ModENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Jason Grundstad
PROVIDER: E-GEOD-23537 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A cis-regulatory map of the Drosophila genome.
Nègre Nicolas N Brown Christopher D CD Ma Lijia L Bristow Christopher Aaron CA Miller Steven W SW Wagner Ulrich U Kheradpour Pouya P Eaton Matthew L ML Loriaux Paul P Sealfon Rachel R Li Zirong Z Ishii Haruhiko H Spokony Rebecca F RF Chen Jia J Hwang Lindsay L Cheng Chao C Auburn Richard P RP Davis Melissa B MB Domanus Marc M Shah Parantu K PK Morrison Carolyn A CA Zieba Jennifer J Suchy Sarah S Senderowicz Lionel L Victorsen Alec A Bild Nicholas A NA Grundstad A Jason AJ Hanley David D MacAlpine David M DM Mannervik Mattias M Venken Koen K Bellen Hugo H White Robert R Gerstein Mark M Russell Steven S Grossman Robert L RL Ren Bing B Posakony James W JW Kellis Manolis M White Kevin P KP
Nature 20110301 7339
Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensi ...[more]
Similar Datasets
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for H3K4me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM385397..GSM385405]: ChIP-chip of H3K4me3 in Drosophila embryos at 12-16 hours of development [GSM386032..GSM386040]: ChIP-chip of H3K4me3 in Drosophila embryos at 0-4 hours of development [GSM386088..GSM386096]: ChIP-chip of H3K4me3 in Drosophila embryos at 4-8 hours of development [GSM386097..GSM386105]: ChIP-chip of H3K4me3 in Drosophila embryos at 16-20 hours of development [GSM386106..GSM386114]: ChIP-chip of H3K4me3 in Drosophila embryos at 20-24 hours of development [GSM386115..GSM386123]: ChIP-chip of H3K4me3 in Drosophila L1 larvae [GSM386125..GSM386133]: ChIP-chip of H3K4me3 in Drosophila L2 larvae [GSM386996..GSM387004]: ChIP-chip of H3K4me3 in Adult Male [GSM418254..GSM418262]: ChIP-chip of H3K4me3 in Drosophila embryos at 8-12 hours of development [GSM442287..GSM442292]: ChIP-chip of H3K4me3 in Pupae [GSM442293..GSM442301]: ChIP-chip of H3K4me3 in Adult Female [GSM442302..GSM442310]: ChIP-chip of H3K4me3 in Drosophila L3 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-06-22 | E-GEOD-15424 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K27me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM384769..GSM384777]: ChIP-chip of H3K27me3 in Drosophila embryos at 0-4 hours of development [GSM384778..GSM384786]: ChIP-chip of H3K27me3 in Drosophila embryos at 4-8 hours of development [GSM384787..GSM384795]: ChIP-chip of H3K27me3 in Drosophila embryos at 12-16 hours of development [GSM384797..GSM384805]: ChIP-chip of H3K27me3 in Drosophila embryos at 16-20 hours of development [GSM384807..GSM384815]: ChIP-chip of H3K27me3 in Drosophila embryos at 20-24 hours of development [GSM384817..GSM384825]: ChIP-chip of H3K27me3 in Drosophila L1 larvae [GSM384826..GSM384834]: ChIP-chip of H3K27me3 in Drosophila L2 larvae [GSM384839..GSM384847]: ChIP-chip of H3K27me3 in Drosophila pupae [GSM385341..GSM385349]: ChIP-chip of H3K27me3 in Drosophila L3 larvae [GSM418225..GSM418233]: ChIP-chip of H3K27me3 in Drosophila Adult male [GSM418239..GSM418247]: ChIP-chip of H3K27me3 in Drosophila embryos at 8-12 hours of development [GSM442006..GSM442014]: ChIP-chip of H3K27me3 in Drosophila Adult female For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-06-22 | E-GEOD-15423 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-seq data generated on Solexa Genome Analyzer for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure.
