|
| Status |
Public on Jun 07, 2022 |
| Title |
WT_HSPCs_3 |
| Sample type |
SRA |
| |
|
| Source name |
WT_HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: WT
cell type: hematopoietic stem and progenitor cells (HSPCs)
|
| Treatment protocol |
4-6 week old mice were injected intraperitoneally with 300 mL of 1 mg/mL PIpC every other day for a total of 7 doses.
|
| Growth protocol |
HSPCs were isolated from mice 4-6 weeks post treatment using red cell lysis and lineage depletion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 1x10^6 cells using Trizol (ThermoFisher Scientific, 15596018) and the manufacturer’s recommended protocol.
Libraries were prepped in exact accordance with the NEBNext Ultra II RNA library prep kit for Illumina (NEB, E7770) in combination with the NEBNext Poly(A) mRNA magnetic isolation module (NEB, E7490), the NEBNext multiplex oligos for Illumina set 1 and set 2 (NEB, E7335 and E7500), and Ampure XP magnetic beads (Beckman Coulter, A6388).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq 500 system used for base calling
RNA seq data were aligned to the mm9 genome using STAR
DESEQ2 was used to obtain a list of differentially expressed genes between genotypes of interest.
Genome_build: MM9
Supplementary_files_format_and_content: Excel spreadsheet and log2FC
|
| |
|
| Submission date |
Sep 15, 2021 |
| Last update date |
Jun 07, 2022 |
| Contact name |
Sridhar Rao |
| E-mail(s) |
sridhar.rao@bcw.edu
|
| Phone |
4149373841
|
| Organization name |
BloodCenter of Wisconsin
|
| Department |
Blood Research Institute
|
| Street address |
8727 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE184176 |
Combinatorial genetics reveals the DOCK1-RAC2 axis as a specific target for the treatment of NPM1;Cohesin mutated AML |
|
| Relations |
| BioSample |
SAMN21441327 |
| SRA |
SRX12194740 |
