|
| Status |
Public on May 13, 2019 |
| Title |
WX1_sRNAseq_run331 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Streptococcus pneumoniae D39 |
| Characteristics |
strain: IU1781
|
| 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 1-6 and 8-9, the library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria and subsequently utilizing the ScriptSeqTM v2 RNA-Seq Library Preparation kit (Epicenter). For samples 7 and 10, the same protocol excpet for TruSeq® Stranded RNA kit (Illumina Inc.) was used to prepare sRNA libraries using 145 - 500 bp size selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rRNA depleted, fragmented (sRNA-seq)
|
| Data processing |
Adapters and low quality bases were trimmed using Trimmomatic (version 0.17)
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2 version 2.0.0-beta7
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)
Supplementary_files_format_and_content: tab-delimited counts file
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
May 13, 2019 |
| Contact name |
Malcolm Winkler |
| Organization name |
Indiana University
|
| Department |
Biology
|
| Lab |
A414
|
| Street address |
1001 E. Third Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL25906 |
| Series (1) |
| GSE124170 |
Redefining the sRNA transcriptome of Streptococcus pneumoniae serotype 2 strain D39 |
|
| Relations |
| BioSample |
SAMN10619133 |
| SRA |
SRX5169360 |
