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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 libraryhttp://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
MacArray™ 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
GSM225156 ,
GSM225157 ,
GSM225158 ,
GSM225159 ,
GSM225160 ,
GSM225161 ,
GSM225162 ,
GSM225163 ,
GSM225164 ,
GSM225165 ,
GSM225166 ,
GSM225167 ,
GSM225168 ,
GSM225169 ,
GSM225171 ,
GSM225173 ,
GSM225174 ,
GSM225175 ,
GSM225176 ,
GSM225177 ,
GSM225178 ,
GSM225180 ,
GSM225181 ,
GSM225182 ,
GSM225184 ,
GSM225185 ,
GSM225186 ,
GSM225187 ,
GSM225188 ,
GSM225189 ,
GSM225191 ,
GSM225192 ,
GSM225193 ,
GSM225194 ,
GSM225196 ,
GSM225198 ,
GSM225200 ,
GSM225201 ,
GSM225202 ,
GSM225203 ,
GSM225204 ,
GSM225205 ,
GSM225206 ,
GSM225208 ,
GSM225209 ,
GSM225210 ,
GSM225211 ,
GSM225212 ,
GSM225213 ,
GSM225214 ,
GSM225215 ,
GSM225216 ,
GSM225217 ,
GSM225219 ,
GSM225220 ,
GSM225221 ,
GSM225222 ,
GSM225223 ,
GSM225224 ,
GSM225225 ,
GSM225226 ,
GSM225227 ,
GSM225228 ,
GSM225229 ,
GSM225230 ,
GSM225231 ,
GSM225232 ,
GSM225518 ,
GSM225522 ,
GSM225523 ,
GSM225524 ,
GSM225526 ,
GSM225527 ,
GSM225528 ,
GSM225529 ,
GSM225532 ,
GSM225533 ,
GSM225535 ,
GSM225543 ,
GSM225546 ,
GSM225548 ,
GSM225551 ,
GSM225554 ,
GSM225557 ,
GSM225560 ,
GSM225562 ,
GSM225569 ,
GSM225573 ,
GSM225576 ,
GSM225580 ,
GSM225822 ,
GSM225826 ,
GSM225830 ,
GSM225834 ,
GSM225837 ,
GSM225838 ,
GSM225839 ,
GSM225840 ,
GSM225841 ,
GSM225842 ,
GSM225843 ,
GSM225845 ,
GSM225847 ,
GSM225850 ,
GSM225853 ,
GSM225856 ,
GSM225858 ,
GSM225862 ,
GSM225865 ,
GSM225869 ,
GSM225870 ,
GSM225872 ,
GSM387378 ,
GSM387379 ,
GSM387380 ,
GSM387381 ,
GSM387382 ,
GSM387383 ,
GSM387384 ,
GSM387385 ,
GSM387386 ,
GSM387387 ,
GSM387388 ,
GSM387389 ,
GSM387390 ,
GSM387391 ,
GSM387392 ,
GSM387393 ,
GSM387394 ,
GSM387395 ,
GSM387396 ,
GSM387397 ,
GSM387398 ,
GSM387399 ,
GSM387400 ,
GSM387401 ,
GSM387403 ,
GSM387404 ,
GSM387405 ,
GSM387406 ,
GSM387407 ,
GSM387408 ,
GSM387409 ,
GSM387410 ,
GSM387411 ,
GSM387412 ,
GSM387413 ,
GSM387414 ,
GSM387415 ,
GSM387416 ,
GSM387417 ,
GSM387418 ,
GSM387419 ,
GSM387420 ,
GSM387421 ,
GSM387422 ,
GSM387423 ,
GSM387424 ,
GSM387425 ,
GSM387426 ,
GSM387427 ,
GSM387428 ,
GSM387429 ,
GSM387430 ,
GSM387431 ,
GSM387432 ,
GSM387433 ,
GSM387434 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
GSE15436 Array CGH analysis of 56 primary gastric cancers for elucidating prognostic biomarkers
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
4045 594 Kbytes .Supplementary data files not provided
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