{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["DCC modENCODE"],"study_type":["ChIP-chip by tiling array"],"organism":["Drosophila melanogaster"],"species":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-44881"],"description":["modENCODE_submission_4181 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 the major histone modifications across the Drosophila melanogaster genome. The modifications 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/27528"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation. 2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization. 3. Hybridize 18hr at 450C with 45 rpm rotation. 4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.","Labeling - 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation. 2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization. 3. Hybridize 18hr at 450C with 45 rpm rotation. 4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.","Nucleic Acid Extraction - Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place. Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experi"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Nicole Riddle","Gary Karpen","DCC modENCODE","Vincenzo Pirrotta","Andrey Gortchakov","Art Alekseyenko","Greg Shanower","Michael Tolstorukov","Sarah Elgin","Aki Minoda","Mitzi Kuroda","Cameron Kennedy","Peter Park","Yuri Schwartz","Peter Kharchenko"],"data_protocol":["Feature Extraction - M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.","Image Adquisition - Standard Affymetrix Array Scanning Protocol was used"],"additional_accession":[]},"is_claimable":false,"name":"H3K23ac.2-4 hr OR embryo","description":"modENCODE_submission_4181 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 the major histone modifications across the Drosophila melanogaster genome. The modifications 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/27528","dates":{"release":"2013-03-06T00:00:00Z","modification":"2023-08-27T01:58:47.403Z","creation":"2022-01-31T16:15:16.622Z"},"accession":"E-GEOD-44881","cross_references":{"GEO":["GSE44881"],"EFO":["EFO_0002762"]}}