|
| Status |
Public on Aug 20, 2023 |
| Title |
CR_6_KO_CH3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lin-cKit+ bone marrow cells
strain: C57BL/6
genotype: Brd4_KO
c&r antibody: Clipping H3(Cell signaling, 1257)
|
| Treatment protocol |
BM c-Kit+ and LSK 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 |
The gemonic DNA covered by indicated antibodies were digested by pAG-Mnase and purified using DNA purification kit(NEB).
The CUT&RUN libraries were prepared using the NEBNext Ultra II DNA library prep kit and sequenced with pared-end 75 bp on an Illumina NextSeq 500 system
CUT&RUN
|
| |
|
| Library strategy |
OTHER |
| 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 homer with options: findPeaks
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary_files_format_and_content: Peak files were generated using homer
|
| |
|
| 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) |
| GSE189833 |
Bromodomain member BRD4 is required for hematopoietic stem cell functions (CUT&RUN) |
| GSE189836 |
Bromodomain member BRD4 is required for hematopoietic stem cell functions |
|
| Relations |
| BioSample |
SAMN23497002 |
| SRA |
SRX13257119 |
