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Platform GPL4035 Query DataSets for GPL4035
Status Public on Jul 28, 2006
Title NKI-CMF Homo sapiens 35k oligo array with DamID annotations
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Homo sapiens
Manufacturer Central Microarray Facility, NKI Amsterdam
Manufacture protocol The Human Genome Oligo Set Version 3.0 arrays contain 34,580 probes representing 24,650 genes and 37,123 gene transcripts. All oligos are 70-mer sequences. The arrays consist of 37632 features (oligos and controls) and are printed in a 28x28 subarray layout using 48 Biorobotic 10K-microspot pins. We use 14 different Bacillus subtilus sequences as spike-controls printed in triplo in every subarray.
Support glass
Coating aminosilane
 
Description This platform is identical to GPL3676. Due to application in DamID experiments custom annotations are provided. The annotations are derived from blast analysis of the oligo to the genomic sequence. The EnsEMBL release used to for retrieving gene, transcript and exon annotations are v31.35. The assembly build that is used as genomic sequence is NCBI35.
 
Contributor(s) Brugman W, Heimerikx M, Sie D, Velds A, Nieuwland M, Kerkhove R, de Wit E, Vogel M
Submission date Jul 26, 2006
Last update date Aug 02, 2006
Contact name Daoud Sie
E-mail(s) d.sie@nki.nl
Organization name Dutch Cancer Institute
Street address Plesmanlaan 161
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Samples (240) GSM124306, GSM124307, GSM124319, GSM124321, GSM124322, GSM124323 
Series (2)
GSE5445 Human Heterochromatin Proteins form Large Domains Containing KRAB-ZNF Genes
GSE14513 Tamoxifen-resistant human breast cancer cell lines

Data table header descriptions
ID
MetaRow Row coordinate of feature block
MetaCol Column coordinate of feature block
SubRow Row coordinate within feature block
SubCol Column coordinate within feature block
Reporter ID Internal DB identifier
oligo_id OMAD oligo identifier
GI-Bacillus GenBank Identifier
Gene Ensembl gene identifier
oligo_start Blast hit start on chromosome
oligo_end Blast hit end on chromosome
chrom Blast hit chromosome
start Start of gene on chromosome
end End of gene on chromosome
orientation Blast hit orientation
location Location relative to exons (Inside, Partial, Outside, Intron, Multiple)
Gene_5 Downstream ensembl exon identifier
start_5 Downstream exon start
end_5 Downstream exon end
Gene_3 Upstream ensembl exon identifier
start_3 Upstream exon start
end_3 Upstream exon end
numberofhits Number of blast hits
SEQUENCE Oligo sequence

