Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

59 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of splenic B cells derived from WT and Itch KO mice

ABSTRACT: We found that the E3 ubiquitin ligase Itch significantly affects early B-cell differentiation. To explore the role of Itch in late B-cell differentiation, we sorted B cells from WT and Itch KO mice. To explore the effect of Itch deficency on gene expression, we determined mRNA profiles in B cells from WT and Itch KO mice by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

INSTRUMENT(S): Agilent 2100 Bioanalyzer, Illumina HiSeq 4000, Ribo-Zero Gold (Illumina)

ORGANISM(S): Mus musculus

SUBMITTER: Renxi Wang

PROVIDER: E-MTAB-8273 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of splenic B cells derived from WT and Itch cKO mice

Project description:We found that the E3 ubiquitin ligase Itch significantly affects early B-cell differentiation. To explore the role of Itch in late B-cell differentiation, we sorted B cells from WT and Itch cKO mice. To explore the effect of Itch deficency on gene expression, we determined mRNA profiles in B cells from WT and Itch cKO mice by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2020-03-01 | E-MTAB-8281 | biostudies-arrayexpress

RNA-seq of splenic and LN B cells from WT and Gm40600 Tg mice with or without LPS stimulation

Project description:We found that Gm40600 significantly affects plasmablast(PB)-like SP 2/0 cells. To explore the role of Gm40600 in B-cell especially plasma cell (PC) differentiation, we developed Gm40600 Transgenic (Gm40600 Tg) mice. B cells from spleen and lymph nodes (LNs) of WT and Gm40600 Tg mice were sorted by using B220 microbeads. B cells were also stimulated for 3 days by 10 ug/ml LPS. To explore the effect of Gm40600 overexpression on gene expression, we determined mRNA profiles in B cells from WT and Gm40600 Tg mice and LPS-stimulated B cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2020-07-31 | E-MTAB-8320 | biostudies-arrayexpress

Single cell RNA-seq and VDJ-seq of B cells from sheep red blood cells-primed WT and Stch cKO mice

Project description:Once activated, B cells produce the antibodies needed to fight against infection. B cells are necessary for adaptive or specific immunity, which focuses on the destruction of foreign invaders that have gotten past the bodies initial defenses. Heat shock protein family is a group of highly conserved molecular chaperones with important functions in protein folding such as antibody and in signal transduction. Stch (Heat shock 70 kDa protein 13) is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins. To explore the role of Stch in B-cell activation and antibody production, we evaluated the transcriptional events and the role of stch pathway on the activation and antibody production of B cells by single cell RNAseq. Splenic lymphocytes were isolated from 7-9-week-old female Stchf/f wildtype (WT) mice and B-cell specific Stch knocked-out (CD19creStchf/f) mice (3 mice/group) using Ficoll (Ficoll-Paque Plus, GE Healthcre). B cells were sorted using B220 microbeads (Cat No. 130-049-501, Miltenyi Biotec, Germany). Their transcriptomes were captured using a 10x chromium system.

2021-03-01 | E-MTAB-8280 | biostudies-arrayexpress

Orientation-specific RAG activity in chromosomal loop domain contribute to Tcrd V(D)J recombination during T cell development

Project description:T cell antigen receptor Î´ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination. Here, we employ a high throughput method to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in developing thymocytes. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, but Trdd1 joining is ordered with joining to Trdd2 a prerequisite for further rearrangement. We also find frequent, previously unappreciated Trdd1 and Trdd2 rearrangements that inactivate Tcrd. Moreover, we find numerous RAG off-targets that are generated via unidirectional RAG tracking across the loop-domain containing Trdd1, Trdd2 and Trdj. Correspondingly, disruption of the upstream domain boundary causes spreading of on- and off-target RAG activity to the proximal Trdv domain. RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq

2016-08-04 | E-GEOD-79892 | biostudies-arrayexpress

An ectopic CTCF binding element disturbs VÎ´ usage at the mouse Tcra-Tcrd locus by regulating contact between VÎ´ and DÎ´ gene segments

Project description:Chromatin looping mediated by the CCCTC binding factor CTCF regulates V(D)J recombination at antigen receptor loci. CTCF-mediated looping can influence recombination signal sequence accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate through-space interactions between recombination signal sequences, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG-tracking, and RAG-independent long-distance interactions. Here, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of EÎ´ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. Moreover, although the ectopic CBE limited directional RAG tracking from the Tcrd recombination center, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent through-space interactions between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility and RAG tracking. RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq

