Public on Aug 08 2008

city: Yokohama, Kanagawa

first: Takeya

last: Kasukawa

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

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary:
Cellular diversity of the brain is largely attributed to the spatial and temporal heterogeneity of progenitor cells. In mammalian cerebral development, it has been difficult to determine how neural progenitor cells are heterogeneous, due to their dynamic changes in nuclear position and gene expression. To address this issue, we systematically analyzed the cDNA profiles of a large number of single progenitor cells at the mid-embryonic stage.
Keywords: single cell analysis

overall_design: We randomly picked up single cells from the ventricular zone(VZ)/subventricular zone (SVZ) of E14 mouse dorsal forebrain, and a total of 102 single-cell cDNA samples were amplified as descibed (Kurimoto et al.Nucreic Acid Res.34:e42, 2006).  After checking the quality of the samples, we then chose 70 samples and applied them to GeneChip analysis.

first: Ayano

last: Kawaguchi

first: Tomoko

last: Ikawa

first: Hiroki

last: Ueda

first: Kazuki

last: Kurimoto

first: Mitinori

last: Saitou

first: Fumio

last: Matsuzaki


title: Genome-wide mapping of RNA Polymerase II binding sites

status: Public on Oct 02 2008

first: Flora

last: Vaccarino

summary:
Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing.

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: Map binding sites of RNA Polymerase II in the genome of K562 & NB4 cells

first: Debasish

last: Raha

first: Michael

last: Snyder


summary:
We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor PolII in HeLa S3 cells. The PolII ChIP was performed according to the same protocol as used for the STAT1 samples except that the cells were not stimulated using gamma-interferon prior to formaldehyde fixation.

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: Examination of the PolII transcription factor in Human HeLa S3.

first: Joel

last: Rozowsky

first: Ghia

last: Euskirchen

first: Mark

last: Gerstein


title: An epigenetic role for maternally inherited piRNAs in transposon silencing

status: Public on Nov 28 2008

first: Colin

middle: Dean

last: Malone

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

summary:
In plants and mammals, small RNAs indirectly mediate epigenetic inheritance  by specifying cytosine methylation.  Here, we find that small RNAs  themselves serve as vectors for epigenetic information.  Crosses between  Drosophila strains that differ in the presence of a particular transposon  can produce sterile progeny, a phenomenon called hybrid dysgenesis.  This  phenotype manifests itself only if the transposon is paternally inherited,  suggesting maternal transmission of a factor that maintains fertility. In  both P- and I-element-mediated hybrid-dysgenesis models, daughters show a  markedly different content of piRNAs targeting each element, depending upon  its parent of origin.  Such differences persist from fertilization through  adulthood.  This indicates that maternally deposited piRNAs are crucial for  mounting an effective silencing response and that a lack of maternal piRNA  inheritance underlies hybrid dysgenesis.

Mappers table contains all of the sequences in our libraries that map to the drosophila genome (release 5)
Nonmappers table contains all of the sequences in our libraries that do not map to the drosophila genome(release 5)

overall_design: 15 small RNA libraries were generated from total RNA of Drosophila melanogaster ovarian and embryo tissues and analyzed for this study

first: Julius

last: Brennecke

middle: D

first: Gregory

middle: J

last: Hannon


title: Genome-wide chromatin state maps of ES cells, ES-derived neural progenitor cells and brain tissue

status: Public on Jul 06 2008

first: Tarjei

last: Mikkelsen

summary:
Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment.
Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison

overall_design: H3K4me3, H3K4me2 and/or H3K4me1 ChIP-Seq in singlicate from mouse embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue suspensions

first: Alexander

last: Meissner

first: Xiaolan

last: Zhang

first: Andreas

last: Gnirke

first: Rudolf

last: Jaenisch

first: Eric

last: Lander


title: Analysis of small RNAs in murine neutrophils by Solexa/Illumina genome analyzer

status: Public on Jul 31 2008

first: Whitehead

last: Institute

summary: To examine the effects of microRNAs including miR-223 on murine neutrophil function, small RNAs cloning and sequencing from neutrophils were performed.

overall_design: Neutrophils were isolated from a wild-type mouse and total RNAs were prepared.  Small RNAs were cloned and sequenced by Solexa/Illumina genome analyzer.

