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RNA-Seq of WT and constitutively methylated mESCs

ABSTRACT: RNA-Seq of WT and constitutively methylated mESCs

PROVIDER: PRJNA495937 | ENA |

REPOSITORIES: ENA

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RNA-Seq of WT and constitutively methylated mESCs

Project description:WT J1 and 3B3L cells (in which Dnmt3B and Dnm3L are constitutively expressed from an exogenous construct) were cultured under both serum/LIF and 2i/LIF conditions. 3B3L cells do not show ground state-associated hypomethylation phenotype. This experiment sought to analyse the gene expression changes between the two conditions.

2019-02-01 | GSE121171 | GEO

Quantitative Analysis of Wild Type(wt) and Setd2 knockout(ko) mESCs Transcriptomes [RNA-Seq]

Project description:Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation. Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR. Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation. One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.

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Project description:Examination of transcriptional changes in WT vs. Prdm15 KO mESCs

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m6A-seq profiling in WT, WtapKO and Mettl3KO mESCs

Project description:m6A-seq profiling in WT, WtapKO and Mettl3KO mESCs

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H3K27me3 ChIP-seq in DNMT triple knock-out mESCs

Project description:We immunoprecipitated formaldehyde crosslinked chromatin from DNMT triple knockout cells using an antibody against methylated lysine 27 on histone H3. Subsequent high-throughput sequencing allowed us to study the genome-wide distribution of this histone mark in the absence of DNA methylation. Examination of a histone modification in mESCs lacking DNA methylation.

2014-03-22 | E-GEOD-56110 | biostudies-arrayexpress

WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

Project description:Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from the knockout of Hira in undifferentiated mouse embryonic stem cells (mESCs) and in day 15 differentiated cardiomyocytes.Methods: RNA extraction was done in duplicate from WT and Hira-null mESCs at day0 and day15 using TRIzol reagent. RNAseq was done onIllumina Nextseq500 and processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R2 package. Gene lists were filtered using adjusted p-value ≤ 0.05 and absolute fold change ≥ 2. Results:We identified 1680 transcripts changed in the absence of HIRA in day 15 differentiated cardiomyocytes. GO term cardiovascular system development was the most downregulated gene set(p-value ≤ 0.01 and FDR ≤0.1. Conclusion: this study analysis the role of HIRA in early cardiac mesoderm development usinf an invitro mESCs model.

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Small RNA profiling of WT E14, Ago2_KO and Ago1_KO mouse embryonic stem cells before and after XEN conversion and small RNA profiling after Immunoprecipitation of AGO1&2 proteins in WT E14, Ago1_KO and Ago2_KO mESCs.

Project description:Purpose: The goals of this study was to obtain the profile total miRNAs in WT E14, Ago2_KO and Ago1_KO mESCs to compare it with Immunoprecipitated microRNAs in AGO1&2 proteins.

2018-02-02 | GSE80211 | GEO

WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

Project description:WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

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