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Platform GPL14731 Query DataSets for GPL14731
Status Public on Apr 16, 2012
Title VTT_KB_Aspergillus nidulans v4.0_135K array
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Aspergillus nidulans FGSC A4
Manufacturer NimbleGen
Manufacture protocol High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
 
Description Nimblegen design name 100608_Anid_KB_exp, Nimblegen design ID 531573. Expression + Tiling design for Aspergillus nidulans FGSC A4 using customer-provided transcript set. Expression portion -- selected 6 probes per transcript for 10546 out of 10597 transcripts (51 not found, 18 less than 6 probes per transcript, 114 duplicate probes/exemplars). 2 replicates of 63,130 probes for a final expression total of 126,260 probes. Tiling portion -- Used customer provided list of 36 long transcripts. Selected 5651 tiling 50-75mers and tiled at a 66bp interval (int=56/win=10/mm=1). 2 replicates on final array for 11302 tiling probes. Created .pos and probe_locations.gff to go with tiling portion. Annotation for these regions can be found in the .ngd file
 
Submission date Oct 13, 2011
Last update date Apr 16, 2012
Contact name Kirsi Bromann
E-mail(s) [email protected]
Organization name VTT Technical Research Centre of Finland
Department TK402, Cell Factory
Lab TK4021, Metabolic Engineering
Street address Tietotie 2
City Espoo
ZIP/Postal code 02044
Country Finland
 
Samples (12) GSM815940, GSM815941, GSM815942, GSM815943, GSM815944, GSM815945 
Series (1)
GSE32954 Expression analysis of Aspergillus nidulans AN1599 (PbcR) overexpression mutant

Data table header descriptions
ID PROBE_DESIGN_ID
SEQ_ID_X_Y SEQ_ID_X_Y
SEQ_ID SEQ_ID
X X
Y Y
CONTAINER CONTAINER
DESIGN_NOTE DESIGN_NOTE
SELECTION_CRITERIA SELECTION_CRITERIA
SEQUENCE PROBE_SEQUENCE
MISMATCH MISMATCH
MATCH_INDEX MATCH_INDEX
FEATURE_ID FEATURE_ID
ROW_NUM ROW_NUM
COL_NUM COL_NUM
PROBE_CLASS PROBE_CLASS
PROBE_ID PROBE_ID
POSITION POSITION
DESIGN_ID DESIGN_ID
GENE_INFO GENE_INFO

