Selected article for: "accession number and genome accession number"
Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance
  • Document date: 2020_1_18
    • ID: bf4qpsy7_72
    Snippet: Read quality was assessed using FastQC. Reads were mapped to the hg38 genome with STAR 2.4.2a (Dobin et al., 2012) . Transcripts were quantified with Salmon 0.8.2 (Patro et al., 2017) using GENCODE v25 transcript annotations. Normalization was performed using DESeq2. TCGA RNA-seq data were downloaded using TCGA-assembler 2 (Wei et al., 2018) as normalized counts. TCGA RNA-seq data for lncRNAs was downloaded from TANRIC (Li et al., 2015) as normal.....
    Document: Read quality was assessed using FastQC. Reads were mapped to the hg38 genome with STAR 2.4.2a (Dobin et al., 2012) . Transcripts were quantified with Salmon 0.8.2 (Patro et al., 2017) using GENCODE v25 transcript annotations. Normalization was performed using DESeq2. TCGA RNA-seq data were downloaded using TCGA-assembler 2 (Wei et al., 2018) as normalized counts. TCGA RNA-seq data for lncRNAs was downloaded from TANRIC (Li et al., 2015) as normalized counts. Cholangiocarcinoma RNA-seq data (Nakamura et al., 2015) was downloaded from the European Genome-Phenome Archive (accession number EGAS00001000950). GTEx Release V7 data was downloaded from the GTEx Portal as gene read counts and normalized with RNA-seq data from primary FLCs using DESeq2. Principal components analysis was performed using the most variable 1000 genes following variance stabilizing transformation (DESeq2).

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