title: Correlation of global micro RNA expression with basal cell carcinoma subtype

first: Christopher

last: Heffelfinger

state: Ct

address: 333 Cedar Street

summary: Basal cell carcinomas (BCCs) are the most common cancers in the US.  Histologic appearance distinguishes several subtypes, each of which can have a different biologic behavior.  In this study global miRNA expression was quantified by high throughput sequencing in nodular BCCs, a subtype that is slow growing, and infiltrative BCCs, aggressive tumors that extend through the dermis and invade structures such as cutaneous nerves.  Principal components analysis correctly classified seven out of eight infiltrative tumors on the basis of miRNA expression.  The remaining tumor, on pathology review, contained a mixture of nodular and infiltrative elements.  Nodular tumors did not cluster tightly, likely reflecting broader histopathologic diversity in this class, but trended toward forming a group separate from infiltrative BCCs.  qPCR assays were developed for six of the miRNAs that showed significant differences between the BCC subtypes, and five of these six were validated in a replication set of four infiltrative and three nodular tumors.  The expression level of miR-183, a miRNA that inhibits invasion and metastasis in several types of malignancies, was consistently lower in infiltrative than nodular tumors and could be one element underlying the difference in invasiveness.  These results represent the first miRNA profiling study in BCCs and demonstrate that miRNA gene expression may be involved in tumor pathogenesis and particularly in determining the aggressiveness of these malignancies.

overall_design: Total RNA was extracted from eight nodular and eight infiltrative basal cell carcinomas. miRNA was then processed into libraries using the Illumina Small RNA Ver 1.5 protocol. Samples were then sequenced on the Illumina GAII system

middle: E

first: Allen

last: Bale

first: Michael

last: Snyder


title: Genome-wide maps of AR binding in prostate cancer cell lines VCaP and VCS2

status: Public on Feb 01 2012

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the high-throughput profiling of AR binding in prostate cancer cells.

overall_design: Examination of AR binding in prostate cancer cell lines VCaP and VCS2

first: Changmeng

last: Cai

middle: H

first: Myles

last: Brown

first: Steven

middle: P

last: Bulk


title: AR binding in prostate cancer cell lines VCaP and VCS2

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

overall_design: Refer to individual Series


title: Genome-wide maps of H3R2me2s in pro-B cells

status: Public on Feb 02 2012

city: Boston

first: Mark

middle: L

last: Borowsky

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: MGH

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3R2me2s in mouse pro-B cells. We find that H3R2 symmetric dimethylation and H3K4 trimethylation colocalized throughout the genome of mouse pro-B cells.

overall_design: Examination of 2 different histone modifications in mouse pro-B cells

first: Chih-Chi

last: Yuan

first: Adam

middle: G

last: Matthews

first: Yi

last: Jin

first: Changfeng

last: Chen

first: Brad

middle: A

last: Chapman

first: Toshiro

middle: K

last: Osumi

first: Karen

middle: C

last: Glass

first: Tatiana

last: Kutateladze

first: Kevin

last: Struhl

first: Marjorie

last: Oettinger


title: Dramatic effects of social behavior on gene regulation in rhesus macaques [Bisulfite seq]

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

type: Methylation profiling by high throughput sequencing

summary: These data are a component of a larger study investigating differences in gene regulation in relationship to rhesus macaque dominance rank. These data compare DNA methylation levels between individuals of different rank on a genome-wide scale using bisulfite sequencing

overall_design: DNA from peripheral blood mononuclear cells sampled from 3 high ranking individuals and 3 low ranking individuals (all adult female rhesus macaques)

first: Yoav

last: Gilad


title: Identification of Transcription Factor CES1::GFP Binding Regions in L3

status: Public on Jan 31 2012

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3081
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ces-1; Strain OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Dramatic effects of social behavior on gene regulation in rhesus macaques

last: Tung

platform_organism:
Macaca mulatta
Homo sapiens


title: Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice is dependent on LXR and correlates with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the role of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligand-regulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. Functional annotation of putative direct LXR target genes revealed a significant association with classical LXR-regulated pathways as well as PPAR signaling pathways, and subsequent ChIP-seq mapping of PPARα binding demonstrated binding of PPARα to 71-88% of the identified LXR:RXR binding sites. Sequence analysis of shared binding regions combined with sequential ChIP on selected sites indicate that LXR:RXR and PPARα:RXR bind to degenerate response elements in a mutually exclusive manner. Together our findings suggest extensive and unexpected cross-talk between hepatic LXR and PPARα at the level of binding to shared genomic sites

overall_design: LXR, RXR, PPARalpha and RNA Polymerase II ChIP-seq on livers from female C57BL/6 wild-type and/or LXRα/β-deficient mice (13 weeks of age, n=1) treated by oral gavage once daily for 14 days with the RXR agonist bexarotene (100 mg/kg body weight [mpk], in 1% carboxymethylcellulose), the LXR agonist T0901317 (T09, 30 mpk) or vehicle alone.

first: Michael

last: Boergesen

first: Barbara

last: Gross

first: Simon

middle: J

last: van Heeringen

first: Dik

last: Hagenbeek

first: Christian

last: Bindesbøll

first: Sandrine

last: Caron

first: Fanny

last: Lalloyer

first: Knut

middle: R

last: Steffensen

first: Hilde

middle: I

last: Nebb

first: Jan-Åke

last: Gustafsson

first: Hendrik

last: Stunnenberg

first: Bart

last: Staels


title: Identification of Transcription Factor GEI-11::GFP Binding Regions in L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_3066
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

last: Reinke


title: Pyrococcus furiosus crRNAs associated with the Cas RAMP module complex

city: Farmington

first: Brenton

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

type: Expression profiling by high throughput sequencing

summary: Analysis of CRISPR RNAs from both total Pyrococcus furiosus RNA and those that co-purify with the Cmr complex, which has been predicted to be involved in RNA-mediated targeting of foreign RNAs in prokaryotes.  Small RNAs (20 - 70 nts) were isolated either from total Pyrococcus furiosus RNA or RNAs isolated from immunopurified Cmr complexes.  The RNAs were cloned and sequenced using the Illumina platform.  Results provide insight into the anatomy of Cmr2-associated CRISPR RNAs.

overall_design: 2 Samples: total small RNAs vs Cmr2-associated small RNAs

first: Caryn

last: Hale

first: Sonali

last: Majumdar

first: Joshua

last: Elmore

first: Neil

last: Pfister

last: Compton

first: Sara

last: Olson

first: Alissas

middle: M

last: Resch

first: Claiborne

middle: V

last: Glover III

first: Rebecca

last: Terns

first: Michael


title: Deep-sequencing of total RNA from manually dissected wild-type Arabidopsis embryos at the globular stage

status: Public on Jan 26 2012

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

summary: This dataset provide deep-profiling of the embryonic transcriptome of total RNA at the globular stage in Arabidopsis. Embryos were derived from a cross between Col0 (mother) and Ler (father). Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm. For details on the method, see PMID: 21620136.

overall_design: 1 sample: cross between Col0 and Ler

first: Célia

last: Baroux

last: Raissig

first: Ueli

last: Grossniklaus

last: Wittig

first: Philip

last: Rosenstiel


title: mRNA-Seq of central cells from the Arabidopsis thaliana female gametophyte

summary: This dataset provides the transcriptome of the central cell of the female gametophyte from Arabidopsis thaliana.

overall_design:
We sequenced two biological replicates. Each replicate started with a pool of 450 central cells collected using laser-assisted microdissection (LAM). Libraries were prepared as described in DOI:10.1038/NMETH.1315. Each library was sequenced on one eight of a slide on the AB SOLiD platform (version 3).

