title: Genome-wide identification of MBD2 and MBD3 binding sites by ChIP-seq

status: Public on Feb 08 2013

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here we show a strong enrichment for MBD2 at methylated CpG sequences, whereas CpGs bound by MBD3 are devoid of methylation. Gene activity of MBD2 bound genes is four fold lower as compared to genes bound by MBD3. When depleting cells for MBD2, the MBD2 bound genes increase their activity, whereas MBD2 plus MBD3 bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes. This suggests a functional connection between MBD2 binding to chromatin and splicing.

overall_design: V5 ChIP followed by high throughput sequencing in HeLa cells transiently transfected with either V5-MBD2b, V5-MBD3 or V5.

first: Katharina

last: Guenther

first: Rainer

last: Renkawitz


title: Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and exon sequences

country: Germany

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effects of FSH knockdown on gene expression

status: Public on Feb 06 2013

city: Basel

first: Tobias

last: Kockmann

address: Mattenstr. 26

department: D-BSSE

country: Switzerland

institute: ETHZ

type: Expression profiling by high throughput sequencing

summary: see Super Series Summary

overall_design: Gene expression profiles of Drosophila S2-DRSC FSH knockdown cells were generated by Illumna RNA sequencing and compared to profiles derived from control cells (eGFP knockdown).


title: TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS

status: Public on Feb 07 2013

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

summary: TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O-GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3-OGT co-localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3-OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step-wise model, involving TET-OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-Seq experiments were performed on Illumina HiScanSQ sequencer in wild-type HEK293T cells for H3K4me3 histone marks, O-GlcNAc and HCF1, for HT-TET2, HT-TET3 and HT-OGT in HEK293T cells overexpressing those three fusion proteins and in TET2 Kd HEK293T cells for H3K4me3 histone marks. ChIP-Seqs were also performed in mouse bone marrow tissues for H3K4me3 histone marks, O-GlcNAc, endogenous Tet2 and in Tet2 Ko bone marrow tissues for H3K4me3 histone marks.

first: Rachel

last: Deplus

first: Benjamin

last: Delatte

first: Marie

middle: K

last: Schwinn

first: Jacqui

last: Méndez

first: Nancy

last: Murphy

first: Mark

middle: A

last: Dawson

first: Michael

last: Volkmar

first: Sarah

last: Dedeurwaerder

first: Pascale

last: Putmans

first: Emilie

last: Calonne

first: Roos

middle: L

last: Levine

first: Olivier

last: Bernard

first: Thomas

last: Mercher

first: Eric

last: Solary

first: Marjeta

last: Urh

first: Danette

last: Daniels

first: François

last: Fuks


title: Sequencing of small RNA libraries prepared from Invertebrate Iridescent Virus 6 (IIV6)-infected S2 cells or adult flies.

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: We observed several hundreds of thousand reads matching the IIV6 genome in IIV6 infected S2 and wild-type flies. The large majority of these reads have a size of 21 nt. This peak was absent from the library prepared from S2 non-infected and infected Dcr-2-/- mutant flies. The virus-derived siRNAs were not uniformally distributed along the viral genome, but rather several hotspots were observed, revealing that specific regions of the viral genome generate the siRNAs.

overall_design: Small RNA profiles of IIV6 infected S2 cells and adult flies were generated by deep sequencing using Illumina 2G Analyzer.

first: Akira

last: Goto

first: Vincent

last: Barbier

first: Simona

last: Paro

first: Laurent

last: Troxler

first: Sébastien

last: Pfeffer


title: Accelerated high-yield generation of limb-innervating motor neurons from human stem cells

city: Cambridge

first: Mackenzie

middle: W.

last: Amoroso

state: MA

address: 52 Oxford St.

country: USA

institute: Harvard University

summary: Human pluripotent stem cells are a promising source of diverse cells for developmental studies, cell transplantation, disease modeling, and drug testing.  However, their widespread use even for intensely studied cell types like spinal motor neurons, is hindered by the long duration and low yields of existing protocols for in vitro differentiation and by the molecular heterogeneity of the populations generated. We report a combination of small molecules that induce up to 50% motor neurons within 3 weeks from human pluripotent stem cells with defined subtype identities that are relevant to neurodegenerative diseases.  Despite their accelerated differentiation, motor neurons expressed combinations of HB9, ISL1 and column-specific markers that mirror those observed in vivo in human fetal spinal cord. They also exhibited spontaneous and induced activity, and projected axons towards muscles when grafted into developing chick spinal cord.  Strikingly, this novel protocol preferentially generates motor neurons expressing markers of limb-innervating lateral motor column motor neurons (FOXP1+/LHX3-). Access to high-yield cultures of human limb-innervating motor neuron subtypes will facilitate in-depth study of motor neuron subtype-specific properties, disease modeling, and development of large-scale cell-based screening assays.

overall_design: We analyzed 3 samples including 2 positive samples and 1 negative sample. Descriptions are as follows: a) Positive Sample 1: SHH-derived, day 21 GFP-high FACS-purified motor neurons. b) Positive Sample 2: S+P-derived, day 21 GFP-high FACS-purified motor neurons. c) Negative: S+P condition, day 21 GFP-off FACS-purified non-motor neurons. Initial analysis of data was performed on ~40% of fastq reads (Amoroso et al., J Neurosci 2013 Jan 9;33(2):574-86. PMID: 23303937).  Further processing of the full dataset has since been carried out and the updated rpkm file and expression analysis reflecting all aligned reads can be accessed at: http://scholar.harvard.edu/amorosornaseq/

middle: W

first: Gist

middle: F

last: Croft

first: Damian

middle: J

last: Williams

first: Sean

last: O’Keeffe

first: Monica

last: Carrasco

first: Anne

middle: R

last: Davis

last: Roybon

first: Derek

middle: H

last: Oakley

first: Tom

last: Maniatis

first: Christopher

middle: E

last: Henderson

first: Hynek

last: Wichterle


title: Effects of pharmacologic FSH inhibition on gene expression

first: Tobias

last: Kockmann

summary: see Super Series Summary

overall_design: We treated Drosophila S2-DRSC cells for 1, 2, 4 and 20 h with 10 µM JQ1 and compared their gene expression to DMSO-treated control cells (1 and 20 h).

