title: Identification of Transcription Factor N2::POL II Binding Regions in Late Embryo

summary:
modENCODE_submission_2436
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: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: late embryo 20dC 4.5 hrs post-early embryo; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage late embryo 20dC 4.5 hrs post-early embryo; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor N2::POL II Binding Regions in Early Embryo

status: Public on Feb 18 2011

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_2435
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: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: early embryo; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage early embryo; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

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: Identification of Transcription Factor LIN-39::GFP Binding Regions in L3

summary:
modENCODE_submission_2432
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: OP18(made_by : R. Waterston and S. Kim 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-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::TY1::EGFP::3xFLAG] official name : OP18 ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene lin-39; Strain OP18(made_by : R. Waterston and S. Kim 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-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::TY1::EGFP::3xFLAG] official name : OP18 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor NHR-6::GFP Binding Regions in L2

summary:
modENCODE_submission_2433
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: OP90(made_by : R. Waterston 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-6::EGFP fusion protein is expressed in the correct nhr-6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] official name : OP90 ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-6; Strain OP90(made_by : R. Waterston 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-6::EGFP fusion protein is expressed in the correct nhr-6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] official name : OP90 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor HLH-1::GFP Binding Regions in Embryos

summary:
modENCODE_submission_2431
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: OP64(made_by : R. Waterston 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 HLH-1::EGFP fusion protein is expressed in the correct hlh-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs64 [unc-119(+) hlh-1::TY1::EGFP::3xFLAG] official name : OP64 ); Developmental Stage: embryo; Genotype: unc-119(ed3) III; wgIs64 [unc-119(+) hlh-1::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene hlh-1; Strain OP64(made_by : R. Waterston 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 HLH-1::EGFP fusion protein is expressed in the correct hlh-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-1 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs64 [unc-119(+) hlh-1::TY1::EGFP::3xFLAG] official name : OP64 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros

summary:
modENCODE_submission_2620
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: OP120(made_by : R Waterston 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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); Developmental Stage: late embryo; Genotype: unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene ceh-30; Strain OP120(made_by : R Waterston 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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq


title: Genome-wide chromatin analysis of wing imaginal discs

status: Public on Feb 17 2011

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: We report the relationship between 'absent, small or homeotic discs 2' (ASH2) occupancy, histone modifications and the transcription machinery using the wing disc as a source of chromatin. Our results indicate that genes related to development and transcriptional regulation are direct targets of ASH2 and that this protein contributes to H3K4me3 of nearby nucleosomes. Moreover, ASH2 occupancy correlates with phosphorylated forms of RNA polymerase II and histone positive marks in active genes. RNA Pol II phosphorylation in Ser5 is reduced in ash2 mutants, indicating that ASH2 plays a role in promoter stalling.

overall_design: Examination of three histone modifications and two polymerase modifications in wing imaginal dics cells.

first: S

last: Perez

first: E

first: A

last: Carbonell

first: D

first: M

first: F

last: Serras

last: Corominas


title: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.pse_WPP on Illumina Genome Analyzer.

status: Public on Feb 15 2011

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.pse_WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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

overall_design:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest.

This submission represents the ChIP-seq component of the study

first: Nicolas

last: Negre

first: Nicholas

middle: A

last: Bild

middle: P


title: Identification of Transcription Factor LIN-11::GFP Binding Regions in L2

first: DCC

last: modENCODE

summary:
modENCODE_submission_2429
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: OP62(made_by : R Waterston 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-11::EGFP fusion protein is expressed in the correct lin-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs62 [unc-119(+) lin-11::TY1::EGFP::3xFLAG] official name : OP62 ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs62 [unc-119(+) lin-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene lin-11; Strain OP62(made_by : R Waterston 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-11::EGFP fusion protein is expressed in the correct lin-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-11 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs62 [unc-119(+) lin-11::TY1::EGFP::3xFLAG] official name : OP62 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

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

first: Wei


title: Identification of Transcription Factor UNC-130::GFP Binding Regions in L1

summary:
modENCODE_submission_2430
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: OP77(made_by : R. Waterston 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 UNC-130::EGFP fusion protein is expressed in the correct unc-130 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-130 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG] official name : OP77 ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene unc-130; Strain OP77(made_by : R. Waterston 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 UNC-130::EGFP fusion protein is expressed in the correct unc-130 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-130 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG] official name : OP77 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

last: Gerstein

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Psq-D2 from D.pse_E0-4h on Illumina Genome Analyzer.

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Psq-D2 from D.pse_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

first: Nicolas


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.sim_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Pcl-D2 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

last: Negre

first: Nicholas


title: Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma: RNA-Seq

status: Public on Apr 07 2011

city: Lausanne

first: Armand

last: Valsesia

address: Bâtiment Génopode

country: Switzerland

institute: Ludwig Institute for Cancer Research

type: Expression profiling by high throughput sequencing

summary: All cancers are diseases of the genome. A combination of somatic point mutations, focal amplifications and deletions, and chromosome level aberrations conspire to disrupt gene expression and the interplay between signaling pathways that control normal growth and tissue homeostasis. Here we investigate transcript levels in 7 melanomas and a pool of melanocytes.

overall_design: The transcriptome from 7 cutaneous melanomas and a pool of 2 normal melanocyte cultures was sequenced using the 454 technology

first: Brian

middle: J

last: Stevenson


title: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.sim_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

last: Bild


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from D.sim_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Kr-D2 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Identification of Transcription Factor N2::POL II Binding Regions in L4

first: DCC

last: modENCODE

summary:
modENCODE_submission_2440
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: N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); Developmental Stage: L4; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene ama-1; Strain N2(genotype : wild type genotype : DR subclone of DB original (Tc1 pattern I) official name : N2 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Hyman


