GEO help: Mouse over screen elements for information.
Status
Public on Aug 11, 2010
Title
URGV Arabidopsis thaliana CHROMO4_2 array
Technology type
spotted DNA/cDNA
Distribution
non-commercial
Organism
Arabidopsis thaliana Manufacturer
URGV
Manufacture protocol
http://urgv.evry.inra.fr/CATdb Support
glass
Coating
aminosilane
Description
The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define repeated and unique segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°C63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis.
Web link
http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/consult_project.pl?array_type_id=6 Contributor(s)
Colot V , Roudier F Submission date
Aug 10, 2010
Last update date
Oct 04, 2010
Contact name
Véronique BRUNAUD
E-mail(s)
veronique.brunaud@inrae.fr Organization name
INRA - CNRS - UPSUD
Lab
IPS2
Street address
rue Noetzlin
City
Gif-sur-Yvette
ZIP/Postal code
91190
Country
France
Samples (92)
GSM603103 , GSM603104 , GSM603105 , GSM603106 , GSM607742 , GSM607743
GSM607744 ,
GSM607745 ,
GSM607746 ,
GSM607747 ,
GSM607748 ,
GSM607749 ,
GSM607750 ,
GSM607751 ,
GSM607752 ,
GSM607753 ,
GSM607754 ,
GSM607755 ,
GSM607756 ,
GSM607757 ,
GSM607758 ,
GSM607759 ,
GSM607760 ,
GSM607761 ,
GSM607762 ,
GSM607763 ,
GSM607764 ,
GSM607765 ,
GSM607766 ,
GSM607767 ,
GSM607768 ,
GSM607769 ,
GSM607770 ,
GSM607771 ,
GSM607772 ,
GSM607773 ,
GSM607774 ,
GSM607775 ,
GSM607776 ,
GSM607777 ,
GSM607778 ,
GSM607779 ,
GSM607780 ,
GSM607781 ,
GSM608373 ,
GSM608375 ,
GSM608377 ,
GSM608379 ,
GSM608381 ,
GSM608383 ,
GSM608385 ,
GSM608387 ,
GSM608389 ,
GSM608391 ,
GSM608393 ,
GSM608395 ,
GSM608397 ,
GSM608399 ,
GSM608401 ,
GSM608403 ,
GSM608405 ,
GSM608407 ,
GSM608409 ,
GSM608411 ,
GSM608413 ,
GSM608415 ,
GSM608417 ,
GSM608419 ,
GSM615049 ,
GSM615050 ,
GSM615051 ,
GSM615052 ,
GSM615053 ,
GSM615054 ,
GSM615055 ,
GSM615056 ,
GSM615437 ,
GSM615438 ,
GSM615439 ,
GSM615440 ,
GSM615441 ,
GSM615442 ,
GSM615443 ,
GSM615444 ,
GSM615445 ,
GSM615446 ,
GSM615447 ,
GSM615448 ,
GSM615449 ,
GSM615450 ,
GSM615451 ,
GSM615452 Series (18)
GSE24494 cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE24646 h3k36me3-Establishing a reference epigenome in arabidopsis seedlings
GSE24647 h3k9me2-Establishing a reference epigenome in arabidopsis seedlings
GSE24648 h3k4me2-Establishing a reference epigenome in arabidopsis seedlings
GSE24649 h3k4me3-Establishing a reference epigenome in arabidopsis seedlings
GSE24650 h3k9me3-Establishing a reference epigenome in arabidopsis seedlings
GSE24651 h3k27me3-Establishing a reference epigenome in arabidopsis seedlings
GSE24652 h3k27me2-Establishing a reference epigenome in arabidopsis seedlings
