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Platform GPL7707 Query DataSets for GPL7707
Status Public on Jan 01, 2009
Title Mouse lincRNA Tiling Array (HD1 Platform)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Mus musculus
Manufacturer NimbleGen
Manufacture protocol see manufacturer's web site www.nimblegen.com
 
Description Platform annotation based on genome build mm8, NCBI Build 36.
The .ndf and .pos files are linked below as supplementary files.
 
Contributor(s) Guttman M, Rinn JL, Lander ES
Submission date Nov 29, 2008
Last update date Jan 01, 2009
Contact name Mitchell Guttman
E-mail(s) mguttman@mit.edu
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Samples (23) GSM346628, GSM346629, GSM346630, GSM346631, GSM346632, GSM346633 
Series (1)
GSE13765 lincRNA Expression

Data table header descriptions
ID
PROBE_DESIGN_ID This a unique, composite key consisting of the DESIGN_ID,ROW_NUM and COL_NUM.
CONTAINER NimbleGen arrays are divided into containers. One method of using containers is to divide the array into quadrants with reference marks.
DESIGN_NOTE A comment field suitable for placing information necessary for data analysis, for instance if you want to analyze sets of probes and/or genes together that don’t separate out using SEQ_ID, PROBE_ID,
SELECTION_CRITERIA Generally contains information about how a probe was selected. For rank selection, contains rank, uniqueness, and frequency. For older designs, will contain a criteria category.
SEQ_ID The NimbleGen sequence identifier. Used to group the probe pairs together to generate average difference values. An NGS SEQ_ID is a 17 character string that looks like: HSAP0001S00001834. The first four letters (HSAP) are the species code. The next four characters (0001) are the sequence build number. The ‘S’ is the designator for sequence (so there’s no confusion with the
SEQUENCE The DNA sequence synthesized on the array
MISMATCH mismatch index of the PROBE_SEQUENCE. This will be 0 (for the perfect match probe) , 1 for the first mismatch, 2 for the next, etc…(for the corresponding mismatch probe).
MATCH_INDEX Integer number that ties probe pairs together. Using the combination of MATCH_INDEX and MISMATCH you can retrieve and distinguish the members of the probe pair. Many controls have a MATCH_INDEX of ‘0’ since they are not paired with a mismatch probe.
FEATURE_ID Unsigned Integer that uniquely identifies a feature. A feature is the set of probes on the array that are to be considered as one entity. A 4:9 array will have 4 probes with the same FEATURE_ID
ROW_NUM The Y coordinate of the feature on the image
COL_NUM The X coordinate of the feature on the image
PROBE_CLASS For internal use. Generally 'experimental' or 'control' or 'fiducial'.
PROBE_ID The NimbleGen probe identifier. A PROBE_ID is a 17 character string that looks like: HSAP00P0001724033. The first four letters (HSAP) are the species code. The ‘P’ is the designator for probe (so there’s no confusion with the similar looking SEQ_IDs) The last ten digits are the probe number.
POSITION Position of the PROBE_SEQUENCE in the sequence/region of interest, starting from the left/5' end. (Genomic Position of probe)
DESIGN_ID This is the NimbleGen identifier for the design.
X The DLP X coordinate of the feature
Y The DLP Y coordinate of the feature
CHROMOSOME chromosome number
RANGE_GB ACCESSION.VERSION of chromosome
RANGE_START the start position (relative to the RANGE_GB accession)
RANGE_END the end position (relative to the RANGE_GB accession)

