Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE158268 | GEO | 2021/12/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome-wide N6-methyladenosine modification profiling in patients with recurrent implantation failure (RIF)

Project description:Purpose:using m6A modified RNA immunoprecipitation sequence (m6A-seq), to establish the m6A methylation transcription profiles in recurrent implantation failure (RIF). Methods: GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) was used to construct RNA libraries for IP and input samples by following the manufacturer's instructions. The library quality was evaluated using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina 6000). Result:using m6A modified RNA immunoprecipitation sequence (m6A-seq), methylated sites in mRNA,lncRNA and circRNA are identified. Conclusions: Our study revealed the m6A methylation landscape by MERIP sequencing.

2022-10-16 | GSE205398 | GEO

Transcriptomic m6A MeRIP-seq in human metastatic ovarian carcinoma and in situ ovarian carcinoma tissue

Project description:To investigate the mRNA m6A modification profiling in human metastatic ovarian carcinoma and in situ ovarian carcinoma tissue, we performed m6A MeRIP-seq(GenSeq®️ m6A MeRIP Kit) with the total RNA extacted from these tissue samples.

2022-07-15 | GSE208023 | GEO

Mettl3-mediated m6A Methylation Determines the Size of Endocrine Progenitor Pool and Postnatal Islet Mass

Project description:To investigate the role of RNA methyltransferase-like 3 (Mettl3)-mediated m6A modification in pancreatic endocrine differentiation in early embryonic period. We then performed m6A MeRIP-seq (GenSeq®️ m6A MeRIP Kit) at E15.5 Mettl3pKO pancreas group and E15.5 WT pancreas group

2023-04-16 | GSE229502 | GEO

mRNA m6A MeRIP-seq of Mesocricetus auratus cell infected with Senecavirus A

Project description:To investigate the mRNA m6A modification profiling in Mesocricetus auratus cells that infected with Senecavirus, we used passage-5 Senecavirus A to infect BSR-T7/5 cells. We then performed m6A MeRIP-seq(GenSeq®️ m6A MeRIP Kit) at at two time points (12hrs or 72 hrs after infection), each time point with three replicates.

2022-06-30 | GSE206974 | GEO

m6A-RIP-seq of mRNA in HeLa cells undergoing EMT

Project description:We report the application of m6A-RIP-seq to indentify the m6A modifications variation in genes invovled in EMT. Briefly, total polyadenylated RNA was isolated from HeLa cells treated with or without 10 ng/ml TGF-β for 3 days by use of TRIZOL reagent followed the using of FastTrack MAGMaxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed according to instructions of manufacture and the previously published protocol (Wang et al., 2015). NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each experiment was conducted in two biological replicates. m6A-seq data were analyzed according to the protocols described before (Wang et al., 2015). Significant peaks with FDR < 0.05 were annotated to RefSeq database (hg19). Sequence motifs were identified by using Homer. Gene expression was calculated by Cufflinks using the sequencing reads from input samples. Cuffdiff was used to find the DE genes.

2019-03-25 | GSE112795 | GEO

The role of m6A methylation modification in CPB2 toxin treatment of porcine small intestinal epithelial cells

Project description:In this experiment, m6A-seq sequencing technology was used to study the functional role of methylated molecules in the process of CPB2 processing porcine small intestinal epithelial cells. In this experiment, an IP library and an input library were built together. The IP library was enriched with m6A specific antibodies to generate methylated RNA, and the influence of m6A methylation modification on its expression was analyzed by bioinformatics. We finally concluded that m6A methylation modification may play a very important role after CPB2 toxin treats small intestinal epithelial cells.

2021-10-05 | GSE167267 | GEO

Identification and N6-Methyladenosine Modification of the different genes in the peri-infarct cortex of PT mice response to circSCMH1 using MeRIP-seq.

Project description:Whole MeRIP-sequencing analysis was performed and analyzed by Lc. Aksomics Co. Ltd. (Shanghai, China). The peri-infarct cortex from sham mice, PT mice with EV-Vector, and PT mice with EV-circSCMH1 was collected in TRIzol. Total RNAs were qualified by agarose gel electrophoresis and quantified using Nanodrop. mRNA was isolated and then fragmented to 100-nucleotide-long fragments. m6A methylated mRNAs were enriched with anti-N6-methyadenosine(m6A) antibody. We use commercial kit for RNA-seq library prepa ration of m6A mRNA and input samples. Completed libraries were qualified and then sequenced on Hiseq 4000 platform.

2022-12-08 | GSE193633 | GEO

MeRIP sequencing reveals angiogenic properties of vascular endothelial cells

Project description:We report the application of MeRIP sequencing technology for high-throughput profiling of RNA m6A modifications in wide-type and knock-down METTL3 or WTAP Human Umbilical Vein Endothelial Cells (HUVECs). Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads. Clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. And, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. qRT-PCR validation was performed using SYBR Green assays. Finally, we find that METTL3/WTAP can regulate the expression level of target genes through m6A modification in HUVECs. This study provides a framework for applying MeRIP sequencing profiles to characterize vascular endothelial cells.

2019-12-20 | GSE142386 | GEO

Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (CLIP-Seq)

Project description:RNA was isolated from control and Mettl3 cKO mouse testes using the TRIzol (Invitrogen) reagent by following the manufactures's instructions. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. For RNA-seq, approximately 2.5 µg of total RNA was then used for library preparation using a KAPA Stranded mRNA-Seq Kit Illumina® platform (KAPABIOSYSTEMS, KR0960) according to the manufacturer’s protocol.For m6A-miCLIP-seq, 6 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403].All the libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

2017-08-16 | GSE99772 | GEO

Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (RNA-Seq)

2017-08-16 | GSE99771 | GEO