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| Status |
Public on Nov 26, 2006 |
| Title |
FHCRC Arabidopsis Tiling Array |
| Technology type |
in situ oligonucleotide |
| Distribution |
custom-commercial |
| Organism |
Arabidopsis thaliana |
| Manufacturer |
NimbleGen Systems Inc. |
| Manufacture protocol |
http://www.nimblegen.com/products/chip/index.html
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| Description |
Arabidopsis tiling array using NimbleGen platform (DesignID=2482). TIGR release 5.0, 1/22/2004 (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/). Entire genome, isothermal probes averaging 50 base pairs at 300 base pair intervals.
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| Web link |
http://www.nimblegen.com
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| Contributor(s) |
Henikoff S, Tran R |
| Submission date |
Jan 18, 2006 |
| Last update date |
Nov 26, 2006 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Samples (35)
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GSM138295, GSM138296, GSM138297, GSM138298, GSM138299, GSM176870
GSM176871, GSM307373, GSM307374, GSM307375, GSM307376, GSM307377, GSM307378, GSM307379, GSM307380, GSM307381, GSM307382, GSM307383, GSM307384, GSM307385, GSM307386, GSM307387, GSM307388, GSM307389, GSM307390, GSM307391, GSM307392, GSM307393, GSM364540, GSM364541, GSM364542, GSM602792, GSM602793, GSM602794, GSM602795
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| Series (6)
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| GSE5974 |
Interdependence between DNA methylation and transcription |
| GSE7336 |
DNA demethylation in the Arabidopsis genome |
| GSE12212 |
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks |
| GSE14570 |
Extensive demethylation of repetitive elements during seed development underlies gene imprinting |
| GSE24474 |
H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants |
| GSE24507 |
Gene expression and H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants |
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| Data table header descriptions |
| ID |
NimbleGen PROBE_DESIGN_ID |
| CONTAINER |
Probes are arranged in sets in different containers |
| DESIGN_NOTE |
Comment field for data analysis |
| SELECTION_CRITERIA |
Information about how the probe was selected |
| SEQ_ID |
NimbleGen sequence identifier |
| SEQUENCE |
DNA sequence synthesized on the array |
| MISMATCH |
Number of mismatches in the PROBE_SEQUENCE. Generally 0 (for the perfect match probe) or 2 (for the corresponding mismatch probe) |
| MATCH_INDEX |
Integer number that ties probe pairs together |
| FEATURE_ID |
Unique number used to tie together multiple features that compose a feature cell |
| ROW_NUM |
Y coordinate of the feature within the CONTAINER holding the feature |
| COL_NUM |
X coordinate of the feature within the CONTAINer holding the feature |
| PROBE_CLASS |
Experimental or Control |
| PROBE_ID |
NimbleGen probe identifier |
| POSITION |
Position of the probe within the parent sequence |
| DESIGN_ID |
NimbleGen identifier for the design |
| X |
Absolute X coordinate of the feature on the array |
| Y |
Absolute Y coordinate of the feature on the array |
| Data table |
| ID |
CONTAINER |
DESIGN_NOTE |
SELECTION_CRITERIA |
SEQ_ID |
SEQUENCE |
MISMATCH |
MATCH_INDEX |
FEATURE_ID |
ROW_NUM |
COL_NUM |
PROBE_CLASS |
PROBE_ID |
POSITION |
DESIGN_ID |
X |
Y |
| 2571_0001_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.71 |
cluster:13867;probe:01 |
CHR4 |
TTGATGTAACCAAGCCGGTTAGAAGCTATTTCTGTATAAGAATCCACCAAGAATTGCTG |
0 |
38746760 |
38746760 |
1 |
1 |
experimental |
CHR400P004152705 |
4152705 |
2571 |
1 |
1 |
| 2571_0004_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000187 |
