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| Status |
Public on Jul 30, 2019 |
| Title |
C3-2 |
| Sample type |
SRA |
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| Source name |
Vibrio cholerae O1 biovar El Tor str. N16961
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| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
strain: N16961
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| Treatment protocol |
Five milliliters of exponential phase cultures expressing (shaking at 37 °C for 2 h, 250 µM IPTG added at OD600 ∼0.05) either empty plasmid or pHLwigRD78E were pelleted
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| Growth protocol |
Cells were grown in LB medium (biological triplicates) until reach to OD600 ∼0.05.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using TRIzol reagent (Ambion), breifly the pellet resuspended and left at ambient temperature for 5 min. Next, 260 µL of chloroform was added, followed by shaking and centrifugation (11,500 × g, 5 min). The upper (aqueous) phase was transferred to a fresh tube, mixed with an equal volume of chloroform, and centrifuged. The upper phase was then transferred to 600 µL of isopropanol, vortexed, and incubated at room temperature for 10 min, followed by centrifugation (12,000 × g, 15 min, 4 °C). The pellet (total RNA) was washed twice with 75% (vol/vol) ethanol and then resuspended in 100 µL of nuclease-free water (Ambion). DNA was removed using the Turbo DNase kit (Ambion).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies), and the RNA integrity was checked with RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA library preparation and sequencing reactions were conducted by Genewiz. Illumina TruSeq Stranded Total RNA Library Prep Kit, clustering, and sequencing reagents were used throughout the process following the manufacturer’s recommendations. The cDNA library was quantified using Qubit 2.0 Fluorometer (Life Technologies) and by qPCR. The samples were clustered on a flow cell using the cBOT. After clustering, the samples were loaded for sequencing of 1 × 50 single read on the Illumina HiSEq. 2500 instrument.
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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 |
The files have been generated by the Illumina pipeline software v2.18. Sequencing data was processed by CLC Genomics Workbench (CLC Bio).
Raw sequencing reads were quality trimmed with the same method with ChIP-Seq reads.
Quality trimmed reads were mapped strand specifically on the reference genome sequence by Transcriptome Analysis Tool with the following parameters: maximum number of mismatches of 2, length fraction, and similarity fraction of both 0.9. Number of mapped reads on each gene was normalized by DESeq2 package in Bioconductor v3.4 (Love et al., 2014). Genes with p-value (padj, DESeq2) lower than 0.001 were scored as differentially expressed genes (DEGs).
Genome_build: (NCBI accession NC_002505.1 and NC_002506.1)
Supplementary_files_format_and_content: gff data files contains total profile and values of reads
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| Submission date |
Jul 29, 2019 |
| Last update date |
Jul 31, 2019 |
| Contact name |
JUNG HO Cornell SHIN |
| E-mail(s) |
jhs0421@gmail.com
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| Phone |
6077935562
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| Organization name |
Weill Institute at Cornell University
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| Department |
Microbiology
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| Lab |
Tobias Doerr
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| Street address |
363 Weill Hall, Cornell University
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL26987 |
| Series (1) |
| GSE135010 |
RNA-Seq for identification of differntially expressed genes by VxrB(D78E) overexpression |
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| Relations |
| BioSample |
SAMN12390008 |
| SRA |
SRX6607839 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3983616_C3_NC_002505_normed_profile.gff.gz |
28.3 Mb |
(ftp)(http) |
GFF |
| GSM3983616_C3_NC_002506_normed_profile.gff.gz |
8.6 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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