Data table
ID SEQ_ID_X_Y SEQ_ID X Y CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID GENE_INFO
531573_0061_0455 CADANIAT00000001_61_455 CADANIAT00000001 61 455 EXPRESSION_REP1 rank_selected rank:03;score:400;uniq:15;count:37;freq:02;rules:1;tm:75.6 TTGCTGGTCAGATATATAATAACCCTGTTTGCAGCCTGAATATAGTCTGTATTTCTGGCT 0 725640 725640 455 61 experimental AnidP00000002 173 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0190_0424 CADANIAT00000001_190_424 CADANIAT00000001 190 424 EXPRESSION_REP1 rank_selected rank:02;score:487;uniq:24;count:37;freq:02;rules:1;tm:72.2 ATACATGCCTTTGCCTTTGTAAACAGATACTATATATTTAGTACTATATACTTCAATGGC 0 725641 725641 424 190 experimental AnidP00000007 322 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0039_0107 CADANIAT00000001_39_107 CADANIAT00000001 39 107 EXPRESSION_REP1 rank_selected rank:05;score:386;uniq:14;count:37;freq:01;rules:1;tm:74.9 CAAGGAGATGTCAGCTTAGTAATATCTATATCTCTACTGGTAGTATAGAATACCTTGACC 0 725642 725642 107 39 experimental AnidP00000012 401 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0011_0569 CADANIAT00000001_11_569 CADANIAT00000001 11 569 EXPRESSION_REP1 rank_selected rank:06;score:386;uniq:24;count:37;freq:02;rules:1;tm:71.5 AATATTTGATAGTGATCTATTTATCCCTGTTCAGACTAGTTGTAAAAGCTATATTAGTCA 0 725643 725643 569 11 experimental AnidP00000014 585 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0271_0105 CADANIAT00000001_271_105 CADANIAT00000001 271 105 EXPRESSION_REP1 rank_selected rank:01;score:518;uniq:25;count:37;freq:02;rules:1;tm:72.9 TAGTGATCTATTTATCCCTGTTCAGACTAGTTGTAAAAGCTATATTAGTCAAGTATCTGT 0 725644 725644 105 271 experimental AnidP00000018 594 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0030_0608 CADANIAT00000001_30_608 CADANIAT00000001 30 608 EXPRESSION_REP1 rank_selected rank:04;score:396;uniq:17;count:37;freq:02;rules:1;tm:74.2 TTGCTTTGGCTATAAATATTAGCCAGGAGATTGCAGTGTTTAATTGCCAATTCTTCAAAG 0 725645 725645 608 30 experimental AnidP00000019 665 531573 EG:CADANIAT00000001 cdna:known chromosome:CADRE2:IV:1268:6235:1 gene:CADANIAG00000001
531573_0163_0629 CADANIAT00000001_163_629 CADANIAT00000001 163 629 EXPRESSION_REP2 rank_selected rank:03;score:400;uniq:15;count:37;freq:02;rules:1;tm:75.6 TTGCTGGTCAGATATATAATAACCCTGTTTGCAGCCTGAATATAGTCTGTATTTCTGGCT 0 863244 863244 629 163 experimental AnidP00000002 173 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0364_0300 CADANIAT00000001_364_300 CADANIAT00000001 364 300 EXPRESSION_REP2 rank_selected rank:02;score:487;uniq:24;count:37;freq:02;rules:1;tm:72.2 ATACATGCCTTTGCCTTTGTAAACAGATACTATATATTTAGTACTATATACTTCAATGGC 0 863245 863245 300 364 experimental AnidP00000007 322 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0405_0449 CADANIAT00000001_405_449 CADANIAT00000001 405 449 EXPRESSION_REP2 rank_selected rank:05;score:386;uniq:14;count:37;freq:01;rules:1;tm:74.9 CAAGGAGATGTCAGCTTAGTAATATCTATATCTCTACTGGTAGTATAGAATACCTTGACC 0 863246 863246 449 405 experimental AnidP00000012 401 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0178_0216 CADANIAT00000001_178_216 CADANIAT00000001 178 216 EXPRESSION_REP2 rank_selected rank:06;score:386;uniq:24;count:37;freq:02;rules:1;tm:71.5 AATATTTGATAGTGATCTATTTATCCCTGTTCAGACTAGTTGTAAAAGCTATATTAGTCA 0 863247 863247 216 178 experimental AnidP00000014 585 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0008_0584 CADANIAT00000001_8_584 CADANIAT00000001 8 584 EXPRESSION_REP2 rank_selected rank:01;score:518;uniq:25;count:37;freq:02;rules:1;tm:72.9 TAGTGATCTATTTATCCCTGTTCAGACTAGTTGTAAAAGCTATATTAGTCAAGTATCTGT 0 863248 863248 584 8 experimental AnidP00000018 594 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0426_0116 CADANIAT00000001_426_116 CADANIAT00000001 426 116 EXPRESSION_REP2 rank_selected rank:04;score:396;uniq:17;count:37;freq:02;rules:1;tm:74.2 TTGCTTTGGCTATAAATATTAGCCAGGAGATTGCAGTGTTTAATTGCCAATTCTTCAAAG 0 863249 863249 116 426 experimental AnidP00000019 665 531573 EG:CADANIAT00000002 cdna:known chromosome:CADRE2:IV:8987:9589:1 gene:CADANIAG00000002
