Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

71 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

ABSTRACT: In this study, we investigated somatic mutations of CD4+ and CD8+ T cells in patients with immune-mediated aplastic anemia (AA). To understand the role of mutations, we performed single-cell level analysis of 6 longitudinal samples of 2 AA patients carrying STAT3 or KRAS and other mutations in CD8+ T cells. The analysis was performed using V(D)J and 5' gene expression platform (10X Genomics). STAT3 mutated clone was clearly distinguishable from other CD8+ T cells and showed a cytotoxic phenotype, attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells can alter T cell phenotype warranting further investigation of their role in the pathogenesis of immune-mediated AA.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Sofie Lundgren

PROVIDER: E-MTAB-9969 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress

Single cell TCR-seq of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-11 | E-MTAB-7918 | biostudies-arrayexpress

Single-cell RNA sequencing and single-cell CRISPR screens of interacting natural killer and blood cancer cells

Project description:To profile the cell states of interacting natural killer (NK) cells and blood cancer cells, we cultured 26 different cell lines representing diverse hematologic neoplasms either alone or with NK cells derived from three healthy human donors. After 24 h co-culture, we labeled the cells from each monoculture or co-culture condition with oligonucleotide-conjugated antibodies against ubiquitously expressed surface proteins (with different oligonucleotide for each mono- or co-culture), enabling multiplexing in the scRNA-seq using the cell hashing method. We additionally performed pooled CRISPR screens with a single-cell transcriptome readout using the CROP-seq platform in blood cancer cells cultured either alone or in the presence of NK cells to study the effects of perturbing genes that influenced sensitivity to NK cell killing in genome-scale CRISPR screens.

2023-07-24 | E-MTAB-13204 | biostudies-arrayexpress

Coupled single-cell RNA, TCR, and barcoded pMHC multimer sequencing, from virus-specific PBMC T-cells

Project description:Virus-specific CD8 T cells from PBMCs of healthy donors and hepatitis patients were enriched for recognition of a panel of feature barcode-labeled pMHC multimers. The phenotypic description was made using gene expression and TCRseq. Samples were pooled and sequenced on the same 10x Genomics sequencing chip and deconvoluted using ADT HashTag antibodies,

2024-05-01 | E-MTAB-13758 | biostudies-arrayexpress

Single-cell mRNA-seq from a healthy skeletal muscle cell derived from human induced pluripotent stem cell

Project description:1 healthy cell - 1 time point (Day 17 of differentiation) - 1 replicate

2020-10-04 | E-MTAB-9510 | biostudies-arrayexpress

Single cell antigen receptor analysis reveals lymphocyte developmental origins

Project description:To test the impact of nonsense-mediated decay (NMD) on BCR/TCR RNA sequences, we treated peripheral blood mononuclear cells (PBMCs) with cycloheximide to block NMD and analyzed treated and untreated cells by scRNA-seq with scVDJ-seq.

2023-02-28 | E-MTAB-12524 | biostudies-arrayexpress

Single-cell RNA sequencing of Ngn2-induced neurons from the pluripotent stem cells of great apes

Project description:We generated induced excitatory sensory neurons (iNeurons, iNs) from pluripotent stem cells of great apes (Human, Chimpanzee and Bonobo) by expressing the transcription factor neurogenin 2 (Ngn2). Single cell-RNA sequencing was performed to identify gene expressions differing in dendrite and synapse development during iNs maturation. Briefly, cultured cells were first dissociated and yield a concentration of 500 to 1000 cells/ml to obtain approximately 3000 cells per lane of a 10X microfluidic chip device. Single cell gene expression libraries were generated using the 10X Chromium Single Cell 3’ v2 Kit following the manufacturer’s instructions. Quantification and quality control of libraries was performed using a High Sensitivity DNA chip for Agilent’s Bioanalyzer and sequenced on a HiSeq2500 in Rapid sequencing mode. Our single-cell RNA-Seq data can be explored using our ShinyApp-based browser called iNeuronExplorer: https://bioinf.eva.mpg.de/shiny/iNeuron_Explorer/ (for details, please see this paper: DOI: 10.7554/eLife.59323). Sequencing raw data for all iNeurons from 409B2 line, one culture of day 35 iNeurons from H9 line and one culture of day 35 iNeurons from SC102A1 line are deposited under Mendeley Data with doi: 10.17632/y3s4hnyvg6, their corresponding gene counts (UMIs) are deposited in this ArrayExpress experiment with accession number MTAB-9233.

2020-12-15 | E-MTAB-9233 | biostudies-arrayexpress

Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scVDJ-seq

Project description:In response to antigen challenge, human B cells clonally expand, undergo selection and differentiate within secondary lymphoid tissues to produce mature B cell subsets and high affinity antibodies necessary for an effective immune response. However, the interplay between affinity, antibody class and different B cell fates has proved challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells from a model secondary lymphoid tissue. Specifically, here we have used single-cell sequencing of antibody repertoires using the 10X Genomics platform to profile unsorted immune cells and sorted memory B cells from paediatric tonsil tissue. Matched gene expression and bulk B cell repertoires are also available for the same patient donors.

2020-05-01 | E-MTAB-9003 | biostudies-arrayexpress

Single-cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish

Project description:The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans, heterozygous germline mutations in GATA2 often lead to a loss of function of one allele, causing GATA2 haploinsufficiency. In mice, Gata2 has an essential regulatory function in hematopoietic stem cell (HSC) generation and maintenance. However, whereas Gata2-null mice are lethal at embryonic day (E) 10.53, Gata2 heterozygous (Gata2+/-) mice survive to adulthood with normal blood values. However, mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness, they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells (HSPCs) and homozygous deletion (gata2b-/-) redirects HSPCs differentiation bias, thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations, we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro-myelodysplasia, a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome, we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow (KM) of WT and mutated zebrafish based on the scatter profile of flow cytometry for single-cell RNA (scRNA) sequencing.

2024-11-05 | E-MTAB-14075 | biostudies-arrayexpress

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