Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts

ABSTRACT: Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts

PROVIDER: PRJNA775989 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16612738_1.fastq.gz	Fastqsanger.gz
	SRR16612738_2.fastq.gz	Fastqsanger.gz
	SRR16612739_1.fastq.gz	Fastqsanger.gz
	SRR16612739_2.fastq.gz	Fastqsanger.gz
	SRR16612740_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts

Project description:Objective: Transcriptional profiling of immune cells is an indispensable tool in biomedical research; however, heterogenous sample types routinely used in transcriptomic studies may mask important cell type-specific transcriptional differences. Techniques to isolate desired cell types are used to overcome this limitation. We sought to evaluate the use of immunomagnetic B cell isolation on RNA quality and transcriptional output. Additionally, we aimed to develop a B cell gene signature representative of a freshly isolated B cell population to be used as a tool to verify isolation efficacy and to provide a transcriptional standard for evaluating maintenance or deviation from traditional B cell identity. Results: We found RNA quality and RNA-sequencing output to be comparable between donor-matched PBMC, whole blood, and B cells following negative selection by immunomagnetic B cell isolation. Transcriptional analysis enabled the development of an 85 gene B cell signature. This signature effectively clustered isolated B cells from heterogeneous sample types in our study and naïve and memory B cells when applied to transcriptional data from a published source. Additionally, by identifying B cell signature genes whose functional role in B cells is currently unknown, our gene signature has uncovered areas for future investigation.

2021-10-28 | GSE186768 | GEO

Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts.

Project description: Not available

| S-EPMC8600718 | biostudies-literature

Membrane-associated transcripts in Arabidopsis; their isolation...

Project description:Membrane-associated, integral membrane and secreted proteins are of key importance in many cellular processes. For most of the 28 952 predicted proteins in Arabidopsis, the actual subcellular localisation has not been demonstrated experimentally. So far, their potential membrane-association has been deduced from algorithms that predict transmembrane domains and signal peptides. However, the comprehensiveness and accuracy of these algorithms is still limited. The majority of membrane-associated and secreted proteins is synthesised on membrane-bound polysomes. Therefore, the isolation and characterisation of mRNA associated with membrane-bound polysomes offers an experimental tool for the genome-wide identification of these proteins. Here we describe an efficient method to isolate mRNA from membrane-bound polysomes and report on the validation of the method to enrich for transcripts encoding membrane-associated and secreted proteins. The sensitivity and reproducibility of the isolation method was investigated by DNA microarray analysis. Pearson correlations between transcript levels obtained from three replicate isolations showed that the method is highly reproducible. A significant enrichment for mRNAs encoding proteins containing predicted transmembrane domains and signal peptides was observed in the membrane-bound polysomal fraction. In this fraction, 301 transcripts were classified by gene ontologies as ‘cellular component unknown’, and potentially encode previously unrecognised secreted or membrane-associated proteins. Keywords: mRNA localisation, mRNA fractionation, predict protein localisation

2006-03-17 | GSE4023 | GEO

Membrane-associated transcripts in Arabidopsis; their isolation...

Project description:Membrane-associated, integral membrane and secreted proteins are of key importance in many cellular processes. For most of the 28 952 predicted proteins in Arabidopsis, the actual subcellular localisation has not been demonstrated experimentally. So far, their potential membrane-association has been deduced from algorithms that predict transmembrane domains and signal peptides. However, the comprehensiveness and accuracy of these algorithms is still limited. The majority of membrane-associated and secreted proteins is synthesised on membrane-bound polysomes. Therefore, the isolation and characterisation of mRNA associated with membrane-bound polysomes offers an experimental tool for the genome-wide identification of these proteins. Here we describe an efficient method to isolate mRNA from membrane-bound polysomes and report on the validation of the method to enrich for transcripts encoding membrane-associated and secreted proteins. The sensitivity and reproducibility of the isolation method was investigated by DNA microarray analysis. Pearson correlations between transcript levels obtained from three replicate isolations showed that the method is highly reproducible. A significant enrichment for mRNAs encoding proteins containing predicted transmembrane domains and signal peptides was observed in the membrane-bound polysomal fraction. In this fraction, 301 transcripts were classified by gene ontologies as âcellular component unknownâ, and potentially encode previously unrecognised secreted or membrane-associated proteins. Membrane-bound (MBP) and free polysomes (FP) were isolated in triplicate from one batch of two weeks old aboveground parts of Arabidopsis seedlings. Each combination of isolated MBP and FP was applied to 4 microarrays, of which two were dyeswapped, giving a total of 12 arrays.

2010-07-01 | E-GEOD-4023 | biostudies-arrayexpress

The effect of cell subset isolation method on gene expression in leukocytes.

Project description:Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes. FACS incurs the least short-term changes in gene expression signature.

2013-08-20 | GSE50008 | GEO

Immunomagnetic enrichment and flow cytometric isolation of breast cancer circulating tumor cells (CTCs) for genomic characterization

Project description:We developed a novel approach to isolate tumor cells with high purity from blood via immunomagnetic enrichment followed by fluorescence activated cell sorting (IE/FACS) and examined copy number alterations in these cells. Magnetic beads coated with EpCAM mAb were added to blood to enrich for tumor cells. Enriched samples were then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. DNA from isolated tumor cells was subjected to whole genome amplification (WGA) and copy number analysis via array comparative genomic hybridization (CGH). The assay was evaluated using BT474 and MCF7 breast cancer cell lines and in CTCs from 5 metastatic breast cancer (MBC) patients with matched archival primary tumors and later extended to an additional 97 MBC patients.

2012-12-31 | GSE27511 | GEO

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

Project description:Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

| PRJNA1144972 | ENA

Sorting of Growth Plate Chondrocytes Allows the Isolation and Characterization of Cells of a Defined Differentiation Status

Project description:Axial growth of long bones occurs through a coordinated process of growth plate chondrocyte proliferation and differentiation. This maturation of chondrocytes is reflected in a zonal change in gene expression and cell morphology from resting to proliferative, prehypertrophic, and hypertrophic chondrocytes of the growth plate followed by ossification. A major experimental limitation in understanding growth plate biology and pathophysiology is the lack of a robust technique to isolate cells from the different zones, particularly from small animals. Here, we report on a new strategy for separating distinct chondrocyte populations from mouse growth plates. By transcriptome profiling of microdissected zones of growth plates, we identified novel, zone-specific cell surface markers and used these for flow cytometry and immunomagnetic cell separation to quantify, enrich, and characterize chondrocytes populations with respect to their differentiation status. This approach provides a novel platform to study cartilage development and characterize mouse growth plate chondrocytes to reveal unique cellular phenotypes of the distinct subpopulations within the growth plate.

2020-02-29 | GSE144362 | GEO

Capybara: A tool to measure cell identity and fate transitions

Project description:Capybara: A tool to measure cell identity and fate transitions

| PRJNA606516 | ENA

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

Project description:Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

| PRJNA1144976 | ENA