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| Status |
Public on Aug 20, 2021 |
| Title |
patient 1 lung rep 1 |
| Sample type |
SRA |
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| Source name |
lung autopsy tissue
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| Organism |
Homo sapiens |
| Characteristics |
replicate type: technical replicate 1
viral rna detected?: yes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the autopsy tissues by first flash freezing each tissue in liquid nitrogen and then using the CryoPREP Tissue Disruption System (Covaris) to pulverize the tissue into a fine powder. The powder was then immediately resuspended in cell lysis buffer and RNA was extracted using the ReliaPrep RNA Tissue Miniprep System (Promega, #Z6112) by following the manufacturer’s instructions. A DNase digestion was also performed during the RNA extraction workflow to remove any potential contamination from carryover genomic DNA (reagents included in the kit). The extracted RNA was then purified using 1.8X RNAClean XP beads (Beckman Coulter) to remove any molecular impurities.
Stranded total RNA libraries were generated according to the manufacturer's instructions, using the TruSeq Stranded Total RNA Gold kit for Illumina sequencing
RNAseq, 2x100 PE reads, Illumina NovaSeq 6000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
s9-lung-rep1
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| Data processing |
The raw RNAseq data was aligned to the hg38 genome using the STAR(v2.7.3a) mapper.
Aligned data were annotated using GENCODE v35 gene annotations and counted using featureCounts(v1.6.3).
Genes with fewer than 50 counts across all samples were excluded from the analysis, and the counts were subsequently log2-transformed for differential gene expression analysis using DESeq2. A pairwise comparison between infected tissues (lung, nasopharynx) and uninfected tissues (olfactory bulb, prefrontal cortex, oropharynx, salivary gland, tongue, heart, liver, kidney) with an adjusted p-value < 0.05 for differentially expressed (DE) genes.
Gene Set Enrichment Analysis (clusterProfiler) was performed to probe for Gene Ontology (GO) categories that were significantly overrepresented and statistically different in infected versus non-infected tissues.
Genome_build: hg38
Supplementary_files_format_and_content: featureCount tsv file summarizes raw counts from featureCounts for each sample.
Supplementary_files_format_and_content: DESeq csv file contains DE genes found by DESeq2.
Supplementary_files_format_and_content: GSEA csv file contains GESA results for GO categories.
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| Submission date |
Aug 17, 2021 |
| Last update date |
Aug 20, 2021 |
| Contact name |
Robert Sebra |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Genetics and Genomic Sciences
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| Street address |
One Gustave L. Levy Place
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE182297 |
Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms [RNA-Seq] |
| GSE182299 |
Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms |
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| Relations |
| BioSample |
SAMN20839521 |
| SRA |
SRX11802673 |
| 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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