NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL5745 Query DataSets for GPL5745
Status Public on Dec 01, 2007
Title KARC Schizosaccharomyces pombe CEN array
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Schizosaccharomyces pombe
Manufacturer National Institute of Information and Communications Technology, and Japan Science and Technology Agency
Manufacture protocol 255 probe sequences from centromere regions were generated by PCR. 173 of these sequences occurred between lys1 to the right edge of cntI. 56 sequences were from cen2, and the remaining 26 sequences from cen3. Probes for cen2 and cen3 were selected only from specific regions unique to each centromere. #50 probes of cen1 were not included in the array because they were not amplified by PCR. To make specific probes for each strand of the sequence, two primer sets were prepared for each sequence. In one set, the 5' end of the forward primer was modified with an amino group. In the other set, the 5' end of the reverse primer was modified with an amino group. A GeneAmp PCR System 9700 (Applied Biosystems) and z-Taq polymerase (TAKARA) were used for PCR. PCR conditions were as follows: 40 cycles of denaturation at 95°C, extension at 72°C, and annealing, depending on the Tm values of the primers, at 54-63°C. The PCR products were purified by using Multiscreen96 (Millipore) or NucleoFast96 (MACHEREY-NAGEL) kits and their concentrations were measured using a SpectraMax190 (Molecular Devices).
For each probe, 4µg of probe DNA was dissolved in 20µl spotting buffer (150mM Na-phosphate buffer pH8.5).These probes were spotted on a Surmodics 3D-Link Slide by a PixSys4500 (Genomic Solutions) to produce the centromere array. Spotting was carried out by the NippnTecnoCrasta e-Array system. 534 spots were applied to each cen array. The diameter of each spot was 380µm and the pitch 920µm. To covalently bind probe DNA to the glass slide, a blocking procedure was carried out as follows: the stamped slides were incubated in a humidity chamber (~75% humidity) for 2 days, and then were soaked in a pre-warmed blocking buffer (50mM ethanolamine, 0.1M Tris-Cl pH9, 0.1% SDS) at 50°C for 15-30 minutes. The slides were rinsed twice with distilled water (DW), soaked in a wash buffer (4xSSC, 0.1% SDS) at 50°C for 15-60 minutes, and again rinsed twice with DW. To remove the unmodified anti sense strand of the probe DNA, the slides were boiled in DW for 2 min. After rinsing twice in DW, the slides were dried.
Support glass
Coating other
 
Description The 534 spots included: 514 spots which correspond to the sense or antisense strands of 257 sequences (ura4, GFP and 255 sequences from cen regions), and 20 negative control spots. ID number 50 and 306 are assigned to the #50 probes that were not included in the array (see the Manufacture Protocol).
 
Web link http://www2.nict.go.jp/w/w103/w131103/CellMagic/index.html
Contributor(s) Chikashige Y, Tsutsumi C, Okamasa K, Haraguchi T, Hiraoka Y
Submission date Aug 15, 2007
Last update date Jan 23, 2023
Contact name Atsushi Matsuda
Organization name National Institute of Information and Communications Technology
Street address 588-2, Iwaoka, Iwaoka-cho, Nishi-ku
City Kobe
ZIP/Postal code 651-2492
Country Japan
 
Samples (2) GSM218193, GSM218194
Series (1)
GSE8782 Gene expression and distribution of Swi6 in partial aneuploids of the fission yeast Schizosaccharomyces pombe

Data table header descriptions
ID
Spot Number Spot Number assigned by constructor of this array.
Organism Schizosaccharomyces pombe
Probe Name Probe Name assigned by constructor of this array.
Systematic Gene Name Systematic name of gene included in the probe
Accession Number Accession number of cosmid or contig including the probe
Centromeres Centromere including the probe. Probes from the unique region on the outside of cen1 indicated by U.
SEQUENCE
ORF GenBank Identifier
GB_ACC
SPOT_ID spot identifier

