biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNick BildChIP-seqDrosophila melanogasterDrosophila melanogasterhttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-25027This 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 CG8478 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 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.biostudies-arrayexpressNucleic Acid Extraction - Drosophila material is crushed in a glass homogenizer in presence of 1.8% of formaldehyde for 15 minutes at room temperature. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the Input reference sample. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation. If used for hybridization on microarrays, the sample will undergo an LM-PCR amplification before labelling.Growth Protocol - 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.Sample Processing - No TreatmentNucleic Acid Extraction - After chromatin immuno-precipitation, the DNA is purified in 30ul of water. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesNicholas BildKevin WhiteNick BildNicolas NegreFeature Extraction - Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.falsemodENCODE_White Lab: genome-wide ChIP data of CG8478 from E16-24h on Illumina Genome Analyzer.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 CG8478 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 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.2010-10-30T00:00:00Z2023-08-10T05:33:04.014Z2022-02-02T12:42:17.399ZE-GEOD-25027GSE25027EFO_0002692