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| Status |
Public on Nov 27, 2023 |
| Title |
COV362, PromethION |
| Sample type |
SRA |
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| Source name |
COV362
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| Organism |
Homo sapiens |
| Characteristics |
cell line: COV362
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| 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
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| 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
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN38301746 |
| SRA |
SRX22560439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7906070_LIB5432313_SAM24385456.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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