|
| Status |
Public on Dec 08, 2021 |
| Title |
mRNA_HPV+OSCC_C3 |
| Sample type |
SRA |
| |
|
| Source name |
OSCC
|
| Organism |
Homo sapiens |
| Characteristics |
hpv status: HPV+
cell type: OSCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Preparing selected tissue，flash frozen on dry ice, and RNA was harvested using trizol reagent.RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method.After library construction, the concentration of library was measured by the Qubit® fluorometer and adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the insert size and concentration of the library was identical, the samples can then be subjected for sequencing
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
C3
|
| Data processing |
the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained
|
| |
|
| Submission date |
Dec 06, 2021 |
| Last update date |
Dec 08, 2021 |
| Contact name |
Yue Wang |
| E-mail(s) |
wy19960401@126.com
|
| Phone |
17862890372
|
| Organization name |
binzhou medical university
|
| Street address |
NO.661 Huanghe Er Road, Binzhou City
|
| City |
binzhou |
| State/province |
shandong |
| ZIP/Postal code |
256600 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE190222 |
Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [mRNA] |
| GSE190224 |
Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation |
|
| Relations |
| BioSample |
SAMN23673029 |
| SRA |
SRX13323383 |
