title: Transcriptional profiling of EJC depletion by RNA-Seq using the SOLiD platform (Applied Biosystems)

city: Montreal

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

department: Genetics

country: Canada

institute: CNRC-IRB

summary: Signaling pathways are controlled by a vast array of post-translational mechanisms. By contrast, little is known regarding the mechanisms that regulate the expression of their core components. We conducted an RNAi screen in Drosophila for factors modulating RAS/MAPK signaling and identified the Exon Junction Complex (EJC) as a novel key element of this pathway. The EJC binds the exon-exon junctions of mRNAs, and thus far, has been linked exclusively to post-splicing events. Here, we report that the EJC is required for proper splicing of mapk transcripts by a mechanism that apparently controls exon definition. Moreover, whole transcriptome and RT-PCR analyses of EJC-depleted cells revealed that the splicing of long intron-containing genes, which includes mapk, is sensitive to EJC activity. These results identify a role for the EJC in the splicing of a subset of transcripts and suggest that RAS/MAPK signaling depends on the regulation of MAPK levels by the EJC.

overall_design:
Transcriptome sequencing (RNA-Seq) of Drosophila S2 cells to monitor the effect of EJC depletion on the cellular mRNA expression profile.
Each treatment (dsRNA knockdown of MAGO (CG9401), dsRNA knockdown of eIF4AIII (CG7483)) was done in biological duplicate and each sample was sequenced separately on a quad slide on the SOLiD 3.0 platform. The reference samples were treated with a dsRNA targeted to GFP.

first: Marc

last: Therrien


title: Cloning of 50-75 nt small RNAs associated with Armitage in OSCs

status: Public on Oct 25 2010

city: Shinjuku-ku

first: Kuniaki

last: Saito

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Armitage (Armi) is a component of Yb bodies and  functions in the primary piRNA processing pathway. Armi interaction with Piwi does not require Yb expression; however, without Yb, the Armi-Piwi complex does not localize at Yb bodies and contains few piR-ILs (small RNAs associated with Armitage complex). These results suggest that only upon its localization at Yb bodies does the Armi-Piwi-Yb complex gain an opportunity to interact with piR-ILs. Currently, however, it remains unclear how piR-ILs are loaded onto the Piwi complex at Yb bodies and which protein(s) within the complex is directly bound to them.

overall_design: 1 sample examined: Ovarian somatic cell (OSC) line

first: Hirotsugu

last: Ishizu

first: Haruhiko

last: Siomi

first: Mikiko

middle: C


title: Dm Canton-S Adult Female Head Aged smallRNA RNA-Seq

status: Public on Oct 18 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3195
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton S; Tissue: Female heads; Developmental Stage: Adult Female; Genotype: wild type; Sex: Female;  EXPERIMENTAL FACTORS: Strain Canton S; Tissue Female heads; Developmental Stage Adult Female

first: Eric

last: Lai


title: Lai-MLDmD32/BS25/BS26

summary:
modENCODE_submission_3514
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmD32; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; EXPERIMENTAL FACTORS: Cell Line ML-DmD32; Replicate type: biological


title: Lai-MLDmD9/BS101/BS102

summary:
modENCODE_submission_3512
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmD9; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; EXPERIMENTAL FACTORS: Cell Line ML-DmD9; Replicate type: biological


title: Small RNAs in S. cerevisiae reconstituted with RNAi

status: Public on Aug 10 2011

city: Cambridge

first: Ines

middle: Anna

last: Drinnenberg

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

summary: The RNA interference (RNAi) pathway is found in most eukaryotic lineages but curiously is absent in others, including that of Saccharomyces cerevisiae. Here, we show that reconstituting RNAi in S. cerevisiae causes loss of a beneficial dsRNA virus, known as killer virus. Incompatibility between RNAi and killer viruses extends to other fungal species, in that RNAi is absent in all species known to possess dsRNA killer viruses, whereas killer viruses are absent in closely related species that retained RNAi. Thus, the advantage imparted by acquiring and retaining killer viruses explains the persistence of RNAi-deficient species during fungal evolution.

overall_design: Employ high-throughput sequencing of endogenous small RNAs from Saccharomyces cerevisiae wild-type and RNAi-reconstituted strains.

first: I

middle: A

first: G

middle: R

last: Fink

first: D

middle: P

last: Bartel


title: Multimodal RNA-seq using single-strand, double-strand, and circligase-based capture yields a refined and extended description of the C. elegans transcriptome

status: Public on Oct 20 2010

city: Stanford

first: Ayelet

last: Lamm

state: CA

address: 300 Pasteur Drive, Lane Bldg Room L302

department: Pathology

institute: Stanford University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single stranded RNA fragments and one involving circular-template PCR (circligase).  We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method.  Of particular note in the analysis were substantial advantages of circligase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the polyA junction. Using datasets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.

overall_design: single-strand-capture, double-strand-capture, and circligase-based RNA-seq

first: A

middle: Z

last: Fire

middle: T


title: Effect of mago nashi depletion on gene expression in Drosophila S2R+ cells

status: Public on Oct 21 2010

city: New York

first: Jessica

middle: E

last: Treisman

state: NY

address: 540 First Avenue

department: Cell Biology (Skirball)

institute: NYUMC

summary:
This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected.

SRA accession number: SRP003001.1

overall_design: Sequencing of poly(A)+ RNA from S2R+ cells treated with either lacZ (control) or mago (experimental) dsRNA

first: Jean-Yves

last: Roignant

first: Stuart

last: Brown

first: Zuojian

last: Tang


title: Dm Canton-S Adult Female Head Heat Shocked smallRNA RNA-Seq

summary:
modENCODE_submission_3190
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq


title: modENCODE_White Lab: genome-wide ChIP data of Trl from E0-8h on Illumina Genome Analyzer.

status: Public on Oct 30 2010

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 high throughput sequencing

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 genome-wide binding profile of the factor Trl from E0-8h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

overall_design:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study.

