|
| Status |
Public on Apr 30, 2024 |
| Title |
Oral verrucouscarcinoma 5 |
| Sample type |
SRA |
| |
|
| Source name |
Oralmucosa
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
tissue: Oralmucosa
disease state: Oral verrucouscarcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the prepared samples using TRIzol Reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
VC5
|
| Data processing |
FASTQ files were trimmed using Trimmomatic (v0.39) 9 to remove adaptors and low-quality reads.
Trimmed sequence reads were mapped to hg38 using salmon
Differential expression analysis of mRNA and lncRNA between two conditions was performed using the DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 05, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
JANGHYUN KIM |
| E-mail(s) |
kphe22@gmail.com
|
| Organization name |
CNUDH
|
| Department |
Oral pathology
|
| Lab |
YKimLab
|
| Street address |
33, YONGBONG-RO, BUK-GU, GWANGJU
|
| City |
Gwangju |
| State/province |
Gwangju |
| ZIP/Postal code |
61186 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE228993 |
The mRNA and lncRNA profiles of verrucoushyperplasia (VH) and verrucouscarcinoma (VC) compared to SCC |
|
| Relations |
| BioSample |
SAMN34074869 |
| SRA |
SRX19873086 |
