 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 07, 2020 |
| Title |
mTECs_from_WT_mice_ATAC-seq_1 |
| Sample type |
SRA |
| |
|
| Source name |
mTECs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6x129SvEv
genotype/variation: WT
Sex: Male
cell type: TECs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5×10e4 mTEChi from 3- to 4-week-old male WT mice, Fezf2fl/fl Foxn1-Cre mice, or Chd4fl/fl Foxn1-Cre mice were used for preparation of ATAC-seq libraries.
Cells were suspended in 100 µl of cold hypotonic lysis buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550 g for 30 min. The pellet was re-suspended in 5 µl of transposition reaction mix [1 µl of Tagment DNA Enzyme and 2.5 µl of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5 µl H2O], and was incubated for 60 min at 37 °C for DNA to be fragmented and tagged. For library preparation, two sequential seven-cycles of PCR were performed to enrich small tagmented DNA fragments. After the PCR, the libraries were selected for large fragments (more than 100 bp) using AMPure XP.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ATAC_WT_1
ATAC-seq for mTECs from WT mice
processed data file: ATAC_WT.bw
|
| Data processing |
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 ver2.3.2.
Duplicates were removed through command line interface.
Generated sam files were converted to bamfiles by using samtools.
bamfiles were converted to bigwig files by using deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files
|
| |
|
| Submission date |
Feb 06, 2020 |
| Last update date |
Feb 08, 2020 |
| Contact name |
Yoshihiko Tomofuji |
| Organization name |
University of Tokyo
|
| Department |
Immunology
|
| Lab |
Takanayagi's lab
|
| Street address |
hongo 7-3-1
|
| City |
bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8654 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE144879 |
Genome-wide maps of chromatin state in Fezf2 or Chd4 KO mTECs |
| GSE144880 |
RNA-seq, ChIP-seq, and ATAC-seq analyses of mTECs |
|
| Relations |
| BioSample |
SAMN14051851 |
| SRA |
SRX7691599 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
