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Sample GSM499645 Query DataSets for GSM499645
Status Public on Jan 26, 2010
Title E0-4h_7T_INPUT_1
Sample type SRA
 
Source name E0-4h_7T_INPUT_1
Organism Drosophila melanogaster
Characteristics development stage: E0-4h
reference: input
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 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.
Extracted molecule genomic DNA
Extraction protocol Drosophila whole animals (embryos, larvae, pupae or adults) are crushed in presence of 1.8% of formaldehyde for 15 minutes with the help of a douncer. 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 E0-4h_7T_INPUT_1
Data processing Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software. Signal files were generated with the R package SPP. Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).
 
Submission date Jan 22, 2010
Last update date May 15, 2019
Contact name Kevin P. White
E-mail(s) kpwhite@uchicago.edu
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 (1)
GSE20000 Genome-wide maps of chromatin state in staged Drosophila embryos and cell lines.
Relations
SRA SRX016154
BioSample SAMN00008267

Supplementary data files not provided
SRA Run SelectorHelp
Processed data not applicable for this record
Raw data are available in SRA

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