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Platform GPL10232 Query DataSets for GPL10232
Status Public on Apr 06, 2010
Title Washington University School of Medicine Microarray Core Brugia malayi microarray V.2
Technology type spotted oligonucleotide
Distribution non-commercial
Organisms Brugia malayi; Onchocerca volvulus; Wuchereria bancrofti; Wolbachia endosymbiont strain TRS of Brugia malayi
Manufacturer Washington University School of Medicine Microarray Core
Manufacture protocol The Brugia malayi Version 2 (V.2) array contains 18,153 oligonucleotides, 878 based on Wuchereria bancrofti ESTs, 1,016 based on Onchocerca volvulus gene indices, 804 from the Wolbachia complete genome, and the remaining 15,455 based on B. malayi ESTs, TIGR gene indices, TIGR gene models, and L3 ESTs.

Oligonucleotide selection:
We patterned our oligo selection algorithm after PICK70 (J. DeRisi, personal communication). The algorithm utilizes two input files in oligo selection: the first is a fasta format file of all genes to be used for oligo selection and the second is a fasta format file of the entire genome sequence. For the input gene sequences, we bias selection of oligos to the 3?-most 1000 bases of sequence (for genes greater than 1000 bp in length) by pre-masking all sequences upstream of this cutoff. The initial portion of the oligo selection routine is designed to mask out any repetitive sequence elements or any highly similar portions (e.g. to other genes) of the input gene sequences. This masking is accomplished by BLAST comparison of genes to genome, using a stringent cut-off to mask out any sequence with 70% or greater similarity to any other sequence in the genome that extends over 66% of the desired oligo length. Once the input gene sequences are masked, they are subjected to the oligo selection algorithm. Here, the algorithm examines each sequence one at a time, starting from base number one and looking at the first contiguous 65 bases (or whatever the input desired oligo length is) with respect to the following parameters, in order:
1.Ensures that all of the bases being considered are either A, C, G or T (e.g. no N?s or masked bases are contained in the putative oligo sequence). If all bases do not conform, the algorithm shifts to base two of the sequence and reiterates the check.
2.If all bases conform, examines the input bases for whether they collectively fall in the desired G/C range of the oligo. If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one, etc.
3.If all bases and the G/C range conform, the algorithm examines the input bases for whether they collectively fall in the desired Tm range of the oligo. If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one. The Tm calculation currently used is nearest-neighbor calculation.
For the next series of checks, the algorithm assigns ?scores? for the input oligo, rather than outright rejection of non-conforming sequence. The score assigned indicates the relative deviation of the oligo from the desired parameter, where a score of zero means that the oligo conforms to the parameter.
4.If the bases conform to the Tm range desired, then the algorithm examines the oligo for percentage of G/C content across the oligo, using a sliding window. If any window has a G/C content that deviates from the average G/C content of all windows by more than a specified amount (the default is 10% of the overall oligo Tm) the oligo score is incrementally increased. This ensures uniformity of G/C content across the oligo.
5.Once the sequence G/C uniformity is scored, the algorithm examines the oligo for homopolymers greater in length than the cut-off length set by the user (we typically stipulate that the same base cannot occur more than 4 times in a row or the oligo score is increased from zero). The number of homopolymer runs in the oligo greater than the cut-off length and the total number of bases encompassed by these runs is also determined and stored.
6.Once the homopolymer content is assessed, the algorithm calculates secondary structure potential. This is done using a fasta comparison of the sequence to itself. The optimal score of the fasta alignment is used here as the score reported for the oligo. An optimal fasta score of zero indicates no potential for self-annealing. The optimal score increases as more regions of potential self-alignment are found. Our examination of many such alignments indicates that oligos with a reverse fasta score lower than 100 lack significant secondary structure.
7.If the algorithm passes through all these checks with the oligo starting at base one of the input sequence, it writes that oligo and its scores to a temporary database and starts over with the next input oligo (bases 2-66 in this example). The algorithm reiterates over the entire input gene and then passes to the next gene.
8.In some stretches of input sequence, multiple oligos will result that differ by only one base in succession, but all conform to the desired oligo parameters. In these cases, the algorithm selects the best scoring sequence for all parameters and selects it as the best oligo sequence representing a particular region.
9.In some input genes, the algorithm may not find any oligos within the desired Tm range. In these cases, the algorithm will lengthen or shorten the oligo length according to the length range input, and re-iterate at each length to determine whether the desired Tm range can be met. If not, the algorithm selects the best oligo that falls outside the range, with the corresponding Tm appearing in the final output file.
10.The final output of the algorithm is a text document containing the optimal oligo for each gene examined, including the oligo names (gene name plus oligo start position as an extension) and sequences, followed by the output of all parameter scores for that sequence
For genes that do not result in an oligo selection, we manually examine the input sequences and then relax certain algorithmic parameters in order to select an oligo (typically we relax the constraint on similarity in the initial masking step, up to 80% identity). In some instances, no oligo that uniquely represents a gene can be found since no sufficient length of the gene sequence is left unmasked due to gene family similarities at the nucleotide level.
Oligos were synthesized from the consensus sequence of selected clusters (n=3569) by standard methods by Illumina (San Diego, CA). The oligonucleotides (50nM in 3x SSC with 0.75M betaine) were printed in duplicate on MWG Epoxy slides (MWG Biotech Inc, High point, NC) by a locally constructed linear servo arrayer.
 
