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Sample GSM4101818 Query DataSets for GSM4101818
Status Public on Sep 10, 2020
Title VC48_1
Sample type SRA
Source name Host and bacteria
Organisms Vibrio parahaemolyticus; Caenorhabditis elegans
Characteristics strain: N2, RIMD 2210633
genotype: WT
tissue: Whole organism
Extracted molecule total RNA
Extraction protocol Total RNA was then isolated from C. elegans containing bacteria using the mirVana kit (Ambion) following the user manual. The isolated total RNA was treated with DNase I (Fermentas) (0.25 U/1 μg of RNA) for 30 mins, followed by purification with ethanol. The Ribo-Zero Magnetic Gold Kit (Epidemiology) from Epicentre/Illumina was used to removed rRNA in the samples following the manufacturer’s instructions.
cDNA libraries for Illumina sequencing were constructed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) following the manufacture instruction. For organism dual RNA-Seq, ~ 100 ng rRNA-depleted RNA were used for cDNA library preparation
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the V. parahaemolyticus RIMD2210633 genome ( ASM19609v1) or C. elegans genome (WBcel235)using Tophat2 with the default parameterization, respectively
Reads aligned to annotated genes were quantified with the htseq-count program using gene annotations from Ensembl release 92
Determined uniquely mapped read counts were served as input to DESeq2 (version 1.14.1) for pairwise detection and quantification of differential gene expression with default parameterization (pmid 25516281)
Genome_build: V. parahaemolyticus RIMD2210633 genome ( ASM19609v1) or C. elegans genome (WBcel235)
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample
Submission date Sep 30, 2019
Last update date Sep 13, 2020
Contact name wenwen Zhang
Organization name Zhang Wenwen
Street address University of Macau, Avenida de Universidade, Taipa
City Macau
ZIP/Postal code no
Country Macau
Platform ID GPL27555
Series (1)
GSE138199 Organism Dual RNA-Seq Reveals the Control on both Pathogen and Host through BarA/UvrY of Vibrio parahaemolyticus for Successful Infection
BioSample SAMN12875955
SRA SRX6927167

Supplementary file Size Download File type/resource
GSM4101818_VC48_1_C.txt.gz 314.7 Kb (ftp)(http) TXT
GSM4101818_VC48_1_V.txt.gz 29.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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