first: Moritz

last: Gerstung

first: Xhinzhou

last: Zhu

first: Daniel

last: Hess

first: Christian

last: Beisel

first: Renato


title: Deep RNA sequencing reveal a complex transcriptional landscape of a bat adenovirus.

city: Wuhan

first: Lijun

last: Wu

address: 44, Xiao hongshan street

country: China

institute: wuhan institute of virology

summary: Bat adenoviruses are a group of recently identified adenoviruses (AdVs) which are highly prevalent in bats yet share low similarity to known AdVs from other species. In this study, deep RNA sequencing was used to analyze the transcriptome at five time points following the infection of a bat AdV in a kidney cell line derived from a myotis bat species. Evidence of AdV replication was observed with the proportion of viral RNAs ranging from 0.01% at 6 h to 1.3% at 18 h. Further analysis of viral temporal gene expression revealed three replication stages; the early stage genes encoding mainly for host interaction proteins, the intermediate stage genes for the DNA replication and assembly proteins, and the late stage genes for most structural proteins. Several bat AdV genes were expressed at stages that differed from their counterpart genes previously reported for human AdV. In addition, single-base resolution splice sites of several genes and promoter regions of all 30 viral genes were fully determined. Simultaneously, the temporal cellular gene expression profiles were identified. The most overrepresented functional categories of the differentially expressed genes were related to cellular immune response, transcription, translation, and DNA replication and repair. Taken together, the deep RNA sequencing provided a global, transcriptional profile of the novel BtAdV and the virus-host interactions, which will be useful for the understanding and investigation of AdV replication, pathogenesis and specific virus-bat interactions in future research.

overall_design: Deep RNA sequencing was used to analyze the transcriptome at five time points(0h,6h,8h, 12h 18h) following the infection of a bat AdV in a bat kidney cell.

first: Peng

last: Zhou


title: The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

summary: Background: The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results: Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread colocalization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions: Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes.

first: Tommy

last: Schlumpf

first: Zhu

last: Xhinzhou

first: Niko

last: Beerenwinkel

last: Paro


title: Generation of chromatin maps for ASH1 and FSH applying ChIP-seq

summary: see Super Series Summary

overall_design: Cross-linked chromatin derived from Drosophila S2-DRSC cells was immunoprecipitated using antibodies targeting ASH1 and FSH. Precipitated chromatin was sequenced applying Illumina sequencing.

last: Xinzhu


title: Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [ChIP-Seq]

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary: The Hippo pathway regulates metazoan growth, acting through the transcriptional co-activators Yorkie (in Drosophila) and Yap and Taz (in vertebrates). Much attention has been focused on upstream regulators of Yorkie and its homologues. In contrast, the mechanisms by which they actually promote transcription have remained poorly understood. Genome-wide chromatin binding experiments support extensive functional overlap between Yorkie and GAF. Chromatin binding identifies thousands of Yorkie sites, the majority of which are associated with elevated transcription, based on genome-wide analysis of mRNA and histone H3K4Me3 modification. Our studies establish a molecular basis for transcriptional activation by Yorkie and implicate it as a global regulator of transcriptional activity in Drosophila.

overall_design: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Ken Irvine at HHMI/Rutgers University and Richard S. Mann at Columbia University.  It contains ChIP-seq data (Illumina) for multiple transcription factor antibodies in Drosophila embryos and larval wing imaginal discs.

first: Matthew

last: Slattery

first: Hyangyee

last: Oh

first: Lijia

last: Ma

first: Alex

last: Crofts

first: Jason

last: Grundstad

first: Richard

last: Mann

first: Kenneth

last: Irvine


title: FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells

status: Public on Feb 05 2013

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki


title: The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey


title: FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells (HTS)

summary: We report the androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell lines, LNCaP-1F5 and VCaP in response to physiological androgen 5a-dihydrotestosterone (DHT) using ChIP-sequencing. We compare the AR recruitment by DHT to that by partial agonist/antagonist cyproterone acetate (CPA), mifepristone (RU486) and bicalutamide (Bica) in LNCaP-1F5 cells. We also report the role of glucocorticoid receptor recruitment in presence of dexamethasone (Dex) in androgen responsive prostate cancer cells. The AR and GR cistrome analysis is subsequently compared with gene expression data and RNA Pol II analysis. The ChIP-seq has been performed using AR, GR, RNA Pol II antibodies.

overall_design: Examination of AR and GR binding sites in LNCaP-1F5 and VCaP cells in presence of DHT and Dex respectively. Further analysis of AR binding sites in LNCaP-1F5 cells treated with partial agonist/antagonists, CPA, RU486 and Bica. Additionally RNA Pol II mapping is performed in cells treated with DHT and Dex.

first: Sahu

last: Biswajyoti

first: Laakso

last: Marko

first: Pihlajamaa

last: Paivi

first: Ovaska

last: Kristian

first: Sinielnikov

last: Ievgenii

first: Hautaniemi

last: Sampsa

first: Jänne

last: Olli


title: Identification of Transcription Factor DPL-1::GFP Binding Regions in L1

status: Public on Feb 04 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3607
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: OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene dpl-1; Strain OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); 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

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq data)

first: Michael

last: Verzi

summary: We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi. This metadata file describes the ChIP-seq componant of that data

overall_design: Intestinal epithelia were collected from mouse jejunum using EDTA-based chelation and ChIP-seq was performed, followed by next generation sequencing.

