|
| Status |
Public on Aug 21, 2019 |
| Title |
H26_ala_3 |
| Sample type |
RNA |
| |
|
| Source name |
Haloferax volcanii H26, L-alanine
|
| Organism |
Haloferax volcanii |
| Characteristics |
genotype: H26 ∆pyrE2
supplement: 10 mM L-alanine, 20 mM glycerol
|
| Treatment protocol |
Haloferax volcanii H26 was grown in glycerol minimal medium with 10 mM ammonium chloride or L-alanine as indicated above (see Characteristics)
|
| Growth protocol |
Hfx. volcanii H26 grown to mid-logarithmic phase (OD600, 0.3 to 0.5) at 42 °C in 20 mM glycerol minimal medium supplemented with 10 ug/mL uracil to complement the ∆pyrE2 deletion. A recipe of the minimal medium is described in The Halohandbook (http://www.haloarchaea.com/resources/halohandbook/).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three biological replicate cultures under each condition using TRI-Reagent (Sigma-Aldrich) according to manufacturer’s instructions. RNA quality was ensured using an Agilent Bioanalyzer 2100. Double-stranded cDNA libraries were created from the extracted RNA using Superscript cDNA synthesis kit according to manufacturer instructions (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
One microgram of cDNA from each biological replicate was labeled with Cy3 dye according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.
|
| |
|
| Hybridization protocol |
Labeled cDNA samples were hybridized to NimbleGen 12 × 135-k feature single-color custom microarray slides (Roche), with containing 98% of the annotated genes in the Hfx. volcanii genome (Hartman et al., 2010) at FSU-NimbleGen certified facility (The Florida State University, Tallahassee, FL) according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.
|
| Scan protocol |
Array scanning was conducted according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.
|
| Description |
This sample is of the Hfx. volcanii H26 strain grown in the presence of 10 mM L-alanine. It is the third of three biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
Raw spot intensities were first normalized within arrays using RMA. The four replicate probes corresponding to the same gene were averaged, followed by further normalization of low signal cutoff (cutoff 1.0 and replace), global normalization (75 percentile) and log2 based transformation using Subio Platform v. 1.22 (https://www.subioplatform.com).
|
| |
|
| Submission date |
May 08, 2019 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Sungmin Hwang |
| E-mail(s) |
[email protected]
|
| Organization name |
Korea Institute of Science and Technology
|
| Department |
Clean Energy Research Center
|
| Lab |
Lee
|
| Street address |
Hwarang-ro 14-gil, Seongbuk-gu
|
| City |
Seoul |
| ZIP/Postal code |
02792 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21414 |
| Series (1) |
| GSE130934 |
Transcription analysis for the growth of Haloferax volcanii on L-alanine and ammonium chloride |
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