|
| Status |
Public on Sep 21, 2017 |
| Title |
MBO24 (E) rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria planktonic culture harvested at OD600nm 0.8.
|
| Organism |
Streptococcus pneumoniae |
| Characteristics |
strain: MBO24
hsds allele: E
hsds allele target recognition domains: 1.1 and 2.3
colony phenotype: 100% transparent
|
| Growth protocol |
For each pneumococcal strain, three independent cultures were grown in 8 mL of Todd-Hewitt broth supplemented with 0.5 % yeast extract in a 37°C water bath. Cultures were harvested at mid-log phase (OD600nm 0.8), centrifuged (12,000 rpm) for 5 min and resuspended in 1 mL PBS containing lysozyme (2 mg/mL). Samples were immediately processed for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from bacteria pellets with lysozyme, followed by clean-up and DNase I treatment with NucleoSpinRNA II kit kit per manufacturer’s recommendations.
The ribosomal RNA was removed from the total bacterial RNA using ribosome reduction for Gram positive bacteria (ArrayStar, Rockville MD). The purified RNA was then processed using the SureSelect Strand Specific RNA-Seq library prep kit from Agilent Technologies (San Diego, CA) following the manufacturer’s protocol. The resulting libraries were quantitated with quantitative PCR (KapaBiosystems, Woburn MA) and the size distribution of the inserts were checked on the Agilent 2100 BioAnalyzer on a High Sensitivity DNA Chip. Library concentration was normalized to 2nM
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate 2
E2
|
| Data processing |
Illumina Casava (bcl2fastq) version 1.8.4 software used for basecalling.
Reads were mapped to the reference S. pneumoniae TIGR4 genome (accession- NC_003028.3) using Bowtie2 2.2.9 (default parameters), and transcript abundance was calculated using summarizeOverlaps function from R package GenomicAlignments
The differential expression analyses were carried out using R package DeSeq2 alognwith generation of normalized read count matrix
Genome_build: NC_003028.3
Supplementary_files_format_and_content: Normalized read count matrix for all samples
|
| |
|
| Submission date |
Aug 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
W Edward Swords |
| E-mail(s) |
[email protected]
|
| Organization name |
Univ. of Alabama at Birmingham
|
| Department |
Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
|
| Street address |
1918 University Blvd. McCallum bldg, Room 798
|
| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL23152 |
| Series (1) |
| GSE103364 |
Streptococcus pneumoniae TIGR4 phase-locked opacity variants differ in virulence phenotypes |
|
| Relations |
| BioSample |
SAMN07585978 |
| SRA |
SRX3152395 |
