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Platform GPL4517 Query DataSets for GPL4517
Status Public on Sep 12, 2007
Title UCT Brombacher lab Mus MEEBO 40K version1
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Mus musculus
Manufacturer Capar Microarray Facility, University of Cape Town, South Africa
Manufacture protocol Platform type: spot printed
Slide surface: Gamma Amino Propyl Silane (GAPS)
Slide dimensions: 25 x 75mm
Spot diameter: 100um from 10K pin set
Spot attachment: ionic during to printing then covalent attachment via UV-crosslinking and baking
Printer: MicroGridII, BioRobotics
Software: TAS, BioRobotics
Printing solution: 50% DMSO
Drying after printing: 12 hour minimum, room temp.
UV crosslinking: 120mJ
Baking: 2hour 80°C
Support glass
Coating aminosilane
 
Description The MEEBO (Mouse Exonic Evidence Based Oligonucleotide) Set contains a collection of oligo probes, largely derived from constitutively expressed exons, allowing interrogation of almost 25,000 mouse genes. The set was designed to enable study of mouse transcription patterns and, as
broadly as possible, alternative splicing. An exon-centric design was selected to allow the differentiation of constitutively expressed versus alternatively expressed exons. This design also supports comparative genome hybridization (CGH) analysis. In addition to the exon-centric probes, the set contains an extensive assortment of controls that facilitate accurate evaluation of expression results.
The MEEBO Set contains 38,467 70mer oligonucleotide probes with an amino modification on the 5’ end. Probes are provided at a final yield of 200pmol each, and delivered in 101 384-well microarray print plates (Genetix model X7020). Probes are Tm normalized, and are designed to minimize cross-hybridization and secondary structure.
 
Web link http://alizadehlab.stanford.edu/
Contributor(s) Schwegmann A, Guler R, Cutler AJ, Arendse B, Horsnell WG, Flemming A, Kottmann AH, Ryan G, Hide W, Leitges M, Seoighe C, Brombacher F
Submission date Nov 02, 2006
Last update date Apr 13, 2011
Contact name Anita R Schwegmann
E-mail(s) SCHANI002@uct.ac.za
Phone 27214066035
Fax 27214066029
Organization name Institute for Infectious Diseases and Molecular Medicine, University of Cape Town
Department Division of Infectious Immunology
Lab S1.21
Street address Institute for Infectious Diseases and Molecular Medicine, UCT medical School, Anzio Rd, Observatory
City Cape Town
State/province Western Cape
ZIP/Postal code 7925
Country South Africa
 
Samples (8) GSM143886, GSM143893, GSM143895, GSM143896, GSM143897, GSM143901 
Series (1)
GSE6256 Identification of genes involved in macrophage activation and effector functions against Listeria monocytogenes.

Data table header descriptions
ID
MEEBO_ID Contains the MEEBO ID for each feature in the oligoneucleotide set.
Block Contains the block number of each block on the MEEBO array (there are 32 blocks).
Column Contains the column number of each column in an individual block.
Row Contains the row number of each row in an individual block.
Plate_Name Contains the name that will appear on the plate label. The MEEBO oligonucleotide set was purchased from Illumina, San Diego, CA, USA.
Plate_Num Contains the plate number used to identify which packing box a plate is located.
Row
Column
Probe_Name Contains the oligo name.
GENE Entrez GENE ID
Gid Contains the GenBank Identifier number.
GB_ACC Contains the GenBank accession number. GenBank Accession number
GB_LIST Contains the a list of GenBank accession numbers. GenBank Accession number
Symbol Contains the gene symbol
SEQUENCE Contains the 70mer oligo probe sequence.
SeqID Contains the unique oligo probe sequence ID
Tm Contains the oligo melting temperature.
GC Contains the percentage of GC content within the probe sequence.
Product Contains the probe target definition.
Description Contains the specific annotation for each 70mer is detailed and is carat (^) delimited as follows: MCC Details: [LLID (060504) ^ Design type ^ cluster ^ Long Oligoname ^ outputset ^ worstxhyb ^ oligo_3_marg] - Where LLID refers to LocusLink ID, which can be linked with gene annotation data through a variety of tools including BatchSource.
organism Contains the organism source of each feature on the MEEBO array.
SPOT_ID

