|
| Status |
Public on Oct 19, 2023 |
| Title |
Isolated HSPCs, Doxorubicin IP, 12-hours_1 Srcap mutant |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem and progenitor cells (HSPCs)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
cell type: Hematopoietic stem and progenitor cells (HSPCs)
genotype: Srcap mutant
treatment: Doxorubicin
time: 12 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from 30,000 sorted HSPCs in the bone marrow and isolated using Allprep DNA/RNA Micro Kit (Qiagen) of each independent Sample for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using True-Seq Stranded mRNA library preparation kit (Illumina, 20020594) based on manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Fastq files quality were controlled using fastqc/multizc
Duplicate reads were removed and unique sequence reads were trimmed for adaptor sequence/low-quality sequence
Paired-end bulk RNA-sequencing reads were mapped to the STAR mouse reference genome index (mm39) using STAR
Quantification of mapped reads for RNA-sequencing was performed using Subread package (featureCount) to obtain count files
Assembly: mm10
Supplementary files format and content: tab-delimited text files including feature counts for each Sample
|
| |
|
| 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) |
| GSE229865 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation [RNA-seq] |
| GSE230155 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation |
|
| Relations |
| BioSample |
SAMN34224113 |
| SRA |
SRX19994554 |
