|
| Status |
Public on Jan 19, 2021 |
| Title |
U2OS PDPK1-FKBP(F36V) RNA-seq DMSO rep1 [DMSO-1] |
| Sample type |
SRA |
| |
|
| Source name |
U2OS PDPK1-FKBP(F36V) RNA-seq DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
engineered genotype: endogenous C-terminal tag on PDPK1, FKBP(F36V)-2xHA
treatment: 0.01% DMSO for 24 hours
|
| Growth protocol |
All cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment. RNA was submitted to GENEWIZ or the Vanderbilt Technologies for Advanced Genomics Core Laboratory for rRNA reduction, library preparation, and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DMSO-1
processed data file: U2OS-PDK1-count.txt
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each Sample
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Jan 19, 2021 |
| Contact name |
Jing Wang |
| Organization name |
Vanderbilt University Medical Center
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN14901710 |
| SRA |
SRX8331195 |
