|
| Status |
Public on Aug 29, 2024 |
| Title |
AC1.112, 0hr, 3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293F
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293F
genotype: WT, clonal
treatment: pre-transfection
|
| Treatment protocol |
HEK293 cells were resuspended in fresh Expi293™ expression medium at a density of 2.5M/ml and triple-transfected with TransIT-VirusGEN and a pHelper plasmid, a RepCap9 plasmid and an ITR containing reporter plasmid.
|
| Growth protocol |
HEK293 cells were maintained in suspension in Expi293™ expression medium on an orbital shaker (125 rpm,19 mm orbital throw) in a 37°C, 5% CO2 incubator.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cell pellets before and during AAV production. RNA was extracted using Direct-zol-96 RNA Kit.
mRNA libraries were constructed by SeqMatic using the Illumina Stranded mRNA prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
Reads were aligned to the human genome via Hisat2 with default parameters.
Genomic features were counted using Subread featurecounts with default parameters.
Assembly: Homo sapiens GRCh38.84
Supplementary files format and content: Individual CSV file for each sample contains raw counts.
|
| |
|
| Submission date |
Jun 10, 2024 |
| Last update date |
Aug 29, 2024 |
| Contact name |
Joshua Tworig |
| Organization name |
Ascend Advanced Therapies
|
| Street address |
1010 Atlantic Ave., Suite 102
|
| City |
Alameda |
| State/province |
CA |
| ZIP/Postal code |
94501 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE269485 |
Transcriptomics-informed pharmacology identifies epigenetic and cell cycle regulators as enhancers of AAV production |
|
| Relations |
| BioSample |
SAMN41775398 |
| SRA |
SRX24858194 |
