Identification of transcription factor HLH-8 binding sites in C.elegans
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Michael Wilson
PROVIDER: E-GEOD-17458 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We, being members of modENCODE consortium, have established an experimetal pipeline in C.elegans that allows global identification of the binding sites for transcription factors using chromatin immunoprecipitation followed by illumina high-throughput sequencing (ChIP-seq). In current study, we identified the binding sites for EOR-1 at L3 stage, which plays important roles in regulating RAS/RAF-mediated signaling during excretory system development and RAS/RAF- and WNT-mediated signaling during P12 fate specification. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EOR-1 was tagged with a dual GFP:3xFLAG tag at the carboxy terminus, whose expression pattern was confirmed through both fluorescence imaging and immunoblot analysis. The binding sites were determined using ChIP-seq. Two biological replicates were used in this study and non-immunoprecipitated chromatin (input) from the same sample served as a control. Concordance between two replicates is about 95% when p-value is 0.05
2009-07-31 | E-GEOD-17456 | biostudies-arrayexpress
Project description:We, being members of modENCODE consortium, have established an experimetal pipeline in C.elegans that allows global identification of the binding sites for transcription factors using chromatin immunoprecipitation followed by illumina high-throughput sequencing (ChIP-seq). In current study, we identified the binding sites for CEH-14 at L2 stage, which is required for specification of the AFD thermosensory neurons and for normal thermotactic behavior. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf CEH-14 was tagged with a dual GFP:3xFLAG tag at the carboxy terminus, whose expression pattern was confirmed through both fluorescence imaging and immunoblot analysis. The binding sites were determined using ChIP-seq. Two biological replicates were used in this study, but replicate1 is at a later L2 stage. Only one Input sample (non-immunoprecipitated chromatin (input) from replicate2 was used as a control. The concordance between two replicates is just above 50% when p-value is 0.05.
2009-07-31 | E-GEOD-17454 | biostudies-arrayexpress
Project description:We identified the DNA binding sites of MAB-5 in C. elegans. MAB-5 was C-terminally tagged with GFP and the expression pattern was examined through fluorescent microscopy. The binding sites were determined using chromatin immunoprecipitation with anti-GFP antibody followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Identification of MAB-5 binding sites at L3 stage
2009-04-11 | E-GEOD-15625 | biostudies-arrayexpress
Project description:modENCODE_submission_660 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: OS3991 (engineered, target gene hlh-17 tagged by 3xFlag::PAB-1); Tissue: CEPsh (YA); Developmental Stage: Young Adult 20dC 72hr post-L1; Genotype: unc-119 (ed1); nsIs191 [unc-119 (+); hlh-17::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain OS3991 (engineered, target gene hlh-17 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage Young Adult 20dC 72hr post-L1; Tissue CEPsh (YA)
2010-08-04 | E-GEOD-23284 | biostudies-arrayexpress
Project description:modENCODE_submission_659 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue reference (L3-L4)
2010-08-04 | E-GEOD-23283 | biostudies-arrayexpress
Project description:modENCODE_submission_2454 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); Tissue: hypodermis (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119(ed1); wdEx626[unc-119+; dpy-7::3xFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue hypodermis (L3-L4)
2010-08-04 | E-GEOD-23287 | biostudies-arrayexpress
Project description:modENCODE_submission_655 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); Tissue: Dopaminergic neurons (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx637 [unc-119 (+); dat-1::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue Dopaminergic neurons (L3-L4)
2010-08-04 | E-GEOD-23279 | biostudies-arrayexpress
Project description:modENCODE_submission_460 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); Tissue: PVD OLLs (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx460 [unc-119 (+); ser-2prom3B::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue PVD OLLs (L3-L4)
2010-08-04 | E-GEOD-23250 | biostudies-arrayexpress
Project description:Condensins are multi-subunit protein complexes that regulate chromosome structure throughout cell-cycle. Metazoans contain two types of condensin complexes (I and II) with essential and distinct functions. In C. elegans a third type of condensin (IDC) functions as part of the X chromosome dosage compensation complex1,2. We mapped genome-wide binding sites of the three condensin types in C. elegans embryos. Characteristics of condensin binding are similar between condensin types. ChIP-seq profiles of C. elegans subunits of the three condensins in 3-6 replicates from mixed stage embryos, controls are included, and RNA-Seq profiles of C. elegans in 5 replicates from mixed staged embryos. Additionally, ChIP-seq profiles of the condensin II subunit KLE-2 in 6 replicates from L3 with controls, and RNA-Seq profiles of KLE-2 mutants in 3 replicates each from L3.
2013-09-16 | E-GEOD-45678 | biostudies-arrayexpress
Project description:To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding. Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05). There were 2 groups and 3x replication for each group, for 6 total samples. The groups were (1) L3 and (2) L3-lethargus. We compared L3-lethargus vs L3 using R/maanova. The permutation based p-values for each test were significant for FDRM-bM-^IM-$5%.
2014-04-18 | E-GEOD-46288 | biostudies-arrayexpress