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Platform GPL6380 Query DataSets for GPL6380
Status Public on Feb 17, 2008
Title University of Washington Human Itsara PWS 388K custom design array, version 1
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer NimbleGen
Manufacture protocol manufactured per NimbleGen protocol. The design utilized b35 coordinates, with 385,000 spaced over 15258127bp, corresponding to a final probe density of 1 oligo per 39 bp.
 
Description Ultra high-density coverage of Prader-Willi region on chr15
 
Contributor(s) Mefford HC
Submission date Jan 16, 2008
Last update date Feb 17, 2008
Contact name Heather Mefford
E-mail(s) hmefford@u.washington.edu
Phone 206-685-7336
Fax 206-221-5795
Organization name University of Washington
Department Genome Sciences
Lab Eichler Lab
Street address 1705 NE Pacific St
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Samples (3) GSM257409, GSM257411, GSM257413
Series (1)
GSE10189 Recurrent 15q13 microdeletions

Data table header descriptions
ID
PROBE_DESIGN_ID Itsara PWS tiling design
CONTAINER
DESIGN_NOTE
SELECTION_CRITERIA
SEQ_ID
PROBE_SEQUENCE
MISMATCH
MATCH_INDEX
FEATURE_ID
ROW_NUM
COL_NUM
PROBE_CLASS
POSITION
DESIGN_ID
X
Y
chrm
RANGE_START coordinates of probe start
RANGE_END coordinates of probe end
genome_build hg17
RANGE_STRAND +
RANGE_GB
INDEX