531573_0112_0356 CADANIAT00000002_112_356 CADANIAT00000002 112 356 EXPRESSION_REP1 rank_selected rank:03;score:346;uniq:09;count:37;freq:03;rules:1;tm:83.1 TGCTGCTATGGGGTTTGTCTCGGGCCAGCAGTCTACTGGCGCGGTGGGTTAACCACAATA 0 725646 725646 356 112 experimental AnidP00000021 2 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0212_0456 CADANIAT00000002_212_456 CADANIAT00000002 212 456 EXPRESSION_REP1 rank_selected rank:06;score:300;uniq:16;count:37;freq:02;rules:1;tm:83.1 TTGGGGCAAAGCAGGCAGGCAGCAGGTATCCCTGCATGGGTTGATTAAGGACTGCTGGAG 0 725647 725647 456 212 experimental AnidP00000024 108 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0078_0582 CADANIAT00000002_78_582 CADANIAT00000002 78 582 EXPRESSION_REP1 rank_selected rank:01;score:404;uniq:17;count:37;freq:02;rules:1;tm:82.4 GGCAAAGCAGGCAGGCAGCAGGTATCCCTGCATGGGTTGATTAAGGACTGCTGGAGACTT 0 725648 725648 582 78 experimental AnidP00000028 112 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0404_0222 CADANIAT00000002_404_222 CADANIAT00000002 404 222 EXPRESSION_REP1 rank_selected rank:05;score:314;uniq:14;count:37;freq:03;rules:1;tm:81.8 AGGCAGCAGGTATCCCTGCATGGGTTGATTAAGGACTGCTGGAGACTTGGTGGTCACAGT 0 725649 725649 222 404 experimental AnidP00000033 124 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0021_0289 CADANIAT00000002_21_289 CADANIAT00000002 21 289 EXPRESSION_REP1 rank_selected rank:04;score:334;uniq:10;count:37;freq:03;rules:1;tm:80.4 TCGCTCCTCAATTGGCTTTACCAGCGATGGCAGTTGGGAAAAGTGGTTGTGGAGCAGAAA 0 725650 725650 289 21 experimental AnidP00000036 200 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0445_0075 CADANIAT00000002_445_75 CADANIAT00000002 445 75 EXPRESSION_REP1 rank_selected rank:02;score:381;uniq:13;count:37;freq:03;rules:1;tm:77.0 GCAAAGCTTCGAACTTACAAACTCTGCTACTATGCAGCCATGTCTTTGATTAGGGAAGAA 0 725651 725651 75 445 experimental AnidP00000040 274 531573 EG:CADANIAT00000003 cdna:known chromosome:CADRE2:IV:12345:13757:-1 gene:CADANIAG00000003
531573_0380_0376 CADANIAT00000002_380_376 CADANIAT00000002 380 376 EXPRESSION_REP2 rank_selected rank:03;score:346;uniq:09;count:37;freq:03;rules:1;tm:83.1 TGCTGCTATGGGGTTTGTCTCGGGCCAGCAGTCTACTGGCGCGGTGGGTTAACCACAATA 0 863250 863250 376 380 experimental AnidP00000021 2 531573 EG:CADANIAT00000004 cdna:known chromosome:CADRE2:IV:14428:15154:1 gene:CADANIAG00000004
531573_0210_0434 CADANIAT00000002_210_434 CADANIAT00000002 210 434 EXPRESSION_REP2 rank_selected rank:06;score:300;uniq:16;count:37;freq:02;rules:1;tm:83.1 TTGGGGCAAAGCAGGCAGGCAGCAGGTATCCCTGCATGGGTTGATTAAGGACTGCTGGAG 0 863251 863251 434 210 experimental AnidP00000024 108 531573 EG:CADANIAT00000004 cdna:known chromosome:CADRE2:IV:14428:15154:1 gene:CADANIAG00000004

Total number of rows: 137604

Table truncated, full table size 49089 Kbytes.




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Supplementary file Size Download File type/resource
GPL14731_100608_Anid_KB_exp.ndf.gz 7.8 Mb (ftp)(http) NDF
GPL14731_100608_Anid_KB_exp.ngd.gz 186.8 Kb (ftp)(http) NGD

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