|
| Status |
Public on Aug 29, 2022 |
| Title |
codY_mutant_2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria cells
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300
medium: RPMI-1640 with 10% Lysogeny broth (LB)
phase: mid-log phase
genotype: codY mutant
|
| Treatment protocol |
the media was RPMI-1640 with 10% Lysogeny broth (LB) ; no other treatments
|
| Growth protocol |
glycerol stocks of S. aureus JE2 and cody mutant strains were inoculated into RPMI-1640 with 10% Lysogeny broth (LB) . The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (gram-positive bacterial kit) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CodY_2
|
| Data processing |
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto each reference genome using bowtie with the maximum insert size of 2000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for DESeq(https://bioconductor.org/packages/release/bioc/html/DESeq.html)
DESeq2 was run with default options with the library type of dUTP RNA-seq and the default normalization method
Genome_build: The reference genome used in this study is: NC_007793.1 for WT and cody mutant strains
Supplementary_files_format_and_content: tab-delimited text file containing TPM values for each sample
|
| |
|
| Submission date |
Dec 16, 2020 |
| Last update date |
Aug 29, 2022 |
| Contact name |
Ye Gao |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25144 |
| Series (1) |
| GSE163312 |
Elucidating the CodY regulon in Staphylococcus aureus USA300 lineage using ChIPexo |
|
| Relations |
| BioSample |
SAMN17089244 |
| SRA |
SRX9689987 |
