|
| Status |
Public on Feb 26, 2024 |
| Title |
HeLa cells, siSRSF1 -1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: epithelial cells
genotype: SRSF1 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using strand-speecific Illumina-compatible cDNA libraries (dUTP protocol)
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_A5
si_CTRL-siSRSF1.gene_exp.diff
si_CTRL-siSRSF1.isoform_exp.diff
|
| Data processing |
Sequence reads were trimmed for adaptors with Cutadapt
Trimmed sequence reads were mapped to hg38 using STAR aligner
Aligned bam files were used to determine alternative splicing using
Cuffdiff was used to generate differential expression files (gene and isoform ending in _exp.diff files) using default parameters for Cuffdiff version 2.2.0
rMATS was used to generate differential expression files (rMATS.tar.gz files) using default parameters of rMATS version 4.0.2
Assembly: hg38
Supplementary files format and content: Cuffdiff and rMATS files
|
| |
|
| Submission date |
Aug 31, 2022 |
| Last update date |
Feb 26, 2024 |
| Contact name |
MANOJ PILLAI |
| E-mail(s) |
MANOJ.PILLAI@YALE.EDU
|
| Organization name |
YALE UNIVERSITY
|
| Lab |
PILLAI LAB
|
| Street address |
300 GEORGE STREET #786
|
| City |
NEW HAVEN |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE212471 |
Effect of SRSF1 depletion on FANCD2 mRNA and isoform expression and effect of FANCD2 depletion or expression of SRSF1 mutants on splicing |
|
| Relations |
| BioSample |
SAMN30619341 |
| SRA |
SRX17386623 |