IMPORTANT: In the alignment files (.bam), we named the mitochondrial and the chloroplastidial chromosomes ChrM and ChrC. This is different from the "chloroplast" and "mitochondrium" names in the whole genome fasta file available on TAIR.

middle: W

first: Anja

last: Schmidt

first: Ulrich

last: Klostermeier

first: Matthias

last: Barann


title: Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

status: Public on Jan 25 2012

city: Leiden

first: Anastasios

last: Mastrokolias

address: LUMC, Building 2 Einthovenweg 20 2333 ZC Leiden

country: Netherlands

institute: Leiden University Medical Center

summary: Transcriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides robust, comparable and highly informative expression profiling data, with several million of tags per blood sample, reticulocyte globin transcripts can constitute up to 76% of total mRNA compromising the detection of low abundant transcripts. We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression.

overall_design: Comparison of 6 whole blood RNA samples versus their globin reduced counterparts

first: A

first: J

middle: T

last: den Dunnen

first: G

last: van Ommen

first: P

last: ’t Hoen

first: W

last: van Roon-Mom


title: Identification of Conserved and Novel MicroRNAs in Cashmere Goat (Capra hircus) by Deep Sequencing

status: Public on Feb 25 2012

city: Huhehot

first: Liu

last: Zhihong

address: Zhaowuda Road 306

country: China

institute: Inner Mongolia Agriculture University

type: Non-coding RNA profiling by high throughput sequencing

summary: The study confirmed a batch of goat skin and hair follicles miRNA, by high-throughput sequencing methods.316 sequences miRNAs were obtained by the means of analysis and we confirmed the authenticity of 68 known miRNAs and discovered 248 novel miRNAs, as well as 22 miRNAs that haven’t been reported before. Through the miRNAs family analysis, we found the co-expressed miRNAs in goat and sheep located in the same region of chromosome, which may play an essential role in skin and follicle development. In addition, the prediction of novel target miRNAs followed by the analysis of target gene pathways indicated that MAPK pathway may have an important effect to the fast growth of skin follicle cell.

overall_design: We sequenced a mixed sample which contains three goat skin in anagen of cashmere

first: Li

last: Jinquan

first: Zhao

last: Yanhong


title: Genome-wide binding profiles of the B-Myb-MuvB complex in HeLa cells

first: Subhashini

last: Sadasivam

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

summary: To identify genomic regions bound by B-Myb and LIN9 (a subunit of the MuvB complex), we performed ChIP-Sequencing (ChIP-Seq) using chromatin from proliferating HeLa cells in which we can detect a robust association between B-Myb and subunits of the MuvB complex. This analysis allowed us identify late cell cycle or G2/M expressed genes as specific targets of the B-Myb-MuvB complex.

overall_design: Examination of B-Myb and LIN9 binding in asynchronously growing HeLa cells

first: James

last: DeCaprio


title: Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

status: Public on Jan 24 2012

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary: Recent epigenomic studies have predicted thousands of potential enhancers in the human genome. However, there has not been systematic characterization of target promoters for these potential enhancers. Using H3K4me2 as a mark for active enhancers, we identified genome-wide enhancer-promoter interactions in human CD4+ T cells. Among the 6,520 long-distance chromatin interactions, we identify 2,067 enhancers that interact with 1,619 promoters and enhance their expression. These enhancers exist in accessible chromatin regions and are associated with various histone modifications and Pol II binding. The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers and their expression levels are positively correlated with the number of interacting enhancers. Interestingly, interacting promoters are co-expressed in a tissue-specific manner. We also find that chromosomes are organized into multiple levels of interacting domains. Our results define a global view of enhancer-promoter interactions and provide a dataset to further understand mechanisms of enhancer targeting and long-range chromatin organization.

overall_design: Two biological replicates of ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) experiment in CD4+ T cells

first: Gang

last: Wei

first: Dara

last: Wangsa

first: Qingsong

last: Tang

first: Keji

last: Zhao


title: [E-MTAB-698] Sexual dimorphism in mice

status: Public on Jan 20 2012

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

summary:
High-throughput sequencing of vomernasal tissues of adult male and female mice.

ArrayExpress Release Date: 2011-06-10

Person Roles: Investigator
Person Last Name: Logan
Person First Name: Darren
Person Mid Initials: W
Person Email: dl5@sanger.ac.uk
Person Phone:
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, Uk
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: sex_design
Experimental Design: in_vivo_design
Experimental Design: co-expression_design
Experimental Factor Name: SEX
Experimental Factor Type: sex


title: [E-MTAB-652] CID island ChIP

summary:
The centromere-specific Histone H3-variant CENH3 (also known as CENP-A) is considered to be an epigenetic mark for establishment and propagation of centromere identity. Pulse-induction of CENH3 (Drosophila CID) in Schneider S2 cells incorporates into noncentromeric regions and generates CID islands that resist clearing from chromosome arms for multiple cell generations. We demonstrate that CID islands represent functional ectopic kinetochores, which are non-randomly distributed on the chromosome and display a preferential localization near telomeres and pericentric heterochromatin in transcriptionally silent, intergenic chromatin domains. Although overexpression of heterochromatin protein 1 (HP1) or increasing Histone acetylation interferes with CID islands formation on a global scale, induction of a locally defined region of synthetic heterochromatin by targeting HP1-LacI fusions to stably integrated Lac Operator arrays produces a proximal hotspot for CID islands formation. These data suggest that the characteristics of regions bordering heterochromatin promote de novo kinetochore assembly and thereby contribute to centromere identity.

ArrayExpress Release Date: 2011-07-15

Person Roles: submitter
Person Last Name: Diehl
Person First Name: Sarah
Person Mid Initials:
Person Email: diehl@immunbio.mpg.de
Person Phone: (+49) 761 5108 795
Person Address: Stuebeweg 51, 79108 Freiburg im Breisgau, Germany
Person Affiliation: Max-Planck-Institute for Immunobiology and Epigenetics

Person Roles: investigator
Person Last Name: Heun
Person First Name: Patrick
Person Mid Initials:
Person Email: heun@immunbio.mpg.de
Person Phone: (+49) 761 5108 717
Person Address: Stuebeweg 51, 79108 Freiburg im Breisgau, Germany
Person Affiliation: Max-Planck-Institute for Immunobiology and Epigenetics

Publication Title: Heterochromatin boundaries are hotspots for de novo kinetochore formation.
Publication Author List: Agata Olszak, Dominic van Essen, Antonio J. Pereira, Sarah Diehl, Thomas Manke, Helder Maiato, Simona Saccani and Patrick Heun

overall_design:
Experimental Design: translational_design
Experimental Design: in_vitro_design
Experimental Design: ChiP-seq
Experimental Factor Name: Immunoprecipitate
Experimental Factor Type: Immunoprecipitate


title: Transcriptional profiling analysis in Populus yunnanensis provides insights into the molecular mechanisms of sexual differences in plant salinity tolerance

city: chengdu

first: Hao

last: Jiang

address: CIB-CAS

institute: CIB-CAS,China

summary: In the present study, we compared transcriptional response to salinity between male and female individuals of Populus yunnanensis. We found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observation that salinity inhibited photosynthetic capacity more in females than in males. In conclusion, our study provided molecular evidence of sexual differences in poplar salinity tolerance. Identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences to salinity stress at the transcription level.