2009-05-12 | E-GEOD-16013 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This Series contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM382158..GSM382166]: ChIP-chip of H3K9me3 in Drosophila embryos at 12-16 hours of development [GSM384690..GSM384698]: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development [GSM384723..GSM384731]: ChIP-chip of H3K9me3 in Drosophila embryos at 4-8 hours of development [GSM384732..GSM384740]: ChIP-chip of H3K9me3 in Drosophila embryos at 16-20 hours of development [GSM384741..GSM384749]: ChIP-chip of H3K9me3 in Drosophila embryos at 20-24 hours of development [GSM384750..GSM384758]: ChIP-chip of H3K9me3 in Drosophila L1 larvae [GSM384760..GSM384768]: ChIP-chip of H3K9me3 in Drosophila L2 larvae [GSM418207..GSM418215]: ChIP-chip of H3K9me3 in Drosophila Adult male [GSM418216..GSM418224]: ChIP-chip of H3K9me3 in Drosophila embryos at 8-12 hours of development [GSM442371..GSM442379]: ChIP-chip of H3K9me3 in Drosophila Adult male - Set2 [GSM442380..GSM442388]: ChIP-chip of H3K9me3 in Drosophila Pupae [GSM442389..GSM442397]: ChIP-chip of H3K9me3 in Drosophila L3 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-06-22 | E-GEOD-15422 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. This SuperSeries is composed of the following subset Series: GSE15422: ChIP-chip of H3K9me3 in Drosophila at different time points of development GSE15423: ChIP-chip of H3K27me3 in Drosophila at different time points of development GSE15424: ChIP-chip of H3K4me3 in Drosophila at different time points of development GSE15425: ChIP-chip of H3K4me1 in Drosophila at different time points of development GSE15426: ChIP-chip of H3K9Ac in Drosophila at different time points of development GSE15427: ChIP-chip of CBP/p300 in Drosophila at different time points of development GSE15430: ChIP-chip of H3K27Ac in Drosophila at different time points of development GSE16013: Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq GSE16702: ChIP-chip of PolII in Drosophila at different time points of development GSE18068: Genome-wide maps of chromatin state in staged Drosophila embryos, RNA-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 ChIP-chip: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays. ChIP-seq: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure. RNA-seq: For each time-point (E-0-4h, E-4-8h, E-8-12h, E-12-16h, E-16-20h, E20-24h, L1, L2, L3, Pupae, Adult Males and Adult Females) a total RNA extraction has been performed. After conversion into double stranded DNA, the samples have been sequenced in duplicate on Solexa Genome Analyzer following Solexa sequencing procedure.
2009-03-20 | E-GEOD-15292 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: CBP/p300 at 12 different time-points of Drosophila development. Current Dataset: [GSM386269..GSM386277]: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development [GSM386279..GSM386287]: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development [GSM418309..GSM418317]: ChIP-chip of CBP in adult female Drosophila [GSM418318..GSM418326]: ChIP-chip of CBP in adult male Drosophila [GSM418335..GSM418343]: ChIP-chip of CBP in Drosophila embryos at 16-20 hours of development [GSM418454..GSM418462]: ChIP-chip of CBP in Drosophila L3 larvae [GSM418463..GSM418471]: ChIP-chip of CBP in Drosophila pupae [GSM442425..GSM442433]: ChIP-chip of CBP in Drosophila embryos at 0-4 hours of development [GSM443119..GSM443127]: ChIP-chip of CBP in Drosophila L1 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-06-21 | E-GEOD-15427 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9Ac at 12 different time-points of Drosophila development. Current Dataset: [GSM386138..GSM386146]: ChIP-chip of H3K9AC in Drosophila embryos at 12-16 hours of development [GSM386148..GSM386156]: ChIP-chip of H3K9AC in Drosophila L1 larvae [GSM386158..GSM386166]: ChIP-chip of H3K9AC in Drosophila L2 larvae [GSM386168..GSM386176]: ChIP-chip of H3K9AC in Adult female Drosophila [GSM418290..GSM418298]: ChIP-chip of H3K9AC in Adult male Drosophila [GSM442311..GSM442316]: ChIP-chip of H3K9AC in Drosophila embryos at 8-12 hours of development [GSM442317..GSM442325]: ChIP-chip of H3K9AC in Adult male Drosophila - Set2 [GSM442326..GSM442334]: ChIP-chip of H3K9AC in Pupae [GSM442335..GSM442343]: ChIP-chip of H3K9AC in L3 [GSM442344..GSM442352]: ChIP-chip of H3K9AC in Drosophila embryos at 20-24 hours of development [GSM442353..GSM442361]: ChIP-chip of H3K9AC in Drosophila embryos at 4-8 hours of development [GSM442362..GSM442370]: ChIP-chip of H3K9AC in Drosophila embryos at 0-4 hours of development For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-10-08 | E-GEOD-15426 | biostudies-arrayexpress
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-seq data generated on Solexa Genome Analyzer for several Transcription Factors and Chromatin associated Proteins. This dataset is called February_1st_datafreeze and is part of the regular datafreezes we produce for the modENCODE project. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each experiment, at least 2 replicates of ChIP have been performed (except Caudal in Adult Female and E4-8h) and compared to an Input sample(s). The factors analyzed in this freeze are: CTCF in S2 cells, Caudal in embryos 0-4h, embryos 4-8h, L3 larvae and Adult Female, EcR in White Pre-Pupae (10 to 11 hours and 30 to 33 hours) and HDAC1, HDAC3, HDAC6, HDAC4a and HDAC11 in Embryos 0-12h. ChIP samples have been sequenced on the Solexa Genome Analyser (36 bp reads) following the standard Illumina protocol.
2010-01-26 | E-GEOD-20000 | biostudies-arrayexpress
Project description: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 hkb from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 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
2010-08-11 | E-GEOD-23123 | biostudies-arrayexpress
Project description: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 Pcl from E0-8h generated by ChIP and analyzed on Illumina Genome Analyzer. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 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
2010-08-11 | E-GEOD-23127 | biostudies-arrayexpress