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Sample GSM8027459 Query DataSets for GSM8027459
Status Public on May 15, 2024
Title 2512322_SJMMNORM080054_C4_HETb_H3K27me3_AB4
Sample type SRA
 
Source name HSC
Organism Mus musculus
Characteristics strain: C57/B6
cell type: HSC
chip antibody: anti-H3K27me3, Cell signaling 9733S
Extracted molecule genomic DNA
Extraction protocol CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used. Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding. Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format
Library strategy: CUT&RUN
 
Submission date Jan 19, 2024
Last update date May 15, 2024
Contact name Michael Walsh
E-mail(s) Michaelp.walsh@stjude.org
Organization name St Jude Children's Research Hospital
Street address 262 Danny Thomas
City Memphis
ZIP/Postal code 38103
Country USA
 
Platform ID GPL24247
Series (2)
GSE253750 Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [Cut&Run]
GSE253753 Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia
Relations
BioSample SAMN39510272
SRA SRX23331135

Supplementary file Size Download File type/resource
GSM8027459_2512322_SJMMNORM080054_C4_HETb_H3K27me3_AB4.CRall.bw 100.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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