|
| Status |
Public on Mar 11, 2019 |
| Title |
IU1781 WT-TEX-3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Streptococcus pneumoniae D39 |
| Characteristics |
strain: IU1781
treatment: none
genotype: wild type
|
| Growth protocol |
Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.15 to 0.2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
For samples 1-3, the library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria, fragmenting RNA reagent (Ambion), removing 5' triphosphates via RNA 5' polyphosphatase, and subsequently utilizing the TruSeq Small RNA library kit. For samples 4-6, the same protocol was used as for Samples 1-3, but prior to RNA 5' polyphosphatase treatment the RNA was treated with Terminator 5'-phosphate-dependent exoribonuclease.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Fragmented rRNA depleted RNA
|
| Data processing |
For libararies constructed with Samples 1-6, adapters were trimmed using Cutadapt. Trimmed reads were mapped on the Streptococcus pneumoniae D39 (CP000410.1) genome using Bowtie2 version 2.0.6. Aligned reads were visualized in IGV to identify peaks corresponding to small RNAs.
Read coverage was generated from BAM files using a combination of SAMtools, Bedtools, and a custom R script to normalize coverage per million reads or paired-end fragments. Paired reads were filtered so that only properly-paired reads of fragments less than 600 nt were included in coverage counts.
Genome_build: CP000410.1
Supplementary_files_format_and_content: bigWig files, read coverage maps
|
| |
|
| Submission date |
Dec 06, 2018 |
| Last update date |
Mar 11, 2019 |
| Contact name |
Nicholas De Lay |
| E-mail(s) |
nicholas.r.delay@uth.tmc.edu
|
| Phone |
713-500-6293
|
| Organization name |
University of Texas Health Science Center
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL25906 |
| Series (1) |
| GSE123437 |
Redefining the sRNA transcriptome of Streptococcus pneumoniae serotype 2 strain D39 |
|
| Relations |
| BioSample |
SAMN10527217 |
| SRA |
SRX5100927 |