Data table
ID PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y CHROMOSOME RANGE_GB RANGE_START RANGE_END
chr10:120082855-120082855 6744_0752_0510 BLOCK1 interval rank target_tm:76.00;probe_tm:78.40;freq:18.22;count:01;rules:0000;score:0743 chr10:120082847-120093122 AAGAGGGTGCCAGGGAGGGAAATGAGGGCTGTTTTCACATAAGGGCAATT 0 63627880 63627880 510 752 experimental CHR10FS120082855 120082855 6744 752 510 chr10 NC_000076.4 120082855 120082904
chr10:120082867-120082867 6744_0555_0573 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq:12.14;count:01;rules:0000;score:0788 chr10:120082847-120093122 GGGAGGGAAATGAGGGCTGTTTTCACATAAGGGCAATTATGCAGCAGAGT 0 63627881 63627881 573 555 experimental CHR10FS120082867 120082867 6744 555 573 chr10 NC_000076.4 120082867 120082916
chr10:120082881-120082881 6744_0748_0122 BLOCK1 interval rank target_tm:76.00;probe_tm:75.10;freq: 9.36;count:01;rules:0000;score:0821 chr10:120082847-120093122 GGCTGTTTTCACATAAGGGCAATTATGCAGCAGAGTTGTTCATTGTAGAG 0 63627882 63627882 122 748 experimental CHR10FS120082881 120082881 6744 748 122 chr10 NC_000076.4 120082881 120082930
chr10:120082891-120082891 6744_0036_0242 BLOCK1 interval rank target_tm:76.00;probe_tm:74.30;freq: 6.17;count:01;rules:0000;score:0835 chr10:120082847-120093122 ACATAAGGGCAATTATGCAGCAGAGTTGTTCATTGTAGAGTTACGATGTG 0 63627883 63627883 242 36 experimental CHR10FS120082891 120082891 6744 36 242 chr10 NC_000076.4 120082891 120082940
chr10:120082899-120082899 6744_0498_0902 BLOCK1 interval rank target_tm:76.00;probe_tm:75.10;freq: 5.47;count:01;rules:0000;score:0859 chr10:120082847-120093122 GCAATTATGCAGCAGAGTTGTTCATTGTAGAGTTACGATGTGAAGCTGGA 0 63627884 63627884 902 498 experimental CHR10FS120082899 120082899 6744 498 902 chr10 NC_000076.4 120082899 120082948
chr10:120082917-120082917 6744_0335_0729 BLOCK1 interval rank target_tm:76.00;probe_tm:75.10;freq:18.31;count:01;rules:0000;score:0772 chr10:120082847-120093122 TGTTCATTGTAGAGTTACGATGTGAAGCTGGAAAAGAACAGAAGTGGAGC 0 63627885 63627885 729 335 experimental CHR10FS120082917 120082917 6744 335 729 chr10 NC_000076.4 120082917 120082966
chr10:120082931-120082931 6744_0206_0688 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq:19.17;count:01;rules:0000;score:0785 chr10:120082847-120093122 TTACGATGTGAAGCTGGAAAAGAACAGAAGTGGAGCCAACGGGTAAACAT 0 63627886 63627886 688 206 experimental CHR10FS120082931 120082931 6744 206 688 chr10 NC_000076.4 120082931 120082980
chr10:120082945-120082945 6744_0053_0685 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq:14.11;count:01;rules:0000;score:0777 chr10:120082847-120093122 TGGAAAAGAACAGAAGTGGAGCCAACGGGTAAACATTGGAGGGAAGAGGT 0 63627887 63627887 685 53 experimental CHR10FS120082945 120082945 6744 53 685 chr10 NC_000076.4 120082945 120082994
chr10:120082959-120082959 6744_0447_0359 BLOCK1 interval rank target_tm:76.00;probe_tm:79.20;freq: 8.78;count:01;rules:0000;score:0779 chr10:120082847-120093122 AGTGGAGCCAACGGGTAAACATTGGAGGGAAGAGGTGGACGTGTCTCAAT 0 63627888 63627888 359 447 experimental CHR10FS120082959 120082959 6744 447 359 chr10 NC_000076.4 120082959 120083008
chr10:120082969-120082969 6744_0604_0866 BLOCK1 interval rank target_tm:76.00;probe_tm:76.80;freq:10.19;count:01;rules:0000;score:0817 chr10:120082847-120093122 ACGGGTAAACATTGGAGGGAAGAGGTGGACGTGTCTCAATAAAGACCATT 0 63627889 63627889 866 604 experimental CHR10FS120082969 120082969 6744 604 866 chr10 NC_000076.4 120082969 120083018