GSE24653 h3k56ac-Establishing a reference epigenome in arabidopsis seedlings
GSE24654 h4k20me1-Establishing a reference epigenome in arabidopsis seedlings
GSE24655 h3-Establishing a reference epigenome in arabidopsis seedlings
GSE24692 chip in silencing suppressor plants or in mirna plants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing
GSE24710 Establishing a reference epigenome in arabidopsis seedlings
GSE24836 Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE24837 Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing
GSE25049 h3k4me2_c24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE25060 h3k4me2_colxc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GSE25061 h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
Data table header descriptions ID Name of probes
ORF ORF Name
SEQUENCE Sequence of probes
SPOT_ID
Data table ID ORF SEQUENCE SPOT_ID BAR
NO INFORMATION
BT
NO INFORMATION
C037
TCGTTTAATAGCAGTTCCATCTATCACTTTATTGTGAAATACCAGATTGGCCCGTTCCGCCATAAGTACCTCCATATTCTGCTGAATGGGATTCGACAATGAGTTTGAGTCAATGATTGCAAAACTTCCTTTTCTCGATCTTGATTTGCGTAGAATTTTAGGTCAGGAACTATGGTCCGATTTGAATCGGAGAGGTCCGAATTCACACGGGTGTCCTAGAATTCCTTTTTTTTAATAGCATATTATTAGGTATCATATGAACAGGCTTGAGAAAAACCTTGTATAGCTTCCTCGATTTCTCGATAAAAAGAAATATGACCAACTGTGGTTCGAATATATATACAAAAATTTTCTTTTTTTACACTTCTTACTATTAGATAGTGTGCATAAATCTCATGATAGTTACCAAAAGATTCATAGTGAACTTCGATAGGAACTTCTCTTGAAGCAATAACGCGTTGATCTAATTGCCACCGAAGCCACAAAGGACTA
NO INFORMATION
C041
TTCACGAGGTACGCCTATCAATTTGAATTTCTGAATCGACCATAGACCAATCGCCTTTTTTTTTATTTGGGAGTATTGAATACACCCACAATTCTGAGCTTCATGTTACTCTTTTCAAGAGACATGTCAGATCGAGGGCATCCCAAATTGATTGAAGGGGATGAGAGTTTATCATTCTTAATCTGTAAAAGAAAAATTTCGATCAAATCACACATCGCAGTATACTAGGCCTTCTAATTCTTTAAGAGGTTTATCTAAAAGATTCGCAATATAACTAGGAAGACGTTTCAAATACCATACATGAGTTACAGGACATGTCAGTTTTATGTATCCCATTTGATATCTTCGTATCCGAGAATCAACAAATTCAACTCCACATTGTTCACAAAACTTTGGGTCTTCTTTTTCATCTCCGATCACTCGATAATTTCCACAAGCGCAAATTCCACTCTTTATAGGTCCAA
NO INFORMATION
C042
TTTCATCTCCGATCACTCGATAATTTCCACAAGCGCAAATTCCACTCTTTATAGGTCCAAAAATCCTTTCACAAAATAATCCATCTTTTTCCGGTTTATTGGTTTTGTAATGAAAAGTATAGGGTTTTGTCACCTCTCCAACTATCTCTCCATTAGGTATTATTTTAGTGGCCCAAGCACTTATTTGCTGAGGAGAAACTAAGCCAATTCGGAGTTGTTGATGTTTATACCGATCGATCATATAAGAAATTTTGTGATTCATTCCGATTAAACTTCCTTCCTATTAATCTGGAAATTCTTCTCAGATACAAGGAAATGATTCAGTTCCAGAGCCAAAGATCGTAGTTCTCGAACAAGTAATCGAAAAGATTCCGGAGCATCTTCTGGTTTAGGTATTGTTCCTCCAATGATAGTGGTACCAAGTACTTCTTGGCGAGCTCTAATATGATCAGATTTATAAGTAAGCATCTCTTGTAAA
NO INFORMATION
C043
