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| Status |
Public on Apr 26, 2018 |
| Title |
SeV_8hr3 |
| Sample type |
SRA |
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| Source name |
R. aegyptiacus derived fibroblasts (RoNi7.1), Sendai Cantell virus
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| Organism |
Rousettus aegyptiacus |
| Characteristics |
cell type: RoNi7.1 (fibroblast like kidney derived)
agent: Sendai Cantell
passage: 4 to 6
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| Treatment protocol |
MOI 1.0 of Sendai (Cantell, Charles River) or mock (DMEM media alone), media changed afer 1 hour of absorption and cells incubated at 5% CO2 and 37C
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| Growth protocol |
10% FBS DMEM, 5% CO2 and 37C
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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)
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| Submission date |
Jan 09, 2018 |
| Last update date |
Jul 19, 2018 |
| Contact name |
Catherine E Arnold |
| E-mail(s) |
catherine.e.arnold13.civ@mail.mil
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| Organization name |
US Army Medical Research Institute of Infectious Diseases
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| Department |
Diagnostic Systems Division
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| Street address |
1425 Porter St
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| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
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| Platform ID |
GPL24487 |
| Series (1) |
| GSE108941 |
Infection of RoNi cells with Sendai Cantell virus at MOI of 1.0 |
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| Relations |
| BioSample |
SAMN08331120 |
| SRA |
SRX3542856 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2916293_SeV8hr3.h5 |
24.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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