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163 results for “HiChIP”
FitHiChIP: Identification of significant chromatin contacts from HiChIP data
<p>FitHiChIP is a computational method for identifying chromatin contacts among regulatory regions such as enhancers and promoters from HiChIP/PLAC-seq data.</p> <p><strong>Functionalities</strong> of FitHiChIP include:</p> <p>1) Calling significant interactions / loops / contacts from a HiChIP / PLAC-seq data </p> <p>2) Identifying peaks (enriched segments) from a HiChIP data (i.e. HiChIP peak caller)</p> <p>3) Finding differential loops among non-differential loci between two different categories of HiChIP samples, each with one or more replicates.</p> <p><strong>GitHub page</strong>: <a href="https://github.com/ay-lab/FitHiChIP">github.com/ay-lab/FitHiChIP</a></p> <p><strong>Documentation</strong>: <a href="https://ay-lab.github.io/FitHiChIP/">https://ay-lab.github.io/FitHiChIP/</a></p> <p><strong>Citation</strong>: Please check the above documentation regarding citation of FitHiChIP</p> <p>About this repository: All the data and results provided here correspond to the published manuscript. The file <strong>Data_Summary.xlsx</strong> summarizes for each figure, corresponding tables storing the related datasets.</p>
MNT-1 HiC and H3K27ac HiChIP data
<p>We performed Hi-C and H3K27ac HiChIP assays in MNT1 cells. Hi-C is a high-throughput method for detecting chromatin interactions at whole genome scale and is often used to identify topologically associating domains (TADs) in the nucleus. H3K27ac HiChIP can identify chromatin interactions enriched for H3K27ac, a histone modification associated with active promoters and enhancers. We performed bridge linker mediated Hi-C and H3K27ac HiChIP using double (Hae3+Alu1) as well as single (Hae3) enzyme digestion in MNT-1 cells. For Hi-C_Hae3+Alu1, Hi-C_Hae3, HiChIP_Hae3+Alu1, and HiChIP_Hae3 assays, respectively, we sequenced 399 million (M), 430 M, 257 M, and 181 M paired reads and obtained 299 M, 305 M, 151 M, and 94 M valid interactions (cis-pairs >= 1 kb and trans-pairs) using pairtools. <br> Using the Hi-C data, we identified 80,333 TADs in MNT-1 cells using onTAD software 60 and the genes located in the same TAD with MFVs. Using four different tools, cooltools-dots, cLoops, mustache and FitHiChIP , we detected 201,862 loops based on Hi-C and H3K27ac HiChIP data and identified 8,569 loops for 597 tested MPRA SNPs. Using the Hi-C and HiChIP data, we constructed a high-resolution chromatin interaction map of MNT-1 cells. This map serves as an invaluable resource for investigating the interactions between the regulatory elements and their target genes in melanoma cells, thereby facilitating the elucidation of regulatory networks underlying human skin phenotype and diseases. </p>
MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
GEO Series GSE119663. Mus musculus. 10 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
H3K27ac BL HiChIP and GRID-seq data of LW and MS
GEO Series GSE189397. Sus scrofa. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [HiChIP]
GEO Series GSE193828. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]
GEO Series GSE137949. Drosophila melanogaster. 30 samples. Type: Other.
Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma.
GEO Series GSE193830. Homo sapiens. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Super-enhancer-driven PPP1R15B/CReP, regulated by C/EBPβ and YY1, is oncogenic in multiple myeloma [HiChIP II]
GEO Series GSE267003. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Coordination of widespread transcription at enhancers and target genes through BRD4 (HiChIP)
GEO Series GSE214591. Homo sapiens. 6 samples. Type: Other.
Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]
GEO Series GSE188380. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PDKCC during chondrogenesis [HiChIP]
GEO Series GSE212226. Homo sapiens. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
H3K27ac HiChIP analysis in GI-MEN DOX-ASCL1 cells
GEO Series GSE214792. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Predictive prioritization of functional enhancers in human pancreas cells [HiChIP]
GEO Series GSE245482. Homo sapiens. 29 samples. Type: Other.
H3K27ac HiChIP analysis in TL-Om1 cells
GEO Series GSE181214. Homo sapiens. 1 samples. Type: Other.
A cis-regulatory lexicon of DNA motif combinations mediating cell type-specific gene regulation [HiChIP-Seq]
GEO Series GSE188401. Homo sapiens. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The effect of STAG2 loss in Ewing sarcoma [HiChIP]
GEO Series GSE165977. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [Rec-1_HiChIP]
GEO Series GSE116875. Homo sapiens. 2 samples. Type: Other.
3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [HiChIP]
GEO Series GSE280796. Homo sapiens. 3 samples. Type: Other.
HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [HiChIP-Seq]
GEO Series GSE245732. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [HiChIP]
GEO Series GSE175529. Homo sapiens. 6 samples. Type: Other.
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International Brain Laboratory public data
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OpenNeuro
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