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Sample GSM2107750 Query DataSets for GSM2107750
Status Public on Feb 20, 2018
Title input DNA for ChIP on thymoctes fixed with formaldehyde#2
Sample type SRA
 
Source name whole thymocyte, fixed with formaldehyde
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: thymocyte
age: adult (8.1 weeks)
Sex: male
genotype: wild type
antibody: NULL
Growth protocol Mice were sacrificed, their thymi were removed, and single-cell suspensions were made.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Briefly, ChIP DNA was purified and end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3’ 'A' base for ligation of NEBNext Multiplex Oligos for Illumina (NEB #E7335) which have a single 3' overhanging 'T' base and a hairpin structure. After ligation, adapters were converted to the ‘Y’ shape by treating with USER enzyme and DNA fragments were size selected using Agencourt AMPure XP beads (Beckman Coulter #A63880) to generate fragment sizes between 250 and 350 bp. Adaptor-ligated DNA was PCR amplified for 18 cycles followed by AMPure XP bead clean up. Libraries were quantified with Qubit dsDNA HS Kit (ThermoFisher Scientific #Q32854) and the size distribution was confirmed with High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies #5067). Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description ChIP-Seq
Data processing Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4.
DNA sequence reads from each ChIP-seq library (single-read) were mapped onto NCBI37/mm9 using Bowtie (bowtie-1.1.1, https://sourceforge.net/projects/bowtie-bio/files/bowtie/) with three or fewer mismatches. Data from multiple lanes of the same biological sample were combined. Uniquely mapped reads were used for further analysis. The obtained data were processed by the Homer v4.7.2 to obtain tag directory followed by conversion to BED files.
Genome_build: mm9
Supplementary_files_format_and_content: tag directory bed
 
Submission date Apr 04, 2016
Last update date May 15, 2019
Contact name Satoshi Hirose
E-mail(s) hirose@caltech.edu
Phone 626-395-4915
Organization name California Institute of Technology
Department Biology and Bioengineering
Lab Rothenberg
Street address 1200 E. California
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
 
Platform ID GPL17021
Series (2)
GSE79874 Integrative analysis of 3D nucleome and chromatin accessibility reveals a chromatin barrier established for T-lineage commitment during early T cell development [ChIP-Seq]
GSE79875 Integrative analysis of 3D nucleome and chromatin accessibility reveals a chromatin barrier established for T-lineage commitment during early T cell development
Relations
BioSample SAMN04605087
SRA SRX1677241

Supplementary file Size Download File type/resource
GSM2107750_15196_mm9_tagdir.bed.gz 323.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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