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.sim_WPP on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Pcl-D2 from D.sim_WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.yak_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Pcl-D2 from D.yak_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.sim_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from D.yak_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Kr-D2 from D.yak_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Psq-D2 from D.yak_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Psq-D2 from D.yak_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.yak_WPP on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.yak_WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.yak_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.yak_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Identification of Pol II Binding Regions in MAB-5::GFP L3

summary:
modENCODE_submission_594
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: OP26(made_by : R. Waterston and S. Kim 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 MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG] official name : OP26 ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ama-1; Strain OP26(made_by : R. Waterston and S. Kim 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 MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG] official name : OP26 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.pse_E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.pse_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: ENCODE Genome Institute of Singapore RNA-Seq

status: Public on Feb 14 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ruan Xiaoan mailto:ruanx@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track is produced as part of the ENCODE Project. It shows high throughput sequencing of RNA samples from tissues or sub cellular compartments from cell lines included in the ENCODE Transcriptome subproject.
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: The RNA-Seq data were generated from high quality polyA RNA, and the RNA-Seq libraries were constructed using SOLiD Whole Transcriptome (WT) protocol and reagent kit. Total RNA in good quality was used as starting materials and purified twice through MACs polyT column aimed to enrich polyA and remove any contaminants (e.g., rRNA, tRNA, DNA, protein etc.). A one microgram enriched polyA RNA sample was then fragmented to small pieces, and a gel-based selection method was performed to collect fragmented random polyA at a size-range of 50-150 nt in length. The collected fragmental RNA was then hybridized and ligated to a mix of adapters provided from ABI, followed by reverse transcription to generate corresponding cDNAs. The resulting cDNA library was further amplified by PCR and sequenced by SOLiD platform for single reads at 35 bp length (new version in 50 bp length). Cells were grown according to the approved ENCODE cell culture protocols. Data: The SOLiD-generated RNA-Seq reads were 35 bp in length. An initial filtering process was performed to remove any non-desirable contamination sequences, such as rRNA, tRNA, and repeats etc. A read-split mapping approach was developed to map the 35 bp reads onto the reference genome (GRCh37/hg19) excluding mitochondrion, haplotypes, randoms and chromosome Y. Mapping parameters: Strand specific mapping was done using Applied Biosystems' SOLiD alignment where all the reads were mapped to the genome, and to exon-exon junction database. Seed and extend strategy is adopted where initial seed length of 25 is mapped with maximum of 2 mismatches and then extended to read length, each color space match is awarded a score of +1 and each mismatch is awarded a penalty of -2. After extension each read is trimmed to its maximum score, shortest length. The color space sequences are then converted into base space and checked to ensure that each sequence has a maximum of 2 base pair mismatches. If any sequence has more than 2 mismatches, then that sequence is discarded.

first: Ruan

last: Xiaoan


title: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.sim_WPP on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.sim_WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Strand specific sequencing illustrates the complex transcriptional response of Legionella pneumophila during infection

status: Public on Feb 11 2011

city: Edinburgh

first: James

last: Prendergast

address: Crewe Road

country: United Kingdom

institute: MRC Human Genetics Unit

summary: Legionella pneumophila is a Gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila in broth growth and in infection of A. castellanii.

overall_design: Examination of 2 infection and 3 broth growth time points


title: IGH analysis in pro-B cells with H3K4me3, H3K4me2, H3K9ac, H3K27me3, Pax5 and CTCF

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Anja

last: Ebert

first: Shane

last: McManus

first: Maria

last: Novatchkova

first: Markus

last: Jaritz


title: IGH analysis in pro-B cells with H3K4me3, H3K4me2, H3K9ac, H3K27me3, Pax5 and CTCF [ChIP-Seq]

summary: VH-DJH recombination of the immunoglobulin heavy-chain (Igh) locus is temporally and spatially controlled during early B-cell development, and yet no regulatory elements other than the VH gene promoters have been identified throughout the entire 2.5-Mb VH gene cluster. Here we discovered novel regulatory sequences that are interspersed in the distal VH gene region. These conserved repeat elements were characterized by the presence of Pax5-dependent active chromatin, the binding of Pax5, E2A, CTCF and Rad21 as well as by Pax5-dependent antisense transcription in pro-B cells. The Pax5-activated intergenic repeat (PAIR) elements were no longer bound by Pax5 in pre-B and B cells consistent with the loss of antisense transcription, whereas E2A and CTCF interacted with PAIR elements  throughout early B-cell development. The pro-B-cell-specific and Pax5-dependent activity of the PAIR elements suggests that they are involved in the regulation of distal VH-DJH recombination at the Igh locus.

overall_design: Analysis of chromatin and TF binding in rag2-/- and wt pro-B, DP T and Mature B cells. Chip-Seq of CTCF and Rad21. The provided data is in mm8 coordinates.


title: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.pse_E0-4h on Illumina Genome Analyzer.

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.pse_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq]

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

summary: Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent transposition. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to their effect on nearby genes. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from Arabidopsis thaliana and a closely related congener with a two- to three-fold higher TE copy number, A. lyrata. We show that TEs, and particularly siRNA-targeted TEs, are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Overall, our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species.

overall_design: 4 A. lyrata mRNA-seq samples

first: Jesse

last: Hollister

first: Lisa

middle: M

last: Smith

first: Ya-Long

last: Guo

first: Detlef

last: Weigel

first: Brandon

last: Gaut


title: modENCODE_White Lab: genome-wide ChIP data of K27me3 from WPP on Illumina Genome Analyzer.

status: Public on Feb 09 2011

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor K27me3 from WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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

