|
Status |
Public on Oct 19, 2023 |
Title |
Isolated B cells, Transplantation, 2-weeks_1 WT |
Sample type |
SRA |
|
|
Source name |
B cells in bone marrow
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL6/J cell type: B cells in bone marrow genotype: WT treatment: Transplantation time: 2 weeks
|
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
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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
|
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 |
SAMN34224111 |
SRA |
SRX19994556 |