|
| Status |
Public on May 15, 2024 |
| Title |
RNA-seq of cKit+ cells from Mga(+/-) C57/B6 mice #4 |
| Sample type |
SRA |
| |
|
| Source name |
HSC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: HSC
genotype: Mga(+/-)
strain: C57/B6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a quick-RNA Microprep kit (Zymo Research, CA).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076940_D1_HET
|
| Data processing |
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.
Supplementary files format and content: tab-delimited text file for gene counts , one gene per row and one sample per column.
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Michael Walsh |
| E-mail(s) |
Michaelp.walsh@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Street address |
262 Danny Thomas
|
| City |
Memphis |
| ZIP/Postal code |
38103 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE253748 |
Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [RNA-seq] |
| GSE253753 |
Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia |
|
| Relations |
| BioSample |
SAMN39511451 |
| SRA |
SRX23332026 |
