GEO DataSets

(Submitter supplied) N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification, present on tRNA, rRNA and recently investigated in eukaryotic mRNA. We report ac4C-seq, a chemical genomic method for single-nucleotide resolution, transcriptome-wide quantitative mapping of ac4C. While we did not find detectable ac4C sites in human and yeast mRNAs, ac4C was induced via ectopic overexpression of eukaryotic acetyltransferase complexes, invariably at a conserved sequence motif. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens; Thermococcus sp. AM4; Thermococcus kodakarensis; Pyrococcus furiosus; Methanocaldococcus jannaschii; Saccharolobus solfataricus

Type:

Other

8 related Platforms

96 Samples

Download data: XLSX

(Submitter supplied) Generation of the "epitranscriptome through post-transcriptional ribonucleoside modification embeds a layer of regulatory complexity into RNA structure and function. Here we describe N4-acetylcytidine (ac4C) as an mRNA modification that is catalyzed by the acetyltransferase NAT10. Transcriptome-wide mapping of ac4C revealed discretely acetylated regions that were enriched within coding sequences. Ablation of NAT10 reduced ac4C detection at the mapped mRNA sites and was globally associated with target mRNA down-regulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL18573

41 Samples

Download data

(Submitter supplied) As obligate parasites, viruses need to navigate a variety of cellular regulatory systems while infecting and replicating in the host cell. Post-transcriptional modifications have recently emerged as an important layer of regulation of viral RNA function. For example, our lab and others have shown that the RNA modification N6-methyladenosine (m6A) can enhance the replication of multiple viruses in cis, including Human Immunodeficiency virus 1 (HIV-1), Influenza A virus, SV40 and Kaposi's sarcoma-associated herpesvirus (KSHV). more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20301 GPL18573 GPL24676

12 Samples

Download data: BED

(Submitter supplied) mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. While cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5’UTRs impacts protein synthesis at the level of initiation. 5’UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. more...

Organism:

Homo sapiens; Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

19 Samples

Download data: TSV, TXT, XLS

(Submitter supplied) To evaluate ac4C acetylation in the spinal dorsal horn of rats with bone cancer pain.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25947

16 Samples

Download data: TXT

(Submitter supplied) NAT10 is an RNA cytidine transferase known to add acetyl group on RNA transcripts thereby promoting translational efficiency. It was reported that NAT10 regulates epithelial to mesenchymal transition (EMT), DNA damage, and cell proliferation in cancers. However, weather NAT10 regulates other crucial pathways is unknown. In our study we conducted gene expression profiling analysis using data obtained from RNA-seq of MCF7 NAT10 KO and scramble control. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: XLS

(Submitter supplied) We show that non-toxic exogenous palmitate uptake in MCF7 cells promotes NAT10 expression and NAT10-dependent ac4C RNA modification. It was previously reported that NAT10 modulates the addition of ac4C on RNA transcripts in normal and cancer conditions. However, no study report the impact of NAT10 in palmitate driven cells. Here we performed RNA immunoprecipitation sequencing (RIP-seq) in palmitate loaded MCF7 knockdown with NAT10 siRNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: BW

(Submitter supplied) tRNAs are subject to numerous modifications including methylation. Mutations in the human N7-methylguanosine (m7G) methyltransferase complex METTL1-WDR4 cause primordial dwarfism and brain malformation yet the molecular and cellular function in mammals is not well understood. We developed m7G methylated tRNA immunoprecipitation sequencing (MeRIP-Seq) and tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome in mouse embryonic stem cells (mESCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

26 Samples

Download data: TXT

(Submitter supplied) We determined the enrichment of mRNA in stress granules in WT and NAT10 KO cells to assess the impact of RNA acetylation on stress granule mRNA localization.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

16 Samples

Download data: TXT, XLSX

(Submitter supplied) To resolve the patterns of TILs in HCC, we performed scRNA-seq on the TILs isolated from the three groups (P: control group, T: immunotherapy group, TR: immunotherapy plus REM group; n=2 per group) at two time points (1 w and 2 w)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

12 Samples

Download data: TAR

(Submitter supplied) Ac4C-binding RNAs were analyzed by imprinting RNA-sequencing of anti-Ac4C antibody-retrieved complexes from macrophages lysate. We then performed gene expression profiling analysis using data obtained from RIP-seq of peritoneal macrophages incubated with IFN-G

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

12 Samples

Download data: TSV

(Submitter supplied) To investigated how NAT10 inhibitor (Remodelin hydrobromide) affected the function of peritoneal macrophages , we treated peritoneal macrophages IFN y，Remodelin hydrobromide and Remodelin hydrobromide with IFN y. We then performed gene expression profiling analysis using data obtained from RNA-seq of peritoneal macrophages with four treaments

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) Using acRIP-seq, we present transcriptome-wide atlases of ac4C in Arabidopsis thaliana and Oryza sativa. Analysis of ac4C distribution reveals ac4C is enriched near translation start sites in rice while near translation start sites and end sites in Arabidopsis. Further analysis shows ac4C contributes to RNA stability, splicing and translation. We then performed NaCNBH3 treatment and RNA-seq to measure C to T mutation and RNC-seq to measure translation efficiency in Arabidopsis.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

28 Samples

Download data: BW, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL23227 GPL24676

46 Samples

Download data

(Submitter supplied) NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. To investigate the effect of NAT10-mediated ac4C acetylation modification on RNA stability at the transcriptome scale, we performed high throughput RNA sequencing experiments of control and NAT10 KD hESCs at three time points each with 3 replicates.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

18 Samples

Download data: XLSX

(Submitter supplied) NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. To investigate the effect of NAT10-mediated ac4C acetylation modification on gene expression level, we performed high throughput RNA sequencing experiments of control and NAT10 KD hESCs each with 4 replicates.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

8 Samples

Download data: XLSX

(Submitter supplied) NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. To explore the transcriptome-wide profile of ac4C modification, we mapped the locations of ac4C modification on wild-type (WT) hESCs and NAT10 KD hESCs by high-throughput ac4C RNA immunoprecipitation sequencing (ac4C-RIP-seq).

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

12 Samples

Download data: XLSX

(Submitter supplied) NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. To explore the transcriptome-wide profile of ac4C modification, we mapped the locations of ac4C modification on wild-type (WT) hESCs and NAT10 KD hESCs by NaCNBH3-based chemical ac4C sequencing (ac4C-seq).

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

8 Samples

Download data: XLSX

(Submitter supplied) We show that NAT10-ac4C axis significantly regulates cell fates. To identify the molecular mechanisms of NAT10-ac4C-ANP32B axis in cell-fate transitions, we construct shNAT10 and shANP32B hESCs. acRIP-seq of shCTR and shNAT10 hESCs. We profiled ATAC-seq in shCTR, shNAT10, and shANP32B hESCs. We profiled H3K4me3 and H3K27me3 modifications and the binding of ANP32B by CUT&Tag in shCTR and shNAT10 hESCs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

44 Samples

Download data: BED, BW, MATRIX, NARROWPEAK, TXT

(Submitter supplied) To investigate the principal mechanism of NAT10 in cervical cancer, RNA-seq was accomplished in SiHa and Hela cells with NAT10 knockdown and in control cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT