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Sample GSM3983615 Query DataSets for GSM3983615
Status Public on Jul 30, 2019
Title C2-2
Sample type SRA
 
Source name Vibrio cholerae O1 biovar El Tor str. N16961
Organism Vibrio cholerae O1 biovar El Tor str. N16961
Characteristics strain: N16961
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
Growth protocol Cells were grown in LB medium (biological triplicates) until reach to OD600 ∼0.05.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Jul 29, 2019
Last update date Jul 31, 2019
Contact name JUNG HO Cornell SHIN
E-mail(s) jhs0421@gmail.com
Phone 6077935562
Organization name Weill Institute at Cornell University
Department Microbiology
Lab Tobias Doerr
Street address ​363 Weill Hall, ​Cornell University
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
 
Platform ID GPL26987
Series (1)
GSE135010 RNA-Seq for identification of differntially expressed genes by VxrB(D78E) overexpression
Relations
BioSample SAMN12390009
SRA SRX6607838

Supplementary file Size Download File type/resource
GSM3983615_C2_NC_002505_normed_profile.gff.gz 26.5 Mb (ftp)(http) GFF
GSM3983615_C2_NC_002506_normed_profile.gff.gz 7.8 Mb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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