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

Dissecting placental host-pathogen interactions: Rift Valley fever virus infection in early human trophoblast stem cells

ABSTRACT: Single-cell RNA-seq (parse biosciences) of in vitro differentiated human trophoblast stem cells, infected with RVFV

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Johan Henriksson

PROVIDER: E-MTAB-16352 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

single-cell RNA-Seq of human induced pluripotent stem cells from a healthy donor and a DMD patient at different time point during myogenic differentiation

Project description:The experiment aimed to validate the gene network regulating cell fate decisions during the myogenic differentiation of iPS cells from a DMD patient. DMD iPSCs were transfected with specific siRNA at Day 7 of the differentiation protocol and collected either at Day 9 or Day 14. As a control, we used a non-specific siRNA. Non transfected DMD cells were also included, together with the healthy control cell line used in our previous experiments.

2026-06-01 | E-MTAB-16077 | biostudies-arrayexpress

Single-cell transcriptomic profiling of patient-derived pancreatic ductal adenocarcinoma primary cell cultures

Project description:Single-cell transcriptomic dataset comprising 41 patient-derived cell cultures (PDCs) established from pancreatic ductal adenocarcinoma (PDAC). The dataset was generated using Evercode™ technology with the Whole Transcriptome v2 kit (Parse Biosciences, ECW02130), based on Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq). For scRNA-seq, PDCs were processed in two batches, 14 samples in the first batch (R1) and 27 samples in the second batch (R2). Sequencing was performed separately for each batch using the Illumina NovaSeq X Plus platform. Paired-end reads were generated on a 10B flow cell with 200 sequencing cycles. FASTQ quality control (QC), barcode correction, alignment to the human reference genome (GRCh38.p13), multiplet detection, and raw count matrix generation were performed using the split-pipe pipeline (v1.1.1, Parse Biosciences) with default parameters. This single-cell collection of experimentally derived models reveals transcriptional heterogeneity both within and across PDCs. The submitted file consists of the count matrix along with the corresponding metadata.

2026-04-15 | E-MTAB-16856 | biostudies-arrayexpress

Single-cell sequencing samples for chemically defined, serum-free, and xeno-free differentiation of alveolar type 2 cells

Project description:HiPSCs were differentiated into alveolar type 2 cells (AT2s) following a stepwise differentiation protocol, mimicking lung development, using a chemically defined, serum-free, and xeno-free differentiation protocol. Raw data contains 8 sublibraries which include hiPSC-derived passage 2 (day 76) AT2 cells.(at2_ep_filt_4_3).

2026-04-01 | E-MTAB-15033 | biostudies-arrayexpress

The dura mater acts as an autonomous B cell niche supporting immune responses during chronic Trypanosoma brucei infection

Project description:The dura mater hosts a rich population of B cell progenitors, yet its capacity to sustain B cell development during systemic lymphopenia remains unclear. Using Trypanosoma brucei infection, which induces peripheral B cell depletion, we demonstrate that the murine dura mater maintains intact B cell lymphopoiesis independently of bone marrow and spleen. We performed a comparative single cell transcriptomic profiling of the calvaria bone marrow, femur bone marrow, and dura mater from naive and Trypanosoma brucei-infected female mice. The sequencing rendered high quality data from the calvaria bone marrow and the dura mater, but the femur bone marrow failed to generated reliable data and was thus excluded from downstream analyses. This data is single-cell RNA sequencing using Parse Biosciences Evercode Whole Transcriptome combinatorial barcoding

2026-02-04 | E-MTAB-16521 | biostudies-arrayexpress

Single cell sequencing of fibroblast-like synoviocytes (FLS) isolated from hind paws of Col6a1-cre Bmal1-flox PER2::LUC mice

Project description:Fibroblast-like synoviocytes (FLS) were isolated from the hind paws of Col6a1-cre Bmal1-flox PER2::LUC mice for single cell sequencing to determine the effect of Bmal1 knockout on FLS cell function. FLS cells were isolated from joint digests by selection for Podoplanin expression, then fixed and barcoded for single cell transcriptomic analysis using a split-pool ligation-based transcriptomic sequencing (SPLiT-seq) approach.

