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Platform GPL2857 Query DataSets for GPL2857
Status Public on Mar 20, 2006
Title KARC Schizosaccharomyces pombe 5K Ver. D 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 60-70C. 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, 95C for denature, 72C for extension, for annealing 54-63C 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 50C, for 15-30 minutes. The slides were rinsed twice with distilled water (DW), and soaked in a wash buffer (4xSSC, 0.1% SDS) at 50C, 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
 
Description The breakdown of 5184 spots is as follows; 4929 fission yeast genes (cdc2, nuc1, and nda3 are excluded) are spotted once on a slide, cdc2, nuc1, nda3, and GFP are spotted once for each block (16 in total). Representative values of r' for these 4 genes were average of their 16 spots. ID numbers from 5185 to 5188 are assigned to their representative values. 11 negative control spots are common to each block (A to P except, 176 in total). The reaction mixture except primers was spotted at negative control spots. Only spotting buffer were spotted at 8 blank spots. Spots for the following 7 ORF, SPAC212.10, SPAC3G9.16c, SPBC19G7.12c, SPCC784.05c, SPCC1442.04c, SPAC8E11.04c, SPBC2A9.08c, are ignored in data processing (see details in http://www-karc.nict.go.jp/d332/CellMagic/index.html).
 
Web link http://www-karc.nict.go.jp/d332/CellMagic/index.html
Contributor(s) Chikashige Y, Tsutsumi C, Haraguchi T, Hiraoka Y
Submission date Sep 20, 2005
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 (39) GSM75419, GSM75420, GSM75421, GSM75422, GSM75423, GSM76685 
Series (3)
GSE3336 Two-step, Extensive Alterations in the Transcriptome from G0 Arrest to Cell Division in Schizosaccharomyces pombe
GSE3515 Meiotic proteins Bqt1 and Bqt2 tether telomeres to promote the bouquet arrangement of chromosomes in fission yeast
GSE4449 A defect in protein farnesylation suppresses a loss of fission yeast tsc2

Data table header descriptions
ID
ORGANISM
ORF Number Open Reading Frame Number assiigned 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 ORF Number ORF D Name Reserved Name Gene Synonyms Obsolete Synonyms status Curation SEQUENCE SPOT_ID
1 Schizosaccaromyces pombe 3.006-02 SPCC613.02 role inferred from homology membrane transporter (46 others); similar to S. pombe SPCC613.01 and SPCC330.07c and SPCC757.11c (paralogs); conserved in A. thaliana (2 others); no apparent S. cerevisiae ortholog (482 others) gtctaaatgggcagaagatagagatatgatgctttatggctttatattgggaatactggctcttgttgtacatcttgttttagacgttcttcacaaggttcgcgtgcagccatactttgttttgtactctgccatgcagtttgggtttagtatcggttccgcaccattaatttcacttgctactaaacaattgcatccgaaatatcatatccttgtcggcattattgttcaaattggtatatctgctgcagatacagttggtgctatctgtggaggcgctatatttgatata
2 Schizosaccaromyces pombe 3.028-08 SPCC16C4.06c role inferred from homology tRNA pseudouridylate synthase (putative) (2 others); involved in tRNA modification (9 others); similar to S. cerevisiae YPL212C and YGL063W (2 others) agccctttcgtttatccaaacctaaactcgactttctaaagcatgcgtgtacgatgtttcggggcacccatcgatttcacagttatacaacggagaagggtttttcggacgccagttctcgaaggtttttattagatgtgcgtgtggataaccttcacattgacaagttaaatcgccaatgggttaagctaatctttcacggccagtcgtttatgaagcatcaaattcgcaaaatggttggcatccttattcatcttacacgcactggatggaatgcgcaagttttgctaaatacatt