first: X

middle: S

last: Liu

first: Hyunjin

last: Shin

first: Ramesh

last: Shivdasani


title: Identification of Transcription Factor HPL-2::GFP Binding Regions in L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_3604
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: YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene hpl-2; Strain YL416(official name : YL416 genotype : unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The HPL-2::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder


title: Identification of Transcription Factor LIN-35::GFP Binding Regions in yA

summary:
modENCODE_submission_3602
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: YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene lin-35; Strain YL402(official name : YL402 genotype : unc-119(ed3) III; vrIs56[pPIE-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the pie-1 promoter. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray


title: Identification of Transcription Factor NHR-77::GFP Binding Regions in L1

summary:
modENCODE_submission_3594
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: OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : 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 NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-77;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene nhr-77; Strain OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : 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 NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu


title: Identification of Transcription Factor NHR-116::GFP Binding Regions in L4

summary:
modENCODE_submission_3599
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: OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : 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 NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-116;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene nhr-116; Strain OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : 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 NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ); temp (temperature) 20 degree celsius

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal


title: Identification of Transcription Factor SPTF-1::GFP Binding Regions in L1

summary:
modENCODE_submission_3601
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: OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 tags : Bombard tag : 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite; Transgene: sptf-1;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene sptf-1; Strain OP196(official name : OP196 genotype : unc119(ed3);wgIs196(sptf1::TY1 EGFP FLAG C;unc119) outcross : 3 transgene : sptf-1 tags : Bombard tag : 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 SPTF-1::EGFP fusion protein is expressed in the correct sptf-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SPTF-1 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor ZK377.2::GFP Binding Regions in L4

summary:
modENCODE_submission_3593
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: OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene sax-3; Strain OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1

summary:
modENCODE_submission_3590
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: OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene sax-3; Strain OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor LIN-15B::GFP Binding Regions in L1

summary:
modENCODE_submission_3589
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: OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) 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 LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene lin-15B; Strain OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) 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 LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor R02D3.7::GFP Binding Regions in L3

summary:
modENCODE_submission_3586
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: OP218(official name : OP218 genotype : unc-119(ed3); wgIs218(R02D3.7: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 R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : Mihail Sarov ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene R02D3.7; Strain OP218(official name : OP218 genotype : unc-119(ed3); wgIs218(R02D3.7: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 R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor ALY-2::GFP Binding Regions in L2

summary:
modENCODE_submission_3383
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: OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-2: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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: L2; Genotype: unc-119(ed3); wgIs217(aly-2:TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene aly-2; Strain OP217(official name : OP217 genotype : unc-119(ed3); wgIs217(aly-2: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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor F45C12.2::GFP Binding Regions in L2

summary:
modENCODE_submission_3379
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: OP212(official name : OP212 genotype : unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : F45C12.2 tags : Bombard tag : 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 F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: F45C12.2;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene F45C12.2; Strain OP212(official name : OP212 genotype : unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : F45C12.2 tags : Bombard tag : 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 F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor DPL-1::GFP Binding Regions in L4

summary:
modENCODE_submission_3366
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: OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene dpl-1; Strain OP105(official name : OP105 genotype : unc119(ed3);wgIs105(dpl-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The DPL-1::EGFP fusion protein has broad expression pattern description : but silence in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor AHA-1::GFP Binding Regions in L4

summary:
modENCODE_submission_3069
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: OP124(official name : OP124 genotype : unc-119(ed3); wgIs124(aha-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 AHA-1::EGFP fusion protein is expressed in the correct aha-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the AHA-1 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L4; Genotype: unc-119(ed3); wgIs124(aha-1::TY1 EGFP FLAG;unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene aha-1; Strain OP124(official name : OP124 genotype : unc-119(ed3); wgIs124(aha-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 AHA-1::EGFP fusion protein is expressed in the correct aha-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the AHA-1 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor LIN-35::GFP Binding Regions in L1

summary:
modENCODE_submission_3603
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: YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene lin-35; Strain YL398(official name : YL398 genotype : unc-119(ed3) III; vrIs55[pGES-1::LIN-35::GFP FLAG: LIN-35 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The LIN-35::GFP fusion protein is driven by the ges-1 promoter and is expressed in the intestine. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius


title: Small RNA sequencing from Arabidopsis adult leaves and profiling of Arabidopsis transcripts in response to flg22 peptide

city: Paris

first: Emmanuelle

last: Lastrucci

address: 46 rue d'Ulm

institute: Institut de Biologie de l’Ecole Normale Supérieure

summary:
DNA methylation is an epigenetic mark that silences transposable elements (TEs) and repeats. Whereas the establishment and maintenance of DNA methylation are relatively well understood, little is known on their dynamics and biological relevance in plant and animal innate immunity. Here, we show that some TEs are demethylated and transcriptionally reactivated during antibacterial defense in Arabidopsis. This effect is concomitant with the down-regulation of key transcriptional gene silencing factors as well as an active demethylation process. DNA demethylation restricts multiplication and vascular propagation of the bacterial pathogen Pseudomonas syringae in leaves and, accordingly, some immune-response genes, containing repeats in their promoters, are negatively regulated by DNA methylation. This study provides evidence that DNA demethylation is part of a plant-induced immune response, potentially acting to prime transcriptional activation of some defense genes linked to Tes/repeats.

