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Sample GSM499652 Query DataSets for GSM499652
Status Public on Jan 26, 2010
Title S2_CTCF500_INPUT_1
Sample type SRA
 
Source name S2_CTCF500_INPUT_1
Organism Drosophila melanogaster
Characteristics cell line: S2
reference: input
Treatment protocol No Treatment
Growth protocol 1. S2 cells are cultivated in Schneider medium according to the recommendations from the Drosophila Genome Ressource Center (DGRC). 2. 1 plate is used for 2 IPs. When cells reach confluence, formaldehyde is added to the plate.
Extracted molecule genomic DNA
Extraction protocol Drosophila cells are cross-linked by the addition of 1.8% of formaldehyde directly in the plate for 15 minutes. The plates are gently rocked every 2 minutes. The cross-linking reaction is quenched by the addition of glycine in the medium for 5 minutes. The cells are then scraped from the plates and pelleted down. 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 S2_CTCF500_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 SRX016161
BioSample SAMN00008274

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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