{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jason Grundstad"],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-25566"],"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 Trem from Adult-Female 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 t"],"repository":["biostudies-arrayexpress"],"sample_protocol":["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 Treatment","Nucleic 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 3M-CM-\"M-^@M-^Y 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Feature Extraction - Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["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, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight ch"],"study_type":["ChIP-seq"],"species":["Drosophila melanogaster"],"pubmed_title":["A cis-regulatory map of the Drosophila genome."],"pubmed_authors":["NM-CM-(gre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP","Nicholas Bild","Kevin White","Jason Grundstad","Nicolas Negre"],"additional_accession":[]},"is_claimable":false,"name":"modENCODE_White Lab: genome-wide ChIP data of Trem from Adult-Female on Illumina Genome Analyzer.","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 Trem from Adult-Female 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 t","dates":{"release":"2010-11-24T00:00:00Z","modification":"2023-08-15T04:03:46.043Z","creation":"2022-03-10T03:45:54.593Z"},"accession":"E-GEOD-25566","cross_references":{"GEO":["GSE25566"],"pubmed":["21430782"],"EFO":["EFO_0002692"],"doi":["10.1038/nature09990"]}}