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3

status: Public on Oct 28 2010

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

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

overall_design: Refer to individual Series

first: Richard

last: Bartfai

first: Wieteke

last: Hoeijmakers

first: Adriana

middle: M

last: Salcedo-Amaya

first: Arne

middle: H

last: Smits

first: Eva

last: Janssen-Megens

first: Anita

last: Kaan

first: Moritz

last: Treeck

first: Tim-Wolf

last: Gilberger

first: Kees-Jan

last: Françoijs

first: Hendrik

middle: G


title: Epigenetic profile of the Plasmodium falciparum intraerythrocytic cycle

summary: This experiment characterizes the localisation of H2A.Z, H3K9ac and H3K4me3 in the epigenome of the human malaria parasite, P. falciparum at 4 different stages of intraerythrocytic development.

overall_design: Examination of H2A.Z, H3K9ac, H3K4me3 and mono-nucleosomal input in 3D7 strain at 4 different stages and H2A in 3D7 strain at 1 stage using native ChIP-seq


title: Kc-Rubin + Ecdysone smallRNA RNA-Seq

first: DCC

last: modENCODE

summary:
modENCODE_submission_2974
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: Kc-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Cell Line Kc-Rubin

first: Eric

last: Lai


title: Canton S Adult ovaries

summary:
modENCODE_submission_2976
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton S; Tissue: Adult ovaries; Developmental Stage: Adult Female; Genotype: wild type; Sex: Female;  EXPERIMENTAL FACTORS: Tissue Adult ovaries

first: Gregory

last: Hannon


title: Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq

status: Public on Oct 19 2010

first: Dali

last: Han

address: 5801 South Ellis Avenue

department: Department of Chemisty

summary: We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs.

overall_design: We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)’s ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. By integrating the ChIP-seq, RNA-seq and small RNA-seq data (previously uploaded to GEO as GSM450615 by our collaborator) with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified previously electronically annotated TSSs at a high resolution, and  predicted some novel TSSs.

first: Yi

last: Liu

first: Yixing

first: Zheng

last: Yan

first: Bin

last: Xie

first: Jing

last: Li

last: Qiao

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich

first: Yuan

last: Gao

first: Jing-Dong

middle: J


title: S2-Rubin + Ecdysone smallRNA RNA-Seq

summary:
modENCODE_submission_2973
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S2-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-Rubin


title: Lai_embryo_2-6hr_BS43-46

summary:
modENCODE_submission_2743
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 2-4h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1];  EXPERIMENTAL FACTORS: Developmental Stage Embryo 2-4h; Strain Y cn bw sp


title: Dcr-2[L811fsX] Ovary smallRNA RNA-Seq

summary:
modENCODE_submission_2975
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Dcr-2L811fsX; Tissue: Adult ovaries; Developmental Stage: Adult Female; Genotype: Dcr-2[L811fsX]; Sex: Female;  EXPERIMENTAL FACTORS: Tissue Adult ovaries


title: Dm 2-18hr non-irradiated embryos smallRNA RNA-Seq

summary:
modENCODE_submission_2971
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: w1118; Developmental Stage: 2-18hr embryo; Genotype: w[1118];  EXPERIMENTAL FACTORS: Developmental Stage 2-18hr embryo; Strain w1118


title: ago2[414] ovary total RNA

summary:
modENCODE_submission_2834
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Ago2 414; Tissue: Adult ovaries; Developmental Stage: Adult Female; Genotype: w;;ago2[414]; Sex: Female;  EXPERIMENTAL FACTORS: Tissue Adult ovaries


title: dcr-2[L811fsX] Ago1 Immunoprecipitation ovary

summary:
modENCODE_submission_2833
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RIP-seq

overall_design: EXPERIMENT TYPE: RIP-seq. BIOLOGICAL SOURCE: Strain: Dcr-2L811fsX; Developmental Stage: Adult Female; Genotype: Dcr-2[L811fsX]; Sex: Female;  EXPERIMENTAL FACTORS: Adult_ovaries


title: Lai - CMEL1/BS28

summary:
modENCODE_submission_2820
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: CME-L1; Tissue: ventral prothoracic disc; Developmental Stage: third instar larval stage; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line CME-L1


title: r2d2 ovary total RNA

summary:
modENCODE_submission_2748
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: r2d2 1; Tissue: Adult ovaries; Developmental Stage: Adult Female; Genotype: w; r2d2[1]; Sb/TM6B; Sex: Female;  EXPERIMENTAL FACTORS: Tissue Adult ovaries


title: Canton S Ago1 Immunoprecipitation

summary:
modENCODE_submission_2744
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RIP-seq

overall_design: EXPERIMENT TYPE: RIP-seq. BIOLOGICAL SOURCE: Strain: Canton S; Developmental Stage: Adult Female; Genotype: wild type; Sex: Female;  EXPERIMENTAL FACTORS: Adult_ovaries


title: Lai_embryo_12-24hr_BS61-64-67-73

summary:
modENCODE_submission_2742
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 14-16h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1];  EXPERIMENTAL FACTORS: Developmental Stage Embryo 14-16h; Strain Y cn bw sp


title: Drosophila melanogaster Canton-S small RNA sequence: Adult Male Body

summary:
modENCODE_submission_2751
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton S; Tissue: Male body; Developmental Stage: Adult male; Genotype: wild type; Sex: Male; EXPERIMENTAL FACTORS: Strain Canton S; Tissue Male body; Developmental Stage Adult male; Replicate type: biological;


title: Lai_CMEW1_Cl_8

summary:
modENCODE_submission_2721
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+


title: Lai_S2-DRSC/BS10/BS11

summary:
modENCODE_submission_3511
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-DRSC


title: Lai_ML-DmBG3-c2/BS179/BS180

summary:
modENCODE_submission_3510
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Replicate type: biological


title: Lai-one day adult male/BS149

summary:
modENCODE_submission_2008
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult male, eclosion + 1 day; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Male;  EXPERIMENTAL FACTORS: Developmental Stage Adult male, eclosion + 1 day; Strain Y cn bw sp


title: Lai-ML-DmBG1-c1/BS176/BS177

summary:
modENCODE_submission_3508
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmBG1-c1; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; EXPERIMENTAL FACTORS: Cell Line ML-DmBG1-c1; Replicate type: biological


title: Dm 2-18hr irradiated embryos smallRNA RNA-Seq

summary:
modENCODE_submission_2972
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq


title: Lai - MLDmD20c5/BS16

summary:
modENCODE_submission_2002
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmD20-c5; Tissue: antenna disc-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line ML-DmD20-c5


title: Lai_GM2/BS32/BS33

summary:
modENCODE_submission_3307
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: GM2; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line GM2


title: Lai_Sg4/BS34/BS35

summary:
modENCODE_submission_3506
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: Sg4; embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line Sg4; Replicate type: biological


title: Lai-one day adult female/BS152

summary:
modENCODE_submission_2009
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RNA-seq

