|
| Status |
Public on May 31, 2019 |
| Title |
GAS_WT_Liquid LC1-3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria - liquid culture
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
strain: NZ131
sample type: WT GAS samples taken from liquid culture
|
| Growth protocol |
Samples grown in liquid medium were grown overnight, diluted and then grown to mid-log phase. In the vaginal tract, samples were inoculated at 10^7 CFU/mouse and bacteria were collected by vaginal lavage at 48 hours post-inoculation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from liquid cultures or vaginal lavage fluid using the Ambion Ribopure Bacterial RNA prep kit (Thermofisher AM1925), for mouse samples, eukaryotic RNA was depleted using MICROBEnrich kit (Thermo Fisher AM1901) rRNA was removed via the MICROBExpress kit (Thermo Fisher AM1905)
cDNA libraries were constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina Platforms (KAPABiosystems, KR0934).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Streptococcus pyogenes grown in chemically defined medium (CDM) replicate 3
sample3_LC-1-3_AGTCAA_L008
|
| Data processing |
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: TopHat v2.0.13
Customized sample merged reference genome for transcripts assembly with featureCounts: cufflinks cuffmerge
Samples gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Genome_build: UCSC mouse genome model: mm10; NCBI bacteria genome model: Streptococcus pyogenes NZ131 Refseq NC_011375.1
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample, and cuffmerge processed reference genome file.
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
May 31, 2019 |
| Contact name |
Yan Li |
| E-mail(s) |
yli22@bsd.uchicago.edu
|
| Phone |
7738344316
|
| Organization name |
The University of Chicago
|
| Department |
Center for Research Informatics
|
| Street address |
900 East 57th St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL20656 |
| Series (1) |
| GSE131982 |
Transcriptomic analysis of Streptococcus pyogenescolonizing the vaginal mucosa identifies hupY, an MtsR-regulated adhesin involved in heme utilization |
|
| Relations |
| BioSample |
SAMN11893975 |
| SRA |
SRX5935562 |
