GEO DataSets

(Submitter supplied) We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL21290 GPL18573

16 Samples

Download data: BED, TXT

(Submitter supplied) In this experiment, we sought to analyze the genes positively or negatively selected during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs) with particular focus on the genes enriched for CTCF boundary disruption at HoxA cluster

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to analyze the genes positively or negatively selected during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs) with particular focus on the genes enriched for CTCF boundary disruption at HoxA cluster

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL19057 GPL17769

13 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to identify the distribution of RAD21 in cervical motor neurons (MNs) that is formed through in vitro differentiation of mESCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

1 Sample

Download data: BW

(Submitter supplied) In this experiment, we sought to identify how the distribution of CTCF and MAZ change in WT and MAZ knock-out (KO) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL19057

18 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) In this experiment, we sought to identify how the distribution of MAZ change in WT, MAZ HoxA(Δ5|6), and MAZ HoxD(Δ4|8) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

11 Samples

Download data: BW

(Submitter supplied) In this experiment, we sought to identify how the distribution of H3K27me3 and H3K4me3 change in WT, MAZ HoxA(delta5|6), MAZ HoxD(delta4|8), and CTCF (delta5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

12 Samples

Download data: BW

(Submitter supplied) In this experiment, we sought to identify how the distribution of CTCF change in WT, MAZ HoxA(Δ5|6), MAZ HoxD(Δ4|8), and CTCF (Δ5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

16 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) In this experiment, we sought to identify how topological organization changes at HoxA cluster in WT, MAZ HoxA(Δ5|6) and CTCF (Δ5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

17 Samples

Download data: BEDGRAPH

(Submitter supplied) In this experiment, we sought to identify how the distribution of CTCF, RAD21, H3K27me3 and H3K4me3 change in WT and double-positive MAZ HoxA(Δ5|6) cervical motor neurons (MNs).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BW

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

Organism:

Mus musculus; synthetic construct

Type:

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

4 related Platforms

138 Samples

Download data: BEDGRAPH, BW, HIC, NARROWPEAK, TXT

(Submitter supplied) In this experiment, we sought to analyze how transcriptome of WT and Maz HoxA(Δ5|6) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to analyze how transcriptome of WT and MAZ knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) In this experiment, we sought to analyze how three dimensional genome organization of WT and MAZ knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

8 Samples

Download data: HIC

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19786 GPL18573

10 Samples

Download data: BAR, BW, CEL

(Submitter supplied) Chromatin insulators partition the genome into the functional units to control gene expression especially in complex chromosomal regions. The CCCTC-binding factor (CTCF) is an insulator-binding protein which functions for transcriptional regulation and higher-order chromatin formation. Here we report that a removable CTCF insulator is responsible for the retinoic acid (RA)-mediated higher-order chromatin remodeling and selective gene expression in the human HOXA gene locus. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BW

(Submitter supplied) Chromatin insulators partition the genome into the functional units to control gene expression especially in complex chromosomal regions. The CCCTC-binding factor (CTCF) is an insulator-binding protein which functions for transcriptional regulation and higher-order chromatin formation. Here we report that a removable CTCF insulator is responsible for the retinoic acid (RA)-mediated higher-order chromatin remodeling and selective gene expression in the human HOXA gene locus. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL19786

4 Samples

Download data: BAR, CEL

(Submitter supplied) We found that posterior HOXA-associated HOTTIP lncRNA is aberrantly activated in MLL-rearranged AMLs and required for the posterior HOXA chromatin structure and gene expression. Knock-out of HOTTIP attenuates leukemic progressions of the transplanted humanized AML mice by blocking posterior HOXA-associated AML gene expression programs while the dCas-VP160 mediated reactivation of HOTTIP restores HOXA locus chromatin structure and HOXA9-A13 gene expression in the CBS7/9 boundary depleted AML cells. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

7 related Platforms

66 Samples

Download data: BED, TXT

(Submitter supplied) Proper Homeobox A (HoxA) cluster genes expression is essential for embryonic stem cells (ESCs) differentiation and individual development. However, the mechanisms controlling the precise spatiotemporal expression of HoxA cluster genes during early ESCs differentiation remain largely unknown. Here, we find a CTCF binding element (CBE+47kb) closest to the 3'-end of HoxA locus within a topologically associated domains (TAD) in ESCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21103 GPL21273

10 Samples

Download data: TXT, WIG

(Submitter supplied) Retinoic acid (RA) induces rapid differentiation of ESCs, partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21273 GPL17021

9 Samples

Download data: TXT, WIG