overall_design: 4 samples examined: males without salinity stress, males exposed to salinity stress, females without salinity stress and females exposed to salinity stress. Nine plants of each sex were exposed to each treatment, and RNA samples from the 9 individuals were pooled with equal proportion.

first: Chunyang

last: Li

first: Shuming

last: Peng

first: Sheng

last: Zhang

first: Xinguo

first: Helena

last: Korpelainen


title: Functional studies of a H2A.Bbd-like histone variant in mouse spermatogenesis

city: Canberra

first: Rohan

last: Williams

state: ACT

address: Garran Rd ACTON

country: Australia

institute: ANU


title: Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae [Sequence Data]

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function.  The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure.  Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing.  Forkhead regulation of origin timing is independent of local levels or changes of transcription.  Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1-phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories.  Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins.  These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.

overall_design: These files contain BrdU-IP-seq files (2 replicates for each strain; 5 strains total where WT was used as control). These files also contain RNA-seq data from Asynchronous and G1 arrested WT and Mutant cells (2 replicates per strain and condition; paired end). These files also contain RNA-pol-chip-seq data from Asynchronous and G1 arrested WT and Mutant cells (2 replicates per strain/condition).

first: Jared

last: Peace

first: A

middle: Z

last: Ostrow

first: Yan

last: Gan

first: Alexandra

middle: E

last: Rex

first: Christopher

last: Viggiani

last: Tavare

first: Oscar

last: Aparicio


title: Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

summary: Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse H2A.Bbd-like histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated

overall_design: Examination of 2 different histone variants in mouse spermatids.

first: Gavin

last: Huttley

first: Anuj

last: Pahwa

first: Maxim

last: Nekrasov


title: [E-MTAB-607] Transcription profiling by high throughput sequencing of the planarian Schmidtea mediterranea during head regeneration

first: ArrayExpress

last: EBI

summary:
The head-regeneration transcriptome of the planarian Schmidtea mediterranea

ArrayExpress Release Date: 2011-07-15

Publication Title: The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Publication Author List: Thomas Sandmann, Matthias C. Vogg, Suthira Owlarn, Michael Boutros, and Kerstin Bartscherer

Person Roles: submitter
Person Last Name: Sandmann
Person First Name: Thomas
Person Mid Initials:
Person Email: t.sandmann@dkfz.de
Person Phone: +49 6221 42 1954
Person Address: Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
Person Affiliation: German Cancer Research Center

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: organism_part_comparison_design
Experimental Design: in_vivo_design
Experimental Design: co-expression_design
Experimental Factor Name: TIME
Experimental Factor Name: ORGANISMPART
Experimental Factor Name: BATCH
Experimental Factor Type: developmental_stage
Experimental Factor Type: organism_part
Experimental Factor Type: batch
Quality Control Type: biological replicate


title: Bisulphite-sequencing of chromatin immunoprecipitated DNA directly informs methylation status of histone-modified DNA

status: Public on Jan 18 2012

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zuerich

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChiP-seq) directly informs methylation status

summary: Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation.

overall_design: Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines

middle: D


title: Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq

status: Public on Jan 17 2012

city: Columbus

first: Dario

last: Motti

state: Ohio [OH]

address: 700 Childrens Drive

department: Research

institute: Nationwide Children's Hospital

summary: To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate.  The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities.  Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance.  Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3’ untranslated regions (3’ UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to illuminate the complex transcriptional landscape in two neuronal populations.

overall_design: RNA was sequenced from cultured peripheral neurons of the dorsal root ganglia (DRG neurons) and cerebellar granular neurons (CGNs) of the central nervous system

first: Jessica

last: Lerch

first: Frank

last: Kuo

first: Richard

last: Morris

first: John

middle: L

last: Bixby

first: Vance

middle: P

last: Lemmon


title: Genome-wide expression analysis of dikaryotic colonies of Schizophyllum commune: wild-type, delta-hom2, delta-fst4

city: Utrecht

last: Wösten

address: Padualaan 8

institute: Utrecht University

summary: The transcription factors Hom2 and Fst4 were shown to be involved in mushroom development in the basidiomycete Schizophyllum commune. When the genes encoding Hom2 or Fst4 were deleted, no mushrooms formed. In this study we performed a genome-wide expression analysis on dikaryons of wild-type, delta-hom2 and delta-fst4.

overall_design: A total of three samples were analyzed. One wild-type and two deletion strains (delta-hom2 and delta-fst4)

first: Robin

middle: A

last: Ohm

first: Luis

middle: G

last: Lugones

first: Han


title: Regulation of Mediator-dependent transcriptional activation of Pol II(G) through TFII

status: Public on Jan 13 2012

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

institute: Uiversity Hospital Zurich

summary: Pol II(G) is a novel form of RNA polymerase II that contains a tightly associated Gdown1 polypeptide. Whereas Pol II suffices for robust activator-dependent transcription in the absence of Mediator, Pol II(G) is highly dependent upon Mediator in a biochemically defined in vitro system. However, the mechanism(s) whereby Gdown1 alters the coactivator-dependence of Pol II is unknown. Here we show that Gdown1 competes with TFIIF for binding to the RPB1 and RPB5 subunits of Pol II in vitro, resulting in inhibition of a critical function of TFIIF in facilitating PIC assembly. The apparent inability of Pol II(G)  to associate with TFIIF suggests that Gdown1 must be removed from Pol II for transcription initiation. However, Mediator can actually help Pol II(G) bind to the promoter prior to subsequent Mediator functions. Complementary cell-based analyses reveal that Pol II(G) is recruited to promoter regions of subsets of actively transcribed genes, where Pol II(G) appears to modulate transcription. Our findings indicate that differential regulation of subsets of genes by Pol II and Pol II(G) occurs through the regulation of TFIIF and consequent alterations in Mediator requirements.

overall_design: Genome-wide localization of PolII and Gdown1 in human IMR90 fibroblast cells using ChIP-seq

first: Miki

last: Jishage

first: Sohail

last: Malik

first: Beatrix

last: Uberheide

first: Averell

last: Gnatt

first: Brian

last: Chait

first: Yasushi

last: Ishihama

first: Bing

last: Ren

first: Robert

last: Roeder


title: Intragenic enhancers act as alternative promoters

status: Public on Jan 30 2012

city: Oxford

first: Monika

middle: S

last: Kowalczyk

state: Oxfordshire

address: Headley Way

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, University of Oxford


title: Transcriptome of mouse erythroid cells (part1) poly(A)+

summary: We report genome-wide maps of transcription in mouse erythroid cells. We used an approach to survey poly(A)+ (mRNA) (GSE26877) and non-polyadenylated RNA poly(A)- (GSE27920) separately. This provides an alternative framework for comprehensive transcriptome profiling in mammalian cells.

overall_design: Two Samples. mRNA-seq from wild type murine Ter119+ cells and mRNA-seq from ΔMCS-P6MCS-R3-/- Ter119+ cells

first: Jim

last: Hughes

first: Jacqueline

last: Sloane-Stanley

first: Chris

last: Ponting

first: William

last: Wood

first: Douglas

last: Higgs


title: Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)

city: Stanford

first: ENCODE

last: DCC

state: CA

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 (Terry Furey mailto:tsfurey@duke.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

