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Platform GPL248 Query DataSets for GPL248
Status Public on Jul 24, 2003
Title Dmel_arrayplatform
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Drosophila melanogaster
 
Description Spotted array using PCR fragments of approximately 95% of the genes in the D. melanogaster BDGP genome.

We followed a sequence of decreasingly stringent tests to pick optimal primer pairs for the PCR fragments on the arrays. For each gene, we looked for (first) a 500b to 2kb sequence at the 3’ end and, failing this, (second) two 200b to 500b sequences in:(1) coding sequence, completely within an EST clot, and unduplicated (BLAST<=10^-4); (2) coding sequence, partially within an EST clot, unduplicated; (3) coding sequence, unduplicated; (4) exon, completely within an EST clot, unduplicated; (5) exon, partially within an EST clot, unduplicated; (6) exon, unduplicated; (7) sequence less than 2kb at the 3’ end. See above for the other details about making these arrays.
 
Contributor(s) Li T, White KP
Submission date Feb 18, 2003
Last update date May 30, 2012
Contact name Tong-Ruei Li
E-mail(s) tong-ruei.li@yale.edu
Phone 203-785-4474
Organization name Yale University School of Medicine
Department Department of Genetics
Lab Kevin White
Street address 333 Cedar St. Rm#NSB386
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Samples (175) GSM3894, GSM3895, GSM3896, GSM4487, GSM4488, GSM4489 
Series (7)
GSE283 sage gene RNAi experiment
GSE540 EcR mutant midgut comparison
GSE541 Whole animal vs. tissues at 18h before puparium formation

Data table header descriptions
ID
Block 32 blocks of spots in 4 columns and 8 rows. Block numbering is from left to right and from higher to lower. The 1st block is at the upper left corner. The 4th block is at the higher right corner. The 29th block is at the lower left corner. The 32nd block is at the lower right corner.
Column The column number of a spot within a block.
Row The row number of a spot within a block.
Internal_ID The internal ID. Representing the ID for primer pairs.
ORF The CG number for a gene used by Flybase.
CLONE_ID Reporter Biosequence Database Entry: The FBgn number used by FlyBase, which is the systematic gene name.
Forward_Primer The sequence for the forward primer that is used in the PCR reaction to amplify a gene fragment.
Reverse_Primer The sequence for the reverse primer that is used in the PCR reaction to amplify a gene fragment.
SEQUENCE The predicted sequence (base on Flybase annotation) of the product from the PCR reaction amplifying a gene fragment.
SPOT_ID

Data table
ID Block Column Row Internal_ID ORF CLONE_ID Forward_Primer Reverse_Primer SEQUENCE SPOT_ID
1 1 1 1 BLANK BLANK
2 1 2 1 BLANK BLANK
3 1 3 1 BLANK BLANK
4 1 4 1 BLANK BLANK
5 1 5 1 BLANK BLANK
6 1 6 1 BLANK BLANK
7 1 7 1 BLANK BLANK
8 1 8 1 BLANK BLANK
9 1 9 1 BLANK BLANK
10 1 10 1 BLANK BLANK
11 1 11 1 BLANK BLANK
12 1 12 1 BLANK BLANK
13 1 13 1 BLANK BLANK
14 1 14 1 BLANK BLANK
15 1 15 1 BLANK BLANK
16 1 16 1 BLANK BLANK
17 1 17 1 BLANK BLANK
18 1 18 1 BLANK BLANK
19 1 19 1 BLANK BLANK
20 1 20 1 BLANK BLANK

Total number of rows: 20000

Table truncated, full table size 7420 Kbytes.






Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

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