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

This submission represents the ChIP-seq component of the study


title: modENCODE_White Lab: genome-wide ChIP data of core from BRC on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor core from BRC generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Gene expression differences among primates are associated with changes in a histone epigenetic modification

first: Carolyn

middle: Elizabeth

last: Cain

address: 920 E. 58th Street - CLSC 301

department: Human Genetics

institute: The University of Chicago

summary: Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression differences between primates is not yet known. Our study focuses on an epigenetic histone modification, H3K4me3, which is thought to promote transcription. To investigate the contribution of H3K4me3 to regulatory differences between species, we collected gene expression data and identified H3K4me3-associated genomic regions in lymphoblastoid cell lines (LCLs) from humans, chimpanzees, and rhesus macaques, using three cell lines from each species. We found strong evidence for conservation of H3K4me3 localization in primates. Moreover, regardless of species, H3K4me3 is consistently enriched near annotated transcription start sites (TSS), and highly expressed genes are more likely than lowly expressed genes to have the histone modification near their TSS. Interestingly, we observed an enrichment of interspecies differences in H3K4me3 at the TSS of genes that are differentially expressed between species. We estimate that as much as 7% of gene expression differences between the LCLs of humans, chimpanzees, and rhesus macaques may be explained, at least in part, by changes in the status of H3K4me3 histone modifications. Our results suggest a modest, yet important role for epigenetic changes in gene expression differences between primates.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Examination of H3K4me3 profiles in lymphoblastoid cell lines (LCLs) from three primate species (human, chimpanzee, and rhesus macaque), using 3 samples from each species, compared to a pooled input control from each species. Expression profiling was also done in the same LCL samples.

middle: E

first: Ran

last: Blekhman

first: John

middle: C

last: Marioni

first: Yoav

last: Gilad


title: Bisulfite sequencing data of one human DNA sample

status: Public on Feb 12 2011

city: Shenzhen

first: Yao

last: Qiong

state: Guangdong

address: Beishan Industrial Zone,Yantian District

country: China

institute: BGI-SZ

type: Methylation profiling by high throughput sequencing

summary: Bisulfite conversion and whole genome-single base next generation sequencing of DNA from a single iPSC clone (CMC28). This method provides exceptional depth of the sequenced methylome.

overall_design: Bisulfite converted DNA from a single iPSC clone (CMC28), and get its high-throughput sequence data with Illumina.

first: Miguel

last: Miguel

first: Feng

last: Li


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from WPP on Illumina Genome Analyzer.

summary: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from WPP generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0

type: Non-coding RNA profiling by high throughput sequencing

summary: Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone.

overall_design: A. thaliana Col-0, Bur-0 & C24 small RNA-seq data, 2 biological replicates each

first: Korbinian

last: Schneeberger

first: Stephan

last: Ossowski

first: Juliane

middle: D

last: Klein

first: Jun

last: Cao

first: Christa

last: Lanz

first: Joffrey

last: Fitz

first: Norman

last: Warthmann

first: Stefan

middle: R

last: Henz

first: Daniel

middle: H

last: Huson


title: modENCODE_White Lab: genome-wide ChIP data of exd-GFP from E16-24h_13T on Illumina Genome Analyzer.

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor exd-GFP from E16-24h_13T generated by ChIP and analyzed on Illumina Genome Analyzer.

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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: modENCODE_White Lab: genome-wide ChIP data of Yki-91 from E0-4 on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Yki-91 from E0-4 generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of GFP from EcR_mF3d on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from EcR_mF3d generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: The Yb Body, a Major Site for Piwi-associated RNA Biogenesis and a Gateway for Piwi Expression and Transport to the Nucleus in Somatic Cells

status: Public on Feb 10 2011

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

summary: Despite exciting progress in understanding the Piwi-associ-ated RNA (piRNA) pathway in the germ line, less is known about this pathway in somatic cells. We showed previously that Piwi, a key component of the piRNA pathway in Drosophila, is regulated in somatic cells by Yb, a novel protein containing an RNA helicase-like motif and a Tudor-like domain. Yb is specifically expressed in gonadal somatic cells and regulates piwi in somatic niche cells to control germ line and somatic stem cell self-renewal. However, the molecular basis of the regulation remains elusive. Here, we report that Yb recruits Armitage (Armi), a putative RNA helicase involved in the piRNA pathway, to the Yb body, a cytoplasmic sphere to which Yb is exclusively localized. Moreover, co-immunoprecipitation experiments show that Yb forms a complex with Armi. In Yb mu-   tants, Armi is dispersed throughout the cytoplasm, and Piwi fails to enter the nucleus and is rarely detectable in the cytoplasm. Furthermore, somatic piRNAs are drastically diminished, and soma-expressing transposons are desilenced. These observations indicate a crucial role of Yb and the Yb body in piRNA biogenesis, possibly by regulating the activity of Armi that controls the entry of Piwi into the nucleus for its function. Finally, we discovered putative endo-siRNAs in the flamenco locus and the Yb dependence of their expression. These observations further implicate a role for Yb in transposon silencing via both the piRNA and endo-siRNA pathways.

overall_design: Examination of the effect of Yb on piRNA pathway


title: modENCODE_White Lab: genome-wide ChIP data of anti-cbt from E16-24h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor anti-cbt from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-h-D1 from E8-16h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-h-D1 from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Opposing regulation of the Il17 locus through direct, reciprocal actions of STAT3 and STAT5

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health


title: Non-canonical compensation of zygotic X transcription in Drosophila melanogaster development revealed through single embryo RNA-Seq

status: Public on Feb 07 2011

city: Berkeley

first: Michael

last: Eisen

address: Stanley Hall 304B

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: We sequenced mRNA from 24 single D. melanogaster embryos (12 male and 12 female) taken from 8 early embryonic timepoints to generate the first sex specific timecourse of gene expression in early Drosophila development

overall_design: Examination of mRNA levels in individual male and female embryos at 8 timepoints between the onset of zygotic transcription and gastrulation

first: Susan

last: Lott

middle: B


title: Genome-wide binding of STAT3 and STAT5 under Th17 conditions (ChIP-Seq)

summary: Interleukin 2 (IL-2), a cytokine linked to human autoimmune diseases, limits IL-17 production. We show that deletion of Stat3 in T cells abrogates IL-17 production and attenuates autoimmunity associated with IL-2 deficiency. While STAT3 induces IL-17 and RORγt and inhibits Foxp3, IL-2 inhibited IL-17 independently of Foxp3 and RORγt. We found that STAT3 and STAT5 bound to multiple common sites across the Il17 genetic locus. The induction of STAT5 binding by IL-2 was associated with a reduction in STAT3 binding at these sites and the inhibition of associated active epigenetic marks. Titrating the relative activation of STAT3 and STAT5 modulated TH17 cell specification. Thus, the balance rather than the absolute magnitude of these signals determines the propensity of cells to make a key inflammatory cytokine.

