Mus musculus
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MODEL1109130000MODEL1703310000MODEL1311110000MODEL1311110001
PROVIDER: PRJNA12247 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Production of biopharmaceuticals relies on the expression of mammalian cDNAs in host organisms. Here we show that the expression of a human cDNA in the moss Physcomitrium patens generates the expected full-length and four additional transcripts due to unexpected splicing. This mRNA splicing results in non-functional protein isoforms, cellular misallocation of the proteins and low product yields. We integrated these results together with the results of our analysis of all 32,926 protein-encoding Physcomitrella genes and their 87,533 annotated transcripts in a web application, physCO, for automatized optimization. A thus optimized cDNA results in about twelve times more protein, which correctly localizes to the ER. An analysis of codon preferences of different production hosts suggests that similar effects occur also in non-plant hosts. We anticipate that the use of our methodology will prevent so far undetected mRNA heterosplicing resulting in maximized functional protein amounts for basic biology and biotechnology.
2022-01-10 | PXD026651 | Pride
Project description:The NIH Mammalian Gene Collection (MGC) program aims to identify, sequence, and provide full-length cDNA clone reagents.
| PRJNA10872 | ENA
Project description:Detailed global proteomics analysis for NF1 deficient cells and tissues is lacking. We investigated proteomes from immortalized human Schwann cells with (+/+) and without (-/-) NF1 to evaluate potential biomarkers and targets in NF1 deficient cells. We identified over 1900 proteins in both cell lines and find 148 proteins with differential expression levels based on genotype. Following Ingenuity Pathway analysis (IPA), we found multiple pathways were altered including decrease in “oxidative phosphorylation,” increases in “mitochondrial dysfunction”, and “glycolysis”, as well as changes in “Myelination Signaling Pathway.” Next, we stably transfected NF1 -/- cells with tagged mNf1 cDNAs (either WT or variant) and again evaluated the global proteome. We identified an overall trend of metabolic differences pertaining to oxidative phosphorylation, mitochondria dysfunction, and glycolysis in the mutant cDNA expressing cells compared to WT cDNA cells. We then validated differential expression of the following proteins: LAMC1, CYB5R3, and SOD2. Additionally, we used the encoded Strep tag on the cDNA to affinity purity NF1 Protein-Protein interactors from the Schwann cells expressing WT and variant cDNAs. We were able to identify 98 PPIs and 9 overlap with prior HEK293 cell datasets while 89 are unique to Schwann cells. GO analysis indicates many of these PPIs play a role in protein-transporting ATP synthase complex or are involved with intermediate filaments. While we were able to show that some of these bind differentially to variant isoforms, variations within NF1 did not significantly impact ability to bind partners. Finally, we show that loss of NF1 impacts Schwann cell mitochondrial respiration via Seahorse validating our proteomics data and indicating that NF1 plays a significant role in in mitochondrial metabolism that results in proteomics changes in Schwann cells.
2025-05-07 | PXD052442 | Pride
Project description:Detailed global proteomics analysis for NF1 deficient cells and tissues is lacking. We investigated proteomes from immortalized human Schwann cells with (+/+) and without (-/-) NF1 to evaluate potential biomarkers and targets in NF1 deficient cells. We identified over 1900 proteins in both cell lines and find 148 proteins with differential expression levels based on genotype. Following Ingenuity Pathway analysis (IPA), we found multiple pathways were altered including decrease in “oxidative phosphorylation,” increases in “mitochondrial dysfunction”, and “glycolysis”, as well as changes in “Myelination Signaling Pathway.” Next, we stably transfected NF1 -/- cells with tagged mNf1 cDNAs (either WT or variant) and again evaluated the global proteome. We identified an overall trend of metabolic differences pertaining to oxidative phosphorylation, mitochondria dysfunction, and glycolysis in the mutant cDNA expressing cells compared to WT cDNA cells. We then validated differential expression of the following proteins: LAMC1, CYB5R3, and SOD2. Additionally, we used the encoded Strep tag on the cDNA to affinity purity NF1 Protein-Protein interactors from the Schwann cells expressing WT and variant cDNAs. We were able to identify 98 PPIs and 9 overlap with prior HEK293 cell datasets while 89 are unique to Schwann cells. GO analysis indicates many of these PPIs play a role in protein-transporting ATP synthase complex or are involved with intermediate filaments. While we were able to show that some of these bind differentially to variant isoforms, variations within NF1 did not significantly impact ability to bind partners. Finally, we show that loss of NF1 impacts Schwann cell mitochondrial respiration via Seahorse validating our proteomics data and indicating that NF1 plays a significant role in in mitochondrial metabolism that results in proteomics changes in Schwann cells.
