|
| Status |
Public on Feb 28, 2019 |
| Title |
Dengue 2 NAI-Map REP1 - NAI |
| Sample type |
SRA |
| |
|
| Source name |
Virus particle
|
| Organism |
dengue virus type 2 |
| Characteristics |
assembly: EU081177.1
tissue: Virus particle
|
| Treatment protocol |
Fresh virus particles are treated with NAI for secondary structure mapping, and with biotinylated psoralen for interactome mapping, at 37C for 10 min. Virions treated with biotinylated psoralen were then crosslinked using UV.
|
| Growth protocol |
Dengue 1-4 are amplified from african green monkey kidney (Vero) cells. Zika strains are amplified by mosquito C6/36 cells. Huh7 cells were grown in DMEM, supplemented with 10% FBS and 1% Pen-Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NAI or biotinylated treated RNA was extracted from virus particles using Trizol extraction. RNA from Dengue1 infected Huh7 cells were extracted using Trizol.
Local secondary structure mapping was performed using SHAPE-map strategy, and long-range interactome mapping was performed using SPLASH. Ribsome profiling was performed using the Artseq ribosome profiling kit (Epicenter).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
local secondary structure mapping
DEN2-NAI-Map.tar.gz
|
| Data processing |
Library strategy: SHAPE-map
NAI-Map files are processed using the ShapeMapper v1.2 script by the Kevin M. Weeks lab (www.chem.unc.edu/rna/software.html) with default settings to generate reactivity profiles (ShapeMapper called local bowtie2 2.3.3 for alignment)
SPLASH data is aligned using bowtie2 2.3.3 against the reference genome; all reads that align to two distinct sites along the reference genome are filtered and included as a bam and csv file;
Ribosome footprinting reads (footprints and mRNA sets) were aligned to the reference genome using bowtie2 (2.3.3) with the options "--local -D 20 -R 3 - N 1 -L 15 -i S,1,0.50 --score-min G,20,8 --ma 2 --mp 6,2 --rdg 5,1 --rfg 5,1"; relative intensities were calculated by dividng read number of the footprint set by the read number of the mRNA set at each nucleotide position along the reference genome
Genome_build: Dengue 1 EU081230.1; Dengue 2 EU081177.1; Dengue 3 EU081190.1; Dengue 4 GQ398256.1; Zika MR766 AY632535.1; Zika BeH815744 KU365780.1; Zika H/PF/2013 KJ776791.2; Zika ZIKV-SG-032 KY241702.1
Supplementary_files_format_and_content: processed NAI-Map files are tar.gz archives and contain 2 pdf files showing shape reactivity and quality scores and 3 text files containing the raw shape reactivity numbers; Processed SPLASH files are tar.gz archives and contain paired read alignments and location summaries as bam and csv respectively; Processed RIBO_PROFILE files are gzipped text files that contain a list of FP/mRNA calculated for each position;
|
| |
|
| Submission date |
Nov 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Roland G Huber |
| E-mail(s) |
rghuber@bii.a-star.edu.sg
|
| Phone |
+6564788321
|
| Organization name |
Agency for Science, Technology and Research (A*STAR)
|
| Department |
Bioinformatics Institute (BII)
|
| Lab |
Structure and Function of RNA
|
| Street address |
30 Biopolis Street
|
| City |
Singapore |
| ZIP/Postal code |
138671 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24218 |
| Series (1) |
| GSE106483 |
Genome organization of dengue and Zika viruses |
|
| Relations |
| BioSample |
SAMN07974377 |
| SRA |
SRX3358869 |
