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| Status |
Public on May 08, 2021 |
| Title |
wildtype-vc0513_rep1 |
| Sample type |
SRA |
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| Source name |
bacteria harvested from broth culture
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| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
genotype: N16961 pHLmob(Piptg-vc0513)
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| Treatment protocol |
N/A
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| Growth protocol |
Overnight cultures were diluted 1:100 and grown shaking in LB broth containing kanamycin (50 ug/mL) and inducer (IPTG, 500 uM) at 37ºC until cultures reached mid-log phase (optical density at 600 nm = 0.5)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested via centrifguation, resuspended in 1X phosphate buffered solution, and treated with RNA protect (Qiagen). mirVana™ miRNA Isolation Kit (Ambion) was used according to manufacturer instructions. Total RNA was treated with DNAfree (Ambion) and precipitated with ethanol and ammonium acetate.
Ribosomal RNA was subtracted by hybridization from total RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
V. cholerae N16961 with vc0513 containing vector; isolated at mid-log phase in LB medium
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| Data processing |
Libraries were sequenced on an Illumina HiSeq instrument with at least 10M reads were generated per library.
Reads were be trimmed for low quality and adaptor sequences with TrimGalore v0.6.0 (Babraham Institute), a wrapper for cutadapt (Martin et al., EMBnet Journal) and fastQC (Babraham Institute) using the following parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC --length 50 --fastqc
Reads were mapped to the reference genome/transcriptome (Vibrio cholerae O1 El Tor N16961 taxonomy ID: 243277) using STAR v2.7.0e (Dobin et al, Bioinformatics, 2013) with the following parameters: --outSAMstrandField intronMotif , --outFilterIntronMotifs RemoveNoncanonical , --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression (Varet et al., PLOS ONE, 2016; Love et al., Genome Biology, 2014) using the following parameters: fitType parametric, cooksCutoff TRUE, independentFiltering TRUE, alpha 0.05, pAdjustMethod BH, typeTrans VST, locfunc median
Genome_build: Vibrio cholerae O1 biovar El Tor str. N16961 (taxonomy ID: 243277)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Combined matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with differential expression values and p-values for each gene
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| Submission date |
May 07, 2021 |
| Last update date |
May 08, 2021 |
| Contact name |
Tobias Doerr |
| E-mail(s) |
tdoerr@cornell.edu
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| Organization name |
Cornell University
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| Department |
Microbiology
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| Lab |
Doerr Lab
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| Street address |
525 N Campus Rd
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL30088 |
| Series (1) |
| GSE174028 |
Transcriptional response to overexpressing Vibrio Seventh Pandemic -II island encoded genes |
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| Relations |
| BioSample |
SAMN19066500 |
| SRA |
SRX10813624 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5284856_vc0513-rep1.txt.gz |
14.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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