|
| Status |
Public on Aug 14, 2023 |
| Title |
SNRNP200 whole cell stress eCLIP rep1 (input) |
| Sample type |
SRA |
| |
|
| Source name |
Human epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human epithelial cell
cell line: HEK293
cell type: Human epithelial kidney
treatment: 500 µM of arsenic
fraction: input
|
| Treatment protocol |
500 µM of arsenic
|
| Growth protocol |
DMEM + glutamine + 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and RBP:RNA complexes were immunoprecipitated with RBP-specific antibody (A301-902A)
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SNRNP200_HEKstress.reproducible_enriched_windows.tsv.gz.bed
|
| Data processing |
Data was processed using the eCLIP pipeline and available at https://github.com/YeoLab/skipper
Unique Molecular Identifiers (UMIs) were extracted using fastp 0.11.5 (https://github.com/OpenGene/fastp)
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples)
Mapping was then performed against the full human genome (hg38) including a database of splice junctions with STAR (v 2.7.6) allowing up to 100 multimapped regions.
Reads were then PCR deduplicated using UMIcollaps (https://github.com/Daniel-Liu-c0deb0t/UMICollapse
Enriched “windows” (IP versus SM-Input) was called on deduplicated reads using a GC-bias aware beta-binomial model. Each window (~100 b.p.) were partitioned from Gencode v38 and associated with a specific type of genomic region (CDS, UTR, proximal introns near splice site… etc). Windows are filtered using FDR < 0.2 and only reproducible windows between two replicates were used.
Data was processed using the eCLIP pipeline and available at https://github.com/YeoLab/skipper
Assembly: hg38
Supplementary files format and content: bed files contain Skipper windows.
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Aug 14, 2023 |
| 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 (1) |
| GSE230717 |
Large-scale map of RNA binding protein interactomes across the mRNA life-cycle |
|
| Relations |
| BioSample |
SAMN34395319 |
| SRA |
SRX20116048 |
