|
| Status |
Public on Jun 22, 2023 |
| Title |
K562_total_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab/nano-COP)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_splicing_status_per_read.txt: text files containing the overall splicing status of each read
|
| |
|
| Submission date |
Jul 14, 2022 |
| Last update date |
Jun 22, 2023 |
| Contact name |
Karine Choquet |
| E-mail(s) |
karine.choquet@usherbrooke.ca
|
| Organization name |
Université de Sherbrooke
|
| Department |
Biochemistry and Functional Genomics
|
| Street address |
3201 rue Jean-Mignault
|
| City |
Sherbrooke |
| State/province |
Québec |
| ZIP/Postal code |
J1E 4K8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE208225 |
Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the transcript life cycle |
|
| Relations |
| BioSample |
SAMN29755138 |
| SRA |
SRX16240939 |