chr10:120082985-120082985 6744_0180_0358 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: 6.86;count:01;rules:0000;score:0829 chr10:120082847-120093122 GGGAAGAGGTGGACGTGTCTCAATAAAGACCATTCTGCATGATGGCTTCA 0 63627890 63627890 358 180 experimental CHR10FS120082985 120082985 6744 180 358 chr10 NC_000076.4 120082985 120083034
chr10:120082991-120082991 6744_0444_0880 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 7.56;count:01;rules:0000;score:0852 chr10:120082847-120093122 AGGTGGACGTGTCTCAATAAAGACCATTCTGCATGATGGCTTCACTACAA 0 63627891 63627891 880 444 experimental CHR10FS120082991 120082991 6744 444 880 chr10 NC_000076.4 120082991 120083040
chr10:120083009-120083009 6744_0197_0695 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 8.83;count:01;rules:0000;score:0841 chr10:120082847-120093122 AAAGACCATTCTGCATGATGGCTTCACTACAAAGGAATGGCCTATGCCAT 0 63627892 63627892 695 197 experimental CHR10FS120083009 120083009 6744 197 695 chr10 NC_000076.4 120083009 120083058
chr10:120083017-120083017 6744_0366_0598 BLOCK1 interval rank target_tm:76.00;probe_tm:78.40;freq: 7.50;count:01;rules:0000;score:0807 chr10:120082847-120093122 TTCTGCATGATGGCTTCACTACAAAGGAATGGCCTATGCCATGACCGAGG 0 63627893 63627893 598 366 experimental CHR10FS120083017 120083017 6744 366 598 chr10 NC_000076.4 120083017 120083066
chr10:120083031-120083031 6744_0510_0872 BLOCK1 interval rank target_tm:76.00;probe_tm:79.20;freq: 7.67;count:01;rules:0000;score:0789 chr10:120082847-120093122 TTCACTACAAAGGAATGGCCTATGCCATGACCGAGGGCTCTGAGCCTGAA 0 63627894 63627894 872 510 experimental CHR10FS120083031 120083031 6744 510 872 chr10 NC_000076.4 120083031 120083080
chr10:120083043-120083043 6744_0017_0947 BLOCK1 interval rank target_tm:76.00;probe_tm:81.70;freq:15.14;count:01;rules:0000;score:0690 chr10:120082847-120093122 GAATGGCCTATGCCATGACCGAGGGCTCTGAGCCTGAAGCTCAGTCAGAG 0 63627895 63627895 947 17 experimental CHR10FS120083043 120083043 6744 17 947 chr10 NC_000076.4 120083043 120083092
chr10:120083057-120083057 6744_0679_0527 BLOCK1 interval rank target_tm:76.00;probe_tm:81.70;freq:17.06;count:01;rules:0000;score:0681 chr10:120082847-120093122 ATGACCGAGGGCTCTGAGCCTGAAGCTCAGTCAGAGGCTTTCTCGCCATC 0 63627896 63627896 527 679 experimental CHR10FS120083057 120083057 6744 679 527 chr10 NC_000076.4 120083057 120083106
chr10:120083075-120083075 6744_0599_0667 BLOCK1 interval rank target_tm:76.00;probe_tm:80.90;freq: 8.36;count:01;rules:0000;score:0749 chr10:120082847-120093122 CCTGAAGCTCAGTCAGAGGCTTTCTCGCCATCCAGTGCTCACCCTGACAA 0 63627897 63627897 667 599 experimental CHR10FS120083075 120083075 6744 599 667 chr10 NC_000076.4 120083075 120083124
chr10:120083089-120083089 6744_0059_0813 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq:10.78;count:01;rules:0000;score:0797 chr10:120082847-120093122 AGAGGCTTTCTCGCCATCCAGTGCTCACCCTGACAAAAAGCCTTTAGATA 0 63627898 63627898 813 59 experimental CHR10FS120083089 120083089 6744 59 813 chr10 NC_000076.4 120083089 120083138
chr10:120083101-120083101 6744_0763_0453 BLOCK1 interval rank target_tm:76.00;probe_tm:76.80;freq:10.94;count:01;rules:0000;score:0811 chr10:120082847-120093122 GCCATCCAGTGCTCACCCTGACAAAAAGCCTTTAGATAATCGGAGGTTTA 0 63627899 63627899 453 763 experimental CHR10FS120083101 120083101 6744 763 453 chr10 NC_000076.4 120083101 120083150

Total number of rows: 385000

Table truncated, full table size 121526 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL7707_071127_MM8_JR_ChIP.ndf.gz 22.7 Mb (ftp)(http) NDF
GPL7707_071127_MM8_JR_ChIP.pos.gz 2.6 Mb (ftp)(http) POS

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