first: Daehyun

last: Baek

first: Judit

last: Villén

first: Chanseok

last: Shin

first: Fernando

last: Camargo

first: Steven

last: Gygi

first: David

last: Bartel


title: A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

status: Public on Jul 03 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

institute: Max Planck Institute for molecular genetics

summary: Transcriptome of HEK and B cells were analyzed by microarray and RNA-Seq parallely. Both platforms were then compared in terms of sensitivity. To assess whether values were a reliable indicator of gene activity, we correlated these values with hypophosphorylated RNA polymerase II (PolIIa) occupancy, used as a landmark of transcription initiation. For HEK, we identified PolIIa islands by chromatin immunoprecipitation and sequencing (ChIP-Seq).

overall_design: For HEK and B cell, samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips. PolIIa Chip-Seq performed on HEK.

first: Marcel

last: Schulz

first: Hugues

last: Richard

first: Alon

last: Magen

last: Klingenhoff

first: Matthias

last: Scherf

first: Martin

last: Seifert

first: Tatjana

last: Borodina

first: Aleksey

last: Soldatov

first: Dmitri

last: Parkhomchuk

first: Dominic

last: Schmidt

first: Sean

last: O'Keeffe

first: Stefan

last: Haas

last: Vingron

first: Hans

last: Lehrach

first: Marie-Laure

last: Yaspo


title: Genome-scale DNA methylation maps of pluripotent and differentiated cells

first: Tarjei

last: Mikkelsen

type: Methylation profiling by high throughput sequencing

summary:
We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for murine embryonic stem (ES) cells, ES-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of ES-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumors. More generally, the results establish RRBS as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
Keywords: High-throughput Reduced Representation Bisulfite Sequencing (RRBS), Illumina, cell type comparison

overall_design:
Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) of 18 murine cell types.

Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000179

first: Alexander

last: Meissner

first: Hongcang

last: Gu

first: Ancreas

last: Gnirke

first: Rudolf

last: Jaenisch

first: Eric

last: Lander


title: Genome-wide maps of transcription factor binding using ChIP-Seq for Human ENCODE

first: Flora

last: Vaccarino

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE12781
SuperSeries of: GSE12782

overall_design: Examination of 2 different transcription factors in Human HeLa S3 cells under two different cellular condtitions.


title: The impact of microRNAs on protein output

first: Whitehead

last: Institute

institute: Whitehead Institute

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

overall_design: Refer to individual Series

first: Daehyun

last: Baek

first: Judit

last: Villén

first: Chanseok

last: Shin

first: Fernando

last: Camargo

first: Steven

last: Gygi

first: David

last: Bartel


title: Conservation of small RNA pathways in platypus

status: Public on May 21 2008

city: Cold spring Harbor

first: ravi

last: Sachidanandam

address: 1 bungtown road

institute: Cold Spring Harbor Laboratory

summary:
Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage.  Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly-evolving cluster of miRNAs on platypus chromosome X1 which is unique to monotremes. Platypus and echidna testes contain a robust piRNA system which appears to be participating in ongoing transposon defense.
Keywords: piRNA

sample_organism:
Ornithorhynchus anatinus
Tachyglossus aculeatus

overall_design: Two size fractions of small RNAs (18-24nt and 25-33nt) were cloned and sequenced from platypus adult testis total RNA; one size fraction (28-24nt) was cloned and sequenced from echidna adult testis total RNA

first: Elizabeth

last: Murchison

first: Gregory

last: Hannon


title: Novel microRNA-target RNA pairs revealed by Parallel analysis of RNA ends

status: Public on Jun 10 2008

city: Newark

first: Marcelo

middle: Ariel

last: German

state: DE

address: 15 Innovation Way

institute: Delaware Biotechnology Institute

summary:
MicroRNAs are important regulatory molecules in most eukaryotes and the identification of their mRNA targets is essential for their functional analysis. From inflorescence tissue of Arabidopsis, >28,000,000 signatures were sequenced from 5’ ends of polyadenylated products of mRNA decay. Within the set of ~27,000 transcripts included in the 3,500,000 non-redundant signatures, several previously predicted but non-validated miRNA targets were found. Like validated targets, most showed a single abundant signature at the miRNA cleavage site, particularly in libraries from a mutant deficient in the 5’ to 3’ exonuclease AtXRN4. Among the most unexpected miRNA targets discovered were miRNA precursor transcripts that are self-targeted by their own mature miRNA. Although the miRNAs of Arabidopsis have been extensively investigated, working in reverse from the cleaved targets, additional novel miRNAs were identified and validated. This deep and versatile approach will impact the study of other aspects of RNA processing beyond miRNA-target RNA pair analyses.
Keywords: miRNA-target RNA pairs, Palallel analysis of RNA ends, PARE, SBS

