|
| Status |
Public on Oct 20, 2020 |
| Title |
p20040_s004_7162_d4 |
| Sample type |
SRA |
| |
|
| Source name |
Group I_d4_PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
animalid: 7162
timepoint: d4
group: Gr_I
tissue: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from PAXgene RNA Blood Tubes using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit (ThermoFisher). RNA was extracted from BAL fluid stored in PAXgene RNA Blood Tubes using the PAXgene Blood RNA Kit IVD (Qiagen).
Globin transcripts in the blood RNA were blocked prior to library prep using the FastSelect Globin Reagent (Qiagen). Libraries were prepared using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) in combination with 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 25 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
p20040_s004_7162_d4_S70
processed data file:
p20040_MacaM_RawCount.txt
p20040_MacaM_DESeq2_NormCount.txt
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Composite reference was generated by concatenating sequence (.fa) and annotation (.gtf) files for host and viral genome references
Reads were mapped to the Composite (MacaM MN985325.1) genomic reference with STAR (v2.7.3a) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized abundace was caluclated with DESeq2 R Package (version 1.26.0)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) (https://www.unmc.edu/rhesusgenechip/index.htm).
Genome_build: MN985325.1, SARS-CoV2 (strain MN985325.1) was downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/MN985325)
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 |
Aug 23, 2020 |
| Last update date |
Oct 20, 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 (1) |
| GSE156701 |
Vascular Disease and Thrombosis in SARS-CoV-2 Infected Humans and Rhesus Macaques |
|
| Relations |
| BioSample |
SAMN15889088 |
| SRA |
SRX8994547 |
