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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single cell RNA sequencing of healthy and trisomy 21 (Down's syndrome) foetal liver and foetal bone marrow

ABSTRACT: Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal liver and bone marrow tissue samples from 15 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 1.1 million cells from three different populations: CD235- (niche and haematopoietic cells depleted of erythrocytes), CD34+/Lin- (haematopoietic progenitors), and CD45+ (all haematopoietic cells).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Marco De Zuani

PROVIDER: E-MTAB-13067 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Multiome scRNA- and scATAC-seq of healthy and trisomy 21 (Down's syndrome) foetal liver

Project description:Here, we performed multiome sequencing (snRNA-seq + snATAC-seq) of human fetal liver samples from 3 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 60,000 CD45+ foetal liver cells.

2024-07-17 | E-MTAB-13070 | biostudies-arrayexpress

Immune cells direct epithelial maturation during early human lung development

Project description:The adult human lung harbours a significant proportion of immune cells, which are known to play a crucial role in both normal lung homeostasis and pathogenesis. In this work, we collected CD45-enriched human lung cells from 6 to 22 week post conception (pcw) and built a single-cell transcriptome and proteome atlas. We showed a biphasic mode of immune cell development peaking at 8-9 and 20 pcw respectively. The developing immune cells potentially modulate the maturation of the epithelium through signalling molecules. We demonstrated using the lung organoid model that IL-1ß was required for epithelium differentiation. Overall, we provide a resource for the community of lung biologists and immunologists and provide insights on the interaction between the innate immune system and epithelium during fetal development.

2022-12-09 | E-MTAB-11528 | biostudies-arrayexpress

Haematopoietic stem and progenitor cells are present in healthy gingiva tissue

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2021-02-23 | E-MTAB-10050 | biostudies-arrayexpress

Single cell RNA-seq atlas of human NSCLC lesions and non-involved tissue

Project description:We performed single cell RNA sequencing (scRNA-seq) of NSCLC tumours and matched, adjacent, non-involved lung tissue from 24 patients. The data set is composed of approximately 900,000 cells from two different populations: CD235- (haematopoietic and non-haematopoietic cells depleted of erythrocytes), and CD45+ (all haematopoietic cells).

2024-04-29 | E-MTAB-13526 | biostudies-arrayexpress

Single-cell RNA+ATAC sequencing of human CRL-1459 colonic fibroblasts

Project description:The 10x multiome (RNA+ATAC) kit was applied to CRL-1459 cells in culture at passage 10 and 15

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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.

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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

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

Single-cell RNA-seq (10x Chromium) of FACS-sorted drl:H2B-Dendra2, etv2:Kaede, fli1:DsRed, and tp1:eGFP transgenic zebrafish embryos

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2023-08-01 | E-MTAB-13196 | biostudies-arrayexpress

Transcription profiling of mouse RLSC and MMH-D3 cell lines

Project description:Increasing evidence provide support that the mammalian liver contains stem/progenitor cells, but their molecular phenotype, embryological derivation, cell biology as well as of their role in the liver cell turnover and regeneration remain to be further clarified. We report the isolation, characterization and reproducible establishment in line of a resident liver stem cell (RLSC) with immunophenotype and differentiative potential distinct from other previously reported liver precursor/stem cells. RLSCs, derived from foetal and neonatal murine livers as well as from immortalized hepatocytic MMH lines and established in lines, are Sca+, CD34-, CD45-, alfa-fetoprotein+, albumin-. This immunophenotype suggests a non-haematopoietic origin. RLSCs transcriptional profile, defined by microArray technology, highlighted the expression of a broad spectrum of âplasticity-related genesâ and âdevelopmental genesâ suggesting a multi-differentiative potential. RLSCs, indeed, spontaneously differentiate into hepatocytes and cholangiocytes and, when cultured in appropriate conditions, into mesenchymal and neuro-ectodermal cell lineages, such as osteoblasts/osteocytes, chondrocytes, astrocytes and neuronal cells. RLSCs capability to spontaneously differentiate into hepatocytes, the lack of albumin expression and the broad differentiative potentiality locate them in a pre-hepatoblast/liver precursor cells hierarchical position. In conclusion, RLSCs may provide an useful tool to improve liver stem cell knowledge and to assess new therapeutic approaches for liver diseases. Experiment Overall Design: We compared the gene expression profile of a RLSC line to that of the previously characterised hepatocytic differentiated cell line MMH-D3 (ref Amicone), using Affymetrix Mouse430_2 GeneChip array.

2008-06-18 | E-GEOD-7038 | biostudies-arrayexpress

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