|
| Status |
Public on Jun 30, 2022 |
| Title |
RNA-seq_IR_KO |
| Sample type |
SRA |
| |
|
| Source name |
Lineage–Sca1+cKit+CD34–Flk2– long-term hematopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: irradiation
strain: C57BL/6
cell type: long-term hematopoietic stem cell
genotype: Twist1 cKO
|
| Treatment protocol |
Long-term hematopoietic stem cells were isolated from bone marow of WT or Twist1 cKO mice 12 days after irradiation treatment or under steady state
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lineage–Sca1+cKit+CD34–Flk2– cells were collected and RNA was harvested using RLT reagent. Qiagen RNeasy Mini Kit (Cat#74104) was used for the construction of sequencing libraries. For ATAC-seq samples nuclei were subjected to Tn5 transposase reaction (Illumina Nextera DNA Sample Preparation Kit) following manufacturer’s instructions and DNA was purified using the Agencourt AMPure XP beads (Beckman Coulter).
RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC-seq was performed as originally described in Buenrostro et al. 2013.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference.
ATAC-seq: skewer 0.1.126 is required for trimming raw data. Parameter: -m pe.
ATAC-seq: BWA 0.7.12-r1039 is required for mapping. Parameter: -T 25 -k 18.
ATAC-seq: deepTools3.0.2 is required for sample analysis. Parameter: --corMethod pearson.
ATAC-seq: MACS2 2.1.0 is required for peak calling. Parameter: -q 0.05 --nomode --call-summits --nomodel.
ATAC-seq: homer findMotifsGenome.pl v4.9.1 is required for identifying motif. Parameter: -gc -len 8,10,12,14.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Gene quantification txt file; ATAC-seq: Signal track bigWig file.
|
| |
|
| Submission date |
Jul 02, 2019 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Xiao Tong Ma |
| E-mail(s) |
maxt@ihcams.ac.cn
|
| Phone |
+862223909405
|
| Organization name |
Chinese Academy of Medical Sciences
|
| Department |
Institute of Hematology & Blood Diseases Hospital
|
| Lab |
State Key Laboratory of Experimental Hematology
|
| Street address |
Blood hospital, 288 Nanjing Road
|
| City |
TianJin |
| State/province |
TianJin |
| ZIP/Postal code |
300020 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE133682 |
TWIST1 is required for HSC maintenance under steady state and stress condition by inhibiting mitochondrial metabolism gene program |
|
| Relations |
| BioSample |
SAMN12184526 |
| SRA |
SRX6387009 |
