|
| Status |
Public on Jul 14, 2018 |
| Title |
WT_scRNA_batch4 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hematopoietic Stem Cells
strain: C57BL/6
genotype: wild type
tissue: Bone Marrow
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone marrow HSCs from WT or Med23-dificient adult mice were isolated by cell sorting (LSKsCD150+CD34-CD48-).
Single mouse hematopoietic stem cells which were isolated by cell sorting, were manually picked, lysed and subjected to first-strand cDNA synthesis by using barcoded oligo-dT primers. Then, second-strand cDNA were synthesized, amplified and fragmented by sonication (Covaris). Final RNA-seq library was prepared by using the KAPA Hyper Prep Kit (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were separated by cell barcodes, trimmed, aligned to the mm9 mouse transcriptome and de-duplicated by UMIs information.
The transcript copy numbers of each gene were counted and used for the subsequent analysis. Single cells with less than 30% mapping efficiency, 2,000 detected genes and 20,000 transcripts were excluded.
Genes with averaged counts above 0.2 among all the retained 586 single cells were used, and the transcripts were normalized.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include expression values (log2(nomalized count +1)). Cells and genes have been filtered.
|
| |
|
| Submission date |
Mar 19, 2018 |
| Last update date |
Jul 14, 2018 |
| Contact name |
Fan Guo |
| E-mail(s) |
guofan@ioz.ac.cn
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
The State Key Laboratory of Stem Cell and Reproductive Biology
|
| Lab |
Group of Reproductive Epigenetics
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE112008 |
Med23 serves as a gatekeeper of the myeloid potential of hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN08734431 |
| SRA |
SRX3811425 |
