|
| Status |
Public on Nov 10, 2020 |
| Title |
p20084-s008_RHz12_BAL_Day4_GEX |
| Sample type |
SRA |
| |
|
| Source name |
bronchoalveolar lavages
|
| Organism |
Macaca mulatta |
| Characteristics |
animalid: RHz12
treatment: Untreated
day post infection: 4dpi
|
| Treatment protocol |
RMs were infected with 1.1x106 plaque forming units (PFU) SARS-CoV-2 via both the intranasal (1 mL) and intratracheal (1 mL) routes concurrently. Two RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. Baricitinib was supplied as a powder that was folded into food items (i.e. honey, yogurt, etc.) or distilled water, which was delivered either orally or as a gavage when animals were being anesthetically accessed, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
single-cell suspensions of 100,000 BAL-derived cells, and approximately 30,000 cells were loaded onto 10X Chromium Controller in the BSL3. Single cells were partitioned into droplets (Gel Beads in Emulsion: GEMs) using Chromium NextGEM Single Cell 5’ Library & Gel Bead kits on the 10X Chromium Controller(Zheng et al., 2017).
The resulting cDNA was amplified and libraries were prepared for transcriptomic analysis according to manufacturer instructions. Gene expression libraries were sequenced as paired-end 26x91 reads on an Illumina NovaSeq6000 targeting a depth of 50,000 reads per cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cell Ranger software was used to perform demultiplexing of cellular transcript data
Cell Ranger v3.1 (10X Genomics) was used to perform mapping and annotation of UMIs and abundance estimation of transcripts for downstream data analysis.
Cell Ranger was used to create a single cell reference with the Macaca mulatta (Mmul10 Ensembl release 100)
Genome_build: Macaca mulatta Mmul10 Ensembl release 100
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.1 containing per cell transcript counts.
|
| |
|
| Submission date |
Oct 07, 2020 |
| Last update date |
Nov 10, 2020 |
| 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 (2) |
| GSE159212 |
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques [scRNA-Seq] |
| GSE159214 |
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques |
|
| Relations |
| BioSample |
SAMN16392924 |
| SRA |
SRX9260457 |
