|
| Status |
Public on Aug 24, 2023 |
| Title |
PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
cell line: HEK293T
cell type: Human embryonic kidney
genotype: PUM1-APOBEC1 PUM2-rABE
treatment: 1000 ng/ml dox
|
| Growth protocol |
HEK 293T cells were cultured in DMEM with 4.5 g / L glucose, L-glutamine & sodium pyruvate (Corning #10-0130CV) and 10% FBS (Avantor #97068-085) at 37 ˚C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular RNA extraction was performed with Direct-zol RNA miniprep Kit (Zymo Research #R2053) following manufacturer’s protocol
We used PacBio Iso-seq Express Template Preparation Kit (PN 101-763-800, v2)
PacBio IsoSeq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Description |
HEK293T cell with dox-inducible expression of PUM1-APOBEC1 and PUM2-rABE, 1000 ng/ul doxcycline, 48h
|
| Data processing |
Sequencing reads were processed with CCS and demultiplexed with lima
Reads were aligned and calibrated with Iso-seq 3 pipeline
Custom script for calling isoform specific PUM1 binding events: github.com/linyz/remora
Assembly: GRCh38
Supplementary files format and content: all_exon_alt_u_v2_all.csv (Isoform specific PUM1 binding events in csv table)
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Aug 24, 2023 |
| Contact name |
Yizhu Lin |
| E-mail(s) |
linyz151@gmail.com
|
| Organization name |
University of California, San Francisco
|
| Department |
Cell and Tissue Biology
|
| Lab |
Stephen Floor
|
| Street address |
513 Parnassus
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL28352 |
| Series (2) |
| GSE241615 |
Directed protein evolution of an RNA editor for single molecule RNA-binding protein co-occupancy (II) |
| GSE241616 |
RNA molecular recording with an engineered RNA deaminase |
|
| Relations |
| BioSample |
SAMN37131179 |
| SRA |
SRX21475026 |
