Project description:The null pacman allele pcm[14] causes at lethaility pupariation. Lethality can be rescued by driving expression of wild-type pacman in somatic cells during development using the UAS-GAL4 system. Use of the driver arm-GAL4 allows adult flies to develop, but pacman is not expressed in the germline cells. RNA was prepared from null pacman testes from rescued flies, parental controls (UAS line and GAL4 line) and from a genetic background control for pcm[14] (a line generated by a neutral excision of the P-element used to induce the pcm[14] deletion). Total RNA was prepared from adult Drosophila testes. Sequencing of each genotype was replicated 3 times with a read depth of 12-15 million reads per replicate.
Project description:Two pcm null alleles (pcm14 and pcm15) were sequenced alongside respective wild-type controls (wild-type 1 and wild-type 2). Each genotype was replicated 3 times. Read depth was 12-17 million reads per replicate. Total RNA was prepared from Drosophila L3 larval wing imaginal discs.
Project description:Testes and testes terminal epithelium/seminal vesicles were dissected and separated from 4-5 day old Oregon-R-modENCODE Drosophila melanogaster males. RNA-sequencing was then performed on these two distinct biological structures.
Project description:XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5′–3′ mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. We compared differentially expressed genes derived from the analysis of the transcriptome and the translatome of HEK293T wild-type (WT) and XRN1-null cells by RNA-Seq and Ribo-Seq, respectively. Two biological replicates of each cell line were analyzed. The RNA-Seq analysis indicated that a substantial fraction of the total 10,105 genes showed significant differences between the two cell lines. 2,906 genes were significantly upregulated whilst 2,900 genes were downregulated using a fold change >0 on log2 scale with an FDR<0.005 to determine abundance. Significantly fewer genes showed differences between the WT and the XRN1-null cells at the level of translation with 433 genes showing an increase in abundance of ribosomal footprints whilst 560 genes were decreased as indicated by the Ribo-Seq analysis. Comparative analysis of translational efficiency (TE) in WT and XRN1-null cells on a genome-wide scale as a ratio of ribosomal occupancy to mRNA abundance identified an increase in TE for 102 genes but a decrease for 598 genes with most of the genes showing no evidence of change in the TE.
Project description:To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.
Project description:To investigate the role of CPES in germ cell differentiation during spermatogenesis in Drosophila testis. We have generated cpes null mutants using ends-out homologus recombination and rescued with Bam-Gal4 and UAS-CPES in cpes mutant background. We then dissected 200 pairs of testes for each of the 3 replicates from wild type, cpes mutant and Rescue (Bam-Gal4 and UAS-CPES) Drosophila males and total RNA was extracted using Trizol and RNA-Clean and concentrater column. About 1ug of RNA in 20ul was submitted for bulk RNAseq using Illumina machine (HWI-ST1276).