|
| Status |
Public on Oct 22, 2019 |
| Title |
WtBfilmGlucose/259_A# |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type Y. pestis grown in glucose in the biofilm state
|
| Organism |
Yersinia pestis |
| Characteristics |
strain: PAN259
genotype/variation: pCD1-
carbon source: Glucose
growth state: Biofilm
|
| Growth protocol |
Y. pestis and ∆crp were grown in defined, minimal TMH media in 0.2% glucose or 0.2% glycerol at 37ºC in 125 mL Erlenmeyer flasks. Adhering bioflm cells were scraped away and separated from planktonic cells after 18 hours of growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were resuspended in RNA protect and extracted using RNA-whiz and precipitated in isoproponol. RNA was treated with Turbo Dnase
Total RNA was checked for quality and quantity on Agilent Bioanalyzer 2100 and Qubit fluorometer. The Illumina TruSeq Stranded Total RNA Library Preparation Kit was used to prepare sequencing libraries from 500 ng of total RNA samples according to manufacturer’s instructions without modifications. This procedure includes rRNA depletion with Ribo-Zero rRNA Removal Kit (Bacteria), remaining RNA purification and fragmentation, cDNA synthesis, 3’-end adenylation, Illumina adapter ligation, library PCR amplification and validation. Illumina NextSeq 500 Sequencer was used to sequence the libraries with the production of single-end, 75 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Wild-type Y. pestis grown in glucose in the biofilm state
|
| Data processing |
The quality of DNA reads, in fastq format, was evaluated using FastQC
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.
The cleaned reads were aligned to the Y. pestis genome (NC_003143.1) and plasmids pPCP1 (NC_003132.1) and pMT1 (NC_003134.1) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for Y. pestis
Read counts for sRNA were obtained using bedtools using the annotated locations
Genome_build: Y. pestis chromosome NC_003143.1, plasmid pPCP1 NC_003132.1, and pMT1 NC_003134.1
Supplementary_files_format_and_content: .xlsx file containing individual tabs comparing treatment conditions with GeneID, log2 fold change, and false discovery rate p values
|
| |
|
| Submission date |
Aug 01, 2019 |
| Last update date |
Oct 22, 2019 |
| Contact name |
Jeremy T Ritzert |
| E-mail(s) |
jritzert@luc.edu
|
| Organization name |
Loyola University Chicago
|
| Department |
Biology
|
| Street address |
1032 W. Sheridan Road
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60660 |
| Country |
USA |
| |
|
| Platform ID |
GPL27001 |
| Series (1) |
| GSE135228 |
The Cyclic AMP Receptor Protein Regulates Quorum Sensig and Global Gene Expression in Yersinia pestis During Planktonic Growth and Growth in Biofilms |
|
| Relations |
| BioSample |
SAMN12421884 |
| SRA |
SRX6631980 |
