|
| Status |
Public on Sep 22, 2021 |
| Title |
HeLa siGI3_1 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: siGl3-control
|
| Treatment protocol |
Cells were plated 24h before transfection and then transfected using the Calcium phosphate method at a confluence of ~50% with either siTFIP11 or siGl3 (control: targeting Gl3 luciferase) with a final concentration of 40 nm.
|
| Growth protocol |
Cells were maintained at 37°C in the presence of 5% CO2 in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using a Nucleospin kit from Macherey/Nagel.
Illumina TruSeq stranded mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter sequences and/or low-quality ends were identified and trimmed using bbduk 35.59
Reads were mapped to the human genome (hg19) using STAR v2.5.2b
PCR duplicates were removed from aligned files using Picard tools
Gene expression was quantified using featureCounts v1.4.6-p5 and GENCODE v. 26 annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated file of read counts per gene per sample
|
| |
|
| Submission date |
Aug 18, 2020 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Tina M O'Grady |
| E-mail(s) |
[email protected]
|
| Phone |
504-988-1169
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE156388 |
RNA-Seq of HeLa cells treated with siTFIP11 |
| GSE156390 |
Role of TFIP11 in U6 snRNA modification and splicing efficiency |
|
| Relations |
| BioSample |
SAMN15846101 |
| SRA |
SRX8960115 |
