|
| Status |
Public on Jun 20, 2024 |
| Title |
COV24H_1 |
| Sample type |
SRA |
| |
|
| Source name |
ex vivo human precision-cut lung slices
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ex vivo human precision-cut lung slices
treatment: SARS-CoV-2
time point: 24h post infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, 3 to 6 slices of the hPCLS were pooled and treated with 1 ml of TRIzol reagent (Invitrogen) at room temperature for 30 min. Total RNAs were then isolated according to the manufacturer’s instruction.
The RNA samples were checked for quality using Bioanalyzer (Agilent 2100) and were sent to Novogene for library construction per company's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The samples were sequenced and analyzed by Novogene. The reads were mapped using STAR (v2.5) to the reference genome and HTSeq (v0.6.1) as used to count the reads mapped to each gene. FPKM of each gene was calculated and differential expression analysis performed using DESeq2 (v2_1.6.3). The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted p-value < 0.05 were considered differentially expressed.
Assembly: GRCh38
Supplementary files format and content: excel file including fpkm of genes.
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Stephanie D Byrum |
| Organization name |
University of Arkansas for Medical Sciences
|
| Street address |
501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor
|
| City |
Little Rock |
| State/province |
Arkansas |
| ZIP/Postal code |
72205 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE226702 |
An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy |
|
| Relations |
| BioSample |
SAMN33600759 |
| SRA |
SRX19568710 |
