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| Status |
Public on Sep 10, 2020 |
| Title |
C36_3 |
| Sample type |
SRA |
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| Source name |
Host
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: WT
tissue: Whole organism
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Sep 30, 2019 |
| Last update date |
Sep 13, 2020 |
| Contact name |
wenwen Zhang |
| E-mail(s) |
yb67620@umac.mo
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| Organization name |
Zhang Wenwen
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| Street address |
University of Macau, Avenida de Universidade, Taipa
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| City |
Macau |
| ZIP/Postal code |
no |
| Country |
Macau |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE138199 |
Organism Dual RNA-Seq Reveals the Control on both Pathogen and Host through BarA/UvrY of Vibrio parahaemolyticus for Successful Infection |
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| Relations |
| BioSample |
SAMN12875921 |
| SRA |
SRX6927154 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4101805_C36_3.txt.gz |
306.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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