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| Status |
Public on Jun 30, 2018 |
| Title |
PGYLI2 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Clostridium perfringens |
| Characteristics |
strain: HN13
growth: PGY liquid
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| Growth protocol |
C. perfringens HN13 cells were grown in duplicate in six conditions: liquid culture to mid-log phase and 1% agar plates of PGY, BHI, and FABG media for 24 hours. Liquid cultures were standardized to OD600=0.500 and cells were scraped from the outer edges of plate grown colonies and resuspended in DPBS to OD600=0.500. Bacteria were pelleted and frozen in liquid nitrogen prior to RNA purification.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in 500 μl Tri Reagent (Zymo Research) using high-impact zirconium beads in a Mini-Beadbeater (Biospec) for one minute and kept on ice. RNA was then purified from cell lysate using a Direct-Zol RNA Mini-Prep Plus Kit according to the manufacturer’s protocol (Zymo Research), including an on-column DNA digestion. RNA integrity was measured using an Agilent BioAnalyzer 2100 (VBI), and samples with a RIN of 8.3 or greater were used for RNA sequencing.
Library construction was performed for Illumina sequencing by Virginia Bioinformatics Institute. All samples were processed with HiSeq Illumina sequencing (VBI) creating 100-bp paired-end reads, and the resulting data was aligned to C. perfringens strain 13 reference genome (NCBI, accession number NC_003366) using the bioinformatics mapper Geneious version 9 with low sensitivity
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PGY liquid
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| Data processing |
Geneious version 9 with low sensitivity
Relative expression levels of annotated coding regions were calculated with units of transcripts per million (TPM). TPM, as proposed by Wagner (3) is calculated as: TPM= (coding Sequence read count x Mean read length x 106)/(Coding sequence length x Total transcript count). Differentially expressed genes were identified by a stringent cutoff of fold-change >4 when media conditions were compared against one another for each gene.
Genome_build: NC_003366
Supplementary_files_format_and_content: excel, raw and average RNA-seq data and compiled sRNA values
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| Submission date |
May 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Melville |
| E-mail(s) |
melville@vt.edu
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| Phone |
5402311441
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| Organization name |
Virginia Tech
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| Department |
Biological Sciences
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| Street address |
217 LS1, Washington St.
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| City |
Blacksburg |
| State/province |
Virginia |
| ZIP/Postal code |
24061 |
| Country |
USA |
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| Platform ID |
GPL20676 |
| Series (1) |
| GSE99224 |
Large-scale differences in gene expression, including genes encoding type IV pili-associated proteins, are seen when Clostridium perfringens is grown in liquid or on surfaces |
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| Relations |
| BioSample |
SAMN07159032 |
| SRA |
SRX2845365 |
| 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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