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult female, eclosion + 1 day; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Female;  EXPERIMENTAL FACTORS: Developmental Stage Adult female, eclosion + 1 day; Strain Y cn bw sp


title: Drosophila melanogaster small RNA sequence

summary:
modENCODE_submission_3193
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: ML-Dm21; Tissue: dorsal mesothoracic disc; Developmental stage: third instar larval stage; Genotype: y v f mal; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line ML-Dm21; Replicate type: biological


title: Lai-1182-4H/BS22/BS23

summary:
modENCODE_submission_3742
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: 1182-4H; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: mh; Sex: Unknown; EXPERIMENTAL FACTORS: Cell Line 1182-4H; Replicate type: biological


title: Small RNA-seq from ENCODE/Cold Spring Harbor Lab

status: Public on Oct 08 2010

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Jonathan Preall jpreall@cshl.edu (Generation 0 Data from Hannon Lab), Carrie Davis davisc@cshl.edu (experimental), Alex Dobin dobin@cshl.edu (computational), Wei Lin wlin@cshl.edu (computational), Tom Gingeras gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

hg18: This data was produced by Hannon lab part of Cold Spring Harbor as part of the ENCODE Project. The series depicts NextGen sequencing information for RNAs between the sizes of 20-200 nt isolated from RNA samples from tissues or sub cellular compartments of cell lines.

hg19: This track depicts NextGen sequencing information for RNAs between the sizes of 20-200 nt isolated from RNA samples from tissues or sub cellular compartments from ENCODE cell lines. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome.
hg19: This cloning protocol generates directional libraries that are read from the 5' ends of the inserts, which should largely correspond to the 5' ends of the mature RNAs. The libraries were sequenced on a Solexa platform for a total of 36, 50 or 76 cycles however the reads undergo post-processing resulting in trimming of their 3' ends. Consequently, the mapped read lengths are variable.

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:
hg18: Small RNAs between 20-200 nt were ribominus treated according to the manufacturer's protocol (Invitrogen) using custom LNA probes targeting ribosomal RNAs (some datasets are also depleted of U snRNAs and high abundant microRNAs). The RNA was treated with Tobacco Alkaline Pyrophosphatase to eliminate any 5' cap structure. Poly-A Polymerase was used to catalyze the addition of C's to the 3' end. The 5' ends were phosphorylated using T4 PNK and an RNA linker was ligated onto the 5' end. Reverse transcription was carried out using a poly-G oligo with a defined 5' extension. The inserts were then amplified using oligos targeting the 5' linker and poly-G extension and containing sequencing adapters. The library was sequenced on an Illumina GA machine for a total of 36, 50 or 76 cycles. Initially 1 lane is run. If an appreciable number of mappable reads are obtained, additional lanes are run. Sequence reads underwent quality filtration using Illumina standard pipeline (Gerlad). The read lengths may exceed the insert sizes and consequently introduce 3' adaptor sequence into the 3' end of the reads. The 3' sequencing adaptor was removed from the reads using a custom clipper program, which aligned the adaptor sequence to the short-reads, allowing up to 2 mismatches and no indels. Regions that aligned were "clipped" off from the read. The trimmed portions were collapsed into identical reads, their count noted and aligned to the human genome (NCBI build 36, hg18 unmasked) using Nexalign (Lassmann et al., not published). The alignment parameters are tuned to tolerate up to 2 mismatches with no indels and will allow for trimmed portions as small as 5 nucleotides to be mapped. We report reads that mapped 10 or fewer times. Data obtained from each lane is processed and mapped independently. The processed/mapped data from each lane is then complied as a single track without additional processing and submitted to UCSC. Consequently, identical reads within a lane were collapsed and their value is reported as the "transfrag" signal value. However, the redundancy between lanes has not been eliminated so the same transfrag may appear multiple times within a signal.

hg19: Small RNAs between 20-200 nt were ribominus treated according to the manufacturer's protocol (Invitrogen) using custom LNA probes targeting ribosomal RNAs (some datasets are also depleted of U snRNAs and high abundant microRNAs). The RNA was treated with Tobacco Alkaline Pyrophosphatase to eliminate any 5' cap structures. Poly-A Polymerase was used to catalyze the addition of C's to the 3' end. The 5' ends were phosphorylated using T4 PNK and an RNA linker was ligated onto the 5' end. Reverse transcription was carried out using a poly-G oligo with a defined 5' extension. The inserts were then amplified using oligos targeting the 5' linker and poly-G extension and containing sequencing adapters. The library was sequenced on an Illumina GA machine for a total of 36, 50 or 76 cycles. Initially, one lane was run. If an appreciable number of mappable reads were obtained, additional lanes were run. Sequence reads underwent quality filtration using Illumina standard pipeline (GERALD). The Illumina reads were initially trimmed to discard any bases following a quality score less than or equal to 20 and converted into FASTA format, thereby discarding quality information for the rest of the pipeline. As a result, the sequence quality scores in the BAM output are all displayed as "40" to indicate no quality information. The read lengths may exceed the insert sizes and consequently introduce 3' adapter sequence into the 3' end of the reads. The 3' sequencing adapter was removed from the reads using a custom clipper program (available at http://hannonlab.cshl.edu/fastx_toolkit/), which aligned the adapter sequence to the short-reads using up to 2 mismatches and no indels. Regions that aligned were "clipped" off from the read. Terminal C nucleotides introduced at the 3' end of the RNA via the cloning procedure are also trimmed. The trimmed portions were collapsed into identical reads, their count noted and aligned to the human genome (version hg19, using the gender build appropriate to the sample in question - female/male) using Bowtie (Langmead B. et al). The alignment parameter allowed 0, 1, or 2 mismatches iteratively. We report reads that mapped 20 or fewer times. Discrepancies between hg18 and hg19 versions of CSHL small RNA data: The alignment pipeline for the CSHL small RNA data was updated upon the release of the human genome version hg19, resulting in a few noteworthy discrepancies with the hg18 dataset. First, mapping was conducted with the open-source Bowtie algorithm (http://bowtie-bio.sourceforge.net/index.shtml) rather than the custom NexAlign software. As each algorithm uses different strategies to perform alignments, the mapping results may vary even in genomic regions that do not differ between builds. The read processing pipeline also varies slightly, in that we no longer retain information regarding whether a read was 'clipped' off adapter sequence.

first: Tom

last: Gingeras

first: Katalin

last: Fejes-Toth

first: Vihra

last: Sotirova

first: Gordon

last: Assaf

first: Jonathan

last: Preall


title: Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: MNase-seq data

city: Boston

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the "default" chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy.