 
Submission date Mar 19, 2010
Last update date Apr 06, 2010
Contact name Uta StrĂ¼bing
Organization name University Hospital Bonn
Department Institute for Medical Microbiology, Immunology and Parasitology
Street address Sigmund-Freud-Str. 25
City Bonn
ZIP/Postal code 53105
Country Germany
 
Samples (38) GSM524476, GSM524477, GSM524478, GSM524479, GSM524480, GSM524481 
Series (3)
GSE20976 Tetracycline-treated Litomosoides sigmodontis vs. untreated control Litomosoides sigmodontis
GSE34976 Effect of Doxycycline on Wolbachia and Brugia malayi adult female worms in vivo
GSE68301 Comparative Analysis of Gene Expression Profiles in Infective and Developing Larvae of Brugia malayi and Brugia pahangi

Data table header descriptions
ID
Oligo_Name Oligo name
GB_ACC GenBank accession
ORF Locus tag
SPOT_ID
SEQUENCE Oligo sequence
Model_Name Model name or EST from which the oligo was designed
Oligo_Source Oligo source
Oligo_Best_Hit Oligo best hit (nraa) or annotation
Blastn_Match Single best Blastn match (e<0.0005,id>=80,length>=50) in Brugia CDS
Pub_Locus Pub locus for Blast match Brugia model name
Annotation Annotation for Blast match Brugia model name

