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| Status |
Public on Feb 01, 2018 |
| Title |
2WB1 |
| Sample type |
SRA |
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| Source name |
BHI pH 5.5
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| Organism |
Listeria monocytogenes |
| Characteristics |
strain: 10403S
genotype/variation: WT
condition: Bile
replicate: 1
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| Treatment protocol |
Total RNA was treated with Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input for removal of 16S and 23S ribosomal RNA and enriched for mRNA
Cultures were diluted into 100ml pH 5.5 BHI with or without 1.1% bile for 10 min.
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| Growth protocol |
strains were streaked from frozen BHI stock, stored at -80°C in 15% glycerol, onto a BHI agar plate, followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into 5 ml of BHI broth in 16 mm tubes, followed by incubation at 37°C with shaking (230 rpm) for 18 h (Series 25 Incubator, New Brunswick Scientific, Edison, NJ). After 18 h, 50 μl BHI culture was inoculated into fresh 100 ml BHI broth and grown in flasks without shaking for 3h (to OD600 ~0.4) at 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using proteinase K, and lysozyme, followed by Tri reagent with bead-beating. Total RNA was incubated with DNase in the presence of RNasin to remove remaining DNA.
Preparation of cDNA fragment libraries was performed using the ScriptSeqTM Complete Kit (Bacteria)-Low Input (Epicentre, Madison, WI), which is composed of Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input, Magnetic Core Kit-Low Input, and ScriptSeqTM v2 RNA-Seq Library Preparation Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
TC_Bile_Control_10403S.xlsx
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| Data processing |
Raw data was generated by the Illumina pipeline software v1.8
the sequence reads were aligned to a 10403S genome using the BWA-MEM with default settings.The output was a SAM files for each sample. Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from BWA and convert them to BAM format. BAM files were converted to strand-specific base count files. Coverage at each base position along the chromosome was calculated by enumerating the number of reads that aligned to a given base for each DNA strand separately.
Differential expression of genes in different strains was statistically assessed using the BaySeq method implemented in the BaySeq 2.2.0 package available from Bioconductor. Genes were considered differentially expressed if they showed a false discovery rate (FDR) < 0.05 and a fold change (FC) ≥ 2.0 (meaning genes were upregulated on Prha-sigB) or FC ≤ 0.5 (meaning genes were downregulated on Prha-sigB).
Genome_build: 10403S genome (genebank accession number: NC_017544) or H7858 permanent draft (BioProject Accession number: PRJNA10752)
Supplementary_files_format_and_content: Each excel spreadsheet contains the normalized count data for each coding gene in 10403S or H7858, likelihood of being differentially expressed and False Discovery Rate (from Bayseq output), as well as the foldchange Bile/No Bile or WT/SigB depending on comparison.
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| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Veronica Guariglia |
| E-mail(s) |
vg93@cornell.edu
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| Phone |
6072805390
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| Organization name |
Cornell University
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| Department |
Food Science
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| Street address |
320 Stocking Hall
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| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850-6302 |
| Country |
USA |
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| Platform ID |
GPL21330 |
| Series (1) |
| GSE103443 |
RNA-sequencing based analysis of Listeria monocytogenes 10403S and H7858 and corresponding ΔsigB mutants under exposure to pH 5.5 with or without bile |
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| Relations |
| BioSample |
SAMN07604267 |
| SRA |
SRX3159156 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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