overall_design: Examination of MNase-digested mononucleosomal chromatin from untreated, mock-treated, and NELF-depleted Drosophila S2 cells.

first: Daniel

last: Gilchrist

first: Gilberto

last: Dos Santos

first: Leping

first: David

last: Fargo


title: Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias and copy number variation

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zuerich

type: Methylation profiling by genome tiling array

type: Methylation profiling by high throughput sequencing

summary: Abstract: DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation but in disease states such as cancer, the DNA methylation landscape is often deregulated.  There are now numerous technologies available to interrogate DNA methylation status of CpG sites in a targeted or genome-wide fashion but each method, due to intrinsic biases, potentially interrogates different fractions of the genome.  In this study, affinity-purification of methylated DNA using two popular genome-wide techniques: methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap) were evaluated, highlighting that each technique operates in a different domain of the CpG density landscape. The effect of whole genome amplification was explored, illustrating that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome.  Using MBDCap, microarray- and sequencing-based readouts were compared, highlighting the impact that copy number variation (CNV) can make in differential comparisons of methylomes.  These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed and consideration must be made in light of GC content, extent of DNA amplification and copy number.

overall_design: Comparison of MeDIP/MBD for DNA methylation profiling, comparison of whole genome amplification techniques, using tiling array for copy number aberration detection and comparisons of tiling array data to sequencing readouts

middle: D


title: Protein arginine methyltransferase AtPRMT5 is involved in pre-mRNA splicing in Arabidopsis thaliana

status: Public on Oct 07 2010

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

summary:
In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5.

Contributed by The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences

overall_design: Investigate the role of AtPRMT5 in pre-mRNA splicing

first: Xian

last: Deng

first: Lianfeng

last: Gu

first: Chunyan

last: Liu

first: Tiancong

last: Lu

first: Falong

first: Zhike

first: Peng

last: Cui

first: Yanxi

last: Pei

first: Baichen

last: Wang

first: Songnian

first: Xiaofeng

last: Cao


title: Combinatorial Transcriptional Control in Blood Stem/Progenitor Cells: Genome-wide Analysis of 10 major Transcriptional Regulators

first: Samuel

middle: David

last: Foster

state: Cambridgeshire

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

department: Department of Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

summary: Combinatorial transcription factor (TF) interactions control cellular phenotypes and therefore underpin stem cell formation, maintenance and differentiation. Here we report the genome-wide binding patterns and combinatorial interactions for 10 key regulators of blood stem/progenitor cells (Scl/Tal1, Lyl1, Lmo2, Gata2, Runx1, Meis1, Pu.1, Erg, Fli-1, Gfi1b) thus providing the most comprehensive TF dataset for any adult stem/progenitor cell type to date. Genome-wide computational analysis of complex binding patterns followed by functional validation revealed the following: First, a previously unrecognized combinatorial interaction between a heptad of TFs (Scl, Lyl1, Lmo2, Gata2, Runx1, Erg, Fli-1). Second, we implicate direct protein-protein interactions between four key regulators (Runx1, Gata2, Scl, Erg) in stabilising complex binding to DNA. Third, Runx1+/-::Gata2+/- compound heterozygous mice are not viable with severe haematopoietic defects at midgestation. Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells.

overall_design: 10 Samples (9 Transcription Factors and 1 Histone Modification) and 1 Control (IgG). All from the same cell line, a haematopoietic progenitor cell line (HPC-7).

first: Nicola

middle: K

last: Wilson

first: Xiaonan

first: Kathy

last: Knezevic

first: Judith

last: Schütte

first: Sarah

last: Kinston

first: Willem

last: Ouwehand

first: Elaine

last: Dzierzak

first: John

last: Pimanda

first: Marella

middle: F

last: de Bruijn

first: Berthold

last: Göttgens


title: Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation

first: Karen

last: Adelman

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Daniel

last: Gilchrist

first: Gilberto

last: Dos Santos

first: Yuan

last: Gao

first: Leping

last: Li

first: David

middle: C

last: Fargo


title: Gastrointestinal stromal tumor GIST: gene expresssion and ChIP analyses

status: Public on Oct 14 2010

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center


title: Ago2[414] Ago1 Immunoprecipitation

first: DCC

last: modENCODE

summary:
modENCODE_submission_2746
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: RIP-seq

overall_design: EXPERIMENT TYPE: RIP-seq. BIOLOGICAL SOURCE: Strain: Ago2 414; Developmental Stage: Adult Female; Genotype: w;;ago2[414]; Sex: Female;  EXPERIMENTAL FACTORS: Adult_ovaries

first: Eric

last: Lai

first: Gregory

last: Hannon


title: Gene expression profiling of human tissue samples using SAGE-Seq

status: Public on Oct 05 2010

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around 5 million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less abundant genes including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

overall_design: Global transcriptome profilings of 7 samples in normal and 7 samples in cancer from clinical breast tissue using Sage-Seq

first: Xiaole

middle: S

last: Liu

first: Zhenhua

last: Wu

first: Clifford

last: Meyer

first: Sibgat

last: Choudhury

first: Michail

last: Shipitsin

first: Reo

last: Maruyama

first: Marina

last: Bessarabova

first: Tatiana

last: Nikolskaya

first: Saraswati

last: Sukumar

first: Armin

last: Schwartzman

first: Jun


title: High throughput sequencing of Piwi bound piRNAs from Drosophila ovaries in which key factors for primary piRNA biogenesis in somatic support cells were knocked down using RNAi

status: Public on Oct 04 2010

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: In Drosophila, PIWI proteins and bound PIWI interacting RNAs (piRNAs) form the core of a small RNA mediated defense system against selfish genetic elements. Within germline cells piRNAs are processed from piRNA clusters and transposons to be loaded into Piwi/Aubergine/AGO3 and a subset of piRNAs undergoes target dependent amplification. In contrast, gonadal somatic support cells express only Piwi, lack signs of piRNA amplification and exhibit primary piRNA biogenesis from piRNA clusters. Neither piRNA processing/loading nor Piwi mediated target silencing is understood at the genetic, cellular or molecular level. We developed an in vivo RNAi assay for the somatic piRNA pathway and identified the RNA helicase Armitage, the Tudor domain containing RNA helicase Yb and the putative nuclease Zucchini as essential factors for primary piRNA biogenesis. Lack of any of these proteins leads to transposon de-silencing, to a collapse in piRNA levels and to a failure in Piwi nuclear accumulation. We show that Armitage and Yb interact physically and co-localize in cytoplasmic Yb-bodies, which flank P-bodies. Loss of Zucchini leads to an accumulation of Piwi and Armitage in Yb-bodies indicating that Yb-bodies are sites of primary piRNA biogenesis.

