Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

597 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNAseq of mouse bone marrow cells (Drop-seq)

ABSTRACT: Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly depleted bone marrow (DBM; Ter119/Cd45 negative cells) were analysed.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Fumio Arai

PROVIDER: E-MTAB-8630 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing.

Stumpf Patrick S PS Du Xin X Imanishi Haruka H Kunisaki Yuya Y Semba Yuichiro Y Noble Timothy T Smith Rosanna C G RCG Rose-Zerili Matthew M West Jonathan J JJ Oreffo Richard O C ROC Farrahi Katayoun K Niranjan Mahesan M Akashi Koichi K Arai Fumio F MacArthur Ben D BD

Communications biology 20201204 1

Biomedical research often involves conducting experiments on model organisms in the anticipation that the biology learnt will transfer to humans. Previous comparative studies of mouse and human tissues were limited by the use of bulk-cell material. Here we show that transfer learning-the branch of machine learning that concerns passing information from one domain to another-can be used to efficiently map bone marrow biology between species, using data obtained from single-cell RNA sequencing. We ...[more]

PMID: 33277618

Similar Datasets

Single-cell RNAseq of human bone marrow cells enriched for stromal and endothelial markers

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Subsets of bone marrow cells were isolated using magnetic cell sorting to enrich for putative skeletal stem cells.

2021-06-30 | E-MTAB-9662 | biostudies-arrayexpress

Single-cell RNAseq of human bone marrow cells (Drop-seq)

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly lineage depleted bone marrow (DBM; CD235a and/or Cd45 negative) and stromal cells (STRO-1 positive or collagenase IV released) were analysed.

2020-11-27 | E-MTAB-8629 | biostudies-arrayexpress

Single-cell RNAseq of human bone marrow cells enriched using RNA probes

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Subsets of bone marrow cells were isolated using fluorescence-assisted cell sorting to enrich for putative skeletal stem cells.

2022-05-31 | E-MTAB-9664 | biostudies-arrayexpress

Cell-specific proteome analyses of human bone marrow upon aging.

Project description:Diminishing potential to replace damaged tissues is a hallmark for aging of somatic stem cells, but the mechanisms leading to aging remain elusive. We performed a proteome-wide analysis of human hematopoietic stem and progenitor cells (CD34+) along with five other cell types that constitute the bone marrow niche, namely, lymphocytes and precursors; monocytes/macrophages and precursors; granulocytic precursors and erythroid precursors, as well as mesenchymal stem/stromal cells. In total, we analyzed 270 samples from 59 human subjects. The data represents a valuable resource for further in-depth mechanistic analyses, and for validation of knowledge gained from animal models.

2018-07-20 | PXD007048 | Pride

Genotyping of human Infant ALL samples to detect MLL-cooperating aberrations

Project description:In this study we explored the genotype of Infant ALL to detect MLL-cooperating aberrations, hidden to conventional techniques. In order to limit further heterogeneity, we focused on patients carrying the t(4;11) translocation, the most frequent genetic abnormality in Infant ALL. Final aim was to get new insights into the leukemia pathogenesis of this rare and aggressive disease, as well as providing the basis for discovering new genes for targeted therapy.

2009-12-03 | E-TABM-511 | biostudies-arrayexpress

Real-time quantitative PCR analysis of human mononuclear cells from bone marrow.

Project description:Activation of non-canonical TGF-β1 signaling indicates an autoimmune mechanism for bone marrow fibrosis in primary myelofibrosis Two condition experiment. Biological replicates: 3 control human healty subjects, 3 PMF patients

2014-09-27 | E-GEOD-61819 | biostudies-arrayexpress

Effect of LPS and the glucocorticoid dexamethasone on the mouse Bone Marrow Derived Macrophage Proteome

Project description:The concentrations and copy number of proteins in the mouse Bone Marrow Derived proteome was determined for control, 10 ng/mL LPS stimulation, and LPS stimulation plus the addition of 100 nM dexamethasone, after an incubation for 24 hours and with four biological replicates for each condition. Over 6000 proteins were detected, 410 of which were upregulated by LPS (> 1.5-fold increase, adjusted p value < 0.05). 125 of these LPS-induced proteins were significantly regulated by Dexamethason > 1.5 fold 899 increase or decrease, adjusted p value <0.05).

2024-01-26 | PXD041375 | Pride

Next generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia_RRBS_samples

Project description:Little is known about the impact of DNA methylation on the evolution/progression of chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. While only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared to controls, ~6,500 differentially methylated CpG sites were found in cells from BC-CML patients. In the majority of affected CpG sites methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes which were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared to CP-CML-derived cells. Several of them are well-known tumor suppressor genes or regulators of cell proliferation. 5-aza-2 -deoxycytidine treatment of CML cells resulted in gene re-expression and in a dose-dependent cell growth reduction. Single nucleotide variants of certain epigenetic modifiers during CML progression were not found. Together, our results demonstrate that methylation changes occur frequently during CML progression and may provide a useful basis for revealing new targets of therapy in advanced CML.

2016-08-01 | E-MTAB-4341 | biostudies-arrayexpress

BMDM mouse ctrl SPM (label free proteomics)

Project description:This project investigates the proteomic changes in bone marrow-derived macrophages (BMDMs) from mouse under two conditions: control (Ctrl) and specialized pro-resolving mediator (SPM) treatment. The study includes 3 biological replicates per condition, aiming to identify proteins involved in macrophage function and inflammation resolution.

2025-09-01 | PXD058466 | Pride

Global Proteomic Profiling of Pediatric AML: A Pilot Study

Project description:Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML’s heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limited. Furthermore, the majority of biological functions within cells are operated by proteins (i.e., enzymes) and most drugs target the proteome rather than the genome or transcriptome, thus, highlighting the significance of studying proteomics.

2023-09-26 | PXD043982 | Pride

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