|
| Status |
Public on Aug 20, 2023 |
| Title |
KO_156_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lin-cKit+ bone marrow cells
strain: C57BL/6
genotype: Brd4_KO
|
| Treatment protocol |
BM Lin-c-Kit+ cells from Mx1Cre+ Brd4 flox/fox and WT littermates were purified by sorting 14 days after poly(I:C) injection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq DNA were treated and extracted following the Omni-ATAC protocol.
TheATACseq libraries were prepared using the NEBNext high-fidelity 2x PCR master mix and sequenced with a paired-end 150 bp on an Illumina NextSeq 500 system.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with MACS2 with options: -g mm -n test -B -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary_files_format_and_content: NarrowPeak files were generated using MACS2
|
| |
|
| Submission date |
Nov 29, 2021 |
| Last update date |
Aug 20, 2023 |
| Contact name |
Hui Yang |
| Organization name |
UTHSCSA
|
| Street address |
5114 medical dr.
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE189832 |
Bromodomain member BRD4 is required for hematopoietic stem cell functions (ATAC-Seq) |
| GSE189836 |
Bromodomain member BRD4 is required for hematopoietic stem cell functions |
|
| Relations |
| BioSample |
SAMN23496236 |
| SRA |
SRX13257099 |
