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Sample GSM1141669 Query DataSets for GSM1141669
Status Public on May 16, 2013
Title CD8+_Input_Biotin_ChIPseq
Sample type SRA
Source name CD8+ cells, Foxo1tagBirA mice
Organism Mus musculus
Characteristics cell type: CD8+, Foxo1tagBirA strepdavidin Input
strain: C57BL/6
ChIP: none
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol phenol-chloroform
Lysates were clarified from sonicated nuclei and Foxo1-DNA complexes were isolated with antibody or Streptavidin. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a kit from Epicentre. The blunt, phosphorylated ends were treated with Taq DNA polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-19 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalls performed using CASAVA v1.4
Bowtie v0.12.7 was used to identify sequences mapping uniquely to the genome
Peak calls were determined using BCP (
Overlapping peaks between antibody and biotin ChIP methods were merged
Genome_build: mm9
Supplementary_files_format_and_content: BED files for uniquely mapping reads and called MACS peaks for Antibody, Biotin, and overlapping peaks are provided
Submission date May 15, 2013
Last update date May 15, 2019
Contact name Willey Liao
Organization name New York Genome Center
Department Bioinformatics
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
Platform ID GPL11002
Series (2)
GSE46943 Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [ChIP-Seq]
GSE46944 Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection
BioSample SAMN02144286
SRA SRX278100

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

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