|
| Status |
Public on Sep 28, 2022 |
| Title |
WT_3h.1 |
| Sample type |
RNA |
| |
|
| Source name |
PCC6803, WT, 3 h HC, replicate 1
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
genotype: WT
treatment: 3 h high carbon conditions
|
| Treatment protocol |
Cells were shifted to LC conditions at an OD750 of 0.8-1. Following the shift, the cultures were sampled after 3 h and 24 h for the transcriptome analysis by filtration.
|
| Growth protocol |
Liquid cultures in buffered BG11 media at 30°C under constant light with an intensity of 130 µmol photons m-2 s-1 and constant bubbling. The media for High Carbon (HC) and Low Carbon (LC) cultures was buffered with TES/KOH until a pH of 8 and 7. HC cultures were bubbled with CO2-enriched air (5%, v/v), while LC cultures with ambient air (0.04% CO2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using a hot phenol-based protocol.
|
| Label |
Cy3
|
| Label protocol |
DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in: Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.
|
| |
|
| Hybridization protocol |
The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays
|
| Scan protocol |
Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays
|
| Description |
Slide Format: 8 x 60 K
Slide Layout: IS-62976-8-V2
Design ID: 75764
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.
|
| |
|
| Submission date |
Oct 04, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Wolfgang R. Hess |
| E-mail(s) |
[email protected]
|
| Phone |
49-761-2032796
|
| Organization name |
University of Freiburg
|
| Department |
Institute of Biology III
|
| Lab |
Genetics & Experimental Bioinformatics
|
| Street address |
Schänzlestrasse 1
|
| City |
Freiburg |
| State/province |
Baden-Würtemberg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21131 |
| Series (2) |
| GSE185294 |
The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [sbtB] |
| GSE185298 |
The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 |
|
