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Sample GSM3291869 Query DataSets for GSM3291869
Status Public on Nov 01, 2018
Title SeV_24hr_rep1
Sample type SRA
 
Source name SeV_24hr_RoNi7.1
Organism Rousettus aegyptiacus
Characteristics cell type: RoNi7.1 (fibroblast like kidney derived)
infection: Sendai Cantell
time: 24hr
passage: 4 to 6
Treatment protocol MOI 1.0 of Sendai (Cantell, Charles River), MARV371bat, MARV371-R301A, or mock (DMEM media alone), media changed afer 1 hour of absorption and cells incubated at 5% CO2 and 37C
Growth protocol 10% FBS DMEM, 5% CO2 and 37C
Extracted molecule total RNA
Extraction protocol Harvested in 1x RNA Lysis/Binding Solution Concentrate (Thermo Fisher Scientific) at 3hr, 8hr and 24hr post-infection, followed by magnetic bead purification and TURBO DNase treatment using the MagMAX-96 Total RNA Isolation Kit (Ambion) according to manufacturer guidelines. RNA extractions were performed on a MagMAX Express 96 Magnetic Particle Processor (Applied Biosystems)
Libraries were generated on the Sciclone G3 Liquid Handling Robot (PerkinElmer) using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). Library quality was evaluated on the Agilent 2200 TapeStation 2200 and quantified by qPCR using the KAPA Complete (Universal) qPCR kit (Kapa Biosystems) for Illumina libraries. Libraries were diluted to 12 pM and cluster generation was performed on the Illumina cBot. Libraries were sequenced on the Illumina HiSeq 2500 using the paired end 2x125 bp, dual-index format.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description SeV_24hr1
Data processing dual index filter: in house software (raw reads index filtered to Q30 cutoff)
trimming : Trimmomatic-0.33 (leading:3, trailing:3, sliding window:4:15, minlen: 80, Q30 cutoff)
alignment and normalization: kallisto 0.43.0 (bootstraps: 100, default parameters)
Genome_build: Raegyp2.0
Supplementary_files_format_and_content: abundance files: h5 (contains transcript_id, length, eff_length (effective length), est_counts (estimated counts) and tpm (transcripts per million) for each gene in the transcriptome, includes bootstrap values (each h5 contains 100 bootstraps that are used for downstream differential gene expression). length, eff_length, est_counts used to calculate tpm. )
Supplementary_files_format_and_content: annotation: gff (contains gene identifiers used in h5 files, genome coordinates, Ensembl IDs, gene symbols, etc)
 
Submission date Jul 19, 2018
Last update date Nov 01, 2018
Contact name Catherine E Arnold
E-mail(s) catherine.e.arnold13.civ@mail.mil
Organization name US Army Medical Research Institute of Infectious Diseases
Department Diagnostic Systems Division
Street address 1425 Porter St
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL24487
Series (1)
GSE117367 Infection of RoNi cells with Sendai Cantell virus, MARV371bat virus, and VP35 mutant MARV371bat-R301A virus at MOI of 1.0
Relations
BioSample SAMN09692180
SRA SRX4408662

Supplementary file Size Download File type/resource
GSM3291869_SeV24hr1.h5 24.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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