Comment[ArrayExpressAccession] E-GEOD-9698
Investigation Title De-regulation of maize C4 photosynthetic development in a mesophyll cell defective mutant: Bundle sheath and Mesophyll
Comment[Submitted Name] De-regulation of maize C4 photosynthetic development in a mesophyll cell defective mutant: Bundle sheath and Mesophyll
Publication Title Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant.
Publication Author List Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP
Publication DOI
PubMed ID 18258693
Experimental Design
Experimental Design Term Source REF
Public Release Date 2008-01-31
Experiment Description During Zea mays (maize) C4 differentiation, mesophyll (M) and bundle sheath (BS) cells accumulate distinct sets of photosynthetic enzymes, with very low photosystem II (PSII) content in BS chloroplasts. Consequently, there is little linear electron transport in the BS and ATP is generated by cyclic electron flow. In contrast, M thylakoids are very similar to those of C3 plants and produce the ATP and NADPH that drive metabolic activities. Regulation of this differentiation process is poorly understood but involves expression and coordination of nuclear and plastid genomes. Here, we identify a recessive allele of the maize Hcf136 homologue that in Arabidopsis thaliana functions as a PSII stability or assembly factor located in the thylakoid lumen. Proteome analysis of the thylakoids and electron microscopy reveal that Zm hcf136 lacks PSII complexes and grana thylakoids in M chloroplasts, consistent with the previously defined Arabidopsis function. Interestingly, hcf136 is also defective in processing the full-length psbB-psbT-psbH-petB-petD polycistron specifically in M chloroplasts. To determine whether the loss of PSII in M cells affects C4 differentiation, we performed cell-type specific transcript analysis of hcf136 and wild-type seedlings. The results indicate that M and BS cells respond uniquely to the loss of PSII, with little overlap in gene expression changes between data sets. These results are discussed in the context of signals that may drive differential gene expression in C4 photosynthesis. To explore the disruption of PSII activity on gene expression, transcript profiles from separated M and BS cells were examined using two-label microarray analysis. Total RNA was isolated from the second leaves of mutant and wild-type silbings. Six biological replicates were used to compare wild-type and mutant transcript profiles in separate M and BS experiments. To maximize biological replication, different seedling pools were used for each of the 12 hybridizations. Microarray experiments and analyses were performed using the Genisphere MPX900 kit and the Maize Array Consortium oligonucleotide platform (GPL5439; GPL5440). Feature intensity values were log-transformed and corrected for local background signal, and a LOWESS procedure (Dudoit et al., 2002) was used to normalize between channels. Features with either low or saturating signal intensity were discarded from further analysis. High expression filtering was less stringent to avoid elimination of previously characterized, high abundance, C4 cell-specific transcripts. After filtering, features that were not assigned an MZ number by the Maize Array Consortium were discarded from further analysis. The moderated t-test (Smyth, 2004) using the R package limma was applied to identify differentially expressed genes. The p-values for each test (gene) were converted to q-values for false discovery rate analysis as described by Storey et al. (2004). To avoid confounding treatment effects associated with direct comparisons of M and BS transcriptomes (Sawers et al., 2007), comparisons were only made using the same cell type across the hcf136 and wild-type sibling genotypes. Bundle sheath (BS) Samples: GSM245063-GSM245164 Mesophyll (M) Samples: GSM245165 - GSM245206
Date of Experiment
Term Source Name EFO
Term Source Version
Term Source File http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl
Person Last Name Brutnell Covshoff Majeran Liu Kolkman van Wijk Brutnell
Person First Name Thomas Sarah Wojciech Peng Judith Klaas Thomas
Person Mid Initials P. M J P
Person Email
Person Affiliation Boyce Thompson Institute for Plant Research
Person Phone
Person Fax
Person Address Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
Person Roles submitter
Person Roles Term Source REF
Person Roles Term Accession Number
Normalization Type
Normalization Term Accession Number
Normalization Term Source REF
Replicate Type
Replicate Term Accession Number
Replicate Term Source REF
Quality Control Type
Quality Control Term Accession Number
Quality Control Term Source REF
Protocol Name P-GSE9698-19 P-GSE9698-15 P-GSE9698-22 P-GSE9698-24 P-GSE9698-20 P-GSE9698-18 P-GSE9698-2 P-GSE9698-7 P-GSE9698-4 P-GSE9698-6 P-GSE9698-23 P-GSE9698-3 P-GSE9698-5 P-GSE9698-11 P-GSE9698-21 P-GSE9698-1 P-GSE9698-12 P-GSE9698-14 P-GSE9698-9 P-GSE9698-13 P-GSE9698-16 P-GSE9698-17 P-GSE9698-8 P-GSE9698-10 P-GSE9698-30 P-GSE9698-29 P-GSE9698-27 P-GSE9698-26 P-GSE9698-33 P-GSE9698-25 P-GSE9698-32 P-GSE9698-28 P-GSE9698-34 P-GSE9698-31
Protocol Description ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_039_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_049_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_051_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_052_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_049_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_052_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_118_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_131_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_120_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_124_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_055_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_126_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_131_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_118_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_050_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_117_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_128_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_048_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_133_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_039_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_050_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_051_A = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_120_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} ID_REF =
VALUE = -[INV_VALUE]
LAB_ID = The unique numerical identifier assigned for statistical analysis
Cy5 Signal Median = Raw data showing Cy5 channel signal median
Cy5 log(SMD,2) = {=log(Cy5signalmedian,2)}
Cy5 Background Median = Raw data showing the Cy5 channel background median
Cy5 log(BMD,2) = {=log(Cy5backgroundmedian,2)}
CL5_base2 = log2 transformed and background-subtracted value for Cy5 {= log2(signal median)-log2(background median)}
Cy3 Signal Median = Raw data showing the Cy3 channel signal median
Cy3 log(SMD,2) = {=log(Cy3signalmedian,2)}
Cy3 Background Median = Raw data showing the Cy3 background median
Cy3 log(BMD,2) = {=log(Cy3backgroundmedian,2)}
CL3_base2 = log2 transformed and background-subtracted value for Cy3 {= log2(signal median)-log2(background median)}
M_117_B = Difference between CL5 and CL3 {=CL5_base2 - CL3_base2}
A = Average of CL5 and CL3 {=(CL5_base2 + CL3_base2)/2}
LOWESS = The LOWESS residual when fitting LOWESS curve
CL5(backTransf) = {=2^CL5_base2}
CL3(backTransf) = {=2^CL3_base2}
INV_VALUE = The LOWESS-normalized log2 ratio between CY5 and CY3 {=M - LOWESS} See: Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8, 12. Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C. RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405. BS strands were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591. M protoplasts were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591. Grown for 13 days in growth chamber (16h/8h light/darkness, 50% humidity, 28°C, approx 40 µmol/s-1/m-2) in soil. BS cells collected from second leaves of 3rd leaf emerging stage seedlings. Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C. Lowess normalization. See: Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8, 12.
Protocol Software
Protocol Hardware
Protocol Contact
Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction grow labeling labeling feature_extraction feature_extraction
Protocol Term Source REF
Protocol Term Accession Number
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Experimental Factor Term Accession Number
Comment[SecondaryAccession] GSE9698
Comment[GEOLastUpdateDate] 2008-05-04
Comment[GEOReleaseDate] 2008-02-01
Comment[ArrayExpressSubmissionDate] 2007-11-27
SDRF File E-GEOD-9698.sdrf.txt