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Sample GSM2927823 Query DataSets for GSM2927823
Status Public on Sep 10, 2018
Title IAV-5T in MDCK replicate 1
Sample type SRA
Source name MDCK
Organism Canis lupus familiaris
Characteristics infection: Influenza A 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 IAV_alignments.xlsx
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
Organization name Ichan School of Medicine at Mount Sinai
Department Microbiology
Street address 1468 Madison Avenue
City New York
State/province NY
ZIP/Postal code 10128
Country USA
Platform ID GPL21400
Series (1)
GSE108995 Profiling of escape kinetics of viruses subjected to RNAi
BioSample SAMN08337134
SRA SRX3547172

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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