2024-06-06 | E-MTAB-13320 | biostudies-arrayexpress

Single cell RNAseq of haploidized HCT116 colorectal carcinoma cells expressing specific p53 mutations treated with either DMSO or Nutlin

Project description:Colorectal carcinoma cell line HCT116 cells were used as a model system to investigate the heterogeneity of different TP53 mutations. To this end, cells were haploidized by deleting an intronic splice site in one of the two wild-type TP53 alleles while the other copy was altered to different loss-of-function mutants via CRISPR/Cas9 gene editing. Cells expressing different haploid TP53 genotypes were treated with either Nutlin or DMSO to investigate the genetic variation between the mutants and the wild-type genotype.

2024-10-16 | E-MTAB-13904 | biostudies-arrayexpress

Volumetric imaging and single-cell RNAseq atlases identify cellular mechanisms of human dental pulp response during tooth decay progression

Project description:Dental decay induces dental pulp’s responses, which are still unclear. Firstly, we performed a complete volumetric imaging. Samples from healthy and diseased teeth were collected, processed into thick sections, transparized, immunolabeled, and imaged. Secondly, we performed single-cell RNA sequencing analyses of human dental pulps across health and various stages of the disease. We generated an extensive imaging atlas of the pulp’s neurovascular systems. We also identified distinct cell population and subpopulations showing the cellular heterogeneity, including large populations of fibroblasts, mesenchymal progenitor and endothelial cells. These results provide a basis for understanding dental tissue response to injury, potentially driving a paradigm shift in patient management. Furthermore, the human tooth seems to be a promising model for investigating systemic diseases and therapeutic responses.

2025-11-01 | E-MTAB-14896 | biostudies-arrayexpress

Bulk RNA-seq of Adult and Fetal Enteroids (Control or Treated with DBZ)

Project description:Bulk RNA sequencing data of both adult and fetal enteroid lines cultured for 1 or 3 days. Conditions include enteroids grown in control basal media and basal media with the notch inhibitor DBZ added.

2022-04-08 | E-MTAB-11619 | biostudies-arrayexpress

Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors

Project description:Here, we report synergistic inhibition of glycogen synthase kinase 3 (GSK3), transforming growth factor β (TGF β), and Notch signaling pathways by small molecules can efficiently convert monolayer cultured hESCs into homogenous primitive neuroepithelium within one week under chemically defined condition. These primitive neuroepithelia can stably self-renew in the presence of leukemia inhibitory factor, GSK3 inhibitor (CHIR99021) and TGF β receptor inhibitor (SB431542); retain high neurogenic potential and responsiveness to instructive neural patterning cues toward midbrain and hindbrain neuronal subtypes; and exhibit in vivo integration. hESCs at about 20% confluence were treated with 3 μM CHIR99021, 2 μM SB431542, 0.1 μM Compound E (γ-Secretase Inhibitor XXI) in neural induction media containing Advanced DMEM/F12:Neurobasal (1:1), 1xN2, 1xB27, 1% Glutmax, 5 μg/ml BSA and 10 ng/ml hLIF, for 7 days. The culture was then split 1:3 for the next six passages using Accutase and cultured in neural induction media supplemented with 3 μM CHIR99021 and 2 μM SB431542 on X-ray inactivated MEF feeders or Matrigel-coated plates. After six passages, the cells were split 1:10 regularly. Global gene expression analysis of primitive neural stem cells

2011-04-28 | E-GEOD-28595 | biostudies-arrayexpress

DNA methylation in marmoset primed and naive pluripotent stem cells, and trophoblast stem cells

Project description:Bisulfite sequencing on bulk populations of marmoset naïve pluripotent stem cells (PSC), primed PSC, and trophoblsat stem cells.

2024-11-21 | E-MTAB-12453 | 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