These tracks display Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) evidence as part of the four Open Chromatin track sets. FAIRE is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements.
Together with DNaseI HS and ChIP-seq experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: DNaseI hypersensitivity (HS) and these FAIRE assays, combined with chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen.
Release 1 (March 2011) of this track consists of a remapping of all previously released experiments to the human reference genome GRCh37/hg19 (these data were previously mapped to NCBI36/hg18; please see the Release Notes section of the hg18 Open Chromatin track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeChromatinMap) for information on the NCBI36/hg18 releases of the data). -There are 12 new FAIRE experiments in this release, on 10 new cell lines. -New to this release is a reconfiguration of how this track is displayed in relation to other tracks from the Duke/UNC/UT-Austin/EBI group. -A synthesis of open chromatin evidence from the three assay types was compiled for Tier 1 and 2 cell lines plus NHEK will also be added in this release and can be previewed in: Open Chromatin Synthesis (http://genome-preview.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromSynth). -Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/supplemental/.

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:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). FAIRE was performed (Giresi et al., 2007) by cross-linking proteins to DNA using 1% formaldehyde solution, and the complex was sheared using sonication. Phenol/chloroform extractions were performed to remove DNA fragments cross-linked to protein. The DNA recovered in the aqueous phase was sequenced using an Illumina (Solexa) sequencing system. FAIRE-seq data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. For some cell types, additional verification was performed using the same material but hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome) along with the input DNA as reference (FAIRE-chip). A more detailed protocol is available at http://hgwdev.cse.ucsc.edu/ENCODE/protocols/general/FAIRE_UNC_procedure.pdf. Also see Giresi et al., 2009.
DNA fragments isolated by FAIRE are 100-200 bp in length, with the average length being 134 bp. Sequences from each experiment were aligned to the genome using BWA (Li et al., 2010) for the NCBI 36 (hg19) assembly. The command used for these alignments was: > bwa aln -t 8 genome.fa s_1.sequence.txt.bfq > s_1.sequence.txt.sai Where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format.
Sequences from multiple lanes are combined for a single replicate using the bwa samse command, and converted in the sam/bam format using samtools. Only those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/supplemental/). The mappings of these short reads to the genome are available for download at http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeOpenChromFaire.
The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data has been generated for several cell lines. These are used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models are meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data is not being generated directly for other cell lines. Instead, a general background model was derived from the available Input data sets. This should provide corrections for sequencing biases and alignment artifacts, but will not correct for cell type specific copy number changes. The exact command used for this step is: > fseq -l 800 -v -b <bff files> -p <iff files> aligments.bed Where the (bff files) are the background files based on alignability, the (iff files) are the background files based on the Input experiments, and alignments.bed are a bed file of filtered sequence alignments.
Discrete FAIRE sites (peaks) were identified from FAIRE-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization, and peaks were called using ChIPOTle (Buck, et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files containing this data can be found in the Downloads directory labeled Validation view (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromFaire).

first: Terry

last: Furey

first: Alan

last: Boyle

first: Lingyun

last: Song

first: Greg

last: Crawford

first: Paul

last: Giresi

first: Jason

last: Lieb

first: Zheng

last: Liu

first: Ryan

last: McDaniell

first: Bum-Kyu

last: Lee

first: Vishy

last: Iyer

last: Flicek

first: Damian

last: Keefe

first: Ewan

last: Birney

first: Stefan

last: Graf


title: Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes.

status: Public on Jan 12 2012

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To clarify these issues we established genome-wide STAT5 binding upon growth hormone (GH) stimulation of wild type mouse embryonic fibroblasts (MEFs) and MEFs overexpressing STAT5A more than 20-fold. Upon GH stimulation 23,827 and 111,939 STAT5A binding sites were detected in wild type and STAT5A overexpressing MEFs, respectively. 13,278 and 71,561 peaks contained at least one GAS motif. 1,586 and 8,613 binding sites were located within 2.5 kbp of promoter sequences, respectively. Stringent filtering revealed 78 genes in which the promoter/upstream region (-10kbp to +0.5kbp) was recognized by STAT5 both in wt and STAT5 overexpressing MEFs and 347 genes that bound STAT5 only in overexpressing cells. Genome-wide expression analyses identified that the majority of STAT5-bound genes was not under GH control. Up to 40% of STAT5-bound genes were not expressed. For the first time we demonstrate the magnitude of opportunistic genomic STAT5 binding that does not translate into transcriptional activation of neighboring genes.

overall_design: Genome-wide mapping of STAT5 binding in MEF cells (WT, KO; Stat5-/- and overexpression; STAT5A-Stat5-/-) upon growth hormone induction

first: B

last: Zhu

first: K

first: J

middle: H

last: Yu

first: W

last: Chen

first: H

last: Smith

first: D

last: Sun

first: L

last: Wei

last: Hennighausen


title: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]

status: Public on Feb 24 2012

city: Chicago

first: Joseph

last: Zullo

state: IL

address: 929 E 57th Street

department: MGCB

institute: University of Chicago

summary: A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts.

overall_design: We characterized DNA regions within LADs that are functionally capable of positioning chromatin domains at the inner nuclear membrane (INM) lamina.  We mapped and characterized the IgH and other LADs in murine fibroblasts.  We show that these murine LADs have a unique chromatin structure with discrete boundaries.  We demonstrate DNA regions within LADs that are capable of directing the association of chromatin domains with the INM-lamina as well as the silencing of a co-integrated reporter gene.

first: Charles

middle: B

last: Epstein


title: The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression

city: Boston

first: Subhashini

last: Sadasivam

first: James

last: DeCaprio


title: Three-dimensional folding and functional organization principles of the Drosophila genome

city: Montpellier

first: Tom

last: Sexton

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS UPR 1142

summary: Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts.

overall_design: One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes

first: Eitan

last: Yaffe

first: Amos

last: Tanay

first: Giacomo

last: Cavalli


title: Functional association of Gdown1 with RNA Polymerase II in Human

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function.

overall_design: 7 ChIP-Seq data for Pol II and Gdown1 in human HeLa cell. See associated publication.

first: David

last: Price


title: Neighboring genomic regions influence differential methylation patterns of CpG islands in endometrial and breast cancers

status: Public on Jan 11 2012

first: Fei

last: Gu

state: Ohio

department: Molecular Virology, Immunology & Medical Genetics

institute: The Ohio State University

summary: We report the global methylation patterns by MBDCap-seq for total 232 primary samples in endometrial cohorts, breast cancer cohorts and breast cancer cell lines. We found total 1,007 differentially methylated regions (DMRs) include CpG islands and shores in endometrial cohorts, and 2529 for Breast Cancer cohorts. We also identified 153 regions that are distinctly different from regular CpG islands at the 5'-ends of genes. Those regions, always contain a chain of 1-2 main islands and a few satellites alone on GC-poor and gene-less region. Majority of CpG atolls contain lowly transcribed or silenced genes in normal controls. This phenomenon provides a new opportunity to develop sensitive biomarkers for cancer diagnosis and prognosis

overall_design: Study of 3 different Cancer type, Endometrial Cancer and Breast Cancer patient samples, and Breast Cancer cell liens, using MBDCap-seq technology.

