Comment[GEAAccession]	E-GEAD-411
MAGE-TAB Version	1.1
Investigation Title	Comprehensive analysis of transcripts in sarcomatoid hepatocellar carcinoma
Experiment Description	The current case-control study demonstrated that sarcomatoid hepatocellular carcinoma (SHCC) had distinct features of histomorphology consisting of one or more of pleomorphic, spindle, or giant cells, transcriptome findings involving upregulated genes related with epithelial-to-mesenchymal transition and inflammatory response, and prominent PD-L1 expression and T cell infiltration. That SHCC is an immunologically hot tumor can have implications for the effectiveness of immunotherapy for SHCC.
Experimental Design	disease state design
Experimental Factor Name	disease_state
Experimental Factor Type	disease_state
Person Last Name	Suzuki
Person First Name	Toshihiro
Person Affiliation	Department of Cancer Immunotherapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center
Person Roles	submitter
Public Release Date	2021-02-09
Protocol Name	P-GEAD-722	P-GEAD-723	P-GEAD-724	P-GEAD-725	P-GEAD-726
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Around 2 to 5 mm squares of fresh tumor tissues from surgically resected specimens of ordinary HCC or sarcomatoid HCC were stored in RNAlater (QIAGEN), and were stocked -80 degree.	Total RNA was isolated by QIAGEN RNeasy Mini Kit, according to standard methods. The quality of RNA was determined using RNA Electrophoresis with the 2100 Bioanalyzer System as the RNA Integrity Number (RIN).	Libraries were prepared from 300 to 800 ng total RNA using the TruSeqTM Stranded mRNA Library prep (Illumina).	RNA sequencing was performed using the NextSeq 550 (Illumina) according to the manufacturer protocol.	Using bowtie2-2.2.9, the reads were aligned to remove rRNA-derived reads and mapped to the human reference genome hg38 with Tophat-2.1.1. To generate a transcriptome assembly, the alignment-reads were provided to Cufflinks packages (Cufflinks-2.2.1), and the expression level of each isoform was calculated and normalized as fragments per kilobase of exon per million reads mapped values (FPKM).
SDRF File	E-GEAD-411.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB10863
Comment[Last Update Date]	2021-02-09