Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell multi-omics profiling of brain organoids

ABSTRACT: Organoids were generated from H9 cells. Single cells were sorted from 4-month-old brain organoids differentiated using the telencephalon organoids protocol.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Chong Li

PROVIDER: E-MTAB-13144 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell CRISPR screening of autism risk genes in brain organoids

Project description:Single-cell RNA sequencing of 4-month-old telencephalon organoids. Organoids were generated from cells infected with pooled lentivirus library. The lentiviral library delivers dual-gRNAs targeting 36 high-risk ASD genes in parallel. Organoids were dissociated after 4 months of in vitro differentiation and maturation. Single cells were sorted and subjected to 10X genomics 3' kits.

2023-07-09 | E-MTAB-13148 | biostudies-arrayexpress

Reduced polymerase pausing compensates for increased chromatin accessibility in the aging liver

Project description:Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation. Here, we used a multi-omics approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase of transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II). We propose that these changes in transcriptional regulation are due to a reduced stability of the pausing complex and may represent a mechanism to compensate for the age-related increase in chromatin accessibility in order to prevent aberrant transcription.

2022-09-15 | PXD034564 | Pride

Transcriptome analysis of H9 hESC derived cerebral organoids

Project description:RNA-seq was utilized to characterize the transcriptome of human embryonic stem cells-derived 3D cerebral organoids. Briefly, H9 hESCs were differentiated into cerebral organoids using previously established methods (Lancaster, 2013). Coding and noncoding genes were analyzed in 1 month and 2 month old cerebral organoid samples.

2016-05-05 | GSE80264 | GEO

Lineage recording in human cerebral organoids (whole organoids)

Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the iTracer data of 12 cerebral organoids.

2021-11-03 | E-MTAB-10974 | biostudies-arrayexpress

Single-cell transcription profiling human dorsal forebrain organoids treated with Hyper-IL-6

Project description:We performed single-cell RNA sequencing of dorsal forebrain organoids at day 53 of differentiation upon treatment with Hyper-IL-6. The study aimed at investigation of the effects of Hyper-IL-6 on transcriptional profiles of dorsal forebrain organoids at single-cell level.

2023-03-08 | E-MTAB-12743 | biostudies-arrayexpress

scGET-seq profile of patient derived organoids

Project description:Two patient-derived organoids from liver metastasis of CRC samples were profiled by scGET-seq to analyze their genomic composition

2021-08-17 | E-MTAB-10219 | biostudies-arrayexpress

scRNA-seq of Human Alveolar Type 2 Cell Organoids

Project description:Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in injury-repair. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development through differentiation of lung progenitor organoids to AT2 cells and benchmarking against primary AT2 organoids.

2023-06-15 | E-MTAB-12960 | biostudies-arrayexpress

Single cell RNA-seq profiles of patient derived organoids

Project description:Three patient-derived organoids from liver metastasis of CRC samples were profiled by scRNA-seq.

2024-02-29 | E-MTAB-13123 | 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 transcriptional profiling of primary human dental follicle and derived organoids

Project description:Knowledge on tooth epithelial stem cells and corresponding biology in humans is sparse. Here, we developed an organoid model, typically replicating epithelial tissue stem cell biology, starting from human tooth. Dental follicle (DF), isolated from extracted wisdom teeth, efficiently generated long-term expandable epithelial organoids. The organoids displayed a tooth stemness phenotype as present in DF’s Epithelial Cell Rests of Malassez, a compartment deemed to contain tooth epithelial stem cells. To further decode the organoids in more granular detail, we applied scRNA-seq analysis on DF-derived organoids (passage 1 (P1) and P4) together with their primary tissue. Additionally, to decipher the amelogenesis-resembling process that takes place in the tooth organoids upon differentiation, we performed scRNA-seq analysis of P4 organoids switched to mineralization-inducing medium for 8 days.

2022-04-01 | E-MTAB-10596 | 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