|
| Status |
Public on Nov 01, 2021 |
| Title |
0W_LSK: control |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem-progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: Hematopoietic stem-progenitor cells
time: 0 week after BCR/ABL expression induced
strain: C57BL/6
sorting antibody: Lineage Cell Depletion Kit (Miltenyi Biotec). Lineage-negative cells were then stained with Biotin Mouse Lineage Panel (BD Pharmingen), Streptavidin APC-Cy7 (BD Pharmingen), Sca1-PE (BD Pharmingen) and c-Kit-APC (Biolegend)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LSKs were sorted by BD FACSAria, total RNA was isolated from LSKs using the miRNeasy mini RNA isolation kit (Qiagen) according to the manual description.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat (version:2.0.9).
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a protocol from Mortazavi A et al., Nat Methods, 2008.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Nov 06, 2018 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Zhiwei Chen |
| E-mail(s) |
chenzhiweimilan@163.com
|
| Organization name |
Shanghai Jiao Tong Universtiy School of Medicine
|
| Department |
Shanghai Institute Of Hematology
|
| Street address |
Room 807, Research and Education Plaza, 197 Ruijin 2nd Road, Luwan District, Shanghai, PRC
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE122213 |
Next Generation Sequencing Facilitates Quantitative Analysis of tetracycline (Tet) inducible Scl/tTA-BCR/ABL (BA) transgenic mouse hematopoietic stem-progenitor cells Transcriptomes |
|
| Relations |
| BioSample |
SAMN10387381 |
| SRA |
SRX4985357 |
