Ontology highlight
ABSTRACT:
PROVIDER: PRJNA766998 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16980320_1.fastq.gz | Fastqsanger.gz | |||
| SRR16980320_2.fastq.gz | Fastqsanger.gz | |||
| SRR16980321_1.fastq.gz | Fastqsanger.gz | |||
| SRR16980321_2.fastq.gz | Fastqsanger.gz | |||
| SRR16980322_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 116 |
Similar Datasets
Project description:Mammalian cells are critical hosts for the production of most therapeutic proteins and many proteins for biomedical research. While cell line engineering and bioprocess optimization have yielded high protein titers of some recombinant proteins, many proteins remain difficult to express. Here we use systems biology methods to deciper the factors influencing yields in Chinese hamster ovary (CHO) cells as they produce proteins from the human secretome.
2024-02-23 | GSE225989 | GEO
Project description:The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined A total of 295 microarray samples were assayed. In addition 9 continous bioprocess variables were also measured.
2011-07-27 | E-GEOD-30321 | biostudies-arrayexpress
Project description:The production of biopharmaceuticals relies on robust cell systems that can produce recombinant proteins at high levels, and grow and survive in the stressful bioprocess environment. Chinese hamster ovary cells (CHO) as the main production hosts offer a variety of advantages including robust growth and survival in a bioprocess environment. Cell surface proteins are of special interest for the understanding of how CHO cells react to their environment while maintaining growth and survival phenotypes, since they enable cellular reactions to external stimuli and potentially initiate signaling pathways. To provide deeper insight into functions of this special cell surface sub-proteome, pathway enrichment analysis of the determined CHO surfaceome was conducted. Enrichment of growth/ survival pathways such as the phosphoinositide-3-kinase (PI3K/AKT), Mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK-STAT) and RAP1 pathways was observed, offering novel insights into how cell surface receptors and ligand mediated signaling enable the cells to grow and survive in a bioprocess environment. When supplementing surfaceome data with RNA expression data, several growth/ survival-receptors were shown to be co-expressed with their respective ligands and thus suggesting self-induction mechanisms, while other receptors or ligands were not detectable. As data about the presence of surface receptors and their associated expressed ligands may serve as base for future studies, further pathway characterization will enable the implementation of optimization strategies to further enhance cellular growth and survival behavior.
2022-10-15 | PXD033581 | Pride
Project description:Gene expression is a key determinant of phenotypes that made Chinese Hamster Ovary (CHO) cells, with their human-like glycosylation profile and high protein titers, one of the most widely used cells for the production of therapeutic proteins and biopharmaceuticals. Engineering CHO gene expression thus holds a key to improve drug quality and cost effective production. However, the success of engineering gene expression or ectopic activation of silent genes to optimize desired pathways requires accurate annotation of the underlying regulatory elements and the transcription start site (TSS). Unfortunately, to date, most TSSs of CHO-expressed genes and the ~50% of hamster genes that are silent in CHO were computationally predicted and are frequently inaccurate. To oust this hurdle, we report revised TSSs annotations for 15,308 Chinese Hamster genes and 4,145 non-coding RNAs based on experimental data from CHO K1 cells and 10 hamster tissues. In the example of the glycosyltransferase gene Mgat3, we further demonstrate how accurate annotations readily facilitate activating silent genes by CRISPRa. Together, we envision that our annotation and data from the Chinese Hamster will provide a rich resource for the CHO community, improve genome engineering efforts and additionally aid comparative and evolutionary studies.
2020-10-06 | GSE159044 | GEO
Project description:We present the first comprehensive genome-wide view of CHO translational activity during recombinant expression by the application of ribosome profiling. The distribution of translational power in CHO cells was analyzed in the context of the recombinant mRNAs and the endogenous mRNA pool. In an antibody-producing CHO cell line, the recombinant mRNAs were found to be the most abundant transcripts and also sequestered a substantial amount of translating ribosomes (up to 15%). The recombinant mRNAs were translated as efficiently as the endogenous mRNAs, and changes in translation and transcription of the recombinant mRNAs were directly reflected in changes in specific productivity. Interestingly, improvements in bioprocess quality attributes were achieved by depleting the highly expressed and translated inert NeoR mRNA by siRNA-mediated knock-down. This resulted in improved cellular growth, which was accompanied by an 18% increase in antibody titers. This study is the first to carefully map the translatome of the CHO cell to the nucleotide level and to demonstrate how recombinant expression affects the cell on the translational level.
