|
| Status |
Public on Jul 01, 2020 |
| Title |
RRB-KO3 |
| Sample type |
SRA |
| |
|
| Source name |
lamina proprial lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Brg1-deficient ILC3s
gender: female
mouse genotype: Rag1-/-Smarca4flox/floxRorc-cre
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library preparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme, Nanjing, China. 1.2X Agencourt AMPure XP beads(Beckman Coulter) were used to purify libraries for sequencing.
150 paired-end sequencing was performed with Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
cells were isolated from small intestinal lamina propria.
ATACrawCountsBrg1
|
| Data processing |
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Quality filtered reads were then mapped to mouse genome (mm10) by Bowtie2, and only uniquely mapped reads were saved.
Peak calling was done using MACS2 with an initial threshold q-value of 0.01 as cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts of sequencing reads from triplicates samples with chromosome ID, chromosome start and end positions.
|
| |
|
| Submission date |
Apr 03, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Ju Qiu |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE148078 |
Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN14535099 |
| SRA |
SRX8055071 |
