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| Status |
Public on Nov 16, 2022 |
| Title |
p21094-s074_RMs8-BAL-Day2-2021-03-17 |
| Sample type |
SRA |
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| Source name |
BAL
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: BAL
day post infection: Day2
day post treament: NA
infection: Infected
treatment: Control
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| Treatment protocol |
NA
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs: Whole blood was collected from the femoral vein in EDTA tubes. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Ficoll-Paque Premium density gradient and resuspended in R10 media. For bulk RNAseq, 250,000 PBMCs were frozen in 700uL of QIAzol.; BAL: To collect BAL, a fiberoptic bronchoscope was used to administer 0.9% NaCl solution into the bronchus and re-aspirate the BAL fluid. BAL was then filtered through a 70μm cell strainer and centrifuged. Following centrifugation, BAL fluid supernatant was removed and the remaining cell pellet was lysed in ACK lysing buffer and resuspended in R10. For bulk RNAseq, 50,000 BAL cells were frozen in 700uL of QIAzol. For 10X, ~125,000 BAL cells from each animal were incubated with one of five TotalSeq-C anti human Hashtags. Following a 30 minute incubation, cells were washed with PBS, filtered with a 40uM cell filter, and resuspended in R10.
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio). Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RMs8,Infected,Control,Day2
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| Data processing |
Illumina bcl2fastq v2.20.0.422 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: Mmul_10/rheMac10
Supplementary files format and content: csv file with raw read counts per gene for each Sample
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| Submission date |
Jun 03, 2022 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
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| Phone |
404-727-7797
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| Organization name |
Yerkes National Primate Research Center
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| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
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| Street address |
954 Gatewood Dr
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE205429 |
Modulation of type-I interferon responses reduces SARS-CoV-2 replication and inflammation in rhesus macaques |
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| Relations |
| BioSample |
SAMN28859209 |
| SRA |
SRX15589717 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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