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Sample GSM5610353 Query DataSets for GSM5610353
Status Public on Sep 28, 2022
Title WT_0h.1_control for DacA
Sample type RNA
 
Source name PCC6803, WT, LC, replicate 1
Organism Synechocystis sp. PCC 6803
Characteristics genotype: WT
treatment: low 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)
GSE185297 The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [dacA]
GSE185298 The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803

Data table header descriptions
ID_REF
VALUE log2 normalized signal intensity

Data table
ID_REF VALUE
1 14.5105613407712
2 9.4077688629713
3 9.40518835755418
4 9.66199826578228
5 9.96729573909477
6 13.4695196276225
7 9.40650078277346
8 10.8733207027336
9 9.40650078277346
10 14.5057846467428
11 9.33224157287147
12 10.2196269001472
13 8.8360318745703
14 10.2666062796542
15 9.07681375706517
16 9.45481193263491
17 9.27417516869566
18 9.35109969928788
19 10.6486200396609
20 9.29942801118768

Total number of rows: 62334

Table truncated, full table size 1383 Kbytes.




Supplementary file Size Download File type/resource
GSM5610353_US90900275_257576410045_S01_GE1_107_Sep09_1_1.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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