All files are provided as tab-delimited text files.

Filtered data (2.5 MB)

-Spot ID -Gene name -Raw ratio data for each fraction -Median reference intensity (the median of the background-subtracted reference channel fluorescence intensities; roughly a measure of the signal strength for that spot)

Doping control normalized data (4.6 MB)

-Spot ID -Gene name -Normalized ratio data for each fraction -Median reference intensity

Final data set (2.0 MB)

-Spot ID -Unique ID (I gave each spot a unique ID number to distinguish the profiles generated by duplicate spots) -Type of feature -Gene name -Length (ORF length for mRNAs, total length for noncoding RNAs) -Max length (feature length plus lengths of adjacent intergenic regions) -Overlaps (1 if feature overlaps another annotated feature) -Similarities (number of other features with significant sequence identity) -Normalized ratio data for each fraction -Median reference intensity -Number of missing data points in the profile -Maximum ratio value -Median ratio value -Maximum value divided by median value (roughly a measure of signal to background) -Number of peaks

Gaussian fit (326 kb)

-Spot ID -Unique ID -Number of Peaks -Precise mobility of each peak in mm from tallest to shortest peak

RACE primers (569 kb)

-ORF name -5'-Inner RACE primer sequence -Tm of that sequence -5'-Outer RACE primer sequence -Tm of that sequence -3' RACE primer sequence -Tm of that sequence

RACE results (6 kb)

-Gene name -3'-UTR length -5'-UTR length -Intron length -ORF length (non-intron corrected) -Total transcript length (UTRs + ORF - Intron)

Figure 3 data (5 kb)

-Gene name -Virtual Northern mobility -RACE measured length -Log of RACE measured length -Calculated Virtual Northern length -Percent difference between RACE measured length and Virtual Northern measured length

Mobility to length (506 kb)

-Spot ID -Unique ID -Precise mobility of each peak in mm from tallest to shortest -Calculated Virtual Northern length

ORF info (406 kb)

-Systematic feature name -Gene name -Feature type -Chromosome -Strand (Watson or Crick) -Coding length (ORF length for mRNAs, total length for noncoding RNAs) -Chromosomal coordinates of the feature -Max -Overlaps (1 if the feature overlaps another) -Lengths of intergenic regions to the left and right of the feature -Max length (sum of coding length and left and right)

Data match to genome (1.1 MB)

-Systematic feature name -Gene name -Feature type -Chromosome -Chromosomal coordinates of the feature -Coding length -Spot ID -Unique ID -Assignment of the top three peaks to a specific gene -Virtual Northern measured lengths for all peaks

Spot to gene (297 kb)

-Gene name -Averaged transcript length -Number of different peaks assigned to that transcript -Spot ID of one of the peaks assigned to that gene -Unique ID of that spot -Length calculated from that peak

Transcript lengths (135 kb)

-Systematic name -Gene name -Feature type -Coding length (ORF length for mRNAs, total length for noncoding RNAs) -Virtual Northern measured transcript length

Test run data (95 kb)

-Spot ID -Test run length (not truly length calibrated) -Virtual Northern length

Accuracy (6 kb)

-Gene name -ORF length -Traditional Northern length -Virtual Northern length

ORF greater than transcript list (4 kb)

-Systematic name -Gene name -ORF length -Virtual Northern length

Adjacent ORFs (4 kb)

-Orientation of ORFs in locus -Overall conclusion -Names of ORFs in locus -Conclusions based on synteny, RT-PCR, and RACE data -Crosshybridization potential of locus

Transcript greater than max length list (8 kb)

-Systematic name -Gene name -ORF length -Max length -Virtual Northern length -Comment

Introns (8 kb)

-Spot ID for all intron spots -Unique ID -Comment -Measured lengths for each peak -Name of ORF containing the intron -ORF length -Measured lengths for each peak from the ORF spot -Intron length -Sum of intron and measured length from ORF (length of unspliced transcript)

Intergenics list (59 kb)

-Systematic name -Genome order -Chromosome -Chromosomal position -Length of intergenic region -Spot ID of spot lying within the intergenic region -Unique ID of that spot -Gene to the left of that intergenic region -Transcriptional orientation of that gene -Gene to the right of that intergenic region -Transcriptional orientation of that gene -Virtual Northern measured length -T < Len (1 if the length of the intergenic region is greater than the Virtual Northern measured length) -Median reference intensity -Number of other features with significant sequence identity

Questionable ORFs list (17 kb)

-Name of ORF from MIPS questionable ORFs list -Conclusion -ORF length -Max length -Virtual Northern measured length

Observed minus expected (444 kb)

-Systematic name -Gene name -ORF length -Virtual Northern length -Expected length based on the average relationship between ORFs and transcripts -Difference between observed and expected lengths -GO annotations for the gene

T values (43 kb)

-GO annotation -Number of genes with that annotation -T-value for that annotation -Type of GO annotation (molecular function, biological process, or cellular component)

Spot to spot sequence identities (391 kb)

-Spot ID -Gene name -Chromosome -Chromosomal position -BLAST hit name -Percent sequence identity between query and target -BLAST hit gene name -BLAST hit chromosome -BLAST hit chromosomal position -Number of hits for that query

Homologous families (3 kb)

-Each column is a list of spots with a high degree of sequence homology to the other spots in the same column