Dataset NIH_mRNA_Dyak_adults

General Information
Name	NIH_mRNA_Dyak_adults	Species	D. yakuba
Dataset type	RNA-Seq transcriptome profiles	FlyBase ID	FBlc0000454
Source & Content
Consists of	cDNA short sequencing reads from high-throughput sequencing. (Malone et al., 2011.8.9)
Created by
Available from
Strain
Stage & tissue

Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Umbrella record for 1 collection of RNA-Seq data from adults. Transcriptome represented as frequency of reads along genome (see GBrowse presentation; data in wiggle format). (Malone et al., 2011.8.9)
Parent collections
Component collection(s)	NIH_Dyak_1_F NIH_mRNA_Dyak_adults_junctions
Number in collection	75,484,498 (Malone et al., 2011.8.9)
Comment on number in collection	Total of uniquely aligned reads for component collections (RNA-Seq transcriptome coverage collections); determined by FlyBase. (Malone et al., 2011.8.9)
Members
Experimental protocol
Vector
Sample preparation	Flies were raised in incubators with no photoperiod at 22 C and 60% humidity. Adults were aged 5-7 days post-eclosion and sorted by sex. (Malone et al., 2011.8.9)
Collection preparation	mRNA was purified from total RNA using a QIAGEN Oligotex mRNA kit (Valencia, California). mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer. Double-stranded cDNAs were made from mRNA using the Superscript II (Invitrogen) and random hexamer primers (Invitrogen). DNA fragment libraries were prepared for sequencing by addition adaptor oligonucleotides; cDNA templates were size-selected by gel purification (300bp +/- 25bp), then amplified by PCR using oligo-specific primers and Phusion polymerase. The amplified product was purified using a QIAquick column. (Malone et al., 2011.8.9)
Mode of assay	Data were generated using Illumina Genome Analyzer II and various versions of the Illumina Genome Analysis Pipeline. Deposited sequence data are high quality sequence reads that passed default parameters of the Illumina quality filter. (Malone et al., 2011.8.9)
Assay platform	Illumina Genome Analyzer II (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10061) (Malone et al., 2011.8.9) Illumina HiSeq 2000 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13307) (Malone et al., 2011.8.9)
Data analysis	Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. A species-specific reference sequence, that determined and/or used by the Drosophila 12 Genomes Consortium (FBrf0200326), was used in each case. The species-specific reference sequence plus ERCC spike-in control sequences were used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to the reference sequence using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals. (Malone et al., 2011.8.9)
Additional data

Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	NIH_mRNA_Dyak_adults
Secondary FlyBase IDs

References ( 1 )
Personal communication to FlyBase	Malone et al., 2011.8.9, mRNA-Seq of adult flies from the genus Drosophila mRNA-Seq of adult flies from the genus Drosophila [FBrf0214763]