Data table
ID Oligo_Name GB_ACC ORF SPOT_ID SEQUENCE Model_Name Oligo_Source Oligo_Best_Hit Blastn_Match Pub_Locus Annotation
1 bm.00205 Bm1_36090 ATACTTGGGAAAAGTGTGCTTCACGATGGTGATACTATTTCTGTCCATAATCCGACATTTTACGC BMC00620 Brugia Chip V1 emb|CAE66932.1| Hypothetical protein CBG12324 [Caenorhabditis briggsae] 14971.m02858 Bm1_36090 Pip kinase protein 1, putative
2 bm.00211 Bm1_52295 TATTTGGAAGAATCTGCTATCTATTTAGCCTTTTCATGTTGGTATCCTAAGGGGTGCCCTGTTCA BMC00634 Brugia Chip V1 emb|CAE72297.1| Hypothetical protein CBG19427 [Caenorhabditis briggsae] 14992.m11424 Bm1_52295 hypothetical protein
3 bm.00229 BMC00726 AAGTTTGGTCTTTTTGGGGAAGGAGGAAAGAACTTATTCTTACAAGTTGGCCGAATTGAAATTCC BMC00726 Brugia Chip V1 ref|NP_001020992.1| C09D4.1b [Caenorhabditis elegans] >gb|AAV34797.1| Hypothetical protein C09D4.1b [Caenorhabditis elegans] no_match
4 bm.00235 Bm1_10970 GAAGGTAATGAGCAAACGGTAGTTGTGAAGGAAGAACAAAAACCGAATGAATGAATTAAGGCTGC BMC00748 Brugia Chip V1 gb|AAR85527.1| 14-3-3b protein [Meloidogyne incognita] 13662.m00125 Bm1_10970 14-3-3-like protein 2, putative
5 bm.00253 Bm1_39300 TACGAAAACTGCAACCTGTTTTCGAACACCGTCGTTCTGATTTGTATTCGTTGATAGTGGTACAG BMC00824 Brugia Chip V1 ref|NP_499556.1| NitFhit family member (nft-1) [Caenorhabditis elegans] >sp|O76463|NFT1_CAEEL Nitrilase and fragile histidine triad fusion protein NitFhit [Includes: Bis(5'-adenosyl)-triphosphatase (Diadenosine 5',5'''-P1,P3-triphosphate hydrolase) (Dinucleosidetriphosphatase) (AP3A hydrolase) (AP3Aase); Nitrilase homolog ] >pdb|1EMS|A Chain A, Crystal Structure Of The C. Elegans Nitfhit Protein >pdb|1EMS|B Chain B, Crystal Structure Of The C. Elegans Nitfhit Protein >gb|AAC39136.1| nitrilase and fragile histidine triad fusion protein NitFhit [Caenorhabditis elegans] >emb|CAB60517.1| Hypothetical protein Y56A3A.13 [Caenorhabditis elegans] 14972.m07562 Bm1_39300 hydrolase, carbon-nitrogen family protein
6 bm.00259 BMC00842 CCAAAATTATTTTACCCTTCCAAATGGGAACGTCCAAACCAAACCTCGTTTTAGTTGAATCCGAA BMC00842 Brugia Chip V1 ref|XP_973403.1| PREDICTED: similar to p47 protein isoform a [Tribolium castaneum] no_match
7 bm.00277 BMC00903 TCCATCATCTTTTATTTAAAGTCCTTTTGCTCGTCAACGTTGCTTTCATATCAAACAGCTCAGCA BMC00903 Brugia Chip V1 gb|AAG09305.3|AF178439_1 embryonic fatty acid-binding protein Bm-FAB-1 [Brugia malayi] >gb|AAR21213.1| FAB1 [Brugia malayi] no_match
8 bm.00283 Bm1_18685 GTGACATGTGCCTGGATGGTGAATTGTTATGGTGGGATCGTATGTTATAATCGTCATGTGAATAC BMC00930 Brugia Chip V1 ref|NP_492001.2| W01A8.4 [Caenorhabditis elegans] >emb|CAA95851.2| Hypothetical protein W01A8.4 [Caenorhabditis elegans] 14379.m00149 Bm1_18685 conserved hypothetical protein
9 bm.00589 Bm1_42170 CGGAATTTTTGGACAAAGCTTTTCCAATTTGGACGTATCCAAAGCACAGTTTCGTTTCTATGTTC BMC02368 Brugia Chip V1 14975.m04370 Bm1_42170 NAD dependent epimerase/dehydratase family protein
