3885 results for "RNA AND sequencing OR transcriptome"

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• Heterogeneous metabolic signatures are linked to cancer cell differentiation in colorectal cancer

  Colorectal cancer (CRC) is characterized by functional intratumor heterogeneity that shares many similarites with the hierarchical organization of the normal intestinal epithelium. In order to relate transcriptional subtypes to functional tumor cell heterogeneity we applied scRNA-seq to 12 patient-derived CRC spheroid cultures. We identified shared expression programs that relate to intestinal lineages and revealed metabolic signatures that are linked to cancer cell differentiation. In addition, we validated and complemented sequencing results by quantitative microscopy using live-dyes and multiplexed RNA fluorescence in situ hybridization, thereby revealing metabolic compartmentalization and potential cell-cell interactions. Finally, we demonstrate functional differences between metabolically distinct lineage subtypes that might have strong implications for future treatment strategies of CRC.

  Dataset EGAD00001005524

• Single cell RNA sequencing of human cord Blood CD34 Cells

  We performed single cell RNA sequencing and ATAC e valuation of human umbilical cord blood. To explore the differentiation pathway for human lymphoid lineage, our target cells contain CD34-positive cord blood. That population is evaluated by single cell RNA sequencing and single cell ATAC.

  Study JGAS000528

• HuBMAP: High Resolution 3D Mapping of Cellular Heterogeneity Within Multiple Types of Mineralized Tissues

  The overall goal of the study was to generate 3D single cell maps of healthy human knee cartilage. Articular cartilage from the weightbearing and non-weightbearing regions of the femoral condyles in healthy knees from young donors (n=12) was analyzed by bulk RNA-sequencing (RNA-Seq), single nuclei RNA (snRNA-seq) and ATAC-sequencing and by spatial transcriptomic methods (GeoMx, MERFISH and Xenium). These multimodal data and additional single cell RNA-sequencing (scRNA-seq) data were integrated to generate a comprehensive molecular, genomic and function annotation of chondrocyte populations. Regulatory mechanisms were derived by linking motifs in expressed genes, transcription factors and chromatin organization.

  Study phs003721

• RNA sequencing of 12 NSCLC samples from 4 patients at MDACC

  Multi-region RNA sequencing of 12 NSCLC samples from 4 patients at MDACC

  Study EGAS00001005951

• Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing in Sporadic ALS

  To identify the genetic cause and modifiers of Sporadic ALS, we performed Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing of Sporadic ALS patients.

  Study JGAS000393

• Total exRNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

  We sequenced small RNAs from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 college athletes ages 18-25 years. Many of the participants provided more than one sample, weeks or months apart, allowing us to assess variability in an individual's exRNA expression levels over time. Several individuals provided all three biofluid types at one time, producing data on individual expression levels across several biofluid types. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid. Additionally, we performed whole transcriptome sequencing on 134 plasma and 115 urine samples and identified circRNA.

  Study phs001258

• Gene Expression between PMD and Control LCLs at Baseline, E2, and E2 Withdrawal

  In this study, lymphoblastoid cell lines (LCLs) derived from women with past perimenopausal depression (PMD) (n = 8) and asymptomatic controls (n = 9) were compared via poly(A)-selected transcriptome sequencing (RNA-seq). LCLs were cultured in three experimental conditions: at vehicle baseline (ovarian steroid-free), during estradiol (E2) treatment, and following E2-withdrawal. Transcriptomic analysis revealed significant differences in transcript expression in PMD LCLs compared to controls in all experimental conditions, and significant overlap in genes that were changed in PMD regardless of experimental condition. Among these, chemokine CXCL10 was upregulated in women with PMD, but most so after E2-WD and CYP7B1, an enzyme intrinsic to DHEA metabolism, was upregulated in PMD across experimental conditions. Finally, this in vitro model identified gene networks dysregulated in PMD which included inflammatory response, early/late E2-response, and cholesterol homeostasis. Data available will include the normalized counts for each subject in the study.

  Study phs003003

• Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease

  Celiac disease is an autoimmune disorder in which ingestion of dietary gluten triggers an immune reaction in the small intestine leading to destruction of the lining epithelium. Current treatment focusses on lifelong adherence to a gluten-free diet. Gluten-specific CD4+ T cells and cytotoxic intraepithelial CD8+ T cells have been proposed to be central in disease pathogenesis. Here we use unbiased single-cell RNA-sequencing and explore the heterogeneity of CD45+ immune cells in the human small intestine. We show altered myeloid cell transcriptomes present in active celiac lesions. CD4+ and CD8+ T cells transcriptomes show extensive changes and we define a natural intraepithelial lymphocyte population that is reduced in celiac disease. We show that the immune landscape in Celiac patients on a gluten-free diet is only partially restored compared to control samples. Altogether, we provide a single cell transcriptome resource that can inform the immune landscape of the small intestine during Celiac disease.

  Study EGAS00001003751

• Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence

  Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. Strikingly, we observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.

  Study EGAS00001006778

• Single cell RNAseq and TCRseq data from tumor and blood samples from 4 patients with muscle invasive bladder cancer

  For this dataset we performed single cell RNAseq paired with single cell TCR-seq on tumor and blood samples from 4 patients. This dataset contains 4 tumor samples as well as 4 blood samples. Each sample is made up of 2 sets of paired fastq files. The first pair contains reads corresponding to RNA transcripts (_Transcripts in file name), while the second pair contain reads corresponding to TCRs (_VDJ in file name). Sequenced on the Illumina NovaSeq6000 platform in a paired-end run using an SP flow cell (v1.5, 300 cycles).

  Dataset EGAD50000001381