Genome wide mapping of transcription factor downstream targets using STAGE
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE6312 | GEO | 2006/11/23
SECONDARY ACCESSION(S): PRJNA100521
REPOSITORIES: GEO
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Project description:Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. ChIP-chip is a powerful technique to map chromosomal targets of transcription factors. We applied ChIP-chip to map downstream targets of the transcription factor E2F4 and c-Myc. E2F4 is a member of the E2F family of transcriptional regulators that functions as a repressor in quiescent and early G1 cells. c-Myc is a oncogenic transcription factor implicated in almost all aspects of tumorigenesis. We mapped E2F4 and c-Myc binding sites in 1% of the human genome using Nimblegen hg17 ENCODE arrays. Keywords: ChIP-chip
2007-01-20 | GSE6375 | GEO
Project description:Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. Here, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNA, then dual priming oligonucleotide system to specifically enrich 5’-end tags for genomic analysis.
2023-01-01 | GSE174479 | GEO
Project description:modENCODE_submission_2622 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: OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene skn-1; Strain OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25810 | biostudies-arrayexpress
Project description:modENCODE_submission_2600 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: OP70(made_by : R Waterston tags : GFP::3xFlag mutagen : Bombard genotype : unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119) official name : WBGene00003218 ); Developmental Stage: embryo; Genotype: unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene mep-1; Strain OP70(made_by : R Waterston tags : GFP::3xFlag mutagen : Bombard genotype : unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119) official name : WBGene00003218 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25800 | biostudies-arrayexpress
Project description:modENCODE_submission_3072 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: YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); Developmental Stage: Young Adult; Genotype: unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene efl-1; Strain YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37799 | biostudies-arrayexpress
Project description:modENCODE_submission_3075 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: YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene dpl-1; Strain YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37802 | biostudies-arrayexpress
Project description:modENCODE_submission_3074 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: YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); Developmental Stage: fed L1; Genotype: unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene efl-1; Strain YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37801 | biostudies-arrayexpress
Project description:modENCODE_submission_3073 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: YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); Developmental Stage: Young Adult; Genotype: unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene dpl-1; Strain YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37800 | biostudies-arrayexpress
Project description:Identifying transcription factor functions and targets by phenotypic activation
| PRJNA96143 | ENA
Project description:modENCODE_submission_4184 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages 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-chip. BIOLOGICAL SOURCE: Strain: HP1c mutant(official name : HP1c[f04929] genotype : w[1118]; PBac{w[+mC]=WH}HP1c[f04929] outcross : unknown transgene : PBac insertion tags : Transposon description : Insertion of PBac transgene disrupts Hp1c gene (Gene disruption project). Developmental Stage: 3rd Instar Larvae; Genotype: w[1118]; PBac{w[+mC]=WH}HP1c[f04929]; Transgene: PBac insertion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain HP1c mutant(official name : HP1c[f04929] genotype : w[1118]; PBac{w[+mC]=WH}HP1c[f04929] outcross : unknown transgene : PBac insertion tags : Transposon description : Insertion of PBac transgene disrupts Hp1c gene (Gene disruption project). Antibody HP1b Q4114 (target is HP1b); Developmental Stage 3rd Instar Larvae
2013-03-13 | E-GEOD-45058 | biostudies-arrayexpress