|
| Status |
Public on Aug 14, 2019 |
| Title |
Agr knock-out nares strain, replicate A |
| Sample type |
SRA |
| |
|
| Source name |
Agr knock-out nares strain
|
| Organism |
Staphylococcus aureus |
| Characteristics |
phenotype: delta-agr
|
| Growth protocol |
Overnight cultures were diluted and grown to late-log phase (~0.80 OD) and stabilized in RNALater
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using the QIAGEN RNeasy Mini Kit. Lysozyme and lysostaphin were used for cell wall degradation, followed by two cycles of two-minute bead beating with 1 ml of 0.1 mm silica beads in a mini bead-beater (BioSpec), and eluted in nuclease-free water. Isolated RNA was treated with 1 uL of Baseline Zero DNase (Epicentre) at 37°C for 30 min and ribosomal RNA depletion was performed using Epicenter Ribo-ZeroTM Magnetic Gold Kit (Illumina), according to the manufacturer’s instructions.
After RNA extraction, barcoded stranded RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina). RNA quality and quantity was assessed using the Agilent Bioanalyzer and Qubit RNA Broad Range Assay kit (Thermo Fisher), respectively. Finally, Libraries were pooled and sequenced on the Illumina HiSeq platform in a 100 bp single-end read run format.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MSSA_pt053_N_164+M_A_DS
|
| Data processing |
Raw reads were first trimmed by removing Illumina adapter sequences from 3’ ends using cutadapt with a minimum match of 32 base pairs and allowing for 15% error rate. Trimmed reads were mapped to the reference genome using Bowtie2, and htseq-count was used to produce strand-specific transcript count summaries. Read counts were then combined into a numeric matrix and used as input for differential gene expression analysis with the limma R package in Bioconductor. Normalization factors were computed on the data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom mean-variance transformation in preparation for Limma linear modeling.
Genome_build: PS00089_1A (genome fasta and annotations included as raw data files)
Supplementary_files_format_and_content: Tab-delimited text files containing the Gene ID and the normalized Log2 count per million reads.
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Kieran Ifan Chacko |
| E-mail(s) |
kieran.chacko@icahn.mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetic & Genomic Sciences
|
| Street address |
One Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19006 |
| Series (1) |
| GSE102637 |
Colonizing and infecting subclones diverge during Staphylococcus aureus infection |
|
| Relations |
| BioSample |
SAMN07503951 |
| SRA |
SRX3092190 |