We have monitored the transcript changes in Arabidopsis plants treated with a flagellin-derived peptide.

overall_design:
DNA methylation is closely related to 24nt sRNAs. This is why we sequenced small RNA population in our study.
5-week-old Col-0 leaf samples (treated with either water or flg22 at 1 ?M concentration for 6 h) and deep sequenced by Fasteris (Geneva) on the Illumina HiSeq 2000 platform.

first: Yu

last: Wang

first: Agnès

last: Yu

first: Anne

last: Abraham

first: Lionel

last: Navarro


title: Transcriptional profiles of PA1 teratoma cells transfected by RIPK1, RIPK2, RIPK3, or RIPK4

city: South San Francisco

first: Jinfeng

last: Liu

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

summary: RIPK4 but not the related kinases RIPK1, RIPK2, and RIPK3 caused similar transcriptional changes to Wnt3a.

overall_design: PA1 cells were transfected by 8ug RIPK1, RIPK2, RIPK3, or RIPK4 for 48h, RNA were extracted and sequenced.

first: XiaoDong

last: Huang


title: Genome-wide mapping of early replication fragile sites (ERFS)

city: Philadelphia

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

summary: DNA double strand breaks (DSBs) in B lymphocytes are thought to arise  stochastically during replication (S phase) or as a result of targeted DNA damage by  activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of  recurrent, early replicating and AID independent DNA lesions, termed early  replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins  DNA double strand breaks (DSBs) in B lymphocytes are thought to arise  stochastically during replication (S phase) or as a result of targeted DNA damage by  activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of  recurrent, early replicating and AID independent DNA lesions, termed early  replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins  DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins  RPA, SMC5, gamma-H2AX, and BRCA1 in B cells subjected to replication stress.

overall_design: Protein-DNA association for four DNA damage response proteins (RPA, SMC5, g-H2AX, BRCA1), BrdU incorporation, and gene transcription in B lymphocytes with and without hydroxyurea treatment were examined.

middle: B

first: Jacqueline

last: Barlow


title: Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [Bisulfite-Seq]

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave. Room W-506

department: Department of Pharmacology

institute: Weill Cornell Medical College

type: Methylation profiling by high throughput sequencing

summary: Maternal 5-HT1A-receptor (R) is required for the timely development of the hippocampus and the establishment of emotional behaviors in Swiss-Webster (SW) mice.  A partial and/or complete loss of maternal 5-HT1AR results in delayed ventral dentate granule cell (v-DGC) development and subsequent anxiety-like phenotype in the wild-type offspring by a non-genetic, presumably epigenetic mechanism.  Here we tested v-DGCs for genome-wide DNA methylation changes elicited by the receptor deficient maternal environment.  We identified a set of hypomethylated regions in the offspring of receptor deficient mothers.  A significant fraction of these maternal-differentially methylated regions (m-DMRs) mapped to strong CpG islands, sequences that are typically not methylated or if methylated, resistant to environmental-induced changes.  Many m-DMRs mapped to exons and some were associated with expression changes.  Their hypomethylation was due to an arrest in de novo methylation and, to a lesser extent, to demethylation during postnatal life indicating that the perturbation in methylation coincides with the developmental delay in DGC maturation in the offspring of receptor deficient mothers.  Inhibiting methylation in differentiating neurons impaired their maturation further suggesting a link between de novo methylation and neuronal differentiation.  These data suggest that methylation at specific exonic CpG-islands may contribute to the mechanism through which maternal 5-HT1AR modulates hippocampal development and consecutively the level of anxiety in the SW offspring.  Reduced 5-HT1AR-binding has been reported in individuals, particularly in association with anxiety/depression, including peri/postpartum depression.  Therefore, maternal receptor deficit may contribute, via a non-genetic mechanism, to the high prevalence and heritability of anxiety disorders in human.

overall_design: Examined 4 samples:  5HT1A wild type offspring with 5HT1A wild type/heterozygous mother or 5HT1A KO offspring with 5HT1A of heterozygous/knock out mother

first: Ji-eun

last: Oh

first: Nyasha

last: Chambwe

first: Judit

last: Gal

first: Stuart

last: Andrews

first: Georgia

last: Gleason

first: Rita

last: Shaknovich

first: Ari

last: Melnick

first: Fabien

last: Campagne


title: Identification of Transcription Factor ZK377.2::GFP Binding Regions in L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_3592
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: OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene sax-3; Strain OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::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 Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

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

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: The Function of Piwi is Independent of Its Slicer Activity

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

summary: In diverse organisms, the highly-conserved Piwi proteins bind to a complex class of small non-coding RNAs called piRNAs, and are essential for germline stem cell maintenance, transposon silencing, fertility, and offspring viability1. By homology with other Argonautes, Piwi proteins have been proposed and later reported to possess endonuclease activity in vitro, effected by its conserved aspartate catalytic triad2,3. Indeed, mutation of these residues in one of the three mouse PIWI proteins, MILI, affects the production of Line 1 piRNAs and spermatogenesis4. In Drosophila, the conserved slicer function has been proposed to be crucial for all Piwi proteins in piRNA amplification and transposon silencing5. Here, we report in vivo evidence that, in contrast to common belief, the catalytic triad of Piwi is not required for the function of PIwi  in the germline for stem cell maintenance, fertility, transposon silencing, or  piRNA biogenesis. In addition, it is not required for piRNA biogenesis in the soma where Piwi is the sole Piwi-subfamily protein involved in the process. These observations, together with the recent findings on MILI and MIWI2 triad mutant, indicate that even though the slicer function may be required for a subset of piRNA-mediated process, it is overall inconsequential for the function of Piwi proteins

overall_design: Assess the role of the endonuclease activity of Piwi in all known biological processes that involve Piwi function in Drosophila ovary

first: Nicole

last: Darricarrère

first: Toshiaki

last: Watanabe

first: Haifan

last: Lin


title: Transcriptome sequencing of the rock pigeon, Columba livia

status: Public on Feb 03 2013

city: Shenzhen

first: tan

last: hao

state: Guangdong

address: Building No.11,Beishan Industrial Zone,Yantian District

department: Department of Science & Technology

institute: BGI-Shenzhen

summary: Deep sequencing of mRNA from the rock pigeon

overall_design: Analysis of ploy(A)+ RNA of different specimens: heart and liver from the rock pigeon (Danish Tumbler, Oriental Frill and Racing)

