Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504034 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Proteogenomics analysis was employed to refine the genome annotation and provide new insights into nitrogen metabolism of Nostoc sp. PCC 7120.
2021-08-05 | PXD027697 | iProX
Project description:A synthesized Chinese Hamster Ovary (CHO) cell genome-scale model (GeM) consisting of iCHO2291 (Yeo. et al 2020) coupled with the secretory machinery presented in iCHO2048 (Gutierrez et al. 2020). This model is the most comprehensive CHO GeM to date, boasting the highest number of genes compared to any previous CHO GeM.
2023-03-06 | MODEL2206100001 | BioModels
Project description:MicroRNAs are small non-coding RNAs that play a critical role in post-transcriptional control of gene expression. Recent publications of genomic sequencing data from CHO cells provide new tools for the discovery of novel miRNAs in this important production system. The current release of the miRNA registry miRBase contains 307 mature miRNAs and 200 precursor sequences. We searched for evolutionary conserved miRNAs in recently published genomic data, derived from hamster and CHO cells, to further extend the list of known miRNAs. With our approach we could identify several dozens novel miRNAs and verify their expression with multiple next-generation sequencing experiments. In addition, a great amount of unexpressed miRNAs could be found, awaiting further confirmation by testing for their transcription in different Chinese hamster tissues. Two batch processes with 6 samples each
2015-03-02 | E-GEOD-59838 | biostudies-arrayexpress
Project description:To optimize the genome annotation, two tissue RNA libraries (i.e. liver and muscle) were constructed using the Illumina mRNA-Seq Prep Kit This study is a part of the Pseudopodoces humilis WGS project (BioProject ID: PRJNA179234) and was used for gene annotation improvement.
2013-11-29 | GSE44779 | GEO
Project description:CRISPR screen targeting 3022 CHO (Chinese hamster) genes to identify those contributing to induction of the Integrated Stress Response by histidinol treatment.
2019-07-26 | GSE134917 | GEO
Project description:MicroRNAs are small non-coding RNAs that play a critical role in post-transcriptional control of gene expression. Recent publications of genomic sequencing data from CHO cells provide new tools for the discovery of novel miRNAs in this important production system. The current release of the miRNA registry miRBase contains 307 mature miRNAs and 200 precursor sequences. We searched for evolutionary conserved miRNAs in recently published genomic data, derived from hamster and CHO cells, to further extend the list of known miRNAs. With our approach we could identify several dozens novel miRNAs and verify their expression with multiple next-generation sequencing experiments. In addition, a great amount of unexpressed miRNAs could be found, awaiting further confirmation by testing for their transcription in different Chinese hamster tissues.
2015-03-02 | GSE59838 | GEO
Project description:Two clones of Chinese hamster ovary (CHO) cells were cultured in 2 different chemical difined custom media. Transcriptional profile were compeared between clones and media.
2022-03-01 | GSE197570 | GEO
Project description:Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems. Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems.
2019-09-25 | PXD014240 | Pride
Project description:Genome annotation improvement of Brassica rapa
| PRJNA244166 | ENA