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Platform GPL4634 Query DataSets for GPL4634
Status Public on Nov 08, 2007
Title Nimblegen Dyak expression custom array/2005-06-03_D_yakuba_50mer
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Drosophila yakuba
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 (12) GSM149665, GSM149666, GSM149668, GSM149669, GSM149670, GSM149671 
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
2214_0001_0001 YAK00P0000161157 GTGCAACGCTTTGCTTGACCTTCTTGCAGCAAGTTGCATCTGAAGATGTG 1 1 yak-EIS-07752 experimental CM000159.2 + 13214201 13214251 dyak_GLEANR_5673 + 28 78 FBgn0239190
2214_0004_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 4 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0006_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 6 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0008_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 8 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0010_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 10 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0012_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 12 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0014_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 14 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0016_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 16 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0018_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 18 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0020_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 20 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0022_0001 CPK6 TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 1 22 FIDUCIAL_UPPER_LEFT fiducial NA NA NA NA NA NA NA
2214_0025_0001 YAK00P0000175127 TCTCGACGAGCTGATTCAGTACGGCCAGATTACGCCCGGATTGGCGTTCA 1 25 yak-EIS-09149 experimental NA NA dyak_GLEANR_7659 + 53 103 FBgn0241062
2214_0027_0001 YAK00P0000208223 TCTTTGGACCCTCTAGTGTCCGCAGTTCCTTGGAGTTTTTCGGGGATTAC 1 27 yak-EIS-12458 experimental CM000160.2 - 14823346 14823396 dyak_GLEANR_8041 + 571 621 FBgn0241459
2214_0029_0001 YAK00P0000194711 AGAAGGGCAACAAGTTGTTGGACAACCTCCGAGACAAGCGGCAGGATTGC 1 29 yak-EIS-11107 experimental CM000160.2 - 20717074 20717124 dyak_GLEANR_7647 + 214 264 FBgn0241049
2214_0031_0001 YAK00P0000159958 TTCCGGATGTGGGATTACGGGTTAATGGTGTGAATTACATTCCGTGCGAG 1 31 yak-EIS-07632 experimental CM000157.2 + 15775703 15775753 dyak_GLEANR_2888 + 1009 1059 FBgn0236473
2214_0033_0001 YAK00P0000094089 AGGTCATCCGCTACATCATCGACAACAAGCCCGAGGAGTGGAAGCAGCTG 1 33 yak-EIS-01043 experimental CM000158.2 + 19893449 19893499 dyak_GLEANR_14489 + 253 303 FBgn0068102
2214_0035_0001 YAK00P0000171284 AAGCTGCCACCGGGCATACTGCCGGGCGATAAGATATTGCAAGTCCACGC 1 35 yak-EIS-08764 experimental NA NA dyak_GLEANR_9629 + 1176 1226 FBgn0243094
2214_0037_0001 YAK00P0000100422 TTGCTACCATTGATTTGCATCGCCATTGGCTATGTTCGGTCCCAACCGGC 1 37 yak-EIS-01677 experimental NA NA NA NA NA NA NA
2214_0039_0001 YAK00P0000064308 GCATCCCCATTTGACTTTGCTGGTTATACAAGGTCGCATTAATGTGTTCT 1 39 yak-GID-04042 experimental CH898290.1 + 13555 13605 NA NA NA NA NA
2214_0041_0001 YAK00P0000205683 AACTGCAACTCGTACTTAGTCACCGATAGCGTTGCCTTTATTGGAACCTC 1 41 yak-EIS-12204 experimental CM000158.2 + 1607086 1607136 dyak_GLEANR_13247 + 1269 1319 FBgn0230704

Total number of rows: 391015

Table truncated, full table size 65503 Kbytes.




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