 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 01, 2021 |
| Title |
VI2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung Cells
|
| Organism |
Mesocricetus auratus |
| Characteristics |
sarscov2_infection: TRUE
vaccination_status: Vaccinated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cranial left lung sections taken at the time of necropsy at 4 dpi from the 5 µg prime-boost group (VI, n=5), mock vaccinated group (MI, n=5) and a naïve group (N, n=4) of hamsters that were mock infected via the IN route with 100 µL of media inoculum. Lung samples were enzymatically digested and homogenized using the Lung Dissociation kit, mouse (Miltenyi Biotec Cat No. 130-095-927) and GentleMACS Dissociator (Miltenyi Biotec) according to the manufacturers protocol. After 30 min of digestion, the samples were filtered through a 70 µM filter, and RBC lysis was performed (ThermoFisher, MA, Cat #00-4333-57). After two washes in PBS containing 0.05 mM EDTA, the cell pellet was re-suspended in 1ml of buffer and filtered through a 40 µM Flowmi Cell strainer (Bel-Art # H13680-0040). The cell viability and concentration were determined on a TC20 cell counter (Bio-Rad, CA). Dead cell removal was performed if the viability was lower than 80% using Dead Cell Removal Kit (Miltenyi Biotec, CA, Cat#130-090-101) as per manufacturers recommendations.
Seven thousand cells were targeted for generation of barcoded gel bead emulsions using the Chromium Single Cell 3’ version 3.0 chemistry (10x Genomics, CA, Cat# 1000077). After reverse transcription, the cDNA was amplified and purified using SPRISelect magnetic beads (Beckman Coulter, CA, Cat#B23317). The purified cDNA was precipitated in 80% ethanol, removed from BSL-4 containment, tested for quality on Bioanalyzer, and 3’ gene expression libraries were prepared as per manufacturer’s instructions. Libraries were quantified, and pooled libraries were submitted for sequencing (~140,000 reads per sample) on Novaseq S1 Flow cell (New York Genome Center).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Genomic and Viral RNA
|
| Data processing |
Cell Ranger 3.1.0 used for data demultiplexing and alignment to the Mesocricetus auratus and SARS-CoV-2 genomes.
STAR 2.7.0 in STARsolo mode used for alignment to the SARS-CoV-2 genome with the addition of 3' and 5' ends of the genome as genes.
Genome_build: MesAur1.0+ASM985889v3
Supplementary_files_format_and_content: h5 matrices (hamster reads) and 10X output sparse matrices in folder format (viral reads)
|
| |
|
| Submission date |
Dec 24, 2020 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Aliza Rubenstein |
| E-mail(s) |
aliza.rubenstein@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1 Gustave L. Levy Pl
|
| City |
Manhattan |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL28997 |
| Series (1) |
| GSE163838 |
mRNA vaccine efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after the challenge |
|
| Relations |
| BioSample |
SAMN17152538 |
| SRA |
SRX9731794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4988086_2_filtered_feature_bc_matrix.h5 |
4.5 Mb |
(ftp)(http) |
H5 |
| GSM4988086_2_viral_reads.tar.gz |
35.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
