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| Status |
Public on Jan 01, 2020 |
| Title |
TX9611 |
| Sample type |
SRA |
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| Source name |
Mimus polyglottos (Mocking Bird)
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| Organism |
West Nile virus |
| Characteristics |
source tissue: dead bird brain homogenate
location: USA: TX, Kingswood (77339)
collection date: 30-Jun-14
molecule subtype: viral RNA
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| Growth protocol |
virus was isolated from the brain homogenate of dead birds by passageing on vero cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the supernatant of infected vero cells using the QIAamp Viral RNA Mini kit according to the manufacturer’s recommendations
Libraries were generated with a TruSeq RNA v2 kit (Illumina) according the the manufactures instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Aptmers and poor quality bases (q< 20) were removedwith Trimmomatic
reads were aligned to the reference (AF196835) with bowtie2 under the sensitive local parameters
a consensus sequence was extracted using the mpileup function in samtools
alignment was repaired by realigning to the new consensus sequence in Bowtie2 under the very sensitive local parameters
reads were sorted by coordinate by the SamSort function of picard tools
Duplicates were removed with the MarkDuplicate function of picard tools
Single nucleotide variants were identified with V-phaser2
Genome_build: AF196835
Supplementary_files_format_and_content: variant caller summary; Each variant entry consists of the following: the reference position (coordinate starts at 1), predicted variant, consensus base, strand-bias p-value, type of variant (Single nucleotide polymorphism (SNP) or Length polymorphism (LP)), frequency of the variant and the profile, where each entry consists of three values: the base, its count in the forward strand, and its count in the reverse strand, separated by Colons.
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| Submission date |
Feb 14, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Daniele Swetnam |
| E-mail(s) |
dmswetnam@ucdavis.edu
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| Phone |
4097397784
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| Organization name |
University of Texas Medical Branch
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| Department |
Experimental Pathology
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| Lab |
Alan Barrett
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| Street address |
301 University Blvd
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| City |
Galveston |
| State/province |
TX |
| ZIP/Postal code |
77555 |
| Country |
USA |
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| Platform ID |
GPL26196 |
| Series (1) |
| GSE126555 |
Deep sequencing of WNV isolates collected in Harris County, TX 2013-2016 |
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| Relations |
| BioSample |
SAMN10929400 |
| SRA |
SRX5374761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3604400_TX9611.fdr.var.txt.gz |
422 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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