Project description:Illumina single-end sequencing of Hela_2 (HeLa cell line). While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. On-line liquid chromatography coupled to high resolution MS and MS/MS yielded more than 150,000 unique peptides that identified more than 10,000 different human proteins encoded by more than 9,000 human genes. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We show that the abundances of more than 90% of proteins and transcripts fall within a 10,000-fold range, and allocate the proteome to different compartments, complexes and functions. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved almost complete coverage of the functional transcriptome and the proteome of a single cell type.
Project description:Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution. Keywords: Gene Regulation Study Examination of gene expression levels in livers from three primate species (human, chimpanzee, and rhesus macaque), using 3 male and 3 female samples from each species.
Project description:Our aim was to investigate the interaction between epidermal differentiation and VZV infection. By means of a calcium-induced keratinocyte differentiation model and RNA-seq we show VZV infection has a profound effect on differentiating keratinocytes and hijacks the normal process of epidermal gene expression to generate a signature resembling patterns of gene expression seen in both heritable and acquired skin-blistering disorders. Analysis of the viral transcriptome provides evidence that VZV replication in skin is tightly linked to differentiation and critically, that late viral gene expression is associated with cellular differentiation. The experiment was performed on human primary keratinocytes under four conditions: undifferentiated/uninfected, uninfected/differentiated, VZV-infected/undifferentiated and VZV-infected/differentiated.
Project description:De novo assembly of transcripts from RNAseq study to examine developmental regulation of S. stercoralis transcripts with a focus on infectious third-stage larvae. Raw read files are part of the submission 'RNAseq of S. stercoralis PV001 strain developmental stages' accession E-MTAB-1164, associated ENA accessions are included where appropriate .
Project description:This study is to investigate the potential impact of an lncRNA NR_126553 (Nostril) in murine intestinal epithelial cells (IEC4.1 cells) in response to Cryptosporidium parvum (C. parvum) infection. NR_126553 (Nostril) was knocked down by using a pool of gene specific siRNAs (SiNostril). Cells treated with a scramble non-specific siRNA were used as the control (siNegative control). After siRNA transfection 24h, cells were exposed to C. parvum infection for 24h. Then total RNA was collected for sequencing via BGISEQ-500 platform to obtain a comprehensive view of the transcriptome.
Project description:The canonical NF-κB pathway is active in 70% of all pancreatic cancer cases and NF-κB Essential Modulator (NEMO) is essential for the activation of this pathway. In our study, we used KC mice, which express the oncogenic KRAS and develop precancerous lesions termed Pancreatic Intraepithelial Neoplasias (PanINs), and KNeC mice, which express the oncogenic KRAS and have NEMO deleted in their pancreatic cells. These mice were injected with cerulein to promote the development of pancreatitis (cerulein dosage= 50μg/kg). Cerulein was injected at 8 hourly intervals for 2 days in total. The first injection day was when mice reached their sixth week of age and the second injection day was 3 days after the first injection day. Both KC and KNeC mice developed PanINs. At the age of 10 months, pancreata of KC and KNeC mice were analyzed. Using laser capture microdissection, PanINs from both groups were excised and their transcriptome was analyzed though RNA-seq.
Project description:Here we explore the striatum transcriptomic effects of alpha-synuclein administration in mice as model of Parkinson´s disease. Moreover, we also explore the neuroprotective effect of cannabonoid-based druga (VCE-003.2) as a potential neuroportective agent in Parkinson´s disease