Data table
ID MEEBO_ID Block Column Row Plate_Name Plate_Num Row Column Probe_Name GENE Gid GB_ACC GB_LIST Symbol SEQUENCE SeqID Tm GC Product Description organism SPOT_ID
1 mCM038128 1 1 1 DC004 100 E 16 AmbionRNASpike8_1800_a_21_1 CGCCGATCGCCTTTGAAGTGCATAAAGGCTGGCATATTCAGTACAACATCGTTTCCCGCGTGACACCGCA mSQ038128 79.4 0.53 DC Details: [Mismatch Controls; Anchored^2026^^Pick70+mutator^Ambion^AmbionRNASpike8^Ambion^AmbionRNASpike8_1800_a_21_1] none
2 mCD037383 1 2 1 DC002 98 F 15 AmbionRNASpike1_222 CATTCTCTGGAAGGTGAACTTTTACATCGTGATGATTTACCTGCGGATGTCGCGGAGCTGGTGCTGTATC mSQ037383 77.7 0.49 DC Details: [Ambion doping sense^776^484^Pick70^Ambion^AmbionRNASpike1^Escherichia coli^AmbionRNASpike1_222] none
3 mCT038320 1 3 1 DC004 100 M 16 AmbionRNASpike8:401-470 ATCTAACGGTCACTCAGTATCGTTTGGTCGTATGGACCAGTATCTCTACCCGTACTATCGCCGCGACGTT mSQ038320 78.3 0.5 DC Details: [DC Tiling^2026^^manual^Ambion^AmbionRNASpike8^Ambion^AmbionRNASpike8:401-470] none
4 mCD036987 1 4 1 DC001 97 F 3 AmbionRNASpike6_688 AGTTCAACAAACCGTGGAGCGAAATCGGCACTGGTCTTTCTGATAAATGCGTTCTCAGCTACGGCGCATT mSQ036987 77.7 0.49 DC Details: [Ambion doping sense^1276^518^Pick70^Ambion^AmbionRNASpike6^Escherichia coli^AmbionRNASpike6_688] none
5 mCA038136 1 5 1 DC004 100 E 24 MJ-5000-158_4832_REVCOMP AAAGTTGGTGTCTTAGGAGCTACTGGAAGCGTGGGGCAGAGATTTGTCCAATTGTTGGCAGACCATCCAA mSQ038136 77.7 0.49 DC Details: [MJDC antisense^5000^^Pick70+mutator^BrownLab^MJ-5000-158^Methanococcus jannaschii^MJ-5000-158_4832_REVCOMP] none
6 mCM038232 1 6 1 DC004 100 I 24 MJ-1000-75_640_a_28_2 AAGTAGCTCACCCACCGCAATAATATCTGGAATGTCTTTAGCTGTAGCTGGGGCAGCTGGACCAAATGCT mSQ038232 77.7 0.49 DC Details: [Mismatch Controls; Anchored^1000^^Pick70+mutator^BrownLab^MJ-1000-75^Methanococcus jannaschii^MJ-1000-75_640_a_28_2] none
7 mCD036891 1 7 1 DC001 97 B 3 AmbionRNASpike5_931 TGATCGACTGCCTGGCTCCGGATCGTCGCGTAGAGATCGAAGTTAAAGGTATCAAAGACGTTGTAACTCA mSQ036891 77.7 0.49 DC Details: [Ambion doping sense^1059^58^Pick70^Ambion^AmbionRNASpike5^Escherichia coli^AmbionRNASpike5_931] none
8 mCA038408 1 8 1 DC005 101 A 8 MJ-5000-163_2650_REVCOMP TGGGCCATAAAGGACAAAGTCTCCTGACGCCATAACTTGGACTAAGTTTGCTCCAACATCACAAACGTGG mSQ038408 77.1 0.47 DC Details: [MJDC antisense^5000^^Pick70+mutator^BrownLab^MJ-5000-163^Methanococcus jannaschii^MJ-5000-163_2650_REVCOMP] none
9 mCD036910 1 9 1 DC001 97 B 22 MJ-1000-75_640 GCCAAGGATATTTGCCGCAATAATATCTGGAATGTCTTTAGCTGTAGCTGGGGCAGTTATGCAGTGCATT mSQ036910 75.9 0.44 DC Details: [MJDC^1000^290^Pick70^BrownLab MJDC^MJ-1000-75^Methanococcus jannaschii^MJ-1000-75_640] none
10 mCM038600 1 10 1 DC005 101 I 8 MJ-1000-75_640_a_21_2 TCTAGGTCTATTTGCCGCAATAATATCTGGAATGTCTTTAGCTGTAGCTGGGGCAGTTATATGACCTACC mSQ038600 75.3 0.43 DC Details: [Mismatch Controls; Anchored^1000^^Pick70+mutator^BrownLab^MJ-1000-75^Methanococcus jannaschii^MJ-1000-75_640_a_21_2] none
