|
| Status |
Public on Jun 13, 2023 |
| Title |
15297X29 Abcb10 knockout cells Day 5 biol rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
MEL
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEL
cell type: Erythroleukemia cells
genotype: Abcb10 knockout
treatment: 1.5% DMSO
time: 5 days treatment
|
| Growth protocol |
DMEM with 1.0 mM Na pyruvate, 1X Glutamax, 1X non-essential amino acids, 100 units/ml penicillin, 100 ug/ml streptomycin. 37 C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymo Research DirectZol RNA Extraction
RNA was processed with Ribo-Zero Globin and stranded RNA seq libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep Gold.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Assembly: mm10
Supplementary files format and content: featureCount output files combined into a single tab-delimited raw count matrix
|
| |
|
| Submission date |
Feb 13, 2023 |
| Last update date |
Jun 13, 2023 |
| Contact name |
W. Zac Stephens |
| Organization name |
University of Utah
|
| Department |
Pathology
|
| Lab |
Round Lab
|
| Street address |
15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84121-3808 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE225218 |
Loss of the mitochondrial protein Abcb10 results in altered arginine metabolism in MEL and K562 cells and nutrient stress signaling through ATF4 |
|
| Relations |
| BioSample |
SAMN33273670 |
| SRA |
SRX19355594 |
