|
| Status |
Public on Nov 01, 2022 |
| Title |
WT LSK, from wt females [639] |
| Sample type |
SRA |
| |
|
| Source name |
BM Lin-Sca-1+c-Kit+ (LSK)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BM Lin-Sca-1+c-Kit+ (LSK)
Sex: female
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.
RNA-seq was performed on Illumina NovaSeq6000 with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
639
|
| Data processing |
Illumina NovaSeq6000
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Bin Zhang |
| Organization name |
City of Hope
|
| Department |
Hem Malignancies Trans Sci
|
| Street address |
1500 E. Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216794 |
Gene profiling changes in BM Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142-/- (KO), miR-142+/+ (WT), miR-142-/- BCR-ABL (BC CML) and miR-142+/+ BCR-ABL (CP CML) mice. [bulk RNA-Seq] |
|
| Relations |
| BioSample |
SAMN31508481 |
| SRA |
SRX18064013 |
