|
| Status |
Public on Jun 13, 2024 |
| Title |
HEK293T_buffer_only_INSCRIBE_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
replicate: 2
molecule subtype: rRNA depleted RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Kinnex full-length RNA kit (PN 103-072-000)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Revio |
| |
|
| Description |
Long-read HEK293T buffer only INSCRIBE rep2
|
| Data processing |
CCS calling (v8.0.0)
read deconcatenation using skera(1.2.0)
read trimming with lima(v2.9.0)
refine reads with isoseq refine (v4.1.1)
read alignment with pbmm2 (v1.13.0)
QC with NanoPlot (v1.32.1)
filter unmapped reads, supplementary alignment reads, reads aligned to the incorrect strand, and reads having read quality below 20
call edits using custom script
remove SNPs
Assembly: hg38
Supplementary files format and content: isoforms level edit detection (.bed)
|
| |
|
| Submission date |
Apr 12, 2024 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Brian Yee |
| E-mail(s) |
brian.alan.yee@gmail.com
|
| Organization name |
UCSD
|
| Department |
Health
|
| Lab |
Yeo
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL34382 |
| Series (2) |
| GSE240326 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells |
| GSE263870 |
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr] |
|
| Relations |
| BioSample |
SAMN40945782 |
| SRA |
SRX24235953 |