3 Schizosaccaromyces pombe 3.050-09 SPCC4B3.10c ipk1 experimentally characterised (or published) inositol 1,3,4,5,6-pentakisphosphate (IP5) kinase (PMID:10960485); similar to S. cerevisiae YDR315C ggtagacccgttggtttttgtcctctacagcttgatttcaacaattggcccaagtttttgtgctgtcttcaaggatttgtgagtcctgatatcgcaatgagattgtttcagtctggtatactacggaagcttcgtgacctacaagagcaatactctcgtactgatgttgcgttagcgatgacccttcgagatgtgactttatacattggtaaagatcacataacattactagatttagatcctaaagacatgaataccaaaatgtctaaatgggaacgtgatgaaaggaattt
4 Schizosaccaromyces pombe 3.032-13 SPCC1020.02 spc7 experimentally characterised (or published) kinetochore protein Spc7p; essential (PMID:15371542) (188 others); coiled-coil (region) (96 others); similar to S. cerevisiae YGL093W S. cerevisiae SPC105 can rescue S. pombe mal3 mutant strains (PMID:15371542); S. Pombe Centromere ctgtaagttccctaacgaaagtaatgcttgcagctcaaatgtgctcgagcatgttgcatcgtcgttttctaaatggcattccaaggtattttctaggaacttacgtcttctgaagaagtatcttaacgatgtttcaatttgttgggaacaaattgtttatcttgtccaagatttccagcgattatggtaccattggccctttttgtcagttgaaaatgatgataagtctattatcataaatgttgagctatacctgcgttcggtatcatctaaggtaaaggttgttttcggtctcccaattgatactat
5 Schizosaccaromyces pombe 2.171-08 SPBC8E4.02c sequence orphan sequence orphan (422 others) gttcgccgagtttaatggaagtggaagcatgcatgctttgttgatgtctattttgtcaaagaaatcttatcacccaacatcctatcgggttggaggatatcggaaccaacttatccgggtgttctgtgtgtgggcatgcattgagctacacagcatcaatccgtggtattctggaatgtatacttttgaaaccggccgattactggttttaaaacaacgacatcgcgtgctttccatggaattgaaaaaaccaaacagctcgacgattaaaccgtgttttacttgggccaattctgtattgt
6 Schizosaccaromyces pombe 2.134-14 SPBC2G2.14 sequence orphan sequence orphan (422 others) gagagtcaaccgactaatctagggaggaaagaatattcaaattcgcctttttctatcagagctagaaaagatgcagcaactactagttcctcatttgaaagttatcacaatacacaaacgatacaatcacctatgaaatttacaaaagcgacgcctttgaaagacaatgagtcagctagtgtcgatgaaagtaaagtaaatgtgttgtcggagaaccagtctttacaggccgataccgctacgttggaacaacttacaccaattccaaaggcaaggtggaaccaacttgcaaataaacacccttc
7 Schizosaccaromyces pombe 2.160-09 SPBC14F5.09c ade8 experimentally characterised (or published) adenylosuccinate lyase (1 others); involved in purine biosynthesis (8 others); similar to S. cerevisiae YLR359W ctaaggttattcaaaaacacattcgtgctgaattgcccttcatggccactgaaaacattatcatggctatgactaagcacggtgctagtcgtcatgagtgtcacgagcagattcgtgtcttgtctcatcaagctggccgagtagtcaaggaagagggaggggataacgacttaattgagcgtattaagaatactccttattttgctcctatttatgatgagctagattctttgttggatgcatccacttttgttggacgtgctcccgagcagactgaatcctttgtaaataaggacgt
8 Schizosaccaromyces pombe 2.146-17 SPBC21C3.17c conserved hypothetical conserved fungal protein (77 others); similar to S. cerevisiae YKL077W (1 others); predicted N-terminal signal sequence (275 others); 1 predicted transmembrane helix (92 others); similar to S. pombe SPCP31B10.04 homology to YKL077W is low but has conserved residues by multiple alignment, conserved N-terminal signal peptide and C-terminal transmenbrane helix gataagaaatggcttatgaagatggacaacattactgcgcgagttgttgctgttcctcaaaatggtaccgccagcacggtatatgtgggtccacaggtcctattagcgaacacgttttactggaagatggtagtggatgtttcccctgcattttctgtaaacccgattgacaagaaacttgcaattgggttatccgttggtttatcctgttgcatactgatcgttctatttcttcattttgcaactaggagagaaagaaggattttaaaaaacgagaaagagctggaaatgtcttcatatag
