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Sample GSM3635629 Query DataSets for GSM3635629
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 (
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 (
Counts of reads aligned to 5’ UTR, CDS and 3’ UTR of each transcript were determined by Htseq-count (
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
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
BioSample SAMN11037835
SRA SRX5444369

Supplementary file Size Download File type/resource
GSM3635629_293T138_8hpi_viralcounts.txt.gz 328 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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