2025-05-07 | PXD052439 | Pride
Project description:Limb development is a powerful model to investigate transcriptional complexity during differentiation and development, as tissue types appear at various stages, with unique transcriptional signatures. So far, most studies have used conventional expression arrays, which can identify only a predetermined set of cDNAs. However there is growing evidence that most of the non-coding part of the genome is transcribed as well. We took advantage of genomic tiling arrays, which cover most of the mouse genome, to look at limb transcriptomes in an unbiased manner, by identifying all genic- and intergenic transcripts. We selected three developmental stages (E11.5 ; E13.5 ; E15.5), covering a large period of limb organogenesis, during which the limb evolves from a mostly homogenous mesenchymal cell population to more specialized tissue types such as cartilage, bone, muscle and skin.
2012-01-23 | GSE27417 | GEO
Project description:BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl.We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. CONCLUSIONS: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies. Keywords: other
2003-07-16 | GSE513 | GEO
Project description:These are the Visium spatial transcriptomic data (10x Genomics) from 9 patients with Head and Neck Squamous Cell Carcinoma (oral cavity) treated in Gustave Roussy. Patients are stratified by their tumoral density of multinucleated giant cells (MGC) : 6 patients have high MGC density (patients 1, 2, 3, 4, 5, 8) and 3 have low MGC density (patients 6, 7, 9). There is one data file for each patient, except for one patient that has 3 data files (patient 1). Accordingly, there are 9 patients but 11 samples. The source code of the is available on GitHub (https://github.com/AhmedAmineAnzali/MGC_Paper_Analysis). The results are published in the paper untitled : Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma (Gessain et al., 2024, Cancer Discovery). Please contact the corresponding author for more information.
2024-09-20 | E-MTAB-14409 | biostudies-arrayexpress
Project description:Used a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. Keywords: Paired End DiTags
2008-12-01 | GSE6694 | GEO
Project description:We tried to find the target genes of miR-100 in MGC-803 and SK-BR-3 cells, thus we uesd specific miR-100 inhibitor to knock down the level of miR-100 in the cells, with this condition, we used this mRNA microarray to find the genes whose amount changed. and they may be the target genes that miR-100 mediated. Total of four chips, MGC-AMO, MGC-NC, SK-AMO, SK-NC. MGC and SK represents MGC-803 and SK-BR-3 cells respectively. AMO is the specific miR-100 inhibitor and NC is negative control.
2014-01-09 | E-GEOD-53909 | biostudies-arrayexpress
Project description:The purpose of this microarray experiment was to validate the Del-Mar 14K Chicken Integrated Systems Microarray for different chicken tissues and to determine the utility of this chicken cDNA microarray for other closely related and more distant avian species. The Del-Mar 14 K array was constructed from cDNAs amplified from EST clones sequenced from five normalized chicken cDNA libraries derived from neuroendocrine (5,929), abdominal fat (4,800), liver (2,635), skeletal muscle (2,398), reproductive tract (2,008), 387 long (70mer) oligonucleotides and 72 quality control spots. The array contains 17,770 cDNA clones, where protein matches were found by BlastX analysis for 68% of chicken contigs and 46% of singleton sequences represented on the array. A reference RNA design was used for the hybridization of total RNA from four chicken tissues (liver, abdominal fat, breast muscle and hypothalamus) and the cross-species hybridization (CSH) of total RNA from tissue from birds representing four orders of the Class Aves [Galliformes (chicken, Coturnix quail and domestic turkey), Anseriformes (Peking duck), Falconiformes (American kestrel) and Passeriformes (American tree sparrow)]. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from chicken liver, abdominal fat, breast muscle and hypothalamus. Each of the 43 microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the avian tissue samples and Cy5-labled cDNA targets from the reference chicken RNA pool. Loess-normalized data were used to determine the number of cDNAs expressed in chicken tissues and the number of genes (cDNAs) detectable by cross-hybridization with various avian tissue samples. The Cy5-labeled reference samples were used to determine the coefficient of variation across the 43 microarrays. This study shows a remarkably high level of cross hybridization of Cy3-labeled cDNA targets from a wide range of avian species to the Del-Mar 14K microarray, where 38 to 62% of the cDNA probes on the chicken array (genes) were detectable. Keywords: Transcriptional profiling, Del-Mar 14K Chicken Integrated Systems Microarray validation, multi-tissues, cross-species hybridization, class Aves
2007-11-12 | GSE9500 | GEO