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Platform GPL8206 Query DataSets for GPL8206
Status Public on Mar 31, 2010
Title FGSC-N. crassa-10918-NC_10/04/05 UCB
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Neurospora crassa
Manufacturer N. Louise Glass's lab in Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
Manufacture protocol To construct a gene-specific microarray of N. crassa genome, we designed 70-mer oligonucleotide immobilized probes using ArrayOligoSelector, and the approximately 10,000 open reading frames (ORFs) derived mainly from the N. crassa databases at the Broad Institute and MIPS. ArrayOligoSelector selects a unique segment to identify each ORF considering the predicted sequences of all genes. The program avoids selecting internal self-annealing structures and internal repeat sequences, and preferentially chooses oligonucleotides within a narrow range of GC content, which are biased towards the 3' terminal region of each gene. Oligomers were synthesized (Illumina, San Diego, CA) for all ORFs. Analysis of oligomer placement in predicted genes indicated the desired strong 3' bias. Oligomers were re-suspended in 3x SSC to a final concentration of 20µM, and spotted. Eight 40mM ArrayControl Sense Oligo spots, which were complementary to the eight ArrayControl RNA spikes (Ambion, Austin, TX, USA), were also included. Amplified DNA may be precipitated in 96-well format with isopropanol, washed with 70% EtOH, and resuspended in a salt spotting solution such as 3X SSC. DNA is commonly spotted on polylysine-coated glass slides or γ-aminopolysilane (GAPS)–coated glass slides (Corning, Corning, NY), using a microarraying robot. GAPS slides are more expensive but have a better shelf life and tend to be less variable in quality than poly-lysine coated slides. An example of cDNA array can be seen here. 10,918 oligomers are on the chip. 10,526 oligos are based on MIPS or Broad Institute predicted ORFs. 8 oligos are Abmion ArrayControl Sense Oligo Spots (#1781). The remaining 384 oligos (ChIP_Chip) were mainly designed in the intergenic regions. 40uM oligos in 3x SSC were printed onto Corning UltraGAPS slides. Slides are not post-processed. Rehydration is optional. Oligos need to be cross-linked with 600mJ UV. Slides should be stable for a year at room temperature in desiccator. Slides may display unacceptable levels of green background and the way we know to remove is using the Pronto!™ Background Reduction Kit (Item #40029) from Corning. It is not 100% effective so we recommend prescanning after prehybridization and identifying spots that are 3x standard deviation above background for possible elimination. For fast, easy, successful fist microarrays, we recommend to use Corning/Promega kit: 40076 Pronto Plus Indirect System and RPN5661 Amersham Post-labeling Reactive Dye Pack, which are expensive but always give brilliant results.
 
 
Web link http://www.yale.edu/townsend/Links/ffdatabase/introduction.html
Submission date Feb 19, 2009
Last update date Mar 31, 2010
Contact name Chen-Hui Chen
E-mail(s) chen-hui.chen@dartmouth.edu
Phone 603-650-1120
Fax 603-650-1233
Organization name Dartmouth College
Department Genetics
Lab Dunlap and Loros lab
Street address 702 Remsen
City Hanover
State/province NH
ZIP/Postal code 03755
Country USA
 
Samples (12) GSM372472, GSM372473, GSM372474, GSM372475, GSM372476, GSM372477 
Series (1)
GSE14909 Molecular characterization of a cryptochrome in Neurospora crassa

Data table header descriptions
ID
Gene ID Name of corresponding NCU gene
Sample ID IDs of genes from which oligos were designed. The last number of the ID indicates distance of the oligomer from the stop codon.
NAME Gene Description
ORF
SEQUENCE
SPOT_ID Spot identifier

