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Platform GPL5772 Query DataSets for GPL5772
Status Public on Jan 17, 2008
Title SNU_Breast_CGH_v1.0
Technology type spotted DNA/cDNA
Distribution commercial
Organism Homo sapiens
Manufacturer Macrogen, Inc.
Manufacture protocol Construction of BAC library
The array used in this study consists of 4,045 human Bacterial Artificial Chromosomes (BACs), which were spaced approximately 1 Mb on average across the entire genome (MacArrayTM Karyo4000 from Macrogen, Inc., Seoul, Korea). BAC clones were selected from the proprietary BAC library of Macrogen, Inc. Briefly, the pECBAC1 vector was digested with HindIII and size-selected HindIII-digested pooled male DNAs were used to generate a BAC library. These vectors were then transformed into and grown in the Escherichia coli DH10B strain.
Construction of BAC-mediated array CGH microarray
All clones were two-end sequenced using an ABI PRISM 3700 DNA Analyzer (Applied Biosystems, Foster City, CA, USA), and their sequences were blasted and mapped according to their positions described in the University of California, Santa Cruz (UCSC) human genome database (http://www.genome.ucsc.edu). Confirmation of locus specificity of the chosen clones was performed by removing multiple loci-binding clones by individual examination under standard fluorescence in situ hybridization (FISH) as described previously. These clones were prepared by the conventional alkaline lysis method to obtain BAC DNA. The DNA was sonicated to generate ~3-kb fragments before mixing with 50% DMSO spotting buffer. The arrays were manufactured by an OmniGrid arrayer (GeneMachine, San Carlos, CA, USA) using a 24-pin format. Each BAC clone was represented on an array as triplicate spots and each array was pre-scanned using a GenePix 4200A scanner (Axon Instruments Inc., Foster City, CA, USA) for proper spot morphology.
Catalog number MacArrayâ„¢ Karyo
 
 
Submission date Aug 25, 2007
Last update date Jan 17, 2008
Contact name Wonshik Han
E-mail(s) hanw@snu.ac.kr
Phone 82-2-2072-1958
Fax 82-2-766-3975
Organization name Seoul National University College of Medicine
Department Dept. of Surgery
Lab Lab of Breast Cancer Biology
Street address 28 Yongon-dong, Chongno-gu
City Seoul
ZIP/Postal code 110-744
Country South Korea
 
Samples (174) GSM224836, GSM224837, GSM224843, GSM224844, GSM225154, GSM225155 
Series (4)
GSE10128 Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer
GSE10129 Genomic copy number alterations as predictive markers of neoadjuvant chemotherapy response in breast cancer
GSE10181 Genomic copy number alterations as predictive markers in breast cancer

Data table header descriptions
ID BAC clone ID
chrNo
RANGE_GB RefSeq accession, NCBI build 36
SPOT_ID
cyto
RANGE_START BAC start position on chromosome, NCBI build 36
RANGE_END BAC end position on chromosome, NCBI build 36
bac_size
Cancer/Gene
STS/Terminal
Spot_Column
Spot_Row
Subarray_Column
Subarray_Row

