|
| Status |
Public on Dec 05, 2022 |
| Title |
WT Neonate 3 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Alveolar macrophages
tissue: Lung
genotype: WT (C57Bl/6J)
age: Postnatal Day 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposed DNA extracted with Qiagen MiniElute.
100bp paired-end
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
pup-w3
|
| Data processing |
alignment; bowtie2 with default parameters
create common peak set; bedops merge with default parameters
sort; samtools sort with default parameters
remove PCR duplicates; picard MarkDuplicates with REMOVE_DUPLICATES=TRUE
peak calling; macs callpeak with parameters -q 0.05 --keep-dup all
create common peak set; bedops merge with default parameters
generate count matrix; featureCounts
Assembly: mm10
Supplementary files format and content: text file; a count matrix with counts of raw reads overlapping peaks in each sample
|
| |
|
| Submission date |
Nov 29, 2022 |
| Last update date |
Dec 05, 2022 |
| Contact name |
Luis B Barreiro |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Lab |
Barreiro Lab
|
| Street address |
900 E 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE219042 |
Early life provision of 12-HETE by neutrophils imprints self-renewing capacity on alveolar macrophages |
|
| Relations |
| BioSample |
SAMN31933379 |
| SRA |
SRX18421069 |
