Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translational co-culture model reveals epithelial-mesenchymal mechanisms of lung fibrosis and identifies NF-κB as potential therapeutic target

ABSTRACT: The interaction of lung epithelial and lung mesenchymal cells was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. We used single-cell RNA sequencing (scRNA-seq) to evaluate the transcriptional fate of the normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) during the course of co-cultivation, and compare the single cell profiles with their counterpart isolated from patients with idiopathic pulmonary fibrosis (IPF). NHLF and normal NHBE cells were grown as co-cultures, cell suspensions were collected at the time points t = 0h, 3h and 18h and analyzed by single-cell RNA-seq on a Chromium Platform. Eight samples were sequenced, resulting in a total of xx single cell transcription profiles.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-11847 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-11832

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq, V(D)J seq, CITE-seq, LIBRA-seq of human CD4+, CD8+ and B lymphocytes PBMCs of 5 donors (3 SARS-CoV-2 experienced and 2 SARS-Cov-2 Naive) before and following two doses of Pfizer/BioNTech BNT162b2 mRNA vaccine

Project description:The experiment aims at characterizing the immune responses elicited by the BNT162b2 vaccine against SARS-CoV-2, initially administered in a two dose regimen (second dose after three weeks followinf the first dose) In particular the transcriptional landscape of circulating T and B lymphocytes has been profiled longitudinnaly by scRNA-seq coupleD with CITE-seq of 19 cell surface markers to better classify T cells subpopulations, LIBRA-seq to assess the Spike-specificity of BCRs and and V(D)J seq to also track T and B cell clones dynamics. Eeach sample was profiled before vaccination (T0), 21 days after the first dose (T1), 2 months after the first dose (1 month after the second dose) (T2). The immune responses were characterized using PBMC from 3 SARS-CoV-2 experienced donors (experiencing SARS-Cov-2 at least 4 months before the first vaccinatin) and 2 SARS-CoV-2 unexperienced donors.

2024-04-18 | E-MTAB-13721 | biostudies-arrayexpress

Integrated longitudinal immunophenotyping, transcriptional and repertoire analyses depict principles of protective immune responses and memory formation in COVID-19 patients

Project description:scRNAsequencing coupled with TCR and BCR sequencing of 6 Covid patients (3 mild and 3 severe) and 2HD in acute and recovery phases

2021-07-30 | E-MTAB-9652 | biostudies-arrayexpress

Clonal and functional patterns of emigrating Treg cells according to locations

Project description:Single-cell TCR and RNA sequencing of recovered T cells in mLN, cLN, tdLN and tumor bed 24 hours post inoculation of CFSE in mLN.

2023-07-01 | E-MTAB-12846 | biostudies-arrayexpress

RNA-seq time series of lung epithelial and lung mesenchymal cells in a novel co-culture model of lung fibrosis

Project description:The interaction of lung epithelial and lung mesenchymal cells (fibroblasts) was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. Primary normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) were fluorescently labelled prior to seeding, then grown either as mono or co-cultures and collected in triplicates for mRNA-seq at the start (T=0h) and after 3h and 18h. Each harvested cell culture was FACS sorted into individual NHLF and NHBE cell populations, which were then then lysed and sequenced.

2022-10-03 | E-MTAB-11832 | biostudies-arrayexpress

Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

2022-12-07 | E-MTAB-11673 | biostudies-arrayexpress

Single-cell RNA-seq of fibroblasts influenced by exosomes derived from melanoma cell line G361

Project description:In this in-vitro study, we demonstrated the different effects of exosomes produced by G361 melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of cutaneous malignant melanoma. Both normal and cancer-associated fibroblasts were cultivated in either DMEM with 10% EDS (exosome-depleted serum) (control) or DMEM with 10% EDS + 10 microg/ml G361 exosomes (EXO). The cells were harvested after 24 hours of cultivation.

2021-12-31 | E-MTAB-10290 | biostudies-arrayexpress

Single cell expression profiling of murine subventricular zone in adult brain three days after focal celebral ischemia

Project description:Ischemic stroke is a serious medical condition that leads to the onset of neurological symptoms such as loss of motor and cognitive functions. Focal cerebral ischemia (FCI) occurs due to the interrupted blood supply to the site of injury, resulting in the demise of brain cells. The subventricular zone (SVZ) is a source of stem and progenitor cells (NS/PCs), which proliferate and differentiate in multiple cell types in order to substitute the injured tissue. We isolated cells from the SVZ and the adjacent striatum three days after middle cerebral artery occlusion (MCAO) in order to map cellular changes and NS/PCs plasticity in adult brain upon injury. Expression profiling of the isolated tissue at the single cell level enables the identification of cell population subtypes in the region and their characteristic gene expression.

2021-01-01 | E-MTAB-9935 | biostudies-arrayexpress

Single cell RNA, BCR and CITE-Seq of longitudinal COVID-19 patients

Project description:6 patients with severe COVID-19 were followed longitudinally during hospitalization and up to 1 year after infection, when they also received a vaccine. For each time point and patient, PBMCs were collected and split into 3 pools: 1/3 was sequenced straight; from 1/3 of the samples B cells were enriched (B cell enrichment kit from StemCell) and from 1/3 of the samples, antigen-specific cells were sorted using barcoded N, S and RBD probes. All samples were further stained using a cocktail of 181 barcoded Abs. For all samples we have sequences gene-expression, B cell receptor and Cell surface proteins.

2022-12-06 | E-MTAB-12392 | biostudies-arrayexpress

Single cell RNA-seq and TCR-seq of coding RNA from single cells in the mouse lung using 10x Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index)

Project description:Single-cell RNA-seq and TCR-seq were conducted using coding RNA of single cells isolated from mouse lung MNCs with or without 7DW8-5 according to the manufacturer’s instructions. In brief, single cells from the mouse lung MNCs were incubated with mouse Fc block and then stained by anti-mouse CD45+ antibody and DAPI. Sorted viable CD45+DAPI- single cells were loaded into 10x genomics ChromiumTM controller (samples were split into 4 lanes, Saline1 and Saline2 without 7DW8-5 treatment, and 7DW1 and 7DW2 with 7DW8-5 treatment) to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library and TCR library were sequenced with Illumina Novaseq. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of the samples Saline1, Saline2, 7DW1, and 7DW2.

2023-06-06 | E-MTAB-11770 | biostudies-arrayexpress

scRNA-seq with paired V(D)J sequencing of synovial B cells from rheumatoid arthritis patients

Project description:scRNA-seq with paired V(D)J sequencing of synovial B cells from rheumatoid arthritis patients.

2023-08-01 | E-MTAB-12833 | biostudies-arrayexpress