Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CpG island mediated linear and spatial gene partitioning (other data sets)

ABSTRACT: In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed diverse published data of DNaseI-seq, MeDIP-seq, LMNB1-DamID-seq, PolII ChIA-pet, and Hi-C analysis.

OTHER RELATED OMICS DATASETS IN: PRJNA319990PRJNA319987PRJNA319992PRJNA319996PRJNA319994PRJNA319989

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE80795 | GEO | 2018/02/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CpG island mediated linear and spatial gene partitioning (MOE430V2)

Project description:In order to study the gene expression change upon transcription factor (MYOD1, SPI1) induction, we reanalyzed published gene expression microarray data. Raw data were preprocessed and normalized with the Robust Multi-array Average (RMA)(Irizarry et al., 2003) method.

2018-02-15 | GSE80792 | GEO

CpG island mediated linear and spatial gene partitioning (ChIP-seq)

Project description:In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.

2018-02-15 | GSE80791 | GEO

CpG island mediated linear and spatial gene partitioning (RNA-seq)

Project description:We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

2018-02-15 | GSE80793 | GEO

CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

Project description:In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

2018-02-15 | GSE80797 | GEO

CpG island mediated linear and spatial gene partitioning (other data sets)

Project description:CpG island mediated linear and spatial gene partitioning (other data sets)

| PRJNA319990 | ENA

DamID (LmnB1/Dam) Log2 ratios of C57Bl/6 fibroblasts and RAG2-/- pro-B cells.

Project description:Comparison of DamID profiles and LAD patterning across cell types reveals regions of variable LADs LmnB1 interactions at the nuclear periphery of C57Bl/6 pro-B cells and fibroblasts were identified by DamID in duplicate for both pro-B and fibroblasts (4 samples total). For each sample, Dam-LmnB1/Dam-only Log2 ratios of chromosomes 11 and 12 were calculated, lifted over to mm9, duplicates were normalized and averaged together.

2014-12-16 | E-GEOD-56990 | biostudies-arrayexpress

Genomic positioning in LBR and Lamin A K562 knockout cells

Project description:To probe the functional consequences of nuclear lamina genome association, we made LMNA, LBR, and double LMNA/LBR K562 knockout lines. We first examined the genome interaction changes with nulcear lamina using LMNB1 DamID seq and further assessed the functional consequences of these changes using RNA-seq and repli-seq.

2024-04-04 | GSE263012 | GEO

CpG island mediated linear and spatial gene partitioning (RNA-seq)

Project description:CpG island mediated linear and spatial gene partitioning (RNA-seq)

| PRJNA319992 | ENA

CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

Project description:CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

| PRJNA319996 | ENA

Mus musculus

Project description:ChIP-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages

| PRJNA318504 | ENA