Map active enhancer and gene promoter regions in the SCN
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ABSTRACT:
PROVIDER: PRJNA901441 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Histone ChIP-seq was performed at varied time of the day to map the gene promoter and active enhancer sites in the central clock; SCN (suprachiasmatic nuclei). Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K4me3 and H3K27ac in adult mouse SCN and cortex at distinct time of the day .
2023-04-24 | GSE217941 | GEO
Project description:Histone H3 lysine 4 methylation on promoter regions plays essential roles in transcriptional regulation in mouse early embryo development. Here, we presented the first genome-wide map of H3K4me1 in mouse pre-implantation embryos and observed a unique establishment process of H3K4me1 pattern on promoter regions, which is strongly correlated with active transcription and the broad H3K4me3 domain formation. We further demonstrate that the histone methyltransferase ASH2L contributes to forming the H3K4me1 DIP pattern on the promoter regions in mouse pre-implantation embryos.
2022-07-10 | GSE179939 | GEO
Project description:Histone H3 lysine 4 methylation on promoter regions plays essential roles in transcriptional regulation in mouse early embryo development. Here, we presented the first genome-wide map of H3K4me1 in mouse pre-implantation embryos and observed a unique establishment process of H3K4me1 pattern on promoter regions, which is strongly correlated with active transcription and the broad H3K4me3 domain formation. We further demonstrate that the histone methyltransferase ASH2L contributes to forming the H3K4me1 DIP pattern on the promoter regions in mouse pre-implantation embryos.
2022-07-10 | GSE179937 | GEO
Project description:Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation. In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells. The resulting map defines 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 un-annotated transcriptional units. The map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome. Further examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. Our results provide a global view of the functional relationship among the transcriptional machinery, chromatin structure, and gene expression in human cells. Keywords = GALA Keywords = gene expression Keywords = nimblegen Keywords = promoter profile Keywords = LICR renlab Keywords: other
2010-07-01 | E-GEOD-2672 | biostudies-arrayexpress
Project description:Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation. In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells. The resulting map defines 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 un-annotated transcriptional units. The map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome. Further examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. Our results provide a global view of the functional relationship among the transcriptional machinery, chromatin structure, and gene expression in human cells. Keywords = GALA Keywords = gene expression Keywords = nimblegen Keywords = promoter profile Keywords = LICR renlab Keywords: other
2005-06-29 | GSE2672 | GEO
Project description:Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition at active promoter regions in budding yeast
| PRJNA384985 | ENA
Project description:To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at –800C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at –80°C before routine processing for GeneChip analysis. Keywords: other
2004-10-09 | GSE1673 | GEO
Project description:To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at â??800C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at â??80°C before routine processing for GeneChip analysis.
2008-06-11 | E-GEOD-1673 | biostudies-arrayexpress
Project description:Purpose: One goal of this study is to identify actively transcribing genes in the mesenchyme (pulp) corresponding to the narrow (lateral) and wide (medial) vane of primary remiges. The other is to pinpoint the active promoter regions of these genes.
2017-03-08 | GSE86414 | GEO
Project description:Actinomadura sp. SCN-SB Genome sequencing
| PRJNA1173323 | ENA