Ea9e3f56-e351-49e2-9ae1-dfe6fbfe3335 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008188 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Targeted sequencing using BD Rhapsody with 462 mRNA and 197 antibodies of healthy young adult bone marrow mononuclear cells from iliac crest aspirations. Please note raw and integrated gene expression data, cell type annotation, metadata and dimensionality reduction are available as Seurat v3 objects through figshare. Access link is https://figshare.com/s/313b5739ff469dac8c01
| EGAD00001008189 | EGA
Project description:Whole transcriptome sequencing using BD Rhapsody with 97 antibodies of a healthy young adult bone marrow (Young3/BM3) mononuclear cells from iliac crest aspirations. Please note raw and integrated gene expression data, cell type annotation, metadata and dimensionality reduction are available as Seurat v3 objects through figshare. Access links is https://figshare.com/s/901bcddb9ee18e226031.
| EGAD00001008186 | EGA
Project description:Targeted sequencing using BD Rhapsody with 462 mRNA of healthy young adult bone marrow mononuclear cells from iliac crest aspirations (BM3/Young3).
| EGAD00001008184 | EGA
Project description:Shallow targeted sequencing with 462 mRNA and 97 antibodies of AML patient’s bone marrow mononuclear cells from iliac crest aspirations from. Please note raw and integrated gene expression data, cell type annotation, metadata and dimensionality reduction are available as Seurat v3 objects through figshare. Access link is https://doi.org/10.6084/m9.figshare.14780127.v1
AMLQ4_SMK1 AML314 male
AMLQ1_SMK2 AML116 female
AMLQ3_SMK3 AML127 female
AMLQ6_SMK4 AML183 male
AMLQ2_SMK5 AML327 female
AMLQ5_SMK6 AML334 male
APLQ5_SMK7 APL124 male
APLQ3_SMK8 APL142 male
APLQ6_SMK9 APL218 female
APLQ4_SMK10 APL147 male
APLQ2_SMK11 APL223 female
APLQ1_SMK12 APL224 female
| EGAD00001008185 | EGA
Project description:This SuperSeries is composed of the SubSeries listed below. The main processed data are organized in the following two Figshare links: Seurat objects: https://doi.org/10.6084/m9.figshare.23290004 ReDeeM-V output: https://doi.org/10.6084/m9.figshare.24418966.v1
2023-11-18 | GSE219015 | GEO
Project description:We performed a targeted scRNA-seq approach using the BD Rhapsody™ Single Cell Analysis Systems (BD Biosciences). Peripheral blood mononuclear cells (PBMCs) were labeled with sample tags (BD Human Single Cell Multiplexing Kit) and AbSeq antibodies (CD1c, CD3, CD4, CD5, CD8, CD11c, CD14, CD16, CD18, CD19, CD20, CD21, CD23, CD24, CD25, CD27, CD28, CD31, CD38, CD40, CD44, CD45RA, CD45RO, CD56, CD62L, CD123, CD127, CD134, CD137, CD161, CD183, CD185, CD186, CD196, CD197, CD272, CD278, CD279, CD303, CD314, CD337, CD357, CD366, HLA-DR, IgD, IgM, TCRαβ, TCRγ8, Vα24-Jα18) and counted. Single-cell capture was performed using the BD Rhapsody Express following manufacturer’s instructions. The libraries were pooled and sequenced on NovaSeq 6000 S2 as a dual index pair-end run. Fastq files were processed using BD's Rhapsody analysis pipeline on the Seven Bridges Platform using default parameters, the GRCh38-PhiX-gencodev29 reference genome and the gencodev29-20181205 transcriptome annotation. Data (molecules per gene per cell based on DBEC error correction) were analyzed using BD SeqGeq v1.8 and the Seurat plug-in to perform dimensionality reduction (UMAP) and differential analysis output for selected cell subsets (CD4+ T cells, CD8+ T cells, NK cells, NKT cells, classical monocytes, intermediate monocytes, non-classical monocytes).
2022-10-16 | GSE215451 | GEO
Project description:Immunotherapy using CD19-directed chimeric antigen receptor (CAR)-T cells has shown excellent results for treatment of B-cell leukaemia and lymphoma. To produce CAR-T cells, the patient’s own T cells are isolated from the blood and modified in a laboratory with a genetic vector to express a tumor antigen-directed CAR on its surface. The CAR-T cells are then expanded in numbers and given back to the patient with the aim to eradicate the tumors. However, some patients display primary resistance to CAR-T treatment while others relapse quickly after CAR-T treatment. In this experiment, we seek to understand whether the quality of the individual CAR-T cell product the patients were given can predict outcome to the therapy. We investigate the transcriptional profile of the individual CAR-T infusion products using single-cell RNA sequencing. In this dataset, we identified a T cell subset correlating with response that could be used as an indicator for clinical outcome. Targeted RNA and protein single-cell libraries were obtained using the BD Rhapsody platform (BD Biosciences). In total four separate targeted libraries were produced with 6 patients per library. Sequencing was performed on NovaSeq 6000 S1 sequencer at the SNP&SEQ Technology Platform (Uppsala, Sweden). The raw scRNA-seq data was pre-processed by BD Biosciences using the Rhapsody Analysis pipeline to convert the raw reads into Unique Molecular Identifier (UMI) counts. UMIs are further adjusted within Rhapsody by applying BD’s Recursive Substitution Error Correction (RSEC) and Distribution-Based Error Correction (DBEC) in order to remove false UMIs caused by sequencing or library preparation errors. Pooled samples were deconvoluted using Sample-tag reads. The scRNA-seq and AbSeq counts were loaded, processed and used for clustering and differential gene expression with Seurat v. 4.0.0.
2023-07-24 | E-MTAB-12407 | biostudies-arrayexpress
Project description:4 groups of mice : Control, antibiotics, antibiotics + 4days of recolonization, antibiotics + 4days of recolonization + Enterocloster clostridioformis. Tumor draining lymph node were harvested after CFSE injection were harvested and CFSE+ cells were sorted and proccessed in order to generate single cell RNA-sequencing using BD Rhapsody mouse immune response targeted panel. Groups were barcoded using BD Rhapsody Multiplexing Kit.
2023-05-31 | E-MTAB-12784 | biostudies-arrayexpress
Project description:We used BD Rhapsody™/scRNA-seq to analyze the heterogeneity of lymphocytes in brain metastasis
2024-08-26 | GSE228379 | GEO
Project description:Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of three well-established high throughput 3’-scRNAseq platforms: Drop-seq, 10x Chromium and BD Rhapsody; using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar but higher gene sensitivity than Drop-seq, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.
2024-09-04 | GSE229765 | GEO