overall_design:
RNA from inflorescence tissue from wildtype Arabidopsis and xrn4 mutants was extracted. Following polyA RNA extraction, libraries for PARE were constructed.

RNA from inflorescence tissue from wildtype Arabidopsis (Col-0),  and rdr2 and dcl2,3,4 mutants was extracted. The material was submitted to Illumina and libraries were constructed for small RNAs. Individual small RNA libraries from inflorescences of Arabidopsis wildtype, rdr2, and dcl2/dcl3/dcl4 were sequenced with SBS at Illumina, Inc. The distribution of small RNA sizes in each library is in agreement with that published previously for the wild type or the respective mutants sequenced with MPSS or 454; however, the presence and abundances of some small RNAs may differ. This may be attributed to the use of different sequencing technologies with different depths, biological differences in the tissue used, or other unknown reasons.

raw data requested but not provided for GSM280226 and GSM280227

first: Manoj

last: Pillay

first: Dong-Hoon

last: Jeong

first: Amit

last: Hetawal

first: Prakash

last: Janrdhanan

first: Vimal

last: Kannan

first: Linda

last: Rymarquis

first: Kan

last: Nobuta

first: Rana

first: Cheng

last: Lu

first: Emanuele

last: DePaoli

first: Shujun

last: Luo

first: Gary

last: Schroth

first: Blake

last: Meyers

first: Pamela

last: Green


title: Drosophila melanogaster small RNA sequence: female heads

status: Public on Apr 23 2008

first: Wei-Jen

last: Chung

address: 430 E 67th St

department: Developmental Biology

institute: Sloan-Kettering Institute

summary:
High-throughput sequencing of Drosophila melanogaster small RNAs.
total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH
Keywords: High-throughput solexa sequencing

overall_design:
Small RNAs were sequenced from D. melanogaster female head. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

Quality scores in the supplementary file for GSM240749 are undefined.  Quality of the bases assessed by (1) identifying for the sequenced linker, which is a known sequence, and (2) mapping the clipped sequence to the genome and taking only perfect hits.

first: Eric

last: Lai


title: Drosophila melanogaster small RNA sequence from 14 libraries

status: Public on Jun 02 2008

summary:
High-throughput sequencing of Drosophila melanogaster small RNAs.
total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

overall_design: Small RNAs were sequenced from D. melanogaster heads (male and female), body (male and female), S2 and Kc cells and different stages of embryo. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt


title: Drosophila melanogaster small RNA sequence: cell lines and imaginal disc

status: Public on May 01 2008

overall_design: Small RNAs were sequenced from D. melanogaster S2 and KC cells. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt


title: The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

status: Public on May 05 2008

first: Zhong

last: Wang

address: 266 Whitney Avn, KBT716

summary:
The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq in which cDNA fragments are subjected to high throughput sequencing. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genomeand demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames were also identified for many yeast genes. We also found unexpected 3' end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
Keywords: RNA-Seq, mRNA expression profiling, Illumina high-throughput sequencing

overall_design: Oligo(dT) primed dataset has one technical and one biological replicates (total 3), Random Hexamer primed dataset has one technical and one biological replicates (total 3).

first: Ugrappa

last: Nagalakshmi

first: Karl

last: Waern

first: Chong

last: Shou

first: Debasish

last: Raha

first: Mark

last: Gerstein

first: Michael

last: Snyder


title: A link between RNA metabolism and silencing affecting Arabidopsis development

status: Public on May 15 2008

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary:
Whole genome small RNA sequencing (wild-type Col-0, abh1-1, ein5-6, ein5-6 abh1-1) and 5'-RACE (GMUCT) (wild-type Col-0 and ein5-6) sequencing of parenthetically indicated genotypes of Arabidopsis using the Illumina Genetic Analyzer. Whole-genome oligonucleotide tiling microarrays were used for gene expression studies of the entire transcriptome for wildtype Col-0, abh1-1, ein5-6, and ein5-6 abh1-1 plants.

