|
| Status |
Public on Aug 14, 2017 |
| Title |
fruK-13_1 |
| Sample type |
SRA |
| |
|
| Source name |
fruKM28stop_bacterial batch culture
|
| Organism |
Streptococcus mutans |
| Characteristics |
parental strain: UA159
genotype/variation: fruKM28stop
media: BHI
|
| Treatment protocol |
Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.
|
| Growth protocol |
Bacterial cells used for extraction of RNA were grown in BHI medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
repeat 1 of 3
|
| Data processing |
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert A Burne |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Florida
|
| Department |
Oral BIology
|
| Lab |
Robert A Burne
|
| Street address |
1395 Center Drive
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL21130 |
| Series (1) |
| GSE102646 |
COORDINATED REGULATION OF THE EIIMAN AND FRURKI OPERONS OF STREPTOCOCCUS MUTANS BY GLOBAL AND FRUCTOSE-SPECIFIC PATHWAYS |
|
| Relations |
| BioSample |
SAMN07504406 |
| SRA |
SRX3092220 |
