|
| Status |
Public on Aug 26, 2022 |
| Title |
Nanopore_sequencing_TEX_2 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: U2OS
treatment: treatment: Nanopore sequencing + TEX
|
| Treatment protocol |
Terminator phosphate-dependent TEX treatment:
For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.
|
| Growth protocol |
HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Nanopore samples, poly(A) selected RNA (500 ng) of control or TEX treated samples were prepared for nanopore direct RNA sequencing generally following the ONT SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. RNA sequencing on the MinION was performed using ONT R9 Flow Cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Nanopore: FASTQ files were aligned to the genome GRCh37.p13.genome using minimap2 (2.17-r941). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Nanopore_Readcounts.txt is tab delimited txt file containing raw read counts obtaned with htseq over exons of protein coding genes. also included is Nanopore_sequencing_TEX_2.psl as psl file
|
| |
|
| Submission date |
Mar 29, 2022 |
| Last update date |
Aug 26, 2022 |
| Contact name |
Pierre-Rene Körner |
| Organization name |
Netherlands Cancer Institute (NKI)
|
| Department |
Oncogenomics
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE149204 |
Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential |
|
| Relations |
| BioSample |
SAMN27063553 |
| SRA |
SRX14659823 |
