Adult fly population cages were maintained at 24 ̊C on a 24-hour light cycle (14 hours light/10 hours dark). After a 2hr pre-lay, embryos were collected on agar plates for a 2 hour interval during a light cycle, aged appropriately, dechorionated and frozen on dry ice.
Frozen samples were homogenized and extracted using the TRIzol reagent protocol (Invitrogen). RNA was purified on an RNeasy spin column (Qiagen), and DNase treated. Polyadenylated RNAs were purified from total RNA extracts via oligo(dT) binding, using standard Illumina protocol. The poly(A)+ RNA was fragmented using divalent cations under elevated temperature, following by first and second strand cDNA synthesis primed with random hexamers. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase, and phosphorylated at their 5' ends with T4 polynucleotide kinase. After adding A bases to the 3' end of the DNA fragments, Illumina adaptor oligonucleotides were ligated to the ends and ~ 300 bp fragments were isolated from an agarose gel, enriched by PCR amplification, and gel-purified again.
Read length (bases):76
The samples were quantitated using a Nanodrop, and loaded onto a flow cell for cluster generation and sequenced on an Illumina Genome Analyzer II using either single read or paired end protocols (Illumina).
Reads were aligned to Dmel_Release_6 using the STAR aligner v2.3.0e (Linux x86_64) with default parameters on the FASTQ files to generate multiply-mapped BAM files. These were filtered to include reads with only 1 aligned hit ( NH:i:1 attribute) to generate uniquely-mapped BAM files. A custom script was used to convert BAM files into bedgraph files (bam2bedgraph.cc).
Note that for each pair of paired-end reads, the two reads were mapped independently, and only those reads mapping uniquely to the genome were included in the data submission to FlyBase. In other words, information from one read was not used to resolve ambiguous mapping of its paired read.
Clusters 1-7 are strongly associated with early-to-mid embryogenesis and adult females.
Clusters 11-17 appear to be primarily associated with late embryogenesis and the larval stage, though several of these show significant peaks of expression during later stages as well.
Clusters 18-20 show low expression during early development followed by a monotonic increase in expression level terminating in adult males � and no significant expression in adult females.