Dataset FlyAtlas-RNA.adult

General Information
Name	FlyAtlas-RNA.adult	Species	D. melanogaster
Dataset type	expression_microarray_profiles	FlyBase ID	FBlc0000157
Source & Content
Consists of	Quantitation of mRNA hybridized to a microarray; array consists of DNA fragments that correspond to regions within postulated genes. (Chintapalli et al., 2010.9.17)
Created by	FlyAtlas: FlyAtlas
Available from	GEO: GSE7763
Strain	Canton-S (Chintapalli et al., 2010.9.17)
Stage & tissue

Cell Line
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Description & Members
Description	Umbrella record for 17 collections that consist of expression microarray data from different dissected tissues of adult flies. (Chintapalli et al., 2010.9.17)
Parent collections
Component collection(s)	FlyAT_A.brain FlyAt_A.head FlyAt_A.eye FlyAt_A.thr_abd_ganglion FlyAt_A.sal_gland FlyAt_A.crop FlyAt_A.midgut FlyAt_A.M_tubule FlyAt_A.hindgut FlyAt_A.heart FlyAt_A.fat FlyAt_AF.ovary FlyAt_AM.testis FlyAt_AM.acc_gland FlyAt_AF.spermatheca_1 FlyAt_AF.spermatheca_2 FlyAt_A.carcass
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	The starting material was wild-type Canton-S adult flies, reared at 22[o]C on a 12:12h light regime, on standard Drosophila diet, 1 week after adult emergence. Tissues were isolated by hand dissection from equal numbers of male and female 7-day old flies (except in the case of gonads). Multiple sample collections were pooled to obtain enough tissue to provide 2 ug of total RNA. (Chintapalli et al., 2010.9.17)
Collection preparation	Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. (Chintapalli et al., 2010.9.17)
Mode of assay	Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol) were hybridized for 16 hr at 45[o]C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the GeneChip scanner 3000 7G. (Chintapalli et al., 2010.9.17)
Assay platform	Affymetrix_GeneChip_v2 (Chintapalli et al., 2010.9.17)
Data analysis	The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. For each tissue, the entire procedure was repeated 4 times, to create 4 independent replicates. (Chintapalli et al., 2010.9.17)
Additional data
	More information is available under: FlyAtlas: FlyAtlas GEO: GSE7763
Associated files
Additional sites
Comments
	Quantitation of expression at gene level: FlyAtlas provided mean coverage levels for Affy2 probe sets, and FlyBase intersected these probe sets with the exons of all FlyBase genes to associate each probe set with one or more FlyBase genes. These values were distributed into five expression level bins for further analysis. (Gelbart and Emmert, 2010.10.13)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	adult transcriptome (Chintapalli et al., 2007) FlyAtlas-RNA.adult
Secondary FlyBase IDs

References ( 3 )
Research paper	Chintapalli et al., 2007, Nat. Genet. 39(6): 715--720 Using FlyAtlas to identify better Drosophila melanogaster models of human disease. [FBrf0200485]
Personal communication to FlyBase	Chintapalli et al., 2010.9.17, FlyAtlas: survey of adult and larval expression. FlyAtlas: survey of adult and larval expression. [FBrf0211869]
FlyBase analysis	Gelbart and Emmert, 2010.10.13, FlyBase High Throughput Expression Pattern Data Beta Version. FlyBase High Throughput Expression Pattern Data Beta Version. [FBrf0212041]