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ABSTRACT: Thymocyte mRNA sequence from Eed conditional knockout mice

PROVIDER: PRJNA1054693 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27290613.fastq.gz	Fastqsanger.gz
	SRR27290614.fastq.gz	Fastqsanger.gz
	SRR27290615.fastq.gz	Fastqsanger.gz
	SRR27290616.fastq.gz	Fastqsanger.gz
	SRR27290617.fastq.gz	Fastqsanger.gz

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Project description:Eed conditional knockout in chondrocytes

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Eed conditional knockout in chondrocytes

Project description:Primary rib chondrocyte were isoloated from P0.5-day old wildtype and Col2-Cre:floxed EED conditional knockout mouse pups,and cultured overnight in 10%FCS containing DMEM. RNA was isolated and subjected to Affymetrix Mouse Gene ST 1.0 array. Primary rib chondrocyte were isoloated from P0.5-day old wildtype and Col2-Cre:floxed EED conditional knockout mouse pups,and cultured overnight in 10%FCS containing DMEM. RNA was isolated and subjected to Affymetrix Mouse Gene ST 1.0 array. Biological duplicate. Mice were in a mixed genetic background of C57/B6 and 129sv.

2015-11-01 | E-GEOD-66862 | biostudies-arrayexpress

Analysis of changes in gene expression in skin epidermis upon conditional knockout of PRC2-subunit Eed

Project description:Analysis of changes in gene expression in skin epidermis upon conditional knockout of the essential Polycomb repressive complex 2 (PRC2) subunit Eed. Loss of Eed in skin epithelium leads to de-repression of key Merkel-differentiation genes, which are known PRC2 targets, and results in ectopic formation of Merkel cells that are associated with all hair types. Gene expression analysis: To determine the changes in gene expression in skin epidermis upon conditional knockout of Eed, total RNA was isolated from skin epidermis in four biologic replicates from cells in different conditions and hybridized to SurePrint G3 Mouse GE 8X60K microarrays (Agilent).

2016-06-14 | E-GEOD-83244 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of peritoneal macrophages Transcriptomes of Dnmt3a macrophage conditional knockout mouse

Project description:Purpose:The purpose of this study is to measure the gene expression profile in Dnmt3a conditional knockout macrophages. Methods:Dnmt3a conditional knockout macrophages mRNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 20 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation during Dnmt3a conditional knockout in macrophages. Dnmt3a conditional knockout mRNA profiles were generated by deep sequencing

2016-05-30 | E-GEOD-74750 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of peritoneal macrophages Transcriptomes of Dnmt3a macrophage conditional knockout mouse

2016-05-30 | GSE74750 | GEO

Next-generation Sequencing Facilitates Quantitative Analysis of Wild Type and EED cKO mice Hippocampus Dentate Gyrus Transcriptomes

Project description:Purpose:Quantification differentially expressed genes and find target genes. The goals of this study are to compare Wild Type and EED cKO hippocampus dentate gyrus transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes Methods: Hippocampus dentate gyrus mRNA profiles of 14-day-old wild-type (WT) and Embryonic Ectoderm Development conditional knockout (EED cKO) mice were generated by deep sequencing, in two biological replicates,using BGISEQ-500 platform.All RNA-Seq data were aligned to mouse genome version mm10 using HISAT.We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. Results:Only transcripts that showed more than 2-fold differential expression compared to control were subjected to relevance network analysis. 1047 candidate genes that were differentially expressed with biological functional groups as compared between WT and EED cKO mice . Conclusions: Our study represents the first detailed analysis of Wild Type and EED cKO mice hippocampus dentate gyrus transcriptomes, with two biologic replicates, generated by RNA-seq technology.

2019-05-11 | GSE131035 | GEO

Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [RNA-seq]

Project description:Polycomb-mediated gene repression plays an important role in adult stem cell maintenance. We knocked out (using the inducible AhCre-LoxP system) Polycomb genes Eed and Ezh2 in the intestine for 6 weeks, after which crypts - the small intestinal stem cell zone - were harvested and RNA sequenced. We found Wnt, Notch and cell cycle pathways to be affected in Eed knockout (KO) but not Ezh2 KO crypts. Direct targets of Eed were determined by comparing this data with ChIP-sequencing. Small intestinal crypt mRNA profiles of 6 weeks-induced 12 weeks old Eed KO, Ezh2 KO and WT mice (all triplicates) as well as 10 days-induced Eed KO and WT organoids (duplicates) were generated by RNA sequencing over two runs and using IlluminaHiseq2000 and Hiseq2500.

2016-07-01 | E-GEOD-81576 | biostudies-arrayexpress

scRNA-seq study of Eed-deleted cerebellar granule neuron progenitors (CGNPs)

Project description:We studied CGNPs with conditional deletion of Eed using scRNA-seq. Eed was deleted in CGNPs by crossing Math1-Cre mice with Eed floxed mice. scRNA-seq seq was performed by Drop-seq. The results may be compared to our prior published data on scRNA-seq in normal CGNPs (GEO accession number GSE129730)

2022-07-08 | GSE207451 | GEO

Analysis of changes in gene expression in skin epidermis upon conditional knockout of PRC2-subunit Eed

2016-06-14 | GSE83244 | GEO

Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and EED-/- mice cerebellum Transcriptomes and Genome-wide maps of chromatin state in Wild Type and EED-/- mice cerebellum

Project description:Purpose: The goals of this study are to compare Wild Type and EED-/- cerebellum transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes. We performed chromatin-immunoprecipitation coupled to sequencing (ChIP-seq) to dissect the relationship between the differentially expressed genes and the occupancy of H3K27me3, H3K27ac and EED. Methods: Cerebellum mRNA profiles of 14-day-old(P14) wild-type (WT) and Embryonic Ectoderm Development conditional knockout (EED-/-) mice were generated by deep sequencing, in triplicate,using Illumina HiSeq 2500 system.All RNA-Seq data were aligned to mouse genome version mm10 using Salmon (v.1.1.0) .We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. we performed ChIP-seq using freshly isolated P14 from Wild Type and EED-/- cerebellar tissues . DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp. Results:Only transcripts that showed more than 1.5-fold differential expression compared to control were subjected to relevance network analysis. 3149 candidate genes that were differentially expressed with biological functional groups as compared between WT and EED-/- mice .We found that the enrichment of H3K27me3 was decreased H3K27ac was highly increased in EED-/- mice. Conclusions: Our study represents the first detailed analysis of Wild Type and EED-/ mice cerebellum transcriptomes, with three biologic replicates, generated by RNA-seq technology. We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in cerebellar cells.

2024-04-02 | GSE169312 | GEO

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