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Items: 1 to 20 of 52

1.

Functional enhancers shape extrachromosomal oncogene amplifications

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; synthetic construct
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
5 related Platforms
20 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE139417
ID:
200139417
2.

Genome-wide maps of CTCF in glioblastoma

(Submitter supplied) Here we have used CTCF ChIP-seq in glioblastoma to understand CTCF elements in the context of chromatin topology genome-wide.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
2 Samples
Download data: BED, BW
Series
Accession:
GSE139416
ID:
200139416
3.

CRISPRi proliferation dropout screen of EGFR cis-regulatory elements

(Submitter supplied) Here we have used using a pooled proliferation dropout screen with KRAB-dCas9 to determine the contribution of cis-regulatory elements around EGFR to cell fitness in EGFR unamplified (GSC23) and amplified (GBM3565) glioblastoma .
Organism:
synthetic construct; Homo sapiens
Type:
Other
Platforms:
GPL15520 GPL17769
3 Samples
Download data: TXT
Series
Accession:
GSE139415
ID:
200139415
4.

Chromosome topology of the EGFR locus in glioblastoma

(Submitter supplied) Here we have used 4C-seq to interrogate the toplogy of the EGFR locus in glioblastoma models that are EGFR unamplified (GSC23) and amplified (GBM3565).
Organism:
Homo sapiens
Type:
Other
Platform:
GPL16791
10 Samples
Download data: TXT
Series
Accession:
GSE139414
ID:
200139414
5.

Genome-wide maps of active chromatin in Wilms tumor

(Submitter supplied) Here we have used H3K27ac ChIP-seq in primary Wilms tumors to identify active promoter and enhancer elements genome-wide.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
5 Samples
Download data: BED, BW
Series
Accession:
GSE126774
ID:
200126774
6.

Ex vivo screen identifies CDK12 as a metastatic vulnerability in osteosarcoma

(Submitter supplied) Despite progress in intensification of therapy, outcomes for patients with metastatic osteosarcoma (OS) have not improved in thirty years. We developed a system that enables preclinical screening of compounds against metastatic OS cells in the context of the native lung microenvironment. Using this strategy to screen a library of epigenetically-targeted compounds, we identified inhibitors of CDK12 to be most effective, reducing OS cell outgrowth in the lung by >90% at sub-micromolar doses. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL16791 GPL24676
34 Samples
Download data: BROADPEAK, BW, TXT
7.

Supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
10 Samples
Download data: BW
Series
Accession:
GSE96872
ID:
200096872
8.

Gene expression changes in the supraorbital cranial mesenchyme after beta-catenin deletion in vivo

(Submitter supplied) Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at e13.5 cranial mesenchyme.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
7 Samples
Download data: TXT, XLSX
Series
Accession:
GSE96871
ID:
200096871
9.

H3K27me3 enrichment in the supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin

(Submitter supplied) H3K27me3 enrichment in the supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
3 Samples
Download data: BW
Series
Accession:
GSE96604
ID:
200096604
10.

Mismatch-repair signature mutations activate gene enhancers across human colorectal cancer epigenomes

(Submitter supplied) We show that mismatch-repair (MMR) signature mutations can activate colorectal cancer (CRC)-specific enhancers, through analysis of enhancer DNA associated with the active enhancer histone mark H3K27ac. We demonstrate that MMR mutations activate enhancers using a xenograft metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16791 GPL21697
13 Samples
Download data: BROADPEAK, BW
Series
Accession:
GSE126188
ID:
200126188
11.

A miRNA-mediated approach to dissect the complexity of tumor-initiating cell function and identify miRNA-targeting drugs

(Submitter supplied) Microarray analysis of miR-181a sensor sorted primary HGSOC cells to determine the ability of miRNA sensor to regulate various cancer related pathways.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL23159
6 Samples
Download data: CEL
Series
Accession:
GSE123121
ID:
200123121
12.

