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Status
Public on Jun 15, 2005
Title
Nimblegen ENCODE tiling array (HG17) with 50mer probe at 38bp interval for RenLab
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism(s)
Homo sapiens Manufacturer
Nimblegen
Manufacture protocol
as described in www.nimblegen.com
Description
ENCODE regions tiled from HG17; NCBI Build 35. 50-mer tiling at 38 bp interval. Only 4 regions were re-tiled: ENm006, ENm014,ENr131,ENr211. For the remainder, the probes from HG16 were renamed and remapped to the HG17 coordinates. 3319 random probes added Mask set trimmed to 148 cycles.
Web link
http://www.nimblegen.com Contributor(s)
Ren B Submission date
Jun 10, 2005
Contact name
Chunxu Qu
E-mail(s)
qchunxu@ucsd.edu Phone
(858)822-5767
Organization name
Ludwig Institute for Cancer Research
Department
Gene Regulation
Lab
RenLab
Street address
City
San Diego
State/province
CA
ZIP/Postal code
92093
Country
USA
Samples (30)
GSM60841 , GSM60842 , GSM60843 , GSM60844 , GSM60845 , GSM60846
GSM60847 ,
GSM60848 ,
GSM60849 ,
GSM60850 ,
GSM60851 ,
GSM60852 ,
GSM147439 ,
GSM147440 ,
GSM147441 ,
GSM147442 ,
GSM147444 ,
GSM147445 ,
GSM147446 ,
GSM147447 ,
GSM147448 ,
GSM159174 ,
GSM159175 ,
GSM159176 ,
GSM159253 ,
GSM159254 ,
GSM159255 ,
GSM159256 ,
GSM159257 ,
GSM159258 Series (7)
GSE2813 ENCODE (HG17) region-wide binding of a few antibodies in IFg treated and untreated HeLa cells using nimblegen array
GSE6392 ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody on GM06990 Cells [unpublished]
GSE6393 ENCODE ChIP-chip for Tetra-acetylated Histone H4 on GM06990 Cells [unpublished]
GSE6394 ENCODE ChIP-chip for RNA Polymerase II using monoclonal antibody (8WG16) on GM06990 Cells [unpublished]
GSE6892 STAT1 (Interferon-alpha) ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array
GSE6899 ENCODE ChIP-chip for Rel A (p65) using polyclonal antibody (C-20) on TNF-alpha-stimulated HeLaS3 Cells [unpublished]
GSE6900 ENCODE ChIP-chip for Rel A (p65) using polyclonal antibody (N-) on TNF-alpha-stimulated HeLaS3 Cells [unpublished]
Data table header descriptions ID SPOT ID Probe id composed with chromosome and position
ENCODE_ID ENCODE region ID
Position Start position (1-based) in the chromosome, the ending position will be this value + 49 (50 bp probe).
SEQUENCE Probe sequence.
Comment Blocks in the array. Block1 is the container for non-control elements.
Data table ID SPOT ID ENCODE_ID Position SEQUENCE Comment 1
CHR01P147971134
ENr231
147971134
GTTGACCTTTCGAGGCCTTAAGCTCTTGAGAGGTTCCTGAGGACAGATTG
BLOCK1
2
CHR01P147971172
ENr231
147971172
GAGGACAGATTGGAATCAGATACTGGGGAACAGAAGAAGTCAGGAGAAAT
BLOCK1
3
CHR01P147971210
ENr231
147971210
GTCAGGAGAAATATGAGGATCTCAATGAGAGAAAACTAGCATTGCCAGAA
BLOCK1
4
CHR01P147971248
ENr231
147971248
GCATTGCCAGAAATGGAAGTGGCATAGGGAGTACTGGGACCTGATGAAAG
BLOCK1
5
CHR01P147971286
ENr231
147971286
ACCTGATGAAAGAGAGAATAGGAATTGAGGAAATCCAAGACAACTAGGAC
BLOCK1
6
CHR01P147971324
ENr231
147971324
GACAACTAGGACTCCCCCTGTACCTTATAGGCCTTGGTGACTACTCGGCG
BLOCK1
7
CHR01P147971362
ENr231
147971362
GACTACTCGGCGCTTCCTTCTTGGCTCTTCTGCTTCTCCATCACTGGATG
BLOCK1
8
CHR01P147971400
ENr231
147971400
CATCACTGGATGGTTCATCCCCTTCATCAATGTCAAAGTCAGAGTCCACT
BLOCK1
9
CHR01P147971438
ENr231
147971438
TCAGAGTCCACTTCGTCCTCTGTGTCTGACTGGTCCCCTTGATACTCATC
BLOCK1
10
CHR01P147971476
ENr231
147971476
TTGATACTCATCATCTCCGGATTCCTAAGGACACAGGGAGATAAGGGTTG
BLOCK1
11
CHR01P147971514
ENr231
147971514
AGATAAGGGTTGGCTGGCAATGGAAGCCTTAATGCCCCTTCAGGAGGAAC
BLOCK1
12
CHR01P147971552
ENr231
147971552
TTCAGGAGGAACAGAATCTCTCGACTTTCTTGATAAGGGCTGCCCTACTC
BLOCK1
13
CHR01P147971590
ENr231
147971590
GCTGCCCTACTCTCCTTCCTAATCCAGCCCTTCATTTTCCTCAGGCAAGA
BLOCK1
14
CHR01P147972274
ENr231
147972274
GATCTAAGTAAAACTTTTCTCTGTCAAGAAACCTTGTTAGCCAACTGCAT
BLOCK1
15
CHR01P147972312
ENr231
147972312
AGCCAACTGCATTTGGCTCCAGCACTGCCTCCTTCCAACACTGATTGCAC
BLOCK1
16
CHR01P147972350
ENr231
147972350
CACTGATTGCACTGTAGGACTGTATGATTTGAAAAGAAGGTTGCATTCCA
BLOCK1
17
CHR01P147972388
ENr231
147972388
GGTTGCATTCCATTTATGGAGAAACTTAAATGTCACACTAATAAACACGC
BLOCK1
18
CHR01P147972426
ENr231
147972426
TAATAAACACGCTTTTAACCTGCAGGCCAGTGATTCTCAATCCCCTCCAT
BLOCK1
19
CHR01P147972464
ENr231
147972464
AATCCCCTCCATCTCCTTATTTTCCCTACCATTGATAATCATTGTTGAGG
BLOCK1
20
CHR01P147972502
ENr231
147972502
TCATTGTTGAGGTAAACTAAAGTTACTGAGAGAAATATGTGTCATTCCTC
BLOCK1
390611 36949 Kbytes .Supplementary data files not provided
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