Micro (mi)RNAs and small-interfering (si)RNAs are abundant endogenous small (sm)RNAs that control transcript expression by post-transcriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5’-3’ exoribonuclease, and CBP80/ABH1, the largest subunit of the mRNA cap binding complex, results in Arabidopsis plants manifesting myriad developmental defects. Through the analysis of ein5 abh1 double mutant plants, we find that CBP80/ABH1 regulates the levels of mature miRNAs, which suggests this protein is a novel component of the miRNA-mediated RNA silencing pathway. Additionally, we show that a novel class of smRNAs are processed from both sense and anti-sense strands of ~130 endogenous transcripts that apparently are converted to double-stranded RNA and subsequently processed into smRNAs, and accumulate in the absence of XRN4/EIN5. Moreover, we demonstrate that accumulation of these smRNAs is often synergistically increased in ein5 abh1 double mutant plants, which suggests that these proteins act coordinately to regulate the substrates from which they are processed. Finally, we find that the parent transcripts of these novel smRNAs accumulate in an uncapped form upon loss of XRN4/EIN5. These results suggest that uncapped endogenous transcripts can shuttle into an RNA silencing pathway where they become smRNA biogenesis substrates. Overall, our results reveal unexpected connections between RNA metabolism and silencing.
Keywords: transcriptome analysis using tiling array; whole genome small RNA sequencing; 5'-RACE sequencing

overall_design: Two biological replicates were done for each of the four genotypes (wild-type Col-0, abh1-1, ein5-6, and ein5-6 abh1-1) for the gene expression studies of the entire transcriptome employing tiling microarrays for the reverse (Crick) and forward (Watson) chromosomal strands, which meant a total of 16 whole-genome oligonucleotide tiling microarrays were used for these studies. The small RNA component of the transcriptome was sequenced from the four genotypes (wild-type Col-0, abh1-1, ein5-6, and ein5-6 abh1-1) using the Illumina Genetic Analyzer. A genome-wide survey of 5'-RACE products was sequenced (GMUCT) from two genotypes (wild-type Col-0 and ein5-6) using the Illumina Genetic Analyzer.

first: Brian

last: Gregory

first: Ronan

last: O'Malley

first: Ryan

last: Lister

last: Urich

first: Julian

last: Tonti-Filippini

first: Huaming

last: Chen

first: Harvey

last: Millar


status: Public on Apr 07 2008

first: wei

last: chen

address: Ihestrasse 73

institute: MPI molecular genetics

summary:
High-throughput sequencing of small RNAs from HeLa cells
Keywords: high-throughput Solexa sequencing

overall_design: Small RNAs were sequenced from HeLa cells


title: Highly integrated epigenome maps in Arabidopsis - transcriptome sequencing

status: Public on Apr 21 2008

summary:
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana.
Keywords: Illumina high-throughput transcriptome sequencing

overall_design: Transcriptome sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

first: Charles

last: Berry

first: A


title: MPI_Chen_domestic_dog_Solexa_2007

summary:
High-throughput sequencing of small RNAs from domestic dog lymphocytes
Keywords: high-throughput Solexa sequencing

overall_design: Small RNAs were sequenced from domestic dog lymphocytes


status: Public on May 28 2008

city: Cambridge

first: Tarjei

last: Mikkelsen

address: 7 Cambridge Center

summary:
Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines obtained by ectopic expression of Oct4, Sox2, Klf4 and c-Myc using constitutive retroviral infection of MEFs (MCV6, MCV8, MCV8.1) or induction of lentivirus in secondary B lymphocytes obtained from iPS-derived chimeric mice (BIV8).
Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison

overall_design: H3K4me3 and H3K27me3 ChIP-Seq in singlicate from three partially reprogrammed cell lines (BIV1, MCV8, MCV6), one iPS cell line (MCV8.1) and MEFs (subsampled from Mikkelsen et al, Nature, 2007))

first: Xiaolan

last: Zhang

first: Eric

last: Lander

first: Alexander

last: Meissner


title: Highly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing

summary:
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana.
Keywords: Illumina high-throughput bisulfite sequencing

overall_design: Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.