first: Guojie

last: Zhang

first: Cai

last: Li


title: Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [RNA-Seq]

first: Miklos

last: Toth

overall_design: Examined transcriptomes of 5HT1A wild type offspring with 5HT1A wild type/heterozygous mother or 5HT1A KO offspring with 5HT1A of heterozygous/knock out mother

first: Ji-eun

last: Oh

first: Nyasha

last: Chambwe

first: Judit

last: Gal

first: Stuart

last: Andrews

first: Georgia

last: Gleason

first: Rita

last: Shaknovich

first: Ari

last: Melnick

first: Fabien

last: Campagne


title: Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus

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

overall_design: Refer to individual Series


title: Histone H3K9 Methyltransferase G9a Represses PPARγ Expression and Adipogenesis [ChIP-Seq and RNA-Seq data]

status: Public on Feb 01 2013

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: PPARγ promotes adipogenesis while Wnt proteins inhibit adipogenesis. However, the mechanisms that control expression of these positive and negative master regulators of adipogenesis remain incompletely understood. By genome-wide histone methylation profiling in preadipocytes, we find that among gene loci encoding adipogenesis regulators, histone methyltransferase (HMT) G9a-mediated repressive epigenetic mark H3K9me2 is enriched on the entire PPARγ locus. H3K9me2 and G9a levels decrease during adipogenesis, which correlates inversely with induction of PPARγ. Removal of H3K9me2 by G9a deletion enhances chromatin opening and binding of adipogenic transcription factor C/EBP-beta to PPARγ promoter, which promotes PPARγ expression. Interestingly, G9a represses PPARγ expression in an HMT activity-dependent manner but facilitates Wnt10a expression independent of its enzymatic activity. Consistently, deletion of G9a or inhibiting G9a HMT activity promotes adipogenesis. Finally, deletion of G9a in mouse adipose tissues increases adipogenic gene expression and tissue weight. Thus, by inhibiting PPARγ expression and facilitating Wnt10a expression, G9a represses adipogenesis.

overall_design: Examination of 3 different histone modification changes in 3T3-L1 preadipocytes

first: Lifeng

last: Wang

first: Shiliyang

last: Xu


title: Identification of Transcription Factor C16A3.4::GFP Binding Regions in L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_3367
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: OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene C16A3.4; Strain OP345(official name : OP345 genotype : unc119(ed3);wgIs345(C16A3.4::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain.  The C16A3.4::EGFP fusion protein has broad expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the C16A3.4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

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

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

city: Ithaca

first: Hojoong

last: Kwak

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a Precision nuclear Run-On and sequencing assay (PRO-seq) to map the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' poly-adenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing . We test this ‘Complex Interaction’ model with insertional mutagenesis of the Drosophila Hsp70 core promoter.

overall_design:
Identification of RNA polymerase active sites in Drosophila S2 cell line using PRO-seq method.
Identification of transcription initiation sites in Drosophila S2 cell line using PRO-cap method.
Identification of changes in RNA polymerase active sites on transgenic Hsp70 promoters upon disruption of DNA sequence elements in 3 transgenic fly lines using PRO-seq method.

first: Nicholas

last: Fuda

first: Leoghton

last: Core

middle: T

last: Lis


title: C. neoformans gene expression in DMEM of WT and rim101 mutant cells

status: Public on Feb 02 2013

city: Durham

first: Teresa

last: O'Meara

state: NC

address: DUMC 3355

institute: Duke University

summary: Purpose: To examine the comparative transcriptional profiles of WT and rim101 mutant cells in host-mimicking in vitro conditions to determine genes that are responsible for the increased virulence of the rim101 strain. The rim101 mutant is able to trigger an overactive inflammatory response, presumably by exposing an antigenic trigger. Using transcriptional profiling, we determined that many genes involved in cell wall processes were differentially transcribed between the wild type and the mutant strain.

overall_design: Whole mRNA profiles of WT and rim101 cells were generated by deep sequencing using Illumina GAII.

first: Andrew

last: Alspaugh


title: Histone H3K9 Methyltransferase G9a Represses PPARγ Expression and Adipogenesis

first: Kai

last: Ge


title: H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence (ChIP-seq)

status: Public on Jan 31 2013

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

summary: Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. We combined quantitative mass spectrometry and ChIP deep-sequencing to identify changes in histone modification occurring during cellular senescence.

overall_design: ChIP-seq was carried out using H3K4me3-specific antibodies in growing, quiescent, senescent, or senescent with shRB targeting Rb, IMR90 cells. The control mock data (ChIP-seq using anti-mouse IgG antibody) is available in GEO Sample GSM497500 (Series GSE19898).

first: Scott

last: Lowe

first: Xiaowo

last: Wang


title: H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence


title: Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Cell Composition

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: By applying RNA-ISH and RNAseq to circulating tumor cells (CTCs), the study provides definitive evidence of epithelial to mesenchymal transition (EMT) across all histological types of breast cancer, identifying mediators such as FOXC1 and TGF-β signaling, and demonstrating dynamic treatment-associated changes in EMT within clusters of CTCs.

overall_design: Epithelial to mesenchymal transition (EMT) has been postulated to contribute to the migration and dissemination of cancer cells, but supporting histopathological evidence is limited. We used a microfluidic device to isolate circulating tumor cells (CTCs), combined with multiplex fluorescent RNA-in-situ hybridization (ISH) and RNA sequencing, to quantify and characterize EMT in breast cancer cells within the bloodstream. Whereas only rare (0.1-10%) cells in the primary tumor expressed both mesenchymal and epithelial markers, such biphenotypic as well as purely mesenchymal cells were enriched among CTCs, across all histological subtypes of breast cancer. In an index patient followed longitudinally, fluctuation in epithelial and mesenchymal states was observed as a function of initial response and subsequent resistance to therapy. Mesenchymal markers were predominant in clusters of tumor cells, many of which had adherent platelets. Finally, RNA sequencing of CTC clusters identified TGF-β and other EMT-related signatures, which were absent from more epithelial CTCs. FOXC1, a known regulator of EMT, was abundantly expressed in mesenchymal CTCs and was detectable within localized regions of the primary breast tumor. Together, these data support a role for EMT in the blood-borne dissemination of breast cancer and point to the dynamic nature of this cell fate change.

