Dataset Information

Genome-wide maps of chromatin state in LUAD and normal tissues

ABSTRACT: We report the application of Hi-C technology for high-throughput profiling of LUAD and normal tissues. By obtaining over three billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of LUAD. We found the main conversion type of compartment is A→B in tumor tissues, 216 tumor-specific TADs and 41 distinct enhancer-promoter loops in tumor tissue. And these chromatin structure variations are mainly on chromosome 3. We also found 5 most important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which were detected in both A→B compartment, TADs and chromatin loops.

ORGANISM(S): Homo sapiens

PROVIDER: GSE161486 | GEO | 2021/04/30

REPOSITORIES: GEO

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Project description:<a href="https://cptac-data-portal.georgetown.edu/study-summary/S056" target="_blank">Proteogenomics of Lung Adenocarcinoma, Gillette et al., 2020 publication is here</a> Lung cancer is a leading cause of cancer death in the United States and in 2019 it is estimated that there will be over 228,000 new cases (<a href="https://www.cancer.org/cancer/non-small-cell-lung-cancer/about/key-statistics.html" target="_blank">American Cancer Society</a>). There are two main types, small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). A majority of patients (85%) have NSCLC, with a significant portion of those individuals having a histological subtype lung adenocarcinoma (LUAD) <a href="https://www.ncbi.nlm.nih.gov/pubmed/29364287" target="_blank">Herbst et al., 2018 Nature</a>. To advance the proteogenomic understanding of LUAD, the CPTAC program has investigated 111 tumors, (with 102 tumors paired with normal adjacent tissue samples) and subjected these samples to global proteome and phosphoproteome analysis. An optimized workflow for mass spectrometry of tissues using isobaric tags (TMT (tandem mass tags)-10) was used (<a href="https://www.ncbi.nlm.nih.gov/pubmed/29988108" target="_blank">Mertins et al., Nature Protocols 2018</a>). Proteome and phosphoproteome data from the LUAD discovery cohort is available below along with peptide spectrum matches (PSMs) and protein summary reports from the CPTAC common data analysis pipeline (CDAP).Clinical Data for LUAD tumors are provided below. Updates will be available as the LUAD cohort characterization proceeds. Genomic Data for LUAD tumors is available from the NCI Genomic Data Commons (GDC), <a href="https://portal.gdc.cancer.gov/projects/CPTAC-3" target="_blank">here</a> Imaging Data for LUAD tumors is available from NCI, The Cancer Imaging Archive (TCIA), <a href="https://wiki.cancerimagingarchive.net/display/Public/CPTAC-LUAD" target="_blank">here</a> This release includes over 4500 files and 914 GB of data. <ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/study-summary/S046">https://cptac-data-portal.georgetown.edu/study-summary/S046</a> on 01/29/21</li></ul>

Dataset Information

Genome-wide maps of chromatin state in LUAD and normal tissues

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