Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

98 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Peter Tessarz

PROVIDER: E-MTAB-12560 | 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

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

Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

Tissue- and stage-specific Capture-C for selected TSS and CRM

Project description:Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from 2-3h whole embryo samples or Mef2-/Elav-sorted nuclei from 6-8h and 10-12h embryo samples. Capture-C was performed on wildtype embryos. Capture-C was performed using two different Capture probe pools, one for TSS and one for CRM. TSS and CRM were hand curated for tissue- and stage-specific activity.

2023-12-07 | E-MTAB-9310 | biostudies-arrayexpress

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

Project description:Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ~3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1,000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes. We isolated replicates of nuclei of untreated mESCs and cells treated for 2, 5, 12.5, 25 and 50 min with 300nM flavopiridol, as well as nuclei treated for 12.5, 25, and 50 min with 500nM triptolide and performed GRO-seq with these.

2014-03-21 | E-GEOD-48895 | biostudies-arrayexpress

Tissue- and Stage-specific ChIP for H3K27ac, CTCF, Beaf and Su(Hw) in D. melanogaster embryos

Project description:This study contains a series of ChIP-seq experiments performed on nuclear material similar to what was used in Tissue- and Stage-specific Capture-C for selected TSS and CRM (BioStudies/ArrayExpress collection E-MTAB-9310). ChIP-seq with chromatin isolated from nuclei isolated from 2-3h whole embryos samples or Mef2-/Elav-sorted nuclei from 6-8h and 10-12h embryo samples was performed using anti-H3K27ac (Anti-Histone H3 (acetyl K27) antibody, Abcam #ab4729, purified polyclonal), anti-CTCF (rabbit anti Drosophila CTCF antibody, Reinkawitz lab, purified polyclonal), anti-Beaf (mouse anti Drosophila BEAF antibody, DSHB #1553420, monoclonal) and anti-Su(Hw) (goat anti Drosophila Su(Hw) antibody, Geyer lab, purified polyclonal) antibodies.

2023-06-30 | E-MTAB-12639 | 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

Capture-C at paralogous gene loci in Drosophila embryos

Project description:Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from fixed 3-18h Drosophila whole embryo samples. Capture-C was performed on wildtype and embryos with deletions or insertions at loop anchors/genes at the respective loci (scyl-chrb or tsh-tio). Capture-C was performed using two different Capture probe pools, one indicated as left (scyl, tsh, salm) and one as right (chrb, tio, salr).

2023-12-07 | E-MTAB-13271 | biostudies-arrayexpress

AcceSssIble: an array-based assay for the study of chromatin accessibility and DNA methylation using the CpG methyltransferase SssI

Project description:Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Intact nuclei are harvested from cells and treated with M.SssI. DNA is then extracted, bisulfite converted and run on an Infinium methylation array, along with a no-enzyme control. Background subtracted beta values (listed below) are used to determine regions that have gained methylation on enzyme treatment compared to the control - and these are used to infer chromatin state

2013-03-08 | E-GEOD-36580 | biostudies-arrayexpress

Functional DNA methylation is accompanied by chromatin accessibility [methylation]

Project description:Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes. Intact nuclei are harvested from cells and treated with M.SssI. DNA is then extracted, bisulfite converted and run on an Infinium methylation array, along with a no-enzyme control. Background subtracted beta values (listed below) are used to determine regions that have gained methylation on enzyme treatment compared to the control - and these are used to infer chromatin state

2013-03-08 | E-GEOD-43851 | 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