overall_design: The genome-wide binding of STAT3 and STAT5 under Th17 conditions was investigated by CHIP-seq.

first: Xiang-Ping

last: Yang

first: Kamran

last: Ghoreschi

first: Scott

last: Steward-Tharp

first: Jaime

last: Rodriguez-Canales

first: Jinfang

last: Zhu

first: John

last: Grainger

first: Kiyoshi

last: Hirahara

first: Hong-Wei

last: Sun

first: Lai

last: Wei

first: Yuka

last: Kanno

last: O’Shea

first: Arian

last: Laurence


title: The Atoh1 targetome in murine postnatal cerebellum

status: Public on Feb 08 2011

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: A relatively small number of proneural transcription factors specify a multitude of neural progenitor populations in the developing mammalian brain. Despite their importance, little is known about their targets, cellular processes they regulate, or what genomic sites they occupy in vivo. We used an integrated experimental and computational approach, combining RNA-seq, Histone-seq, and Atoh1 ChIP-seq in cerebellar tissue, to identify over 600 targets of Atoh1, an important developmental transcription factor. We validated 10% of these targets and found that Atoh1 directly regulates genes involved not only in early proliferation but also later differentiation, migration, cell adhesion, metabolism, and cytoskeletal organization by recognizing a novel 10 nucleotide Atoh1 E-Box associated motif (AtEAM). This Atoh1 “targetome” is not only a resource for studies aimed at understanding the molecular mechanisms involved in cerebellar development, but our integrated approach provides a framework for future in vivo studies of transcription factors and their targetomes.

overall_design: Examination of RNA-seq WT and null expression data (2 reps each), 2 different histone modifications (2 rep each) and IgG control, and Atoh1 DNA-binding (2 reps each) and control in the developing cerebellum

first: Tiemo

last: Klisch


title: modENCODE_White Lab: genome-wide ChIP data of Hr4_GFP from E0-12 on Illumina Genome Analyzer.

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Hr4_GFP from E0-12 generated by ChIP and analyzed on Illumina Genome Analyzer.

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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: [E-MTAB-189] Genomewide Analysis of Histone Modifications in Normal Human Islets

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
This experiment used ChIP-seq technology to create a genome-wide profile of histone marks in normal human pancreatic islets.  In the current work we analyzed two histone marks associated with gene expression (H3K4me3, H3K4me1) and marks associated with gene repression (H3K27me3). Each mark was anayzed using samples obtained from four donors (n=4). Chromatin Immunoprecipitations (ChIPs) for histone marks were performed using specific anti-histone antibodies. Enrichment of each sample was calulated with respect to its  individual input using qPCR.  Samples were sequenced with Solexa and sequenced DNA from both Input (n=4) and ChIP (n = 4) samples were aligned to the NCBI Genome Build 36.1 Hg18 to determine regions that were enriched for binding by modified histones.

ArrayExpress Release Date: 2010-02-17

Publication Title: Genome-wide analysis of histone modifications in human pancreatic islets
Publication Author List: Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, Naji A, Kaestner KH

Person Roles: submitter
Person Last Name: Bhandare
Person First Name: Reena
Person Email: bhandare@mail.med.upenn.edu
Person Phone:
Person Address: 771 Clinical Research Building, 415 Curie Blvd, Philadelphia, PA, 19104
Person Affiliation: Department of Genetics, University of Pennsylvania

overall_design:
Experimental Design: high_throughput_sequencing
Experimental Design: chromatin_immunoprecipitation_design
Experimental Design: ChIP-seq
Experimental Factor Name: Immunoprecipitate
Experimental Factor Name: Age
Experimental Factor Name: Sex
Experimental Factor Name: Phenotype
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: age
Experimental Factor Type: sex
Experimental Factor Type: phenotype


title: Mapping origins of replication in Arabidopsis thaliana

status: Public on Feb 06 2011

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary:
Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. Here we have profiled origins in Arabidopsis thaliana by high-throughput sequencing of purified nascent DNA strands. We have identified 1543 replication origins, which were uniformly distributed across the Arabidopsis genome and enriched in binding signals of two replication initiation proteins, CDC6 and ORC1. We have also analyzed novel epigenome maps of various histone modifications and found links between origins and epigenetic signatures, which differ from or have not been reported for other eukaryotic systems. Arabidopsis origins tend to be embedded in G+C-rich regions within the 5’ half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated H4, and depleted of H3K4me1 and H3K9me2. Our data establish the basis for the understanding of the epigenetic specification of origins of replication in Arabidopsis and have implications for the mechanisms of origin specification in other eukaryotes.

