NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5556925 Query DataSets for GSM5556925
Status Public on Sep 25, 2021
Title HCCW26T
Sample type SRA
 
Source name Human tumor tissue
Organism Homo sapiens
Characteristics tissue: Hepatocellular carcinoma
treatment: treatment-naive
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from fresh frozen tumor tissues using AllPrep DNA/RNA/Protein Kit (Qiagen).
RNA library was prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequence reads were generated by Novaseq system (Illumina).
Sequenced reads were aligned to human transcript reference sequence [Homo_sapiens (human) GRCh38/hg38] using HISAT2.
Raw read count and TPM were calculated using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM_Matrix_HCC.txt: Tab-delimited text file includes Transcripts per million (TPM) values for each Sample.
 
Submission date Sep 03, 2021
Last update date Sep 25, 2021
Contact name Yutaka Kurebayashi
E-mail(s) y_kurebayashi@keio.jp
Organization name Keio University School of Medicine
Street address 35 Shinanomachi
City Shinjuku-ku
State/province Tokyo
ZIP/Postal code 160-0016
Country Japan
 
Platform ID GPL24676
Series (1)
GSE183406 Human hepatocellular carcinoma RNAseq data
Relations
BioSample SAMN21216418
SRA SRX12008845

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap