PanCan_snATAC_publication

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PanCan_snATAC_publication

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# PanCan_snATAC_publication

This is a repo for the publication:

Terekhanova, N.V., Karpova, A., Liang, W.W., et al. "Epigenetic regulation during cancer transitions across 11 tumour types." Nature (2023): 1-10.

[[Link](https://www.nature.com/articles/s41586-023-06682-5)]

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**Repo structure**

* Fig1: Overview of chromatin accessibility pattern across 11 cancer types.

* Fig2: CREs regulating transcriptional programs in cancer.

* Fig3: Pan-Cancer and cancer-specific regulons.

* Fig4: Transcriptional programs activated in cancer metastasis.

* Fig5: Genetic drivers impact on chromatin accessibility.
  
Use Sample_ID_Lookup_table.xlsx to find raw fastq, bams and count matrix data on HTAN DCC, GDC and CDS

Cell type annotation for tumor GBM and ccRCC samples is available on GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE240822 (please see supplementary files). For all other samples cell type annotation is available via HTAN DCC: https://humantumoratlas.org/ (WUSTL dataset L4 level files).

Synapse project ID with SCENIC results and inferCNV results syn51364714

PanCan_snATAC_publication

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