2016-12-21 | GSE79512 | GEO
Project description:The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined
2011-07-28 | GSE30321 | GEO
Project description:Biologics have emerged as leading blockbuster therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here we identify bottlenecks limiting expression of challenging recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293. Surprisingly, one third of the challenging human proteins displayed an improved secretion upon host cell swapping from CHO to HEK293. While most components of the secretory machinery showed comparable expression levels in both expression hosts, a key set of genes with extreme expression variation was identified. Among these, ATF4 and SRP9 were validated as general productivity boosters in CHO. Further, we found that more heavily glycosylated products benefit more from the elevated activities of the N- and O-glycosyltransferases found in HEK293 cells. Collectively, our results demonstrate the utilization of HEK293 cells for expression rescue of human proteins and suggest a strategy for identification of secretory pathway components improving yield and quality in HEK293 and CHO.
2022-06-22 | GSE157729 | GEO
Project description:γ-secretase is an intra-membrane-cleaving aspartyl protease implicated in the processing of a wide range of type I membrane proteins including the Notch receptor and the amyloid-β precursor protein (APP). It thus regulates a diverse array of cellular and biological processes including the differentiation of neuronal embryonic stem cells, or intestinal stem cells, with the latter controlling the self-renewing of the intestinal epithelium. Indeed, proteolysis of these proteins by γ-secretase triggers signaling cascades by releasing intracellular domains (ICDs) which, following association with adaptor proteins and nuclear translocation, modulate the transcription of different genes by binding directly to their promoters. The pronounced proliferative and regenerative effects of Notch signaling and its implication in the generation of the Aβ-peptides, makes γ-secretase a therapeutic target for several types of cancer and for Alzheimerâs disease. To investigate the broad effects of γ-secretase activity onto the cellular transcriptome, Chinese hamster ovary (CHO) cells with enhanced γ-secretase were compared to cells with abolished γ-secretase activity via a microarray designed for a genetically close species, mouse. Our findings will potentially help to decipher the biology of γ-secretase, including a better understanding of the roles of this enzyme in gene transcription. We compared the transcriptomes of two CHO cell lines displaying extreme differences in γ-secretase activity. The S-1 cell line overexpressed the four components of γ-secretase (NCT, APH1aL, PS1, and PEN2) and was characterized by a marked increase in the level of PS1 heterodimers associated with 8-fold increased γ-secretase activity compared to untransfected controls. The other cell line consisted of wild type CHO cells incubated with DAPT, a well-known γ-secretase inhibitor. The two cell lines were used in combination with a mouse microarray to analyze gene transcription under enhanced γ-secretase. Two samples, S1 and DAPT treated CHO- were used in biological triplicates each.
2010-05-15 | E-GEOD-16379 | biostudies-arrayexpress
Project description:The development of next-generation sequencing technologies has opened new opportunities to better characterize complex eukaryotic cells. Chinese hamster ovary (CHO) cells play a primary role in therapeutic protein production, with currently five of the top ten blockbuster selling drugs produced in CHO. However, engineering superior CHO cells with improved production features has had limited results to date and cell lines are still developed through generation and screening of large strain pools. Here, we applied RNA sequencing to contrast a high and a low monoclonal antibody producing cell line. Rigorous experimental design achieved high reproducibility between biological replicates, remarkably reducing variation to less than 10%. More than 14,000 gene-transcripts were identified and surprisingly 58% were classified as differentially expressed, including 2,900 with a fold change higher than 1.5. The largest differences were found for gene-transcripts belonging to regulation of apoptosis, cell death and protein intracellular transport GO term classifications, which were found to be significantly enriched in the high producing cell line. RNA sequencing was also performed to lower producing subclones, where down-regulation of genes encoding secreted glycoproteins was found to be the most significant change. The large number of significant differences even between subclones suggests a substantial genetic fluidity in CHO lines and challenges the notion of identifying and manipulating a few key genes to generate high production CHO cell lines.
2018-02-12 | GSE100908 | GEO