|
| Status |
Public on Jul 25, 2022 |
| Title |
OG1 untreated s3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Enterococcus faecalis |
| Characteristics |
strain: OG1
treatment: untreated
|
| Treatment protocol |
bacitracin was added to some cultures at 128 ug/ml for 15 min at 37 C; cultures that did not receive bacitracin received vehicle only (DMSO)
|
| Growth protocol |
Exponentially growing bacterial cultures in Mueller-Hinton broth in shaking flasks at 37 C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified from cells, then subjected to rRNA depletion
TruSeq stranded libraries were prepared using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Casava 1.7 software used for basecalling.
TrimGalore v. 0.4.5 used to quality filter and trim reads
Bowtie 2 v. 2.3.4.3 used to align trimmed reads to reference (OG1RF: NC_017316.1)
Samtools v. 1.3 used to convert SAM to BAM and sort alignments
HTSeq was used to count reads; stranded set to reverse (-s reverse), -t gene -f bam
DESeq2 was used for differential expression testing.
Genome_build: NC_017316.1
Supplementary_files_format_and_content: tab-delimited files containing raw counts (output of HTSeq) for each sample
|
| |
|
| Submission date |
Jan 04, 2022 |
| Last update date |
Jul 25, 2022 |
| Contact name |
CHRIS KRISTICH |
| E-mail(s) |
ckristich@mcw.edu
|
| Organization name |
MCW
|
| Street address |
8701 WATERTOWN PLANK RD
|
| City |
MILWAUKEE |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL31169 |
| Series (1) |
| GSE193042 |
CroR-regulated genes in Enterococcus faecalis OG1 |
|
| Relations |
| BioSample |
SAMN24614299 |
| SRA |
SRX13602695 |
