Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide analysis of RNA N6-methyladenosine in Adriamycin-resistant acute myeloid leukemia cells

ABSTRACT: N6-Methyladenosine (m6A) is the most abundant post-transcriptional modification in eukaryotes, the imbalance of which is reported to be associated with various pathological processes, including drug resistance. In this study, we analyzed the methylated RNA immunoprecipitation combined with next-generation sequencing (MeRIP-seq) data of AML cell line HL60 and its adriamycin-resistant cell line HL60/ADR. We found a total of 40550 peaks, representing 15640 genes in HL60, and a total of 38834 peaks, representing 15285 genes in HL60/ADR. A total of 4437 differentially methylated m6A peaks within 3461 genes have been found between HL60 and HL60/ADR. Among them, 3587 differentially m6A peaks within 2790 genes were hyper-methylated, and 850 m6A peaks within 671 genes were hypo-methylated. KEGG pathway analysis showed that pathways were enriched in tumor and drug-resistant related signaling pathway. Results of MeRIP-seq showed that fold enrichment of global m6A peaks was higher in HL60/ADR compared to HL60. This study provides a framework for the application of comprehensive mRNA m6A profiling towards acute myeloid leukemia cell line (HL60) and its adriamycin-resistant acute myeloid leukemia cell line (HL60/ADR).

ORGANISM(S): Homo sapiens

PROVIDER: GSE192618 | GEO | 2021/12/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of m6A methylome in ABRO1 Knockout heart

Project description:To find the m6A methylation targets of ABRO1, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in ABRO1 Knockout or Wild type (WT) mice heart. The analysis of the distribution of m6A peak density in mRNA transcripts showed that m6A peaks are mainly found in coding sequences (CDS) and a considerable amount of m6A peaks enriched around start codon and stop codon regions in mRNA transcripts from ABRO1 KO and WT hearts. Among the total RNA transcripts with m6A sites, more than half (59.4%) of mRNA transcripts contain ≤ 2 m6A peaks, 27.4% mRNA transcripts comprise 3 to 5 m6A peaks and more than 5 m6A peaks exist in 13.2% of mRNA transcripts. MeRIP-seq analysis results from ABRO1 deleted hearts showed that a total of 3444 m6A peaks were upregulated and 4631 m6A were downregulated compared to WT hearts.

2023-12-01 | GSE188518 | GEO

RNA seq analysis of A2780 and A2780-ADR

Project description:We compared the global RNA expression level between doxorubicin-sensitive human ovarian cancer cell line A2780 and the adriamycin-resistant cell line A2780-ADR to elucidate the drug resistant related molecular mechanisms or targets.

2022-12-09 | GSE177038 | GEO

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

Project description:In present study, we first tried to reveal the transcriptome-wide m6A methylation pattern in boar fresh sperm (Fs) and frozen-thawed sperm (Fts) through MeRIP-seq, which demonstrates occurrence the diverse m6A modiﬁcation patterns during cryopreservation. Results: the expression of m6A modification enzymes were significantly dysregulated in sperm during cryopreservation. Furthermore, the m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. In Fts, a total of 1754 differentially methylated m6A genes containing 1928 differentially methylated peaks were identified as compared to Fs. Bioinformatics analysis revealed the role of these genes containing significantly altered m6A peaks (DMMGs) were significantly enriched in terms of metabolism and transcription, as well as a number of DMMGs were annotated to ubiquitin mediated proteolysis, AMPK, mTOR and MAPK signaling pathways. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusion: Our study is first to reveal the dynamic m6A modification in mRNAs of boar sperm during cryopreservation, and provides a new evidence regarding the potential roles of m6A in modulating sperm motility, apoptosis and metabolism. Keywords: N6-methyladenosine (m6A); Boar sperm; Cryopreservation; MeRIP-seq

