|
| Status |
Public on Jun 01, 2023 |
| Title |
WT microglia - ATAC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FACS-sorted microglia
strain: C57BL/6
genotype: WT
treatment: untreated
|
| Treatment protocol |
N.A.
|
| Growth protocol |
Microglia were non-enzymatically isolated from a 3-month-old WT and IRF8KO brain.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-sorted microglia were lysed in NP-40 lysis buffer.
As manufacturer's protocol, the isolated nuclei were tagmented using the Nextera DNA library prep kit (Illumina). The library was amplified by 12-cycle PCR and size-selected.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq without the acceptance of index mismatch
After removing the adapter and low-quality sequences, the data were aligned to the mm10 genome with Bowtie2.
Peaks were called on aligned sequences using MACS2 v2.1.1.20160309 with -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all options.
All peaks were further filtered with less than 0.01 irreversible differential rates.
The bigwig files were generated with Deeptools to visualize the RPGC-normalized, average peaks of each genotype.
Assembly: mm10
Supplementary files format and content: Peak files (.xlsx) consist of peak regions and tag density generated by MACS2
Supplementary files format and content: A bigwig file contains RPGC-normalized, average peaks of each genotype.
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Keita Saeki |
| E-mail(s) |
keita.saeki@nih.gov
|
| Organization name |
NIH/NICHD
|
| Street address |
6 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE231401 |
Genome-wide open chromatin status in WT and IRF8KO microglia [ATAC-seq] |
| GSE231406 |
IRF8 configures enhancer landscape in postnatal microglia and directs microglia specific transcriptional programs |
|
| Relations |
| BioSample |
SAMN34507540 |
| SRA |
SRX20177938 |
