|
| Status |
Public on Nov 20, 2013 |
| Title |
AcH3_Butyrate (S01037) |
| Sample type |
SRA |
| |
|
| Source name |
Naïve T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
marker: CD3+CD4+CD44loCD62Lhi
cell type: Naive T cells
culture conditions: Treg-inducing condition
agent: Butyrate
antibody: AcH3 (Millipore, 06-600, Lot: 2068182)
|
| Treatment protocol |
10 ng/mL IL-2, 0.2 ng/mL TGF-beta, and 0.1 mM Butyrate
|
| Growth protocol |
Naïve T cells were isolated from spleen and were cultured in the presence of TCR signaling, IL-2, TGF-beta and in the presence or absene of Butyrate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sheared chromatin DNA was extracted using Magnify ChIP kit and Covaris S220 accroding to manufacture's procedure followed by precipitation of chromatin-DNA complex
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra DNA Library Prep kit for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.1.0 with default parameters.
Reads of control experiment were normalized using total reads of the experiment (read per million reads per kilobase genome) and those of treated cells were normalized using internal control (5 positions from Rpl13a).
Wiggle files were generated using our in-house program with window size 50bp and cutoff value 5 reads per window.
TDF files were converted from wiggle files using IGVTools version 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files and TDF files containing identical summary data (ie, histone acetylation).
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL15103 |
| Series (2) |
| GSE49653 |
Genome-wide measurement of acetylated histone H3 in naïve cells under Treg-inducing conditon |
| GSE49655 |
Commensal microbe-derived butyrate epigenetically induces colonic regulatory T cells |
|
| Relations |
| BioSample |
SAMN02313889 |
| SRA |
SRX332739 |