2021-06-09 | GSE164691 | GEO

Genome-wide identification of N6-methyladenosine by microarray

Project description:Although internal PolyA RNA modification N6-methyladenosine (m6A) plays essential roles in diverse biological processes, technology to detect precise m6A sites at transcriptome-wide scale is lacking. Here, we discovered that m6A interferes A (Adenine) – U (Uracil) or A-T (Thymidine) pairing. Based on differential hybridization between methylated vs. unmethylated RNAs to a DNA probe, we developed tiling microarray to pinpoint m6A sites in mouse transcriptome. We validated some of the identified sites and provided evidence to suggest that one functional mechanism of m6A is to block small RNA targeting to methylated mRNA. We designed a custom tiling array with to examine the precise location of m6A within meRIP-seq peaks from mouse embryonic stem cells determined in our previous publication (Wang et al., 2014). Each custom two-channel Agilent tiling array harbors 947,952 probes. Each probe is 25 nucleotides (nt), and any two adjacent probes in the genomic coordinate overlap each other by 19 nt. The Cy5 or red channel corresponds to Mettl14 knockout (M14) or DZA mutant mESC cell line, and Cy3 or green channel is associated with wild type cell line treated with scramble hairpin (SCR). Thus, in principle a higher Cy5/Cy3 signal for each probe reflects an increased hybridization to the oligonucleotide due to de-methylation of a particular RNA molecule in M14 or DZA condition relative to the SCR control. Moreover, we employed additional arrays with both channels dedicated for M14 as an external control for technical difference between the Cy5 and Cy3 dye (details below). For each comparison, we have three biological replicates, and therefore there are 9 tiling arrays in total (i.e., 3 arrays for M14 vs SCR, 3 arrays for DZA vs SCR, and 3 arrays for M14 vs M14).

2015-09-08 | E-GEOD-62530 | biostudies-arrayexpress

MeRIP sequencing

Project description:In this study, we aimed to systematically profile global RNA N6-methyladenosine (m6A) modification patterns in a mouse model of diabetic cardiomyopathy (DCM). Patterns of m6A in DCM and normal hearts were analyzed via m6A-specific methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). A total of 973 m6A peaks were detected in DCM samples and 296 differentially methylated sites were selected for further study, including 106 hypermethylated and 190 hypomethylated m6A sites (fold change (FC) > 2, p < 0.05). Gene ontology and KEGG Pathway analyses indicated that unique m6A-modified transcripts in DCM were closely linked to cardiac fibrosis, myocardial hypertrophy, and myocardial energy metabolism. Overall, m6A modification patterns were altered in DCM, and modification of epitranscriptomic processes, such as m6A, is a potentially interesting therapeutic approach.

2021-05-25 | GSE173384 | GEO

MeRIP-seq of mRNAs in MEFs with or without nutrient starvation

Project description:To investigate the dynamic m6A modification during starvation-induced autophagy, we performed MeRIP-seq in MEFs with or without nutrient deprivation and identified the variations of m6A modification on mRNAs. Briefly, the total polyadenylated mRNAs in MEFs cultured with or without nutrient-deprived medium for 2 hours were isolated using RNAiso plus reagent (Takara) followed Dynabeads mRNA Purification Kit (Invitrogen). The m6A RNA immunoprecipitation was performed using GenSeq m6A RNA IP Kit. NEBNext Ultra II Directional RNA Library Prep Kit (NEB) was used for library generation. Each experiment was conducted in two biological replicates. Methylated sites on peaks were identified by MACS2 peak-calling software (Zhang et al., 2008). Differentially methylated sites were identified by diffReps (Shen et al., 2013) with default setting.

2021-12-30 | GSE158268 | GEO

Analysis of m6A methylome in CHAPIR overexpressed heart [MeRIP]

Project description:To elucidate the molecular mechanism by which cardiac-hypertrophy-associated piRNA (CHAPIR) regulates m6A modification, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control or CHAPIR-overexpressing mice heart. The sequential analysis of m6A peaks showed that RGACH motif was highly enriched within m6A sites in heart and that is aligning with the classical consensus sequence of mammals ‘RGACH’, where ‘R’ indicates purine (A/G) and ‘H’ indicates non-guanine base (A/C/U). In CHAPIR treated heart, m6A mostly occurred in mRNAs (89.5%) and only about 10.5% were identified in non-coding RNAs. The majority of mRNAs contain one or two m6A peaks (89.2%) and 10.8% mRNA contain >2 m6A peaks . M6A peaks were predominantly distributed in coding sequences (CDSs), 3’ untranslated regions (3’UTRs) and near stop codon.

2020-07-24 | GSE154699 | GEO

m7G-MeRIP-sequencing of mRNA in drug-resistant acute myeloid leukemia

Project description:m7G-MeRIP-sequencing for AML cells(HL-60) and drug-resistant AML Cells(HL60/MX2).

2022-04-23 | GSE201096 | GEO

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [RNA-seq]

Project description:To determine the targets underlying ALKBH5 during head and neck squamouse cell carcinoma progression, Methylated RNA immunoprecipitation (MeRIP) with an m6A specific antibody followed by RNA sequencing (MeRIP-seq) and next generation sequencing were combined to screen the potential targets haboring m6A modificatios and mRNA level alteration after ALKBH5 knockdown in a HNSCC cell line.

2022-04-13 | GSE185886 | GEO

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq]

2022-04-13 | GSE185885 | GEO