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Sample GSM5203015 Query DataSets for GSM5203015
Status Public on Apr 01, 2024
Title WT_input
Sample type SRA
 
Source name LSK HSPC
Organism Mus musculus
Characteristics organ: BM
genotype: WT
cell type: LSK HSPCs
antibody: none
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 Nuclei extraction using NP40 buffer and digested into nucleosomes using Mnase.
ChIP-seq libraries of fragmented DNA were prepared using the KAPA Hyper Kit (KAPA) according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
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.
MACS2 to call peaks
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak
 
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)
GSE169430 Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [Bulk H3K27ac ChIP]
GSE169431 Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing
Relations
BioSample SAMN18439530
SRA SRX10420977

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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