first: Min

last: Yu

first: Aditya

last: Bardia

first: Shannon

last: Stott

first: Malgorzata

last: Smas

first: David

last: Ting

first: Steven

last: Isakoff

first: Jordan

middle: C

last: Ciciliano

first: Marissa

middle: N

last: Wells

first: Ajay

middle: M

last: Shah

first: Kyle

last: Concannon

first: Lecia

middle: V

last: Sequist

first: Elena

last: Brachtel

first: Dennis

last: Sgroi

first: Jose

last: Baselga

first: Sridhar

last: Ramaswamy

first: Mehmet

last: Toner

first: Daniel

last: Haber

first: Shyamala

last: Maheswaran


title: Multiple roles of RNase Y in Streptococcus pyogenes mRNA metabolism

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

summary:
Streptococcus pyogenes (Group A streptococcus, GAS) is an important human pathogen that causes a variety of infectious diseases and sequelae. Recent studies showed virulence factor expression was controlled at multiple levels, including the post-transcriptional regulation.
In this study, we examined the global half-lives of S. pyogenes mRNAs and explored the role RNase Y played in mRNA metabolism with microarray analysis.
key word: genetic modification

overall_design:
Streptococcus pyogenes NZ131 wild-type cells and Δrny strains were grown in C-medium until late exponential phase. Rifampicin was added to the cell culture and samples were collected before and after rifampicin addition. The transcriptional profile of the whole genome before and after rifampicin addition was examined with microarray.

Please note that mRNA decay assay resulted in considerable variations in the datasets. Samples were taken after rifampicin addition and subsequent incubation for different time intervals. During that time no new RNA is produced and the remaining RNA is degraded to various degrees.

first: Zhiyun

last: Chen

first: Joseph

last: Ferretti


title: Antitumor activity of a pyrrole-imidazole polyamide

city: Pasadena

first: Fei

last: Yang

address: 1200 E. California Blvd.

institute: California Institute of Technology

summary: We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) polyamide interferes with RNA polymerase II (RNAP2) activity in cell culture.  Genome-wide mapping of RNAP2 binding shows reduction of occupancy preferentially at transcription start sites (TSS), while occupancy at enhancer sites are is unchanged.

overall_design: Genome-wide mapping of RNA polymerase II in LNCaP cells treated with DHT and DHT with Py-Im polyamide.


title: Small non-coding RNA expression in mouse elongated spermatids

city: Beijing

first: Qi

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Reproductive Biology

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: In order to discover novel small RNAs expressed in elongated spermatids, we isolated elongated spermatids from mouse testis. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA.

overall_design: RNAs extracted from elongated spermatids were used for high throughput sequencing analysis

first: Hongying

last: Peng

first: Junchao

last: Shi

first: Ying

last: Zhang

first: He

first: Shangying

last: Liao

first: Li

last: Lei

first: Chunsheng

last: Han

first: Lina

last: Ning

first: Yujing

last: Cao

first: Enkui

last: Duan


title: RUNX1 is a key target gene in t(4;11) leukemias and contributes to gene activation by interacting with the AF4-MLL complex

city: Oxford

first: Erica

last: Ballabio

address: headley way

department: The Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: Univeristy of Oxford

summary: The Mixed Lineage Leukemia 1 protein (MLL1) is an important epigenetic regulator required for the maintenance of gene activation during development. MLL1 chromosome translocations produce novel fusion proteins that cause aggressive leukemias in humans. Individual MLL1 fusion proteins have distinct leukemic phenotypes even when expressed in the same cell type, but how this distinction is delineated on a molecular level is poorly understood. Here we highlight a unique molecular mechanism whereby MLL-AF4 specifically activates the RUNX1 gene and the RUNX1 protein interacts with the product of the reciprocal AF4-MLL translocation. These results support a mechanism of leukemic growth whereby two oncogenic fusion proteins cooperate by activating a target gene and then interacting directly with its downstream product

overall_design: ChIP-seq using RUNX1 antibody in SEM cells

first: Huimin

last: Geng

first: Thomas

middle: A

last: Milne


title: RNA-seq analysis of single bovine blastocysts

city: Davis

first: James

middle: Lee

last: Chitwood

address: 1 Shields Avenue

department: Animal Science

institute: University of California, Davis

summary: Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology

overall_design: RNA was extracted from individual D7  bovine blastocysts (Arcturus Picopure), cDNA was synthesized and amplified (Nugen Ovation) and indexed libraries were created for sequencing (Nugen Encore)

first: Pablo

last: Ross


title: Stochastic genome - nuclear lamina contacts are linked to histone H3K9 dimethylation

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Methylation profiling by genome tiling array


title: Stochastic genome - nuclear lamina contacts are linked to histone H3K9 dimethylation (RNA-seq data)

summary: The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina-associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs in single cells using a novel 'molecular contact memory' approach. In each interphase nucleus, only ~30% of LADs are positioned at the periphery; these LADs are in intermittent molecular contact with the NL but remain constrained to the periphery. Upon mitosis, LAD positioning is not detectably inherited but instead is stochastically reshuffled. Contact of individual LADs with the NL correlates with their degree of H3K9 dimethylation in single cells, and inactivation of the H3K9 methyltransferase G9a reduces the NL contact frequencies. These results indicate that nuclear positioning and histone modification of LADs are both stochastic yet linked in single cells. Collectively, these results highlight principles of the dynamic spatial architecture of chromosomes.

