|
| Status |
Public on Apr 01, 2024 |
| Title |
KO LSK 1 |
| Sample type |
SRA |
| |
|
| Source name |
Fli-1 KO LSK HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Fli-1 knockout
tissue: BM
cell type: LSK HSPC
|
| Treatment protocol |
Fli-1 alleles deletion was induced using 4-OHT
|
| Growth protocol |
LSK cells were sorted and co-cultured with E4orf1 vascular niche cells in StemSpan serum free media supplemented with SCF, Flt3, and TPO and with knockout serum replacemnt media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LSK HSPCs were isolated by fluorescence-activated cell sorting and subjected to Omni-ATAC-seq protocl
ATAC-seq libraries of DNA fregments were prepared accordingly to the OMNI-ATAC-seq protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FastQC (v0.11.8) to check FASTQ quality.
Trim Galore (v0.6.4) for adapter trimming
Bowtie2 (v2.3.5) to align reads
Picard (v2.21.1) to remove duplicate reads.
Samtools (v1.9) to remove reads multimapped (MAPQ > 30), unmapped, not primary aligned, failing platform, and mitchondrial reads.
Reads shifted + 4bp and - 5bp for the plus and negative strand respectively.
MACS2 to call peaks
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrix
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Tomer Itkin |
| E-mail(s) |
toi2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Medicine
|
| Lab |
Rafii
|
| Street address |
1300 York Avenue, A-869
|
| City |
NY |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE169397 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [Bulk ATAC-Seq] |
| GSE169431 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing |
|
| Relations |
| BioSample |
SAMN18437389 |
| SRA |
SRX10417587 |
