|
| Status |
Public on Jan 18, 2024 |
| Title |
KEO.L34.Wi.CMo.48.1 |
| Sample type |
SRA |
| |
|
| Source name |
stem-cell derived otic progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: stem-cell derived otic progenitor cells
cell line: WI
virus: Mock
agent: CMV
heat inactivated_virus: No
hours post_infection: 48
|
| Treatment protocol |
Infections of OPCs were performed at multiplicities of infection calculated using BHK-21 infectious units for ZIKVPR and HFF infectious units for hCMVGFP. Virus was added to cells in minimal volume and incubated with intermittent rocking for 1 hr at 37o C. Inoculum was then removed and replaced with fresh medium.
|
| Growth protocol |
Cells were cultured in DFNB basal medium (DMEM/F12 with 1% N2 and 2% B27, Gibco by Life Technologies), supplemented with difluorobenzeneacetamid (DBZ, Tocris Bioscience) at 5 μM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen Rneasy extraction kit following standard procedures
High-throughput ZAPR
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
d238024
|
| Data processing |
Novaseq S1 using v3 NovaSeq Control Software v1.7.0 and RTA v3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the hg38 human assembly with the Ensembl version 106 annotation using Salmon version 1.6.0. Gene level summaries were prepared using tximport version 1.24.0
Assembly: hg38 with ensembl 106 annotation
Supplementary files format and content: tab delimited text file with ensemble gene IDs and either integer count data for each sample
Supplementary files format and content: tab delimited text files with ensemble gene IDs and log2 TPM (with a +1 offset) for each sample
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
[email protected]
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE234062 |
Human Otic progenitor cell models of congenital hearing loss applied to to Zika virus and cytomegalovirus infections |
|
| Relations |
| BioSample |
SAMN35573611 |
| SRA |
SRX20581161 |