first: Yi-Wen

last: Huang

first: Yu-I

last: Weng

first: Brian

last: Kennedy

middle: C

last: Liu

first: Paul

last: Spellman

last: Mutch

first: Pearlly

last: Yan

first: Joe

last: Gray

middle: J

last: Goodfellow

first: Victor

middle: X

last: Jin

first: Tim


title: Notch1-driven epigenetic changes in a mouse model of T cell Acute Lymphoblastic Leukemia (T-ALL)

status: Public on Jan 10 2012

city: Yorktown Heights

first: Aristotelis

last: Tsirigos

address: 1101 Kitchawan Road, Route 134

department: Computational Biology Center

institute: IBM Research

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we used a mouse model of T-ALL through the overexpression of the intarcellular transcriptionally active part of Notch1 (N1-IC). This model faithfully recapitulates the major characteristics of the human disease. Comparison of the leukemic cells from peripheral tumors(thymoma) of this mouse model to normal thymic cells Double Positive (DP) for the markers CD4 and CD8 that express very low levels of Notch1 showed major expression changes (please see GSE34554) in pathways controlling the transition from physiology to disease. Further correlation of the data to ChIP-Seq data from the same cell populations led us to identify a hitherto unknown antagonism of the Notch1 oncogenic pathway and the polycomb complex (PRC2) in leukemia. Importantly exome sequencing in primary samples from human patients with T-ALL revealed that the PRC2 complex is frequently mutated and inactivated, further supporting the tumor suppressor role of the complex in this disease.

overall_design: Gene expression profiles from CD4+/8+ Double Positive (named DP) derived from normal thymus and Notch1-IC over-expressing tumors (named T-ALL) were analyzed for the genomewide enrichments of two major activating epigenetic marks (Histone 3 Lysine 9 acetylation (H3K9ac) and lysine 4 trimethylation (H3K4me3)), one reprressive mark (Histone 3 lysine 27 trimethylation, H3K27me3) and the major oncogene Notch1.

first: Panagiotis

last: Ntziachristos


title: Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes

status: Public on Jan 07 2012

city: Cambridge

first: Tony

last: Jia

address: 12 Oxford St.

department: Chemistry and Chemical Biology

institute: Harvard University

summary: RNA-Seq is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification.  We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq.  Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends.  After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences.  Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence.  We optimized the barcodes to be unambiguously identifiable even in the presence of multiple sequencing errors.  This method allows counting with single copy resolution despite sequence-dependent bias and PCR amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of E. coli with more accurate and reproducible quantification than conventional RNA-Seq.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We analyzed two replicates of the same bulk E. coli transcriptome sample. In each sample, we included internal standards to demonstrate that the digital RNA-Seq system may accurately count fragments correctly.

first: Katsuyuki

last: Shiroguchi

first: Peter

last: Sims

first: X

last: Xie


title: TCERG1 regulates alternative splicing of Bcl-x gene by modulating the rate of RNAPII transcription

city: Kansas City

first: Marco

last: Blanchette

institute: Stowers Institute for Medical Research

summary: Complex functional coupling exists between transcriptional elongation and pre-mRNA alternative splicing. Pausing sites and changes in the rate of transcription by RNAPII may therefore have a fundamental impact in the regulation of alternative splicing. Here, we show that the elongation and splicing-related factor TCERG1 regulates alternative splicing of the apoptosis gene Bcl-x in a promoter-dependent manner. TCERG1 promotes the splicing of the short isoform of Bcl-x (Bcl-xs) through the SB1 regulatory element located in the first half of exon 2. Consistent with these results, we show evidence for in vitro and in vivo interaction of TCERG1 with the Bcl-x pre-mRNA. Transcription profile analysis reveals that the RNA sequences required for the effect of TCERG1 on Bcl-x alternative splicing coincide with a putative polymerase pause site. Furthermore, TCERG1 modifies the impact of a slow polymerase on Bcl-x alternative splicing. In support of a role for an elongation mechanism in the transcriptional control of Bcl-x alternative splicing, we found that TCERG1 modifies the amount of pre-mRNAs generated at distal regions of the endogenous Bcl-x. Most importantly, TCERG1 affects the rate of RNAPII transcription of endogenous human Bcl-x. We propose that TCERG1 modulates the elongation rate of RNAPII to relieve pausing, thereby activating the pro-apoptotic Bcl-xS 5’ splice site.

overall_design: ChIP-Seq

first: Mart

last: Montes

first: Alexandre

last: Cloutier

first: Noemí

last: Sánchez-Hernández

first: Laetitia

last: Michelle

first: Bruno

last: Lemieux

first: Cristina

last: Hernández-Munain

first: Benoit

last: Chabot

first: Carlos

last: Suñé


title: Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [MRE-seq]

status: Public on Jan 06 2012

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. The differentiation phenotype due to Tet1 depletion positively correlated with the extent of 5hmC loss. Meta-analyses of genomic datasets suggested interaction between Tet1 and leukemia inhibitory factor (LIF) signaling. LIF signaling is known to promote self-renewal and pluripo-tency in mESCs partly by opposing MAPK/ERK mediated differentiation. Withdrawal of LIF leads to differentiation of mESCs. We discovered that Tet1 depletion impaired LIF-dependent Stat3-mediated gene activation by affecting Stat3's ability to bind to its target sites on chromatin. Nanog overexpression or inhibition of MAPK/ERK signaling, both known to maintain mESCs in the absence of LIF, rescued Tet1 depletion, further supporting the dependence of LIF/Stat3 signaling on Tet1. These data support the conclusion that analysis of mESCs in the hours/days immediately following efficient Tet1 depletion reveals Tet1’s normal physiological role in maintaining the pluripotent state that may be subject to homeostatic compensation in genetic models.

overall_design: Genome-wide mapping of 5hmC and microarray gene expression profiling in E14Tg2a mESCs after transfection with indicated siRNAs: Tet1 siRNA #1 (Invitrogen, MSS284895), Tet1 siRNA #2 (Invitrogen, MSS284897), and Control siRNA duplex targeting firefly luciferase.

first: Guang

last: Hu

first: Johannes

last: Freudenberg


title: Phaeo CDF 2011 - stressor exposed vs control

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

summary: Initial work for profiling contaminant response in Phaeodactylum cells exposed to contaminants and non contaminant stressors

overall_design: Two colour arrays: Control versus exposed.  5 biological replicates per treatment, 6 split controls one replicate per array

first: Hannah

last: Osborn


title: Isl1-Lhx3 fusion specifies motor neuron fate by inducing motor neuron genes and concomitantly suppressing the interneuron programs

status: Public on Feb 03 2012

city: Brockport

first: Rongkun

last: Shen

state: New York

address: 350 New Campus Dr

department: Biology

institute: SUNY Brockport

summary: Combinatorial transcription codes generate the myriad of cell types during development, and thus likely provide crucial insights into directed differentiation of stem cells to a specific cell type. The LIM-complex composed of Isl1 and Lhx3 directs the specification of spinal motor neurons (MNs) in embryos. Here, we report that Isl1-Lhx3, a LIMcomplex-mimicking fusion, induces a signature of MN transcriptome and concomitantly suppresses interneuron differentiation programs, thereby serving as a potent and specific inducer of MNs in stem cells. We show that an equimolar ratio of Isl1 and Lhx3 and the LIM-domain of Lhx3 are crucial for generating MNs without upregulating interneuron genes. These led us to design Isl1-Lhx3, which maintains the desirable 1:1 ratio of Isl1 and Lhx3 and the LIM-domain of Lhx3. Isl1-Lhx3 drives MN differentiation with high specificity and efficiency in the spinal cord and embryonic stem cells, bypassing the need for sonic hedgehog. RNA-seq analysis revealed that Isl1-Lhx3 induces the expression of a battery of MN genes that control various functional aspects of MNs, while suppressing key interneuron genes. Our studies uncover a highly efficient method for directed MN generation and MN gene networks. Our results also demonstrate a general strategy of utilizing embryonic transcription complexes for producing specific cell types from stem cells.

