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| Status |
Public on May 15, 2024 |
| Title |
2512306_SJMMNORM080054_C1_WTa_H3K27Ac_AB5 |
| Sample type |
SRA |
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| Source name |
HSC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57/B6
cell type: HSC
chip antibody: anti-H3K27Ac, Cell signaling 8173S
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| 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
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jan 19, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Michael Walsh |
| E-mail(s) |
Michaelp.walsh@stjude.org
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| Organization name |
St Jude Children's Research Hospital
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| Street address |
262 Danny Thomas
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| City |
Memphis |
| ZIP/Postal code |
38103 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN39510282 |
| SRA |
SRX23331125 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8027449_2512306_SJMMNORM080054_C1_WTa_H3K27Ac_AB5.CRall.bw |
85.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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