This SuperSeries is composed of the SubSeries listed below.


title: [E-TABM-828] ChIP-Seq in human MCF7 and HEPG2 cells

summary:
ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314)

ArrayExpress Release Date: 2010-05-12

Publication Title: A CTCF-independent role for cohesin in tissue-specific transcription
Publication Author List: Dominic Schmidt, Petra C. Schwalie, Caryn S. Ross-Innes, Antoni Hurtado, Gordon D. Brown, Jason S. Carroll, Paul Flicek and Duncan T. Odom

Person Roles: submitter
Person Last Name: Schwalie
Person First Name: Petra Catalina
Person Email: schwalie@ebi.ac.uk
Person Address:
Person Affiliation: EBI

overall_design:
Experimental Design: binding_site_identification_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: ChIP-seq


title: ORC Meta-peak generation

first: DCC

last: modENCODE

summary:
modENCODE_submission_3388
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
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: The linked output file represents the union of the coordinates of peak data from other submissions.  Meta-peaks show where peaks from the combined data overlap.

first: David

last: MacAlpine

first: Terry

last: Orr-Weaver

first: Jarred

last: Norman

first: Sharon

last: Li

first: Joseph

last: Prinz


title: modENCODE_White Lab: genome-wide ChIP data of KW4-Fer3-D1 from E16-24h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW4-Fer3-D1 from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Regulation of alternative splicing by the core spliceosomal machinery

status: Public on Feb 01 2011

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary: Abstract: Alternative splicing (AS) plays a major role in the generation of proteomic diversity and in gene regulation. However, the role of the basal splicing machinery in regulating AS remains poorly understood. Here we show that the core snRNP protein SmB/B’ self-regulates its expression by promoting the inclusion of a highly-conserved alternative exon in its own pre-mRNA that targets the spliced transcript for nonsense-mediated mRNA decay (NMD). Depletion of SmB/B’ in human cells results in reduced levels of snRNPs and in a striking reduction in the inclusion levels of hundreds of alternative exons, with comparatively few effects on constitutive exon splicing levels. The affected alternative exons are enriched in genes encoding RNA processing and other RNA binding factors, and a subset of these exons also regulate gene expression by activating NMD. Our results thus demonstrate a role for the core spliceosomal machinery in controlling an exon network that appears to modulate the levels of many RNA processing factors.

overall_design:
HeLa cells were transfected with a control non-targeting siRNA pool (siNT), or with siRNA pools designed to knockdown SmB/B' or SRSF1 (also known as SF2/ASF/SFRS1). Sequence reads were aligned to exon-exon junction sequences in a database of EST/cDNA-mined cassette-type alternative splicing events.
Processed data files (.bed and .txt) provided as supplementary files on the Series record.  Processed data file build information: hg18.

first: Arneet

middle: L

last: Saltzman

first: Benjamin

last: Blencowe


title: Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer

city: Salt Lake City

first: Michael

middle: Bryan

last: Warf

state: UT

address: 15 N Medical Dr East, room 4800

department: Biochemistry

institute: University of Utah

summary: MicroRNAs (miRNAs) are small regulatory RNAs that are essential in all studied metazoans. Research has focused on the prediction and identification of novel miRNAs, while little has been done to validate, annotate, and characterize identified miRNAs. Using Illumina sequencing, ~20 million small RNA sequences were obtained from Caenorhabditis elegans. Of the 175 miRNAs listed on the miRBase database, 106 were validated as deriving from a stem–loop precursor with hallmark characteristics of miRNAs. This result suggests that not all sequences identified as miRNAs belong in this category of small RNAs. Our large data set of validated miRNAs facilitated the determination of general sequence and structural characteristics of miRNAs and miRNA precursors. In contrast to previous observations, we did not observe a preference for the 59 nucleotide of the miRNA to be unpaired compared to the 59 nucleotide of the miRNA*, nor a preference for the miRNA to be on either the 59 or 39 arm of the miRNA precursor stem–loop. We observed that steady-state pools of miRNAs have fairly homogeneous termini, especially at their 59 end. Nearly all mature miRNA–miRNA* duplexes had two nucleotide 39 overhangs, and there was a preference for a uracil in the first and ninth position of the mature miRNA. Finally, we observed that specific nucleotides and structural distortions were overrepresented at certain positions adjacent to Drosha and Dicer cleavage sites. Our study offers a comprehensive data set of C. elegans miRNAs and their precursors that significantly decreases the uncertainty associated with the identity of these molecules in existing databases.

overall_design: Deep sequencing of small RNAs in wild-type (N2) mixed stage C. elegans, roughly 20 million sequencing reads were obtained

first: M

first: W

last: Johnson

first: Brenda

last: Bass


title: Mammalian Dpy-30 regulates genomic H3K4 methylation and is essential for ES cell fate specification

city: New York

first: Hao

last: Jiang

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: H3K4 methylation is associated with active genes and, along with H3K27 methylation, is part of a bivalent chromatin mark that typifies poised developmental genes in ESCs. However, its functional roles in ESC maintenance and differentiation are not established. Here we show that mammalian Dpy-30, a core subunit of SET1/MLL complexes, biochemically modulates H3K4 methylation in vitro, and directly regulates chromosomal H3K4me3 throughout the mammalian genome. Depletion of Dpy-30 does not affect ESC self-renewal, but significantly alters the differentiation potential of ESCs, particularly along the neural lineage. The differentiation defect is accompanied by defects in gene induction and H3K4 methylation at key developmental loci. Our results provide strong experimental evidence for the hypothesis that H3K4 methylation is an essential functional component of the bivalent mark during activation of developmental genes in ESCs.

overall_design:
Total RNAs from control or knockdown cells before and after RA-mediated differentiation were subjected to Illumina microarray analyses.

ChIP-enriched DNA from mouse ES cells was analyzed by Solexa sequencing.

first: H

first: R

middle: G

last: Roeder


title: mut-16 and other mutator-class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

city: Boston

first: Taiowa

last: Montgomery

state: MA

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals.  In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood.  To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing.

overall_design: Small RNA analysis in wild type and mut-16 mutant C. elegans strains


title: Genome-wide maps of histone modifications in Arabidopsis thaliana

status: Public on Feb 02 2011

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

summary: Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species.

overall_design:
ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf.

