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| Status |
Public on Oct 13, 2023 |
| Title |
p20185.s120_20.14_15.104_D3 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Blood
cell type: PBMC
time point: D3
vaccine dose: 5x10^10 vp
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| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific).
Ten nanograms of the globin-depleted 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 Nextera XT DNA Library Preparation kit (Illumina).
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with SR100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The quality of the raw reads was assessed using multiQC. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Human-sequenced data were aligned to the Homo Sapiens NCBI reference genome assembly version GRCh38, and the rhesus macaques data were aligned to the Mmul10-100 and the MacaM assemblies and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a, and transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing both a raw and normalized read count table.
Assembly: Mmul_10 (GCA_003339765.3)
Supplementary files format and content: CSV file (read count matrix), 2014.forGeo.csv
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| Submission date |
Dec 11, 2022 |
| Last update date |
Oct 13, 2023 |
| Contact name |
Dan Barouch |
| Organization name |
BIDMC
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| Department |
CVVR
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| Lab |
Barouch Lab
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| Street address |
3 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE220659 |
Activation of Coagulation and Proinflammatory Pathways in Thrombosis with Thrombocytopenia Syndrome and Following COVID-19 Vaccination |
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| Relations |
| BioSample |
SAMN32153339 |
| SRA |
SRX18638651 |
| 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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