Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic Single-Cell Dissection of Cell Cycle and TGFβ-Induced State Transitions Underlying Gemcitabine Resistance in 3D Pancreatic Tumor Tissue

ABSTRACT: Study Description for ArrayExpress Submission: This study investigates cellular heterogeneity and mechanisms of gemcitabine resistance in pancreatic cancer using single-cell RNA sequencing of PANC-1 cells cultured in a 3D environment (and 2D control). Cells were seeded onto a decellularized porcine intestinal matrix to mimic the tumor microenvironment. The experiment analyzed transcriptional profiles before gemcitabine treatment, with particular attention to invasion and resistance states induced by TGFβ. Single-cell RNA-seq was used to map the transcriptional landscape of 3D pancreatic tumor tissues, capturing cell state transitions, differentiation trajectories, and resistance-associated profiles. The analysis identified cell cycle–dependent resistance signatures (late S to G2(/M) phase), tissue differentiation-associated states, and TGFβ-induced epithelial-to-mesenchymal transition (EMT) pathways contributing to chemoresistance. The dataset includes untreated samples with and without TGFβ stimulation, enabling identification of attractor states and transitional paths leading to gemcitabine resistance. This study provides insight into tumor cell plasticity and dedifferentiation in a 3D matrix environment, supporting early diagnostic and therapeutic research in pancreatic cancer.

INSTRUMENT(S): Cell culture incubator (37 °C, 5 % CO₂), Biological safety cabinet, centrifuge, 40 µm strainer, Linux server (GPU/CPU cluster), Illumina NovaSeq 6000, Standard cell culture setup

ORGANISM(S): Homo sapiens

SUBMITTER: Johannes Balkenhol

PROVIDER: E-MTAB-17360 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-sequencing of mouse embryonic fibroblasts, ESCs, and control and Hic2 overexpressing intermediate reprogramming cells

Project description:Nanog-GFP MEFs were reprogrammed using the piggyBac MKOS reprogramming system with overexpression of genes of interest (BFP as a control, or Hic2). Cells were collected on days 2, 4, 6 and 9, alongside Nanog-GFP MEFs and Nanog-GFP mESCs.

2025-09-12 | E-MTAB-13029 | biostudies-arrayexpress

Single-Cell RNA Sequencing of Mouse Synovial Tissue Across Developmental Time Points

Project description:Synovial joints harbor a protective lining layer, consisting of fibroblasts and macrophages, which form an epithelial-like barrier. In inflamed joints, lining macrophages regulate both early inflammatory cell influx and resolution. Despite these critical functions, it is currently unknown at what stage during development the synovial macrophage lining is established, and which signals drive this process.

2026-06-09 | E-MTAB-17170 | biostudies-arrayexpress

Single-cell RNA-seq of differentiating inducible knockdown (with CTCF and GATA4 shRNA) Left Ventricle cardioids

Project description:This dataset comprises droplet-based single-cell RNA-seq (10x Genomics) from first heart field–derived left ventricle (LV) cardioids generated from WTC11 hiPSCs (TTN-mEGFP) carrying tetracycline-inducible shRNAs targeting GATA4 or CTCF, as well as a scrambled (SCR) control. Cardioids were profiled at day 4.5 and day 7.5 to capture early and later stages of LV differentiation under ± tetracycline (isogenic) conditions, with two biological replicates per time point. The dataset enables comparison of cellular composition, cardiomyocyte maturation trajectories (pseudotime), and knockdown-specific shifts in LV development. In brief, GATA4 KD expands immature/mesodermal populations and yields less-mature CM clusters, whereas CTCF KD produces more-mature CM states at day 4.5 and alters CM abundance by day 7.5 (as readouts; see figure panels for details). Each cell is annotated with the following information: line/perturbation (GATA4, CTCF, SCR), treatment (±Tet), time point (d4.5, d7.5), and replicate. Method details for scRNA-seq preparation (pooling 16 cardioids/condition, CMO multiplexing, FACS, library prep, and sequencing) are provided in the paper’s Methods and Supplementary Methods.

2025-10-14 | E-MTAB-15711 | biostudies-arrayexpress

Proof of principle for iPS2-10X-seq: cardioids experiment during 3D cardiac differentiation

Project description:Proof of principle and optimization experiment on cardioid with10X-based-iPS2-seq was performed on two batches of hPSC-derived cardioids at day 7.5 and pooled together after sample multiplexing. hPSC were primed and treated with Tetracycline 5 days prior cardiac differentiation. CG000388 Rev B (when multiplexing) User Guide was followed with sample multiplexing, provided information of the multiplexing for the cellranger aggr is provided. Sequencing has been performed on a Nextseq 1000 on a P2 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.

