 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 27, 2023 |
| Title |
OVKATE, PromethION |
| Sample type |
SRA |
| |
|
| Source name |
OVKATE
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OVKATE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using Qiagen’s RNeasy Plus Mini kit (Cat. #74134) according to manufacturer’s instructions.
Library preparation for nanopore sequencing was performed according to the LSK-110 kit protocol with the exception of the end-repair step time which was increased to 30 min.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Nanopore reads were aligned to the reference genome using minimap2 (v2.24-r1122)
Transcript expression quantification was performed using Isosceles (v0.0.3), using the Ensembl 90 annotations
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file containing the mapping between Isosceles transcript IDs and Ensembl gene and transcript IDs
Supplementary files format and content: comma-delimited text files containing Isosceles transcript read count and TPM quantifications for each sample
|
| |
|
| Submission date |
Nov 17, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Tim Sterne-Weiler |
| Organization name |
Genentech
|
| Department |
Oncology Bioinformatics
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE248114 |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [RNA-seq] |
| GSE248118 |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles |
|
| Relations |
| BioSample |
SAMN38301749 |
| SRA |
SRX22560436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7906067_LIB5432310_SAM24385453.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
