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Platform GPL5577 Query DataSets for GPL5577
Status Public on Dec 01, 2007
Title KARC Schizosaccharomyces pombe 5K Ver. D2 ORF 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 Probe DNA used for the microarray was generated by PCR from the code region of each gene that has been described in annotated fission yeast genome sequences(Wood et al., 2002 Nature 415, 871-880). The continuous 300bp+/- 10bp exon sequence nearest to the 3'-end of the gene was selected as a probe. When the longest exon of the gene is shorter than 290bp, the longest exon was used as a probe. The primer used for PCR was designed by using the primer design supporting tool, Primer3(http:://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi). The length of each primer is 30+/-3bp. Tm of the primer is 60-70°C. The forward primers are modified by the amino group at their 5' end. Wild type L972 strain's genome DNA was used as the temperate of the first rounds of PCR. For the second and later round of PCR, the PCR products of the first round of PCR were used as a temperate. GeneAmp PCR System9700(Applied Biosystemes) and z-Taq polymerase(Takara) were used for PCR. PCR was done as follows: 40 cycles, 95°C for denature, 72°C for extension, for annealing 54-63°C according to the Tm value of primers.
The PCR product was purified by using Multiscreen96(Millipore) or NucleoFast96(MACHEREY-NAGEL) and measured the density by using SpectraMax190(Molecular Devices). A part of the product was confirmed by agarose gel electrophoresis. The dried up probe DNA 4 micro g is dissolved in 20 microl spotting buffer (150mM Na-phosphate buffer pH8.5). Probe DNA was stamped on Surmodics 3D-Link Slide by GTMASS STAMPER (Nippon Laser Electronics). 16 pins of GTMASS STAMPER stamp 324(18x18) times respectively on a slide to form 16 blocks (A to P) including 5184(16x18x18) spots in total. The diameter of each spot is about 150 microm, and the pitch is 190microm. The stamped slides are incubated in a humidity chamber (about 75% in humidity) for 2days, then are 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), and soaked in a wash buffer (4xSSC, 0.1% SDS) at 50°C, for 15-60 minutes. then, are rinsed twice with DW, and boiled in DW for 2 minutes. After rinsing twice in DW, the slides were dried up.
Support glass
Coating unknown
 
 
Web link http://www-karc.nict.go.jp/d332/CellMagic/index.html
Contributor(s) Chikashige Y, Tsutsumi C, Haraguchi T, Hiraoka Y
Submission date Jul 17, 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 (12) GSM210914, GSM210915, GSM210916, GSM210917, GSM210918, GSM210919 
Series (3)
GSE8782 Gene expression and distribution of Swi6 in partial aneuploids of the fission yeast Schizosaccharomyces pombe
GSE13554 Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.
GSE14626 Distinctive responses to nitrogen starvation in the dominant active mutants of the fission yeast Rheb GTPase.

Data table header descriptions
ID
ORGANISM
Spot Number Spot Number assigned by constructor of this array.
ORF Number Open Reading Frame Number assigned by constructor of this array. Nctrl is negative control spot.
ORF Systematic name according to http://www.genedb.org/genedb/pombe/index.jsp
D The ORFs checked with d in this column are ignored in data processing.
Name according to http://www.genedb.org/genedb/pombe/index.jsp Nctrl is negative control spot.
Reserved Name according to http://www.genedb.org/genedb/pombe/index.jsp
Gene Synonyms according to http://www.genedb.org/genedb/pombe/index.jsp
Obsolete Synonyms according to http://www.genedb.org/genedb/pombe/index.jsp
status according to http://www.genedb.org/genedb/pombe/index.jsp
Curation according to http://www.genedb.org/genedb/pombe/index.jsp
