|
| Status |
Public on Jun 13, 2024 |
| Title |
hSAECs, Input, RNA-IP, Rep-2 |
| Sample type |
SRA |
| |
|
| Source name |
hSAECs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hSAECs
cell type: epithelium
treatment: RSV, 1 MOI, 24 hpi
|
| Treatment protocol |
100 mm of hSAECs were infected with RSV at a multiplicity of infection (MOI) of 1. After an hour of adsorption, the unbound virus was removed by PBS, and supplemented by fresh culture medium.
|
| Growth protocol |
Small Airway Epithelial Cell Growth Medium (Ready-to-use) - Includes Basal Medium and SupplementMix (C-21070, PromoCell, Heidelberg, Germany)
|
| Extracted molecule |
other |
| Extraction protocol |
At 24 hpi, cells were fixed with 1% formaldehyde for 10 min at room temperatrue. After quenching and cell lysis by RIPA, lysates were briefly sonicated. During the preparation process, we employed the iron chelator deferoxamine mesylate (252750, Millipore-Sigma) to prevent additional oxidation. The supernatant was treated with RNase A (20 µg/mL) and RNase T1 (5U) at 37°C for 30 min to digest naked viral RNA. We then subjected the supernatant to IP with an anti-OGG1 antibody (PA5-86046, Invitrogen) for 4 hours, using head-over-tail rotation for effective mixing. We incubated the ribonucleoprotein-antibody complexes with magnetic beads for 1 hour at 4°C and subsequently washed them five times with RIPA buffer. After proteinase K digestion and reversing the crosslinks, we extracted the RNA samples using TRIzol. The libraries were processed for Illumina sequencing.
stranded RNA-seq library
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
| |
|
| Description |
OGG1-Ab-vs-Input-cell-hg38-enriched.bedgraph
|
| Data processing |
reads aligned to RSV genome with bowtie2 and aligned to human reference genome using STAR 2.7.11a
Assembly: hg38
Supplementary files format and content: Forward and reverse alignment to RSV in bigwig format
Supplementary files format and content: log ratio of hg38 alignment between IP and input in bedgraph format
|
| |
|
| Submission date |
Jun 13, 2024 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Haiping Hao |
| E-mail(s) |
hahao@UTMB.EDU
|
| Phone |
4097726349
|
| Organization name |
University of Texas Medical Branch
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1005 strand st
|
| City |
Galveston |
| State/province |
Texas |
| ZIP/Postal code |
77555 |
| Country |
USA |
| |
|
| Platform ID |
GPL22790 |
| Series (1) |
| GSE269769 |
8-Oxoguanine DNA glycosylase 1 hijacked by nucleoprotein conceals guanine oxidation in respiratory syncytial virus RNA |
|
| Relations |
| BioSample |
SAMN41817515 |
| SRA |
SRX24911277 |
