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Status
Public on May 27, 2005
Title
Nimblegen ENCODE Array
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Homo sapiens
Description
ENCODE tiling array designed and manufactured by NimbleGen Systems Inc (Madison WI). The array tiles all the non-repetitive forward strand DNA sequence of the ENCODE regions with 50mer oligonucleotides spaced every 38bps (overlapping by 12bps). The array is designed on the NCBIv34 build (hg16) of the Human Genome. The array has approx 390,000 features.
Contributor(s)
Rozowsky JS Submission date
May 26, 2005
Last update date
Jun 16, 2005
Contact name
Joel Rozowsky
E-mail(s)
rozowsky@csb.yale.edu Phone
203-432-5405
Organization name
Yale University
Department
Molecular Biophysics & Biochemistry
Lab
Gerstein Lab
Street address
266 Whitney Ave, Bass 437
City
New Haven
State/province
CT
ZIP/Postal code
06520
Country
USA
Samples (68)
GSM52505 , GSM52506 , GSM52507 , GSM52509 , GSM52510 , GSM78080
GSM78081 ,
GSM78082 ,
GSM78083 ,
GSM78084 ,
GSM78085 ,
GSM78086 ,
GSM78087 ,
GSM81496 ,
GSM81497 ,
GSM81498 ,
GSM81499 ,
GSM81500 ,
GSM81501 ,
GSM81502 ,
GSM81503 ,
GSM98893 ,
GSM147430 ,
GSM147431 ,
GSM147432 ,
GSM147433 ,
GSM147434 ,
GSM147435 ,
GSM147436 ,
GSM147437 ,
GSM147438 ,
GSM159240 ,
GSM159241 ,
GSM159242 ,
GSM159243 ,
GSM159244 ,
GSM159245 ,
GSM159246 ,
GSM159247 ,
GSM159248 ,
GSM159249 ,
GSM159250 ,
GSM159251 ,
GSM159252 ,
GSM177379 ,
GSM177380 ,
GSM177381 ,
GSM177383 ,
GSM177384 ,
GSM177385 ,
GSM177387 ,
GSM177388 ,
GSM177389 ,
GSM178545 ,
GSM178547 ,
GSM178548 ,
GSM199995 ,
GSM199996 ,
GSM199997 ,
GSM252780 ,
GSM252781 ,
GSM252782 ,
GSM601093 ,
GSM601094 ,
GSM601095 ,
GSM601096 ,
GSM601097 ,
GSM601098 Series (23)
GSE2714 ENCODE ChIP-chip for STAT1 on Human Hela S3 Cells
GSE3448 ENCODE ChIP-chip for JUN on Human Hela S3 Cells
GSE3449 ENCODE ChIP-chip for FOS on Human Hela S3 Cells
GSE3450 ENCODE ChIP-chip for TAF II p250 on Human Hela S3 Cells
GSE3549 ENCODE ChIP-chip for BAF155 on Human Hela S3 Cells
GSE3550 ENCODE ChIP-chip for BAF170 on Human Hela S3 Cells
GSE4334 DNaseI/Array GM06990
GSE6389 ENCODE ChIP-chip for Tetra-acetylated Histone H4 on HeLaS3 Cells [unpublished]
GSE6390 ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody (N-20) on HeLaS3 Cells [unpublished]
GSE6391 ENCODE ChIP-chip for RNA Polymerase II using monoclonal antibody (8WG16) on HeLaS3 Cells [unpublished]
GSE6895 Ini1 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]
GSE6896 BAF170 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array [unpublished]
GSE6897 Ini1 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array
GSE6898 BAF155 ChIP-ChIP from K562 Cells using the NimbleGen ENCODE Array [unpublished]
GSE7370 Brg1 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]
GSE7371 SMARCA6 ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]
GSE7372 NRSF ChIP-ChIP from HeLaS3 Cells using the NimbleGen ENCODE Array; [unpublished]
GSE8073 Me3K27 Histone H3 ChIP DNA from HeLa S3 cells
GSE8177 DNaseI/Array multiple cell types
GSE10004 ENCODE Spike-In, Yale Group
GSE10114 Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
GSE24382 Lamin binding profiles in the ENCODE regions
GSE24398 Diverse roles and interactions of the SWI/SNF chromatin-remodeling complex revealed using global approaches
Data table header descriptions ID Probe ID Chromosome_Position (build NCBIv34)
RANGE_GB GenBank/RefSeq chromosome accession number