SEQUENCE
SPOT_ID

Data table
ID ORGANISM Spot Number ORF Number ORF D Name Reserved Name Gene Synonyms Obsolete Synonyms status Curation SEQUENCE SPOT_ID
1 Schizosaccaromyces pombe 4302 1.000-01 SPAC212.11 . . . . . experimentally characterised (or published) RecQ type DNA helicase (1 others); no apparent orthologs (135 others); likely to be present at all telomere ends (minimally chr 1 and 2) (1 others); contains dh repeats (1 others) CGAGTGTATAAAGATGAATGTCTAAGTTGCactcttggtaacccagacacagaaattcgtgctcataccgggaaagcatgccccgtacgcttatctacttgttataaatgtggcaaggccgaccacaacttgcgagaatgtaaactacgtattcgatttcaaggactttgtttattttgtggtttgacaaagtttgaacatgccgacagtgatatggcttacacttctgactgtaggtcatgggctagaaaggcaaacttgatatCGTTAGTTTACTATGCTTGGAACAATGTAC
2 Schizosaccaromyces pombe 1692 1.000-02 SPAC212.10 . . . . . pseudogene pseudo-malic acid transport protein (0 Others); truncated C at terminal (0 Others) AAAGCTTTTCATTGCTACTTGTCTTCTTTCGttatccactttcatcgacatgcttgccatatacgcctatgctgatacgggcgagtggatggtatgggtgattcgaattctttattacatttttgttgcagtagcttttatatactgtgtaagtgcttttttcacaattttcaacaatcatgtatataccattgaaaccgcatctcctgcttggattcttcccatttttcctcctatgatttgtggtgttattgctggcgctgtCAATGCTACACAACCTGCTCGTCAATTATA
3 Schizosaccaromyces pombe 967 1.000-03 SPAC212.09c . . . . . pseudogene pseudo-malic enzyme with 2 frameshifts TTCTCAATGCAATAATGCTCTTCTTTACCCtgctctaggtgttgcatgtgtgttatcccgttgcaaattgttgagcgatggaatgctgaaagcagcttccgatgctttggccactgttcctagatctttgtttgtcgccgatgaagctctcttgccagatctggacaatgctcgagaaatctctcgtcacatcgtttttgcggttttgaagcaagccatttctgaaggaatgagcacagtggatttacccaaagatgatgccaagttgaaggaatgGATTATTGAACGAGAATGGAACCCTGAATA
4 Schizosaccaromyces pombe 3762 1.000-04 SPAC212.08c . . . . . S. pombe specific families 66294 domain (1 others); possibly S. pombe specific (78 others); telomeric duplication (36 others); predicted N-terminal signal sequence (275 others); localization cell surface (predicted) (68 others) TTATTCTGGTCTCAAACTAAATAGCTCTGCtattaataaaaggtcttacttttatcctcaggattcctttcttgtgagtcatgccgaatggcaagatggtaatggtatatggacggatacggattatttcgcagctatggcggattgtgacttcttgggtcaaaatcttggtttctggcttgcaagttcctatccaaacgcatataagtgggaaacacaactgtggcgcaccgtaggaataaacctaaacggtaatataatatacccggggCAACTCATTATGCAGACATTTAACGGTA
5 Schizosaccaromyces pombe 3453 1.000-05 SPAC212.07c . . . . . pseudogene pseudo-similar to S. pombe specific protein family TTATTTGCTGGATATAAGAAGTCGCTCATCaggaaattgtcaacggcgagatcccaaagcctatggtgacaattgagtttgattctttcagatctaatacactcgtaacattaaagtttccatgacatattttcttgtcattttctattgtacttggcttattctcattgttatgggcggctgttcgttgtatttgtagccccagtaaattacgtcttatttaagttcacttgctctgttgttttcctttttaatcttaaatcatcccGTAAATCAACGAACCTTAAGCATTGATGAC
6 Schizosaccaromyces pombe 3287 1.000-06 SPAC212.06c . . . . . pseudogene pseudo-truncated C terminal of DNA helicase in rearranged telomeric region AGCAAGGGATTTGGACTCGGTATCAACtatatgggagtgcgtttagtagtacactatagattaccagcttcatctatggattatgtacaggagacaggtcgagctggaagagatggcaagtatgcgattgcagcattgttttacgagaaatatgattctacatggtcgagctacgtggaggattcgatgaaaaactttcttaatgataatacgatgtgtgttcgatcgtttctcgCAAGTGAAATGGATGGCGAATGTGTATGT
7 Schizosaccaromyces pombe 4835 1.000-07 SPAC212.05c . . . . . pseudogene pseudogene (14 others); truncated by rearrangement and LTR fragment similar to hypothetical protein-duplicated in telomeric region ATGGCTTTCGGTTTAAAAGTTGAGCCATCgggaggtggtgtccttacttctgacagtcttcctacacataatggaaaaacggcattacagtcagatgcaacagttggttctgacattcaacaaatagaattacaaaatatgcctactCCTGTGAAAAAATTAATCTTTATCGTTTTCATG