overall_design: small RNA libraries were prepared from Piwi immuno-precipitates of five different genotypes

first: Daniel

last: Olivieri


title: Genome wide localization of Activation induced cytidine deaminase (AID), Spt5, and RNA Polymerase II (PolII) in mouse

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Activation induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes. Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these key transactions little is known about how AID finds its target sites. To examine AID regulation we performed an shRNA screen. We found that Spt5, a factor associated with paused RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for class switch recombination (CSR).  Spt5 interacts with AID, it is required for the association of AID and Pol II, and for AID recruitment to switch regions. ChIP-seq experiments reveal that Spt5 co-localizes with AID and stalled Pol II. Further, Spt5 accumulation at sites of Pol II pausing is predictive of AID-induced mutation. Our data suggest that Spt5 acts as an adaptor, which brings AID to Pol II on target DNA.

overall_design:
PolII, AID, and Spt5 were immunoprecipitated from in vitro activated B cells.  For Spt5 and AID, two different antibodies were used in separate, biological replicates.

Notes:  Peaks of enrichment relative to a random background model were identified with SICER 1.03 (Zhang et al., 2009).  For AID, the parameters used were window size = 100, gap size = 100, e = 0.000001, redundancy = 1, fragment size   = 127 (AID+/+, ab1), 115 (AID-/-, ab1), and 125 (AID+/+, ab2).  Fragment size estimates were calculated from the data based on a shifting algorithm that attempts to minimize a Shannon entropy measure.  Read counts were adjusted for library size and are given as reads per million non-redundant aligned reads (RPM). Densities were then filtered to only display windows falling onto enriched regions as identified by SICER.  AID-/- densities were additionally scaled by a factor of 0.592 to correct for an overestimation of background levels at 104 genes that displayed higher read densities in AID-/- cells than AID+/+ cells.  Corrected values were used to calculate RPKM values in Table S1 of Yamane et al. (PMID 21113164) and for display in browser tracks. Please note a typo in Fig. 1a of Yamane et al. (PMID 21113164) where the Y axes of AID+/+ and AID-/- samples should read 0.15-1.2, instead of 0-1.2.

first: Anna

last: Gazumyan

first: Arito

last: Yamane

first: Bernardo

last: San-Martin

first: Camilo

last: Ansarah-Sobrinho

first: David

last: Root

first: Davide

last: Robbiani

first: Hong-wei

last: Sun

first: Isaac

last: Klein

first: Michel

last: Nussenzweig

first: Michela

last: Di Virgilio

first: Mila

last: Jankovic

last: Kuo

first: Rafael

last: Casellas

first: Rushad

last: Pavri

first: Thomas

last: Neiland

first: Vasco

last: Barreto

first: Wolfgang

last: Resch

first: Zhiyu

last: Li


title: Comprehensive analysis of orphan CpG islands identifes novel promoters with conserved DNA methylation dynamics

city: Edinburgh

first: Adrian

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

institute: The University of Edinburgh

summary: We report the application of single molecule-based sequencing technology in combination with CXXC affinity purifcation (CAP-seq), MBD affinity purification (MAP-seq) and chromatin immunoprecipitation (ChIP-seq) to generate reciprocal methylation and chromatin modifcation maps in human and mouse. We find that contrary to sequence based prediction methods that humans and mice possess highly equivalent compliments of CpG islands (CGIs). The majority of these CGIs are positive for the active histone modification; H3K4me3 in embryonic stem cells (ES cells) the magnitude of which is correlated with the local density of non-methylated CpG. Approximately half of the human and mouse CGIs are distal to annotated gene promoters, yet more than 40% identify unanticipated transcription start sites as defined by RNA polymerase occupancy and published RNA mapping data. These orphans CGIs preferentially acquire DNA methylation in somatic cells, and this corresponds with a loss of H3K4me3 and RNA polymerase II at these sites. Conversely abnormal CGI methylation found in colorectal tumours showed a distinct distribution relative to that found in normal somatic tissues displaying preferential association with loci marked by H3K27me3 in human ES cells. This study provides a comprehensive functional assessment of CGIs in normal and diseased tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of CGI methylation status in human and mouse primary tissues.

first: Robert

last: Illingworth

first: Ulrike

last: Gruenewald-Schneider

first: Shaun

last: Webb

first: Alastair

last: Kerr

first: Keith

last: James

first: Daniel

last: Turner

first: Colin

last: Smith

last: Harrison

last: Andrews


title: Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

summary: The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation requires formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we use high-throughput sequencing to interrogate all base-paired RNA in Arabidopsis thaliana, and identify ~200 new small (sm)RNA-producing substrates of RNA-DEPENDENT RNA POLYMERASE 6. Our comprehensive analysis of paired RNAs reveals conserved functionality within introns and both 5’ and 3’ untranslated regions (UTRs) of mRNAs, as well as a novel population of functional RNAs, many of which are the precursors of smRNAs. Finally, we identify intra-molecular base-pairing interactions to produce a genome-wide collection of RNA secondary structure models. These findings highlight the importance of base-paired RNAs in eukaryotes, and present an approach that should be widely applicable for the analysis of this key structural feature of RNA.

overall_design: Double-stranded (dsRNA) specific RNA sequencing (dsRNA-seq) in the unopened flowerbuds of wild-type col-0 plants and rdr6 mutant plants, including 2 samples of col-0 dsRNA (1X- or 2X- Ribominus-treated samples) and 1 sample of rdr6 dsRNA. Corresponding two smRNA libraries (smRNA-seq) of both wild-type col-0 plants and rdr6 mutant plants of the same tissue are also presented.

first: Paul

last: Ryvkin

first: Fan

first: Isabelle

last: Dragomir

first: Otto

last: Valladares

first: Jaime

last: Yang

first: Kajie

last: Cao

first: Li-San

last: Wang

first: Brian

last: Gregory


title: H3K27me3, H3K79me2, and Suz12 ChIP-Seq in Human Embryonic Stem Cells (BG03).

