Molecular profiling of stem cell-like female germ line cells in Drosophila delineates networks important for stemness and differentiation

We characterize the transcriptome of germline stem cell (GSC)-like cells isolated from bag of marbles (bam) mutant Drosophila ovaries by next generation RNA sequencing (RNA-seq) and compare it to the transcriptome of germline cells isolated from wild type ovaries. We further refine this dataset by utilizing an RNA-immunoprecipitation strategy to identify transcripts bound to the master differentiation factor Bam. Transcriptomes of bam mutant and wild type (Vasa-GFP) ovaries were characterized and compared by paired-end mRNA sequencing, in triplicate. Further, transcripts bound to Bam-GFP were delineated by RNA-immunoprecipitation followed by mRNA sequencing, also in triplicate.