9 Schizosaccaromyces pombe 2.113-05 SPBC1703.05 role inferred from homology RIO1 domain (1 others); protein kinase (predicted) (PMID:12690111); involved in rRNA processing (predicted) (48 others); similar to S. cerevisiae YNL207W tttccgcaaatggtatctactagtcatcctgatgcgcaattttattttgatagagacgtacagtgcattgtgcaatattttgaaaaaaactatcaatacaaaggtgatgttcctaatttcgaagacatatcgaaaatggaaaaggaaaataatttggatatcatgattgaggcttcaggatttaataagaaacaatctaaagaactagaaaaatatagacaagaagaagaaaaaagaaaagaaaatggtgatgatttatctgataactatgaagaagaagaagaagagaaggaatga
10 Nctrl Nctrl CONTROL
11 Schizosaccaromyces pombe 1.150-03 SPAC15E1.03 rpl36a experimentally characterised (or published) 60S ribosomal protein L36/L42; similar to S. cerevisiae YNL162W and YHR141C gtgaacattcccaagacccgtaagacttactgtcctggtaagaactgccgcaagcacactgtccacagagtcacccaatacaagaagggacctgattccaagcttgctcagggtaagcgtcgttatgaccgcaagcaaagtggttttggtggtcaaactaagcccgttttccacaagaaggctaaggttaccaagaaggttgtccttcgtttggaatgcgtctcttgcaaatacaagaatcaattggttttgaagcgttgcaagcatttcgagcttggtggtgaaaagaaga
12 Schizosaccaromyces pombe 1.005-03 SPAC11D3.03c conserved hypothetical conserved eukaryotic protein (236 others); similar to D. melanogaster CG10208; no apparent S. cerevisiae ortholog (482 others) cagagtttgacgtccatgatgtattgaatgtctttcaagtcaccgggcttaacgaatatgatcaatacttcatggaaacgtgtcccgcaacttcaaaagattatttccaatgtttcgcagaacaagatttattggttgcaattagtgcttgtcctggtggagacttatcaaattggggctggggagaggacgctactgatgttgaaagcagcaaaatggtggattgctgtaggcctttggctatagaagtctatgagttagaagatgaagagaactcattgaaaggttgggtt
13 Schizosaccaromyces pombe 1.207-13 SPAC29A4.09 conserved hypothetical conserved eukaryotic protein (236 others); similar to S. cerevisiae YDR412W; localization cytoplasm (predicted) (43 others); involved in rRNA processing (predicted) (48 others) gagttgaatagctcgctagaaaatgatgaagaatcttcacagcaagaagattcctcatctaaatctgacagcgaggaagagtcatcaatggagcctaaaactactgagtatgacgaagatgataagcatgttacggtagaaattgtagaggacgatgatgatgaagaaattgcttatcctaaagaaggttttgtcacgcctcgtatttctcctccaccagatgttcctttgcgtccccacaagcctaaaaatgccgccaaaaagaaatttcggtatgagagcaaatttgaacgtacac
14 Schizosaccaromyces pombe 1.165-17 SPAC23A1.18c mrp51 role inferred from homology mitochondrial ribosomal protein small subunit mrp51; similar to S. pombe SPBC2G2.07c; similar to S. cerevisiae YPL118W (1 others) cagatgcctctactgcatactacggtttagggggcttgattctgaggctacctcgaacagttgtctttaatagaaatcggtcatctcccctcttttcccaggaacagcgcatttcttatacagtctataaaaatggtcgactccgactagttcccttttccggtcccgagttagaaacacatcttgcctatccctcggaagactcggaggttgaatcgttttttaacagagatattcaattggtagccaaaagagattcatctctcgatgctcccgtatcctatcaacggggtattatgaaatt
15 Schizosaccaromyces pombe 1.199-12 SPAC1B3.11c ypt4 experimentally characterised (or published) GTPase (18 others); Ypt subfamily (3 others); no apparent S. cerevisiae ortholog (482 others) ggtgctgttttagtctatgatgtgacaaacaaggactcgtttgaagaattgtcgtcttggctgtctgatattcgagctatggctccatcaacaatatgtgttgtattggctggtagcaaatctgatttacaaaaccaacgacaagtctctactgaagaggcagctgagttttgctcagaaaagcatatatctagtgcgcatgaaactagttcttatacaggaagcaacgttgaagagtgttttctttccgttgtctccaccataataactaggattgagttgggtgaaat