11 mCM038696 1 11 1 DC005 101 M 8 MJ-1000-74_823_d_6_2 GTTGGCGAGGGAGCTTCTACCGAAGAAGGTTGTCTGTATTCACAACCCTGTCTTAACGGGTTTGGATGGA mSQ038696 78.3 0.5 DC Details: [Mismatch Controls; Distributed^1000^^Pick70+mutator^BrownLab^MJ-1000-74^Methanococcus jannaschii^MJ-1000-74_823_d_6_2] none
12 mCD037413 1 12 1 DC002 98 G 21 AmbionRNASpike6_688 AGTTCAACAAACCGTGGAGCGAAATCGGCACTGGTCTTTCTGATAAATGCGTTCTCAGCTACGGCGCATT mSQ036987 77.7 0.49 DC Details: [Ambion doping sense^1276^518^Pick70^Ambion^AmbionRNASpike6^Escherichia coli^AmbionRNASpike6_688] none
13 mCD037195 1 13 1 DC001 97 N 19 AmbionRNASpike2_516 TCGTCACGAAATCCTTCGCTTAATTGCCGCACTTTGATGGTCAGTCGAAAACTATCATCGGAGGGGCTAC mSQ037195 77.7 0.49 DC Details: [Ambion doping sense^776^190^Pick70^Ambion^AmbionRNASpike2^Escherichia coli^AmbionRNASpike2_516] none
14 mCT038608 1 14 1 DC005 101 I 16 MJ-1000-74:559-628 AAAAAGTTTTTGAAGCAATGGGGTTAAAGGCAAAATATGTTTATGGAAGTGAATTCCAGCTTGATAAGGA mSQ038608 71.2 0.33 DC Details: [DC Tiling^1000^^manual^BrownLab^MJ-1000-74^Methanococcus jannaschii^MJ-1000-74:559-628] none
15 mCD037698 1 15 1 DC003 99 C 18 AmbionRNASpike4_918 AATTATGCAGCGTTATATCAGTATGAACGTGACGCAAAAGCCGTTCGATAACCCGAAGGTCCGTGAGGCG mSQ037698 77.7 0.49 DC Details: [Ambion doping sense^1027^39^Pick70^Ambion^AmbionRNASpike4^Escherichia coli^AmbionRNASpike4_918] none
16 mCA038424 1 16 1 DC005 101 A 24 MJ-4000-143_1623_REVCOMP CTTGCCCACAATCTTAAGGCATCTGCTCCATACTTAGCTATAATTTCATCTGGCTCTACAACATTTCCCC mSQ038424 75.3 0.43 DC Details: [MJDC antisense^4000^^Pick70+mutator^BrownLab^MJ-4000-143^Methanococcus jannaschii^MJ-4000-143_1623_REVCOMP] none
17 mCA038520 1 17 1 DC005 101 E 24 MJ-2000-81_1760_REVCOMP GAAACCCATTAGCAGACCCCTACCTAATGGGAGTTGCAAGTGGGGCATCGTTAGGAGTTGTTTTATACCT mSQ038520 77.1 0.47 DC Details: [MJDC antisense^2000^^Pick70+mutator^BrownLab^MJ-2000-81^Methanococcus jannaschii^MJ-2000-81_1760_REVCOMP] none
18 mCA038616 1 18 1 DC005 101 I 24 MJ-4000-129_3873_REVCOMP TCCCACGCCGTACCAGGCTGGGCCACCCCCGCAATAAAAGCAAACACTAATTGGGTATAAGGTATATATA mSQ038616 77.7 0.49 DC Details: [MJDC antisense^4000^^Pick70+mutator^BrownLab^MJ-4000-129^Methanococcus jannaschii^MJ-4000-129_3873_REVCOMP] none
19 mCD036964 1 19 1 DC001 97 E 4 AmbionRNASpike7_1334 ATTCGCCGAGATGCACGACATTGAAATCACGGTGATTGATAACGACACACGCCTGCCAGCGTTTAAAGAC mSQ036964 77.7 0.49 DC Details: [Ambion doping sense^1474^70^Pick70^Ambion^AmbionRNASpike7^Escherichia coli^AmbionRNASpike7_1334] none
20 mCM000584 1 20 1 002-CTRL 2 I 8 gi|31981422|ref|NM_011740.2|_20_a_42_1 GI_31981422 NM_011740 NM_011740 Ywhaz AGCCTTAGGGGCCTTTCAGCGCTCTTACAGTCTGCCTGGGATTCTATTCACCGGCCCCAGTACCGTACTT mSQ000584 80.6 0.56 Mus musculus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide (Ywhaz), mRNA. PC Details: [Mismatch Controls; Anchored] Mus musculus

Total number of rows: 39200

Table truncated, full table size 11774 Kbytes.




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