 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 08, 2007 |
| Title |
Nimblegen Dsim expression custom array/2005-06-03_D_simulans_50mer |
| Technology type |
in situ oligonucleotide |
| Distribution |
custom-commercial |
| Organism |
Drosophila simulans |
| Manufacturer |
NimbleGen Systems Inc. |
| Manufacture protocol |
Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html
|
| |
|
| Description |
Nimblegen custom design array for Drosophila species expression: An average of 10 array element probes per predicted genes was selected without-bias vis-a-vis position within the gene model. Sources of gene predictions include EIS (Annotations from Eisen lab v.1.0, Feb. 2005), GID (ab-initio GeneID predictions on draft assembly), and GBK (EST sequence from GeneBank). Probes have been remapped to final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and genome annotation (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation). Arrays are described in detail on http://intramural.niddk.nih.gov/research/multifly/multifly.htm.
|
| |
|
| Contributor(s) |
Sturgill D, Zhang Y, Oliver B |
| Submission date |
Dec 05, 2006 |
| Last update date |
Apr 25, 2012 |
| Contact name |
Brian Oliver |
| E-mail(s) |
briano@nih.gov
|
| Phone |
301-204-9463
|
| Organization name |
NIDDK, NIH
|
| Department |
LBG
|
| Lab |
Developmental Genomics
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Samples (14)
|
GSM149655, GSM149656, GSM149657, GSM149658, GSM149660, GSM149661
|
| Series (1) |
| GSE6640 |
Profiling of sex-biased expression in Drosophila species |
|
| Data table header descriptions |
| ID |
NimbleGen PROBE_DESIGN_ID |
| PROBE_ID |
NimbleGen probe identifier |
| SEQUENCE |
DNA sequence synthesized on the array |
| ROW_NUM |
Y coordinate of the feature on the array |
| COL_NUM |
X coordinate of the feature on the array |
| SEQ_ID |
Target Sequence identifier |
| PROBE_CLASS |
different control or experimental spots |
| RANGE_GB |
location of probe on genome CAF1 assemblies |
| RANGE_STRAND |
strand of probe on genome CAF1 assemblies |
| RANGE_START |
start on genome CAF1 assemblies |
| RANGE_END |
end on genome CAF1 assemblies |
| GleanRgeneID |
remapped GleanR gene ID |
| GleanRgene_strand |
strand of probe on GleanR gene set |
| GleanRgene_start |
start on GleanR gene set |
| GleanRgene_end |
end on GleanR gene set |
| flybaseID |
remapped Flybase gene ID |
| Data table |
| ID |
PROBE_ID |
SEQUENCE |
ROW_NUM |
COL_NUM |
SEQ_ID |
PROBE_CLASS |
RANGE_GB |
RANGE_STRAND |
RANGE_START |
RANGE_END |
GleanRgeneID |
GleanRgene_strand |
GleanRgene_start |
GleanRgene_end |
flybaseID |
| 2212_0001_0001 |
SIM00P0000099206 |
AGCAGGAAAAGCACCAGTCAGCGACTGATAAGCGACAAGCGGATGCAATA |
1 |
1 |
sim-EIS-04856 |
experimental |
CM000364.1 |
+ |
12467700 |
12467750 |
dsim_GLEANR_4298 |
+ |
1474 |
1524 |
FBgn0191991 |
| 2212_0004_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
4 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0006_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
6 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0008_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
8 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0010_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
10 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0012_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
12 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0014_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
14 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0016_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
16 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0018_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
18 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0020_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
20 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0022_0001 |
CPK6 |
TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN |
1 |
22 |
FIDUCIAL_UPPER_LEFT |
fiducial |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0025_0001 |
SIM00P0000148058 |
CCGCCGAGCCCAAGGTGAACCGGGAGTACCTTCCGCCCACCGAAGCTGCG |
1 |
25 |
sim-EIS-08927 |
experimental |
CM000363.1 |
+ |
15895981 |
15896031 |
dsim_GLEANR_14644 |
+ |
445 |
495 |
FBgn0186323 |
| 2212_0027_0001 |
SIM00P0000013920 |
TTTCCCCAGCAATTTCGGGCCTGGTTGCGATTTCCCTGTTACTCCGCCCG |
1 |
27 |
sim-GBK-00697_rc |
experimental |
|
|
NA |
NA |
NA |
NA |
NA |
NA |
NA |
| 2212_0029_0001 |
SIM00P0000081181 |
GCAGGACTTCGAGAAACAGTCGGAAATGATGGACATGAAGGAGGAGATGA |
1 |
29 |
sim-EIS-03354 |
experimental |
CM000364.1 |
+ |
21730539 |
21730589 |
dsim_GLEANR_5024 |
+ |
377 |
427 |
FBgn0192707 |
| 2212_0031_0001 |
SIM00P0000151840 |
GCCCTACATGCCCTACTCGTCCAGTCCGCTTATGGTGCAGTCGTATCCGC |
1 |
31 |
sim-EIS-09242 |
experimental |
CM000364.1 |
- |
14645353 |
14645403 |
dsim_GLEANR_2536 |
+ |
1250 |
1300 |
FBgn0190245 |
| 2212_0033_0001 |
SIM00P0000009126 |
GTACCAAGTCCTTAGTTCTACACGCGTGGTTCATGTGCCTACCATTTACA |
1 |
33 |
sim-GBK-00497 |
experimental |
CM000361.1 |
+ |
21645922 |
21645972 |
dsim_GLEANR_8078 |
+ |
890 |
940 |
FBgn0195691 |
| 2212_0035_0001 |
SIM00P0000097506 |
GGCGCATATGATGCACCGTCCGCCCGGAGATCCGGGCTTCCACCAGGGCT |
1 |
35 |
sim-EIS-04714 |
experimental |
CM000364.1 |
+ |
15043237 |
15043287 |
dsim_GLEANR_4491 |
+ |
1370 |
1420 |
FBgn0192184 |
| 2212_0037_0001 |
SIM00P0000047811 |
TGTGGCTGATAGCGATAACATTTTTGAGTGTTGGTTTCGGTGATATTGTT |
1 |
37 |
sim-EIS-00573 |
experimental |
CM000366.1 |
+ |
4065173 |
4065223 |
dsim_GLEANR_16918 |
+ |
43 |
93 |
FBgn0188316 |
| 2212_0039_0001 |
SIM00P0000016481 |
TAAGTTTCTCCATTCGGGCTCGCGATGACCAATGTCCATTGCAACACACT |
1 |
39 |
sim-GBK-00890_rc |
experimental |
CH990716.1 |
- |
390 |
440 |
NA |
NA |
NA |
NA |
NA |
| 2212_0041_0001 |
SIM00P0000170877 |
ACCCACACAACAGAGCAGCAGACGCCATATCAGATCGGAAGATGGCTTCA |
1 |
41 |
sim-EIS-10829 |
experimental |
|
|
NA |
NA |
dsim_GLEANR_14867 |
+ |
92 |
142 |
FBgn0186543 |
Total number of rows: 390209
Table truncated, full table size 63912 Kbytes.
| Supplementary data files not provided |
|
|
|
|
 |
Less...
More...