overall_design: Examine the RNA expression profiles of inducible motor neurons-embryonic stem cells (iMN-ESCs) with or without Dox treatment, with biological duplicates.

first: Seunghee

last: Lee

first: Soo-Kyung


title: Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos

first: Michael

last: Nodine

address: 9 Cambridge Center

institute: Whitehead Institute

summary: In animals, maternal gene products deposited into eggs regulate embryonic development before activation of the zygotic genome. In plants, an analogous period of prolonged maternal control over embryogenesis is thought to occur based on gene-expression studies. However, other gene-expression studies and genetic analyses show that some transcripts must derive from the early zygotic genome, implying that the prevailing model does not fully explain the nature of zygotic genome activation in plants. To determine the maternal, paternal and zygotic contributions to the early embryonic transcriptome, we sequenced the transcripts of hybrid embryos from crosses between two polymorphic inbred lines of Arabidopsis thaliana and used single-nucleotide polymorphisms (SNPs) diagnostic of each parental line to quantify parental contributions. Although some transcripts appeared to be either inherited from primarily one parent or transcribed from imprinted embryonic loci, the vast majority of transcripts were produced in near-equal amounts from both maternal and paternal alleles, even during the initial stages of embryogenesis. Results of reporter experiments and analyses of transcripts from genes that are not expressed in sperm and egg indicate early and widespread zygotic transcription. Thus, in contrast to early animal embryogenesis, early plant embryogenesis is mostly under zygotic control.

overall_design: Col-0 and Cvi-0 seed stocks were obtained from the Arabidopsis Biological Resource Center. Plants were grown at 22° C in a Conviron growth chamber with a 16-h light/8-h dark cycle. Flowers were emasculated one day before crossing, and pools of twenty 1-cell/2-cell, 8-cell and ~32-cell embryos were hand-dissected approximately 40, 64 and 78 hours after pollination, respectively. Embryo dissections, RNA isolation, linear amplification of poly(A) RNA and strand-specific RNA-Seq was as described (Nodine and Bartel, 2010, Genes & Development), except that embryos were extensively washed prior to RNA isolation. After removing adaptor sequences, reads were mapped to both the A. thaliana genome and transcript models (Col-0 genome reference, TAIR10) with the Bowtie short-read aligner. Reads were also mapped to a ‘pseudo’ Cvi-0 genome and Cvi-0 transcript models, in which SNPs in the Col-0 genome and transcript models were replaced with Cvi-0 variants (ftp://ftp.arabidopsis.org/home/tair/Sequences/Ecker_Cvi_snps.txt) generated by the 1,001 Genomes Project. Reads that both perfectly and uniquely matched either the genomes or transcript models were retained, and those overlapping transcribed regions of annotated genes were evaluated for overlap with SNPs. To normalize for differences in library sizes, the numbers of reads representing each transcript were divided by the total number of reads matching the genome and transcript models. SNP-overlapping reads were assigned to one of the parental genomes and tallied for each transcript, combining tallies for multiple SNPs within the same transcript.

first: David

last: Bartel


title: Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

summary: Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.

overall_design: 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

first: Tina

last: Kyndt

first: Annelies

last: Haegeman

first: Geert

last: Trooskens

first: Tim

last: De Meyer

first: Wim

last: Van Criekinge

first: Godelieve

last: Gheysen


title: Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope, and longevity of chromatin-targeted dsRNA effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of H3K9 trimethylation, with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from among all 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9 methylation, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost.  These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries.

overall_design: H3K9me3 nucleosome-IP sequencing and small RNA sequencing in C. elegans populations that underwent RNAi

first: Julia

last: Pak

first: Shouhong

last: Guang

first: Jay

last: Manniar

first: Scott

last: Kennedy

first: Andrew

last: Fire


title: A Multiplicity of Factors Contributes to Selective RNA polymerase III occupancy of a Subset of RNA polymerase III Genes in Mouse Liver

status: Public on Jan 19 2012

city: Lausanne

last: Bernasconi

address: Quartier Sorge, Bat. Génopode

department: CIG

institute: University of Lausanne

summary: The genomic loci occupied by RNA polymerase (pol) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitation experiments followed by deep sequencing (ChIP-Seq).  These studies have in particular shown that only about 40 % of the annotated 622 human tRNA genes and pseudogenes are occupied by pol III, and that these genes are often in regions of open chromatin rich in active pol II transcription units.  Here we have used ChIP-Seq to characterize pol III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver pol III-occupied loci and point to a conserved pol III-occupied mammalian interspersed repeat (MIR) as a potential regulator of a pol III subunit-encoding gene.  They reveal that synteny relationships can be established between a number of human and mouse pol III genes, and that the expression levels of these genes are significantly linked.  They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence can strongly affect pol III occupancy of tRNA genes.  They reveal correlations with various genomic features that together describe the pol III occupancy scores over some 50% of tRNA genes.  In mouse liver, pol III-occupied loci represented in the NCBI37/mm9 genome assembly comprise fifty 5S genes, fourteen known non-tRNA genes, nine 4.5S genes, and some twenty nine SINEs.  In addition, out of the 433 annotated tRNA genes, half are occupied by pol III.  Transfer RNA gene expression levels reflect both an underlying genomic organization that is conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.

overall_design: 12 samples examinded, 4 on pol III, 2 on pol II, 2 on H3K4me3, 2 on H3k36me3, 2 input samples.

first: Donatella

last: Canella

first: Nouria

last: Hernandez

first: Mauro

last: Delorenzi


title: Functional and epigenetic studies reveal multistep differentiation and plasticity of in vitro and in vivo follicular T helper cells

status: Public on Jan 05 2012

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: Follicular T helper cells (Tfh) provide critical help to B cells for germinal center (GC) formation. Mutations affecting SLAM-associated Protein (SAP) prevent GC formation due to defective T-B cell interactions, yet effects on Tfh cell differentiation remain unclear. We describe the in vitro differentiation of functionally-competent “Tfh-like” cells that expressed Interleukin-21, Tfh markers, and Bcl6, and rescued GC formation in SAP-deficient hosts better than other T helper (Th) cells. SAP-deficient Tfh-like cells appeared virtually indistinguishable from wildtype, yet failed to support GCs in vivo. Interestingly, both Tfh-like and in vivo-derived Tfh cells could produce effector cytokines in response to polarizing conditions. Moreover, Th1, Th2 and Th17 cells could be reprogrammed to obtain Tfh characteristics. ChIP-Seq analyses revealed positive epigenetic markings on Tbx21, Gata3 and Rorc in Tfh-like and ex vivo Tfh cells, and Bcl6 in other Th cell populations, supporting the concept of plasticity between Tfh and other Th cells.

overall_design: Epigenetic modifications were evaluated in ChIP-Seq studies by profiling histone H3K4 and H3K27 trimethylation marks between Th1, Th2, Th17, Tfh-like, and CXCR5+PD-1+ sorted Tfh-like in vitro generated T helper cell populations and ex vivo derived Tfh cells.

first: Kristina

middle: T

last: Lu

first: Hongwei

last: Sun

first: John

last: O'Shea

first: Pamela

last: Schwartzberg


title: [E-MTAB-831] GENCODE PCR-Seq Batch VI

status: Public on Jan 04 2012

city: Hinxton

first: ArrayExpress

last: EBI

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch VI, which targets annotations from Gencode 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data.

