Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analyses of barcode repertoire in hematopoietic cells

ABSTRACT: We compared the barcode repertoire in circulating leukocytes, and cardiac and renal macrophages.

ORGANISM(S): Mus musculus

PROVIDER: GSE160072 | GEO | 2024/02/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analyses of barcode repertoire in hematopoietic cells

Project description:Analyses of barcode repertoire in hematopoietic cells

| PRJNA671729 | ENA

HIFI-Barcode-se400

Project description:HIFI-Barcode-se400

| PRJEB29212 | ENA

Inference and effects of barcode multiplets in droplet-based single-cell assays

Project description:A widespread assumption for single-cell analyses specifies that one cell’s nucleic acids are predominantly captured by one oligonucleotide barcode. However, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call “barcode multiplets”. We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.

2020-01-07 | GSE143197 | GEO

Proteus mirabilis strain:Barcode 2

Project description:Proteus mirabilis strain:Barcode 2 Assembly

| PRJNA1067309 | ENA

mais barcode

Project description:Calmodulin gene as a barcode locus for identification of mycotoxigenic fungal species occurring on maize

| PRJEB31140 | ENA

Plasma cell infiltrate populating the muscle tissue of patients with inclusion body myositis feature distinct BCR repertoire properties

Project description:Inclusion body myositis (IBM) is an autoimmune and degenerative disorder of skeletal muscle. The B cell infiltrates in IBM muscle tissue are predominantly fully differentiated antibody-secreting plasma cells, with scarce naïve or memory B cells. The role of this infiltrate in the disease pathology is not well understood. To better define the humoral response in IBM, we used adaptive immune receptor repertoire sequencing to generate large B cell receptor (BCR) repertoire libraries from IBM muscle biopsies and compared them to those generated from dermatomyositis (DM), polymyositis (PM), and circulating CD27+ memory B cells, derived from healthy controls and antibody secreting cells (ASC) collected following vaccination. The repertoire properties of the IBM infiltrate included: expanded clones that equaled or exceeded the highly clonal vaccine-associated ASC repertoire; reduced somatic mutation selection pressure in the complementary determining regions and framework regions; and enriched usage of class switched IgG and IgA isotypes, with a minor population of IgM expressing cells. These IBM IgM-expressing population revealed unique features, including an elevated somatic mutation frequency and distinct CDR3 physicochemical properties., These findings demonstrate that the IBM muscle BCR repertoire is highly distinct from DM and PM and circulating antigen-experienced subsets, suggesting that it may form through selection by a disease-specific set of antigens.

2023-04-25 | GSE227124 | GEO

Human transcriptome analysis of acute responses to glucose ingestion reveals a role of leukocytes in hyperglycemia induced inflammation.

Project description:Objective was to examine acute gene expression responses to physiologic oral glucose ingestion in human circulating leukocytes. Microarray study of human circulating leukocytes sampled before, 1 hour after and 2 hours after glucose ingestion was performed. The present study demonstrated 36 genes which showed acute gene expression change in human leukocytes within 1 hour after glucose ingestion and suggest that leukocytes participate in the inflammatory process induced by acute hyperglycemia. Microarray study of human circulating leukocytes sampled before, 1 hour after and 2 hours after glucose ingestion

2013-01-06 | E-GEOD-32909 | biostudies-arrayexpress

Bone invigorates metstatic seeding [evolving barcode]

Project description:Bone invigorates metstatic seeding [evolving barcode]

| PRJNA675669 | ENA

High-throughput sequencing and analyses of the TCR repertoire

Project description:High-throughput sequencing and analyses of the TCR repertoire

| PRJNA688233 | ENA

Characterization of tumor-infiltrating T cells by TCR-β repertoire analyses

Project description:Local administration of IFN-α-producing proliferating myeloid cells (IFN-α-iPSC-pMCs) inhibited the tumor growth not only at the treatment site but also at the distant site (left). T cell receptor (TCR)-β chain repertoire and complementarity determining region 3 (CDR3) gene sequence analyses of tumor-infiltrating lymphocytes (TILs) showed marked enrichment of T cells with identical TCR-β chains in bilateral tumor tissues.

2019-02-13 | GSE126278 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data