2016-09-02 | E-GEOD-81351 | biostudies-arrayexpress

RNA-seq of mouse myeloma cell line SP 2/0 cells compared to naive B cells

Project description:Both multiple myeloma (MM) and systemic lupus erythematosus (SLE) are characterized with abnormal production of plasma cells. In both diseases, the process of B cells differentiate into plasmablast/plasma cell is disordered. Despite the continuous research on the development of prognostic factors and introduction of new agents, dysregulation of plasmablast/plasma cells in MM and SLE is still uncontrolled. Thus, it is necessary to explore the novel therapeutic target to plasmablast/plasma cells. Because of plasmablast-like, Mus musculus myeloma SP 2/0 cell line was selected to explore the novel therapeutic target to plasmablast/plasma cells. To explore the novel therapeutic target to plasmablast/plasma cells, we determined mRNA profiles in SP 2/0 cells compared to naive B cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.

2019-07-31 | E-MTAB-7112 | biostudies-arrayexpress

RNA-seq of peripheral blood mononuclear cell (PBMC) derived from normal healthy donors and multiple myeloma (MM) patients

Project description:Multiple myeloma (MM), also known as plasma cell myeloma, is a cancer of plasma cells, a type of white blood cell normally responsible for producing antibodies. There is no cure for MM. In addition, the mechanism underlying abnormal production of plasma cells is not clear. In this experiment, peripheral blood was obtained from normal healthy donors and multiple myeloma (MM) patients. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll separation solution. Samples of four donors were pooled and Samples of four MM patients were pooled. The aim was to characterize the mRNA profile of MM patients compared to healthy donors and find the new target of diagnosis or treatment for MM.

2020-08-14 | E-MTAB-7146 | biostudies-arrayexpress

Microarray for LPS-stimulated B cells compared to unstimulated B cells

Project description:Both multiple myeloma (MM) and systemic lupus erythematosus (SLE) are characterized with abnormal production of plasma cells. To explore the novel therapeutic target to plasma cells, we determined the gene expression profile in plasma cells by affymetrix microarrays. LPS could effectively in vitro induce the production of plasma cells. The splenocytes were separated from three C57BL/6 mice per group. B cells were sorted by B220 microbeads, and stimulated for 3 days in vitro by 10 ug/ml LPS. The transcripts in LPS-stimulated B cells were determined by Affymetrix Microarrays.

2019-08-01 | E-MTAB-7109 | biostudies-arrayexpress

RNA-seq of peripheral blood mononuclear cell (PBMC) derived from normal healthy donors and systemic lupus erythematosus (SLE) patients

Project description:Systemic lupus erythematosus (SLE), also known simply as lupus, is an autoimmune disease. There is no cure for SLE. The mechanism involves an immune response by autoantibodies against a person's own tissues. However, the mechanism underlying imbalance of autoantibodies is not clear. In this experiment, peripheral blood was obtained from normal healthy donors and systemic lupus erythematosus (SLE) patients. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll separation solution. Samples of four (total eight) donors were pooled and Samples of four (total eight) SLE patients were pooled. The aim was to characterize the mRNA profile of SLE patients compared to healthy donors and find the new target of diagnosis or treatment for SLE.

2020-08-14 | E-MTAB-7145 | biostudies-arrayexpress

Microarray for B cells of TACI-IgG-treated MRL/lpr mice compared to control mice

Project description:Both multiple myeloma (MM) and systemic lupus erythematosus (SLE) are characterized with abnormal production of plasma cells. In both diseases, the process of B cells differentiate into plasmablast/plasma cell is disordered. Despite the continuous research on the development of prognostic factors and introduction of new agents, dysregulation of plasmablast/plasma cells in MM and SLE is still uncontrolled. Thus, it is necessary to explore the novel therapeutic target to plasmablast/plasma cells. We and other researchers have shown that BAFF inhibitor atacicept (TACI-IgG), leads to some degree of B cell depletion. BAFF-specific targeted therapy specifically affects early-stage B cells in the periphery without affecting late-stage compartments such as plasma cells. Specifically depletion of plasma cells could hold great potential for the treatment of autoimmune diseases. To explore the novel therapeutic target to plasma cells, we determined the gene expression profile in B cells (mainly plasma cells) from atacicept (TACI-IgG)-treated lupus-prone MRL/lpr mice by affymetrix microarrays.

2019-07-30 | E-MTAB-7106 | 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