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Sample GSM892322 Query DataSets for GSM892322
Status Public on Jun 18, 2012
Title Mod(mdg4)BTB_ChIPseq
Sample type SRA
 
Source name Kc cells
Organism Drosophila melanogaster
Characteristics chip antibody: Mod(mdg4)BTB
cell type: Kc167 Drosophila Embryonic Cell line
Growth protocol Kc cells were maintained in HyClone CCM3 Serum-free media.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments. Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC. Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against Mod(mdg4)BTB
Data processing Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome Build:
Modmdg4BTB.bed: DM3
Modmdg4BTB.wig: DM3
 
Submission date Mar 09, 2012
Last update date May 15, 2019
Contact name Kevin Van Bortle
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Dr
City Palo Alto
State/province CA
ZIP/Postal code 94043
Country USA
 
Platform ID GPL13304
Series (1)
GSE36393 Distribution of Drosophila insulator proteins Mod(mdg4) and L(3)mbt in Kc cells
Relations
SRA SRX128326
BioSample SAMN00810071

Supplementary file Size Download File type/resource
GSM892322_Modmdg4BTB.bed.gz 105.6 Kb (ftp)(http) BED
GSM892322_Modmdg4BTB.wig.gz 46.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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