|
| Status |
Public on Nov 11, 2020 |
| Title |
MesAur_Trachea_mock_2 |
| Sample type |
SRA |
| |
|
| Source name |
trachea
|
| Organism |
Mesocricetus auratus |
| Characteristics |
age: 3-5 weks old
Sex: male
tissue: trachea
virus: -
dosage: -
time point: -
|
| 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_trachea_count_matrix.csv
HAB14_day1_PBS_trachea
|
| 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 |
SAMN16727537 |
| SRA |
SRX9470381 |
