|
| Status |
Public on Sep 21, 2019 |
| Title |
WT_A_Dox3h RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Normal HSPCs
group: treatment
|
| Treatment protocol |
Dox (1 mg/ml, Sigma) was used at a concentration of 2 μg/ml
|
| Growth protocol |
MLL-AF9-induced AML cells were maintained in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/ml mIL-3 and 50 ng/ml mSCF (PeproTech). Mouse HSPCs were cultured in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/mL mIL-3, 50 ng/ml SCF, 20 ng/ml thrombopoietin (TPO, PeproTech) and 10 ng/ml Flt3 ligand (Flt3-L, PeproTech).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were prepared using rRNA depletion and strand-specific library construction method. RNA was extracted using TRlzolTM (invitrogen) and followed by rRNA removal (Ribo-ZeroTM rRNA Removal Kits) before library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® Kit).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reads were aligned to mm10 mouse genome assembly by STAR Viersion 2.5.1 with ENCODE recommended parameters.
Data were filtered using Samtools Version 1.3 with parameters view -q 4-f 2
Counts number were called using HTSeq Version 0.10.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene raw count number for each Sample
|
| |
|
| Submission date |
Oct 11, 2018 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Kuangyu Yen |
| E-mail(s) |
kuangyuyen@ihcams.ac.cn
|
| Organization name |
Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College
|
| Department |
State Key Laboratory of Experimental Hematology
|
| Street address |
Nanjing Road
|
| City |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE121122 |
Selective eradication of leukemia cells with reprogramming factors (RNA-Seq) |
| GSE121123 |
Selective eradication of leukemia cells with reprogramming factors |
|
| Relations |
| BioSample |
SAMN10231564 |
| SRA |
SRX4862720 |
