|
| Status |
Public on Jul 14, 2023 |
| Title |
3-Uninfected Sheared |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived alveolar organoids
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Uninfected
tissue: iPSC-derived alveolar organoids
tissue type: Sheared
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from iPSC-derived alveolar organoids by using Tri reagent
The Illumina Stranded mRNA Prep kit was employed for library preparation, following the manufacturer's reference guide and checklist (Document # 1000000124518 v02). In Summary, 100 ng of total RNA input is used for each library prep. First step, the Oligo(dT) magnetic beads purify and capture the mRNA molecules containing polyA tails. The purified mRNA is fragmented and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. In a second strand cDNA synthesis step, dUTP replaces dTTP to achieve strand specificity. Then, add adenine (A) and thymine (T) bases to fragment ends and ligate adapters. The resulting products are purified with magnetic beads. Then, add indexes to the anchor-ligated DNA fragments with PCR. The resulting products are purified and selectively amplified for sequencing on an Illumina system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of the human genome (GRCh38/hg38) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Assembly: GRCh38/hg38
Supplementary files format and content:
Gene expression file generated by cuffdiff analysis
differential gene expression between infected and uninfected samples; gene count and fpkm
*_count: the estimated count of fragments or reads mapped to a particular feature (e.g., gene, transcript) in a given sample; an estimate of the expression level of that feature.
*_count_variance: the estimated variance of the count for a particular feature in a sample; the variability or dispersion in the count measurement for that feature.
*_count_uncertainty_var: the uncertainty variance associated with the count estimate for a specific feature in a sample; the level of uncertainty in the count measurement, taking into account various sources of variability.
*_count_dispersion_var: the dispersion variance associated with the count estimate for a particular feature in a sample. Dispersion refers to the degree of heterogeneity or variability in the expression levels across samples. The dispersion variance reflects the amount of dispersion associated with the count measurement for that feature.
|
| |
|
| Submission date |
Jul 11, 2023 |
| Last update date |
Jul 14, 2023 |
| Contact name |
CHAOQUN HUANG |
| E-mail(s) |
chaoqh@okstate.edu
|
| Phone |
405-744-3410
|
| Organization name |
Oklahoma State University
|
| Department |
Physiological Sciences
|
| Lab |
Lundberg-Kienlen Lung Biology and Toxicology Laboratory
|
| Street address |
264 McElroy Hall
|
| City |
Stillwater |
| State/province |
OK |
| ZIP/Postal code |
74078 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE237059 |
The use of human iPSC-derived alveolar organoids to explore SARS-CoV-2 variant infections and host responses |
|
| Relations |
| BioSample |
SAMN36406138 |
| SRA |
SRX20981997 |
