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Sample GSM4462403 Query DataSets for GSM4462403
Status Public on Apr 10, 2020
Title Series14_FerretTrachea_SARS-CoV-2_d3_1
Sample type SRA
Source name SARS-CoV-2 infected 4 month old Ferret
Organism Mustela putorius furo
Characteristics tissue/cell type: Trachea
treatment: SARS-CoV-2 infected (5E4 PFU)
strain: USA-WA1/2020
time after treatment: 3 days
Extracted molecule polyA RNA
Extraction protocol TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Mf-Tr-16
processed data file: RawReadCounts_Ferret.tsv
Data processing cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.
Submission date Apr 08, 2020
Last update date Apr 12, 2020
Contact name Daniel Blanco Melo
Organization name Icahn School of Medicine at Mount Sina
Department Microbiology
Lab tenOever Lab
Street address One Gustave L. Levy Place, Box 1124
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platform ID GPL28369
Series (1)
GSE147507 Transcriptional response to SARS-CoV-2 infection
BioSample SAMN14563403
SRA SRX8089331

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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