|
| Status |
Public on Dec 10, 2019 |
| Title |
Viral genome sequencing dataset: PR8 virus stock |
| Sample type |
SRA |
| |
|
| Source name |
PR8 virus stock
|
| Organism |
Influenza A virus (A/Puerto Rico/8/1934(H1N1)) |
| Characteristics |
virus strain: PR8
|
| Treatment protocol |
NA
|
| Growth protocol |
PR8 virus stock was plaque purified and propagated in MDCK cells.
|
| Extracted molecule |
other |
| Extraction protocol |
Viral genomic RNA (vRNA) of the virus stocks used in the infection assay was extracted using RNeasy Mini Kit (Qiagen).
vRNA was amplified using multi-segment reverse-transcription PCR (M-RT-PCR) and then subject to Illumina library preparation with Nextera DNA library prep kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: amplicon sequencing
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 10, 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 |
GPL25468 |
| Series (1) |
| GSE118773 |
Cell-to-cell variation in defective virus expression and effect on host response during influenza virus infection |
|
| Relations |
| BioSample |
SAMN09863786 |
| SRA |
SRX4578928 |
