|
| Status |
Public on Dec 25, 2015 |
| Title |
rcsB, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
isogenic P. mirabilis rcsB mutant
|
| Organism |
Proteus mirabilis |
| Characteristics |
genotype: HI4320 rcsB mutant
|
| Treatment protocol |
RNAprotect Bacteria Reagent was used at a 1:1 ratio (Qiagen).
|
| Growth protocol |
Cells were grown in LB broth to an optical density A600 of 1.1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using MasterPure reagent from Epicentre
RNA purity was confirmed on the Agilent 2100 Bioanalyzer (Agilent Technologies). DNA-free samples were then enriched for mRNA using MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion). Two rounds of rRNA depletion were performed and RNA purity was confirmed on an Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were constructed from HI4320 and rcsB::strR mRNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). The cDNA libraries were purified by phenol extraction and ethanol precipitation. Sequences were analyzed on an Illumina HiSeq2000 instrument with 50 bp paired end reads and matched to the HI4320 genome using CLC Genomics Workbench (CLC Bio-Qiagen, Aarhus Denmark).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CLC Genomics workbench was used to analyze the data. The number of reads per transcript was determined and normalized to get RPKM values. A Baggerly¹s proportion test was used to find differentially expressed transcripts over the control sample and was accounted for multiple testing.
Raw data were lost and therefore are not included in this submission
|
| |
|
| Submission date |
Dec 24, 2015 |
| Last update date |
Dec 25, 2015 |
| Contact name |
Philip Rather |
| E-mail(s) |
philiprather@gmail.com
|
| Phone |
678 634-4356
|
| Organization name |
Emory University
|
| Department |
Microbiology
|
| Street address |
3001 Rollins Research Bldg
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30338 |
| Country |
USA |
| |
|
| Platform ID |
GPL21281 |
| Series (1) |
| GSE76341 |
RNA-Seq between Proteus mirabilis HI4320 and an rcsB mutant |
|
| Relations |
| BioSample |
SAMN04370484 |