title: Small RNA profile in fully grown mammalian oocytes

status: Public on Mar 28 2008

first: ravi

last: Sachidanandam

summary:
We aim to comprehensively characterize the small RNA population in oocytes
Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals.
Keywords: small RNAs profile

overall_design: Total RNA was isolated and size-fractionated by PAGE either into 19-24nt and 24-30nt, or 19-30nt. These were independently processed and sequenced on Illumina 1G platform.

first: Oliver

last: Tam

first: Alexei

last: Aravin

first: Paula

last: Stein

first: Angelique

last: Girard

first: Elizabeth

last: Murchison

first: Sihem

last: Cheloufi

first: Emily

last: Hodges

first: Martin

last: Anger

first: Ravi

last: Sachindanandam

first: Richard

last: Schultz

first: Gregory

last: Hannon


title: Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment

status: Public on Feb 08 2008

city: Plymouth

first: Jack

middle: Anthony

last: Gilbert

state: Devon

address: Prospect Place

country: United Kingdom

institute: Plymouth Marine Laboratory

summary:
Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome.
Keywords: metatranscriptome, mesocosm, ocean acidification

overall_design:
This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples.

The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics.

Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm.

first: Dawn

last: Field

first: Weizhong

last: Li

first: Rob

last: Edwards

first: Ian

last: Joint


title: Dynamic regulation of nucleosome positioning in the human genome

status: Public on Feb 09 2008

city: Bethesda

first: Dustin

last: Schones

address: Building 10, Room 7B20A, 9000 Rockville Pike

institute: NHLBI/NIH

summary:
The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription.  However, nucleosome mapping has been performed for only limited genomic regions in humans.  We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique.

We find that nucleosome phasing relative to the transcription start sites (TSSs) is directly correlated to RNA polymerase II binding.  Furthermore, the first nucleosome downstream of TSSs exhibits differential positioning in active and silent genes.  TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression.  Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position.  Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome.

This microarray dataset is the gene expression data from resting and activated CD4+ T cells.  We used this data to look at nucleosome positioning, Pol II and a few chromatin modifications at genes that are silent and activated in both resting and activated T cells as well as genes that are induced or repressed with T cell activation.
Keywords: nucleosome mapping, expression data complementary to Solexa ChIP-Seq data

overall_design: Gene expression data from resting  (M0 and T0) and activated (M18 and T18) T cells.

first: Kairong

last: Cui

first: Suresh

last: Cuddapah

first: Tae-Young

last: Roh

first: Artem

last: Barski

first: Zhibin

last: Wang

first: Gang

last: Wei

first: Keji

last: Zhao


title: Highly integrated epigenome maps in Arabidopsis - small RNA sequencing

first: Joseph

last: Ecker

summary:
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana.
Keywords: Illumina high-throughput small RNA sequencing

overall_design: Small RNA sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

first: Ryan

last: Lister

first: Ronan

last: O'Malley

first: Julian

last: Tonti-Filippini

first: Brian

last: Gregory

first: Charles

last: Berry

first: A

last: Millar


title: Retinoic Acids Exposure Alters TGFbeta1 -Induced Epithelial Mesenchymal Transition via Wnt5b expression.

status: Public on Aug 05 2006

city: Dublin

first: Andrea

middle: Patricelli

last: Malizia

address: 21, Nelson Street

country: Ireland

institute: University College Dublin

summary:
Idiopathic pulmonary fibrosis (IPF) is a refractory and lethal interstitial lung disease; EBV has previously been localised to alveolar epithelial cells of IPF patients. The molecular process of the epithelial mesenchymal transition (EMT) in IPF remains still unknown. Using an oligonucleotide array analysis, we observed dysregulated expression of members of non-canonical Wnt family in EBV infected A549 after TGF?1 exposure. TGF?1 exposure induced EMT increasing ?-Smooth Muscle Actin (ACTC) and Wnt5b gene expression, but decreasing E-cadherin and DKK1. When data were analyzed as a function of Wnt5b in EMT, significance differences in ACTC and E-cadherin gene expression, active TGF?1 protein levels and collagen deposition could be detected. Treatment with 9-cis Retinoic Acid (9-cisRA) significantly inhibited Wnt5b expression in both EBV infected and non-infected A549, followed by decreased collagen deposition and active TGF?1 protein level. Specific non-canonical Wnt-signalling genes are dysregulated in EBV infected cells and A549 treated with TGF?1; while, 9-cisRA treatment appears to attenuate EMT process in vitro.
Keywords: EBV infection, EMT and non-canonical Wnt pathway in A549 detected by oligonucleotide array

