|
| Status |
Public on Aug 01, 2023 |
| Title |
WTRep1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
ls2 mutant: Wildtype
cell type: S2 cells
|
| Treatment protocol |
Cells were treated with 500 micromolar copper sulfate for 53 hours to induce LS2 expression.
|
| Growth protocol |
Copper-inducible genes encoding LS2 mutants were integrated into S2 cells, and integrated were selected using a hygromycin gene on the LS2-containing plasmid.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using a Qiagen Rneasy Mini kit
polyA RNA was selected using OligodT, and standard Illumina sequencing libraries were constructed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the dm6 transcriptome using STAR (BDGP6, Ensembl 88)
Alternative splicing was analyzed using rMATS
Genome_build: dm6, DBGP6, Ensembl 88
Supplementary_files_format_and_content: Tab separated plain text, kallisto transcript quantification measurements
|
| |
|
| Submission date |
Aug 13, 2020 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Matthew Taliaferro |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Biology
|
| Street address |
12801 E 17th Ave, RC1 South Room 10403D
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE156213 |
Structural evolution of the tissue-specific U2AF paralog and alternative splicing factor LS2 |
|
| Relations |
| BioSample |
SAMN15814089 |
| SRA |
SRX8944668 |
