|
Status |
Public on Aug 24, 2023 |
Title |
rABE, 1000 ng/ml dox, rep1 |
Sample type |
SRA |
|
|
Source name |
kidney
|
Organism |
Homo sapiens |
Characteristics |
tissue: kidney cell line: HEK293T cell type: Human embryonic kidney genotype: 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 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 |
SAMN37131198 |
SRA |
SRX21475007 |