GTTGATACATAATTAATGGAATGCTTAGAGTATCACCATTGCCCGAAAAAACGATCTTCTCAGTGTCAGTATAAAGGATTTTTCCCTCGTGTTCGGCTATAGCGGGAACCCCTGAATCTAAAGCCACTTGGCGTTCCAACCCAGTTCCAACAATGCACTTTTCGGACCGAGAAAGTGGAACTGCTTGACGTTGCATATTAGAACTCATTAAAGCTCGATTCGCATCATTATGTTCGATAAAAGGAATTAGAGAAGCTCCAATGGAAAAATATTGGAAAGGGAAAATGCTTCGAAGATGAACCTCTTCCCATGCGATAGTCAAAAATTCTTGGCGGTATCGAGCTGGAACAGCCTGTTCTTCTTGAATGCCCCGATTAAGAGCCAAAGAATTTCCTGCCGCTATCATATAATATTCATCTTGACTTGGTGATAAAAAAAGCATCCGTATCCGTGCT
NO INFORMATION
C065
TTAATGGAACTTTAGCTTTAGCTGGTCGTGACCAAGAAACCACCGGTTTCGCTTGGTGGGCCGGGAATGCCCGACTTATCAATTTATCTGGTAAACTTTTGGGAGCTCATGTAGCCCATGCCGGATTAATCGTATTCTGGGCCGGAGCAATGAACTTATTTGAAGTGGCCCATTTTGTACCTGAAAAGCCCATGTATGAACAAGGATTAATTTTACTTCCCCACCTAGCCACTTTAGGATGGGGGGTAGGTCCTGGGGGAGAAGTTATAGACACCTTTCCGTACTTTGTATCTGGAGTACTTCACTTAATTTCTTCTGCAGTTTTGGGCTTTGGCGGTATTTATCATGCACTTCTGGGACCCGAAACTCTTGAAGAATCTTTTCCCTTTTTCGGTTATGTATGGAAAGATAGAAATAAAATGACCACCATTTTGGGTATTCACTTAATTTTGTTAGGTGTAGGTGCCTTTCTTCTAGTATTCAAGGC
NO INFORMATION
C100
GAATTCTAATACAATACAGAAGAACTACCAAAGTGTTTCAAAGAAGGGTTCTCTTGACGTAGGTTTGCTTTTGGTCTAGATCAACTTAAGTTAAATATAGTCTCTAACATCCTGATTAAAAAATCAAACATGAAACTTGATACACCTTAAGGTTCATAGGACGAAAAGATCATTTTTGAGTTCCTTATACTCATTCTACCTAGCATTGAGTAGACTGGGTATTCACCCTATCAATATCTCAAATCAATGATGGGTTCTATTCATTCCCTACCTAACGGGGTACTTTAATAGGACCTAATGTCAGGCTGTTGTTCTCCTCTTTTTTCCTAAAAAAAAGTCATGGAGTAAGACATCGATTTCTTAATAAGATCAATCAATTAGTTTGATTGCGTGATGGACTCCTCTGAAAAACTTTGGCGCACGTGTAAACGAGGTGCTCTACCTAACTGAGCTATAGCCCTTGTGTTTGTGATACACATTT
NO INFORMATION
C150
AAATATTTGGAGGCTGATTACGTTAACTAGTCCCCGTGTTCCTCGAATGGATCTCTTAGTTGTTGAGAGGGTTGCCCAAAGGCAGTATATAGAGCATACCCAGTAAAACTTACAAGTAACCCAGATATAAAGATGGCGACTAGGGTTGCTGTTTCCATTATTATAGAATTGAAAGACCACACCGGATCTATGCTAAGATCATTTATTTACAACGGAATGGTATACAAAGTCAACAGATCGTAATGAATACAAAATAAGATTTATGGCTACACAAACTGTTGAAGATAGTTCTAGATCTGGTCCAAGAAGCACTACTGTAGGGAAGTTATTGAAACCATTGAATTCCGAATATGGTAAAGTAGCTCCCGGATGGGGAACGACCCCTTTGATGGGTGTTGCAATGGCTCTATTTGCGGTATTCCTATCTATTATTTTGGAGATTTATAATTCTTCTGTTCTACTGGATGGAATTTCAGTGAATT
NO INFORMATION
C160
CATGTTCCTTCTATTTCGCCAAGTAAAGCTCTTCGCATCGCAATGCCTATTGTGTCGGCTTGGCCTTTCATAAGTGGAGACAGAATAAAGCGTCCATAATAAAGACGCTTACTGTCTCTTTTTGATTCAACACACTTCCACTGTAGTGTCCGAGTAGATACTTTGACTTTCTCTCGAACCATAGTAATTTTATTTGATCAGATCGTTGAATCGTTTATTTCTCTTGAAACCCTTTTAGCCTTTTTTTAGTTCTATACACGTCTTTTTTTAGGGGGTCTACAACCATTATGTGGCATAGGGGTTACATCTCGTACGAAACTTAAAAGTATACCGCTTCTACGAATAGCTCGTAATGCCGCATCTCTTCCGAGTCCAGGGCCTTTTATCCTTACTTCAGCTCGTTGCATACCTTGATCCACTACTGCTCGAATAGCATTTCCTGCTGCGGTTTGGGCAGCAAAGGGTGTTCC
NO INFORMATION
C227
AATAACGAGCTAATGAATCTCCTTGTTTTTGCCATTGAATTTCCCATTCAAATTCATCGTAAGACTCATAACGATCAATTTTACGAAGATCCCATGGTATTCCGGATGCGCGTAGCATTGGTCCGGATAAACCCCAATTTATTGCTTCTTCCCCACCAATAATCCCAACTCCTTCAACCCGTTCTAAAAAAATAGGATTTCGTGTAATGAGTTTTTGATATTCAACAACCTCTGTTAAAAAATAATCACAAAAATCCAAGCATTTATCTATCCAACCATAAGGTAAATCAGCCGCTATTCCTCCAATACGAAAAAAATTATGCATCATTCTCATACCGGTGGCAGCTTCGAATAGATCATATACAAATTCTCGTTCTCTGAAAATATAGAAAAAGGGAGTCTGTGCACCAATATCTGCCATAAAAGGGCCGAGCCATAACAGATGAGAAGCTATACGACTCAATTCCAGCATAATTACTCTGATATAGCTGGCCCTTT
