NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL11307 Query DataSets for GPL11307
Status Public on Oct 01, 2011
Title Agilent custom Kluyveromyces lactis 11K Array [G2509F]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Kluyveromyces lactis
Manufacturer Agilent
Manufacture protocol See manufacturer's website
 
Description catalog number G2509F (november 2007), Custom Microarray GE 8X15K Custom Microarray GE 8x15K 60mer, sold in multiples of 1-1'x3' slides, 8 microarrays per slide
oligoset design: /K. lactis /NRRL Y-1140 genome version 3 (S. Casaregola, personal communication) was used as a reference for microarray design. Probe design was performed using ROSO software completed with in-house scripts. ROSO takes a number of parameters into account to design effective oligonucleotide probes: (i) uniqueness among the genomes and lack of cross-hybridization against exclusion genomes; (ii) melting temperature (Tm); (iii) lack of secondary structures; and (iv) distance from the 3' end of the gene. ROSO was run on the 5,270 candidate target genes. Our objective was to obtain one probe with a length of between 40 and 60 nucleotides per target gene. Probes have to be in exons and are preferably located at the 3' end of the gene. The genomes of /Arthrobacter aurescens /TC1/, Arthrobacter sp./ (strain FB24), /Corynebacterium glutamicum,/ /Lactococcus lactis/ IL1403, /Debaryomyces hansenii/ CBS767, /Brevibacterium aurantiacum/ATCC9174 (formerly /B. linens/) and /Yarrowia lipolytica/ CLIB99 were used as exclusion genomes, creating prospects for transcriptomic ecosystem studies.
 
Submission date Dec 10, 2010
Last update date Oct 01, 2011
Contact name Jean-Marie Beckerich
E-mail(s) Jean-Marie.Beckerich@grignon.inra.fr
Phone 00 33 01 30 81 54 43
Organization name INRA
Lab MICALIS
Street address Campus Agroparistech
City Thiverval-Grignon
ZIP/Postal code 78850
Country France
 
Samples (30) GSM638289, GSM638290, GSM638291, GSM638292, GSM638293, GSM638294 
Series (2)
GSE26013 Exploration of the sulfur metabolism in the yeast Kluyveromyces lactis
GSE55128 Exploring the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8 and KlYap1

Data table header descriptions
ID FeatureNumber
Row Row
Col Col
SEQUENCE Probe sequence
ProbeUID Probe ID
ControlType Control type
ProbeName Probe Name
ORF ORF Name
SystematicName Systematic Name
Description Description
SPOT_ID Spot identifier

Data table
ID Row Col SEQUENCE ProbeUID ControlType ProbeName ORF SystematicName Description SPOT_ID
1 1 1 0 1 GE_BrightCorner GE_BrightCorner --GE_BrightCorner
2 1 2 1 1 DarkCorner DarkCorner --DarkCorner
3 1 3 1 1 DarkCorner DarkCorner --DarkCorner
4 1 4 GCTCAGATCAAGGATAAATCATATGACAAAGTCAGAGTTGGTTTCAAATATCAAGGTAAG 3 0 KLLA0B06754g_1 KLLA0B06754g KLLA0B06754g Unknown
5 1 5 CTATCTTCGTTCAAGTGCCAAGTGGTGTTGCATCTCAAAGCTCTCTATTA 4 0 KLLA0F02816g_1 KLLA0F02816g KLLA0F02816g Unknown
6 1 6 CAAGGCATAGTGATCTGTTCGGATGAGGACATTATTAATTTATATGATTTATTTGCAAGC 6 0 KLLA0F11363g_1 KLLA0F11363g KLLA0F11363g Unknown
7 1 7 GATCATCGACGAATTGCCAGAATTACAACCGCATGTGGAATCTATTATCG 7 0 KLLA0B10714g_1 KLLA0B10714g KLLA0B10714g Unknown
8 1 8 TTGACTTACGATTTGCAATATATTACTAGTCCAGGAAAGTTCGATGAAGTGGTAGAGCAA 9 0 KLLA0F18150g_1 KLLA0F18150g KLLA0F18150g Unknown
10 1 10 GACAGCAGTGATATCTCTACTTTGCAAGCTATGCTTCGAGCAATATCAAC 12 0 KLLA0D14531g_1 KLLA0D14531g KLLA0D14531g Unknown
11 1 11 CCATGAAACTCAATTCTTGATTACAGATTGCTTCCAGAGGTGGATTGAAATAAATTTGAG 13 0 KLLA0C06006g_1 KLLA0C06006g KLLA0C06006g Unknown
12 1 12 TGGTTAGCCAACATAAGATGCTCGAACTCTGACCCACTTATTACATCATCATTTATTAGT 14 0 KLLA0A08690g_1 KLLA0A08690g KLLA0A08690g Unknown
13 1 13 GATGTTGTCAAGACAAGGATGCAAAGCAAATACACTTGGTCTTTATACAGGAATTCTTTG 15 0 KLLA0A00979g_1 KLLA0A00979g KLLA0A00979g Unknown
16 1 16 CAGCTAGATCCGAAAGATTGGCTAAATTGAACCAATTGCTAAGAATTGAAGAAGAATTGG 19 0 KLLA0A09185g_1 KLLA0A09185g KLLA0A09185g Unknown
18 1 18 GTAGAGGATTAATGAATGAACTACAAAGTACCGCTAACAAACGTGGCCAA 21 0 KLLA0E11815g_1 KLLA0E11815g KLLA0E11815g Unknown
21 1 21 TCACTGATGTAAAGATTCCTCCTGGTAAACAATGCGGATTTGTCAAATACAACGAAAGAT 24 0 KLLA0C05522g_1 KLLA0C05522g KLLA0C05522g Unknown
22 1 22 TTACGACATAACAAACAAATCCAACTTCTGCTTCATGACTTGATATCCGGTGATATCTGT 26 0 KLLA0D08976g_1 KLLA0D08976g KLLA0D08976g Unknown
24 1 24 AATTCTCAAGGGTTTCACAGGTTTGTACGAAGAGTTTACTACAAGGTCAACGGTATTAAT 29 0 KLLA0D19140g_1 KLLA0D19140g KLLA0D19140g Unknown
26 1 26 CTCGTCTGGCTTGTCCTCAGTCTATATTACGACATTTCCAACAAATTTGG 31 0 KLLA0F05863g_1 KLLA0F05863g KLLA0F05863g Unknown
27 1 27 GATTTACCTGCATACGATTCATACGAACAATTGCGTGGTTCTTTGTTATTAGCGATTAAC 32 0 KLLA0B01804g_1 KLLA0B01804g KLLA0B01804g Unknown
28 1 28 GGCCAAACTGAGAATGATATGTCCACATATTCCAAATTCCTATGTTTGTATACAAGAAAC 34 0 KLLA0C06765g_1 KLLA0C06765g KLLA0C06765g Unknown

Total number of rows: 11168

Table truncated, full table size 1325 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