|
| Status |
Public on Aug 03, 2013 |
| Title |
JK05162-Dde_2665-LysX-rich |
| Sample type |
RNA |
| |
|
| Source name |
Desulfovibrio alaskensis str. G20 mutant str. JK05162, rich media
|
| Organism |
Oleidesulfovibrio alaskensis G20 |
| Characteristics |
genotype/variation: Dde_2665 gene disrupted by a transposon
carbon source: lactate (60 mM)
electron acceptor: sulfate (30 mM)
added nutrient: yeast extract (.1%)
growth_phase: early stationary
|
| Treatment protocol |
We transferred pellets to new media, resuspended the pellets, waited one hour, then collected the pellets and stored them in -80C until RNA extraction. The choline mutant was transferred to a 30 mM choline/ 30 mM sulfate media and a lactate/sulfate media. The lysX mutant was transferred to minimal media with .3 mM lysine and to rich media (.1% Yeast extract). G20 was transferred to choline/sulfate media, a lactate/sulfate media, a lactate/choline/sulfate media, a rich lactate/sulfate media, a minimal lactate/sulfate media with lysine.
|
| Growth protocol |
We collected expression data of Desulfovibrio alaskensis str. G20 and 2 mutants with transposon insertions in regulator proteins. We grew the cultures in minimal 60 mM lactate/ 30mM sulfate media in an anaerobic chamber at 30C until cells reached early stationary phase. Basal salts - 8mM MgCl2, 20mM NH4Cl, 2mM K2PO4 (dibasic), .6mM CaCl2, 30mM Tris-HCl. Thauer's vitamins and trace elements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated total RNA with RNeasy mini kit (Qiagen).
|
| Label |
Alexa fluor 555
|
| Label protocol |
Prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen).
|
| |
|
| Hybridization protocol |
Standard NimbleGen protocol.
|
| Scan protocol |
Standard NimbleGen protocol.
|
| Description |
lysXrich
|
| Data processing |
Quantile normalized the probe intensities to match the G20 rich lactate/sulfate media, averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.
|
| |
|
| Submission date |
Aug 02, 2013 |
| Last update date |
Aug 03, 2013 |
| Contact name |
Jennifer V Kuehl |
| E-mail(s) |
jvkuehl@lbl.gov
|
| Phone |
5106435683
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Physical Biosciences
|
| Lab |
Arkin
|
| Street address |
1 Cyclotron Road
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL17530 |
| Series (2) |
| GSE49528 |
Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX |
| GSE49530 |
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20 |
|