overall_design:
12 RNA-seq experiments for 6 samples, each with a biological replicate:
m6ATracer-VP16+/DamLaminB1+
m6ATracer-VP16+/DamLaminB1-
m6ATracer-VP16-/DamLaminB1-
m6ATracer-GFP+/DamLaminB1+
m6ATracer-GFP+/DamLaminB1-
m6ATracer-GFP-/DamLaminB1-

first: Jop

last: Kind

first: Ludo

last: Pagie

first: Havva

last: Ortabozkoyun

first: Shelagh

last: Boyle

first: Wendy

last: Bickmore


title: Circular RNAs are a large class of animal RNAs with regulatory potency (RNA-Seq)

status: Public on Feb 28 2013

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrueck Center for Molecular Medicine

summary: Circular RNAs (circRNAs) in animals are an enigmatic class of RNAs with unknown function. To systematically explore circRNAs, we sequenced and computationally analyzed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, with oftentimes tissue/developmental stage specific expression. Sequence analysis suggested important regulatory functions for circRNAs. Indeed, we discovered that human circRNA CDR1as is densely bound by miRNA effector complexes and harbors 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebra fish impaired midbrain development similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, indicating previously unrecognized regulatory potential of coding sequences.

overall_design: 1 Sample

first: Markus

last: Landthaler


title: small RNA deep-sequencing of mature sperm, testis and uterus in mice

first: Qi

last: Chen

summary: In order to discover novel small RNAs expressed in mature sperm, we isolated mature sperm from mouse cauda epididymis, comparing with data from adult tesis and uterus. The small RNA fraction (18-40nt) was cloned and sequenced from total RNA of mature sperm, testis and uterus of mice.

overall_design: RNAs extracted from mature sperm, adult testis and uterus were used for high throughput sequencing analysis

first: Hongying

last: Peng

first: Junchao

last: Shi

first: Ying

last: Zhang

first: He

first: Shangying

last: Liao

first: Li

last: Lei

first: Chunsheng

last: Han


title: Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

status: Public on Jan 29 2013

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory TNF. The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steadystate total RNA and should be useful in many biological settings.

overall_design: Analysis of the effect of TNF exposure in nascent gene expression and in transcript stability

first: Michelle

last: Paulsen

first: Artur

last: Veloso

first: Jayendra

last: Prasad

first: Karan

last: Bedi

first: Emily

first: Ya-Chun

last: Tsan

first: Ching-Wei

last: Chang

first: Brendan

last: Tarrier

first: Joseph

middle: G

last: Washburn

first: Robert

last: Lyons

first: Daniel

middle: R

last: Robinson

first: Chandan

last: Kumar-Sinha

first: Thomas

last: Wilson


title: Combined deficiency of Tet1 and Tet2 is compatible with development but leads to epigenetic instability

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet1 and Tet2 mediate 5hmC generation in mouse embryonic stem cells (ESCs) and various embryonic and adult tissues. To investigate the effects of combined deficiency of Tet1 and Tet2 on pluripotency and development, we have generated Tet1 and Tet2 double knockout (DKO) ESCs and mice. DKO ESCs were depleted of 5hmC, but remained pluripotent with subtle defects in differentiation and changes in gene expression. Double mutant embryos and chimeras exhibited mid-gestation defects and postnatal DKO mice displayed partially penetrant neonatal lethality and stochastic perturbation of imprinting. Viable DKO animals developed normally to adulthood but had reduced 5hmC level, increased 5mC level and lacked 5hmC in germ cells. Nevertheless, DKO mice of both sexes were fertile with females having smaller ovaries and reduced fertility. Our data suggest that both Tet1 and Tet2 contribute to 5hmC levels during development. Their combined loss does not block differentiation and embryogenesis, but leads to partially penetrant embryonic and perinatal abnormalities and compromised viability. Moreover, the presence of substantial levels of 5hmC in DKO embryos and adult mice suggests a significant contribution of Tet3 in hydroxylation of 5mC during development.

overall_design: Methylation patterns in tissue samples from a series of wt and Tet1/Tet2 DKO embryos, neonates and adults were generated using methylated DNA immunoprecipitation with antibodies against 5mC (MeDIP) and 5hmC (hMeDIP) followed by deep sequencing.

first: Frank

last: Lyko

first: Achim

last: Breiling


title: A High-Resolution Enhancer Atlas of the Developing Telencephalon

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

summary: The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. While many of the genes required for its development have been identified, the distant‐acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified over 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web‐based enhancer atlas comprising over 33,000 sections. We show how this large collection of annotated telencephalon enhancers can be used to study the regulatory architecture of individual genes, to examine the sequence motif content of enhancers, and to drive targeted reporter or effector protein expression in experimental applications. Furthermore, we used epigenomic analysis of human and mouse cortex tissue to directly compare the genome‐wide enhancer architecture in these species. This atlas provides a primary resource for investigating gene regulatory mechanisms of telencephalon development and enables studies of the role of distant‐acting enhancers in neurodevelopmental disorders.

overall_design: Examination of p300 binding in mouse embryonic stage 11.5 forebrain, mouse postnatal (P0) cortex tissue and human fetal (gestational week 20) cortex

middle: J

first: Axel

last: Visel


title: NOT2 proteins promote Pol II-dependent transcription and interact with multiple miRNA biogenesis factors in Arabidopsis

status: Public on Jan 30 2013

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: MicroRNAs (miRNAs) play key regulatory roles in numerous developmental and physiological processes in animals and plants. The elaborate mechanism of miRNA biogenesis involves transcription and multiple processing steps. Here, we report the identification of a pair of evolutionarily conserved NOT2_3_5 domain containing proteins, NOT2a and NOT2b (previously known as At-NOT2 and VIP2, respectively), as components involved in Arabidopsis miRNA biogenesis. NOT2 was identified by its interaction with the Piwi/Ago/Zwille (PAZ) domain of Dicer-like 1 (DCL1), an interaction that is conserved between rice and Arabidopsis. Inactivation of both NOT2 genes in Arabidopsis caused severe defects in male gametophytes, and weak lines show pleiotropic defects reminiscent of miRNA pathway mutants. Impairment of NOT2s decreases the accumulation of pri-miRNAs and mature miRNAs and increases DCL1-containing nuclear speckle number in vivo. In addition, NOT2b protein interacts with Pol II and other miRNA processing factors including two cap-binding proteins, CBP80/ABH1, CBP20 and SERRATE (SE). Therefore, these results suggest that NOT2 proteins promote MIR transcription and facilitate efficient DCL1 recruitment in Arabidopsis.