ChIRP-seq of lincDUSP in colon cancer cells

(Submitter supplied) The genome-wide occupancy of lincDUSP was determined by using chromatin isolation after RNA purification to detemine the genomic sites where lincDUSP directly interacts with chromatin.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
2 Samples
Download data: BW, XLSX
Series
Accession:
GSE112602
ID:
200112602
13.

Differentially expressed genes post knock down of lincDUSP26

(Submitter supplied) Total RNA from V703 and V481 cells (negative control vs KD of lincDUSP) were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs was calculated as FPKM values.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
12 Samples
Download data: CSV, XLSX
Series
Accession:
GSE101342
ID:
200101342
14.

Positively selected enhancer elements endow tumor cells with metastatic competence

(Submitter supplied) Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in signature enhancer-histone marks between near-isogenic pairs of high and low lung-metastatic osteosarcoma cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL11154 GPL16791
91 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE74230
ID:
200074230
15.

Transcription elongation factors are in vivo-specific cancer dependencies in glioma

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL16791
26 Samples
Download data: BED, BIGWIG, TDF
Series
Accession:
GSE74529
ID:
200074529
16.

Epigenetic Profile in Transcription elongation factors are in vivo-specific cancer dependencies in glioma

(Submitter supplied) Glioblastoma ranks as one of the most lethal human cancers, with no effective therapies. To discover novel therapeutic targets, here we performed parallel in vivo and in vitro RNA interference screens of epigenetic regulators and show that transcription elongation factors are essential for human glioblastoma cell survival in vivo, but not in vitro. Context-specific dependency in vivo is driven by microenvironment-induced global changes in the cancer epigenome. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
17 Samples
Download data: BED, BIGWIG, TDF
Series
Accession:
GSE74520
ID:
200074520
17.

RNA-seq Profiles in Transcription elongation factors are in vivo-specific cancer dependencies in glioma

(Submitter supplied) Glioblastoma ranks as one of the most lethal human cancers, with no effective therapies. To discover novel therapeutic targets, here we performed parallel in vivo and in vitro RNA interference screens of epigenetic regulators and show that transcription elongation factors are essential for human glioblastoma cell survival in vivo, but not in vitro. Context-specific dependency in vivo is driven by microenvironment-induced global changes in the cancer epigenome. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
9 Samples
Download data: TXT
Series
Accession:
GSE74516
ID:
200074516
18.

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

(Submitter supplied) We sought to identify hotspots of aberrant enhancer activity in colorectal cancer (CRC) through interrogation of the enhancer epigenomes of a large cohort of genetically diverse CRC samples and normal colonic crypts, representing the cell type of origin for CRC. Through characterization of loci that exhibit differential enhancer activity, we identified sets of enhancers that are recurrently commissioned and decommissioned in CRC relative to normal crypts. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9052 GPL15456 GPL16791
139 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE77737
ID:
200077737
19.

Gene expression changes in dorsal dermal fibroblasts after beta-catenin deletion in vivo

(Submitter supplied) Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at E10.5 in dermal fibroblasts. Method: Skin tissues were treated in 0/25% trypsin for 15 min at 37 degrees C to obtain single cells for FACS sorting and collected in RNA later. RNA was extracted with Karcturus pico pure kit. The RT and amplification was done using Nugen's ovation RNA-seq system V2. Libraries for sequencing were prepared with Illumina TruSeq kit. Transcriptome of FACS sorted E13.5 Engrailed1; RRYFP lineage-marked dorsal dermal fibroblasts was generated next-gen sequencing, in triplicate, using Illumina HiSeq machine. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 33-49 million sequence reads per sample and obtained 76-79% of uniquely mapped percentage. We assembled the reads to the mouse ref genome (build mm10).
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
5 Samples
Download data: XLSX
Series
Accession:
GSE75944
ID:
200075944
20.

Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL9250
14 Samples
Download data: BED, BIGWIG, TSV, TXT
Series
Accession:
GSE57409
ID:
200057409
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