|
| Status |
Public on Dec 10, 2019 |
| Title |
single-cell RNA-seq dataset: PR8-infected A549 cells at 12hpi |
| Sample type |
SRA |
| |
|
| Source name |
adenocarcinomic human alveolar basal epithelial cells
|
| Organisms |
Homo sapiens; Influenza A virus (A/Puerto Rico/8/1934(H1N1)) |
| Characteristics |
cell types: A549
infection time points: 12 hours post-infection
virus strain: PR8
|
| Treatment protocol |
A549 cells were infected with PR8 virus at a MOI of 5.
|
| Growth protocol |
A549 cells (ATCC) were maintained in Kaighn’s modified Ham’s F-12 medium (F-12K) supplemented with 10% fetal bovine serum (FBS) prior to infection. A549 cells were infected in A549 infection media (F-12K supplemented with 2% bovine serum albumin (BSA) and 1% antibiotic-antimycotic).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were trypisinized, extensively washed, and re-suspended in PBS containing 0.04% BSA.
Cells were subject to 10X Genomics single cell library preparation with Chromium 3’ v2 chemistry following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.
|
| |
|
| Submission date |
Aug 20, 2018 |
| Last update date |
Dec 12, 2019 |
| Contact name |
Chang Wang |
| E-mail(s) |
chang.wang@nyu.edu
|
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Ghedin
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL25466 |
| Series (1) |
| GSE118773 |
Cell-to-cell variation in defective virus expression and effect on host response during influenza virus infection |
|
| Relations |
| BioSample |
SAMN09863816 |
| SRA |
SRX4578902 |
