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Status
Public on Apr 11, 2012
Title
NimbleGen Custom Mouse Hox Tiling Array
Technology type
spotted oligonucleotide
Distribution
custom-commercial
Organism
Mus musculus Manufacturer
Nimblegen
Manufacture protocol
Nimblegen manufacture protocol
Support
glass
Description
Custom NimbleGen tiling microarrays were designed using http://genome.ucsc.edu/MM9 NCBI37. Co ordinates of Mouse Hox A, B, C and D clusters, and several other genes were included in the design. For genes other than Hox clusters, we have included 2 KB upstream TSS and 2KB downstream TES. We have chosen probes that may match up to 10 places in the genome as necessary to fill gaps in coverage; average probe spacing is 46 bases; four copies of each probe to be placed on the array. For details about designing and manufacture http://www.nimblegen.com/
Contributor(s)
Marulasiddappa PM , Eskeland R Submission date
Mar 14, 2011
Last update date
Mar 24, 2011
Contact name
Pradeepa M Madapura
E-mail(s)
p.m.madapura@qmul.ac.uk, manthankumar.patel@qmul.ac.uk Organization name
Queen Mary University of London
Lab
Pradeepa Madapura
Street address
4 Newark Street, Whitechapel
City
London
State/province
UK
ZIP/Postal code
E1 2AT
Country
United Kingdom
Samples (46)
GSM697402 , GSM697403 , GSM697404 , GSM697405 , GSM697406 , GSM697407
GSM697408 ,
GSM697409 ,
GSM697410 ,
GSM697411 ,
GSM1056579 ,
GSM1056580 ,
GSM1195118 ,
GSM1195119 ,
GSM1195120 ,
GSM1195121 ,
GSM1195122 ,
GSM1195123 ,
GSM1195124 ,
GSM1195125 ,
GSM1195126 ,
GSM1195127 ,
GSM1195128 ,
GSM1195129 ,
GSM1195130 ,
GSM1195131 ,
GSM1195132 ,
GSM1195133 ,
GSM1195134 ,
GSM1195135 ,
GSM1195136 ,
GSM1195137 ,
GSM1195138 ,
GSM1195139 ,
GSM1195140 ,
GSM1195141 ,
GSM1195142 ,
GSM1195143 ,
GSM1195144 ,
GSM1195145 ,
GSM1195146 ,
GSM1195147 ,
GSM1195148 ,
GSM1195149 ,
GSM1195150 ,
GSM1195151 Series (7)
GSE28153 Psip1 ChIP using A300-847 antibody (Immunoprecipitates mainly p52 isoform of Psip1) Chip-chip from Mouse MEFs cells with H3K36me3, H3K4me3, Psip1 ChIP using A300-847 antibody
GSE43099 Gain and loss of H4K16 acetylation during ES cell differentiation [NimbleGen ChIP-chip]
GSE43103 H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction
GSE49179 Comparision of Psip1/p75 binding and Mll1 binding sites on Hox and non-Hox genes
GSE49180 Comparision of Psip1/p75, Mll and Menin binding on the Hox and non-Hox genes
GSE49181 Comparision of Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II binding on Hox and non-Hox genes
GSE49182 Psip1/p75 restrains Hox gene expression by recruiting both trithorax and polycomb group proteins
Data table header descriptions ID SEQUENCE Probe sequence
chr Chromosome number
RANGE_GB GenBank Accession number
RANGE_START Probe start position on chromosome
length Probe length in nucleotides
RANGE_END
Data table ID SEQUENCE chr RANGE_GB RANGE_START length RANGE_END CHR01FS136453759
GCAAGGGGAAGCGTCTTCTGAGGGGCGGGGGAGCGGTTGCCTTTAAGTAG
1
NC_000067.5 136453759
50
136453808
CHR01FS136453804
AGTAGAGATCCCTCTCAGGCCCTAGGTTCTCTTGACTAGGTTGGCAACCG
1
NC_000067.5 136453804
50
136453853
CHR01FS136453849
AACCGCCGACTCCCTCAGCGTCTCTCTGGGTTGATCTGTAGCATCTCATC
1
NC_000067.5 136453849
50
136453898
CHR01FS136453884
CTGTAGCATCTCATCATTTAGGATCACTACCAGAAATGGAGGAAGCAGCA
1
NC_000067.5 136453884
50
136453933
CHR01FS136453929
CAGCACTAGTAGACCTTGAAAGTTGGGAGAGAAGATGACTAGGTCATAGT
1
NC_000067.5 136453929
50
136453978
CHR01FS136453989
ACTTCCTAAGTTCGTACCTTCCAGTTACATACCCACAATTCATGTCCAGAG
1
NC_000067.5 136453989
51
136454039
CHR01FS136454034
CCAGAGGTCTGAAAATTATAACCTACTTGGTTTGTAGGATGCTAACGTCAAAGG
1
NC_000067.5 136454034
54
136454087
CHR01FS136454069
AGGATGCTAACGTCAAAGGTGAAAGTACTGTCCTTTCCCAAAGCAGAGAA
1
NC_000067.5 136454069
50
136454118
CHR01FS136454114
GAGAACATGACAGAAAGTCAACTCCAGGAAGACCCCCAAACACACACAAC
1
NC_000067.5 136454114
50
136454163
CHR01FS136454159
ACAACGTTTATAACATCCAGGGTCAGGGCCAAGAGCGAAAATAAAGGATTTT
1
NC_000067.5 136454159
52
136454210
CHR01FS136454219
TCAGTCAATATGACAGGTCATCTGAAATCTTAGCCTTTGGGAATGAGGTCAG
1
NC_000067.5 136454219
52
136454270
CHR01FS136454289
TTCCAGGCCAGCTTTGGCTACAAGTATGCAATCCCATTTCAATTTTTCCC
1
NC_000067.5 136454289
50
136454338
CHR01FS136454339
CCTCAATACATTATCACGGAAAAAAAAATCAGCAAGGTTTAAAAATATGTCAAGC
1
NC_000067.5 136454339
55
136454393
CHR01FS136454414
TAATCCTAGCACCTCCGAGTTAGAAGCCAGCCAATATGTGAGTTTCAGGC
1
NC_000067.5 136454414
50
136454463
CHR01FS136454474
TACATAGTGAAACCTTGACTCAAAAATGTGGTAAATTCTATACTTCTTCCCTAGG
1
NC_000067.5 136454474
55
136454528
CHR01FS136454519
CTTCCCTAGGTTTCCCACGATTTTATAACCTGCTGTATCACCTCATTTTACAATGA
1
NC_000067.5 136454519
56
136454574
CHR01FS136454579
TTTTTAATGAACAGATTATTGTCTAAGACAATATTATTGTCTTATTTTATTATTAT
1
NC_000067.5 136454579
56
136454634
CHR01FS136454629
TATTATTTAAGACAATATATGTCTTATTCAGGCTCCAAATCCCTGTAGAGCTAAGAAAA
1
NC_000067.5 136454629
59
136454687
CHR01FS136454674
TAGAGCTAAGAAAAGTTTTGCCTTCTTCAAGAATTGCTGAACTGTTTTAGAGGCCAG
1
NC_000067.5 136454674
57
136454730
CHR01FS136454709
GCTGAACTGTTTTAGAGGCCAGGTACTTCGATAGAGCTTATTAAAGACTGG
1
NC_000067.5 136454709
51
136454759
179493 18785 Kbytes .Supplementary file Size Download File type/resource GPL13276_100428_PM_MM9_Hox_plus_ChIP.pos.gz
1.4 Mb
(ftp) (http) POS
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