ArrayExpress Release Date: 2011-11-25

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

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:
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: organism_part


title: Widespread regulated alternative splicing of single codons accelerates proteome evolution

first: Robert

middle: K

last: Bradley

state: MA

address: 77 Massachusetts Avenue, 68-223A

institute: MIT

summary: Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. Further, alternative splicing of human NAGNAGs was associated with an order of magnitude increase in the frequency of exon length changes at orthologous mouse/rat exon boundaries, suggesting that NAGNAGs accelerate exon evolution. Together, our analyses show that NAGNAG alternative splicing constitutes a major generator of tissue-specific proteome diversity and accelerates evolution of proteins at exon-exon boundaries.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
mRNA-Seq of sixteen human and eight mouse tissues.

Supplementary files:
human.nagnag.junctions.gff and mouse.nagnag.junctions.gff are the annotation files (in GFF3 format) corresponding to the 'bwtout' mapped reads files linked to the Sample records.

Raw data files provided for Samples GSM742937-GSM742952 only.

first: Jason

last: Merkin

first: Christopher

last: Burge


title: [E-MTAB-737] GENCODE PCR-Seq Batch V

summary:
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch V, based on annotations from Gencode 6 (November2010).

ArrayExpress Release Date: 2011-08-22

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

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:
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type:


title: Production of Virus-Derived Ping-Pong-Dependent Piwi-like RNAs in the Mosquito Soma

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Biotechnology Center

department: Fralin Life Science Institute

institute: Virginia Tech

summary: The natural maintenance cycles of many mosquito-borne pathogens require establishment of persistent non-lethal infections in the invertebrate host. The mechanism by which this occurs is not well understood, but we have previously shown that an antiviral response directed by small interfering RNAs (siRNAs) is important in modulating the pathogenesis of alphavirus infections in the mosquito. However, we report here that infection of mosquitoes with an alphavirus also triggers the production of another class of virus-derived small RNAs that exhibit many similarities to ping-pong-dependent piwi-interacting RNAs (piRNAs). However, unlike ping-pong-dependent piRNAs that have been described previously from repetitive elements or piRNA clusters, our work suggests production in the soma and a role for dsRNA in biogenesis. We also present evidence that suggests virus-derived piwi-like RNAs are capable of modulating the pathogenesis of alphavirus infections in dicer-2 null mutant mosquito cell lines defective in viral siRNA production. Overall, our results suggest that a non-canonical piRNA pathway is present in the soma of vector mosquitoes and may be acting redundantly to the siRNA pathway to target alphavirus replication.

sample_organism:
Aedes aegypti
Aedes albopictus

platform_organism:
Aedes aegypti
Aedes albopictus

overall_design: Comparison of virus derived small RNAs in several mosquito cell types

first: Elaine

middle: M

last: Morazzani

first: Michael

middle: R

last: Wiley

first: Marta

last: Murreddu

first: Zach

middle: N

last: Adelman


title: Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary:
Oestrogen receptor-a (ER) is the defining and driving transcrip- tion factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic under- standing of ER function has been restricted to model systems13. Here we map genome-wide ER-binding events, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), in primary breast cancers from patients with different clinical outcomes and in distant ER-positive metastases. We find that drug-resistant cancers still recruit ER to the chromatin, but that ER binding is a dynamic process, with the acquisition of unique ER-binding regions in tumours from patients that are likely to relapse. The acquired ER regulatory regions associated with poor clinical outcome observed in primary tumours reveal gene signatures that predict clinical outcome in ER-positive disease exclusively. We find that the differential ER-binding programme observed in tumours from patients with poor outcome is not due to the selection of a rare subpopulation of cells, but is due to the FOXA1-mediated reprogramming of ER binding on a rapid
time- scale. The parallel redistribution of ER and FOXA1 cis-regulatory elements in drug-resistant cellular contexts is supported by histological co-expression of ER and FOXA1 in metastatic samples. By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes.

overall_design: Oestrogen receptor alpha (ER) binding was mapped genome wide in 15 primary ER-positive breast tumours and 3 ER-positive distant metastases. As a control, ER binding was also mapped in 2 ER-negative breast tumours. For cell line experiments, ER was mapped, in at least duplicate, in three ER-positive cell lines that respond to tamoxifen treatment, and 2 ER-positive cell lines that are resistant to tamoxifen treatment. Both ER and FOXA1 binding was mapped in MCF-7 cells, in duplicate, before and after treatment with a cocktail of mitogens (i.e. IGF-1, TNF-alpha, EGF and IL-6).

first: Caryn

last: Ross-Innes

first: Rory

last: Stark


title: sRNA sequencing from wild-type Arabidopsis (diverse tissue types)

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

summary: This set consists of small RNAs sequenced from wild-type Arabidopsis samples from multiple tissue types (floral, leaf, seedling, silique). Samples were prepared in two different labs and presumably under different (unknown) growth conditions, hence type A (UEA) and type B (University of Cambridge) samples.

overall_design:
4 biological replicates (7 technical replicates) of Floral A; 3 biological replicates of Floral B; 1 biological replicate of Leaf B; 2 biological replicates of Leaf A; 3 biological replicates of Seedling; 1 biological replicate of Silique.
Note that GSM415783, GSM415784 and GSM415785 form part of the 'Floral A' category; GSM415783, GSM415784 are technical replicates.

first: Thomas

last: Hardcastle

first: Ericka

last: Havecker

first: Susi

last: Heimstaedt

first: Iain

last: Searle

first: Rebecca

last: Mosher

first: Natasha

last: Yelina

first: Antonis

last: Giakountis


title: Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity

first: Raja

last: Jothi

state: NC

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

overall_design: Refer to individual Series

first: Guang

last: Hu

first: Johannes

last: Freudenberg


title: E2F7 represses a transcriptional network of oscillating cell cycle genes to control S-phase progression.

