|
| Status |
Public on Oct 19, 2018 |
| Title |
M3-wt-1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria grown in THY
|
| Organism |
Streptococcus sp. 'group A' |
| Characteristics |
strain: MGAS10870
serotype: M3
molecule subtype: RNA after rRNA depletion
|
| 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 late-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 |
17-10870-1
|
| Data processing |
The raw reads in FASTQ format were aligned to the reference genome, MGAS10870 (M3) or MGAS5005 (M1) 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.
Please note that the MGAS10870 strain and its derivative strains get mapped to the publicly available MGAS315 genome (NC_004070.1/AE014074.1). For strain MGAS2221 and its derivatives, we map to the publicly available strain MGAS5005 (NZ_CP000017.1/CP000017.2). MGAS10870 and MGAS2221 are very closely related to MGAS10870 and MGAS2221, respectively.
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: MGAS315 (NC_004070.1/AE014074.1) and MGAS5005 (NZ_CP000017.1/CP000017.2) genomes
Supplementary_files_format_and_content: normalize counts
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Oct 21, 2018 |
| 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) |
| GSE121313 |
Evaluating the effect of CovR phosphorylation on group A streptococcus global gene expression |
|
| Relations |
| BioSample |
SAMN10246512 |
| SRA |
SRX4892130 |
