|
| Status |
Public on Sep 30, 2013 |
| Title |
TIGR4 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Streptococcus pneumoniae TIGR4 adherent to pharyngeal epithelial cells
|
| Organism |
Streptococcus pneumoniae TIGR4 |
| Characteristics |
strain: TIGR4
treatment: adherence to D562 human pharyngeal epithelial cells
time: 2 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol in a lysing matrix containing silica beads and a FastPrep Instrument. Purification was done using i) phase separation with TRIzol and ii) column exclusion with the RNeasy Mini Kit. Contaminating genomic DNA was removed by DNase treatment.
The library was prepared with the mRNA-Seq Sample Prep Kit. The poly-A selection step was omitted.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
total RNA depleted of rRNA
|
| Data processing |
Basecalls performed using Illumina Bustard 1.4
sequence reads were mapped to reference genome TIGR4 (AE005672) using ELAND aligner
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated per gene
Genome_build: AE005672
Supplementary_files_format_and_content: space-delimited text file with RPKM values
Genome_build: ASM688v1
|
| |
|
| Submission date |
Mar 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jerry Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
IGS
|
| Street address |
801 W. Baltimore St.
|
| City |
Baltimore |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL16764 |
| Series (1) |
| GSE44947 |
Transcriptional Characterization of Streptococcus pneumoniae Interacting with Human Pharyngeal Cells |
|
| Relations |
| SRA |
SRX247309 |
| BioSample |
SAMN01940975 |