2025-10-27 | E-MTAB-14066 | biostudies-arrayexpress

Single-cell RNA sequencing of hiPSC-derived cardiac organoids patterned toward chamber-specific fates (left ventricle, right ventricle, atrium)

Project description:Summary Single-cell RNA sequencing was performed on cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP) to investigate chamber-specific lineage commitment. Organoids were collected at day 7.5 of differentiation, using protocols designed to direct progenitors toward left ventricle, right ventricle, or atrium fates. This dataset enables the characterization of transcriptional programs and cellular heterogeneity underlying the early specification of the cardiac chamber. Dataset: This dataset contains single-cell RNA sequencing (scRNA-seq) data generated to compare the development of cardiac organoids differentiated from WTC11 hiPSCs (TTN-mEGFP reporter line). Organoids were harvested at day 7.5 of differentiation, a stage at which chamber-specific programs begin to emerge. Each sample corresponds to a distinct differentiation protocol designed to direct the commitment of progenitors toward a specific cardiac chamber identity: the left ventricle, the right ventricle, or the atrium. The experimental rationale, illustrated in Supplementary Figure 4 (Figure S4) of Becca et al. (2025), highlights the use of scRNA-seq to resolve the cellular heterogeneity of these chamber-directed organoids and to define transcriptional signatures associated with early cardiac chamber specification.

2025-10-14 | E-MTAB-15693 | biostudies-arrayexpress

iPS2-10X-seq experiment on specific clones targeting with an shRNA either SMAD2 or B2M

Project description:We transfected hiPSCs WTC11 with specific shRNAs targeting SMAD2 or B2M. hiPSCs transfected were selected, cultured, and clones were picked and expanded for follow-up validations. Among these validations, we obtained this scRNAseq dataset. We cultured hiPSCs and differentiated them into cardiac organoids for 7.5 days with and without Tetracycline treatment. This experiment allowed to identify the role of SMAD2 during cardiac differentiation.

2025-10-27 | E-MTAB-15307 | biostudies-arrayexpress

scRNAseq of mouse colorectal organoids in FOLFIRI treatment

Project description:The aim of the experiment is to elucidate changes in tumor heterogeneity upon chemotherapy treatment. The experiment includes non-treated samples, samples right after chemotherapy treatment (FOLFIRI) and organoids recovered from FOLFIRI. It was conducted in two different genetic backgrounds, AKP (Apc KO, KrasG12D and P53 KO) and APS (Apc KO, P53 and Smad4KO). In addition to that, the organoids carry an inducible Cre-ERT2 knock-in allele in the mex3a locus. Upon 4-OH-Tamoxifen induction, Mex3a cells will recombine the tracing allele stop-TdTomato, enabling the tracing of this subpopulation. To understand the fate of the traced cells, samples right after chemotherapy and in the recovery setting were sorted based on their tomato expression. This enables a single cell tracing experiment.

2022-05-13 | E-MTAB-11145 | biostudies-arrayexpress

scRNAseq of AKP Mex3a KO mouse colorectal organoids in FOLFIRI treatment

Project description:Mex3a is an RNA binding protein of unknown function. To elucidate the contribution of Mex3a to tumoral heterogeneity, Mex3a KO organoids engineered by CRISPR were sequenced in three different conditions. Live organoids (DAPI negative) were sorted in Control, after 2 days of FOLFIRI and after 5 days of treatment. Two WT organoids (parental and a derived clone) and two KO (KO1 and KO2, two independent clones) were used for this experiment.

2022-05-16 | E-MTAB-11146 | biostudies-arrayexpress

iPS2-10X-seq Neural organoid differentiation

Project description:iPS2-10X-seq on Neural organoid differentiation after 35days of differentiation. This experiment is a proof of principle that iPS2seq can be applied to different differentiation strategies without risk of silencing. This experiment also showed how neuro-iPSC clones differentiate preferentially towards specific neuronal lineages, which are essential to detect and exclude from the analysis to avoid misleading results.

2025-10-27 | E-MTAB-15308 | biostudies-arrayexpress

Effects of the Sox17∆50 mutation on SOX17 function in mouse embryonic biliary development

Project description:To determine the role of specific cis-regulatory elements within the Sox17 endoderm-preferential TSS2 promoter, we generated Sox17∆50 mutant animals and surveyed how this mutation altered Sox17 expression. EPCAM+/CXCR4+ endodermal cells were isolated from E10.5 Sox17∆50/∆50 and Sox17+/+ embryos (n = 1 of each genotype). Posterior foregut and midgut regions of embryos were dissected by removal of embryonic head, heart, tail, limb buds, posterior and dorsal body trunk. Sox17+/+ and Sox17Δ50/Δ50 cell samples were labelled with barcodes from 3'CellPlex Kit (10X Genomics) and subsequently pooled together for single isolation, library preparation and sequencing.

2024-10-31 | E-MTAB-14000 | 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