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Sample GSM1123915 Query DataSets for GSM1123915
Status Public on Apr 02, 2014
Title control streptavidin ChIP-seq of BirA expressing Beko cells
Sample type SRA
 
Source name Beko-bio cells
Organism Mus musculus
Characteristics cell type: Beko-bio cells
strain: TCRb KO
chip antibody: Streptavidin Dynalbeads (Invitrogen)
Extracted molecule genomic DNA
Extraction protocol ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Illumina pipeline version >1.8.0 used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)
 
Submission date Apr 16, 2013
Last update date May 15, 2019
Contact name Susan Chan
E-mail(s) scpk@igbmc.fr
Phone 33 3 88 65 34 72
Organization name IGBMC
Street address 1, rue Laurent Fries
City Illkirch
ZIP/Postal code 67404
Country France
 
Platform ID GPL11002
Series (1)
GSE46114 Mapping of Notch1 binding sites in a mouse immature T cell line
Relations
BioSample SAMN02046649
SRA SRX268231

Supplementary file Size Download File type/resource
GSM1123915_wigs_for_Beko-bio_bio-ChIP.wig.gz 189.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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