Data table
ID Spot Number Organism Probe Name Systematic Gene Name Accession Number Centromeres SEQUENCE ORF GB_ACC SPOT_ID
1 1 Schizosaccaromyces pombe C1-001F SPAP7G5.04c AL353014 U ctaatgagttggagcgcctccacgaccaccagccgatgcaagcttctccaaagtagcttcatttattttgacttcaggaagctttttaccttctaaagtaggttttggcaaaaatccaatagctaccagatatgacaaatataagcccatctcatgttccaaaattgcagctccattagaaacatccacgttagtccaagatgcatcacgtttcaagatttcacgtgtgtttgtatcatctaattcaggagcttttgtattagcaggaagattatctaacacaaagtgaagtaagggata SPAP7G5.04c AL353014
2 2 Schizosaccaromyces pombe C1-002F SPAP7G5.04c AL353014 U atgcatcacgtttcaagatttcacgtgtgtttgtatcatctaattcaggagcttttgtattagcaggaagattatctaacacaaagtgaagtaagggatacaaagcactatcatgagactcattaatgacaaagcgctccaaagcaatacgccaattgacgtattcggaaagcttggtattgaagccaaaagtggaaagagttcctaggaattggttgaaacgaagtcggggatgactagttacgtgagcaacaattactccttgttcgggatggaaagcactggcagttaccacgcgag SPAP7G5.04c AL353014
3 3 Schizosaccaromyces pombe C1-003F SPAP7G5.04c AL353014 U gttcctaggaattggttgaaacgaagtcggggatgactagttacgtgagcaacaattactccttgttcgggatggaaagcactggcagttaccacgcgagcaacgtgatcggcaggaaccatatttacagtattattgatgttcgggtacagacccaattcaatgcaccctttgaccattcgaaccaaaaagtcgtcggtattaatagcaccagacttggagtcgcctaaaatgtatccaggacgcacaacaacaccacgaaggccacgtaatcccgcttgccttactaaatattcagat SPAP7G5.04c AL353014
4 4 Schizosaccaromyces pombe C1-004F SPAP7G5.04c AL353014 U attaatagcaccagacttggagtcgcctaaaatgtatccaggacgcacaacaacaccacgaaggccacgtaatcccgcttgccttactaaatattcagatacccatttgctttgtccgtaaccggtatgcaaatctttcgaagaaccttgcaaaggatcggattctgggattccatttcctccctttgaagtaatttcgttcgaaaggttaacgtaatactcagtatcaacagttgatgtggatgaaacaaaactcaaggatttaccttttcctaaagagcaaagttttaatgcagtaat SPAP7G5.04c AL353014
5 5 Schizosaccaromyces pombe C1-005F SPAP7G5.04c AL353014 U tcgaaaggttaacgtaatactcagtatcaacagttgatgtggatgaaacaaaactcaaggatttaccttttcctaaagagcaaagttttaatgcagtaattgtacccataacattaggacctctgagtttagaatatggataaacccaatgtacaagggcaccattatgaataacataatcgacgacttcagtaagcttgttccatttcctttcttctataccccagttttcgagagcaagatcaccattgacaacagaaattttttgggcccatgattcatcccatacaccatacgcgg SPAP7G5.04c AL353014
6 6 Schizosaccaromyces pombe C1-006F SPAP7G5.04c AL353014 U ttccatttcctttcttctataccccagttttcgagagcaagatcaccattgacaacagaaattttttgggcccatgattcatcccatacaccatacgcggtacaactgtctttaagacgttttagaccatgttcttccgatgaggcgcggactaaggcaatgactttcaagttagagcttctggtcataaggtctcttaatataaagacaccaaggtagccgttagcaccagttaagaaaacggtttttggctcatcaatacccaagtctttagaggttggaaattctttaggaattaaa SPAP7G5.04c AL353014
7 7 Schizosaccaromyces pombe C1-007F SPAP7G5.04c AL353014 U tataaagacaccaaggtagccgttagcaccagttaagaaaacggtttttggctcatcaatacccaagtctttagaggttggaaattctttaggaattaaatctactaaatcaagtgcatctttaccatattcaatttcaggttctctagtctcttctttgcctatatccatcacgctaatcatctcacccgatttcattctttcaatctctttggccaaaccttcaatagtaggttcactgaaaactaaacctaaaggtacattcacagcaaattttttgcgaagttcaaaaattaagcg SPAP7G5.04c AL353014