37331612 |
1 |
4 |
fiducial |
CPK6 |
0 |
2571 |
4 |
1 |
| 2571_0006_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000197 |
37331622 |
1 |
6 |
fiducial |
CPK6 |
0 |
2571 |
6 |
1 |
| 2571_0008_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000198 |
37331623 |
1 |
8 |
fiducial |
CPK6 |
0 |
2571 |
8 |
1 |
| 2571_0010_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000199 |
37331624 |
1 |
10 |
fiducial |
CPK6 |
0 |
2571 |
10 |
1 |
| 2571_0012_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000200 |
37331625 |
1 |
12 |
fiducial |
CPK6 |
0 |
2571 |
12 |
1 |
| 2571_0014_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000201 |
37331626 |
1 |
14 |
fiducial |
CPK6 |
0 |
2571 |
14 |
1 |
| 2571_0016_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000202 |
37331627 |
1 |
16 |
fiducial |
CPK6 |
0 |
2571 |
16 |
1 |
| 2571_0018_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000203 |
37331628 |
1 |
18 |
fiducial |
CPK6 |
0 |
2571 |
18 |
1 |
| 2571_0020_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000204 |
37331629 |
1 |
20 |
fiducial |
CPK6 |
0 |
2571 |
20 |
1 |
| 2571_0022_0001 |
NGS_CONTROLS |
upper left fiducial |
bright |
FIDUCIAL_UPPER_LEFT |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
0 |
2000205 |
37331630 |
1 |
22 |
fiducial |
CPK6 |
0 |
2571 |
22 |
1 |
| 2571_0025_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.60 |
cluster:14793;probe:01 |
CHR4 |
AGATCATTCCAACTTCAGATGACTGGTCTAAACTCAAAGCACCGAAGGTCAAT |
0 |
38747686 |
38747686 |
1 |
25 |
experimental |
CHR400P004411913 |
4411913 |
2571 |
25 |
1 |
| 2571_0027_0001 |
RANDOM |
|
21-25 |
RANDOM_GC21_GC25 |
CTGTCCCTCTGACAGCTAGCAACTGTCAGAATTGAAGGGAAAGTGTGGCA |
0 |
39308778 |
39308778 |
1 |
27 |
|
RANDOM00005477 |
0 |
2571 |
27 |
1 |
| 2571_0029_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.45 |
cluster:13037;probe:01 |
CHR4 |
GGTGGCGACTCAACATACTGTTCCCCCCTATCAGAATTATCTATAGA |
0 |
38745930 |
38745930 |
1 |
29 |
experimental |
CHR400P003891963 |
3891963 |
2571 |
29 |
1 |
| 2571_0031_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.52 |
cluster:39386;probe:01 |
CHR1 |
TTTTCTGATATTCTACTGAGTCTGTAACCTTTTGCAGTGTGTGTGAGTCCCTAAATCTCAA |
0 |
38832380 |
38832380 |
1 |
31 |
experimental |
CHR100P011947074 |
11947074 |
2571 |
31 |
1 |
| 2571_0033_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.81 |
cluster:12116;probe:01 |
CHR1 |
AGGTCCCACATCGACTTGAGAAGAAAAGATGACATGACAACAGATGAAGACTATTTGA |
0 |
38805110 |
38805110 |
1 |
33 |
experimental |
CHR100P003474432 |
3474432 |
2571 |
33 |
1 |
| 2571_0035_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.81 |
cluster:08113;probe:01 |
CHR3 |
TTTGGCTCATAACCAATTCTCATGAAATGACCTCAAGGAAAATTCCGATATTACCCGC |
0 |
38664203 |
38664203 |
1 |
35 |
experimental |
CHR300P002364529 |
2364529 |
2571 |
35 |
1 |
| 2571_0037_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.91 |
cluster:76376;probe:01 |
CHR5 |
AAGTGTACTATTGTGAGCCGCCTTGTGAAGCATACCAACTTTGAAGTTTGAAGTGTT |
0 |
38583748 |
38583748 |
1 |
37 |
experimental |
CHR500P023982240 |
23982240 |
2571 |
37 |
1 |
| 2571_0039_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.80 |
cluster:53025;probe:01 |
CHR2 |
TCCAAGTGAAGAACATTTAGTTCCGTCAGATTGAGAGACATGACTCATGATTCATGAAATGTCTT |
0 |
38646652 |
38646652 |
1 |
39 |
experimental |
CHR200P016905788 |
16905788 |
2571 |
39 |
1 |
| 2571_0041_0001 |
BLOCK1 |
target_tm:76.00;probe_tm:75.60 |
cluster:16845;probe:01 |
CHR4 |
AATATTCCCTAGCAAAATGTATCATCATCCAAGGTGGCGTACAAACAGTTGGC |
0 |
38749738 |
38749738 |
1 |
41 |
experimental |
CHR400P005012093 |
5012093 |
2571 |
41 |
1 |
Total number of rows: 391015
Table truncated, full table size 81870 Kbytes.
| Supplementary data files not provided |
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