|
| Status |
Public on Nov 16, 2022 |
| Title |
RMj8-KV31, Day 4, BAL, Hashtag antibody library |
| Sample type |
SRA |
| |
|
| Source name |
Bronchoalveolar lavage (BAL)
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Bronchoalveolar lavage (BAL)
timepoint: Day 4 post-infection
infection status: SARS-CoV-2-infected
treatment: IFNant (RMj8), IFNant (KV31)
library type: HTO
antibodies/tags: Anti CD298+/B2M: RMj8 - TotalSeq-C0253; KV31 - TotalSeq-C0254
|
| Treatment protocol |
One group of RMs received a four-day course of IFNmod (1mg/day, intramuscularly) beginning 1 day prior to infection (day-1) and ending on day 2 post infection while the control group of animals remained untreated
|
| Extracted molecule |
protein |
| Extraction protocol |
Brochoalveolar lavage (BAL) fluid was collected at baseline (BL) before initiation of treatment or infection of animals, then collected at 2 days post infection (dpi), and, depending on necropsy date, at 4dpi and 7dpi. Lung samples were collected upon necropsy.
Library was prepared using Chromium Single Cell 5สน protocol (10x Genomics). Cellular mRNA and hashtag-antibody oligos were reverse-transcribed to generate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). These cDNAs were then each prepared for sequencing according to manufacturer instructions. Sequencing was performed on the Illumina NovaSeq 6000 targeting 50k reads/cell for the gene expression libraries and 5k reads/cell for the hashtag-antibody libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s007_RMj8-KV31_D4_S7.filtered_feature_bc_matrix.h5
|
| Data processing |
Sequence reads for each sample were demultiplexed and converted to a count matrix using Cellranger v3.1
Downstream analysis was carried out on Seurat v4.1
Assembly: mmul10
Supplementary files format and content: 10x genomics output of gene expression and HTO barcode counts in sparse matrix ".h5" format
|
| |
|
| Submission date |
Sep 27, 2022 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL27943 |
| Series (1) |
| GSE205429 |
Modulation of type-I interferon responses reduces SARS-CoV-2 replication and inflammation in rhesus macaques |
|
| Relations |
| BioSample |
SAMN31038589 |
| SRA |
SRX17723889 |