status: Public on Oct 01 2010

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

summary: H3K27me3 is a chromatin modification depositied by Suz12, a component of the Polycomb Group 2 complex, and is associated with transcriptional repression. In contrast, H3K79me2 is a chromatin modification associated with active gene transcription.  It is deposited by the histone methyltransferase Dot1L and generally is localized just downstream of the transcriptional start site and extends down the body of the gene.  To gain insight into the transcriptional state of genes in hES cells, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide occupancy of the H3K27me3 and H3K79me2 chromatin modifications and genome-wide occupancy of the Suz12.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing A sample of whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against H3K27me3, H3K79me2, and Suz12 (Abcam).

first: Rahl

last: Peter


title: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (high-throughput sequencing)

status: Public on Sep 30 2010

city: Los Angeles

first: Yi

last: Sun

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

summary: MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as post-transcriptional regulators of gene expression. Many miRNAs are expressed in the developing brain and regulate multiple aspects of neural development including neurogenesis, dendritogenesis and synapse formation. Rett syndrome (RTT) is a progressive neurodevelopmental disorder caused by mutations in the gene encoding Methyl-CpG binding protein 2 (MECP2). While Mecp2 is known to act as a global transcriptional regulator, miRNAs that are directly regulated by Mecp2 in the brain are not known.  Using massively parallel sequencing methods, we have identified miRNAs whose expression is altered in cerebella of Mecp2-null mice before and after the onset of severe neurological symptoms.  In vivo genome-wide analyses indicate that promoter regions of a significant fraction of dys-regulated miRNA transcripts, including a large polycistronic cluster of brain-specific miRNAs, are DNA methylated and directly bound by Mecp2. Functional analysis demonstrates that the 3’ untranslated region (UTR) of messenger RNA encoding Brain-derived neurotrophic factor (Bdnf) can be targeted by multiple miRNAs aberrantly up-regulated in absence of Mecp2.  Taken together, these results suggest that dys-regulation of miRNAs may contribute to RTT pathoetiology, and also provide a valuable resource to further investigate the role of miRNAs in RTT.

overall_design: Two pooled total RNA samples (4 pairs of wild-type (WT) and Mecp2-null (KO) male mice; postnatal 6-week, the pre-/early-symptomatic stage) were sequenced in a multiplexed configuration (with distinct barcode sequences). And, six samples (two litters, one WT and two KO male mice in each litter; postnatal 8-week, the symptomatic stage) were sequenced individually.

first: Hao

last: Wu


title: ChIP-Seq data in secondary fibroblast with dox-inducible cassettes for Oct4, Sox2 and Klf4.

summary: The conversion of fibroblasts to induced pluripotent stem cells (iPS) by forced expression of Oct4, Sox2 and Klf4 is among the earliest demonstrations of reprogramming to a pluripotent state by forced expression of transcription factors. To gain insights into the transcriptional state of genes required for reprogramming, we profiled RNA polymerase II, H3K27me3 and E2F4.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibodies to RNA polymerase II, H3K27me3 and E2F4.

first: Steve

last: Bilodeau


title: Mapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).

first: Yu

last: Chen

summary: ETV1 is highly expressed in GIST and their presumed precursors--the interstitial cells of Cajal. ETV1 is required for survival for both GIST and ICC and regulates GIST signature genes. Here, using Illumina-Solexa based next-generation sequencing of ETV1 chromatin immunoprecipates (ChIP-Seq), we define ETV1 binding sites in the GIST48 cell line.

overall_design:
Crosslinked ChIP using input control ETV1 ChIP in GIST48 cells.
Details: GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with anti-ETV1 antibody (Abcam Ab81086, Lot 787879), washed, eluted, reverse cross-linked, and purified. Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer. All reads (~36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline. Unique reads mapped to a single best-matching location with no more than two mismatches were kept and used to generate genome-wide distribution of ETV1-binding and for peak identification. Redundant reads were considered once.

first: Ping

last: Chi

first: Deyou

first: C

last: Allis

first: Charles

middle: L

last: Sawyers


title: Protein profiling reveals five principal chromatin types in Drosophila cells

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary:
The local protein composition of chromatin is important for the regulation of transcription and other functions. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin types that are defined by unique, yet overlapping combinations of proteins, and form domains that can extend over >100 kb. We identify a novel repressive chromatin type that covers about half of the genome and lacks classic heterochromatin markers. Furthermore, transcriptionally active euchromatin consists of two distinct types that differ in molecular organization and H3K36 methylation, and regulate distinct classes of genes. Finally, we provide evidence that the different chromatin types act as guides that help to target DNA-binding factors to specific subsets of their recognition motifs. These results uncover basic principles of chromatin organization in a higher eukaryote.
For this study, we generated whole-genome DamID binding profiles of 45 chromatin proteins in Drosophila Kc167 cells. Additionally, we perused published binding data of 8 chromatin proteins and generated a binding profile of one exogenous (yeast) DNA binding factor in Kc167 cells. On the same array platform, we obtained ChIP-on-chip profiles of histone H3, H1, H3K9me2, H3K27me3, H3K4me2, and H3K79me3. See supplementary files below.  Gene expression was measured by RNA tag profiling.  See GeneCounts supplementary file below.

overall_design:
[1] RNA tag sequences were optained on an Illumina GAII with the digital gene expression (DGE) module from duplicate RNA samples.

[2] All DamID and ChIP experiments were done in Drosophila Kc167 cells in duplicate. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation, where Dam-fusion material was hybridized over Dam-only material. For ChIP, immunoprecipitated material was hybridized over ChIP input material.
18 previously-submitted Samples were included in this study.
10 of 18 Samples have been renormalized for the GSE22069 study:
GSM509087, GSM509088, GSM509089, GSM509090, GSM509091, GSM509092, GSM509093, GSM509094, GSM509095, GSM509096
New GSM accession numbers have been issued for these 10 samples.
8 of 18 Samples are identical in the original studies and in GSE22069:
GSM423290, GSM423291, GSM423298, GSM423299, GSM493592, GSM493593, GSM509085, GSM509086

[3] The genomic locations in files
GSE22069_norm_aggregated_discretized_tiling_arrays.txt
and GSE22069_norm_aggregated_tiling_arrays.txt are relative to FlyBase release 5 (BDGP R5/dm3).

first: Guillaume

last: Filion

first: Joke

last: van Bemmel

first: Ulrich

last: Braunschweig

first: Wendy

last: Talhout

first: Jop

last: Kind

first: Luke

last: Ward

first: Wim

last: Brugman

first: Ines

last: de Castro Genebra de Jesus

first: Ron

last: Kerkhoven

first: Harmen

last: Bussemaker


title: Epigenomic profiling of 3T3-L1 adipogenesis

first: Tarjei

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary: 3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogenic media.

