Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA

ABSTRACT: Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA. Nuclei from three biological replicates were isolated by detergent lysis, fractionated, then three chromatin and three soluble RNA samples were converted to cDNA using Illumina TruSeq stranded protocol, and sequenced on Illumina HiSeq2000

ORGANISM(S): Homo sapiens

SUBMITTER: Alex Ruthenburg

PROVIDER: E-GEOD-66478 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation

Project description:The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation

2019-08-29 | PXD014287 | Pride

GUN1 controls the accumulation of NEP-dependent transcripts in Arabidopsis cotyledons

Project description:GUN1 proteins controls protein homeostasis in chloroplast development in cotyledons of the model plant Arabidopsis thaliana, via coordination of nuclear encoded polymerase (NEP)-dependent chloroplast genes expression with plastid encoded polymerase (PEP)-dependent chloroplast genes expression. Lack of GUN1 leads to development of abnormal plastids and, consequently, accumulation of nuclear-encoded chloroplast-targeted (NECT) proteins which in many cases have been found still in their precursor form. Data dependent acquisition (DDA) mass spectrometry analysis of cotyledons soluble fractions, as well as targeted proteomics analysis of specific FtsH protease forms recognized by FtsH antibodies in western blotting, have been performed to identify peptides from the chloroplast transit peptide (cTP) of NECT in cotyledons extracts of wild type and GUN1 knocked-out mutant plants. The aim was to compare the number of cTPs found in 6 days after sowing (DAS) seedlings grown on plates with or without the inhibitor of plastid translation lincomycin.

2019-11-15 | PXD015078 | Pride

Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA

Project description:Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA.

2015-03-04 | GSE66478 | GEO

Chromatin-enriched RNA sequencing of HL-1 mouse cardiomyocytes

Project description:Biochemical fractionation of HL-1 mouse cardiomyocyte nuclei and RNA-seq of chromatin-enriched and soluble-nuclear RNA

2023-12-31 | GSE164126 | GEO

Identification and functional characterization of long noncoding RNAs in breast cancer

Project description:In this study, we have integrated RNA-seq data from subcellular fractionated RNA (i.e., cytoplasm, nucleoplasm, and chromatin-associated) with GRO-seq data using a novel bioinformatics pipeline. This has yielded a comprehensive catalog of polyadenylated lncRNAs in MCF-7 cells, about half of which have not been annotated previously and about a quarter of which are estrogen-regulated. Knockdown of selected lncRNAs, such as lncRNA152 and lncRNA67 followed by RNA-seq suggest that these lncRNAs regulate the expression of cell cycle genes. characterization of long noncoding RNAs

2015-07-30 | E-GEOD-63189 | biostudies-arrayexpress

High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.

Project description:DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, implying that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis, as in cancer, or meiosis, leading to epiallelic variation. Here, we demonstrate the existence of an efficient and faithful mechanism that protects against transgenerational loss of DNA methylation in the plant Arabidopsis. This process is specific to the subset of heavily methylated genomic repeats that are targeted by the RNAi machinery, and does not spread into flanking regions. Remethylation is often progressive over two to four sexual generations. This differential and incremental correction of epigenetic defects may preserve genome stability while increasing adaptive opportunities. 2 samples examined: wild type, and ddm1 mutant.

2009-02-02 | E-GEOD-13419 | biostudies-arrayexpress

Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 3)

Project description:When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Ago2/microRNA machinery has been shown to participate in stress-induced translational upregulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by CLIP-seq. Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3` UTR and CDS sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2 binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA-seq. Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian microRNAs in mediating the translational component of the stress response. In this sub-series, CLIP and RNAseq data from the hippuristanol treatment experiment are presented. Experiments on 293S cells +/- hippuristanol treatment, in 2 biological replicates. Here, for each treatment/replicate sample, an aliquot was used for RNA-seq, and the rest was split into three aliquots to perform 3 parallel CLIP-seq protocols with different antibodies. So, each RNA-seq dataset here corresponds to 3 CLIP-seq datasets.

2013-07-15 | E-GEOD-44378 | biostudies-arrayexpress

Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 2)

Project description:When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Ago2/microRNA machinery has been shown to participate in stress-induced translational upregulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by CLIP-seq. Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3` UTR and CDS sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2 binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA-seq. Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian microRNAs in mediating the translational component of the stress response. In this sub-series, CLIP and RNAseq data from the emetine treatment experiment are presented. Experiments on 293S cells +/- emetine treatment, in 1 biological replicate. Here, for each treatment/replicate sample, an aliquot was used for RNA-seq, and the rest was split into three aliquots to perform 3 parallel CLIP-seq protocols with different antibodies. So, each RNA-seq dataset here corresponds to 3 CLIP-seq datasets.

2013-07-15 | E-GEOD-44377 | biostudies-arrayexpress

A Multi-omic Atlas of Human Embryonic Skeletal Development -Multiome GEX+ATAC

Project description:Two distinct and anatomically restricted modes of ossification, which are endochondral ossification and intramembranous ossification, govern osteogenesis and joint formation throughout the human skeleton and, to our knowledge, the cellular bases by which they form and mature remain incompletely described in human development at single-cell resolution. To address this, we apply single-nuclei paired RNA and ATAC sequencing to decipher the molecular gene regulatory programmes that mediate maturation of the distinct bone and joint-forming niches in the cranium and appendicular skeleton across space and time from 5-11 PCW.

2024-10-09 | E-MTAB-14385 | biostudies-arrayexpress

Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Project description:Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by UV light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain completely new insights into chromatin and its regulation in the future.

2020-10-20 | PXD020290 | Pride

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