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Sample GSM401412 Query DataSets for GSM401412
Status Public on May 12, 2009
Title AdultFemale_H3K27Ac_ChIPSeq_1
Sample type SRA
Source name AdultFemale
Organism Drosophila melanogaster
Characteristics tissue: AdultFemale
antibody: H3K27Ac
antibody manufacturer: Abcam
antibody catalog number: ab4729
antibody lot number: 34629
Treatment protocol No Treatment
Growth protocol 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Female 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.
Extracted molecule genomic DNA
Extraction protocol Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. 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 reference samples. 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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description H3K27Ac_ChIPSeq_1
corresponding input record: GSM400671
Data processing Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).
Submission date May 11, 2009
Last update date May 15, 2019
Contact name Kevin P. White
Organization name University of Chicago
Department Institute for Genomics and Systems Biology
Street address 900 E. 57th STR. 10th FL.
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
Platform ID GPL9058
Series (2)
GSE15292 Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq
GSE16013 Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq
SRA SRX013034
BioSample SAMN00005183

Supplementary file Size Download File type/resource
GSM401412_AdultFemale_H3K27Ac_Input_tag36_mfold4_250_peaks_1fdr_filtered.bed.gz 62.1 Kb (ftp)(http) BED
GSM401412_H3K27Ac_density.bedgraph.gz 19.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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