Expression: Gene expression in the histone deacetylase 1 mutant was generated using t-DNA insertion. mRNA expressions in leaf and flower of the AtHD1 mutant were compared with those of the wild type plants. We conducted 8 replicates of dual-channel microarrays, including 4 biological replicates and individual dye swaps.

first: Danny

middle: W

last: Ng

first: Wen-Hsiung

first: Zengjian

last: Chen

first: Lu

last: Tian


title: Chromatin marks and RNA Pol II in human hematopoietic stem and progenitor cells

status: Public on Jan 31 2011

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The transcriptional status of genes can be determined from the enrichment pattern of RNA polymerase at the transcription start site (TSS) and across the body of the gene. Active elongating genes are enriched for H3K79me2, and Polycomb paused genes are marked by H3K27me3.

overall_design: Human CD133-positive Umbilical Cord Blood (UCB) cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against total RNA Pol2 (Covance 8WG16), H3K27me3 (Abcam ab6002) and H3K79me2 (Abcam ab3594).

first: Lee

middle: N

last: Lawton


title: Comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum during infection on different insects

city: Shanghai

first: Chengshu

last: Wang

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: We used RNA-Seq to compare transcriptional responses of M. anisopliae and M. acridum to infection of the optically clear hind wings of adult locusts and cockroaches. It was calculated that >82% of predicted M. anisopliae genes and >88% of predicted M. acridum genes were expressed during pre-penetration growth. Germination and growth by M. anisopliae and M. acridum on either insect triggered high level expression of genes associated with translation and post-translational modifications. Between 6 to 10% of the genes that were highly expressed by M. anisopliae and M. acridum on host cuticles encoded cell wall proteins. Consistent with early host recognition events being key to establishing specificity, M. acridum but not M. anisopliae transcribed different Pth11-like GPCRs on locust and cockroach cuticles, thus differential activation of different signaling pathways.

sample_organism:
Metarhizium anisopliae
Metarhizium acridum

overall_design: Examination of gene differential expressions by two different Metarhizium speceis on two different insects cuticles

first: Guohua

last: Xiao


title: [E-MTAB-332] H-NS and Fis binding to E. coli K12

first: ArrayExpress

last: EBI

summary:
Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear. Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.

ArrayExpress Release Date: 2010-07-29

Person Roles: submitter
Person Last Name: Sai Narain Seshasayee
Person First Name: Aswin
Person Mid Initials:
Person Email: aswin@ebi.ac.uk
Person Phone:
Person Address:
Person Affiliation: EBI

overall_design:
Experimental Design: growth_condition_design
Experimental Design: in_vivo_design
Experimental Design: binding_site_identification_design
Experimental Design: ChIP-seq
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: GENOTYPE
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: growth_condition
Experimental Factor Type: genotype


title: Profiling of AGO104-dependent gene expression in maize ovaries

status: Public on Jan 26 2011

city: Montpellier

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

summary: Maize plants defective for the AGO104 protein show defects in chromatin condensation during meiosis, and subsequent failure to segregate chromosomes. AGO104 is  a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob repeat DNA. Digital Gene Expression Tag Profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Thus, female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize.

overall_design: Profiling of gene expression in mutant versus wilt type ovaries.

first: Manjit

last: Singh


title: Solexa sequencing of small RNAs in Singapore grouper iridovirus (SGIV)-infected grouper cells

status: Public on Jan 29 2011

city: Guangzhou

first: Yang

last: Yan

address: West Xingang Road

institute: South China Sea Institute of Oceanology Chinese Academy of Sciences

summary: We applied Solexa sequencing technology to identify Singapore grouper iridovirus (SGIV) encoded microRNAs during its infection. A small RNA library arising from SGIV infected grouper cells (GP) was constructed and sequenced. We recovered 6,802,977 usable reads, of which 34,400 reads represented the small RNA sequences encoded by SGIV. Among them, 16 novel SGIV encoded miRNAs were identified by a computational pipeline. Generally, these 16 miRNAs are dispersed throughout the SGIV genome, while three of them are located within open reading frame 057L (ORF057L) region. Meanwhile, We identified 138 conserved microRNA genes between grouper fish and zebrafish.

overall_design: 18-30 nt small RNAs from SGIV-infected GP cells were sequenced in one Solexa lane.

first: Huachun

last: Cui

first: Qiwei

last: Qin


title: Genome-wide characterization of long nonpolyadenylated RNAs, experiment II

status: Public on Jan 28 2011

first: Ling-Ling

address: 320 Yue-Yang Road

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

summary: We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from two standard cell lines, HeLa cells and human embryonic stem cell (hESC) H9 cells.

overall_design: Examination of nonpolyadenylated and polyadenylated in 2 cell types.

first: Li

last: Yang

first: Michael

middle: O

last: Duff

first: Brenton

last: Graveley

first: Goardon

last: Carmichael


title: [E-MTAB-387] RNA sequencing in E. coli K12

summary:
Transcriptome sequencing of E.coli K12 in LB media in early exponential phase and transition to stationary phase

ArrayExpress Release Date: 2010-09-30

Person Roles: submitter
Person Last Name: Martincorena
Person First Name: Inigo
Person Mid Initials:
Person Email: martinco@ebi.ac.uk
Person Phone:
Person Address:
Person Affiliation: EBI

overall_design:
Experimental Design: growth_condition_design
Experimental Design: in_vivo_design
Experimental Design: RNA_sequencing_design
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: GENOTYPE
Experimental Factor Type: GrowthCondition
Experimental Factor Type: Genotype


title: Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae

city: Rochester

first: Vincent

last: Isabella

address: 601 Elmwood Ave

department: Microbilogy and Immunology

institute: University of Rochester

summary: Maintenance of an anaerobic respiratory system in the obligate human pathogen, Neisseria gonorrhoeae, suggests that an anaerobic lifestyle may be important during the course of infection.  However, at this point there have been no studies analyzing the complete gonococcal transcriptome response to anaerobiosis.  Here we performed deep sequencing to compare the gonococcal transcriptomes of aerobic and anaerobically grown cells. We found that the anaerobic stimulon in gonococci was large, and that 198 chromosomal genes were found to be differentially expressed.  We also observed a large induction of genes encoded within the cryptic plasmid, pJD1.  Secondary analysis of genes found to be differentially expressed by RNA-seq using translational-lacZ fusions or RT-PCR demonstrated the RNA-seq results to be very reproducible.  Surprisingly, many genes of prophage origin were induced anaerobically, as well as several transcriptional regulators previously unknown to be involved in anaerobic growth.  We also confirmed expression and regulation of a small RNA, likely a functional equivalent of fnrS in the Enterobacteriaceae family.  Several novel factors were identified to be anaerobically regulated, as well as a large number of hypothetical proteins were induced.