overall_design: Examination of 6 histone modifications and CTCF at 4 time points and PPARG at 1 time point using ChIP-Seq

first: Zhao

last: Xu

first: Jeffrey

last: Gimble

first: Eric

last: Lander

first: Evan

last: Rosen


title: Unbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression

status: Public on Sep 28 2010

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation and disease.  To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse liver, and for livers of male mice feminized by continuous infusion of growth hormone (GH).  We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-differences.  Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male liver.  We also identified broad genomic regions (up to ~100kb) showing sex-dependent hypersensitivity and similar patterns of GH response. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100kb from sex-specific genes.  By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism, and several new candidates for further investigation.  This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions.

overall_design: Global DNase Hypersensitivity in male, female, and continuous growth hormone-treated male mouse liver tissue. 10 samples: Male liver (2 replicates), Female liver (2 replicates), GH-treated male liver (2 replicates), DNase digested genomic control (from male and female liver separately) and sonicated genomic control (from male and female liver separately).

first: Guoyu

last: Ling

first: Aarathi

last: Sugathan

first: Tali

last: Mazor

first: Ernest

last: Fraenkel


title: The Drosophila melanogaster Transcriptome by Paired-End RNA-Sequencing

status: Public on Sep 24 2010

city: Houston

first: Bryce

last: Daines

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages.  In total, 142.2 million uniquely mapped 64-100bp paired-end reads were generated on the Illumina GA II yielding 356x sequencing coverage.  More than 95% of FlyBase genes and 90% of splicing junctions were observed.  Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events.  A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation.  Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms.  Much of this splicing is subtle such as tandem alternate splice sites.

overall_design: Poly(A)+ transcripts from 10 distinct stages during the live cycle of D. melanogaster were isolated to generated cDNA libraries which were sequenced on the Illumina GA II instrument.

first: Rui

last: Chen


title: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome

first: Yi

last: Sun

type: Non-coding RNA profiling by genome tiling array


title: Comparative Epigenomic Analysis of Murine and Human Adipogenesis


title: Global Changes following N-deprivation in Chlamydomonas

status: Public on Sep 25 2010

city: East Lansing

first: Guangxi

last: Wu

state: MI

address: S308 Plant Bio Bld

institute: Michigan State University


title: Global Changes following N-deprivation in Chlamydomonas: 454 sequencing

summary: Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient-deprived. To begin studying the mechanisms underlying this process, N-deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and non-induced conditions was applied as a first approach to study molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment.  Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of 8 biologically independent libraries (2 454 libraries, 6 Illumina libraries), four for each condition, N-replete and N-deprived, that allowed a statistically sound comparison of expression levels under the two tested conditions. Inferences on metabolism based on transcriptional analysis can only be indirect but were supported in parts by biochemical experiments. N-deprivation led to a marked redirection of metabolism as the carbon source acetate was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogensis, but funneled directly into fatty acid biosynthesis. Protein biosynthesis and photosynthesis were down-regulated and genes of gametogenesis activated.  A notable finding was that the genes encoding photosynthetic accessory PSBS proteins of currently unclear function in C. reinhardtii were strongly expressed following N-deprivation, providing a clue to their physiological role. Lipase-encoding genes were found to be some of the most regulated following N-deprivation, suggesting a remodeling of membranes under these conditions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae.

overall_design: Examing N-replete and N-deprived conditions. One biological replicate each condition.

first: Christoph

last: Benning


title: modENCODE_White Lab: genome-wide ChIP data of KW4-CG8478-D1 from E8-16h on Illumina Genome Analyzer.

status: Public on Sep 16 2010

first: Kevin

last: White

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

institute: University of Chicago

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 genome-wide binding profile of the factor KW4-CG8478-D1 from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

overall_design:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study.

first: Nicolas

last: Negre

first: Nicholas

last: Bild

middle: P


title: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E1-6h on Illumina Genome Analyzer.

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 genome-wide binding profile of the factor NW-GFP-Goat[eve] from E1-6h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[Dfd] from E0-8h on Illumina Genome Analyzer.

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 genome-wide binding profile of the factor NW-GFP-Goat[Dfd] from E0-8h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Chromatin enrichment of TRIM24, estrogen receptor and H3K4me2 in estrogen-treated and -untreated MCF7 cells

status: Public on Sep 17 2010

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary: TRIM24 PHD-Bromo domains exhibit preferential binding to unmethylated H3K4 and acetylated H3K27.  TRIM24 is a co-activator of estrogen receptor (ER).  The results suggest that specific ER-binding sites are depleted of H3K4me2 with estrogen treatment.  TRIM24 binds these sites preferentially and facilitates ER-regulated gene expression, cell survival and proliferation.

overall_design: ChIP performed on MCF7 cells +/- estrogen with antibodies against ER, TRIM24 and H3K4me2.  ChIP assays of ER, co-activator TRIM24 and H3K4me2 were performed with two concentrations of antibody, without and 6h with estrogen treatment of MCF7 cells. Antibody-enriched samples were sequenced two times, and compared to an IgG negative control and Input. Enriched DNA sequenced by Illumina Solexa.

first: Michelle

last: Barton

first: Kadir

last: Akdemir

first: Curtis

last: Jameson

first: Mehdi

last: Keddache

first: Teresa

middle: T

last: Yiu


title: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[tll] from E0-4h on Illumina Genome Analyzer.

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 genome-wide binding profile of the factor NW-GFP-Goat[tll] from E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Deep sequencing analysis of transcription-induced chimeras in human prostate adenocarcinoma and reference samples

status: Public on Sep 23 2010

city: South San Francisco

first: Thomas

middle: D.

address: 1 DNA Way

institute: Genentech, Inc.