8 Schizosaccaromyces pombe 843 1.000-08 SPAC212.04c . . . . . S. pombe specific families DUF999 (9 others); telomeric duplication (36 others); 4 predicted transmembrane helices (36 others); localization cell surface (predicted) (68 others); possibly S. pombe specific (78 others) repeat expansion SQRSQRS TCTACCGTTAATCAGTATGGTTATAGCATGGgtcggtgtggttatagcagcgttcagtgtgattatcactgcaacaatagcaggagttatagcagcgttcagtgtgattatcactgcaacaatagcaggagttatagcagctatggttggaatcttatatttcggccattggctggtctacaagattttaattttggctttcggctttaaaattgtgacatcaggagacgtctgtgtttctaacactcttcctacacataacgGAGAAACAGCATTACATTCAGATGCAAC
9 Schizosaccaromyces pombe 3435 1.000-09 SPAC212.03 . . . . . S. pombe specific families hypothetical protein (130 others); possibly S. pombe specific (78 others); similar to S. pombe SPBCPT2R1.03; telomeric region has transcript profile on microarray GACAGTTCAAGACATAATATGAACATGACTCAGctgatgcaattaggtgcgtttgatagacgctcaggcgacgatttcatggtccaagacttcaaaaacggtatacgtgattgttcaggaataccagttaataatcgaaatttagcatttaaggcttatgatgctgttaaacagaagtgcgatagttccataaaagtttttaacatacaggatataactataaaaggagcaacatggcagcaccataactgccaaagtacaggCAAATGGTATTCCCAGCTTTACGATTATC
10 Schizosaccaromyces pombe 124 1.000-10 SPAC212.02 . . . . . sequence orphan sequence orphan (422 others); telomeric duplication (36 others) has transcript profile on microarray TTTATAATGACGGAGAGATTTCCAGGATAGttctactcagaactttggtaactcaatctgcggatgatgctacatggataatcaacttgacagatgatgtgcttaatggattaccactgctgaagaagcgagaccgatacaccacacaatgtcatagtacaaatatggcaagcacatatgactgtgacactggagccaatgctgttggagcccgaggtggagccacgttagcagccgactatagaggtgattggggggggggggtaatgttatacaaacCTTTGGTAGTAAAAGCGTGTCTTACTGAGA
11 Schizosaccaromyces pombe 825 1.000-11 SPAC212.01c . . . . . S. pombe specific families DUF999 (9 others); telomeric duplication (36 others); 4 predicted transmembrane helices (36 others); localization cell surface (predicted) (68 others); possibly S. pombe specific (78 others) repeat expansion SQRSQRS ATTATAGCAGTCTTGGGTGCAGTCTTGggtatgattatagcagtcttgggaatgattatagcagccttgggaatgattatagcagccctgggtgcaactataactggccttttgtattttggtcattgggctctttacaaacttgtaatattgtctttaggctttaaaattgtgacaccaggagacgtctgtgtttctaacactcttcctacacataacggagaaacagcattacattcagaaacaacagttggttctgatattgaacaaataGAACTACAAAATATGCCTACTCCTGTGAAAA
12 Schizosaccaromyces pombe 1724 1.002-01 SPAC977.01 . . . . . S. pombe specific families telomeric duplication (36 others); possibly S. pombe specific (78 others); similar to S. pombe SPAC750.05C and SPBC1348.02 and SPBPB2B2.19C; localization cell surface (predicted) (68 others) cagagatttttgacatgatccagtatgaggtatctcctgcaatttgggtgtattctatttgtcatttattgaaacaatgcacgtctgtaacaacttacgaaaatgcttcaaaagccagatttttcagaagaatgctaaatgcatttatctttatattctgtgcatctccaatgttgcattacctgtcgaatattatatttggaaactttgattacagactgtcggtgatcattggtgatcttttcacttttatggagaaaattgcttttccatgttacataatgtttcccacccataat
13 Schizosaccaromyces pombe 3780 1.002-02 SPAC977.02 . . . . . S. pombe specific families telomeric duplication (36 others); possibly S. pombe specific (78 others); 1 predicted transmembrane helix (92 others) ccctctatttataccaagactaagcctcacagtgaaatattgtctagcagtaaaattgctgatttatttattatattgttggtacatttactcggaagtaccatcggcttcatctaaattccgatcctttacatttggatgcgtcgtagtatatcataacaaattttttcctcgtttcattagaactcactccattaactccattagaacgttttctaaatttcaagtcattatacttttctctattgagaaagtcactaggtcagaaagcaagaatcattcttactcgaaaaccgatattagtgatc
14 Schizosaccaromyces pombe 4320 1.002-03 SPAC977.03 . . . . . role inferred from homology sterol methyltransferase (putative) (2 others); similar to S. pombe SPBC1348.04 and SPAC750.03C; telomeric duplication (36 others); no apparent S. cerevisiae ortholog (482 others) agatatttagccagtcttggatataaagtcgtgggtattgatatttccgaaagggctatttctaaagcaatcgataaaacatctagtgaaaaaagtaatgtcaactttaatcaacgcgatttttcaagattaaatgaattcaaggggcatttcgacactgtgattgacattggttgttttcattcaattctaaatagtgatcatgagccacacacagcttcgttaagtcatatatgtcactctgatagctccgttttcctaagagcgtttagcgaaacaaacaaatcacgttatagacggt
