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Status |
Public on Mar 09, 2009 |
Title |
HudsonAlpha Illumina Homo sapiens Methyl-seq |
Technology type |
other |
Distribution |
virtual |
Organism |
Homo sapiens |
Manufacturer |
NIH |
Manufacture protocol |
n/a
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Description |
1G Genome Analyzer sequencing machine
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Submission date |
Mar 09, 2009 |
Last update date |
Jan 18, 2013 |
Contact name |
Rami Rauch |
E-mail(s) |
rrauch@stanford.edu
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Organization name |
Stanford U
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Street address |
300 Pasteaur Dr
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305-5317 |
Country |
USA |
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Data table header descriptions |
ID |
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region chromosome |
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RANGE_GB |
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RANGE_START |
region start coordinate |
RANGE_END |
region end coordinate |
number of MspI sites above threshold in region |
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region length |
bp |
CpGs in region |
number of CpGs in region |
CpG density of region |
#CpGs in region/length of regions in bp |
region overlaps CpG island? |
yes or no |
region overlaps 7x Regulatory Potential? |
yes or no |
region classification |
promoter=PROM, 5'UTR, coding exon=CODING, 3'UTR, INTRON, intergenic=INTGEN |
Refseq id for overlapping gene |
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Gene symbol for overlapping gene |
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region overlaps with histone modifications |
bivalent, H3K4_only, H3K27_only, neither |
region overlaps with promoter classifications |
HCP, ICP, LCP, NA |
list of MspI/HpaII sites in region |
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Data table |
ID |
region chromosome |
RANGE_GB |
RANGE_START |
RANGE_END |
number of MspI sites above threshold in region |
region length |
CpGs in region |
CpG density of region |
region overlaps CpG island? |
region overlaps 7x Regulatory Potential? |
region classification |
Refseq id for overlapping gene |
Gene symbol for overlapping gene |
region overlaps with histone modifications |
region overlaps with promoter classifications |
list of MspI/HpaII sites in region |
1 |
chr1 |
NC_000001.9 |
744000 |
744037 |
2 |
37 |
4 |
0.108108108 |
no |
no |
INTGEN |
NA |
NA |
neither |
NA |
744000 744037 |
2 |
chr1 |
NC_000001.9 |
752582 |
752656 |
2 |
74 |
11 |
0.148648649 |
yes |
yes |
INTGEN |
NA |
NA |
H3K4_only |
HCP |
752582 752656 |
3 |
chr1 |
NC_000001.9 |
795274 |
795330 |
2 |
56 |
7 |
0.125 |
yes |
no |
INTGEN |
NA |
NA |
neither |
NA |
795274 795330 |
4 |
chr1 |
NC_000001.9 |
799061 |
799101 |
2 |
40 |
2 |
0.05 |
no |
yes |
INTGEN |
NA |
NA |
neither |
NA |
799061 799101 |
5 |
chr1 |
NC_000001.9 |
830102 |
830182 |
3 |
80 |
9 |
0.1125 |
yes |
no |
INTGEN |
NA |
NA |
neither |
NA |
830102 830142 830182 |
6 |
chr1 |
NC_000001.9 |
830679 |
830716 |
2 |
37 |
5 |
0.135135135 |
no |
no |
INTGEN |
NA |
NA |
bivalent |
NA |
830679 830716 |
7 |
chr1 |
NC_000001.9 |
831917 |
832072 |
4 |
155 |
6 |
0.038709677 |
no |
no |
INTGEN |
NA |
NA |
H3K27_only |
NA |
831917 831981 832006 832072 |
8 |
chr1 |
NC_000001.9 |
835110 |
835293 |
4 |
183 |
19 |
0.103825137 |
yes |
no |
INTGEN |
NA |
NA |
H3K27_only |
NA |
835110 835174 835239 835293 |
9 |
chr1 |
NC_000001.9 |
835600 |
835710 |
3 |
110 |
8 |
0.072727273 |
yes |
no |
INTGEN |
NA |
NA |
H3K27_only |
NA |
835600 835673 835710 |
10 |
chr1 |
NC_000001.9 |
836081 |
836146 |
2 |
65 |
2 |
0.030769231 |
no |
yes |
INTGEN |
NA |
NA |
H3K27_only |
NA |
836081 836146 |
11 |
chr1 |
NC_000001.9 |
838456 |
838525 |
2 |
69 |
4 |
0.057971014 |
no |
yes |
INTGEN |
NA |
NA |
H3K27_only |
NA |
838456 838525 |
12 |
chr1 |
NC_000001.9 |
843476 |
843514 |
2 |
38 |
2 |
0.052631579 |
no |
no |
INTGEN |
NA |
NA |
H3K27_only |
NA |
843476 843514 |
13 |
chr1 |
NC_000001.9 |
846162 |
846214 |
2 |
52 |
2 |
0.038461538 |
no |
yes |
INTGEN |
NA |
NA |
H3K27_only |
NA |
846162 846214 |
14 |
chr1 |
NC_000001.9 |
846506 |
846556 |
2 |
50 |
5 |
0.1 |
no |
yes |
INTGEN |
NA |
NA |
H3K27_only |
NA |
846506 846556 |
15 |
chr1 |
NC_000001.9 |
848842 |
848949 |
4 |
107 |
12 |
0.112149533 |
yes |
yes |
INTGEN |
NA |
NA |
H3K27_only |
NA |
848842 848892 848910 848949 |
16 |
chr1 |
NC_000001.9 |
849068 |
849301 |
5 |
233 |
42 |
0.180257511 |
yes |
yes |
INTGEN |
NA |
NA |
neither |
NA |
849068 849127 849192 849238 849301 |
17 |
chr1 |
NC_000001.9 |
849393 |
849439 |
2 |
46 |
8 |
0.173913043 |
yes |
yes |
PROM |
NM_152486 |
SAMD11 |
neither |
NA |
849393 849439 |
18 |
chr1 |
NC_000001.9 |
849544 |
849590 |
2 |
46 |
10 |
0.217391304 |
yes |
no |
PROM |
NM_152486 |
SAMD11 |
neither |
NA |
849544 849590 |
19 |
chr1 |
NC_000001.9 |
850217 |
850263 |
2 |
46 |
7 |
0.152173913 |
yes |
no |
PROM |
NM_152486 |
SAMD11 |
neither |
NA |
850217 850263 |
20 |
chr1 |
NC_000001.9 |
850526 |
850562 |
2 |
36 |
6 |
0.166666667 |
yes |
no |
PROM |
NM_152486 |
SAMD11 |
neither |
NA |
850526 850562 |
Total number of rows: 90612
Table truncated, full table size 10771 Kbytes.
Supplementary data files not provided |
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