|
Status |
Public on Nov 11, 2020 |
Title |
MesAur_Lung_day8_CoV2_100pfu_2 |
Sample type |
SRA |
|
|
Source name |
whole lung
|
Organism |
Mesocricetus auratus |
Characteristics |
age: 3-5 weks old Sex: male tissue: lung virus: SARS-CoV-2, USA-WA1/2020 strain dosage: 100 pfu time point: 8 days
|
Treatment protocol |
Syrian golden hamsters were infected with SARS-CoV-2 or IAV intranasally with 100µl of inoculum (virus in PBS) under anaesthesia with ketamine/xylazine at doses indicated and organs were collected at the times indicated. All hamsters were perfused before the collection of organs.
|
Growth protocol |
N/A
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Tissues were homogenized in 1ml TRIzol reagent (invitrogen) and RNA total RNA was extracted my phenol/chloroform extraction following manufacturer's protocol. All libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Starting material: 1µg total RNA
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
HAG_lung_count_matrix.csv HAG14_day8low_lung_D03
|
Data processing |
automated base-calling performed with bcl2fastq (Illumina) fastq files were aligned using RNA-Seq Alignment application (Basespace, Illumina). total counts were extracted and comiled in .csv files for each tissue Genome_build: Ensembl MesAur1.0 Supplementary_files_format_and_content: All processed data files are .csv files containining total counts of each gene after alignment. Each file contains counts from one tissue.
|
|
|
Submission date |
Nov 10, 2020 |
Last update date |
Nov 11, 2020 |
Contact name |
Rasmus Moeller |
E-mail(s) |
rasmus.moeller@icahn.mssm.edu
|
Phone |
9293751400
|
Organization name |
Icahn School of Medicine at Mount Sinai
|
Department |
Microbiology
|
Lab |
tenOever lab
|
Street address |
1 Gustave L. Levy Place
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
|
|
Platform ID |
GPL24490 |
Series (1) |
GSE161200 |
Temporal and dosage-dependent transcriptional response to SARS-CoV-2 in lung, trachea, brain, olfactory bulb and small intestine of Syrian golden hamsters |
|
Relations |
BioSample |
SAMN16727615 |
SRA |
SRX9470356 |