|
| Status |
Public on Jan 31, 2024 |
| Title |
MCP-evoAPOBEC1_Replicate-2 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
treatment: doxycycline-induced expression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Ilumina TruSeq Stranded mRNA Library Prep (Cat # 20020594)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
remove adapter with Cutadapt
align to human genome using STAR 2.7.6a
align unmapped reads from above to 12X MS2 stem-loop reporter mRNA using STAR 2.7.6a
SAILOR analysis of data for C-to-U edits
SAILOR analysis of data for A-to-I edits
Assembly: GRCh38
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: The processed data files are in .bed format. They contain SAILOR-identified C-to-U or A-to-I edit information for endogenous transcripts (*non.construct.bed) and the 12X stem-loop-bearing-bearing reporter mRNA (*reporter.construct.bed).
|
| |
|
| Submission date |
May 15, 2023 |
| Last update date |
Jan 31, 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 |
GPL24676 |
| Series (2) |
| GSE232514 |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2) |
| GSE232520 |
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies |
|
| Relations |
| BioSample |
SAMN35084978 |
| SRA |
SRX20341389 |
