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Platform GPL4633 Query DataSets for GPL4633
Status Public on Nov 08, 2007
Title Nimblegen Dvir expression custom array/2005-06-03_D_virilis_50mer
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Drosophila virilis
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 (9) GSM149712, GSM149713, GSM149714, GSM149715, GSM149718, GSM149719 
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
2213_0001_0001 VIR00P0000018354 GAAGTGCTGGATCCCTACCTCACCATACGTTGCCGAAAGTCGGTTGACTT 1 1 vir-GID-01388 experimental CH940649.1 - 12825337 12825387 dvir_GLEANR_816 + 2694 2744 FBgn0209894
2213_0004_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 4 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0006_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 6 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0008_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 8 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0010_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 10 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0012_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 12 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0014_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 14 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0016_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 16 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0018_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 18 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0020_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 20 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0022_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 22 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2213_0025_0001 VIR00P0000146533 CAGCGTCAAGTTTGCTCCAGAATGAACTTCCTTTATCAGGCGTCAAACTT 1 25 vir-EIS-06507 experimental CH940660.1 - 1694480 1694530 NA NA NA NA NA
2213_0027_0001 VIR00P0000056374 CAAAACTCCACTACCCCATCTCCCATTGTACCGAATCCTGGTGGAACCCC 1 27 vir-GID-04565 experimental CH940659.1 + 1535221 1535271 NA NA NA NA NA
2213_0029_0001 VIR00P0000094764 GGCTGTGGCTCCGGTGGTGCGTTTTACTCCAGTTAAGCGACGCAAAGTCC 1 29 vir-EIS-02191 experimental CH940648.1 - 7215631 7215681 dvir_GLEANR_6158 + 2066 2116 FBgn0207880
2213_0031_0001 VIR00P0000065064 TCAGTTCCGACTTATCGAGTATACTCAACGCCAAGCTTATCCTAAGGAGC 1 31 vir-GID-05305 experimental CH940658.1 - 2619111 2619161 NA NA NA NA NA
2213_0033_0001 VIR00P0000150536 GCGCGCCAAGTACTGCGTGACCAAGGACCTAACCGCATTCAATGTGGGCT 1 33 vir-EIS-06840 experimental CH940647.1 - 8298838 8298888 dvir_GLEANR_12159 + 797 847 FBgn0199424
2213_0035_0001 VIR00P0000008658 ATTTAAATGTACCCATTGAACTGGCCGTGGAATCACCGCTAGCGCAACAA 1 35 vir-GID-00580 experimental CH940648.1 - 10874844 10874894 dvir_GLEANR_5980 + 1291 1341 FBgn0207688
2213_0037_0001 VIR00P0000128560 AAATTGTGCAGTCGCATCCGCCGATTCCCAACACACAAGTGCCGCCACAA 1 37 vir-EIS-05008 experimental CH940649.1 + 11362640 11362690 dvir_GLEANR_1976 + 1978 2028 FBgn0204549
2213_0039_0001 VIR00P0000105539 GTGAAGCTTAGCAAGGGCCACAATGGGGTCACGACCTCCTCATCCTCGAC 1 39 vir-EIS-03089 experimental CH940682.1 - 69357 69407 dvir_GLEANR_16482 + 249 299 FBgn0203248
2213_0041_0001 VIR00P0000139333 GCCCAACGAGCTGACTGTGAAGACGGTGAACAACAGCGTCGTCATCGAGG 1 41 vir-EIS-05906 experimental CH940647.1 - 19488886 19488936 dvir_GLEANR_11511 + 221 271 FBgn0198734

Total number of rows: 391015

Table truncated, full table size 66873 Kbytes.




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