|
| Status |
Public on Apr 07, 2014 |
| Title |
Uhrf1 fl/fl Tconv |
| Sample type |
SRA |
| |
|
| Source name |
Uhrf1 fl/fl Tconv
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Uhrf1 cKO
cell type: Non-Treg
cell population: CD3+CD4+hCD2-(Foxp3-)
|
| Treatment protocol |
N.D.
|
| Growth protocol |
Sorted
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 15 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 |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
His-tagged MBD1
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
MeDIP-seq reads were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Mapped reads were normalized with total mapped reads and bin size (50bp) with cutoff threshold 1 reads / bin for Tconv and 2 reads / bin for Treg.
Genome_build: mm9
Supplementary_files_format_and_content: WIG format having normalized read counts (per million reads per kilobase)
|
| |
|
| Submission date |
Apr 07, 2014 |
| 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) |
| GSE56543 |
Genome-wide measuement of methylated cytosin in regulatory T cells (Treg) and conventional T cells (Tconv) depleted with Uhrf1 |
| GSE56544 |
The epigenetic regulator Uhrf1 facilitates functional expansion of colonic regulatory T cells |
|
| Relations |
| BioSample |
SAMN02720897 |
| SRA |
SRX512211 |