RANGE_START Starting chromosome position of oligonucleotide (build NCBIv34)
RANGE_END Ending chromosome position of oligonucleotide (build NCBIv34)
RANGE_STRAND Strand
ENCODE_REGION Encode Region
CHROMOSOME Chromosome
SEQUENCE Sequence of 50mer oligonucleotide
X_POSITION x position of feature on microarray
Y_POSITION y position of feature on microarray
NIMBLEGEN_PROBE_ID Internal Nimblegen Probe ID
Data table ID RANGE_GB RANGE_START RANGE_END RANGE_STRAND ENCODE_REGION CHROMOSOME SEQUENCE X_POSITION Y_POSITION NIMBLEGEN_PROBE_ID chr7_115365024
NC_000007.10
115365024
115365073
+
ENm001
chr7
TCTTTACATAACAAGGTTGGAGATCTGAATATAAAAATTCCCTATAAGAT
305
31
ENm000P0000000001
chr7_115365062
NC_000007.10
115365062
115365111
+
ENm001
chr7
TCCCTATAAGATATAGGCAGAGAACATTCAGCAGATCACATATGCTCATA
185
265
ENm000P0000000002
chr7_115365100
NC_000007.10
115365100
115365149
+
ENm001
chr7
CATATGCTCATATGTGCCTGAAGCTCTTATCTGCCTACAGGCTTGGGATG
514
620
ENm000P0000000003
chr7_115365138
NC_000007.10
115365138
115365187
+
ENm001
chr7
AGGCTTGGGATGCACAATTGGGAAGAAGGGTGTTGGGGGTGAGGAGGGGG
660
10
ENm000P0000000004
chr7_115365176
NC_000007.10
115365176
115365225
+
ENm001
chr7
GTGAGGAGGGGGAATGTGCAGGAACTGGGGAAAGAAGTTCAGATAAGACA
530
546
ENm000P0000000005
chr7_115365214
NC_000007.10
115365214
115365263
+
ENm001
chr7
TCAGATAAGACAAGTCCAGGGTAAGGAAGCAGCAGGCACCTGGAAAGGGG
517
437
ENm000P0000000006
chr7_115365252
NC_000007.10
115365252
115365301
+
ENm001
chr7
CCTGGAAAGGGGATCAATCCAGTAGTTGATAGAAGTTCTGACACAAACTC
659
863
ENm000P0000000007
chr7_115365290
NC_000007.10
115365290
115365339
+
ENm001
chr7
TGACACAAACTCCAAATAAGTTGAGAACAAACCTGAGAACAATTGAATGG
39
965
ENm000P0000000008
chr7_115365328
NC_000007.10
115365328
115365377
+
ENm001
chr7
ACAATTGAATGGGTGCTCCACTTCACACCTTGGGGAACAGTAGAACAGCA
622
552
ENm000P0000000009
chr7_115365366
NC_000007.10
115365366
115365415
+
ENm001
chr7
AGTAGAACAGCAAGAGCAGATAAACAAGTCCCGTCACATGGAGCAGGGTA
747
185
ENm000P0000000010
chr7_115365404
NC_000007.10
115365404
115365453
+
ENm001
chr7
TGGAGCAGGGTAGTCCTACATCTTCTGCCTGTCTCCTGAGGAACAAGAAA
104
906
ENm000P0000000011
chr7_115365442
NC_000007.10
115365442
115365491
+
ENm001
chr7
AGGAACAAGAAATGATACAGAATTGCCCATGTATGGGAGAAGGCAGATAG
199
505
ENm000P0000000012
chr7_115365480
NC_000007.10
115365480
115365529
+
ENm001
chr7
GAAGGCAGATAGCATGAGCTTACCTGGGGAGTCTGGATAAGGAGAAAGTT
180
206
ENm000P0000000013
chr7_115365518
NC_000007.10
115365518
115365567
+
ENm001
chr7
AAGGAGAAAGTTAATTTACATACAGCACAAAGCTTTGGGATCAACTTCCC
530
920
ENm000P0000000014
chr7_115365556
NC_000007.10
115365556
115365605
+
ENm001
chr7
GATCAACTTCCCATGTCAGGGATTGAATGAGAGTCACAGCTATATCTTTG
561
491
ENm000P0000000015
chr7_115365594
NC_000007.10
115365594
115365643
+
ENm001
chr7
GCTATATCTTTGGGCAAGTTCTACTAAGCCAGAAATAGTGAACCAGATGG
97
937
ENm000P0000000016
chr7_115365632
NC_000007.10
115365632
115365681
+
ENm001
chr7
TGAACCAGATGGTGGAGGTGACTTGATCAGATAACAGAGGTGACCAAGTT
424
222
ENm000P0000000017
chr7_115365670
NC_000007.10
115365670
115365719
+
ENm001
chr7
GGTGACCAAGTTCCCCAGAGCAATCTCCTCACCATGTCAAGGCCAAGAGA
607
767
ENm000P0000000018
chr7_115365708
NC_000007.10
115365708
115365757
+
ENm001
chr7
AAGGCCAAGAGAACAGACCACAAATTGTACCACCTAAAGACACATTAAAA
676
362
ENm000P0000000019
chr7_115365746
NC_000007.10
115365746
115365795
+
ENm001
chr7
GACACATTAAAAGTGGCAGCAGTATGGAGTCCTCAACCATGGCCCCAGTG
80
126
ENm000P0000000020
382884 51228 Kbytes .Supplementary data files not provided
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