overall_design: EBV infected cells and A549 were cultured in RPMI1640+5%FCS, and exposed to 10ng/ml TGF beta1 for 4hours. RNA isolation, cDNA synthesis, in vitro transcription and microarray analysis were performed as previously reported (Kieran et al., 2003). All analysis were microarrayed in duplicate. Image files were obtained through Affymetrix GeneChip software (MAS5), subsequently robust multichip analysis (RMA) was performed.  Expression data were compared to control, p<0.05 correlated values and a signal log ratio of 0.6 or greater (equivalent to a fold change in expression of 1.5 or greater) were taken to identify significant differential regulation (Bolstad et al., 2003). All the SLRs data resulting from the comparative analyses in duplicate were reported in a scatter plot graph to determine the reliability of the assay and the linearity by r2. For all the microarray assays r2 value was higher than 0.98. Using normalised RMA values by Gene Cluster Software, Average Linkage Hierarchical Cluster Analysis was performed using TreeView analysis software (Eisen et al., 1998). Lists of dysregulated genes in both TGF?1 exposed cell lines were curated via the publicly available DAVID, Gene-Ontology (GOCharts) and Functional Annotation Clustering databases (Dennis et al., 2003).

first: Dominic

last: Keating

first: Sined

last: Smith

first: Dermot

last: Walls

first: Alfred

last: Wood

first: Peter

last: Doran

first: Jim

last: Egan


title: Changes in gene expression following ADNP knockout

status: Public on Jan 09 2007

city: Tel Aviv

first: Illana

last: Gozes

address: Einstein

country: Israel

institute: Tel Aviv University

summary:
The putative transcription factor, activity-dependent neuroprotective protein (ADNP) is a zinc finger and homeodomain - like profile containing protein. ADNP knockout mice die at day 9 of gestation. To reveal ADNP-associated pathways, a 22,690- Affymetrix probe array was used on ADNP knockout and control embryos.
References:
Complete sequence of a novel protein containing a femtomolar-activity-dependent neuroprotective peptide.
J Neurochem. 1999 Mar;72(3):1283-93.
PMID: 10037502 [PubMed - indexed for MEDLINE]
Cloning and characterization of the human activity-dependent neuroprotective protein.
J Biol Chem. 2001 Jan 5;276(1):708-14.
PMID: 11013255 [PubMed - indexed for MEDLINE]
Activity-dependent neuroprotective protein: a novel gene essential for brain formation.
Brain Res Dev Brain Res. 2003 Aug 12;144(1):83-90.
PMID: 12888219 [PubMed - indexed for MEDLINE]
Keywords: Comparative gene knockout results

overall_design: To identify downstream target genes of ADNP, we examined global gene expression profiles of whole E9 knockout embryos (KO - ADNP -l-), their wild-type (WT - ADNP +l+ ) and their heterozygous (H - ADNP –l+ ) littermates, using the Affymetrix  Murine Genome 430A oligonucleotide microarrays.  Gestation day 9 was chosen as it is the period at which embryos lacking ADNP exhibit distinct morphological and developmental changes prior to degeneration and in uterus absorption.  Total RNA was extracted from four ADNP knockout embryos, four normal embryos and six heterozygous embryos. A pool of two genotype identical littermates was used on seven different arrays (pooling of two embryos was necessary to obtain enough RNA on each of the gene microarrays).

