Project description:We report the result of testing the splicing potential of random human genomic sequences. We used randomly fragmented HEK293 DNA in a splicing reporter assay to survey the genome for genomic sequences capable of splicing autonomously as a typical internal exon. From ~10 billion sequenced reads we obtained millions of sequences in the human genome capable of splicing autonomously. A read threshold of 100 yields ~1.25 million exons while also capturing most human mRNA exons.
Project description:We investigated genome-wide gene alterations in the temporal cortex of a well-characterized cohort of Alzheimer’s disease (AD) patients using Affymetrix exon arrays.
Project description:We report the transcriptomic comparisions between key processes required for various stages of fungal carnivory in nematode-trapping fungus Arthrobotrys oligospora when induced with nematodes. The reference assembly used for remapping is A. oligospora TWF154 (GenBank assembly accession: GCA_004768765.1)
Project description:Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. Fitness-promoting exons are enriched in essential and highly expressed genes and frequently overlap protein domains and interaction interfaces. This contrasts fitness-suppressing exons that are enriched in low-expressed, non-essential genes and tend to overlap intrinsically disordered regions. In-depth mechanistic investigation of a screen hit, the alternative exon-8 in TAF5, reveals that its inclusion controls the assembly of the TFIID general transcription initiation complex regulating gene expression outputs. Collectively, by applying orthogonal exon perturbation screening strategies we have interrogated phenotypically important exons at genome-scale and uncovered mechanisms that control gene expression and cell fitness.
Project description:Investigation of whole genome expression profiles during four time points during the intraerythrocytic lifecycle of the malaria parasite Plasmodium falciparum for transcript isoforms using Exon Arrays. The samples used in this study are further described in Turnbull et. al., Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in the Human Malaria Parasite (in review)
Project description:Investigation of whole genome expression profiles during four time points during the intraerythrocytic lifecycle of the malaria parasite Plasmodium falciparum for transcript isoforms using Exon Arrays. The samples used in this study are further described in Turnbull et. al., Simultaneous Genome-Wide Gene Expression and Transcript Isoform Profiling in the Human Malaria Parasite (in review)
Project description:We investigated genome-wide gene alterations in the temporal cortex of a well-characterized cohort of AlzheimerM-bM-^@M-^Ys disease (AD) patients using Affymetrix exon arrays. The AD patients and controls are subjects originally recruited into OPTIMA (Oxford Project to Investigate Memory and Ageing). Subjects underwent annual clinical and neuropsychological assessments, including the Cambridge Cognitive Examination (CAMCOG). Among subjects who died with autopsy consent given by next of kin, 1 cm3 blocks of grey matter from BA22 were dissected from fresh frozen brains of AD subjects. Tissues from elderly controls, followed longitudinally in life and with CAMCOG scores >80 at the last assessment before death, were collected. Affymetrix exon array was carried out in 8 control and 8 AD samples. The samples processed in each hybridization run were matched for AD vs. control, sex and postmortem interval (PMI) as far as possible. This submission includes the exon-level analysis.