8 8 Schizosaccaromyces pombe C1-008F SPAP7G5.04c AL353014 U tttcaatctctttggccaaaccttcaatagtaggttcactgaaaactaaacctaaaggtacattcacagcaaattttttgcgaagttcaaaaattaagcgagtagctaaaatagaatgtcctccaatatcaaagaaacttgcttttttgttgacatcagtagcgtgtggaatgatacgcaaccagatatcacgtatatccctttcagtggctgtaagagtttcatcaactccatgtttagaatgtgaacgagatgcggcagcaagttgtgatgtgtctgggaaaggcagagcaggtttat SPAP7G5.04c AL353014
9 9 Schizosaccaromyces pombe C1-009F SPAP7G5.04c AL353014 U ctttcagtggctgtaagagtttcatcaactccatgtttagaatgtgaacgagatgcggcagcaagttgtgatgtgtctgggaaaggcagagcaggtttatctatctttccattaggattgagaggcattttatgaaggggaacaattacagaaggaatagcataactaggaagtttagtcttaagatattcccgtatatcatgtataagcttcctgtacttcttcaaaccattgacgacaatatcttccgactcagtagcgctatcaaagtcatctttatttaaaccttgaggtacaatg SPAP7G5.04c AL353014
10 11 Schizosaccaromyces pombe C1-010F SPAP7G5.04c AL353014 U atgtataagcttcctgtacttcttcaaaccattgacgacaatatcttccgactcagtagcgctatcaaagtcatctttatttaaaccttgaggtacaatgtatgcaactagcgtgggttcttcatccttatcacgtcgaacaagggtaatattttcacggacattaggatgacgagaaagatgggtattaatttcacctaactcaattcggaaaccacgaattttaatttgatcgtcggcacgaccgctacattctacattaccagttgggagatagcggcccaagtcaccagaacgata SPAP7G5.04c AL353014
11 12 Schizosaccaromyces pombe C1-011F SPAP7G5.04c AL353014 U actcaattcggaaaccacgaattttaatttgatcgtcggcacgaccgctacattctacattaccagttgggagatagcggcccaagtcaccagaacgatacatacgatcgcgtattccgaaccaataaggtttccagggcgcattttctggagttcggtctacaaacttggagggatcagcaaaccaactctttaagaattttttgctagtcaattcatcatttccaaggtagccctcagccaatccaccagcacgaagatatatttcaccaacttctccgataccgcatatcttgttag SPAP7G5.04c AL353014
12 13 Schizosaccaromyces pombe C1-012F SPAP7G5.04c AL353014 U tttttgctagtcaattcatcatttccaaggtagccctcagccaatccaccagcacgaagatatatttcaccaacttctccgataccgcatatcttgttagtatcaaaacgattgatcaccaaaagttggacattcttcatgccacgtccggctggaatgacatctttttgcgattccaaaaatgtttgatcttgagaccgcgcaggtactacaaagtacgaaactgaacgctgagtctctgtcgttccatacatgttaacaacgttaacgttgttagcaaggacttgtaagcgaagacaa SPAP7G5.04c AL353014
13 14 Schizosaccaromyces pombe C1-013F SPAP7G5.04c AL353014 U cgcaggtactacaaagtacgaaactgaacgctgagtctctgtcgttccatacatgttaacaacgttaacgttgttagcaaggacttgtaagcgaagacaatcacgtttcgtcaaaatatcacctacaaaaaatgcatggtgtaatgaaggaattggctcatcagcctgagcagctaacagttgacccatagctggggtgagatgagttacagtaaccttatacttgttagcccattgggctaattgaccaggggtgccaatgtcttcagcagtgggtacgattaaggatgcgccaaggaa SPAP7G5.04c AL353014
