Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNAseq of gastric tumors and adjacent mucosa from Twist2Cre;Lkb1fl/+;Rosa26RTdtomato/+ mice

ABSTRACT: 5000 target cells per sample where sequenced from 2 gastric tumor samples and 1 sample of adjacent gastric mucosa Twist2Cre;Lkb1fl/+;RosaRTdtomato+/- mice. Drop-seq 10X Genomics (10X v3 library kit) was used for single cell barcoding and library preparation. Samples were sequenced with Novaseq6000.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Eva Domènech-Moreno

PROVIDER: E-MTAB-13624 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-Sequencing of testis tissue from 3 mouse species and their immediate crosses

Project description:We performed an inter-species comparison of murine spermatogenesis using the inbred strains C57B6J, CAST/EiJ and CAROLI/EiJ to investigate the cell type-specific evolution of gene expression levels among closely related species. We also used F1 crosses of C57B6J and CAST/EiJ to investigate context-specific regulatory effects on gene expression in cis and trans by measuring allele-specific expression (Goncalves et al. 2012; Wittkopp et al. 2021). To this end, single-cell RNA-Sequencing data was generated from dissociated testicular tissue in each mouse strain using the 10x Genomics scRNA-Seq platform.

2023-12-11 | E-MTAB-11602 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract during aging in C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract during ageing in ovary, oviduct and uterus. Tissues of aged mice were collected at the age of 9,12 and 15 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2024-01-31 | E-MTAB-12889 | biostudies-arrayexpress

scRNA-seq of stromal vascular cells from 48 week (aged) mouse subcutaneous adipose tissue compared to control 10 week (young) mouse SVF

Project description:Adipose tissue mass and adiposity change throughout the lifespan. During aging, while visceral adipose tissue (VAT) tends to increase, peripheral subcutaneous adipose tissue (SAT) decreases significantly. Unlike VAT, which is linked to metabolic diseases, SAT has beneficial effects. However, the molecular details behind aging-associated loss of SAT remain unclear. Here we compare scRNA-seq of total SVF of SAT from young and aging mice to identify a novel Aging-dependent Regulatory Cell (ARC) that emerges in SAT of aged mice. Inguinal white adipose tissue (iWAT) was used as a representative SAT; iWAT pads of 2 mice from each age group were subjected to collagenase digestion and treated with a hypotonic buffer to remove red blood cells before subjection to scRNA-seq by 10X Genomics Chromium Single Cell Kit. The findings showed that ARCs express adipogenic markers but lack adipogenic capacity and inhibit differentiation of neighboring adipose precursors.

2021-03-25 | E-MTAB-10221 | biostudies-arrayexpress

Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells

Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 2 chemistry) system on ~6,000 mouse endothelial cells derived from aorta.

2019-05-27 | E-MTAB-7149 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract in young, pregnant and aged C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract across the four stages of estrus cycle in young adult mice (ovary, oviduct, uterus, cervix and vagina, with spleen as a comparison) and compared this with similar analyses of decidualization (uterus) and ageing (ovary, oviduct, uterus, cervix, vagina and spleen). Vaginal smears were used to stage the estrus cycle in young mice. To collect the decidualized uteri mice were mated and uterine tissue was collected from pregnant mice at day 5.5 after mating. Tissues of aged mice were collected at the age of 18 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2023-02-01 | E-MTAB-11491 | biostudies-arrayexpress

Single-cell RNA-seq of the human Lineage– cells derived from the adipose stromal vascular fraction across depots

Project description:We used single-cell RNA-seq to characterize the heterogeneity of the human Lin- stromal vascular fraction across five adipose depots. We mollecularly assessed Lin- SVF cells from subcutaneous, omentum, mesocolic, and perirenal fat depots, as well as gallbladder-associated fat using 10x Genomics.

2023-09-30 | E-MTAB-12893 | biostudies-arrayexpress

Single cell RNA and CITE sequencing of cells from synovial tissue biopsies of healthy donors, and Rheumatoid Arthritis (RA) patients with active disease or sustained clinical remission

Project description:Synovial biopsies were taken using 14G Precisa Needle (HS Hospital Service, Italy) in ultrasound-guided protocol, and digested as described previously (Alivernini et al, 2020). Live CD45+ cells from the synovial tissue (ST) of healthy donors (n=3), patients with active RA (n=5) and patients in sustained remission (n=2) were sorted for single cell RNA (scRNA) or CITE (scCITE) sequencing using the 10x Genomics platform. Maximum 20,000 immune cells from tissue were sorted into Protein LoBind 1.5 ml Eppendorf tube containing 300 μl of RPMI media with 10% of FSC. Cells were loaded onto a Chromium Controller (10X Genomics) for single-cell partitioning, followed by library preparation using Single-Cell 3’ Reagent Kits v3.1. For 3 healthy ST and 4 ST from active RA (Figure S1), Totalseq Hashtag were used (Biolegend #394601, #394603, #394605, #394607, #394609) to combine 2 samples per run, and TotalSeq™-A Human Universal Cocktail (V1.0) was used to collect protein expression (CITEseq) data together with transcriptome data. Single-cell libraries were sequenced on the Illumina HiSeq 4000 system to a minimum depth of 50k reads/cell.

2024-12-06 | E-MTAB-14213 | 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 RNA sequencing of small intestinal dendritic cells from C57BL/6, RORgt-/- and RORgt-Cre x Ltb-flox mice

Project description:Cryptopatches (CP) and isolated lymphoid follicles (ILF) are evolutionary ancient lymphoid structures found in the intestines of all vertebrates. These structures are demarcated by a poorly characterised subset of mononuclear phagocytes (MPh), called CP/ILF-associated (CIA)-MPh. We could demonstrate that CIA-MPh derive from a pre-DC from the bone marrow and thus are boafide dendritic cells. We called these newly identified cDC cells : cryptopatch and ILF associated dendritic cells (CIA-DC). To obtain unbiased insights into how CIA-DC are integrated into the intestinal cDC landscape, we performed single cell RNA-sequencing (scRNA-seq) of purified CD45+ CD64- I-A/I-E+ CD11chigh cells from C57BL/6 mice using the 10X Genomics droplet-based technology. Finally, to study the role of ILC3 in the final differentiation of CIA-DC, we performed single cell RNA-sequencing (scRNA-seq) of cDC from Rorc(γt)-/- and Ltb∆ILC3,T mice, using the 10X Genomics droplet-based technology.

2020-11-24 | E-MTAB-9522 | biostudies-arrayexpress

Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues

Project description:In an effort to define transcriptional heterogeneity in the stromal cell compartment of lymph nodes scRNA-seq analysis of CD45- cells from skin-draining LNs (SLN) was performed. Flow sorted CD45 depleted single cell suspension from SLN of ten mice were profiled by 10x 3’ single-cell RNA-sequencing in two runs, each containing cells from five mice.

2021-04-10 | E-MTAB-10197 | 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