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Sample GSM2387501 Query DataSets for GSM2387501
Status Public on Aug 01, 2017
Title WT Treg_2 (ChIP-seq)
Sample type SRA
 
Source name Treg cells from FoxP3WT:hCD2 mice
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: lymph nodes and spleen cells
cell type: CD4(+)hCD2(+) Treg cells
sorted from: FoxP3WT:hCD2 mice
chip antibody: FoxP3 (affinity purified rabbit polyclonal antibody, generated in house)
Treatment protocol none
Growth protocol freshly isolated cells
Extracted molecule genomic DNA
Extraction protocol Magnetically sorted hCD2(+) WT and A384T Treg cells (approx. 1x10e7 cells per reaction, prepared in triplicates) were fixed for 30 min at room temperature with 1% formaldehyde, washed with PBS, and stored at -80 °C. Cells were resuspended in lysis buffers and sonicated for solubilization and shearing of crosslinked DNA. The cell extract was incubated overnight at 4 °C with 4 µg of the anti-FoxP3 antibodies and then with Dynabeads protein G (Dynal). Bound complexes were washed and eluted from the magnetic beads by heating at 65°C with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. The immunoprecipitated DNA and whole-cell extract input DNA were treated with RNase A and proteinase K, purified using MinElute PCR purification kit (QIAGEN)
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB) according to the manufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4.
DNA sequence reads were aligned to the mouse reference genome (UCSC mm9) using the Bowtie 2 software (Langmead and Salzberg, 2012).
FoxP3 ChIP-seq peaks were called with Model-based Analysis for ChIP-Seq (MACS) (Zhang et al., 2008) (v2.1.0) using input chromatin as control and FDR q-value of <10e-10.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular files in txt format generated by the MACS2 peak-calling program, which contains information about called peaks.
 
Submission date Nov 10, 2016
Last update date May 15, 2019
Contact name Shohei Hori
E-mail(s) shohei.hori@riken.jp
Phone +81-45-503-7069
Organization name RIKEN Center for Integrative Medical Sciences
Lab Laboratory for Immune Homeostasis
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL18480
Series (2)
GSE89743 Genome-wide maps of FoxP3 binding in FoxP3WT and FoxP3A384T Treg cells
GSE89744 Analyses of a mutant FoxP3 allele reveal BATF as a critical transcription factor in the differentiation and accumulation of tissue regulatory T cells
Relations
BioSample SAMN06008924
SRA SRX2341415

Supplementary file Size Download File type/resource
GSM2387501_WT13_peaks.txt.gz 49.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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