|
| Status |
Public on Sep 25, 2021 |
| Title |
HCCW25T |
| 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 |
SAMN21216417 |
| SRA |
SRX12008844 |