overall_design: Two biological replicates of cells grown aerobically or anaerobically with nitrite were analyzed, for a total of four samples subject to SOLiD RNA sequencing.

first: Virginia

last: Clark


title: Transcription factor ChIP-seq in expanded human hematopoietic stem and progenitor cells

first: Richard

middle: A

summary: While many individual transcription factors are known to regulate hematopoietic differentiation, major aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression and analysis of cis-elements in gene promoters to decipher the general organization of their regulatory circuitry. We identified modules of highly co-expressed genes, some of which are restricted to a single lineage, but most are expressed at variable levels across multiple lineages. We found densely interconnected cis-regulatory circuits and a large number of transcription factors that are differentially expressed across hematopoietic states, suggesting a more complex regulatory system than previously assumed. We functionally validated a subset of candidate factors using RNA interference and ChIP-Seq. Our dataset, analytic tools, and findings, available on a web-based portal, provide a unique resource to study the regulatory architecture of hematopoiesis.

overall_design:
Human CD133-positive Umbilical Cord Blood (UCB) cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), PU.1/SPI1 (Santa Cruz SC-352X), IKAROS (Santa Cruz SC-9859X) and MEIS1 (Abcam ab19867).

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


title: MNase digestion-sensitive nucleosomes in Saccharomyces cerevisiae

status: Public on Jan 24 2011

first: Yuanxin

last: Xi

summary: The structural complexity of nucleosomes underlies their functional versatility.  Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion.  Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.

overall_design: Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.

first: Jianhui

last: Yao


title: Expression data from Pseudomonas putida KT2440 (RNA-Seq data)

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

institute: Medical School Hannover

summary: We used cDNA generated from total mRNA for RNA-Seq analysis (Genome Analyzer II at GATC Biotech AG)  to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C

overall_design: Culture was grown in minimal medium supplemented with succinate at 30°C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10°C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.


title: Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA

status: Public on Jan 21 2011

city: Bern

last: Nilsson

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern

summary: Unlike other eukaryotes, the protein coding genes of Trypanosoma cruzi are arranged into large polycistronic gene clusters transcribed by polymerase II (Pol II). Thus, trypanosomes rely on post-transcriptional processes to regulate gene expression. Here, we show that the glucosylated thymine DNA base (-D-glucosyl hydroxymethyluracil or base J) is present within sequences flanking the polycistronic units (PTU) in T. cruzi. loss of base J at sites of transcription initiation, via deletion of the two enzymes that regulate J synthesis (JBP1 and JBP2), correlates with an increased rate of Pol II transcription and subsequent genome-wide increase in gene expression. genes include virulence genes and the resulting parasites are defective in host cell invasion and egress. These studies indicate that base J represents an epigenetic factor regulating Pol II transcription initiation in kinetoplastids, and provides the first biological role of the only hyper-modified DNA base in eukaryotes. This entry contains the results using SLT, digital gene expression profiling of tags read off the spliced leader sequence of all mature trypanosomatid messages, for the life-cycle of T. cruzi, four stages, in wild-type as well as JBP1 KO cells.

overall_design: This entry contains the results using SLT, digital gene expression profiling of tags read off the spliced leader sequence of all mature trypanosomatid messages, for the life-cycle of T. cruzi, four stages, in wild-type as well as JBP1 KO cells, for eight libraries in total.

first: D

middle: K

last: Ekanayake

first: Todd

last: Minning

first: Brent

last: Whetherly

first: Kapila

last: Gunasekera

first: Rick

last: Tarleton

first: Torsten

last: Ochsenreiter

first: Robert

last: Sabatini


title: A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology)

status: Public on Jan 27 2011

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

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

overall_design: Refer to individual Series


title: Graded Nodal/Activin Signaling Governs ES Cell Fate Decisions via Differential Recruitment of Phospho-Smad2 to Oct4 and Distinct Target Gene Subsets.

city: Singapore

first: Yuriy

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: The Nodal/Activin morphogens are secreted signaling molecules that form concentration gradients during early embryogenesis providing stem cells with positional information and differentiation instructions important for embryonic patterning. The molecular basis driving stem cell interpretation of signaling gradients and the undertaking of distinct cell fate decisions remains poorly understood. We show that perturbation of endogenous Nodal/Activin signaling in ES cells leads to exit from self renewal towards mesendodermal differentiation at high signaling and trophectoderm induction during low signaling. ChIP-seq of Phospho-Smad2, the downstream transcription factor of the Nodal/Activin pathway reveals binding to distinct subsets of target genes in a dose dependent manner including the promoter region of the Oct4 master regulator of stemness. Consequently, both Oct4 mRNA and protein levels are directly driven by graded Nodal/Activin signaling. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titers self renewal against alternative differentiation programs.

overall_design: 3 pSmad2 ChIP samples corresponding to ES cells pretreated for 6 hours in 10uM SB followed by 18 hours in 25ng/ml Activin, 1/5000 DMSO and 10uM SB in 20% KSR media. Controls include the corresponding input DNA for each treatment.

first: Kian

last: Lee

first: Bing

last: Lim


title: ChIP-Seq data for REST, MCAF1, Ring1b and H4K20me3 in mouse embryonic stem (ES) cells

status: Public on Jan 19 2011

last: Young

summary: Multiple protein complexes and histone marks have been implicated and/or associated with gene repression in ES cells. To gain insights into repressive complexes present at repressed genes and their associated chromatin state, we profiled REST, MCAF1, Ring1b and H4K20me3 in mouse ES cells.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against REST, MCAF1, Ring1b and H4K20me3.

