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Platform GPL11196 Query DataSets for GPL11196
Status Public on Aug 21, 2011
Title Custom NimbleGen Nucleosome Position Analysis Array [080108_HG18_GS_ChIP]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer NimbleGen
Manufacture protocol NimbleGen custom array spotting technology (circa 2008)
 
Description Custom array for mapping nucleosome positions on glucocorticoid receptor and cell-cycle regulated genes. Oligos on the array all map to a single location in the human hg18 genome build (also called 36.1). Closely tiled genomic microarray for Chip2 and nucleosome position analysis, covering ~50kb regions of select human genes that are regulated by human SWI/SNF and/or GR. Probes selected from OID12189_redo, int2, length 50 of various HG18 regions and customer supplied sequences, mean 9bp, median 10.
DESIGN_ID: 6938
DESIGN_NAME: 080108_HG18_GS_ChIP
 
Submission date Nov 11, 2010
Last update date Aug 21, 2011
Contact name Gavin R. Schnitzler
E-mail(s) gavin.schnitzler@gmail.com
Phone 6086950428
Organization name Tufts Medical Center
Department Molecular Cardiology Research Institute
Lab c/o Navin Kapur
Street address 800 Washington St. Box 80
City Boston
State/province MA
ZIP/Postal code 02111
Country USA
 
Samples (11) GSM622048, GSM622049, GSM622050, GSM622051, GSM622052, GSM622053 
Series (1)
GSE25281 Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

Data table header descriptions
ID The ID format is chr#:start-end. The format for PROBE_ID in the .ndf file could not be used directly, since the PROBE_IDs for forward & reverse oligos at the same positions differed
SEQUENCE Sequence of oligo. Note, this is the sequence for the Forward oligo (tiled in two locations) and is the reverse complement of the reverse oligos (also tiled in two places on the array)
Chromosome Chromosomal location
RANGE_START Chromosomal start position of oligo (referenced to human genome build hg18)
LENGTH Oligo length
RANGE_END Chromosomal end position of oligo
GB_RANGE RefSeq[start..end]

Data table
ID SEQUENCE Chromosome RANGE_START LENGTH RANGE_END GB_RANGE
chr1:110234986-110235035 TTATTCCCACTGTACCTGTTCTGATTCATGTTATTGCCACCAGTCTCCTA chr1 110234986 50 110235035 NC_000001.9[110234986..110235035]
chr1:110234990-110235039 TCCCACTGTACCTGTTCTGATTCATGTTATTGCCACCAGTCTCCTAACAT chr1 110234990 50 110235039 NC_000001.9[110234990..110235039]
chr1:110235000-110235049 CCTGTTCTGATTCATGTTATTGCCACCAGTCTCCTAACATTACATTGCTT chr1 110235000 50 110235049 NC_000001.9[110235000..110235049]
chr1:110235010-110235059 TTCATGTTATTGCCACCAGTCTCCTAACATTACATTGCTTCTTAACTGAT chr1 110235010 50 110235059 NC_000001.9[110235010..110235059]
chr1:110235022-110235071 CCACCAGTCTCCTAACATTACATTGCTTCTTAACTGATTTATCTGCTCCA chr1 110235022 50 110235071 NC_000001.9[110235022..110235071]
chr1:110235030-110235079 CTCCTAACATTACATTGCTTCTTAACTGATTTATCTGCTCCACCCTTTCC chr1 110235030 50 110235079 NC_000001.9[110235030..110235079]
chr1:110235042-110235091 CATTGCTTCTTAACTGATTTATCTGCTCCACCCTTTCCCTCCAACTTTCC chr1 110235042 50 110235091 NC_000001.9[110235042..110235091]
chr1:110235050-110235099 CTTAACTGATTTATCTGCTCCACCCTTTCCCTCCAACTTTCCCCAGCTCC chr1 110235050 50 110235099 NC_000001.9[110235050..110235099]
chr1:110235060-110235109 TTATCTGCTCCACCCTTTCCCTCCAACTTTCCCCAGCTCCCCCTTCCAGG chr1 110235060 50 110235109 NC_000001.9[110235060..110235109]
chr1:110235076-110235125 TTCCCTCCAACTTTCCCCAGCTCCCCCTTCCAGGGGAGAGAGGACAAAGA chr1 110235076 50 110235125 NC_000001.9[110235076..110235125]
chr1:110235084-110235133 AACTTTCCCCAGCTCCCCCTTCCAGGGGAGAGAGGACAAAGAGAGGACAC chr1 110235084 50 110235133 NC_000001.9[110235084..110235133]
chr1:110235096-110235145 CTCCCCCTTCCAGGGGAGAGAGGACAAAGAGAGGACACTCCTAGAAATAA chr1 110235096 50 110235145 NC_000001.9[110235096..110235145]
chr1:110235106-110235155 CAGGGGAGAGAGGACAAAGAGAGGACACTCCTAGAAATAAACTCTCCAAA chr1 110235106 50 110235155 NC_000001.9[110235106..110235155]
chr1:110235114-110235163 AGAGGACAAAGAGAGGACACTCCTAGAAATAAACTCTCCAAAATACACCC chr1 110235114 50 110235163 NC_000001.9[110235114..110235163]
chr1:110235122-110235171 AAGAGAGGACACTCCTAGAAATAAACTCTCCAAAATACACCCTTCCCACA chr1 110235122 50 110235171 NC_000001.9[110235122..110235171]
chr1:110235134-110235183 TCCTAGAAATAAACTCTCCAAAATACACCCTTCCCACAGCCGTCAGCAGA chr1 110235134 50 110235183 NC_000001.9[110235134..110235183]
chr1:110235140-110235189 AAATAAACTCTCCAAAATACACCCTTCCCACAGCCGTCAGCAGAGCCTCT chr1 110235140 50 110235189 NC_000001.9[110235140..110235189]
chr1:110235150-110235199 TCCAAAATACACCCTTCCCACAGCCGTCAGCAGAGCCTCTGCAAAATGCG chr1 110235150 50 110235199 NC_000001.9[110235150..110235199]
chr1:110235164-110235213 TTCCCACAGCCGTCAGCAGAGCCTCTGCAAAATGCGGGTCAGTTTAGATG chr1 110235164 50 110235213 NC_000001.9[110235164..110235213]
chr1:110235176-110235225 TCAGCAGAGCCTCTGCAAAATGCGGGTCAGTTTAGATGACTCCTGTCATG chr1 110235176 50 110235225 NC_000001.9[110235176..110235225]

Total number of rows: 86118

Table truncated, full table size 11381 Kbytes.




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

Supplementary file Size Download File type/resource
GPL11196_080108_HG18_GS_ChIP.ndf.gz 21.1 Mb (ftp)(http) NDF
GPL11196_080108_HG18_GS_ChIP.pos.gz 2.7 Mb (ftp)(http) POS

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