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene profiling of TRA1 and tra1-L3733A

status: Public on Sep 20 2010

city: London

first: Christopher

last: Brandl

address: 1151 Richmond St.

department: Biochemistry

institute: University of Western Ontario

summary: Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase kinase family that contain a C-terminal PI3K domain followed by a 35-residue FATC domain. We analyzed alleles with single residue changes in the FATC domain. Of these tra1-L3733A had the most pronounced effects, resulting in phenotypes similar but not identical to those resulting from mutations in the PI3K domain or SAGA or NuA4 components. To analyze the transcriptional effects of the tra1-L3733A allele, we performed gene profiling of wild-type and tra1-L3733A strains. Expression of 11 genes was elevated ≥ 2-fold, 79 genes were decreased ≥ 2-fold. Of the 11 genes with elevated expression, four (HSP26, PIR3, DDR2 and GRE1) have roles in cellular stress response. The only gene ontology process significantly enriched in the genes with decreased expression greater than 2-fold was lysine biosynthesis (GO: 0009085). Broader analysis of gene ontology processes revealed expression of genes involved in cellular respiration (GO:0045333) and the overlapping process generation of precursor metabolites and energy (GO: 0006091) showed an average upward shift of ~10% relative to the total collection of genes. A similar trend of less magnitude was seen for vitamin metabolic processes (GO:0006766). A slight downward shift was seen for genes involved in translation (GO:0006412) and membrane organization (GO:0016044).

overall_design: Examination of gene expression changes in tra1-L3733A

first: Stephen

last: Hoke

first: Ana

middle: I

last: Mutiu

first: Julie

last: Genereaux

first: Michael

last: Buck

last: Yu

first: Gregory

middle: B

last: Gloor


title: Polymorphic cis- and trans-regulation of human gene expression

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Expression levels of human genes vary extensive among individuals.  Gene expression determines cell function and characteristics thus this variation likely contributes to phenotypic variation.  Genetic studies have shown that there is a heritable component to gene expression variation, and have identified genomic regions that contain polymorphic regulators.  However, most of these regions are quite large, and few regulators have been identified.  In this genetic of gene expression study, we used a large sample to search the genome for polymorphic regulators that influence gene expression, and followed up the results with deep sequencing of transcriptomes and molecular analyses.
Key word(s): Transcriptome Analysis

overall_design: genetics of gene expression study, 41 Coriell cell line samples examined.

first: Vivian

last: Cheung


title: Elucidating the stromal expression pattern in response to tumor-derived Shh

city: berkeley

first: henk

last: roelink

address: 16 barker hall

department: MCB

institute: UC Berkeley

summary: Most tumors of the upper gastrointestinal tract are known to depend on an excessive expression of Shh. It was recently discovered that this Shh does not signal on the tumor cells, but rather the stromal cells that in turn produce an unknown set of reciprocal signals that act as growth- or survival cues for the tumor cells. This sequencing effort aims to identify the reciprocal signals.

overall_design: Mouse fibroblasts and Shh-expressing human pancreatic adenocarcinoma cells were either grown alone, or in a non-adherent coculture system. To be able to assess the effect of Shh on fibroblast gene expression (being the reciprocal signal), 5E1 blocking antibody was added to the cells and after 5 days, RNA was isolated. n=1

first: Maarten

last: Bijlsma

first: Henk

last: Roelink


title: Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples

last: Wu

summary: Prostate adenocarcinoma and matched adjacent normal samples were profiled by deep transcriptional sequencing to analyze transcription-induced chimeras and gene fusions.  Reference samples from the MAQC and brain and universal reference libraries were also sequenced.

overall_design: Two-condition experiment plus reference samples: Prostate adenocarcinoma versus matched normal from three separate patients, plus brain and universal reference samples from the MAQC project.

first: Somasekar

last: Seshagiri

first: Gary

last: Schroth

first: Irina

last: Khrebtukova


title: Characterization of the single-cell transcriptional landscape by highly multiplex RNA-Seq

status: Public on Sep 21 2010

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constitutent cell types. Here we propose a novel strategy to access such complex samples. Hundreds of single-cell RNA-Seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data was projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves—all without need for known markers to classify cell types. The feasibility of the strategy is demonstrated by analyzing the complete transcriptomes of 436 single cells of three distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology and disease.

overall_design: Comparison of single-cell mRNA expression in 436 single cells from three cell types

first: Saiful

last: Islam

first: Una

last: Kjällquist

first: Annalena

last: Moliner

first: Jian-Bing

last: Fan


title: Comparison of GNC and GNL Overexpression with ga1 and pif1345

status: Public on Sep 15 2010

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

country: Germany

institute: Claus Schwechheimer

summary:
We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 5 days-old Arabidopsis ga1 mutants, pif1345 mutants (Leivar et al., 2008) and transgenic lines overexpressing the regulators GNC and GNL/CGA1 to the wild type. All mutants or transgenic lines are in the Columbia-0 background.
Three independent biological samples were prepared for each genotype.

overall_design: Three replicate measurements of three biological samples were prepared for each genotype.

first: Carina

last: Behringer

first: René

last: Richter


title: Next Gen(etics): targeted genome enrichment and next-generation sequencing enhances phenotype-driven forward genetics and gene-driven reverse genetics

status: Public on Sep 13 2010

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

type: Genome variation profiling by high throughput sequencing

summary: Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest.

first: Isaac

last: Nijman


title: Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers

status: Public on Sep 08 2010

city: Cambridge

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

summary:
Aneuploidy is a hallmark of human cancers, but most mouse cancer models lack the extensive aneuploidy seen in many human tumors. The zebrafish is becoming an increasingly popular model for studying cancer. Here we report that malignant peripheral nerve sheath tumors (MPNSTs) that arise in zebrafish as a result of mutations in either ribosomal protein (rp) genes or in p53 are highly aneuploid. Karyotyping reveals that these tumors frequently harbor near-triploid numbers of chromosomes, and they vary in chromosome number from cell-to-cell within a single tumor. Using array CGH (aCGH) we found that, as in human cancers, certain fish chromosomes are preferentially over-represented while others are under-represented in many MPNSTs. In addition, we detected evidence for recurrent sub-chromosomal amplifications and deletions that may contain genes involved in cancer initiation or progression. One striking amplification included the c-met proto-oncogene. Our results suggest that the zebrafish may be a valuable model in which to study aneuploidy in human cancer and in which to identify candidate genes that may act as drivers in fish and potentially also in human tumors.

For GSM587250-GSM587255: This Illumina sequencing data is for validation of a larger array-CGH dataset (GSM580580-GSM580621).

overall_design:
For GSM580580-GSM580621: Two-condition (x3) experiment: (1) genomic DNA: MPNST (rp gene mutation) vs normal tail : 31 replicates; (2) MPNST (p53 mutation) vs normal tail: 5 replicates; (3) normal tail vs. normal tail (6 replicates)

For GSM587250-GSM587255: Six samples total, in three pairs of tumor (MPNST) and normal tail control

first: GuangJun

last: Zhang

first: Adam

last: Amsterdam

first: Charles

last: Whittaker

first: Jacqueline

last: Lees

first: Nancy

last: Hopkins