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Sample GSM3842220 Query DataSets for GSM3842220
Status Public on Aug 15, 2019
Title KD08: siRoq#1, 72h, Rep#1
Sample type SRA
 
Source name Fibroblast, infected
Organism Homo sapiens
Characteristics primary cell: Human foreskin fibroblast
virus strain: HCMV Toledo strain
Growth protocol Human foreskin fibroblasts (HFFs) (ATCC, passages 10–15) were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin, and 50 µg/mL streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNAs from HFFs were isolated using the Trizol reagent. For CLIP-seq samples, Roquin-RNA complexes were isolated using antibodies.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdapt version 1.10, in-house python program, and FASTX-Toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2 version 2.2.7 (-t -k 2 --very-sensitive)
Tophat version 2.1.1 [command-line parameters: with–no-coverage-search–b2-very-sensitive (−b2- score-min L, −0.6, −0.9 only for CLIP-seq due to the high error rate)] was used to align the reads against human and viral genome.
RSEM version 1.2.30 was used to estimate transcript abundance. Differentially expressed genes were assessed using the limma package in R, and voom transformation was applied.
We applied Fisher’s exact test to detect significant peaks (CLIP-seq enriched regions over reference seq) and p-values were calculated for every genomic position in the whole genome background, then adjusted using qvalue package in R.
Genome_build: human (GRCh37.p13), HCMV Toledo (GU937742.2)
Supplementary_files_format_and_content: Files starting with "KD_": tab-delimited text files include genes, transcripts, fold change values and differential expression probabilities, which were made using RSEM.
Supplementary_files_format_and_content: Files starting with "514A_", "515A_", or "Overlap_": CLIP peaks identified using Roquin antibodies. tab-delimited text files include genomic loci of peaks and adjusted p-values. "Overlap" peaks were built by overlapping (by one nucleotide) the libraries derived from the two different antibodies.
 
Submission date Jun 03, 2019
Last update date Aug 15, 2019
Contact name Jaewon Song
E-mail(s) jwsong421@snu.ac.kr
Organization name Seoul National University
Street address 504-407, School of Biological Sciences, College of Natural Sciences, 1 Gwanak-ro, Gwanak-gu
City Seoul
State/province Seoul
ZIP/Postal code 08826
Country South Korea
 
Platform ID GPL16791
Series (1)
GSE132081 Analysis of Roquin targetome during HCMV infection
Relations
BioSample SAMN11936505
SRA SRX5952918

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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