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

Coilin's RNA, DNA and protein interactomes redefine the Cajal body as a hub for small non-coding RNAs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Karla Neugebauer

PROVIDER: E-GEOD-58451 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

iCLIP mapping of coilin-RNA interactions in HeLa and P19 cells

Project description:Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis. 5 biological replicates from P19 and 2 biological replicates from HeLa cells after UV-crosslinking. Negative control samples prepared from GFP-NLS fusion protein are stored uder accession E-MTAB-747.

2014-11-06 | E-GEOD-58448 | biostudies-arrayexpress

Coilin ChIP-seq in cycling HeLa cells

Project description:To investigate location of Cajal bodies (CB) inside the cell nucleus, we created a stable cell line expressing the GFP version of CB-marker protein coilin at endogenous levels and performed ChIP-seq with anti-EGFP antibody. ChIP-seq revealed close association of CBs wih U3 genes, snRNA genes and histone genes in histone cluster 1 and 2. 1 biological replicate of coilin ChIP-seq and input sample

2014-11-06 | E-GEOD-58449 | biostudies-arrayexpress

iCLIP analysis of EZH2-interacting RNAs

Project description:RNAs directly interacting with EZH2 were isolated from human colorectal HCT116 cells using an in vivo crosslinking and immunoprecipitation strategy (iCLIP, König J et al, Nat Struct Mol Biol 2010) coupled to an ultrasequencing approach. RIP sequencing for 1 Human sample

2012-04-23 | E-GEOD-36070 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-28 | E-GEOD-77634 | biostudies-arrayexpress

Genome wide mapping of long range contacts unveils DNA Double Strand Breaks clustering at damaged active genes.

Project description:Translocations, that occur when two DNA Double Strand breaks (DSBs) are abnormally rejoined, represent highly deleterious genome rearrangements favoring cancer apparition and progression. However, the mechanisms that drive their formation are yet poorly deciphered. One prerequisite for translocation is the juxtaposition of two distant DSBs, an event that would be favored if DSB cluster, i.e. are brought together in close spatial proximity within the nucleus. Whether DSB cluster in higher eukaryotes has been subjected to a strong controversy over the past decade, due to conflicting results obtained using microscopy based methods1-9. Here we used for the first time a high throughput chromosome conformation capture assay (Capture Hi-C10) to investigate DSB clustering. We unambiguously found that DSBs do cluster in human nuclei but only when induced in transcriptionally active genes. Clustering of damaged genes mainly occur during the G1 cell cycle phase and coincide with delayed repair. Moreover DSB clustering depends on the MRN complex, as well as the Formin 2 (FMN2) nuclear actin organizer and the LINC (LInker of Nuclear and Cytoplasmic skeleton) complex, suggesting that active mechanisms promote DSB clustering. This work reveals that when damaged, active genes exhibit a very peculiar behavior compared to the rest of the genome, being mostly left unrepaired and clustered in G1 while being repaired by homologous recombination in post-replicative cells.

2017-04-19 | E-MTAB-4846 | biostudies-arrayexpress

Androgen Promotes Differentiation of Promyelocytic Leukemia Zinc Finger (PLZF)+ Spermatogonia pool via Indirect Regulatory Pattern

Project description:We examined a regulatory role of the AR during the process of spermatogenesis. Using a SSCs-Sertoli cells co-culture system, we demonstrated that androgen negatively regulated Plzf in SSCs that co-exist with Sertoli cells. In addition, we identified Gata2 as a target of AR in Sertoli cells, and subsequently observed that Wilms tumor 1 (WT1) and β1-integrin as two putative intermediate molecules to transfer the differentiation signals to SSCs. This signal pathway was further verified using androgen pharmacological deprivation mice model. These results demonstrate a regulatory pattern of androgen in SSCs niche, that androgen turns off the stemness maintenance switch PLZF in undifferentiated spermatogonia populations to promote spermatogenesis in an indirect way via multiple steps of signal transduction.

2019-02-28 | E-MTAB-7129 | biostudies-arrayexpress

Herbal formula YYJD induces lung cancer cell apoptosis via activation of EGR1

Project description:In this study,we demonstrated the transcription factor EGR1 is activated by TCM YYJD and such activation mediated YYJD-induced apoptosis in lung cancer cells and provided a novel insight to understand the anti-tumor mechanism of Chinese herb YYJD.

2018-11-01 | E-MTAB-7236 | biostudies-arrayexpress

ChIP-Seq mapping of histone modifications at multiple DNA Double Strand Breaks

Project description:DNA Double Strands Breaks (DSBs) are highly detrimental since they can lead to mutations and chromosomes rearrangements (amplification, deletion, translocation and chromosome loss). Here, we used in a standardized system, where multiples DSBs are induced at defined positions across the human genome (U2OS-DIvA cells), to describe the distribution of eighteen histone modifications before and after damage using ChIP-Seq. This provides a comprehensive picture of the chromatin landscape induced at DSBs.

2018-09-27 | E-MTAB-5817 | biostudies-arrayexpress

Individual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments. 3 biological replicates of hnRNP L-specific and control (Flag) co-immunoprecipitated RNA after UV-crosslinking in HeLa cells

2014-02-13 | E-GEOD-37560 | 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