overall_design: Examination of transcriptome of not2 and wild type by RNA-seq.

first: Lulu

last: Wang

first: Xianwei

last: Song

first: Liangfeng

last: Gu

first: Xin

last: Li

first: Shouyun

last: Cao

first: Chengcai

last: Chu

first: Xia

last: Cui

first: Xuemei

last: Chen

first: Xiaofeng


title: Brinker regulates wing disc growth in part via repression of Myc expression

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: The molecular mechanisms regulating tissue size represent an unsolved puzzle in developmental biology. One signaling pathway controlling growth of the Drosophila wing is Dpp. Dpp promotes growth via repression of the transcription factor Brinker. The transcriptional targets of Brinker that control cell growth and proliferation, however, are not yet fully elucidated. We report here a genome-wide ChIP-seq of endogenous Brinker from wing imaginal discs. We identify the growth regulator Myc as a target of Brinker and show that Myc together with the microRNA bantam explain a large fraction of the growth inhibition caused by Brinker. This work sheds light on the effector mechanisms by which Dpp signaling controls tissue growth.

overall_design: Identification of Brinker binding sites  in Wing imaginal discs cells

first: Nikolaos

last: Doumpas

first: Marina

last: Ruiz-Romero

first: Bruce

last: Edgar

first: Montserrat

last: Corominas

first: Aurelio

last: Teleman


title: Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites using GRO-seq

status: Public on Jan 28 2013

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Braveheart is a long non-coding RNA necessary for cardiac lineage commitment

city: Cambridge

first: Laurie

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

summary:
Purpose: Long non-coding RNAs (lncRNAs) display development-specific gene expression patterns, yet we know little about their precise roles in lineage commitment. Here, we discover a novel mammalian heart-associated lncRNA, AK143260, necessary for cardiac lineage specification.
Methods: Gene expression profiles of mouse ESCs and differentiated organs were analyzed for master regulators of lineage commitment. The AK143260 transcript was shown to be strongly expressed in mESCs and in cells undergoing cardiac differentiation. Its role in cardiac differentiation was examined using depletion and in vitro differentiation systems, with morphological and gene expression profiling at different time-points.
Results: mESCs depleted of AK143260, named Braveheart, fail to differentiate into cardiomyocytes and to activate a core cardiac gene regulatory network including key transcription factors driving cardiogenesis. We show that Braveheart functions upstream of MesP1 (mesoderm posterior 1), a transcription factor critical for specification of the earliest known multi-potent cardiovascular progenitor and in promoting epithelial-mesenchymal transition (EMT). Consistent with this, Braveheart depletion leads to morphological defects and loss of cardiogenic potential in a defined in vitro cardiomyocyte differentiation system. Furthermore, Braveheart is necessary to maintain myocardial gene expression and myofibril organization in neonatal cardiomyocytes.
Conclusions: These findings reveal that Braveheart is an important regulator of cardiac commitment and implicate lncRNAs as potential therapeutic targets for cardiac disease and regeneration.

overall_design:
Gene expression profiles from control and Bravheart-depleted mESCs were obtained by RNA-Seq on an Illumina HiSeq2000 instruments at Days 0,3,6 and 9.

Gene expression profiles from mESCs, MEFs, partially reprogrammed MEFs and miPS cells were obtained by RNA-Seq on Illumina GAII/GAIIx instruments.

first: Carla

last: Klattenhoff

first: Mohammedsharif

last: Tabebordbar

middle: L


title: The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

summary: The histone modifying complexes PRC2 and TrxG/MLL play pivotal roles in determining the activation state of genes controlling pluripotency, lineage commitment, and cell differentiation. Long non-coding RNAs (lncRNAs) can bind to either complex, and some have been shown to act as modulators of PRC2 or TrxG/MLL activity. Here we show that the lateral mesoderm-specific lncRNA Fendrr is essential for proper heart and body wall development in the mouse. Embryos lacking Fendrr displayed upregulation of several transcription factors controlling lateral plate or cardiac mesoderm differentiation, accompanied by a drastic reduction in PRC2 occupancy along with decreased H3K27 trimethylation and/or an increase in H3K4 trimethylation at their promoters. Fendrr binds to both the PRC2 and TrxG/MLL complexes, suggesting that it acts as modulator of chromatin signatures that define gene activity. Thus, our work identifies a lncRNA that plays an essential role in fine-tuning the regulatory networks which control the fate of lateral mesoderm derivatives.

overall_design: The transcriptomes of ventricles isolated from wildtype (WT) and Fendrr knock-out (KO) E12.5 embryos, obtained from tratraploid complementations of embryonic stem cells, were analyzed by strand-specific RNA-Seq of ribosomal RNA-depleted, total RNA.

first: Phillip

last: Grote

first: Lars

last: Wittler

first: Sandra

last: Währisch

first: David

last: Hendrix

first: Arica

last: Beisaw

first: Manuela

last: Scholze

first: Karol

last: Macura

first: Gaby

last: Bläss

first: Manolis

last: Kellis

first: Martin

last: Werber

first: Bernhard

last: Herrmann


title: Identification of Biologically Relevant Enhancers in Human Erythroid Cells

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University