10 bm.00595 Bm1_36280 ATTGGACTTGGCTTGTAACCAATCAGGTCTTCACGGCTACAAGTGTTTCAATCTACAAATTACTG BMC02383 Brugia Chip V1 ref|NP_501743.1| T13F2.8 [Caenorhabditis elegans] >sp|Q94051|CAV1_CAEEL Caveolin-1 >gb|AAB48388.1| caveolin >emb|CAB03359.1| Hypothetical protein T13F2.8 [Caenorhabditis elegans] 14972.m06945 Bm1_36280 Caveolin-1, putative
11 bm.00613 BMC02432 TTGATTCTAGCGGTCACCCAAAAATGGATGCTGAATAATGGAACTCTAATTTTCAGTTTCATGAC BMC02432 Brugia Chip V1 emb|CAE60197.1| Hypothetical protein CBG03758 [Caenorhabditis briggsae] no_match
12 bm.00619 Bm1_34100 ATATCAAGAATGACCCGTCTCCAGATGAAGTGAACACCATTGCTGTCGTGGCTGCATTTATAAAA BMC02458 Brugia Chip V1 ref|NP_509186.3| Carbonic AnHydrase family member (cah-5) [Caenorhabditis elegans] >sp|Q10462|CAH5_CAEEL Putative carbonic anhydrase 5 precursor (Carbonate dehydratase 5) >gb|AAA80437.6| Carbonic anhydrase protein 5 [Caenorhabditis elegans] 14961.m05317 Bm1_34100 Eukaryotic-type carbonic anhydrase family protein
13 bm.00637 BMC02537 GTTAATGGAAAACACACCAGCTGTTTTTTTGCTGCATATGTTTGCTGCATCACTGTGCATAATTT BMC02537 Brugia Chip V1 no_match
14 bm.00643 BMC02553 TGAACCGGGCAAGATACCAATGAGTAGTATGAGTCCAATGATTGTTTATAATACTAAAACTGGAA BMC02553 Brugia Chip V1 gb|AAD09400.1| gamma-glutamyl transpeptidase precursor [Brugia malayi] no_match
15 bm.00661 BMC02637 ATGCTCATGTGTATCACCAACATCTCGAACTTATTGGTATGTAACTTCGATTGTTCCAAATTCGT BMC02637 Brugia Chip V1 ref|NP_956494.1| MOB1, Mps One Binder kinase activator-like 1A [Danio rerio] >gb|AAH45952.1| MOB1, Mps One Binder kinase activator-like 1A (yeast) [Danio rerio] >gb|AAH63989.1| MOB1, Mps One Binder kinase activator-like 1A (yeast) [Danio rerio] no_match
16 bm.00667 BMC02664 TCATTCGACACATATATCGGGCTGAGACATATGCTAAATCAATAGCAATAATTTCTGCACCATTT BMC02664 Brugia Chip V1 no_match
17 bm.00973 Bm1_30365 AGGTCATCAGCAGCATCATACCAAATCAGGTTCATATAAAAGGCTGCAACAACGAATAGTAACAA BMC03946 Brugia Chip V1 ref|NP_492111.1| Deacetylase Complex Protein family member (dcp-66) [Caenorhabditis elegans] >emb|CAA96601.1| Hypothetical protein C26C6.5a [Caenorhabditis elegans] >emb|CAB07229.1| Hypothetical protein C26C6.5a [Caenorhabditis elegans] 14952.m01371 Bm1_30365 hypothetical protein
18 bm.00979 Bm1_48340 GCATTTAACTGTAAGCAATGGGCCTTGTAGTTCTGCTTCGGAATTGCAGCTACAGAAATATTTTG BMC03977 Brugia Chip V1 14990.m07791 Bm1_48340 Phosphatase regulatory subunit family protein
19 bm.00997 Bm1_03295 GTTGAGAATATACGCTTGCAAGGATTGGAACTTGTTATTTCGCTGCTGCTCTAGAGCAAAAAATT BMC04047 Brugia Chip V1 dbj|BAB14983.1| unnamed protein product [Homo sapiens] 12811.m00145 Bm1_03295 Brix domain containing protein 1 homolog, putative
20 bm.01003 BMC04072 ACAAAAAGCGGAGTGCCGCCAAATTGTCGAGCCTATTGTAATGGTAAATCAATAAAAAACATTGA BMC04072 Brugia Chip V1 emb|CAE73208.1| Hypothetical protein CBG20612 [Caenorhabditis briggsae] no_match

Total number of rows: 36248

Table truncated, full table size 8273 Kbytes.




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