|
| Status |
Public on Dec 21, 2021 |
| Title |
Knockout replicate 1 (ko1) |
| Sample type |
SRA |
| |
|
| Source name |
MHCII-high medullary thymic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
background mouse strain: C57BL/6
genotype: Kat7 knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA was prepared and extracted as described by Corces et al "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues" (Nature methods 2017). DNA was cleaned using the Zymo DNA Clean and Concentrator-5 Kit (Zymo) according to the manufacturer’s instructions.
ATAC-seq libraries were prepared as described by Corces et al (2017).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read pairs were aligned to the mm10 genome using Rsubread version 1.32.2.
Read-pairs were counted for each gene promoter region using Rsubread's featureCounts function. Promoter regions were defined using Rsubread's promoterRegions() function and Rsubread's inbuilt RefSeq annotation as 3kb upstream to 2kb downstream of each Entrez Gene transcription start site. Putative promoter regions were not extended past the end of the gene or outside the relevant chromosome, so for very short genes the promoter region can be less than 5kb in width.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with seven columns. Columns give Entrez Gene ID, chromosome, start and end genomic locations of the promoter region, strand, gene symbol and read count respectively. The supplementary file GenewiseCounts.txt.gz consolidates the read counts for all the samples into one file.
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Dec 21, 2021 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE188868 |
ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice |
| GSE188871 |
RNA-seq and ATAC-seq profiling of thymic epithelial cells from wildtype and Kat7 knockout mice |
|
| Relations |
| BioSample |
SAMN23167391 |
| SRA |
SRX13142956 |
