|
| Status |
Public on Jan 30, 2023 |
| Title |
Patient Sample PS10 |
| Sample type |
SRA |
| |
|
| Source name |
Saliva_patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: oral squamous cell carcinoma patient
organ: Oral cavity
type of saliva: Unstimulated
tissue/sample type: Saliva
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cell-free saliva of healthy donors and OSCC patients using TRIzol method
Small RNA library was prepared using Ion Total RNA-Seq Kit v2.0 as per manufacturer's instructions
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
processed data file: LincRNA_matrix_file.txt, miRNA_matrix_file.txt, Protein_coding_matrix_file.txt, Total_transcripts_matrix_file.txt
|
| Data processing |
Adapter removal pre-processing using Cutadapt
Human genome alignment using Bowtie2
miRBase (v. 22) for miRNAs alignments, and gencode (v. 19) annotation file for other RNA species alignments.
WG Rescue alignment using Bowtie2 and read counting using FeatureCount, differential expression analysis using RUVseq and DESeq2
Microbial species alignment using ONE CODEX platform
Genome_build: hg19
Supplementary_files_format_and_content: Text files-read counts, Excel sheet -microbial reads
|
| |
|
| Submission date |
Jun 03, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
srivatsava naidu |
| E-mail(s) |
srivatsava.naidu@iitrpr.ac.in
|
| Organization name |
indian institute of technology ropar
|
| Department |
biomedical engineering
|
| Lab |
non-coding RNAs lab
|
| Street address |
bhara phool
|
| City |
ropar |
| State/province |
punjab |
| ZIP/Postal code |
140001 |
| Country |
India |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE176077 |
RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma |
|
| Relations |
| BioSample |
SAMN19546243 |
| SRA |
SRX11051961 |
