|
| Status |
Public on Apr 17, 2020 |
| Title |
HEK293T_Tg-1 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic kidney cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
tissue: human embryonic kidney
treatment: 4 hours at 37C-UPR Activator
|
| Treatment protocol |
Cells were treated with DMSO or compound for 4 hours
|
| Growth protocol |
HEK293T cells were maintained in standard DMEM supplemented with 10%FBS and 1%PSQ at 37C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three independent experiments were performed. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard protocols at BGI
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Basescaling was performed by BGI
Single end, 100 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Counts Data were analyzed using DESeq
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX files contain counts data for each sample and DESeq differential expression analysis of test conditions vs. DMSO
|
| |
|
| Submission date |
Apr 16, 2020 |
| Last update date |
Apr 17, 2020 |
| Contact name |
R. Luke Wiseman |
| Organization name |
The Scripps Research Institute
|
| Department |
Molecular Medicine
|
| Lab |
Wiseman
|
| Street address |
10550 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE148802 |
Pharmacologic IRE1/XBP1s Activation Confers Targeted ER Proteostasis Reprogramming |
|
| Relations |
| BioSample |
SAMN14608507 |
| SRA |
SRX8127345 |