NO INFORMATION
C228
GCCGAGCCATAACAGATGAGAAGCTATACGACTCAATTCCAGCATAATTACTCTGATATAGCTGGCCCTTTTAGGAACTTGAATATTTCCCAATTGTTCTGGTCCATTTACTGTTATTGCTTCTGTAAACATAGTAGCTAAATAATCCCATCGCGTTACATACGGTAAATATTGTATAATTGCTCGGTTTTCTGCAATTTTTTCCATTCCTCTGTGTAAATAACCTAATATGGGTTCACAGTCAACAACATCCTCACCATCTAGAGTAACAATTAAGCGAAGAACACCATGCATGGATGGGTGGTGAGGTCCCATATTGACTATCATAAGATCTTTTCCTGTAACTGGTCTCTTCATAAGTTTTTCCTTGATTCGTTCTGGCATGAATTAGATTTCTGAA
NO INFORMATION
GFP
NO INFORMATION
GLOBIN
NO INFORMATION
GUS
NO INFORMATION
HPH
NO INFORMATION
LUC
NO INFORMATION
M001
TGTAAAGATCTCGATGACCGCTTAATTCATCTTTCCTTTCCCGCTCCTGAATGAAAAGTGGTTTTTTTTATTCCTACGGTCTTGGCGTGATCTCTGAAACTGAAATTCGACTGAAAAGTTACCAATAGAATAGGCTTTAGAGTAGCTCTTTCCAAATAGGTCGAGTAGCCATTTCTAGAAATAGAATGAATTAAAAGGAGCCAAATAGTTGGGATTCACACGCACAGCCTTATCCTATGAGTCTGCCTATGCTACGCGCCTGCCTTTGAGAGCCTTTACCGCTGGTTCCCTTCATCGGCGTCATTGAACCTCGTTAGCATTTCGAAAAGAATTGGAGGCTCAAAACGAATGGTCAAAGGAATTGATGATTCGTGTTTAGTCTCCGATCTTCGCCTAGTCTTAGAACCTGCACTGTAGAGAGGCGCTGCGCTGCCTCTTTCTGCCGCTCTCCTCCCAGATGTAGGTCTTCCCGGAAGTGAGAACACTGCTGCCCAACTTATAATTCGGTCACTCCCCGTCTTCATCCTAGACGCCACTGGTACTATTCATCT
NO INFORMATION
M005
CGATCGATTATCTACCCAAGAAGATAGAGAGTCCCACATACGAGAAAAGGTCACAAATAGAGTTGAACCAAGTAACATTGCAAAGGCATAATGATAGTAGGGTCGGGATATCCCCGCCCTCCGAACCGGACGTGAAGGTCTCCCCTCATCCGGCTCTCCGCAGGGGAATCTCCACTCACTGCTTCCCCTAATATCCTCCTTTACCACATCATGGGGGTTTACAGGAGATCCCAGAGGCACGCACGGAAAGGCTGCTATACCATACCTTTGACTCAACTCTACTCTAGTAGTCATAGACTCACTAGAATAGTCCGTCCGGCTGCTCTTGCTGAAATACATTACTCTTCATTCTCCCGTGCTCTAGCAATTGCGCTCCCTAGACCACTACCATGTAGTTAGGTAGGGACATCCGTAATGACGGGAATCTAGGAATGAATGGGGATCCCTATCAATAAGAATATGAAGAATATCTAATTAGTTACACTACCTTTCTCTCACTCAATAGATCTATCTGGTCTGGATACGGTACAGTACAATACGAGACGATGGAATGCTATGGG
NO INFORMATION
M006
CGGTACAGTACAATACGAGACGATGGAATGCTATGGGATGGATGGTAGAGGGATGCCAGCGCCCAAAAGCGATGATTCACTTGTCCCCTTGTCCATAGGGACCTCGTGGCATACAACCGAAACGACTCCCGCTAGATAGCCGCCCCTATCTCTCTTTTTACAGCCTCGTGGACGGACGAAAGAAGGCAAGTTACAGAACGGTGCAGTGAAGGCTCGCGAAGTAGACAGCAAGCAACTGCTTTTCAGCCCCTTCTCTATTATATTAGTAAAGGGAAGGGGACTCTATCAGGATCTTACGAATCTAAAGATCTCCAAATTGAAGAACGGACTCTTTTGCTGCCCCCGGAGCGTAAGCACTTCACTCGCTAGGGGATGGGATTCATTCACTTGCATTCCTGCTAGCACTACAAAAAGCTCGGTCTTAACGCCCTTACTACTGCTGTGCAGCCTTTCCTCGGGTTCGTAGAGTCGGGTTTCCCGTTTACCCACAACGGAGGAGGGCCCCCCACCAGGCAGGCGGCCACGGGTCATAACGCACTCTTCGCACAACAAATCCACTT
NO INFORMATION
21800 20383 Kbytes .Supplementary file Size Download File type/resource GPL10772.gal.gz
243.4 Kb
(ftp) (http) GAL
GPL10772_Bio_bank_CHROMO4_2.txt.gz
230.4 Kb
(ftp) (http) TXT
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