|
| Status |
Public on Sep 30, 2018 |
| Title |
Mx1-Jak2V617F HSC RNA-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic Stem Cell (HSC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Mx1-Jak2V617F
age: 10-weeks (2 months post-pIpC)
cre-driver: Mx1-CRE
cell type: Hematopoietic Stem Cell (HSC)
indexes: CCGGACC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and MPPs (Lin-, cKit+, Sca1+, CD150-, CD48-) were sorted from a pooled sample of 5 male and 5 female 8-week old mice. HSCs and MPPs were purified from three biological replicates (composed of pooled WBM from three male and three female mice) of either control or tests cohorts. Total RNA was isolated from the samples using the NucleoSpin RNA XS kit.
The SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with Subread:featureCount v1.4.5 as well as htseq-count v0.8.0
For RNA-seq QC was performed with RSeQC v2.3
For RNA-seq quantification and normalization of gene RPKM was performed using Partek Genomics Suite Software version 6.6
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw gene counts
|
| |
|
| Submission date |
Sep 27, 2018 |
| Last update date |
Sep 30, 2018 |
| Contact name |
Hamza CELIK |
| E-mail(s) |
[email protected]
|
| Phone |
314-362-0986
|
| Organization name |
Washington University in St Louis
|
| Department |
Internal Medicine
|
| Lab |
Challen Lab
|
| Street address |
660 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE120595 |
Jarid2 Functions as a Tumor Suppressor in Myeloid Neoplasms by Repressing Self-Renewal in Hematopoietic Progenitor Cells |
|
| Relations |
| BioSample |
SAMN10140238 |
| SRA |
SRX4746900 |
