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Sample GSM5201890 Query DataSets for GSM5201890
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

Supplementary file Size Download File type/resource
GSM5201890_WT1_peaks.narrowPeak.gz 2.1 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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