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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

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


Sample GSM3 Query DataSets for GSM3
Status Public on Oct 18, 2000
Title testis a
Sample type RNA
 
Source name y w[67c1]/Y testis
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Testis dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = gonad, male, sex
 
Submission date Oct 18, 2000
Last update date May 27, 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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM4 Query DataSets for GSM4
Status Public on Oct 18, 2000
Title testis b
Sample type RNA
 
Source name y w[67c1]/Y testis
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Testis dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w67c1.
 
Submission date Oct 18, 2000
Last update date Mar 04, 2020
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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM5 Query DataSets for GSM5
Status Public on Oct 18, 2000
Title male a
Sample type RNA
 
Source name y w[67c1]/Y male
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Whole adult male minus gonads (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1]
Keywords = soma, male, sex
 
Submission date Oct 18, 2000
Last update date May 27, 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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM6 Query DataSets for GSM6
Status Public on Oct 18, 2000
Title male b
Sample type RNA
 
Source name y w[67c1]/Y
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Whole adult male minus gonads (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1]
Keywords = soma, male, sex
 
Submission date Oct 18, 2000
Last update date May 27, 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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM7 Query DataSets for GSM7
Status Public on Oct 18, 2000
Title ovary a
Sample type RNA
 
Source name y w[67c1] ovary
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = gonad, female, sex
 
Submission date Oct 18, 2000
Last update date May 27, 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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM8 Query DataSets for GSM8
Status Public on Oct 18, 2000
Title ovary b
Sample type RNA
 
Source name y w[67c1] ovary
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = gonad, female, sex
 
Submission date Oct 18, 2000
Last update date May 07, 2012
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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM9 Query DataSets for GSM9
Status Public on Oct 18, 2000
Title female a
Sample type RNA
 
Source name y w[67c1] female
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Whole adult female minus gonads (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = soma, female, sex
 
Submission date Oct 18, 2000
Last update date May 27, 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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Sample GSM10 Query DataSets for GSM10
Status Public on Oct 18, 2000
Title female b
Sample type RNA
 
Source name y w[67c1] female
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Description Whole adult male minus (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
 
Submission date Oct 18, 2000
Last update date Mar 09, 2006
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
 
Platform ID GPL5
Series (1)
GSE462 Analysis of transcription in the Drosophila melanogaster testis


Series GSE462 Query DataSets for GSE462
Status Public on Jul 16, 2003
Title Analysis of transcription in the Drosophila melanogaster testis
Organism Drosophila melanogaster
Experiment type Expression profiling by array
Summary Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.
Keywords: other
 
 
Contributor(s) Andrews J, Bouffard GG, Cheadle C, Lü J, Becker KG, Oliver B
Citation(s) 11116097
Submission date Jun 25, 2003
Last update date Mar 04, 2020
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
 
Platforms (1)
GPL5 Dmel.testis.1.0
Samples (8)
GSM3 testis a
GSM4 testis b
GSM5 male a
Relations
BioProject PRJNA85069

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp


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