15 Schizosaccaromyces pombe 231 1.002-04 SPAC977.04 . . . . . pseudogene pseudogene (14 others) 5' end of gene missing. Full length gene found in cosmid c1348 13572 - 15029. Possible deletion between SPAC977.03 and SPAC977.04 (maybe as telomeric); N terminal truncated membrane transporter aataggaattttacttttcggttggactgcaagatataagattttttggtttgtgccaacaattggatcagccattatgggtggtgggtacattatgacttccaatcccttaaacatgtatgtggtagattcatatggaatttactcagccagtgcgtcagcgggtgtaaaaatatttcaactattattaggagccatctttccattatttgctgaaagtctatttcgtcgactgaactacggatgggggtgtactttacttgcctttattttattagcttgtggctgtagtcttccaatcttattca
16 Schizosaccaromyces pombe 2841 1.002-05 SPAC977.05c . . . . . conserved hypothetical hypothetical protein (130 others); telomeric duplication (36 others); similar to S. pombe SPBC1348.06C and SPBPB2B2.15; similar to S. cerevisiae YOR387C and YGL258W (1 others); predicted N-terminal signal sequence (275 others); localization cell surface (predicted) (68 others) acaacgtatttgaaaacatgcaatcctcaaagtattgaaaatgcaatgatcccttttgtgaatactgttaccagtgaaatttcttttgatgcatgggcgtatacagcacaaaattcaagtcggataacgggtcttagcaaccaactgatgaattctactctatataatgttcaagtagcaacatgtactcccggattctctgcgttattgttagatagtcctacaatcaatgtttttaataacgaggaaggcatgccaagttggtgtcagcccattgaacttataccagtttgtcctttgga
17 Schizosaccaromyces pombe 2604 1.002-06 SPAC977.06 . . . . . S. pombe specific families DUF999 (9 others); 3 predicted transmembrane helices (42 others); localization cell surface (predicted) (68 others); possibly S. pombe specific (78 others); telomeric duplication (36 others) tctttaccaacatcatcaagcctcaaaaagataaaataaacattaagacagataaaataaagttctttttaaataacctttttactgaattttctaaatttcatgatagttgttatcctgatggtaggatttctacccgcagtaaacttcgttggcccttgcttattatttggtgtattttgattgttttcgcaatagacaagaactttgaagtcaaagattttctttcaatttggataaatgaaagttttataaatgaaaatcggttttacagtgaaatttgggggcctattgctattta
18 Schizosaccaromyces pombe 1404 1.002-07 SPAC977.07c . . . . . S. pombe specific families glycoprotein (predicted) (60 others); serine/threonine-rich (6 others); possibly S. pombe specific (78 others); predicted N-terminal signal sequence (275 others); telomeric duplication (36 others); similar to S. pombe SPAPB2C8.01 and SPAC1F8.06 and SPBC1348.08c; localization cell surface (predicted) (68 others) acaccctagtcgttaacaatgtagatgatgttttctttggttggtttggtgataaagctatttctggttggtccaataataactttgatgcgtattcttattggcatgagtcgcctaatatgggtttaggaactgtgggcatgggaaatttcactgtaggcaattatcctgaaggctactttttgcccgttagatttgttgtagcaaatggagcatatatcggtggatttgatttttactttacttctgattcaacgggtccacttgctactacctcttattcttacacgaaaacatgca
19 Schizosaccaromyces pombe 3152 1.002-08 SPAC977.08 . . . . . role inferred from homology short chain dehydrogenase (putative) (15 others); telomeric duplication (36 others); similar to S. pombe SPBC1348.09; no apparent S. cerevisiae ortholog (482 others) gtattatggtaccaagtatgcaatcgaaggtatttctgaagctctgacttgggaaatgcaaagcattggtgtaaaagtcaagattatagaacctggttttacagcaactgaatttagggttgaagagggtgcaggtaaacattatgctgagtacgacaatctgaaacaaaagttgtacgaagacttgctacctaaattgaaaacagctacaccaccgcaaaaaatcgcagaagtgatattgcaagcggcaacggatgaaagtgatgagctacgataccctactggagattatgttgttgaat
20 Schizosaccaromyces pombe 1728 1.002-09 SPAC977.09c . . . . . role inferred from homology phospholipase (putative) (11 others); telomeric duplication (c1348); similar to S. pombe SPBC1348.10C and SPAC1A6.03c and SPCC1450.09c and SPAC1786.02 and SPAC1A6.04c; similar to S. cerevisiae YMR008C and YMR006C and YOL011W (5 others) ataataccccacctctccttgtatactttccaaattacccttggacttattattccaatatatcgacatttactatgagcatggacgacaagatggctaatggaattcttgagaatgcatttatgtcgactacgcaaaacaataatgaatcttttgcagtttgcttagcatgcgctataattcaacgctctttggaacgcaagaaattgagtactcctacccagtgctcttcttgtttccaagaatactgttgggacggaactcttgcaactagtacggcttctgtatatgatcctac

Total number of rows: 5239

Table truncated, full table size 2701 Kbytes.




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