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Platform GPL6182 Query DataSets for GPL6182
Status Public on Feb 11, 2008
Title NimbleGen custom murine genomic tiling array
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Mus musculus
Manufacturer NimbleGen
Manufacture protocol 1.Contain probes interrogating 402 genes and 4 gene clusters at a 100bp tiling interval.
2.Sequences derived from 20 miRNA genes; 7 imprinted loci; 7 germ cell marker genes; 1 oocyte gene; 155 genes expressed in ES cells; 129 genes expressed in differentiated cells.
3.The single array contains more than 360,000 50mer probes selected from 57 megabases of murine sequence and we surveyed 50 kb surrounding each gene.
 
Description annotations based on mm5 genome build
 
Contributor(s) Ng HH
Submission date Nov 23, 2007
Last update date Feb 11, 2008
Contact name jun cai
Organization name UIUC
Street address Springfield Ave, DCL
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Samples (15) GSM244512, GSM244513, GSM244514, GSM244515, GSM244516, GSM244517 
Series (2)
GSE9535 Identifying targets of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells
GSE9774 ChIP-chip on custom NimbleGen genomic tiling arrays

Data table header descriptions
ID PROBE_ID = The NimbleGen probe identifier. Used to identify a probe sequence within a design.
SEQ_ID The NimbleGen sequence identifier.
CHROMOSOME Chromosome
GENOME_COUNT The uniqueness count of the probe in the target genome.
SEQUENCE The DNA sequence synthesized on the array. Always shown 5’ to 3’.
LENGTH Length of the probe in base pairs.
GB_RANGE RefSeq accession with probe start and end coordinates
SPOT_ID identifies random probes

Data table
ID SEQ_ID CHROMOSOME GENOME_COUNT SEQUENCE LENGTH GB_RANGE SPOT_ID
CHR1P136835685 chr1_136682175_136901392 chr1 1 TTGGGTTTCCCGGCCAGAGCGCACAGCCTACCATTGAGTCCAAGAGCTCT 50 NC_000067.1[136835685..136835734]
CHR14P30719572 chr14_30668726_30840915 chr14 1 GCACTCGCAGCCTCAGGTGAGGGTTTCTGTTTGCCCATTCCACTCTCCTC 50 NC_000080.1[30719572..30719621]
CHR1P136821781 chr1_136682175_136901392 chr1 1 CGCCCTCACAGGCTTGTCTCAGATCATCCTGGAACCTGAAAACCCAAAAG 50 NC_000067.1[136821781..136821830]
CHR2P57055949 chr2_57010885_57127288 chr2 1 TTGTTGCATCGGGATGTGGACACACGTGTACATCACGCGTACGGCGTGGG 50 NC_000068.1[57055949..57055998]
CHR1P72727507 chr1_72682489_72873479 chr1 1 GCAGGGATCAGTAGCTCAAAATTCAAACCACAGTTTGCCTGTGGTTTCAC 50 NC_000067.1[72727507..72727556]
CHR4P98268525 Pgm2 chr4_98225534_98383039 chr4 1 TTCAGCTCTTCTTGATGCTGGTTCAGTGATTCTGATGAAATTGTCTTTGG 50 NC_000070.1[98268525..98268574]
CHR10P120135652 chr10_120001945_120217367 chr10 1 CCCCACAGGACTCTCTCTAGATTCATTTGCCTGCTCCGCCAGAGTGCCTA 50 NC_000076.1[120135652..120135701]
CHR3P99141471 chr3_99127398_99327786 chr3 1 AATGGTTGTGTATTTTAAATCTGGATCCAGCCACCTCTGGTCACACTTAC 50 NC_000069.1[99141471..99141520]
CHR1P120394665 En1 chr1_120326028_120431347 chr1 1 AGGTGACTTGATGGGGAAAGGAGGAGAGGGGTGACAAGTTCTATCTGTGC 50 NC_000067.1[120394665..120394714]
CHR1P180795564 chr1_180716861_180820845 chr1 1 TGTACGTGTTCTCTAGGCCTTTTAGGAAACGTGGTGTTGTTCCTTTGGCC 50 NC_000067.1[180795564..180795613]
CHR18P35656063 chr18_35508924_35744775 chr18 1 GTTAGATAACTTTTCAGACATGAATGTTTATGGTTAGTGTTATATAAATG 50 NC_000084.1[35656063..35656112]
CHR5P4900143 chr5_4760451_5436916 chr5 1 TGCCAGTTCGGGTCCTCAGTTCACTGCCTAGCAGTGCTTTTGAAGGTTAT 50 NC_000071.1[4900143..4900192]
CHR18P69917706 chr18_69819951_70259952 chr18 1 GAAGAGCCGCACTTTTTAGGGCCTGGTGCACAGACACAAAATGCCCAGTC 50 NC_000084.1[69917706..69917755]
CHR9P23190711 chr9_23117838_23486710 chr9 1 TGTGGGGCTGCCGGGAGACCTTTGCTTATACGATGTACGGTATAATAAAA 50 NC_000075.1[23190711..23190760]
CHR4P72620261 chr4_72476250_72658007 chr4 1 TATTGACTGAAAACTATTTTTATGACTTTCTAAGAAGTGGATGTTATTCT 50 NC_000070.1[72620261..72620310]
CHR11P51883804 chr11_51842343_51972310 chr11 1 TCGTGAAGAACAATTGTCATAGACATCTACCTAGAAGCAGAACTTCAAAA 50 NC_000077.1[51883804..51883853]
CHR13P14784360 GLI3 chr13_14769517_15133250 chr13 1 CTAAAAATAATTGGGTTGATCTCTAACATAATTGACCCTCTTCTTTAATC 50 NC_000079.1[14784360..14784409]
CHR3P128157866 chr3_127975356_128165308 chr3 1 TCACTGTAGGGCCCTGGCAGCTCCAGGAATCATGGGAAATGCTGAATGAA 50 NC_000069.1[128157866..128157915]
CHR13P109532128 chr13_109488347_109642277 chr13 1 AACTGCCCTGGAACAGGTATGCATTCCTAATTAAAAGACACAAAAGATTC 50 NC_000079.1[109532128..109532177]
CHR9P120894066 chr9_120878941_121005960 chr9 1 TATACCAGAGGCCACATGTGGCACATCGTTTGACTCTCTCTCCTAAGCCC 50 NC_000075.1[120894066..120894115]

Total number of rows: 385180

Table truncated, full table size 50598 Kbytes.




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

Supplementary file Size Download File type/resource
GPL6182_2006-12-19_GIS_mESC_mm5.ndf.gz 19.5 Mb (ftp)(http) NDF
GPL6182_2006-12-19_GIS_mESC_mm5.pos.gz 4.6 Mb (ftp)(http) POS

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