|
| Status |
Public on Dec 09, 2020 |
| Title |
WT-3 |
| Sample type |
SRA |
| |
|
| Source name |
wild type_Bone Marrow LSK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
tissue: bone marrow
cell type: LSK cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Micro Kit (QIAGEN) from sorted Lin- Sca-1+ c-Kit+ (LSK) cells cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, Palo Alto, CA, USA). The ds-cDNA was fragmented using S220 Focused- ultrasonicator (Covaris)
cDNA libraries were generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
TopHat (version 2.0.13; with default parameters) was used to mapped to the reference genome (UCSC/mm10) with annotation data from iGenomes (Illumina).
The levels of gene expression were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: bedGraph files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 29, 2018 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Koichi Murakami |
| E-mail(s) |
[email protected]
|
| Organization name |
Keio University School of Medicine
|
| Street address |
Shinanomachi 35
|
| City |
Shinjuku-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE116433 |
Regulation of mitophagy by O-linked N-acetylglucosamine transferase is essential for hematopoietic stem cell maintenance |
|
| Relations |
| BioSample |
SAMN09519105 |
| SRA |
SRX4325343 |
