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Platform GPL5 Query DataSets for GPL5
Status Public on Oct 08, 2000
Title Dmel.testis.1.0
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Drosophila melanogaster
 
Description The array was assembled using 1,681 testes ESTs, representing 1,527 Drosophila melanogaster EST sequences and 144 anonymous clones from the bs collection (CLONE_ID).
An aliquot of the same DNA preparation used in the sequencing reactions (GB_ACC), diluted 2/50 in TE, provided material for the PCRs.
Inserts were PCR amplified (1X PCR buffer [Life Technologies], 1.5 mM MgCl2, 0.2 mM dNTPs, 1 µM T7 22-mer primer, 1 µM T3 20-mer primer, 2 µl of plasmid DNA dilution [approximately 10 ng], 0.035 U/µl recombinant Taq DNA polymerase [Life Technologies], in a volume of 100 µl, cycled 94C 2 min, 30X[94 C 0.5 min, 55 C 0.5 min, 2.5 min 72 C], 10 min 72 C in a PTC-225 DNA Engine Tetrad [MJ Research]), and successful amplification was confirmed by agarose gel electrophoresis (PCR-QC: passed = product present, failed = no product).
Samples of approximately 5 nl of 250 µg/ml DNA, in 0.1 N NaOH were printed in 300 µm spots in subarrays (SUB-ARRAY) of 12 x 12 clones (ROW and COLUMN indicated) at 665 µm spacing on Supercharge nytran membranes (Schleicher & Schuell) using a GMS 417 arrayer (Genetic Microsystems).
Subarrays were printed in duplicate (DUPLICATE a or b).
Printing was validated (SPOT_QC) by hybridization of one array with the short vector sequence common to all amplicons (pBluescript SK, 626-791 bp).
SPOT_QC values are hybridization intensity. BEST-HIT and associated E value for ESTs aligned with the nr database are given.
Keywords = germline sex testis, membrane, filter
 
Contributor(s) Oliver B, Andrews J, Bouffard GG, Cheadle C, Lu J, Becker KG
Citation(s) 11116097
Submission date Oct 03, 2000
Last update date Oct 28, 2005
Contact name Brian Oliver
E-mail(s) briano@helix.nih.gov
Phone 301-496-5495
Organization name NIDDK, NIH
Department LCDB
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Samples (8) GSM3, GSM4, GSM5, GSM6, GSM7, GSM8 
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis

Data table header descriptions
ID
GB_ACC GenBank accession number
BSCC_ID bs collection clone identifier
CLONE_ID Flybase identifier
SUB-ARRAY sub-array number
DUPLICATE dupilcate number
ROW row number
COLUMN column number
PCR_QC PCR quality control
SPOT_ID spot identifier
BEST_HIT BLAST best hit against nr database
E_VAL E value of best hit
SPOT_QC spot quality control

Data table
ID GB_ACC BSCC_ID CLONE_ID SUB-ARRAY DUPLICATE ROW COLUMN PCR_QC SPOT_ID BEST_HIT E_VAL SPOT_QC
1 AI944549 bs03g07 FBgn0033989 1 a 1 1 passed gi|4929571|gb|AAD34046.1|AF151809_1 (AF151809) CGI-51 protein [Homo sapiens] 2.00E-08 44364
2 AI944695 bs04c11 FBgn0032821 1 a 1 2 passed 16957
3 AI944741 bs04h01 FBgn0034374 1 a 1 3 passed 17896
4 AI944801 bs05f04 FBgn0039421 1 a 1 4 failed gi|4505995|ref|NP_002697.1|PPPM1B| protein phosphatase 1B (formerly 2C), magnesium-dependent, betaisoform >gi|3378168|emb|CAA06704| (AJ005801) PP2C [Homosapiens] 1.00E-25 16363
5 AI945043 bs08c11 FBgn0045370 1 a 1 5 passed 83502
6 AI945083 bs08g08 FBgn0038111 1 a 1 6 passed 42524
7 AI945145 bs09e03 FBgn0051910 1 a 1 7 passed 46880
8 AI945213 bs10c05 FBgn0017545 1 a 1 8 passed gi|2739184 (AF034971) ribosomal protein S3a [Drosophila melanogaster] 1.00E-79 26328
9 AI945419 bs12f08 FBgn0030263 1 a 1 9 passed gi|1825601 (U88168) weak similarity to rat TEGT protein (GI:456207)[Caenorhabditis elegans] 1.00E-36 29968
10 AI945457 bs13b04 FBgn0033287 1 a 1 10 passed 44401
11 AI945488 bs13d12 FBgn0038248 1 a 1 11 passed 20117
12 AI945524 bs13g12 FBgn0027348 1 a 1 12 passed gi|3080499|emb|CAA18696.1| (AL022602) putative long chain fatty acid-coA ligase [Mycobacteriumleprae] 3.00E-10 15553
13 AI944544 bs03g02 FBgn0045416 1 a 2 1 passed 30578
14 BE662011 bs04c08 FBgn0045413 1 a 2 2 passed 30384
15 AI944737 bs04g09 FBgn0033287 1 a 2 3 passed 35299
16 AI944792 bs05e07 FBgn0045785 1 a 2 4 passed 40102
17 AI945040 bs08c08 FBgn0038694 1 a 2 5 passed 38381
18 AI945081 bs08g06 FBgn0030319 1 a 2 6 passed 36872
19 AI945141 bs09d11 FBgn0033793 1 a 2 7 passed 42734
20 AI945196 bs10a12 FBgn0003435 1 a 2 8 passed 27107

Total number of rows: 3456

Table truncated, full table size 411 Kbytes.






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