|
Status |
Public on Apr 01, 2024 |
Title |
Control LSK 1 |
Sample type |
SRA |
|
|
Source name |
WT LSK HSPCs
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: WT 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 |
SAMN18437392 |
SRA |
SRX10417590 |