NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1150998 Query DataSets for GSM1150998
Status Public on May 30, 2013
Title LDLLL_CT13.5_day2
Sample type RNA
 
Source name whole cell
Organism Synechocystis sp. PCC 6803
Characteristics light regime: LDLLL
sample time point: CT13.5
Treatment protocol Cell concentrations were measured by determining the optical densities of the culture at 750 nm (OD750). Cultures were synchronized with three cycles of light/dark 12h:12h prior sampling.
Growth protocol The glucose-tolerant and motile wild-type strain of Synechocystis sp. PCC 6803 originally obtained from S. Shestakov (Moscow State University, Russia) was routinely grown photoautotrophically in BG11-medium at 30°C under continuous illumination with white light of 80 µmol of photons/m^2s and a continuous stream of air.
Extracted molecule total RNA
Extraction protocol 15 ml of cyanobacterial culture were filtered rapidly through Supor 0.45 µm membrane filters (PALL), immediately stowed with TRIzol reagent (Invitrogen) and frozen in liquid nitrogen. Total RNA samples stored at -20°C were transferred directly to a 65°C water bath for 5 min, mixed with 0.2 ml chloroform per ml of TRIzol and incubated for further 15 min. The dissolving of the membrane and lyses of the cells were supported by vortexing. Centrifugation at maximum speed for 10 min at 4°C separated the phases. The RNA in the supernatant was precipitated by adding 1 volume of isopropanol. Finally isolated total RNA was treated with RNase-free Turbo™DNase (Ambion) by following the manufacturer's instructions, resulting in 40 µl purified RNA solution.
Label Cy3
Label protocol The 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.
 
Hybridization protocol The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.5 µg of labeled RNA.
Scan protocol Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays.
Description subjective night
Data processing Raw data were processed using GNU R and MATLAB. Signal intensity was probe-wise LOS normalized, using a oscillation threshold of 0.7.
 
Submission date May 29, 2013
Last update date May 30, 2013
Contact name Christian Johannes Beck
Organization name Humboldt-University Berlin
Department Institute for Theoretical Biology
Lab AG Axmann
Street address Invalidenstrasse 43
City Berlin
State/province Berlin
ZIP/Postal code 10115
Country Germany
 
Platform ID GPL15867
Series (1)
GSE47482 A daily temporal program for rhythmic expression of protein-coding and non-coding genes in response to light and dark in Synechocystis sp. PCC 6803

Data table header descriptions
ID_REF
VALUE log2 intensities, background subtracted, normalized according to a least oscillating probe set

Data table
ID_REF VALUE
12 11.98465
13 11.22592
14 11.17448
15 12.43679
16 11.16337
17 11.10699
18 11.7201
19 12.04955
20 12.87859
21 11.90159
22 11.15457
23 12.26152
24 11.11398
25 13.21554
26 11.29661
27 11.59925
28 18.98572
29 11.14127
30 11.66205
31 10.94691

Total number of rows: 42292

Table truncated, full table size 594 Kbytes.




Supplementary file Size Download File type/resource
GSM1150998_48h_LDLLL_CT13_2.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap