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Sample GSM239127 Query DataSets for GSM239127
Status Public on Jun 01, 2008
Title Yeast mitochondrial associated RNA prep 04 replicate 3 dye swap
Sample type mixed
 
Channel 1
Source name Mitochondrial associated RNA from WT (CW252) strain labeled with Cyanine-5 (red).
Organism Saccharomyces cerevisiae
Characteristics CW252 WT strain
Mitochondria extracted from CW252 spheroplastic cells
Growth protocol Cell growth overnight at 28°C in galactose rich medium (1% bactopeptone, 1% yeast extract, 2% galactose, 0.1% KH2PO4 and 0.12% (NH4)2SO4) to an OD = 1.0
Extracted molecule other
Extraction protocol Spheroplastic cell are fractionated by differential centrifugation. The pellet corresponding to mitochondria is store at -80°C. RNA associated to mitochondria are then extracted using RNEasy Mini Kit (Quiagen)
Label Cy5
Label protocol 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy5.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.
 
Channel 2
Source name Total RNA extracted from WT (CW252) strain labeled with Cyanine-3 (green).
Organism Saccharomyces cerevisiae
Characteristics CW252 WT strain
Total RNAs
Growth protocol Cell growth overnight at 28°C in galactose rich medium (1% bactopeptone, 1% yeast extract, 2% galactose, 0.1% KH2PO4 and 0.12% (NH4)2SO4) to an OD = 1.0
Extracted molecule total RNA
Extraction protocol Hot phenol extract procedure and RNEasy Mini Kit (Quiagen)
Label Cy3
Label protocol 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy3.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.
 
 
Hybridization protocol 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65¡C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37¡C. The array slides are then air dryed and ready for scaning.
Scan protocol Scanned on a genepix 4000B scanner (Axon)
Description Biological replicate 3 of 3 (6?), S. cerevisiae Wild Type strain grown on galactose medium at 28°C.
Data processing Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 50000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

VALUE column reports log2(Mitochondrial associated RNA/Total RNA) ratios.
 
Submission date Oct 22, 2007
Last update date Aug 14, 2011
Contact name Stéphane LE CROM
Organization name École normale supérieure
Department Biology Institute - IBENS
Lab Genomic platform
Street address 46 rue d'Ulm
City Paris
ZIP/Postal code 75013
Country France
 
Platform ID GPL6035
Series (1)
GSE9393 Looking for mitochondrial associated RNA

Data table header descriptions
ID_REF ENS feature number
VALUE log2 (Cy5/Cy3)
MEAN_INTENSITY (log2(Cy5) + log2(Cy3)) /2

Data table
ID_REF VALUE MEAN_INTENSITY
1 -0.06 5.61
2 0.1 6.37
3 -0.18 5.64
4 -0.07 5.55
5 -0.58 8.63
6 0.14 4.81
7 -0.06 5.3
8 -0.01 4.78
9 -0.04 5.57
10 0.85 7.13
11 -0.5 9.46
12 0.06 5.25
13 0.15 5.37
14 1.19 7.41
15 -0.04 5.07
16 0 4.73
17 1.15 8.23
18 -0.05 9.9
19 -0.17 4.85
20 -0.06 4.8

Total number of rows: 15743

Table truncated, full table size 240 Kbytes.




Supplementary file Size Download File type/resource
GSM239127.gpr.gz 1.3 Mb (ftp)(http) GPR
GSM239127.tif.gz 11.7 Mb (ftp)(http) TIFF
Processed data included within Sample table

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