|
Status |
Public on Jun 22, 2023 |
Title |
K562_total_rep1 |
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 |
SAMN29755137 |
SRA |
SRX16240938 |