Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord

ABSTRACT: To analyse lesion-induced gene regulation in macrophage and microglia at single cell resolution, we performed single cell RNAseq on FACS-isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post-lesion (hpl) after spinal injury at 3 days post-fertilisation (dpf), compared to age-matched uninjured animals.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Danio rerio

SUBMITTER: Louisa Drake

PROVIDER: E-MTAB-10379 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord

Project description:To analyse lesion-induced gene regulation in progenitor cells at single cell resolution, we performed single cell RNAseq on FACS-isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post-lesion (hpl) after spinal injury at 3 days post-fertilisation (dpf), compared to age-matched uninjured animals.

2021-05-24 | E-MTAB-10390 | biostudies-arrayexpress

10x single cell RNAseq of chick ectoderm from stages HH5 to ss4

Project description:The vertebrate ectoderm gives rise to a variety of cell lineages, including neural, neural crest, placodal and non-neural cell fates. How cell fates are specified at the neural plate border (the region surrounding the neural plate) is not fully understood. We therefore carried out 10x scRNAseq of the chick epiblast to investigate cell fate specification at the neural plate border. Embryos were dissected and pooled according to stage. The tissue was then dissociated and FAC sorted to remove dead cells and remaining doublets before cells were stored in MeOH. Due to the time required to dissect embryos, multiple rounds of collections were carried out, with collections from the same stage pooled prior to 10x sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at the Francis Crick Institute, London. This collection was a follow up to E-MTAB-10408.

2023-08-25 | E-MTAB-11444 | biostudies-arrayexpress

Single-cell RNA-seq data of cardiac cells derived from a human induced pluripotent stem cell control line

Project description:Characterization of cell-type diversity obtained after cardiac differentiation of hiPSC using single-cell RNA-Seq.

2022-12-05 | E-MTAB-11817 | biostudies-arrayexpress

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

Project description: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.

2021-03-24 | E-MTAB-9969 | biostudies-arrayexpress

Proteomics analysis of zebrafish spinal cord regeneration

Project description:Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling of the lesion site was performed at 1 dpl and 2 dpl as well as corresponding age-matched unlesioned control tissue (4 dpf as control for 1 dpl; 5 dpf as control for 2 dpl).

2023-09-06 | PXD037590 | Pride

scRNAseq libraries of pooled kidney samples from wild type (ZF1) versus CRISPR-targeted renin knockout (ZF2) zebrafish

Project description:Libraries were made to compare the transcriptome of renin lineage cells (RLCs) from wild-type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren-/- zebrafish, which carried ren:RFP and acta2:EGFP reporter genes, allowing the isolation of renin-expressing cells and smooth muscle cells.

2022-06-10 | E-MTAB-11079 | biostudies-arrayexpress

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 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 RNA sequencing of mouse macrophage

Project description:A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains.

2022-06-21 | E-MTAB-11814 | biostudies-arrayexpress

Human pluripotent stem cell-derived ROR1e lens epithelial cell single cell RNA-sequencing

Project description:Detailed transcriptomic analyses of differentiated cell populations derived from human pluripotent stem cells is routinely used to assess the identity and utility of the differentiated cells. In particular, single cell RNA-sequencing (scRNA-seq) can provide insights into both the cellular and transcriptional heterogeneity of differentiated cell populations. Here we provide scRNA-seq data obtained from ROR1-expressing lens epithelial cells (ROR1e LECs) obtained via directed differentiation of CA1 human embryonic stem cells. Through the use of principal component analysis, heat maps and gene ontology assessments, we demonstrate that ROR1e LECs represent a highly purified and large-scale population of lens cells. These data provide a resource for future characterisation of both normal and cataractous human lens biology.

2020-11-27 | E-MTAB-9178 | 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