Cynomolgus monkey testicular cDNAs for discovery of novel human genes
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ABSTRACT:
PROVIDER: PRJNA85239 | ENA |
REPOSITORIES: ENA
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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.
2010-06-05 | E-GEOD-513 | biostudies-arrayexpress
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:TMT-based quantitative proteomics of young and old cynomolgus monkey heart.
2022-09-13 | PXD036689 | iProX
Project description: Not available
| S-EPMC140308 | biostudies-literature
Project description:RNA sequencing of aorta tissue of cynomolgus monkey
| PRJNA636167 | ENA
Project description:Genome of Cynomolgus monkey Macaca fascicularis
| PRJEB2223 | ENA
Project description:Precise temporal development is an important event during embryo development. However, transcriptional changes in the temporal development of early epiblast cells (EPI), primitive endoderm (PrE) and trophectoderm (TrB) cells remain unclear. Long terminal repeat elements (LTRs) of ERVs (Endogenous retroviruses) are dynamically expressed in blastocysts of mammalian embryos. However, the expression of LTRs in monkey blastocyst is still unknown. By analyzing publicly available single-cell RNA-sequencing (seq) data, LTRs of several ERV families, including MacERV6, MacERV3, MacERV2, MacERVK1 and MacERVK2 were highly expressed in pre-implantation embryo cells including EPIs, TrB and PrE but absent in post-implantation. We knockdown MacERV6-LTR1a in cynomolgus monkey with short hairpin RNA (shRNA) strategy to examine the potential function of MacERV6-LTR1a in early development of monkey embryo. The silence of MacERV6-LTR1a mainly postpone trophectodermal cell differentiation and cell polarity of TrB, and the genes relate to epithelial proliferation, differentiation and development were downregulated in EPI of shRNA-treated embyos. Addtionally, stem cell differentiation relate genes were downregulated in PrE when MacERV6-LTR1a was silenced. Moreover, we have comfirmed MacERV6-LTR1a can recruit ESRRB (Estrogen Related Receptor Beta). Actually, recent reports demonstrated that ESRRB plays a important role in maintenance of self-renewal and pluripotency of embryonic and trophoblast stem cells through different signaling pathways including FGF and Wnt signaling pathways. In summary, these results suggest that MacERV6-LTR1a potentially regulates the temporal development of pre-implantation embryo of cynomolgus monkey.
2021-10-25 | GSE182061 | GEO
Project description:In vitro culture of cynomolgus monkey embryos beyond gastrulation
| PRJNA533988 | ENA
Project description:Gastrulation is a milestone event of embryonic development, during which germ layers are specified and reassigned into the body plan. Due to the inaccessibility in vivo at this stage and the ethical limitations, gastrulation currently remains a mystery in primates. Here, we report the establishment of an in vitro system to culture cynomolgus monkey embryos after up to 20 days to develop beyond the initiation of gastrulation. The histology, immunostaining and single cell sequencing results showed that the in vitro cultured embryos largely recapitulated the key events of early post-implantation development, and initiated gastrulation in primates. Considering the high similarities between monkeys and humans, this system will provide a unique platform for the investigations of human early post-implantation development at physiological, pathological and environmental conditions.
2019-11-01 | GSE130114 | GEO
Project description:Cynomolgus monkeys are well-established translational models for biomedical research and drug testing. Cynomolgus monkeys are outbred species and exhibit substantial levels of genetic variation which can affect the outcome and interpretation of biomedical studies. Copy number variations (CNVs) are a significant source of genetic diversity and a comprehensive understanding of the genomic impact of CNVs on phenotypic traits is limited. A custom 4.2 million probes comparative genomic hybridization (CGH) array (Design-ID: 120405_Cynomolgus5_CGH_UX1) has been designed on the basis of the Cynomolgus monkey genome (Ebeling et al. (2011) Genome Research; PMID: 21862625) to assess genome-wide copy number variation among Cynomolgus monkeys. Using Cynomolgus monkey specific NimbleGen CGH Microarrays we profiled the genomes of 21 Cynomolgus monkeys. Germline DNA from 21 Cynomolgus monkeys with different origin was tested against a Cynomolgus monkey reference. Cynomolus monkey samples were derived from breeding centers located in the Philippines (3 females and 3 males), in Vietnam (2 males and 2 females), in China for animals from Mainland Southeast Asia (3 females), or in Mauritius (4 females and 4 males). Furthermore genome-wide expression profiles were analyzed in 5 vitally important tissue samples (heart, kidney, liver, lung, spleen) from the same animals using a custom Cynomolgus monkey specific NimbleGen gene expression microarray (design ID: 120419_Cynomolgus_v5_TH_exp_HX12) to associate CNV genotypes with expression changes of proximal genes using a cis expression quantitative trait loci (cis-eQTL) mapping approach. Expression data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession numbers GSE76560. The array CGH results analyzed in this study are further described in Gschwind A.R. et al. (2016) "Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis". under submission
2016-02-24 | GSE76707 | GEO