Data table
ID PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS POSITION DESIGN_ID X Y chrm RANGE_START RANGE_END genome_build RANGE_STRAND RANGE_GB INDEX
CHR15P031709366 4016_0433_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.70;freq:17.93;count:01;rules:0000;score:0786 chr15:19099848-33170780 TCTGTTTTCCCATGCAGTGCCAGCTGGTCAAAACTTAAATCACATTCTTTCTTATGTCA 0 62903201 62903201 133 433 experimental 31709366 4016 433 133 chr15 31709366 31709424 hg17 + NC_000015.8 252623
CHR15P019334411 4016_0435_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq:13.53;count:03;rules:-300;score:0302 chr15:19099848-33170780 GCTATGTTTTCCTATGTACACAGGTCACTGGTAGACATGCAAAAAAGTACCTTG 0 62594679 62594679 133 435 experimental 19334411 4016 435 133 chr15 19334411 19334464 hg17 + NC_000015.8
CHR15P032156345 4016_0437_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.60;freq: 9.59;count:01;rules:0000;score:0829 chr15:19099848-33170780 GGTCATTAGCCACAGTCACCACCATGTTACTCACAAGATTCAAACC 0 62915326 62915326 133 437 experimental 32156345 4016 437 133 chr15 32156345 32156390 hg17 + NC_000015.8 264654
CHR15P023606907 4016_0439_0133 FORWARD interval rank target_tm:76.00;probe_tm:83.00;freq: 5.58;count:01;rules:0000;score:0736 chr15:19099848-33170780 ACGGTCTGAAAAACGAGCCAGCACCGCCCTGGGCAGGACGAGGAG 0 62694023 62694023 133 439 experimental 23606907 4016 439 133 chr15 23606907 23606951 hg17 + NC_000015.8 88171
CHR15P026269249 4016_0441_0133 FORWARD interval rank target_tm:76.00;probe_tm:78.40;freq:19.06;count:03;rules:-400;score:0139 chr15:19099848-33170780 GTTCTTGCATCTTCGCTTCCTGCTCACACATCTTCCCCTCCTGCT 0 62763868 62763868 133 441 experimental 26269249 4016 441 133 chr15 26269249 26269293 hg17 + NC_000015.8
CHR15P022300681 4016_0443_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.80;freq:17.86;count:03;rules:0000;score:0588 chr15:19099848-33170780 GATGTCTCTGGTGTTTTCCTAATGATTGGATGACTGTTGTGAATTTAGCAGAGGAAAC 0 62659053 62659053 133 443 experimental 22300681 4016 443 133 chr15 22300681 22300738 hg17 + NC_000015.8
CHR08P006842752 4016_0445_0133 FORWARD interval rank target_tm:76.00;probe_tm:76.60;freq: 9.77;count:03;rules:0000;score:0624 chr8:6840230-6845423 ATAGCTCTACTGGGAGAAGGCTCGGAGACAAGAAACCTTCCTCAA 0 62965132 62965132 133 445 experimental 6842752 4016 445 133 chr8 6842752 6842796 hg17 + NC_000008.9
CHR15P031390441 4016_0447_0133 FORWARD interval rank target_tm:76.00;probe_tm:84.80;freq: 3.65;count:01;rules:0000;score:0731 chr15:19099848-33170780 GGAGGAGAAAGAGCGCAGCAGCAGTCAGCGCACGCCGAGCGGCTG 0 62893848 62893848 133 447 experimental 31390441 4016 447 133 chr15 31390441 31390485 hg17 + NC_000015.8 243323
CHR15P022414953 4016_0449_0133 FORWARD interval rank target_tm:76.00;probe_tm:76.60;freq:17.00;count:01;rules:-400;score:0384 chr15:19099848-33170780 TCAGAGAAGGACCAAGGGATAGAGAAGGGGAGATGCTCCATATCT 0 62662024 62662024 133 449 experimental 22414953 4016 449 133 chr15 22414953 22414997 hg17 + NC_000015.8 56975
CHR07P090680960 4016_0451_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.30;freq:23.41;count:01;rules:-500;score:0259 chr7:90677628-90685457 TTTTGTGGGGGAGATTTTTCATCTCCACTTCTTACTTCTCAGCTACCC 0 62963322 62963322 133 451 experimental 90680960 4016 451 133 chr7 90680960 90681007 hg17 + NC_000007.11 10516
CHR15P021509697 4016_0453_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.80;freq:29.66;count:01;rules:0000;score:0751 chr15:19099848-33170780 CCTCTTCACATGTCATATAAAGACTTCATGACAGTAAATTTCCAATCTCTCCCTCCCA 0 62641430 62641430 133 453 experimental 21509697 4016 453 133 chr15 21509697 21509754 hg17 + NC_000015.8 43809
CHR15P030206870 4016_0455_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.90;freq:56.97;count:01;rules:0000;score:0706 chr15:19099848-33170780 TTATAAGAAACTGCCATACTCTTTTCCAGAGTGGCCGTTCCCACCTAAGT 0 62863374 62863374 133 455 experimental 30206870 4016 455 133 chr15 30206870 30206919 hg17 + NC_000015.8 224278
CHR15P022685926 4016_0457_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.90;freq:13.95;count:01;rules:0000;score:0808 chr15:19099848-33170780 TTCCTCCATACTGAATGTGCATCCCTACATGTTCATGTTGTTGTTTCATAGGTAGTG 0 62667796 62667796 133 457 experimental 22685926 4016 457 133 chr15 22685926 22685982 hg17 + NC_000015.8 62621
CHR15P020413952 4016_0459_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.70;freq:21.23;count:01;rules:0000;score:0774 chr15:19099848-33170780 CCTGGAAATGTCATCATTTACCCAGAAGATGCTGAAACTCTGGGC 0 62615740 62615740 133 459 experimental 20413952 4016 459 133 chr15 20413952 20413996 hg17 + NC_000015.8 29500
CHR15P096753933 4016_0461_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.60;freq:15.28;count:01;rules:0000;score:0795 chr15:96749663-96756481 GCCCAGGGAAGGTTCAAACAAATTTGAGTATGCTGAAATGATTTTAGTGAGGG 0 62939419 62939419 133 461 experimental 96753933 4016 461 133 chr15 96753933 96753985 hg17 + NC_000015.8 283866
CHR15P027571642 4016_0463_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq:11.55;count:01;rules:-400;score:0414 chr15:19099848-33170780 GCTGTACCATAGACATCCCCATTTATTGCATGTAACTTACTTCACTTCTCAACC 0 62793251 62793251 133 463 experimental 27571642 4016 463 133 chr15 27571642 27571695 hg17 + NC_000015.8 172710
CHR15P030326069 4016_0465_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq: 8.53;count:02;rules:0000;score:0735 chr15:19099848-33170780 TAGGAATCATAATGCAACCAGCAAGTCAACTTCCAGGATTAAGGCTAGAAGAGA 0 62866466 62866466 133 465 experimental 30326069 4016 465 133 chr15 30326069 30326122 hg17 + NC_000015.8
CHR15P024935123 4016_0467_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.90;freq:15.63;count:01;rules:0000;score:0800 chr15:19099848-33170780 CCCTGTATTTCTGGTTCCTTAAGGTGATCTTCATGAATGAGTGTTCAGTGTTGTCAA 0 62728790 62728790 133 467 experimental 24935123 4016 467 133 chr15 24935123 24935179 hg17 + NC_000015.8 121725
CHR15P022113703 4016_0469_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq:10.75;count:03;rules:0000;score:0619 chr15:19099848-33170780 GTGAGGTGAGATAAAGGTGGTATTCATCTGTCTTATATGGAGTAGTCACCTTGA 0 62654786 62654786 133 469 experimental 22113703 4016 469 133 chr15 22113703 22113756 hg17 + NC_000015.8
CHR15P028138455 4016_0471_0133 FORWARD interval rank target_tm:76.00;probe_tm:75.70;freq: 8.06;count:01;rules:0000;score:0843 chr15:19099848-33170780 ATGAGAACCAAGAAGGTTCTCACTGGCAACCTTAACGGAAGAGTG 0 62806446 62806446 133 471 experimental 28138455 4016 471 133 chr15 28138455 28138499 hg17 + NC_000015.8 185716

Total number of rows: 388001

Table truncated, full table size 117717 Kbytes.




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