|
| Status |
Public on Jan 31, 2024 |
| Title |
MCP-evoCDA1_Replicate-1 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
rbp-rbe fusion: MCP-evoCDA1
replicate: 1
treatment: doxycycline-induced expression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Nextera XT DNA Library Preparation Kit (Illumina, Cat # FC-131-2002 or Cat # FC-131-1024)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
remove adapter with Cutadapt
align to genome using bowtie2 or bwa-mem
generate count tables along reporter sequence using Pysamstats
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: pysamstats tables that contain the read counts for RNA bases at each position along the reporter mRNA sequence
|
| |
|
| 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 |
GPL15520 |
| Series (2) |
| GSE232513 |
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1) |
| GSE232520 |
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies |
|
| Relations |
| BioSample |
SAMN35084902 |
| SRA |
SRX20341222 |
