Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

59 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of organoids derived from young and old mice livers

ABSTRACT: We set up liver-derived organoids to study the ageing progenitor population. We detected epigenetic and transcriptional memory in organoids derived from old mice accompanied by alterations in drug and fatty acid metabolism pathways, similar to phenotypes observed in the liver itself.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Swati Parekh

PROVIDER: E-MTAB-11097 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scATAC-seq of mouse liver tissue derived from young and old mice

Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 4838 nuclei prepared from 3 young liver tissues and 3361 nuclei from 3 old liver tissues.

2023-02-20 | E-MTAB-12706 | biostudies-arrayexpress

scATAC-seq of mouse liver tissue derived from young and old mice II

Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 old liver tissues.

2023-11-09 | E-MTAB-12560 | biostudies-arrayexpress

Bulk RNA-seq of cerebral organoids investigating the role of CHD8 in cortical development

Project description:We used cerebral organoids generated from wildtype and CHD8 +/- human ES cells to study the effects of CHD8, one of the top ASD risk genes, on early cortical development. CHD8 +/- hESC were generated using the CRISPR/Cas9 system to create a deletion within the helicase domain. Cerebral organoids were generated according to the protocol from Lancaster et al 2013 with minor modifications.

2022-02-01 | E-MTAB-9933 | biostudies-arrayexpress

4tU RNA-seq from wild-type and Rpb7-QHF cells

Project description:Our structural and biochemical studies show that S. cerevisiae RNA Polymerase II (RNAPII) homodimerizes through the stalk domain (formed by the Rpb4-Rpb7 subunits). To explore the biological impact of disrupting this interaction we introduced a triple point mutation at the RNAPII dimerization interface in Rpb7 (Q96A, H97A, F109K). To test the impact of the dimerization mutant on RNA synthesis and 3' end processing in WT and Rpb7-QHF cells, we labelled nascent transcripts with 4tU which enabled subsequent biotinylation and purification of newly-synthesized transcripts. Nascent transcripts were then used to prepare strand-specific RNA-seq libraries.

2023-12-31 | E-MTAB-13370 | biostudies-arrayexpress

Single nuclei sequencing of human and Mice HFrEF data (Heart Failure with reduced ejection fraction)

Project description:Here we provide snRNA-seq datasets from heart failure patients with reduced ejection fraction and snRNA-SEQ of the corresponding LAD mouse model (permanent ligation of the left anterior descending artery)

2023-08-20 | E-MTAB-13264 | biostudies-arrayexpress

RNA-seq of total and nascent RNA after depletion of Mpe1

Project description:To test the role of Mpe1 in transcription termination we inserted a mini-auxin induced degron (mAID) at the C-terminal end of the endogenous MPE1 locus in the yeast Saccharomyces cerevisiae. We treated Mpe1-mAID cells (JRY101) or wild type cells (WT, YMK728) with 1 mM auxin for 30 minutes and labeled the nascent RNA with 4-thiouracil (4tU) for 6 minutes. The nascent RNA fraction was prepared by biotinylating the 4tU-labeled RNA followed purification with streptavidin beads. Nascent and total RNA fractions were depleted of ribosomal RNA and strand-specific libraries prepared. Libraries were single-end sequenced using an Ilummina HiSeq 4000 instrument.

2021-12-31 | E-MTAB-10820 | biostudies-arrayexpress

Choroid plexus organoids as a model of the blood-cerebrospinal fluid barrier to study Streptococcus suis infection

Project description:Streptococcus suis is a zoonotic pathogen that can invade the central nervous system (CNS) and cause meningitis in pigs and humans. The vascularized choroid plexus (ChP) epithelium, known as the blood-cerebrospinal fluid barrier (BCSFB), serves as a route for S. suis invasion of the CNS. In this study, we aimed to use human induced pluripotent stem cells (iPSC)-derived ChP organoids as an in vitro model to investigate S. suis interaction and infection at the BCSFB and the responses of ChP organoids to S. suis using transcriptomics. We also investigated whether the known plasminogen (Plg) binding to S. suis surface enolase and its conversion to proteolytic plasmin (Pln) would facilitate S. suis translocation across the ChP organoid epithelium and alter the ChP response to infection.

2025-02-13 | E-MTAB-14229 | biostudies-arrayexpress

Genotyping of EM93

Project description:Genotype of 480 EM93 segregants using 2965 genetic markers to study the genomic structure and recombination in EM93

2011-09-01 | E-TABM-1174 | biostudies-arrayexpress

Single-cell RNAseq of mouse bone marrow cells (Drop-seq)

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly depleted bone marrow (DBM; Ter119/Cd45 negative cells) were analysed.

2020-11-27 | E-MTAB-8630 | biostudies-arrayexpress

Single-nucleus RNA-seq of the human musculotendinous unit, the myotendinous junction

Project description:Identification of cell types in the interphase between muscle and tendon by single-nuclei RNA-seq of three human semitendinous muscle-tendon biopsies. With special focus on the myotendinous junction specific myonuclei, transcripts were identified and confirmed to myotendinous junction with immunofluorescence.

2023-03-02 | E-MTAB-12529 | 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