Data table
ID Gene ID Sample ID NAME ORF SEQUENCE SPOT_ID
1 NCU01175.2 123a4_020_804 MIPS:farnesyl-pyrophosphate synthetase BROAD:FARNESYL PYROPHOSPHATE SYNTHETASE (FPP SYNTHETASE) (FPS) (FARNESYL DIPHOSPHATE S NCU01175.2 ATTGTCACACCCGAGCAACGCAAAACGCTCGAGGAGAACTACGGCCGCAAGGACAAGGCCAAGGAAGCTG
2 NCU10360.2b 123a4_100_2243 MIPS:conserved hypothetical protein BROAD:hypothetical protein NCU10360.2b GGTGAACCCTCAAAAGTCGGAGTGGCGGACCGTGAGAAGCGACGAGGATTGGAGCTTGATTTACAGCTGG
3 NCU01160.2 123a4_200_1367 MIPS:probable RNA helicase DBP5 BROAD:hypothetical protein NCU01160.2 TACCGAGAGGAAGGTGCAAGAAGTTATCAAGTCGAGCAGGGCCCAAGCGGAGTACGTTCCCAGCGCTACT
4 NCU01370.2 15e6_030_1569 MIPS:related to origin recognition complex subunit 2 BROAD:hypothetical protein ( (AL353822) related to origin recognition complex subunit NCU01370.2 ACATCAGGGGCAGGAGACTTTGCAGCGGGAGGAGAAGGGCCGGGGGTAGAGTATAGGATGCTTTACAACA
5 NCU01361.2 15e6_130_2358 MIPS:conserved hypothetical protein BROAD:hypothetical protein ( hypothetical protein 15E6.130 [imported] - Neurospora cra NCU01361.2 TGTCTCTCCACAGCTTTACGCATCGCCCCCACCCCCACACTCCAAGAGATCCTCAATGCATTCCGAAGAG
6 NCU03742.2 17e5_010_969 MIPS:hypothetical protein BROAD:hypothetical protein ( (AL513467) hypothetical protein [Neurospora crassa] ) NCU03742.2 AGAGGCGAGCTGCCGAATTGCAAGAAAGCTTCTCTGATGCTGTGCACATGGGGATGTCAAGGGGCTGGTG
7 NCU01033.2 1a9_090_2678 MIPS:related to regulatory protein wetA BROAD:hypothetical protein NCU01033.2 AAGAAAGTTATCCGAGGCCATGGTGAAAGTCGTCGAGGCTGCTGGGGGAGATGTTAGGAAGCTGGGGGAG
8 NCU01021.2 1a9_200_757 MIPS:related to translation initiation factor 3 (47 kDa subunit) BROAD:hypothetical protein NCU01021.2 CGCTCGGCCAGTACCTCATGAATGCCCTTTCCCTCGCTCCCAAGGTGTCCAATTTGGCCATCGAGAACGA
9 NCU08052.2 1nc100_050_1022 MIPS:related to aquaporin BROAD:hypothetical protein NCU08052.2 CGCGCATCAAGATGGATTGAAACACACTCCTACCAACCTTACGCAACCCCTCGCTAATGGCGAGGCGGCT
10 NCU07439.2 1nc120_140_103 MIPS:putative protein BROAD:predicted protein NCU07439.2 CTGATAGTGCCAAGGCCACGTTCGAGCAGGCGTCAAAGGCCATGCCCGGTCCCGCCATCTCGCAGAACAT
11 NCU07448.2 1nc120_220_732 MIPS:related to tol protein BROAD:hypothetical protein NCU07448.2 GGTAATGGTCCCGTTGGTCCACAACTAAGGCGTGAGTATGGGCCTTTTCTCACCTCTCGACGGCCTAGAG
12 NCU07456.2 1nc130_010_555 "MIPS:probable riboflavin synthase, alpha chain BROAD:hypothetical protein" NCU07456.2 CGGGTGGTGGTGGCAGGAAAAAAAGTGGGCGAGACGGTGAATGTGGAGGTGGATATGACGGCCAAGTATG
13 NCU09093.2 1nc200_250_1514 MIPS:related to ATP-dependent RNA helicase BROAD:hypothetical protein NCU09093.2 TTACACTGAGCGTGACGAAGATCTCGCTTCTGTTCTCACTCGCACCCTCCTCGAGACCGGCCAGGAAGTT
14 NCU09101.2 1nc200_330_1009 MIPS:related to acetyl-CoA transporter BROAD:hypothetical protein NCU09101.2 TCGAGATCGGTTTGGGATACTACGCAGGAAAGTGGTCACAGGAGTTCACGCCCATGCGTCTCTGGTGCTG
15 NCU09806.2 1nc250_050_83 MIPS:putative protein BROAD:predicted protein NCU09806.2 GGAGGCTATCAAATCCATCATGCCTGGGGCCTTGACCGATTGCTCGCAGTTCGAATTCTCTAAGGAGTGC
16 NCU01941.2 1nc320_020_163 MIPS:hypothetical protein BROAD:predicted protein NCU01941.2 CTGCCTATCCTGAACGACAGTCTGTCAGCTTTCCGAAACGCGAGGTGCCCATCAAGTGGCCACCCATTAA
17 NCU01950.2 1nc320_100_1041 MIPS:related to step II splicing factor SLU7 BROAD:hypothetical protein NCU01950.2 GCCGGCCTGATCAAGGGGGCACCGAAGAAGGTCGGCAAGTCCAAGTATCTCGAGGACGTTTACATCAACA
18 NCU01959.2 1nc322_010_989 MIPS:Mating type protein A-2 BROAD:hypothetical protein NCU01959.2 TCAGGAGCGCCCACTTAGCATTCTCTCCCATGTTTTCACTCGACCCGCACTTTGGGGAGAGGGTTTGGAG
19 NCU02130.2 1nc356_090_1090 MIPS:hypothetical protein BROAD:predicted protein NCU02130.2 CACGTGTCACCGAAGAGTCTATAGTTGGCTCACCTCGGCCGCCGCTCAGAGTCCCGTTGTTTTCTCAAAG
20 NCU02139.2 1nc356_170_1981 MIPS:related to annexin XIV BROAD:predicted protein NCU02139.2 ATCTTGTCGGAGAAGTCCTAGCCCACATTCTCAACGGCGTCATCAATAAGCCCGTCCGCGACGCCATGCT

Total number of rows: 10788

Table truncated, full table size 1850 Kbytes.




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