Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

78 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitoribosome profiling (MitoRiboSeq) data from HEK WT and mtRF1 knockout cell lines

ABSTRACT: Mitochondrial translation was investigated by mitochondrial ribosome profiling (mitoRiboSeq) in three HEK293 cell lines: HEK293 wildtype, mtRF1 knockout 1, and mtRF1 knockout 2

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Yong Liu

PROVIDER: E-MTAB-11687 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChRO-seq on TeloHAEC cells before and after TNFα stimulation

Project description:We performed chromatin run on and sequencing (ChRO-seq) on TeloHAEC cells before and after TNFα stimulation to map locations of RNA polymerase and quantify nascent transcription at RELA peaks.

2020-08-20 | E-MTAB-9425 | biostudies-arrayexpress

Regulation of co-transcriptional splicing by RNA-binding protein PTBP1

Project description:We examined the role of PTBP1 in regulation of co-transcriptional splicing process by depleting this RNA-binding protein from embryonic stem cells using the auxin-inducible degron technology and analysing the total and chromatin-associated RNA fractions by RNA-seq. We also performed mNET-seq and ChIP-seq analyses using RNA polymerase II- and PTBP1-specific antibodies, respectively. Our data suggest that PTBP1 activates co-transcriptional splicing of hundreds of introns, a surprising effect given that PTBP1 is better known as a splicing repressor. Importantly, some co-transcriptionally activated introns fail to be spliced post-transcriptionally without PTBP1. In a striking example of this regulation, lasting retention of a PTBP1-dependent intron triggers nonsense-mediated decay of mRNAs encoding DNA methyltransferase DNMT3B, explaining their natural expression dynamics in development. Our further analyses suggest that this mechanism may protect differentiation-specific genes from aberrant methylation. We conclude that PTBP1-activated co-transcriptional splicing underlies biologically important decisions.

2023-01-08 | E-MTAB-11544 | biostudies-arrayexpress

HyPro-seq analysis of HeLa and ARPE-19 cells

Project description:The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. We developed a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. To generate the HyPro-seq dataset reported here, fixed and permeabilized human cells were hybridized with digoxigenin-labeled oligonucleotide probes against noncoding RNAs 45S, NEAT1 or PNCTR and transcripts co-localizing with these RNAs were biotinylated in situ using a custom-engineered HyPro enzyme containing a digoxigenin-binding domain. Biotinylated RNAs were then purified and sequenced using the NextSeq 500 Illumina platform.

2021-11-05 | E-MTAB-10365 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Project description:Rag1 and Rag2 gene expression in CD4+CD8+ double positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes. Sequencing of Satb1-ChIP and input control from 6 wk old thymus

2015-02-25 | E-GEOD-66248 | biostudies-arrayexpress

A comparison of the effects of duplex-specific nuclease, antisense oligonucleotides, and riboZero rRNA depletion on ribo-Seq data from mouse

Project description:Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. A key step is the depletion of ribosomal RNA that allows sufficient depth of sequencing of the mRNA undergoing ribosomal translation. These data are designed to compare four strategies for ribosomal depletion; a novel strategy based on duplex-specific nuclease using either one or two cycles, the antisense oligonucleotides described in Ingola et al (2012) and the commercially available RiboZero kit (with a no treatment control).

2015-10-16 | E-MTAB-3583 | biostudies-arrayexpress

Translation Complex Profiling analysed using sequencing (TCP-seq) applied to fission yeast cells (Schizosaccharomyces pombe)

Project description:Translation complexes are stabilised in vivo using formaldehyde. Cells are lysed, and cell extracts are treated with RNase I to produce protected RNA fragments (FPs or footprints). Extracts are then run through sucrose gradients to separate small ribosomal subunits and full ribosomes. FPs are isolated from each of these fractions and analysed by sequencing. Note this is a modified version of ribo-seq (a.k.a. ribosome profiling)

2022-12-02 | E-MTAB-12264 | biostudies-arrayexpress

Transposable element expression at unique loci in single cells with CELLO-seq

Project description:We introduce a novel method (CELLO-seq) for long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and Transposable Element (TE) expression at unique loci. We use CELLO-seq to assess the widespread expression of TEs in 2-cell mouse blastomeres as well as human induced pluripotent stem cells (hiPSCs). Across both species, old and young TEs showed evidence of locus-specific expression, with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed surprising heterogeneity, with TEs within a class showing different patterns of correlation, suggesting distinct regulatory mechanisms. CELLO-seq thus represents a significant advance in the research of TEs, highlighting that studying TEs in single cells and at single loci resolution is necessary for understanding how such elements are regulated and for gaining insight into their role during development.

2020-10-01 | E-MTAB-9577 | biostudies-arrayexpress

CUT&RUN of histone modifications, chromatin remodelers, and transcription factors in forelimbs, hindlimbs, liver and branchial arches of E10.5 and E11.5 JAX/Swiss mouse embryos

Project description:Using CUT&RUN, we systematically measured the genome-wide binding profiles of key transcription factors and cofactors that track the activity of ontogenetically relevant signaling pathways in developing mouse tissues. This produced numerous genome-wide biding tracks for different tissues at two developmental stages in biological duplicate. Submitted files include raw fastq files, bigwig files from merged biological replicates, and peak sets.

2024-08-12 | E-MTAB-14340 | biostudies-arrayexpress

PRO-seq (Precision Run-On sequencing) to profile nascent RNA of H3.3 mutant (K9A; K27A; K79A) and control mESCs

Project description:Mouse embryonic stem cells (i.e., mESCs; line ESC 129-B13) were genetically modified using CRISPR-Cas9 to mutate the H3f3b locus, in order to carry homozygous lysine-to-alanine substitution of residues K9 or K27. Two control mESC lines carrying knock-out of the H3f3a gene were used as background for the editing. To profile nascent RNA levels in H3.3 mutant and control mESCs, two rounds of PRO-seq experiment were performed. In the first round, three replicates each of H3.3K9A and control (i.e., Ctrl_9) mESCs were used. In the second round, two replicates each of H3.3K27A and control (i.e., Ctrl_27) mESCs were used. After permeabilization of the mESCs (and addition of 5% Drosophila S2 cells spike-in), a 2 biotin run-on reaction using biotin-11-UTP and biotin-11-CTP was carried out to label nascent transcripts. Biotinylated nascent RNA was then enriched as part of the library preparation process. Sequencing was performed on a NextSeq500 platform in single-end mode (75bp reads). The experiment allows for an assesment of the changes in the activity of cis-regulatory elements, upon removal of H3.3 K9 or K27 residues.

2024-09-04 | E-MTAB-12869 | 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