Dataset RE_cDNA cDNA library

General Information
Name	RE_cDNA	Species	D. melanogaster
Dataset type	cDNA library	FlyBase ID	FBlc0000015
Source & Content
Consists of	cDNA clones in plasmid vector (Stapleton et al., 2002)
Created by	BDGP: cDNA & EST FAQ
Available from	Selected clones available from the DGRC; other sources listed at BDGP, Materials. BDGP: Materials DGRC: Vectors, cDNAs, ESTs
Strain	iso-1 (Stapleton et al., 2002)
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage organism (Stapleton et al., 2002) embryonic stage 1 -- 17 (Stapleton et al., 2002) Comment:0-22 hr AEL
Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Cloned cDNAs prepared from polyadenylated RNA isolated from 0-22-hr embryos. (Stapleton et al., 2002)
Parent collections	mE_Transcription_Start_Sites
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector	pFlc1 (Stapleton et al., 2002)
Sample preparation	The RE (Riken embryo) library was made from RNA extracted from Drosophila 0-22hr mixed stage isogenic y; cn bw sp strain embryos, polyA+ selected twice, RNA made by Ling Hong. cDNA was synthesized by priming with the oligo(dT) primer adapter (5'-GAGAGAGAGAGGATCCAATACTGGAGAGTTTTTTTTTTTTTTTTVN-3'). The first strand was synthesized in presence of trehalose, which increases the full-length cDNA synthesis (Carninci, P. et al. 1998. Proc. Natl. Acad. Sci. U.S.A. 95(2): 520-524; Carninci, P. et al. 1999. Methods Enzymol. 303: 19-44). (Stapleton et al., 2002)
Collection preparation	Full-length cDNA was selected with the biotinylated cap-trapper (Carninci, P. et al. 1996. Genomics 37(3): 327-336). A linker was then ligated to the single-strand cDNA following the published protocol (Shibata, Y., et al. 2001. Biotechniques 30(6): 1250-1254). Subsequently, the cDNA was normalized by using RoT=1.0 as published (Carninci, P., et al. 2000. Genome Res. 10(10): 1617-1630). Second strand cDNA was primed with the (5'-AGAGAGAGAGCTCGAGCTCTAATAAGGTGACACTATAGAACCA-3') primer. After restriction digestion of the hemimethylated cDNA with BamHI and XhoI, the cDNA was cloned in the lambda FLC-I vector. Subsequently, the library was bulk-excised into pFLC-I plasmid as described (Carninci, P., et al. 2001. Genomics 77(1-2): 79-90). cDNAs were transformed into DH5-alpha TonA strain. (Stapleton et al., 2002)
Mode of assay
Assay platform
Data analysis
Additional data
	More information is available under: UniGene: D. melanogaster RE
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	RE (Stapleton et al., 2002, ) RE_cDNA RE EST (Stapleton et al., 2002) Riken embryo library
Secondary FlyBase IDs

References ( 3 )
Research paper	Hoskins et al., 2011, Genome Res. 21(2): 182--192 Genome-wide analysis of promoter architecture in Drosophila melanogaster. [FBrf0213090] Stapleton et al., 2002, Genome Res. 12(8): 1294--1300 The Drosophila Gene Collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. [FBrf0152058]
Supplementary material	Hoskins et al., 2011, Genome Res. 21(2): Supplemental Material. [FBrf0213251]