NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1123942 Query DataSets for GSM1123942
Status Public on Apr 02, 2014
Title input sample for RBPJ ChIP experiment 1
Sample type SRA
 
Source name T29 cells
Organism Mus musculus
Characteristics cell type: T29 cells
strain: mixed C57Bl/6/129sv
chip antibody: none
Treatment protocol T29-IKER cells were treated with 4OHT (100 nM) for 24h.
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 v1.3 to v1.6 are used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using GERALD. Only 2 mismatch reads were kept for further analysis.
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)
GSE46119 Mapping of Ikaros and RBPJ binding sites in the mouse T cell leukemia cell line T29
Relations
BioSample SAMN02046759
SRA SRX266507

Supplementary file Size Download File type/resource
GSM1123942_wigs_for_T29_input_1.wig.gz 82.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap