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| Status |
Public on May 15, 2024 |
| Title |
Mga(-/-) Mouse Rep2 |
| Sample type |
SRA |
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| Source name |
HSC
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| Organism |
Mus musculus |
| Characteristics |
cell type: HSC
genotype: Mga(-/-)-Vav1-cre(tg/+)
strain: C57/B6
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| Growth protocol |
MOLM-13 cells or Lin-,cKit+ HSPCs were harvested at 50,000 cells.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Open chromatin status was assessed using the assay for transposase-accessible chromatin via sequencing (ATAC-seq) kit (Active Motif, CA) following the manufacturer’s protocols.
Library prep, included in kit, was done following the manufacturer’s protocols (Active Motif, CA).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4, Krueger F. (2012)), in order to remove potential adapters and quality trim 3’ end of reads with cutadapt program, followed by FastQC analysis
A quality score cutoff of Q20 was used and the first 15bp of each reads were also clipped to reduce the GC bias. Next, reads were mapped to the human reference genome (hg38; GRCh38.p12) with BWA mem (0.7.17-r1188), then converted to BAM format and deduplicated with fq2bam (v3.0.0.6)
Subsequently, uniquely mapped properly paired reads were extracted with samtools (v1.2), and fragments were extracted with bedtools(v2.24.0)
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format
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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) |
| GSE253752 |
Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [ATAC-seq] |
| GSE253753 |
Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia |
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| Relations |
| BioSample |
SAMN39510436 |
| SRA |
SRX23331087 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8027489_2512342_SJMMNORM080060_C1_MET36_HOMOb.free.bw |
111.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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