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GEO help: Mouse over screen elements for information. |
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| 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
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| |
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| 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@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 (8)
|
GSM3, GSM4, GSM5, GSM6, GSM7, GSM8
|
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
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|
| 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
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| |
|
| Submission date |
Oct 18, 2000 |
| Last update date |
May 27, 2005 |
| 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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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.
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| |
|
| Submission date |
Oct 18, 2000 |
| Last update date |
Mar 04, 2020 |
| 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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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
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| |
|
| Submission date |
Oct 18, 2000 |
| Last update date |
May 27, 2005 |
| 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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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@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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
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|
| 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@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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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@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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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@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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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@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 |
| |
|
| Platform ID |
GPL5 |
| Series (1) |
| GSE462 |
Analysis of transcription in the Drosophila melanogaster testis |
|
|
|
| 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
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| |
|
| |
|
| 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@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 |
| |
|
| Platforms (1) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA85069 |
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