GEO DataSets

(Submitter supplied) The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

143 Samples

Download data: BED, CSV, H5

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21273 GPL20795

1743 Samples

Download data: HIC, PAIRS, TXT

(Submitter supplied) The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

778 Samples

Download data: HIC, PAIRS, TSV, TXT

(Submitter supplied) The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21273

822 Samples

Download data: HIC, PAIRS, TSV, TXT

(Submitter supplied) We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified, suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

50 Samples

Download data: TXT

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

1 Sample

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: BED, BW, MCOOL, PAIRS

(Submitter supplied) The monoallelic expression of olfactory receptor (OR) genes is governed by a large number of intergenic enhancer elements that are located in intergenic regions of OR gene clusters. In mature olfactory sensory neurons (OSNs), multiple OR enhancers colocalize in an interchromosomal enhancer hub together with the active OR allele. Here we show that in OSNs OR enhancers are bound by Ldb1, but not general purpose mediators of nuclear architecture (CTCF or the cohesin complex subunit Rad21). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057 GPL17021

28 Samples

Download data: BED, BIGWIG

(Submitter supplied) The monoallelic expression of olfactory receptor (OR) genes is governed by the formation of large domain of heterochromatin over OR clusters and by enhancer elements embedded within these heterochromatic domains. Here we show that OR enhancers are bound by Ebf and Lhx2 in mature olfactory sensory neurons (OSNs), and that in the same cell population these sites are flanked by a histone modification characteristic of active enhancers (H3K7ac) as well as modifications characteristic of heterochromatin (H3K9me3 and H3K79me3). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

38 Samples

Download data: BIGWIG

(Submitter supplied) We performed single-cell chromatin conformation capture with our recently developed method, Dip-C, on mouse sensory neurons in visual and olfactory systems, and reconstructed their 3D genomes.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21103 GPL17021

409 Samples

Download data: BED, HIC, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL25244 GPL21306

429 Samples

Download data: BW, TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

1 Sample

Download data: TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

1 Sample

Download data: TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL25244

14 Samples

Download data: BW

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

384 Samples

Download data: BW, TSV