14 15 Schizosaccaromyces pombe C1-014F SPAP7G5.04c AL353014 U gatgagttacagtaaccttatacttgttagcccattgggctaattgaccaggggtgccaatgtcttcagcagtgggtacgattaaggatgcgccaaggaaaagtggtgtgaaaatatctctttgaataggatcatgagcaattccacttaacatcgtaaaccggtctgattcagataaattaaattcctgagccatccaatcaaaatagtaagcaagactgaaatgtctaccttttacacctttaggaattccttcacttccgctagtaaaactaagtgtgggagtactatcagggccta SPAP7G5.04c AL353014
15 16 Schizosaccaromyces pombe C1-015F SPAP7G5.04c AL353014 U tcaaaatagtaagcaagactgaaatgtctaccttttacacctttaggaattccttcacttccgctagtaaaactaagtgtgggagtactatcagggcctacaacaacgccagtttgttcggacttcaagtgtaaaacgtgttgcaagatatcgtcagctccttttgagactgatcctcccgttaaagaaccatctttagcaagttttaaagctggtacataagtttttagttcaaggcttttctcaacatactctacgactgtgggagacaaaacacctgcatcttccaaaacaactaag SPAP7G5.04c AL353014
16 17 Schizosaccaromyces pombe C1-016F SPAP7G5.04c AL353014 U aagttttaaagctggtacataagtttttagttcaaggcttttctcaacatactctacgactgtgggagacaaaacacctgcatcttccaaaacaactaaggctctgggcttagcaacgctcagatatataatctgacgagcaggtggatatgctggatcgataactgagaatgtggcaccagctttaagtacacccatgaccgcgacaactaaatccacacctcgataagcataaaccataactacatcacccctctcaattccattctttacgagatggtgagccaggatgttagaaga SPAP7G5.04c AL353014
17 18 Schizosaccaromyces pombe C1-017F SPAP7G5.04c AL353014 U ccgcgacaactaaatccacacctcgataagcataaaccataactacatcacccctctcaattccattctttacgagatggtgagccaggatgttagaagactcgtcgatttgtcgatacgtgtaactagtgacaggagcatcaattgtgaccgaaggagtgactactatgcattctctatcagggaatttagcagcgttggatgcgaaaatatcttgaatggctccacgataaccactccaatcaagatcaacagttggatctggaagaacattcatttgggtaggtgtcattaggtcca SPAP7G5.04c AL353014
18 19 Schizosaccaromyces pombe C1-018F SPAP7G5.04c AL353014 U gatgcgaaaatatcttgaatggctccacgataaccactccaatcaagatcaacagttggatctggaagaacattcatttgggtaggtgtcattaggtccagagcaccgataggacctgtaacatctttggaagctgaaaccactaactttaatagctgatcagccacaatattaaccctactctcagaaaacaacaactgattatagattaatttcaattgtaaatcggggaaagtaaattgggagcgtaaagaagttaattgatcagaaggtttttttaccgaaaccagaacagtcaaa SPAP7G5.04c AL353014
19 20 Schizosaccaromyces pombe C1-019F SPAP7G5.04c AL353014 U attatagattaatttcaattgtaaatcggggaaagtaaattgggagcgtaaagaagttaattgatcagaaggtttttttaccgaaaccagaacagtcaaatccacatctaatcccgtggtagaaagaaagttttcagaaggagcgtctggagcattgtaaaaacgaagatgaacaagagttttacgagggtcatctttcttagaaagtttagcgttcaaaaaattaattaaatcagaaaaatctacagcatcagaggagccttccttttccagatcgcacactttggctaaaaggtcaag SPAP7G5.04c AL353014
20 21 Schizosaccaromyces pombe C1-020F SPAP7G5.04c AL353014 U tagaaagtttagcgttcaaaaaattaattaaatcagaaaaatctacagcatcagaggagccttccttttccagatcgcacactttggctaaaaggtcaagaaaagaatcgcttggttgaatgaaagttctcaaaacgaatggaattgcattctcagaactagtaccgatgctaatgtcctcatctccagtcatgcgactaacgaggattataaaaatcgtcaaaagaatattgaaaggagttactaatattcctttagcttgagcagcaacataaaccttaataagagctgtttttgcat SPAP7G5.04c AL353014

Total number of rows: 536

Table truncated, full table size 188 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap