Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell ATAC-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control

ABSTRACT: This study used snATAC-seq to profile Chromatin accessibility in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using a cold-active protease. Nuclei were extracted and profiled using the 10X Genomics Single-cell ATAC reagent kit v1.1. Libraries were sequenced using paired-end reads on an Illumina NovaSeq 6000. Initial processing was performed using CellRanger ATAC v1.2.0 (10X Genomics).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: John Crean

PROVIDER: E-MTAB-11139 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control

Project description:This study used scRNA-seq to characterise the transcriptome in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using a cold-active protease. Nuclei were extracted and profiled using the 10X Genomics Single-cell 3' V3 kits. Libraries were sequenced using paired-end reads on an Illumina NextSeq 500. Initial processing was performed using CellRanger v3.1.0 (10X Genomics).

2023-04-30 | E-MTAB-11138 | biostudies-arrayexpress

Single cell RNA-seq of hiPSC-derived kidney organoids differentiated within self-assembling peptide hydrogels and the animal-derived matrix Matrigel

Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.

2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress

snATAC-seq of the gray short-tailed opossum cerebellum in two developmental stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 19,204 nuclei in the opossum (Monodelphis domestical) cerebellum across two developmental stages (postnatal day 21 and adult). The study included two biological replicates per stage, one from each sex, and an additional adult sample enriched for white matter. Cerebelli were dissected in two halves, nuclei were extracted from one half and profiled using 10x single-cell ATAC reagent kit (v1.1) and a Chromium controller. The white matter enriched sample was dissected from coronal cerebellum slices. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-10533 | biostudies-arrayexpress

snATAC-seq of the developing mouse cerebellum across eleven stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-9765 | biostudies-arrayexpress

Single cell ATAC-seq of human peripheral blood mononuclear cells under resting and stimulated conditions

Project description:Single cell ATAC-seq of PBMC - resting and stimulated. Used for comparison to asses the capabilies of the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication).

2021-04-13 | E-MTAB-10382 | biostudies-arrayexpress

Single-cell multiome analysis of human in vitro activated CD4 T cells

Project description:This study looks at the ATAC+RNA profiles of human CD4 T cells under bioreactor-like conditions as ACT. Cells were stimulated toward Th1,Th2,Treg and Th17 under anti-CD3/28 activation, and profiled on day 5.

2024-01-31 | E-MTAB-13711 | 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

Single Cell Multi-Omics Profiling Using ISSAAC-seq

Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.

2022-06-15 | E-MTAB-11264 | 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

Single-cell transcriptome of cerebral organoids with and without methanol fixation

Project description:To study how methanol fixation affects single-cell transcriptomic measurement, two cerebral organoids were dissociated. Cell suspension of each organoid was split into two aliquots. Methanol fixation was applied to one of the two aliquots. Single-cell RNA-seq with 10x Genomics was applied to the two aliquots separately.

2020-08-31 | E-MTAB-9473 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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