first: Shmuel

last: Mandel

first: Gideon

last: Rechavi

first: Jasmine

last: Jacob-Hirsch


title: Circadian skeletal muscle_wt and Clock mutants

status: Public on Feb 08 2007

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), the left leg muscle from 5 wildtype mice, and the right leg muscle from the same wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints.  Total RNA from each side (left or right) were separately pooled to make a single sample for amplification and hybridization.  Therefore, duplicate arrays (from left and right side) were performed at each time point. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected. As for the wildtype mice, right and left sides were collected, prepared, amplified, and hybridized in separate pools. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ?l RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at –80?C until use.
Keywords: time course

overall_design: duplicates consisted of pools from independent mice

first: Brooke

middle: H

last: Miller

first: Erin

middle: L

last: McDearmon

first: Satchidananda

last: Panda

first: Jessica

last: Andrews

first: Martin

last: Straume

first: Karyn

last: Esser

last: Hogenesch

first: Joseph

last: Takahashi


title: Deep sequencing of small RNA libraries from chicken embryo

status: Public on May 12 2008

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

summary:
MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in chickens we used a deep sequencing approach developed by Solexa (now Illumina Inc.). We sequenced three small RNA libraries prepared from different developmental stages of the chicken embryo (days 5, 7, and 9) to produce over 9.5 million short sequence reads. We developed a bioinformatics pipeline to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected almost all of the previously known chicken miRNAs and their respective miRNA* sequences. In addition we discovered 449 putative new chicken miRNAs. Of these, 430 miRNAs appear to be specific to the avian lineage. Another 6 new miRNAs had evidence of evolutionary conservation in at least one vertebrate species outside of the bird lineage. The remaining 13 putative miRNAs appear to represent chicken orthologs of known vertebrate miRNAs. We discovered 39 additional putative miRNA candidates originating from miRNA generating intronic sequences known as mirtrons.
Keywords: miRNA discovery, mirtrons, chicken embryo

overall_design: 3 samples

first: Pauline

last: Cottee

first: Wesley

last: Barris

first: Robert

last: Moore

first: Brian

last: Dalrymple

first: Mark

last: Tizard


title: Circadian rhythm in clock mutants

status: Public on Feb 07 2007

summary:
One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. At timepoints 34 through 58 hours in DD, tissues from age-matched male C57BL/6J Clock/Clock homozygous mutant mice that had been treated with the same light entrainment protocol as the wildtype were collected. Tissues were collected from 5 Clock/Clock mutants at each timepoint except for 34 and 46 hours after the onset of DD, when tissues from 10 Clock/Clock mice were collected and run as independent replicates. Mice were sacrificed by cervical dislocation, and the optic nerves were severed in complete darkness; brain dissection was performed using illumination from an infrared viewer (FJW Industries, Palatine, IL). SCNs were dissected out, pooled at a density of 5 per tube in 100 ul RNAlater (Ambion, Austin, TX), frozen on dry ice, and stored at –80 degrees C until use.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
This reference Series links data in the following related Series:
GSE3746 Circadian skeletal muscle_wt and Clock mutants
GSE3748 Circadian liver_wt and Clock mutants


title: Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells

status: Public on Apr 11 2008

city: Worcester

first: Hervé

last: Seitz

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary:
Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA as a defense against viral infection. Here, we identify 21-nt long, endogenous siRNAs (endo-siRNAs) corresponding to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to mRNAs: these siRNAs disproportionately mapped to the complementary regions of overlapping mRNAs predicted to form dsRNA in vivo. Normal accumulation of somatic endo-siRNAs requires the siRNA-generating ribonuclease, Dicer-2, and the RNAi effector protein, Ago2. We propose that endo-siRNAs generated by the fly RNAi pathway silence selfish genetic elements in the soma much as piRNAs do in the germ line.
Keywords: Small RNA detection and quantification.

overall_design: Small RNAs (18-30 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants, and WT expressing an inverted repeat directed against exon 3 of the gene "white") and S2 cells (transgenic for a construct expressing siRNAs against white and GFP) were sequenced using a Solexa Genome Analyzer instrument.

first: Megha

last: Ghildiyal

first: Michael

last: Horwich

first: Chengjian

last: Li

first: Tingting

last: Du

first: Soohyun

last: Lee

first: Jia

last: Xu

first: Ellen

last: Kittler

first: Maria

last: Zapp

first: Zhiping

last: Weng

first: Phillip

last: Zamore


title: Highly integrated single base resolution maps of the epigenome in Arabidopsis

first: Joseph

last: Ecker

summary:
Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.

Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation.

This SuperSeries is composed of the SubSeries listed below.

first: Ryan

last: Lister

first: Ronan

last: O'Malley

first: Julian

last: Tonti-Filippini

last: Gregory

first: Charles

last: Berry

first: A

last: Millar