Data table
ID chrNo RANGE_GB SPOT_ID cyto RANGE_START RANGE_END bac_size Cancer/Gene STS/Terminal Spot_Column Spot_Row Subarray_Column Subarray_Row
5771 1 NC_000001.9 1p36.33 711634 789889 78255 LOC388578, FLJ40008, FLJ22639, LOC284591, RH66043, RH18527, RH65042, WI-12626, SHGC-145224, RH25952, D1S2217, 4 16 1 3
2485 1 NC_000001.9 1p36.33 727410 821316 93906 LOC388578, FLJ40008, FLJ22639, LOC284591, FAM41C, LOC388579, RH18527, RH65042, WI-12626, SHGC-145224, RH25952, D1S2217, RH76697, 25 8 1 4
5706 1 NC_000001.9 1p36.33 778566 865959 87393 LOC284591, FAM41C, LOC388579, FLJ39609, LOC441867, SAMD11, RH25952, D1S2217, RH76697, SHGC-145870, SHGC-145703, SHGC-146656, 32 15 1 1
323 1 NC_000001.9 1p36.33 1510667 1685578 174911 ATAD3A, C1orf70, SSU72, CDC2L1, LOC400730, SLC35E2, NADK, RH65507, RH64278, RH56400, RH10603, RH70327, RH36904, RH27214, RH45084, SHGC-132055, RH13866, RH104480, RH25018, RH69193, RH10348, RH49860, RH12898, RH48431, STSG32748FS, RH45111, 18 2 1 6
705 1 NC_000001.9 1p36.33 1575434 1670760 95326 FLJ37183, ATAD3B, ATAD3A, C1orf70, SSU72, CDC2L1, LOC400730, SLC35E2, RH65507, RH64278, RH56400, RH10603, RH70327, RH36904, RH27214, RH45084, SHGC-132055, RH13866, RH104480, RH25018, RH69193, RH10348, RH49860, RH12898, 24 3 1 7
1391 1 NC_000001.9 1p36.33 2085982 2192431 106449 PRKCZ, C1orf86, LOC440554, SKI, SHGC-131099, RH64431, STSG33324FS, RH11740, RH49991, RH98469, RH103396, RH50661, RH13378, AFM214YG7, SHGC-3360, 18 6 1 4
122 1 NC_000001.9 1p36.33 2192427 2278109 85682 SKI, FLJ13941, RH14633, SHGC-149729, SHGC-80908, RH79610, RH46562, SHGC-33418, RH16553, 23 1 1 2
452 1 NC_000001.9 1p36.32 3549885 3650185 100300 WDR8, TP73, KIAA0495, RH32465, RH13601, AFM280WE5, SHGC-147180, SHGC-147179, D1S1310, RH69438, RH68672, RH67161, RH48939, 10 2 1 7
2557 1 NC_000001.9 1p36.32 3571724 3660988 89264 TP73, KIAA0495, FLJ32825, RH13601, AFM280WE5, SHGC-147180, SHGC-147179, D1S1310, RH69438, RH68672, RH67161, RH48939, 14 8 1 2
2492 1 NC_000001.9 1p36.32 3655702 3797394 141692 FLJ32825, LOC388588, LRRC47, KIAA0562, DFFB, LOC339448, RH104015, D1S1403, STSG29150, RH76499, RH98454, RH36221, RH67525, RH47124, SHGC-152746, SHGC-57243, RH78144, STSG27752, RH64257, 10 8 1 3
1379 1 NC_000001.9 1p36.32 4749058 4832802 83744 LOC388589, STSG33122FS, RH16669, RH17008, RH63947, SHGC-106227, RH64739, 17 6 1 8
2054 1 NC_000001.9 1p36.31 6504288 6606150 101862 FLJ23323, TAS1R1, HKR3, KLHL21, PHF13, SHGC-63524, GCT15G02, SHGC-145696, RH78576, RH71462, RH64576, RH64806, RH24947, 16 6 1 2
2887 1 NC_000001.9 1p36.31 6508455 6652603 144148 FLJ23323, TAS1R1, HKR3, KLHL21, PHF13, THAP3, DNAJC11, GCT15G02, SHGC-145696, RH78576, RH71462, RH64576, RH64806, RH24947, RH13732, WI-6196, RH49941, RH36717, RH67207, 1755, SHGC-57899, AFMB039ZG9, RH46494, 16 9 1 8
2533 1 NC_000001.9 1p36.23 7886394 7994543 108149 TNFRSF9, PARK7, MIG-6, RH91876, RH64464, RH17617, RH64183, D1S1406, RH50179, D1S2407, RH66928, 28 8 1 3
2974 1 NC_000001.9 1p36.23 7886594 7995607 109013 TNFRSF9, PARK7, MIG-6, RH91876, RH64464, RH17617, RH64183, D1S1406, RH50179, D1S2407, RH66928, 5 10 1 7
3027 1 NC_000001.9 1p36.23 8297052 8387510 90458 DNB5, RERE, DKFZp566H0824, WI-9408, RH10121, SHGC-132483, RH50665, RH44393, RH64510, RH68112, 24 10 1 3
4568 1 NC_000001.9 1p36.22 9802379 9889579 87200 CLSTN1, CTNNBIP1, WI-9616, RH12006, RH14623, RH78141, RH64194, STSG33326FS, 10 12 1 3
2730 1 NC_000001.9 1p36.22 11104460 11201073 96613 FRAP1, ANGPTL7, SHGC-56461, SHGC-132902, RH46207, D1S1298, SHGC-79836, RH46072, 23 9 1 2
296 1 NC_000001.9 1p36.22 11114879 11263108 148229 FRAP1, ANGPTL7, TERE1, SHGC-56461, SHGC-132902, RH46207, D1S1298, SHGC-79836, RH46072, RH47621, RH45419, RH78828, 1 2 1 4
2330 1 NC_000001.9 1p36.22 11250787 11342606 91819 TERE1, RH78828, RH45740, D1S1292, RH25933, RH49932, 16 7 1 7

Total number of rows: 4045

Table truncated, full table size 594 Kbytes.




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