Experiment: Cold acclimation
Please note that TAIR stopped accepting new microarray data submissions in June 2005. Newer and more comprehensive microarray data sets are available at GEO, ArrayExpress and NASCArrays.
Experiment Summary
Submission Number	ME00369
TAIR Accession	ExpressionSet:1008805059
Author(s)	Arnd Heyer , Dirk Hincha , Matthew Hannah
Experimental Variables	temperature
Variable Type	Environment
Experiment Category	abiotic treatment
Experiment Goals	response to cold
Date of Completion	2005-01-08
Description	This experiment investigates the effect of 14 days cold acclimation at 4C on greenhouse grown Col-0 plants at the bolting stage. We also hybridised our samples to MWG 25-k oligo arrays to validate the Affymetrix data. A description of the MWG experiment and the datafiles are available in the experiment directory on the ftp.
Data Counts	Number of Slides     Number of Replicate Sets     Number of BioSamples 6   2   2
Sample Information
Sample: Non-acclimated Treatment Description:   No treatment Sample Description:   Whole shoot pooled from 10 soil-grown plants Organism:   Arabidopsis thaliana Tissue Origin :   seed Germplasm:   CS1092 Plant Structure Keywords:   shoot system Plant Structure Description:   shoot Development Keywords :   IL.00 inflorescence just visible stage   Developmental Stage Description:   43-46d after germination, plants just started to bolt (inflorescence 1-2cm) Sample Type :   reference Probe Type (concentration) :   polyA RNA( unknown) Extraction Protocol:   Trizol Labeling Protocol:   Affymetrix
Environmental Conditions & Treatments
condition type name value duration variable control  no treatment      yes  growth media substrate  soil    43-45 days  no  light  light intensity  200 uE/cm2 s  43-45 days  no  light  photoperiod  16 hr  43-45 days  no  temperature  day temperature  20 C  43-45 days  no  temperature  night temperature  18 C  43-45 days  no  tissue  age  43-45 days    no
Sample: Cold-acclimated Treatment Description:   Transferred to 4 oC growth chamber, 16h photoperiod (90?E) for 14d. Sample Description:   Whole shoot pooled from 10 soil-grown plants Organism:   Arabidopsis thaliana Tissue Origin :   seed Germplasm:   CS1092 Plant Structure Keywords:   shoot system Plant Structure Description:   shoot Development Keywords :   IL.00 inflorescence just visible stage   Developmental Stage Description:   43-46d after germination, plants just started to bolt (inflorescence 1-2cm) Sample Type :   test Probe Type (concentration) :   polyA RNA( unknown) Extraction Protocol:   Trizol Labeling Protocol:   Affymetrix
Environmental Conditions & Treatments
condition type name value duration variable temperature  cold  4 C  14 days  yes  growth media substrate  soil    43-45 days  no  light  light intensity  200 uE/cm2 s  43-45 days  no  light  photoperiod  16 hr  43-45 days  no  temperature  day temperature  20 C  29-31 days  no  temperature  night temperature  18 C  29-31 days  no  tissue  age  43-45 days    no
Slide Information
Slide Details
Slide Name External ID Replicate (id :name) Replicate type Control replicate Sample Experimental variables Label Get Data COLNA1 N/A 1786: Non-acclimated biological  N/A  Non-acclimated no treatment   Biotin COLNA2 N/A 1786: Non-acclimated biological  N/A  Non-acclimated no treatment   Biotin COLNA3 N/A 1786: Non-acclimated biological  N/A  Non-acclimated no treatment   Biotin COLACC1 N/A 1787: Cold-acclimated biological  1786   Cold-acclimated cold (4 C, 14 days)   Biotin COLACC2 N/A 1787: Cold-acclimated biological  1786   Cold-acclimated cold (4 C, 14 days)   Biotin COLACC3 N/A 1787: Cold-acclimated biological  1786   Cold-acclimated cold (4 C, 14 days)   Biotin
Analysis Info
Slide : COLNA1
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.568
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	2.01
Background average (standard deviation)	54.5 (0.52)
Central minus: Count (Average)	9 (4491.0)
Corner minus: Count (Average)	32 (5473.0)
Corner plus: Count (Average)	32 (59.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Slide : COLNA2
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.657
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	1.96
Background average (standard deviation)	53.05 (0.57)
Central minus: Count (Average)	9 (5006.0)
Corner minus: Count (Average)	32 (6579.0)
Corner plus: Count (Average)	32 (63.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Slide : COLNA3
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.441
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	2.35
Background average (standard deviation)	60.13 (0.51)
Central minus: Count (Average)	9 (10123.0)
Corner minus: Count (Average)	32 (11956.0)
Corner plus: Count (Average)	32 (98.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Slide : COLACC1
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.763
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	1.97
Background average (standard deviation)	52.61 (0.61)
Central minus: Count (Average)	9 (3739.0)
Corner minus: Count (Average)	32 (5609.0)
Corner plus: Count (Average)	32 (69.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Slide : COLACC2
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.506
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	2.22
Background average (standard deviation)	60.75 (0.49)
Central minus: Count (Average)	9 (4624.0)
Corner minus: Count (Average)	32 (6493.0)
Corner plus: Count (Average)	32 (70.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Slide : COLACC3
Normalization Info :
User Normalization Description:	GCOS/MAS5 (although GCRMA v1.1.0, using the gcrma package (www.bioconductor.org) was used for publication)
Scaling Factor:	0.335
Analysis Info:
Scanning software	GCOS
Scanning hardware	GeneChip Scanner 3000
Scanning parameters	2.5 pixel size
Analysis Parameters:
TGT value	100.0
SRT	0.0
Noise	2.81
Background average (standard deviation)	74.13 (0.99)
Central minus: Count (Average)	9 (12324.0)
Corner minus: Count (Average)	32 (14881.0)
Corner plus: Count (Average)	32 (107.0)
Alpha1	0.05
Alpha2	0.065
TAU	0.015
Array Information
Array Info :
Name:	Affymetrix 25k
Manufacturer:	Affymetrix
Platform type :	in situ synthesized oligos
Surface type :	glass
Number of elements :	22814
Slides:	all slides had this array design
Hybridization Info: