|
| Status |
Public on Apr 01, 2018 |
| Title |
Alone Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Biofilm of Glutamicibacter arilaitensis growing on cheese curd agar
|
| Organism |
Glutamicibacter arilaitensis |
| Characteristics |
strain: JB182
treatment: growing alone
tissue: experimental biofilm
|
| Treatment protocol |
For the + Penicillium sp. #12 treatment, approximately 100,000 CFUs of Penicillium were co-inoculated onto the plates with G. arilaitensis JB182. Plates were at > 90% relative humidity at 24 °C for 5 days.
|
| Growth protocol |
For each experimental unit, approximately 80,000 CFUs of G. arilaitensis JB182 were spread across the surface of a 100mm Petri dish containing 20 mL of cheese curd agar.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rind biofilms were harvested by scraping the cheese curd surface and stored in RNAProtect Reagent (Qiagen) and RNA was extracted using a standard phenol-chloroform protocol.
To confirm that the samples were free of DNA contaminants, a PCR of the 16S rRNA gene was performed with standard primers (27f and 1492r). Overall quantity and quality of the RNA preps were confirmed by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. RNA-seq libraries were constructed from purified mRNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Pooled library samples were be sequenced using paired-end 100bp reads on an Illumina HiSeq Rapid Run by the Harvard Bauer Core Sequencing Core Facility. Each library yielded 6.8-8.9 million forward reads that were used for analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GlutiPenRNAseqforGEO.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were mapped and gene expression values were calculated using default parameters in Rockhopper version 2.0.3 (De novo assembly of bacterial transcriptomes from RNA-seq data. Brian Tjaden. Genome Biology, 16:1, 2015.)
Genome_build: ASM287867v1
Supplementary_files_format_and_content: Rockhopper output with raw and normalized expression values [GlutiPenRNAseqforGEO.txt]
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Apr 01, 2018 |
| Contact name |
Benjamin Wolfe |
| E-mail(s) |
benjamin.wolfe@tufts.edu
|
| Organization name |
Tufts University - Biology
|
| Department |
Biology
|
| Lab |
Wolfe
|
| Street address |
Tufts University - Biology, 200 Boston Ave, Suite 4700
|
| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL24753 |
| Series (1) |
| GSE112092 |
Gene expression of the bacterium Glutamicibacter arilaitensis when grown with Penicillium in cheese |
|
| Relations |
| BioSample |
SAMN08743342 |
| SRA |
SRX3824676 |
