Project description:This experiment was designed to obtain the polyA+ transcriptome in E14 ESCs PolyA+ RNA was extracted and purified from two separate clones of E14, which were treated as biological replicate
Project description:This experiment sought to determine the chromatin structure and PRC2 occupancy at the promoters of all genes in mouse ESCs ChIP-seq for EZH2, SUZ12, and H3K27me3 were performed on WT E14 cells in 2 biological replicates each. In addition H3K27me3 ChIP-seq was also performed on a clone of E14 cells expressing a tagged version of EZH2, which for the purpose of this study was used as replicate #3.
Project description:More than 2x10E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7x10E6 single nucleotide variant. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variant are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of this cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because of it could be target of DNA methylation. We performed a reduced representation bisulfite sequencing on E14 cell line to test our new genome assembly with respect to the mm9 genome reference. After mapping and methylation status calling, we obtained an increase of about 120,000 called CpG and we avoided about 20,000 wrong CpG calling. genotyping of E14 embryonic stem cells (ESCs) and Reduced representation Bisulfite Sequencing (RRBS) of E14 ESCs.
Project description:Purpose: The goals of this study was to obtain the profile total miRNAs in WT E14, Ago2_KO mESCs to compare with Ago2_KO-AGO1 overexpressing AGO1.
Project description:Analysis of gene expression in Mouse E14-TG2a.IV strain ES cells Single end RNA-seq analysis of PolyA selected RNA from E14-TG2a.IV ES cells
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.
Project description:We report the application of single-molecule-based sequencing technology for REST and its cofactors genome wide binding sites in E14 cells.We then combine these binding sirtes with REST regulating gene profiling, to understand REST binding and regulation in E14 cells. Examination of REST and 5 cofactors(RCOR1, RCOR2,RCOR3,SIN3A,SIN3B) in E14 cells, REST and SIN3A endogenous antibody were used for ChIP experiment. The stable E14 cells expressing low level exogenous RCOR1, RCOR2, RCOR3,and SIN3B with V5 tag were used for ChIP experiment with V5 antibody to obtain individual ChIP DNA.
Project description:This experiment was designed to indentify RNAs making direct contact JARID2 as mouse ESCs differentiate E14 WT were left untreated or differentiated with 2 M-BM-5M RA for 24 hrs. In both cases, ceslls were pulsed with 4-SU, irradiated with UV, and subjected to JARID2 immunoprecipitation.