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

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

summary: E2F transcription factors are known to be important for timely activation of G1/S and G2/M genes required for cell cycle progression, but transcriptional mechanisms for deactivation of cell cycle regulated genes are unknown. Here, we show that E2F7 is highly expressed during mid to late S-phase, occupies promoters of G1/S regulated genes and represses its transcription. ChIP-seq analysis revealed that E2F7 binds preferentially to genomic sites containing the TTCCCGCC motif, which closely resemble the E2F consensus site. We identified 89 target genes that carry E2F7 binding sites close to the transcriptional start site and that are directly repressed by short term induction of E2F7. Most of these target genes are known to be activated by E2Fs and are involved in DNA replication, metabolism and DNA repair. Importantly, induction of E2F7 during G0-G1/S resulted in S-phase arrest and DNA damage, whereas expression of E2F7 during G2/M failed to disturb cell cycle progression. These findings provide strong evidence that E2F7 controls directly the downswing of oscillating G1/S genes during S-phase progression.

overall_design: 2 samples: E2F7 ChIP-seq and input control, E2F7 ChIP-seq sample was sequenced in 2 independent runs and data were combined for the analysis. Additional sample on Dec. 29, 2015: E2F8 ChIP-seq sample.

first: Bart

last: Westendorp

first: Marian

last: Koerkamp

first: Frank

last: Holstege

first: Edwin

last: Cuppen

first: Alain

last: de Bruin


title: Identification of Host-Chromosome Binding Sites and Candidate Gene Targets for KSHV LANA

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: LANA is essential for tethering the KSHV genome to metaphase chromosomes and for modulating host-cell gene expression, but the binding sites in the host-chromosome remain unknown. Here, we use LANA-specific chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to identify LANA binding sites in the viral and host-cell genomes of a latently infected pleural effusion lymphoma cell line BCBL1. LANA bound with high occupancy to the KSHV genome terminal repeats (TR), and to a few minor binding sites within the latency control region encoding that LANA transcript.  We identified 256 LANA binding peaks with p < 0.01 and overlap in two independent ChIP-Seq experiments. We validated several of the high-occupancy binding sites by conventional ChIP assays and quantitative PCR.  Two candidate DNA sequence motifs were identified, and confirmed to bind purified LANA protein, although with weaker affinity compared to viral TR binding site.  More than half of the LANA binding sites (170/256) could be mapped to within 2.5 kb of a cellular gene transcript.  Pathways and Gene Ontogeny (GO) analysis revealed that LANA binds to genes within the p53 and TNF regulatory network.  Further analysis revealed partial overlap of LANA binding sites with STAT1 binding sites in several interferon (IFN)-g regulated genes.  We show that ectopic expression of LANA can down-modulate IFN-g mediated activation of a subset of genes, including the TAP1 peptide transporter and proteasome subunit beta type 9 (PSMB9) required for class I antigen presentation.  Our data provides a potential mechanism through which LANA may regulate several host cell pathways by direct binding to gene regulatory elements.

overall_design: Study of KSHV LANA

first: Fang

last: Lu

first: Kevin

last: Tsai

first: Horng-Shen

last: Chen

last: Wikramasinghe

first: Julie

last: Norseen

first: Ramana

middle: V

last: Davuluri

first: Louise

last: Showe

first: John

last: Domsic

first: Ronen

last: Marmorstein

first: Paul

last: Lieberman


title: Yy1 activity in mouse embryonic stem cells

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

first: Pietro

last: Vella


title: Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

type: Genome binding/occupancy profiling by genome tiling array


title: Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq)

status: Public on Jan 03 2012

first: Richard

middle: A

last: Young

institute: Whitehead Institute for Biomedical Research

summary: Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development.  Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation.  Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs).  LSD1 occupies enhancers of active genes critical for control of ESC state.  However, LSD1 is not essential for maintenance of ESC identity.  Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation.  We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states.

overall_design:
This is the ChIP-seq part of the study.

NOTE: We are unable to provide the sequencing data for the IgG control sample because it was never generated. The IgG control sample described in Figure 3c of Whyte et al., 2012 served as a control for the co-immunoprecipation and western blot experiments performed and shown in Figure 3. It was not used in sequencing experiments, and therefore was not sequenced and uploaded to GEO. Please inform those requesting this dataset of this fact.

first: Warren

last: Whyte

first: Steve

last: Bilodeau

first: Heather

last: Hoke

first: David

last: Orlando

first: Garrett

last: Frampton


title: Small RNA deep-sequencing identifies microRNAs and other small non-coding RNAs from human herpesvirus 6 (HHV-6B)

status: Public on Jan 01 2012

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Roseolovirus, or human herpesvirus 6 (HHV-6) is a ubiquitous human pathogen infecting over 95% of the population by the age of two years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived micro (mi)RNAs in modulating both cellular and viral gene expression. An initial report, which computed the likelihood of various viruses to encode for miRNAs, did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6 encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant 60-65 nucleotide RNA of unknown function derived from the lytic origin of replication (OriLyt) that gave rise to smaller RNA species of 18-19 nucleotides in length. In addition, we identified four pre-miRNAs, whose mature forms accumulated in Argonaute 2. In contrast to other beta-herpesviruses, HHV-6B miRNAs are expressed from direct repeat regions (DRL and DRR) located at either side of the genome. All miRNAs are conserved in the closely related HHV-6A variant, and one of them is a seed ortholog of the human miR-582-5p. Similar to alpha-herpesvirus miRNAs, they are expressed antisense to immediate early ORFs and thus have the potential to regulate key viral regulators.

overall_design: Small RNA sequencing from total RNA or Ago2 associated small RNAs extracted from HHV-6 infected Sup-T-1 cells

first: Lee

last: Tuddenham

first: Jette

middle: S

last: Jung

first: Béatrice

last: Chane-Woon-Ming

first: Lars

last: Dölken


title: High-resolution view of the yeast meiotic program revealed by ribosome profiling

city: San Francisco

first: Gloria

last: Brar

address: 1700 4th Street, BH404

institute: UCSF

summary: Meiosis is a complex developmental process that generates haploid cells from diploid progenitors. We measured mRNA abundance and protein production through yeast sporulation and found strong temporal control for most genes, achieved through both mRNA levels and translational regulation. Monitoring the timing of protein production revealed novel factors involved in recombination and helped to illuminate the molecular basis of the broad restructuring of meiotic cells. We also found a strong increase in noncanonical translation at short open reading frames (sORFs) on unannnotated transcripts and upstream regions of known transcripts (uORFs). Ribosome occupancy at near-cognate uORFs was associated with more efficient ORF translation; while some AUG uORFs, often on regulated leader extensions, acted comptetitively. This work reveals a pervasive role for meiotic translational control and great complexity in genomic coding.

overall_design: Fine mapping of gene expression through meiosis reveals extensive regulation of protein synthesis and widespread non-canonical translation.

first: Moran

last: Yassour

first: Nir

last: Friedman

first: Aviv

last: Regev

first: Nicholas

last: Ingolia

first: Jonathan

last: Weissman


title: Yy1 occupancy of mouse ES cell genome

first: Diego

last: Pasini

summary: These data include the genome wide location analyses of Yy1 by bioChIPs of Fbio-Yy1.

overall_design: Streptavidin precipitation of formaldehyde cross-linked chromatin prepared from Fbio-Yy1 and control expressing mouse ES cells

first: Pietro

last: Vella


title: [E-MTAB-684] GENCODE PCR-Seq Batch IV

first: ArrayExpress

last: EBI

state: Cambridgeshire

summary:
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch IV, based on chromosome 3, 4 and 5 annotations from Gencode 4 (January 2010). The sequences in this submission were obtained from two different RNA amplifications of the same original RNA for each tissue (called cdna1 and cdna2 in the assay names). In addition testis cDNA1 and lung cDNA2 were sequenced twice (rep1, rep2), and sequences originated from a new dilution of brain and testis cDNA1 (newdil) have also been included.

ArrayExpress Release Date: 2011-08-22

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

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:
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Type: organism_part


title: Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

city: Baltimore

first: Sarah

last: Wheelan

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

summary: Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern.

overall_design: TIP-seq recovery of transposon insertion junctions in haploid and diploid yeast

first: Jef

middle: D

last: Boeke