|
| Status |
Public on Jul 20, 2017 |
| Title |
ATACseq_Adult_WT |
| Sample type |
SRA |
| |
|
| Source name |
adult pre-selection DP thymocyte
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: adult
genotype/variation: control
cell type: thymocyte
|
| Growth protocol |
TCRb low CD24 high CD4+CD8+ pre-selection thymocytes were prepared from newborn mice or 4-6 week old mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were prepared from 25,000-sorted cells. The transposase reactions were carried using Nextera DNA Library Preparation Kit (Illumina).
Purified DNA fragments were amplified by PCR. The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Control adult thymocyte
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumulated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase
|
| |
|
| Submission date |
Dec 07, 2016 |
| 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 |
GPL18480 |
| Series (2) |
| GSE90989 |
Chromatin structures in pre-selection DP thymocytes of WT and Bcl11b hypomorphic mutant |
| GSE90990 |
Bcl11b hypomorphic mutant thymocytes |
|
| Relations |
| BioSample |
SAMN06116078 |
| SRA |
SRX2402004 |
