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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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M6A-RIP sequencing from primary human foreskin keratinocytes (HFKs) and HPV 31 positive cervical keratinocytes (CIN 612).

ABSTRACT: Differentially m6A modified transcripts were identified between normal and HPV positive cells

INSTRUMENT(S): Illumina HiSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Conor Templeton

PROVIDER: E-MTAB-16071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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m6A-RIP sequencing from primary human foreskin keratinocytes (HFKs) and HPV 31 positive cervical keratinocytes (CIN 612).

Project description:m6A-RIP sequencing from primary human foreskin keratinocytes (HFKs) and HPV 31 positive cervical keratinocytes (CIN 612).

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RNA-sequencing of scrambled control CIN 612 cells and CIN 612 cells depleted of senataxin (SETX) through stable expression of shRNAs

Project description:HPV 31 positive cervical keratinocytes (CIN 612 cells) were transduced with lentiviruses to stably express either a scramble control sequence (Scrm CIN 612) or shRNAs targeting the RNA helicase, senataxin (SETX). RNA sequencing was performed on these cell lines to identify cellular genes whose expression was regulated by SETX expression. The experiment was done in biological duplicate, and two different shRNA sequences were used (shSETX1/13 and shSETX2/30).

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Chromatin immunoprecipitation sequencing of senataxin binding within CIN 612 cells

Project description:Analysis of sentaxin binding sites within HPV 31 positive CIN 612 cells using chromatin immunoprecipitation assays

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An integrative multi-omic analysis reveals a major metabolic rewiring between baby foreskin keratinocytes and adult female abdominal keratinocytes.

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m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency

Project description:N6-methyladenosine (m6A) has been recently identified as a conserved epitranscriptomic modification of eukaryotic mRNAs, but its features, regulatory mechanisms, and functions in cell reprogramming are largely unknown. Here, we report m6A modification profiles in the mRNA transcriptomes of four cell types with different degrees of pluripotency. Comparative analysis reveals several features of m6A, especially gene- and cell-type-specific m6A mRNA modifications. We also show that microRNAs (miRNAs) regulate m6A modification via a sequence pairing mechanism. Manipulation of miRNA expression or sequences alters m6A modification levels through modulating the binding of METTL3 methyltransferase to mRNAs containing miRNA targeting sites. Increased m6A abundance promotes the reprogramming of mouse embryonic fibroblasts (MEFs) to pluripotent stem cells; conversely, reduced m6A levels impede reprogramming. Our results therefore uncover a role for miRNAs in regulating m6A formation of mRNAs and provide a foundation for future functional studies of m6A modification in cell reprogramming. m6A-seq in ESC, iPSC, NSC and sertoli cells.

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Placental epitranscriptome-wide analysis of revealed the m6A modification level at 5’ UTR related fetal growth

Project description:To further understand the relationship between the level of gene expression and protein translation in human placenta, we focused on N6-methyladenosine: m6A, which is a methylation modification of mRNA acting as a post-transcriptional regulation which has drawn attention in recent years. It is said that m6A affects the fate of mRNA. In addition, it is thought that m6A affects gene expression in the placenta of preeclampsia which is a representative disease of perinatal period and fetal growth abnormality, and the placentas of children who were small for date (SFD) or heavy for date (HFD) were studied in addition to appropriate for date (AFD) preganancies. The SFD placentas contained half of the cases with PE. HEK293T cell was used to confirm the experimental system. PolyA RNA was purified from each tissue and cell, and libraries were prepared from immunoprecipitated (IP) samples using anti-m6A antibody and input samples, and sequenced with Hiseq 1500/2500 and RNAseq was carried out.

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Profiling of mRNA N6-Adenosine Methylation (m6A) in Arabidopsis

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m6a peak analysis in normal, FTO deficient and five stages of adipogenesis (D-2/0/2/5/10) in Mouse embryo fibroblast 3T3-L1 pre-adipocytes

Project description:Total RNA was extracted using TRI® Reagent (Sigma). cDNA was synthesized by RevertAid™ First Strand cDNA Synthesis Kit with Oligo dT primers (K1622, Fermentas) following manufacturer’s recommendations. PCR reactions were carried out on a DNAEngine® Thermal Cycler (PTC-0200G, Bio-Rad) in 25 μl reaction volume containing 1 μl cDNA, 200 nM primer pairs and components of TaKaRa Taq™ kit (R001A, Takara). All samples were analyzed in triplicate RT-qPCR.mRNAs were extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen). Then mRNAs were fragmented into 100-200nt length and subjected to immunoprecipitation with m6A specific antibody.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane. discovery of the binding motif of m6a in normal, FTO deficient and five stages of adipogensis (D-2/0/2/5/10) in Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes

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m6A mapping in human RNA (untreated)

Project description:We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Identification of m6A modified sequences in HepG2 cells.

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Metabolic rewiring in keratinocytes by miR-31-5p identifies therapeutic intervention for psoriasis.

Project description: Not available

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