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Sample GSM1938083 Query DataSets for GSM1938083
Status Public on Nov 13, 2015
Title PCC6803_#642_isoprene_producer_rep2
Sample type RNA
 
Source name PCC6803_#642_isoprene_producer
Organism Synechocystis sp. PCC 6803
Characteristics genotype: ispS+
Treatment protocol no special treatment was applied
Growth protocol Axenic cultures of the cyanobacterium Synechocystis sp. PCC 6803 were grown photoautotrophically under continuous illumination of 175 µmol photons/m2 s (warm white fluorescent tubes, Osram L 32) at 29° C. For isoprene production, cultures were pre-cultivated at high CO2 (5%) in BG11 medium. After 24 h, the pre-cultures were used to inoculate the main cultures in closed 0,1 L Schott flasks at OD750 of about 1 in 50 ml of BG11 supplemented with 50 mM NaHCO3. The cultures were incubated at 30° C, with an illumination of about 150 µmol photons/m2 s under continuous stirring with 150 rpm. After 24 h, samples were taken for RNA isolation
Extracted molecule total RNA
Extraction protocol Synechocystis 6803 cells were collected by centrifugation (4000 rpm, 4°C, 4 min) and the cells were dissolved in 500 µl PGTX solution (Pinto et al., 2009) with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine thiocyanate, 0.48 M guanidine hydrochloride. The samples were incubated for 15 min at 65°C and put on ice for 5 minutes. After addition of 500 µl chloroform/isoamylalcohol (24:1), samples were incubated at room temperature for 10 minutes. Samples were centrifuged at 6,000 rpm, 20°C for 10 min. The upper aqueous phase was transferred into a new tube and the same volume of chloroform/isoamylalcohol (24:1) was added and mixed. Samples were centrifuged as described above and the aqueous phase removed again and combined with an equal volume of isopropanol. After gently inverting the tube, RNA was precipitated over night at -20°C. RNA was pelleted through centrifugation (13,000 rpm, 4°C, 30 min). The pellet was washed with 1 ml of 70% ethanol (13,000 rpm, 20°C, 5 min), allowed to air dry for approximately 10 min and resuspended in 30 µl H2O.
Label Cy3
Label protocol The RNA was labeled directly, without cDNA synthesis with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.
 
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 protocol GE1_107_Sep09 for one-color arrays
Data processing Raw data were processed with the R package Limma. Median signal intensity was normexp background corrected and quantile normalized
 
Submission date Nov 12, 2015
Last update date Nov 13, 2015
Contact name Jens Georg
E-mail(s) [email protected]
Organization name University of Freiburg
Street address Schänzlestr. 1
City Freiburg
ZIP/Postal code 79104
Country Germany
 
Platform ID GPL21131
Series (1)
GSE74940 CO2-neutral isoprene production using the cyanobacterium Synechocystis sp. PCC 6803

Data table header descriptions
ID_REF
VALUE pre-processed log2 signal intensity

Data table
ID_REF VALUE
1 14.92394936
2 7.370886083
3 7.554274995
4 9.106292212
5 11.2507923
6 11.58168151
7 7.423301241
8 10.68430182
9 8.402571115
10 15.20824233
11 7.461658009
12 10.00161447
13 6.548586734
14 9.693796747
15 7.639496791
16 7.977761115
17 7.350316266
18 9.035545739
19 9.470448535
20 7.370886083

Total number of rows: 62334

Table truncated, full table size 1078 Kbytes.




Supplementary file Size Download File type/resource
GSM1938083_US90900275_257576410002_S01_GE1_107_Sep09_2_2.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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