The MEEBOChip feature set is a modular collection of 70-mer oligos partitioned 
into a total of 101 384-well plates.  This includes 96 384-well plates which 
contain oligos that primarily measure mouse genes (plates 001-096), as well as 5 
384-well plates which contain features designed to measure spiked-in doping 
control transcripts (plates DC001-005).
 
Plates 001 to 096 are further partitioned as follows:
1. plates 001-CTRL, 002-CTRL, and 004-MCC contain positve control features as 
detailed below and as specified in the comment field accompanying each oligo 
within the Excel document. These are crucial plates to include in the order 
specified by the plate name as detailed below.
2. plates 002-CTRL through part of plate 050-MCC include mouse exonic probes 
designed using genomic annotations derived from the MouSDB3 annotation project 
at Rockefeller University (scl)
3. the latter part of plate 050-MCC through part of 069-MCC include mouse exonic 
probes designed using genomic annotations derived from the loc2ucsc annotation 
project at UCSF/Stanford University, these complement item #2 above with a small 
degree of overlap (scl0)
4. the latter part of plate 069-MCC through part of 082-MCC include mouse probes 
designed from mouse mRNA sequences (instead of exonic sequences annotated within 
the genome using transcripts), and accordingly, these 70mers may span exon 
junctions (scl00)
5. the latter part of plate 082-MCC through plate 093-MCC include 70mers 
designed to detect alternatively spliced exons based on a unified annotation 
project combining 5 sources of supporting data (scl000)
 
6. plate 094-MCC contains (a) non-coding RNA pairs exhibiting cis-antisense 
transcription similar to those described by Yelin R et al 2003 (scl0000), (b) 
probes designed to detect microRNAs when used with corresponding templates 
during cDNA synthesis (miRNA-TT), (c) mitochondrial DNA probes, (d) ribosomal 
RNAs, (e) transgenic and vector sequences such as GFP, YFP, etc.
7. plate 095-MCC contains regional probes for V,D, J and C regions of BCR and 
TCR loci
8. plate 096-MCC contains probes for murine viral sequences 
 
We strongly recommend that users include at a minimum plates 001-CTRL through 
093-MCC as these plates contain exonic and genic probes for most mouse genes.  
 
The recommended nominal printing order is specified in the numbering of the 
384-well plates.  Assuming that users employ a 48-tip printing configuration on 
their arrayers with a sector width of 28 or 29 features, this printing order 
will result in the placement of positive and negative control features at 
specific locations to simplify processes such as:
 
(a) PMT adjustment during image acquisition (using highly expressed and variably 
expressed genes placed within the first row of each sector), 
(b) easier spot-finding during gridding (using replicas of Ubiqutin C as a 
brightly expressed "corner markers"), 
(c) improved normalization including intensity dependent normalization using 
Loess shemes by distributing features of variable intensity uniformly between 
sectors
(d) better negative control of experiments using uniform distribution of 
negative control features including random sequences and empty wells
(e) better positive control of experiments using uniform distribution of 
positive control features including:
     (1) partially mismatched probes containing a range of centrally anchored 
and randomly distributed nucleotide identity (to allow control for hybridization 
and wash stringencies), 
     (2) tiling probes spanning 5' to 3' (to control for end-biased 
amplification and labeling strategies), 
     (3) replication controls for assessing reproducibility
 
Doped control features (DC plates):
There are five 384-well plates which contain features designed to measure 
spiked-in doping control transcripts that not all users may employ (plates 
DC001-DC005).  Nevertheless, the MEEBOChip Consortium strongly recommends all 
users to include these 5 latter DC plates within printings if possible to allow 
for standardization of experimental conditions and data analyses.  These 
analyses include robust normalization, dynamic range calculations, estimations 
of sensitivity, specificity, and linearity of intensity measurements just to 
name a few.  We recommend integrated the 5 DC plates within the print order, but 
not before plate 0004.  To ensure uniform distribution of doped control We 
recommend printing DC001 immediately after plate 004-MCC, DC002 after plate 
027-MCC, DC003 after plate 050-MCC, DC004 after plate 073-MCC, and finally DC005 
after plate 096-MCC.