|
| Status |
Public on Mar 19, 2019 |
| Title |
Yan2_S2 |
| Sample type |
SRA |
| |
|
| Source name |
pediatric patient H73
|
| Organism |
Homo sapiens |
| Characteristics |
viral contents: RSV strain A Full-length (FL) genome and Defective Viral Genomes
repeat: Replicate pool 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples from 2 RSV strain A infected pediatric samples were prepared as follows: RNA extracted from TRIzol reagents as manufacture's introduction.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq files were aligned to self-developed algorithm VODKA to identify possbile copy-back defective viral genomes
Genome_build: RSV isolate NCBI accesion number KJ672447
Supplementary_files_format_and_content: output from VODKA: txt file contain the breakpoint position, sequences, length, READID, CIGAR score of all DVG junction reads.
|
| |
|
| Submission date |
May 25, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Carolina B Lopez |
| E-mail(s) |
clopezzalaquett@wustl.edu
|
| Phone |
3142737026
|
| Organization name |
Washington University in St. Louis
|
| Street address |
425 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE114948 |
Signal sequences in the viral genome regulate the generation of copy-back defective viral genomes |
|
| Relations |
| BioSample |
SAMN09265940 |
| SRA |
SRX4127621 |
