|
| Status |
Public on Apr 02, 2024 |
| Title |
K3_20_n2 |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
genotype: p53 -/- PTEN -/-
tissue: mouse embryonic fibroblasts
treatment: 20 microM vitamin K
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE vM5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.
|
| |
|
| Submission date |
Apr 02, 2020 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Sarah D Diermeier |
| E-mail(s) |
sarah.diermeier@otago.ac.nz
|
| Organization name |
University of Otago
|
| Department |
Biochemistry
|
| Lab |
Diermeier
|
| Street address |
710 Cumberland Street
|
| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE148011 |
Pro-oxidant therapy by a vitamin K precursor targets PI 3-Kinase VPS34 function |
|
| Relations |
| BioSample |
SAMN14527587 |
| SRA |
SRX8048398 |
