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Annotation of estrogen-regulated enhancer RNAs [PRO-cap]

ABSTRACT: To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used precision nuclear run-on and sequencing of capped RNA (PRO-cap) to determine the transcription start sites of eRNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE175467 | GEO | 2022/06/16

REPOSITORIES: GEO

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Annotation of estrogen-regulated enhancer RNAs [RNA-seq]

Project description:To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used RNA-sequencing of polyA-depleted and polyA-enriched RNA fractions to assemble the gene bodies of eRNAs.

2022-06-16 | GSE175468 | GEO

Annotation of estrogen-regulated enhancer RNAs [PRO-cap]

Project description:Annotation of estrogen-regulated enhancer RNAs [PRO-cap]

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PRO-cap from K562 (ENCSR604EBH)

Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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PRO-cap from K562 (ENCSR261KBX)

Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and PCR amplification was performed before sequencing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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PRO-cap from K562 (ENCSR756TPG)

Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and no PCR amplification was done. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2022-12-04 | GSE219707 | GEO

PRO-cap from K562 (ENCSR149ZRX)

Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and PCR amplification was performed before sequencing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2022-12-04 | GSE219507 | GEO

Characterization of human malaria parasite Plasmodium falciparum eIF4E homologue and mRNA 5â² cap status

Project description:The mRNA 5â² cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5â² capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5â² cap binding activity. We used this protein to purify P. falciparum full-length 5â² capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5â² capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA The microarray data were obtained from four hybridizations using RNA from two independent GST-PfeIF4E purifications from separate malaria cultures.

2010-06-10 | E-GEOD-6356 | biostudies-arrayexpress

Characterization of human malaria parasite Plasmodium falciparum eIF4E homologue and mRNA 5′ cap status

Project description:The mRNA 5′ cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5′ capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5′ cap binding activity. We used this protein to purify P. falciparum full-length 5′ capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5′ capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA

2007-07-07 | GSE6356 | GEO

The RNA NAD+ cap is widespread in the Arabidopsis transcriptome and probably promotes translation

Project description:As the most common mRNA cap, the m7G cap impacts the fate of an mRNA in eukaryotes. The metabolite and redox agent, nicotinamide adenine diphosphate (NAD+), can be used as an initiating nucleotide in RNA synthesis to result in NAD+-capped RNAs. Such RNAs have been identified in bacteria, yeast, and human cells, but it is not known whether they exist in plant transcriptomes. The functions of the NAD+ cap in RNA metabolism or translation are still poorly understood. Here, through NAD captureSeq, we show that NAD+- capped RNAs are widespread in Arabidopsis thaliana. NAD+-capped RNAs are predominantly messenger RNAs encoded by the nuclear and mitochondrial genomes but not the chloroplast genome. NAD-capped transcripts from the nuclear genome appear to be spliced and polyadenylated. Furthermore, although NAD+-capped transcripts constitute a small proportion of the total transcript pool from any gene, they are enriched in the polysomal fraction and associate with translating ribosomes. Our findings implicate the existence of as yet unknown mechanisms of translation initiation on NAD+-capped mRNAs. More importantly, our findings suggest that cellular metabolic and/or redox states may influence, and maybe regulated by, mRNA NAD capping.

2019-06-03 | GSE127002 | GEO

Effect of cold atmospheric plasma (CAP) on MCF-7 breast cancer cell (Illumina HumanHT-12 V4.0 beadchip)

Project description:genom-wide expression profiling of MCF-7, MCF-7 and CAP-treated MCF-7 cell. In result, cold atmospheric plasma different effect the CAP-treated MCF-7 breast cancer cell.

2019-07-26 | GSE110117 | GEO

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