|
| Status |
Public on Mar 31, 2022 |
| Title |
Ctrl-2-poly |
| Sample type |
SRA |
| |
|
| Source name |
BEAS-2B cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEAS-2B
transient expression: Control
|
| Treatment protocol |
BEAS-2B cells were nucleofected with the Lonza T1 kit using pcDNA3.4 plasmids expressing ORF9c-3xFLAG, and the empty pcDNA3.4 vector.
|
| Growth protocol |
Standard cell culture in PneumaCult+supplements media on matrigel coated plates for BEAS-2B cells.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were treated with CHX at 100 µg/ml before fractionation. Total and polysome derived RNA were extracted using Trizol reagent.
Illumina polyA Total RNA kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ribosome profiling
mRNA from polysome fraction from BEAS-2B cells transiently expressing empty vector rep2
|
| Data processing |
Library strategy: Ribo-Seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt (v1.14). Trimmed reads were mapped against RepBase (v18.05) to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner (v2.5.2b). Raw read counts were generated from all mapped reads using featureCounts (v1.5.3) package.
Normalized counts were derived from DESeq output.
Assembly: hg19 (GRCh37)
Supplementary files format and content: counts_for_pub.txt contains featureCounts output in comma-delimited format.
Supplementary files format and content: diffexp.tsv files contain DESeq2 output in tab-separated format.
|
| |
|
| Submission date |
Mar 17, 2022 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE173508 |
Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins |
| GSE198899 |
Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq] |
|
| Relations |
| BioSample |
SAMN26752410 |
| SRA |
SRX14495057 |
