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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

ABSTRACT: Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

PROVIDER: PRJNA874833 | ENA |

REPOSITORIES: ENA

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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

Project description:Single-cell RNA sequencing (scRNA-seq) has proven to be an invaluable tool for the study of tumor evolution. However, interrogating regulatory epigenetic alterations during cancer progression at the resolution of single-cells has remained a major challenge due to the lack of sensitivity of current assays. Here, we developed the highly-sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived cell lines. We find that the epigenome can employ diverse modes to contribute towards cancer progression. Notably, we demonstrate that gene expression changes during cancer progression are co-modulated by alterations in both copy number and chromatin activity to drive epigenetic rewiring of cell-states. Furthermore, intratumor epigenetic heterogeneity may predispose sub-clonal populations within the primary tumor to acquire malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to existing toolkit of single-cell assays to dissect the function of the epigenome during cancer progression.

2024-11-18 | GSE212249 | GEO

Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [bulk RNAseq]

2024-11-18 | GSE212247 | GEO

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]

Project description:Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]

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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN

Project description:Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN

| PRJNA874747 | ENA

The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

Project description:We performed cleavage under targets and release using nuclease (CUT&RUN) sequencing to characterize ATAC peaks identified by snATAC-seq.

2023-04-28 | GSE213150 | GEO

Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

| PRJNA686390 | ENA

Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [bulk RNAseq]

Project description:Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [bulk RNAseq]

| PRJNA874706 | ENA

The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

Project description:The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

| PRJNA879346 | ENA

CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors

Project description:We introduce CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/) as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. We illustrate the functionality of CUT&RUNTools through analysis of CUT&RUN data acquired for GATA1, a master regulator in erythroid lineage cells. Results were compared initially to published GATA1 ChIP-seq data for cells under the same conditions. We performed de novo analysis of CUT&RUN peaks to retrieve not only GATA1’s primary motif, but also the GATA1-TAL1 composite motif, and co-factor motifs GCCCCGCCTC, CMCDCCC, and RTGASTCA that correspond to SP1, KLF1, and NFE2 co-factors. Cofactor binding was verified by independent TAL1 and KLF1 CUT&RUN, and other ChIP-seq experiments. CUT&RUNTools also generated base-pair resolution motif footprint for sequence-specific binding factors, and located likely direct binding sites by quantifying log-odds of binding scores. Overall, CUT&RUNTools should enable biologists to realize advantages of cleavage data provided by CUT&RUN, and make high-quality footprinting analysis accessible to a broad audience.

2019-08-24 | GSE136251 | GEO

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