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Sample GSM2927804

Query DataSets for GSM2927804

Status

Public on Sep 10, 2018

Title

SFVGsplit-5T passage 0 replicate 2

Sample type

SRA

Source name

BHK-21

Organism

Mesocricetus auratus

Characteristics

infection: Semliki Forest virus, targeted

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

SFVG_alignments.xlsx
VV3-SFVG5T-BHK-pass0-Rep2_S13

Data processing

Libraries were run on an Illumina NextSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Raw sequencing reads were aligned to the corresponding reference viral genome using Bowtie2 with default paramaters
BAM files from each lane were consolidated into a single file
The resulting aligned reads were visualized, and the read counts for each residue per site obtained, using the Integrative Genomics Viewer (IGV)
Relative read counts and variation analyses were performed using in-house Perl scripts. Major variant for each site was defined as the residue (nucleotide) with higher read counts compared to all other possible residues for the same site.
For the analysis of junction sites, raw sequencing reads were aligned to the corresponding reference viral genome using HISAT2
Resulting alignments were filtered for low mapping quality reads using samtools(-q 10), and junction counts were obtained using regtools
Further consolidation of junction sites and their corresponding counts was performed using in-house Perl scripts.
Genome_build: As these are recombinant viruses, they do not have references on UCSC or NCBI that are perfect matches. See viral_genome sequences linked to the Series record.
Supplementary_files_format_and_content: Processed excel spread sheets contain, for each sample, Variability Ratio, Total Read Number, Number of Minor Variable reads, Number of mapped reads, Percentage, Coverage, and Minor Variable Reads for each position in the indicated viral genome

Submission date

Jan 10, 2018

Last update date

Sep 10, 2018

Contact name

Benjamin tenOever

E-mail(s)

benjamin.tenoever@mssm.edu

Organization name

Ichan School of Medicine at Mount Sinai

Department

Microbiology