|
| Status |
Public on Jan 24, 2015 |
| Title |
covS-T284A-2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria grown in high magnesium nutrient rich broth
|
| Organism |
Streptococcus sp. 'group A' |
| Characteristics |
strain/variation: CovS-T284A
|
| Treatment protocol |
RNA protect was added at 2x volumes to cells and then cells were harvested by centrifugation, snap frozen, and stored at -80 C.
|
| Growth protocol |
GAS strains grown in THY +15 mM MgCl2 to mid-exponential phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed using a fast FastPrep approach and RNA was isolated from ruptured cell using an RNeasy Kit (Qiagen)
cDNA was fragmented to 200 bp (mean fragment size) with the S220 Focused-ultrasonicator (Covaris) and used to make barcoded sequencing libraries on the SPRI-TE Nucleic Acid Extractor (Beckman-Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA after rRNA depletion
|
| Data processing |
The raw reads in FASTQ format were aligned to the reference genome, MGAS10870, using MOSAIK alignment software with parameters of -hs 15, -mmp 0.06, -mmal, -minp 0.5, -act 35, -mhp 100, and -m all
The overlaps between aligned reads and annotated genes were counted using HTSeq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). The gene counts were normalized using the scaling factor method implemented in the R package of DESeq2 (version 1.2.10). If the number of overlapped read of any given gene is less than one per million total mapped read for all samples, this gene was excluded from further analysis.
A negative binomial generalized linear model was fit to each gene expression with strain type as covariates. Then a likelihood-ratio test was applied to examine if there is any difference in the expression of a gene among six strains. The Benjamini-Hochberg method was used to control false discovery rate (FDR). The pairwise comparisons were performed to compare the gene expressions between WT vs any other strain using Wald's tests. The Holm's method was used to calculate adjusted p-value to correct for multiple testing. The calculation was conducted using R (version 3.0.1) with the package of DESeq2 (version 1.2.10)
Genome_build: MGAS10870
Supplementary_files_format_and_content: excel file with normalize counts
|
| |
|
| Submission date |
Jan 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Samuel Shelburne |
| E-mail(s) |
[email protected]
|
| Phone |
713-792-3629
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Infectious Diseases
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19691 |
| Series (1) |
| GSE65226 |
Evaluation of covS polymorphisms on group A streptococcal global gene expression |
|
| Relations |
| BioSample |
SAMN03292309 |
| SRA |
SRX851015 |