first: Peter

last: Rahl

first: Steve

last: Bilodeau


title: Total RNA Pol2 ChIP-seq in mES cells treated with flavopiridol (Cdk9 inhibitor) after DSIF and NELF knockdown

first: Richard

summary: Recent studies have found that promoter-proximal pausing occurs at most Pol2-regulated genes.  DSIF and NELF function as negative elongation factors and promote Pol2 pausing.  P-TEFb, whose enzymatic activity lies in the kinase Cdk9, positively regulates the transition into productive elongation by phosphorylating subunits in DSIF, NELF and Pol2.  To gain insights into the interplay between these factors in regulating transcriptional pause release, we tested if knockdown of either pausing factor could bypass P-TEFb function.  We find that P-TEFb function is still required for transcriptional elongation after DSIF or NELF knockdown.

overall_design: mES cells were infected with a shRNA hairpin to knockdown Spt5, Spt4, NelfE or control.  The resulting cells were then treated with flavopiridol (1uM for 60 minutes).  DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against total RNA Pol2 (Rpb1 N-terminus, Santa Cruz sc-899).


title: Global Mapping of H3K4me1 and H3K4me3 in human CD4+CD25+FOXP3+ Treg cells

city: Chongqing

first: Ni

last: Bing

address: PLA, Third Military Medical University

department: Institute of Immunology

institute: PLA, Third Military Medical University

summary: Regulatory T cells (Treg) contribute to the crucial immunological processes of self-tolerance and immune homeostasis. However, the mechanisms underlying Treg function and cell fate decisions to differentiate between Treg and conventional T cells (Tconv) remain to be fully elucidated, especially at the histone modification level. Covalent modifications of histones establish and maintain chromatin structure, and regulate gene transcription events by facilitating access to cis-elements by trans-acting factors during mammalian development and cellular differentiation. We aimed to investigate the role of the methylation form of histone modification as related to Treg function and phenotype. High-resolution maps of the genome-wide distribution of monomethylated histone H3 lysine 4, H3K4me1, and the trimethylated form H3K4me3 were generated for human activated conventional CD4+CD25+FOXP3- T cells (aTconv) and CD4+CD25+FOXP3+ regulatory T cells (Treg) by sequencing using the Solexa 1G Genetic Analyzer. We found 2115 H3K4me3 regions corresponding to proximal promoter regions; the genes associated with these regions in Treg cells included the crucial transcription factor forkhead box P3 (FOXP3) and the chemokine receptor CCR7. We also identified 41024 Treg cell type-specific H3K4me1 regions. The majority of the H3K4me1 regions differing between the Treg and aTconv cells were located at promoter-distal sites, some of which were selected and consolidated to further examine enhancer activity in in vitro reporter gene assays. The findings from our study provide a comprehensive genome-wide dataset of lineage-specific H3K4me1 and H3K4me3 patterns in Treg and aTconv cells, which may control the differentiation decision, lineage commitment and cell type-specific gene regulation. This basic principle is likely not confined to the two closely-related T cell populations, but may apply generally to somatic cell lineages in adult organisms.

overall_design: Genome-wide distribution of monomethylated histone H3 lysine 4, H3K4me1, and the trimethylated form H3K4me3 in human activated conventional CD4+CD25+FOXP3- T cells (aTconv) and CD4+CD25+FOXP3+ regulatory T cells (Treg) (5 samples in total)

first: Yi

last: Tian

first: Zhengcai

last: Jia

first: Jun

last: Wang

first: Jianxun

last: Song

first: Zeming

last: Huang

first: Yanhua

last: Zheng

first: Xiaolan

last: Fu

first: Yan

last: Tang

first: Di

last: Yang

first: Qinghong

first: Zhiqiang

last: Zhang

first: Yuzhang

last: Wu

last: Ni


title: ChIP-Seq data for histone marks in mouse embryonic fibroblasts

summary: The conversion of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPS) by forced expression of Oct4, Sox2 and Klf4 is among the earliest demonstrations of reprogramming to a pluripotent state by forced expression of transcription factors. To gain insights into the chromatin state of genes required for reprogramming, we profiled H3K4me3, H3K27me3 and H3K9me3.

overall_design:
DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K4me3, H3K27me3 and H3K9me3.

Sample GSM555166 (GSE22320) was used as the negative control for the MEF cells, and Samples GSM602780 and GSM602781 (GSE24471) were used as the negative controls for the secondary fibroblasts.


title: Pluripotency Factors Regulate Definitive Endoderm Specification through Eomesodermin

status: Public on Jan 25 2011

first: Matthew

last: Trotter

address: West Forvie Building, Forvie Site, Robinson Way

department: Department of Surgery

institute: University of Cambridge

summary: Understanding the molecular mechanisms controlling early cell fate decisions in mammals is a major objective towards the development of robust methods for the differentiation of human pluripotent stem cells into clinically relevant cell types. Here, we used human embryonic stem cells (hESCs) to study specification of definitive endoderm in vitro. Using a combination of whole genome expression and ChIP-seq analyses, we established a hierarchy of transcription factors regulating endoderm specification. Importantly, pluripotency factors, namely NANOG, OCT4 and SOX2 have an essential function in this network by actively directing differentiation. Indeed, these transcription factors control the expression of EOMES, which marks the onset of endoderm specification. In turn, EOMES interacts with SMAD2/3 to initiate the transcriptional network governing endoderm formation. Together, these results provide for the first time a comprehensive molecular model connecting the transition from pluripotency to endoderm specification during mammalian development.

overall_design:
ChIP-Seq of Eomesodermin binding in human embyonic stem cells, differentiated towards an endodermal fate for 48h in chemically-defined culture media. Includes an input DNA control.

Supplementary file GSE26097_README.txt contains descriptions of the raw data files and processed data files.

first: Adrian

last: Teo