Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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 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

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: DCC modENCODE

PROVIDER: E-GEOD-25793 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein Mark B MB Lu Zhi John ZJ Van Nostrand Eric L EL Cheng Chao C Arshinoff Bradley I BI Liu Tao T Yip Kevin Y KY Robilotto Rebecca R Rechtsteiner Andreas A Ikegami Kohta K Alves Pedro P Chateigner Aurelien A Perry Marc M Morris Mitzi M Auerbach Raymond K RK Feng Xin X Leng Jing J Vielle Anne A Niu Wei W Rhrissorrakrai Kahn K Agarwal Ashish A Alexander Roger P RP Barber Galt G Brdlik Cathleen M CM Brennan Jennifer J Brouillet Jeremy Jean JJ Carr Adrian A Cheung Ming-Sin MS Clawson Hiram H Contrino Sergio S Dannenberg Luke O LO Dernburg Abby F AF Desai Arshad A Dick Lindsay L Dosé Andréa C AC Du Jiang J Egelhofer Thea T Ercan Sevinc S Euskirchen Ghia G Ewing Brent B Feingold Elise A EA Gassmann Reto R Good Peter J PJ Green Phil P Gullier Francois F Gutwein Michelle M Guyer Mark S MS Habegger Lukas L Han Ting T Henikoff Jorja G JG Henz Stefan R SR Hinrichs Angie A Holster Heather H Hyman Tony T Iniguez A Leo AL Janette Judith J Jensen Morten M Kato Masaomi M Kent W James WJ Kephart Ellen E Khivansara Vishal V Khurana Ekta E Kim John K JK Kolasinska-Zwierz Paulina P Lai Eric C EC Latorre Isabel I Leahey Amber A Lewis Suzanna S Lloyd Paul P Lochovsky Lucas L Lowdon Rebecca F RF Lubling Yaniv Y Lyne Rachel R MacCoss Michael M Mackowiak Sebastian D SD Mangone Marco M McKay Sheldon S Mecenas Desirea D Merrihew Gennifer G Miller David M DM Muroyama Andrew A Murray John I JI Ooi Siew-Loon SL Pham Hoang H Phippen Taryn T Preston Elicia A EA Rajewsky Nikolaus N Rätsch Gunnar G Rosenbaum Heidi H Rozowsky Joel J Rutherford Kim K Ruzanov Peter P Sarov Mihail M Sasidharan Rajkumar R Sboner Andrea A Scheid Paul P Segal Eran E Shin Hyunjin H Shou Chong C Slack Frank J FJ Slightam Cindie C Smith Richard R Spencer William C WC Stinson E O EO Taing Scott S Takasaki Teruaki T Vafeados Dionne D Voronina Ksenia K Wang Guilin G Washington Nicole L NL Whittle Christina M CM Wu Beijing B Yan Koon-Kiu KK Zeller Georg G Zha Zheng Z Zhong Mei M Zhou Xingliang X Ahringer Julie J Strome Susan S Gunsalus Kristin C KC Micklem Gos G Liu X Shirley XS Reinke Valerie V Kim Stuart K SK Hillier LaDeana W LW Henikoff Steven S Piano Fabio F Snyder Michael M Stein Lincoln L Lieb Jason D JD Waterston Robert H RH

Science (New York, N.Y.) 20101222 6012

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of trans ...[more]

PMID: 21177976

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Project description: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 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

Project description: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 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

Project description: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 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

Dataset Information

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

Publications

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

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