|
| Status |
Public on Nov 27, 2023 |
| Title |
Cell line mix, PromethION |
| Sample type |
SRA |
| |
|
| Source name |
Mix (IGROV1, SK-OV-3, COV504)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Mix (IGROV1, SK-OV-3, COV504)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
IGROV1, SK-OV-3 and COV504 cells were trypsinized and pooled together at a 1:1:1 ratio at a concentration of 1000 cells / μl and submitted for single cell long read sequencing.
Illumina whole transcriptome dual-indexed library was prepared using the standard 10x Genomics protocol. 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 single cell |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
The Illumina sequencing data was preprocessed using CellRanger (v6.0.1).
The Nanopore sequencing data was preprocessed using the Sicelore workflow (v2.0)
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: text file containing CellRanger filtered barcodes for Illumina data
Supplementary files format and content: text files and matrix file containing Isosceles transcript read count quantifications for Nanopore data
|
| |
|
| 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) |
| GSE248115 |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [scRNA-seq] |
| GSE248118 |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles |
|
| Relations |
| BioSample |
SAMN38301905 |
| SRA |
SRX22560608 |
