Similar Datasets
Project description:IP with m6A-specific antibodies and Input sequencing for every sample.
2021-03-05 | GSE154555 | GEO
Project description:Purpose: Evaluation of the m6A modification of PRV and PK15 transcripts during PRV infection Methods: Porcine kidney cell line PK15 was uninfected or infected with PRV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 300-nucleoside-long fragments. Fragmented mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq libraries construction. The libraries were forwarded to sequencing run on Illumina NovaSeq 6000. Results: PRV transcripts were m6A modified during PRV infection and PRV infection changed m6A modification profiles of PK15 transcripts.
2022-11-02 | GSE209949 | GEO
Project description:Purpose: Evaluation of the m6A modification of EBV and BJAB transcripts during EBV infection Methods: Human B lymphoma cell line BJAB was uninfected or infected with EBV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 100-nucleoside-long fragments. m6A methylated mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq library construction. Sequencing was performed using an Illumina HiSeq 4000. Results: EBV EBNA2 and BHRF1 transcripts were m6A modified and m6A modification of BJAB transcripts changed during EBV infection. Conclusions: Our study found that some EBV transcripts were m6A modified during EBV infection and EBV infection changed m6A modification profiles of BJAB transcripts.
2021-07-10 | GSE133936 | GEO
Project description:N6-methyladenosine (m6A) is one of the most prevalent and abundant epigenetic modifications in various fundamental bioprocesses. We hypothesized that m6A-mediated inflammation pathway contributes to diabetes. Total RNA was extracted from the retinas of wide type rat and their littermates with diabetes by STZ injection. A total amount of 1 μg RNA per sample was used as an input for the RNA sample preparations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia), the reagents used in library preparation are NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) .After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. The MeRIP-seq was carried out in Novogene (Beijing, China). Briefly, 2 μg total RNA was extracted from the retinas of both wide type mice and their littermates with diabetes. The integrity and concentration of extracted RNA was detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented RNA (~100 nt) was incubated for 2 hours at 4 ℃ with anti-m6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated RNA or input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with three independent biological replicates.
2021-07-01 | GSE176353 | GEO
Project description:N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNA and potential regulatory functions of m6A have been shown by mapping the RNA m6A modification landscape. M6A modification in active gene regulation manifests itself as altered methylation profiles. However, the profiling of m6A modification and its potential role in gestational diabetes mellitus (GDM) has not yet been studied. In this work, placental samples were collected from GDM and control patients. MeRIP-seq was performed to identify differences in m6A methylation. Fragmented mRNAs were incubated for 2 h at 4 °C in the presence of 2 μg m6A antibodies (Synaptic Systems, 202003) in a 500 μl IP reaction system, and some of the fragments were used as input. RNA-seq libraries for m6A antibody-enriched mRNAs and input mRNAs were prepared using the KAPA Stranded mRNA-seq Kit (Illumina, CA, USA). Altered peaks of m6A-modified transcripts were primarily associated with mTOR signaling pathway, Notch signaling pathway, TGF-beta signaling pathway and so on. Our data provide novel information regarding m6A modification alterations in GDM and help our understanding of the pathogenesis of GDM.
2021-12-31 | GSE154413 | GEO
Project description:We report the application of specific antibodies and high-throughput sequencing technologies (methylated RNA immunoprecipitation sequencing, MeRIP-seq) for high-throughput profiling of m6A modifications in breast cancer herceptin resistant cells. We generated maps of m6A modified transcripts in BT474 and BT474.TtzmR cells. We find that the m6A level was significantly increased in BT474.TtzmR cells compared to the BT474 cells. We show that there was a close correlation between the m6A modification and herceptin resistance.
2024-11-18 | GSE189160 | GEO
Project description:MeRIP-Seq data aligned to the genome (GRCh38) for cells with IDH1-Mut or IDH1-WT genotypes. Aligned data (BAM) are separated into input RNA and m6A immunoprecipitated RNA for each cell sample.
2024-02-19 | E-MTAB-13765 | biostudies-arrayexpress
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
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
Project description:To investigate the role of m6A modification,MeRIP-seq was used to identify differential m6A modifications in lung adenocarcinoma .
2022-06-27 | GSE198288 | GEO