Ontology highlight
ABSTRACT:
PROVIDER: PRJNA668433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12808110.fastq.gz | Fastqsanger.gz | |||
| SRR12808111.fastq.gz | Fastqsanger.gz | |||
| SRR12805491.fastq.gz | Fastqsanger.gz | |||
| SRR12805492.fastq.gz | Fastqsanger.gz | |||
| SRR12805493.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.
2022-08-18 | GSE198128 | GEO
Project description:We performed spatial transcriptome sequencing of mouse embryos to provide spatial cell atlas of mouse organogenesis.
2023-02-19 | GSE178636 | GEO
Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.
2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress
Project description:In this study, we analyzed the differential spatial transcriptome of Triple-Negative Breast Cancer (TNBC) patients who responded in an opposite manner to neoadjuvant chemotherapy (NACT): we compared responders displaying pathological complete response (pCR) with no-responders who showed disease progression during therapy. Diagnostic TruCut biopsies were analyzed using the GeoMx Cancer Transcriptome Atlas (Nanostring).
2023-10-12 | E-MTAB-13069 | biostudies-arrayexpress
Project description:To further characterized the serrated pathway, we used the novel Digital Spatial Profiling (DSP) technology and its mRNA Cancer Transcriptome Atlas (CTA) panel, which includes over 1800 target gene, to investigate the underlying gene expression changes and pathways involved in sessile serrated lesion (SSL) and traditional serrated adenoma (TSA), two precancerous lesions to carcinoma in serrated pathway.
2023-12-31 | E-MTAB-12465 | biostudies-arrayexpress
Project description:The human adrenal glands are highly dynamic endocrine organs that are involved in the secretion of various hormones such as steroids and catecholamines. Here we present a single-nuclei and spatial transcriptomic analysis of healthy adult human adrenal glands to provide a complete adrenal gland atlas. With this, we show how such an atlas can be taken advantage when studying adrenocortical diseases, such as adrenocortical adenomas (ACA). Using nornal adrenal as reference, we showed a high intra-tumoural heterogeneity in the single-nuclei transcriptome of ACA, revealing the presence of specific cell populations associated with cortisol secretion and genetic background.
2023-01-01 | E-MTAB-12129 | biostudies-arrayexpress
Project description:Deciphering the connectome, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a cost-effective Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a comprehensive integrated single-cell spatial molecular, cellular and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, we predicted neuron projections with high accuracy by combining gene profiles and spatial information via machine learning. This study facilitates our understanding of brain multi-modal network and neural computation.
2024-11-29 | GSE273066 | GEO
Project description:The World Health Organization has recognized testicular function with temperature dependence. Testicular heat exposure caused by occupational factors, lifestyle and clinical disease, etc., can lead to different degrees of reproductive obstacles. The aim of this study is to reveal the transcriptional regulatory network and their potential crucial roles in testicular heat exposure. After passing quality control, the high throughput sequencing data of mouse testicular tissue for scrotum heat exposure and control group were carried out various analyses including differentially expressed transcriptome exploration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and network regulation. Differential transcriptome expression analysis revealed that 279 miRNAs (138 upregulation and 141 downregulation) were identified as significant differential expression in the mouse testicular tissue of heat exposure compared with control group using the cut-off of log2fold change >= 0.585, p value <= 0.05 and q value <= 1.00. This research provides high throughput sequencing data of transcriptome in testicular heat exposure model and lays the foundation for further study on the miRNA in male reproductive diseases related to elevated testicular temperature.
2021-01-29 | GSE165697 | GEO
Project description:Mammalian embryos exhibits sophisticated cell organizations that are intricately orchestrated at both molecular and cellular level. It has recently become apparent that cells within the animal body display significant heterogeneity, both in terms of their cellular properties and their spatial distributions. However, current spatial transcriptomics profiling either lack three-dimensional representation or are limited in their ability to capture the complexity of embryonic tissues and organs. Here, we present a represented spatial transcriptome atlas of all major organs at embryonic day 13.5 (E13.5) in the mouse embryo, and provide a three- dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating this spatial transcriptome data with corresponding single-cell transcriptome data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine.
2023-08-09 | GSE237308 | GEO
Project description:We report the small RNA transcriptome of testicular extracellular vesicles in mouse testis. We established a testis dissociation protocol to isolate testicular extracellular vesicles. After treatment with proteinase K and RNase A, the RNA inside the extracellular vesicles was extracted and sequenced by small RNA-seq.
2022-01-31 | GSE158402 | GEO