|
| Status |
Public on Jul 01, 2021 |
| Title |
HOK-16B CBD rep3 |
| Sample type |
SRA |
| |
|
| Source name |
human oral keratinocyte
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HOK-16B
cell type: human oral keratinocyte
treatment: treated with CBD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
the immortalized human oral keratinocyte HOK-21B cell line
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 09, 2020 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Quan Yuan |
| E-mail(s) |
yuanquan@scu.edu.cn
|
| Organization name |
West China Hospital of Stomatology, Sichuan University
|
| Lab |
State Key laboratory of Oral Diseases
|
| Street address |
14 Third section, Renmin Nan Road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE152088 |
Effects of cannabidiol on the inflammation-stimulated keratinocytes |
|
| Relations |
| BioSample |
SAMN15185440 |
| SRA |
SRX8508291 |
