|
| Status |
Public on Oct 19, 2023 |
| Title |
CaR, HSPC, Mut, NT, H2AZ, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Isolated Srcap mutant HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
cell type: Isolated Srcap mutant HSPCs
antibody: H2AZ (CST, #50722S)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 sorted HSPCs from the bone marrow were permeabalized with 0.05% Digtonin to perform antibody binding and Mnase digestion. The antibody-enriched DNA fragments were released and used for library construction
Cut-and-run sequencing library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Germline
|
| Data processing |
Fastq files quality were controlled using fastqc/multizc
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
Library strategy: Cut-and-run sequencing
|
| |
|
| Submission date |
Apr 17, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Margaret Goodell |
| E-mail(s) |
goodell@bcm.edu
|
| Phone |
7137921265
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plz, Rm N1030
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE229864 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation [Cut & Run] |
| GSE230155 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation |
|
| Relations |
| BioSample |
SAMN34217884 |
| SRA |
SRX19985734 |
