|
| Status |
Public on Jan 14, 2021 |
| Title |
AGM6_Medialstinal Lymph Node |
| Sample type |
SRA |
| |
|
| Source name |
Medialstinal Lymph Node
|
| Organism |
Chlorocebus aethiops |
| Characteristics |
virus: SARS-CoV-2
virus subtype: Active
tissue: Medialstinal Lymph Node
|
| Treatment protocol |
8 animals received active SARS-CoV-2 and 2 received irradiated SARS-CoV-2
|
| Growth protocol |
Samples were extracted and process directly from African Green Monkeys during necropsy
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues were manually disaccociated, digested with liberase, filtered, and treated with ACK lysis before being processed on the 10X genomics NextGEM instrument
Libraries were prepped according to the 10X genomics V3.0 library prep kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
10X Genomics single-cell RNA Sequencing
|
| Data processing |
reads demultiplexed and bcl to fastq conversion using cellranger mkfastq v3.0.2
reads aligned and counted using cellranger count v3.0.2
Genome_build: GCF_000409795.2 & NC_045512.2
Supplementary_files_format_and_content: features.tsv, barcodes.tsv, and matrix.mtx (set of 3 files)
|
| |
|
| Submission date |
Aug 24, 2020 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Craig Martens |
| E-mail(s) |
[email protected]
|
| Phone |
406-363-9415
|
| Organization name |
NIAID
|
| Department |
DIR
|
| Lab |
RTB
|
| Street address |
903 S. 4th St
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL29061 |
| Series (1) |
| GSE156755 |
SARS-CoV-2 infection dynamics in lungs of African green monkeys |
|
| Relations |
| BioSample |
SAMN15893759 |
| SRA |
SRX8998646 |
