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]
Repo structure
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Fig1: Overview of chromatin accessibility pattern across 11 cancer types.
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Fig2: CREs regulating transcriptional programs in cancer.
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Fig3: Pan-Cancer and cancer-specific regulons.
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Fig4: Transcriptional programs activated in cancer metastasis.
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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