|
| Status |
Public on Nov 10, 2020 |
| Title |
p20097-s084_RQv9_4dpi |
| Sample type |
SRA |
| |
|
| Source name |
bronchoalveolar lavages
|
| Organism |
Macaca mulatta |
| Characteristics |
animalid: RQv9
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. Four 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 |
50,000 cells were lysed directly into 700 ul of QIAzol reagent. RNA was isolated using RNeasy Mini or Micro kits (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20-25 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3.(Dobin et al.)
The STAR index was built by combining genome sequences for Macaca mulatta (Mmul10 Ensembl release 100), SARS-CoV2 (strain MN985325.1 - NCBI) and ERCC sequences. The gffread utility (https://github.com/gpertea/gffread) was used to convert gff3 file for SARS-CoV2 and the resulting gtf file for SARS-CoV2 was edited to include exon entries which had the same coordinates as CDS to get counts with STAR. The combined genomic and gtf files were used for generating the STAR index.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(Sandler et al., 2014).
DESeq2 was used for normalization(Love et al.), producing a normalized read count table
Genome_build: Macaca mulatta Mmul10 Ensembl release 100
Genome_build: SARS-CoV2 (strain MN985325.1 - NCBI)
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| 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) |
| GSE159213 |
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques [RNA-Seq] |
| GSE159214 |
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques |
|
| Relations |
| BioSample |
SAMN16392936 |
| SRA |
SRX9260472 |
