|
| Status |
Public on Apr 27, 2020 |
| Title |
293T138_8hpi_PAR-CLIP |
| Sample type |
SRA |
| |
|
| Source name |
293Tcontrol cells derived from 293Tcontrol cells infected
|
| Organisms |
Homo sapiens; Human alphaherpesvirus 1 |
| Characteristics |
tissue: Kidney
cell line: 293T
genotype: control
infection status: infected with HSV-1 for 8 hours
|
| Treatment protocol |
For infection, cells were infected with wild-type HSV-1 (strain KOS) for 4 and 8 hpi (MOI = 1) before PAR-CLIP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA crosslinked and immunoprecipitate with Agonaute was extracted according to standard PAR-CLIP protocol (Danan, C., Manickavel, S., and Hafner, M. (2016). PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. Methods in molecular biology 1358, 153-173.)
RNA libraries were prepared for sequencing using TruSeq Small RNA Library Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
small RNA
Control cells, Infected with HSV-1 for 8 hours
|
| Data processing |
Reads were trimmed to discard adapters and low-quality reads and reads less than 21 base long using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/).
Using the “grep” command to retain only reads that contain this sequence CACCAGC (binding site of the miR-138 seed region). These reads were aligned with the mouse (mm10 version) genome using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml)
Counts of reads aligned to 5’ UTR, CDS and 3’ UTR of each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral or mouse/human gene
|
| |
|
| Submission date |
Feb 28, 2019 |
| Last update date |
Apr 28, 2020 |
| Contact name |
Dongli Pan |
| E-mail(s) |
pandongli@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
110058 |
| Country |
China |
| |
|
| Platform ID |
GPL26236 |
| Series (2) |
| GSE127503 |
Identification of herpes simplex virus 1 and host targets of miR-138 by comparative PAR-CLIP in Neuro-2a and 293T cells |
| GSE127504 |
Identification of herpes simplex virus 1 and host targets of miR-138 by combined RNAseq/PARCLIP |
|
| Relations |
| BioSample |
SAMN11037835 |
| SRA |
SRX5444369 |