Data table
ID MetaRow MetaCol SubRow SubCol Reporter ID oligo_id GI-Bacillus Gene oligo_start oligo_end chrom start end orientation location Gene_5 start_5 end_5 Gene_3 start_3 end_3 numberofhits SEQUENCE
1 12 4 28 28 334575 H300009761 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 TTAATCTGACCTGTGAAAAACACTGTCCAGAGGCTAGGTGCGGTGGCTAACGCTTGTAATCCCAGCACTT
2 12 4 27 28 333055 H300009722 NA 56195011 56195080 16 NA NA 1 Outside ENSG00000159618 56134068 56183094 ENSG00000159618 56259658 56281476 1 TGTTGCTGACTCGAAGTCTGAAGGAAAGTTCGATGGTGCAAAAGTTAAAGTTGCCTGGAAAAAGGTAGAC
3 12 4 26 28 331915 H300000470 NA 21440640 21440709 15 NA NA 1 Outside ENSG00000179455 21361914 21364679 ENSG00000179455 21482492 21483457 1 AAGCTGGGCTACCATACAGGGAATTTGGTGGCATCCTATTTAGACAGGCCCAAGTTTGGCCTTCTGATGG
4 12 4 25 28 330395 H300000646 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 230 AATGCAGAAGCCTCAGGAGCCGATGCAATCAACTGGAAGAAAAGGTATCAGCAATGGAAGATGAAATGAA
5 12 4 24 28 328875 H300004276 NA 8243265 8243334 10 NA NA 1 Outside ENSG00000107485 8136673 8157170 ENSG00000107485 10256199 10256546 1 CGCGGCACCAACCCTCAATATCTGGTGGGGAAGATCATTCGAATGCGAATCTGTGAGTCCAAGCACTGGA
6 12 4 23 28 327355 H300009441 ENSG00000128585 130634078 130634147 7 130469890 130638645 1 Inside ENSE00001418249.1 130629621 130629976 ENSE00000882392.4 130642278 130646522 1 TGGCTGTGGCAGCTTTAATGGAGAAACCTGTGTTGGCCTCTTTTTCTGGCATTAGGATCTCTTGTCATAG
7 12 4 22 28 326215 H200010775 ENSG00000172653 31206258 31206326 17 31206073 31220008 -1 Inside ENSE00001185610.2 31198023 31198350 ENSE00001185482.1 31206781 31206867 1 AAGTCCATCACCAAAGTAGGCCAAAAGAAAACGCCTGCTTTCCCACCGTGCTGCTCGAAACCACGAAAA
8 12 4 21 28 324695 H300011218 ENSG00000169855 79150406 79150475 3 78729080 79721751 -1 Inside ENSE00001149762.3 79070441 79070767 ENSE00001222628.2 79257296 79257379 1 ACTGACAAGCGTCCGGAAAGGTCGACGAGTAATTGCCCTGAAAACTCTTGGCTAATTGACCCACGTTGCT
9 12 4 20 28 323175 H200001801 ENSG00000167005 55039223 55039291 16 55020554 55042766 -1 Inside ENSE00001108681.1 55038039 55038102 ENSE00001108688.2 55042500 55042766 1 GAGGAGGACTGTAGAAGGGGTTCTGATTGTACATGAGCACCGGCTACCCCATGTGTTACTGCTGCAGCT
10 12 4 19 28 323145 H300021090 ENSG00000166938 64402896 64402965 15 64372714 64413289 1 Inside ENSE00001107948.1 64402079 64402326 ENSE00001259492.2 64405223 64405756 1 ATTATCTAGCAGATCGTCGCTATGACATGCTGCCTTCCGTCCTCAGTGCAGATTTGTGTTCCCTTCTGGG
11 12 4 18 28 322005 H300003239 ENSG00000164746 47873376 47873445 7 47848348 47874131 1 Inside ENSE00001260672.1 47867432 47867443 ENSE00001294226.3 47901481 47901760 1 CAGTGTCTCAGAACTGATCACTTGCTCCTCCTATTGTGTGAACCACTCTTAGCAGGCATTGCTACTGGAT
12 12 4 17 28 320841 H200000124 ENSG00000162772 209181876 209181944 1 209170507 209182509 1 Inside ENSE00001369912.2 209180783 209180988 ENSE00001276431.1 209186021 209186707 1 CTGGTTTCTAAGAGTTTTGGGGGGCGGGGCTGTCACCACGTGCAGTATCTCAAGATATTCAGGTGGCCA
13 12 4 16 28 319351 H300017172 NA 30606554 30606623 X NA NA 1 Outside ENSG00000198814 30431133 30508381 ENSG00000198814 30608111 30637454 1 TCTTGTAGTCAGTTGGTATGTACAGACAATTGGCATGGAAGTGGTAGGATATAAATCGGATGACGCCTGG
14 12 4 15 28 318229 H300020511 ENSG00000152990 22102098 22102167 4 22065597 22193954 -1 Inside ENSE00001152281.1 22098778 22098981 ENSE00001071989.1 22113203 22113358 1 AGCTAAAGCCTGCAGTAGGATTGTGCAGTGTCTTCAGCGCATTGCTACCTACCGGCTAGCCGGTGGAGCT
15 12 4 14 28 317095 H300010411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 3 AAAGAGGCTGTGTGCAAGAATCCAGTCCCATGGGGATTGGAATGTAGTCTGGGATCGTGGGACTATCCTG
16 12 4 13 28 315883 H300016485 ENSG00000143376 148484232 148484301 1 148397735 148484624 1 Inside ENSE00000959691.1 148478973 148479032 ENSE00001355684.1 148487954 148488997 1 TAATCTAGGGTATGTGGGAAGGTCAGGGCTGTGGTAAGGAATAGAATCAAAGAGGGGAGTGATACGGGGT
17 12 4 12 28 314743 H200006036 ENSG00000139180 4634255 4634323 12 4628535 4666658 1 Inside ENSE00000997514.1 4633719 4633889 ENSE00000936882.1 4637175 4637266 1 GCATGGGGTCACAGGTAATCATACCCTATCGGTGTGATAAATATGACATCATGCACCTTCGTCCCATGG
18 12 4 11 28 313645 H200015671 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2 AAGGAAACTTACAAACTGCAACGCAGAGAAACTATTAAAGGTATTCAGAAACGTGAAGCCAGCAATTGT
19 12 4 10 28 312885 H300005545 ENSG00000133937 94304584 94304653 14 94304314 94306252 -1 Inside ENSE00001409196.1 94262301 94263331 ENSE00001011272.1 94305048 94305307 1 GACGTCGTCGTCGAAGGCGTCACCGGAGAAGAGGGAAGAGGAAGGTAAAAGCGATTTGGACTCGGACAGC
20 12 4 9 28 311775 H200014240 ENSG00000130202 50073803 50073871 19 50041425 50083476 1 Inside ENSE00001159580.1 50069427 50069575 ENSE00000893918.1 50077308 50077461 1 CTTGTTCGTCTGGACGACACTGGAGTGGAACACTGCCTCCCACTTTCTTGGGACTTGGAGGGAGGTGGA

Total number of rows: 37632

Table truncated, full table size 7775 Kbytes.




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