Ab07ded7-815c-47f8-b1ef-e7dd7d5ed774 - samples
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ABSTRACT:
PROVIDER: EGAD00001008184 | 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:Targeted sequencing using BD Rhapsody with 462 mRNA and 97 antibodies of healthy young and aged adult as well as AML 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/0fda29b169c719223ee3.
| EGAD00001008188 | 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:To investigate the role of aging in the regulation of ILC3 development and function, we used the young mice as control and carried out single-cell RNA sequencing (BD Rhapsody) on young gut ILC3s.
2023-06-07 | GSE210193 | GEO
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: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: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:Purpose: studying of immunity-related genes in CD235a erythroid cell in order to validate previous findings on the subject using single cell RNA sequencing (scRNA-seq) and its benefits such as mRNA co-localization in a single cell and cell specific marker gating of populaions of interest. Methods: we extracted mononuclear cells from the fetal liver, the fetal thymus, the cord blood and the adult bone marrow, performed magnetic separation of CD235a (Erythroid) cells, marked magnetically separated cells with BD Sample Tags, loaded the cells on a BD Rhapsody cartridge, lysed the cells, performed reverse transcription, cDNA library preparation, QC of final cDNA libraries by BioAnalyzer 2000 and Qubit 4, pooled the final cDNA libraries, sequenced them on a Illumina NextSeq 550 sequencer. Then, we processed FASTQ R1 and R2 files using the BD Pipeline V1.9 and got final metrics in a mols_per_cell.tsv file. Results: in this work, we investigated other possible immunity-related functions on a single cell level using RNA sequencing of adult bone marrow, cord blood and fetal liver NECs and found that NECs from every studied origin expressed ARG1, CXCL5, CXCL8, DEFA3, DEFA4, IL1B, IL15, IL18, IGHE (secreted), LGALS3, LAGLS9, TGFB3 and VEGFA. Conclusions: our study allows to access new potential immunological roles of CD235a erythroid cells, both validated and discarded previous results regarding cytokine and chemokine gene expression in erythroid cells.
2022-05-04 | GSE199230 | 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