16 Schizosaccaromyces pombe 1.198A-02 SPAC4F10.02 role inferred from homology aspartyl aminopeptidase (predicted); metallopeptidase (16 others); peptidase family M18; similar to S. cerevisiae YHR113W gtaaaaagttttctagtttctgctgacatggctcatgccatgcatcccaattactcatctcgctatgaaaattcgaataccccatttttgaacaaaggaactgtaattaaagttaatgcgaatcagcgttatacgactaattccgcaggcatagtccttttaaagaaagtagctcaactcgccgatgtgccaattcagtcattcgtggtgcgaaatgattctccttgtggaagcactattggtcccaaacttgctgccatgacaggaatgcgtacactcgatttaggaaatcctatgctttctatg
17 Schizosaccaromyces pombe 1.025-05 SPAC1F3.05 role inferred from homology VHS domain (2 others); GAT domain (inferred from context) (1 others); ubiquitin binding (ISS) (1 others); involved in intracellular protein transport (predicted) (44 others); involved in vesicle-mediated transport (39 others); involved in Golgi to vacuole transport (predicted) (2 others); localization Golgi (predicted) (9 others); adaptin C-terminal domain (1 others); similar to S. pombe SPBC25H2.16c; similar to S. cerevisiae YHR108W and YDR358W (1 others) gtcaatgttatcatccctttctaactctatgtcgtctacgtcgaatggagctttgaattcaccttcttatagtcaagcagcaatccccaacactaattcatctttgacatctattcttcaatctgattcattaatgatttctactcaattaacttcggttcaaaaaagctctggctttgcttcatactccgttcagttctctaattgctcccttacctggccagtgtccgaagtagtcttccaggtcgcggttgtgaaatctctcaagttacagctacttcctcatactg
18 Schizosaccaromyces pombe 1.126-02 SPAC1786.02 role inferred from homology phospholipase (putative) (11 others); similar to S. pombe SPAC977.09c and SPAC1A6.03c and SPCC1450.09c and SPBC1348.10c and SPAC1A6.04c; GPI anchored protein (predicted) (PMID:12845604) (pers. comm. Birgit Eisenhaber) (38 others); glycoprotein (predicted) (60 others); similar to S. cerevisiae YMR008C and YMR006C and YOL011W (5 others) ctactttctttggctgcgatggtagaaacactactcgtggtgacgttcctgttgaccacaacacccctcctttggttgtttacatgcccaacactccttggacaatgaaatccaaccttgtcgatcatcgctatcgtattgcaaacagcgagattcaagctttgatccaaaacggatttgtcgccactactcaagacaactctactgactttgcctcttgtttggcttgtgccgtcgtccaacgctctttggaacgtcgcaatcaatctacttctgctgcttgtcaacaatgcttta
19 Schizosaccaromyces pombe 3.030-06 SPCC18B5.06 erf1 sup45 role inferred from homology translation release factor eRF1; omnipotent nonsense suppressor; similar to S. cerevisiae YNL001W atccttcattctagcactggtcatattcattcccttaatgaaattttgaaggaccctgctgttgaatcaaaactagccgacacaaaatacgtacaagaaattcgcgttctgaataaattttacgatgtcatgaatgaagatgatagaaaggcatggtatggtccaaatcatgttttgaaggcttttgaacttggcgcgatcggagaacttctgattagcgattctctgttcaggagttctgacattgctactagaaaaaaatgggtttcattagtagaaggtgttaaggagat
20 Schizosaccaromyces pombe 3.038-06 SPCPB16A4.06c dubious dubious (88 others) aatcctcagaaggacagctttcaacttctcctcctcgtcgttggcgcaattgcactctgcaacgacacggctcaagagcctcggcagatgaattttgcgaacaatatcgctctcgctcacatggccctcaaggtaggagaagcttagagcatgataaccagttttttaatagtcgaacatattacggcaatggtggtaatacgactgatacagaagctctgcaaaaatccgttggtagtcaatctgccgatgagtttgaaacgttaagagagcaaactgtacctaacccaattgctgaagctt

Total number of rows: 5188

Table truncated, full table size 2652 Kbytes.






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