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GEO help: Mouse over screen elements for information. |
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Status |
Public on Oct 19, 2023 |
Title |
ATAC, HSPC, Mut, Trx, rep 2 |
Sample type |
SRA |
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Source name |
Isolated HSPCs
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6/J cell type: Isolated HSPCs treatment: Trx_12wk genotype: Srcap mutant
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Extracted molecule |
genomic DNA |
Extraction protocol |
20,000 sorted HSPCs from the bone marrow were washed, permeabalized, and treated with Tn5 transposase. The treated genomic DNA were isolated and used for library construction ATAC-seq library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 2000 |
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Data processing |
Fastq files quality were controlled using fastqc/multiqc Cut-and-run paired-end reads were trimmed from 3' end using Trimmomatic and unique reads were mapped to the mouse genome (mm10) using Bowtie2 BigWig file for each biological replicates were generated using deepTools (bamCoverage) with counts-per-miillion (CPM) normalization and blacklist subtraction Cut-and-run reads from biological replicates were then merged for peak calling using MACS3 Quantification of peaks for Cut-and-run sequencing was performed using Subread package (featureCounts) Assembly: mm10 Supplementary files format and content: bigWig
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Submission date |
Apr 17, 2023 |
Last update date |
Oct 19, 2023 |
Contact name |
Margaret Goodell |
E-mail(s) |
goodell@bcm.edu
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Phone |
7137921265
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Organization name |
Baylor College of Medicine
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Street address |
1 Baylor Plz, Rm N1030
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City |
HOUSTON |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platform ID |
GPL30172 |
Series (2) |
GSE229862 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation [ATAC-Seq] |
GSE230155 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation |
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Relations |
BioSample |
SAMN34223653 |
SRA |
SRX19994473 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7179168_ATAC_Mut_Trx_2.bw |
210.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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