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| Status |
Public on Dec 08, 2021 |
| Title |
miRNA_HPV+OSCC_C3 |
| Sample type |
SRA |
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| Source name |
OSCC
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| Organism |
Homo sapiens |
| Characteristics |
hpv status: HPV+
cell type: OSCC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Preparing selected tissue，flash frozen on dry ice，and RNA was harvested using trizol reagent.A total amount of 3 µg total RNA per sample was used as input material for the small RNA library
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generat
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
C3
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| Data processing |
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively
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| Submission date |
Dec 06, 2021 |
| Last update date |
Dec 08, 2021 |
| Contact name |
Yue Wang |
| E-mail(s) |
wy19960401@126.com
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| Phone |
17862890372
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| Organization name |
binzhou medical university
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| Street address |
NO.661 Huanghe Er Road, Binzhou City
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| City |
binzhou |
| State/province |
shandong |
| ZIP/Postal code |
256600 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE190223 |
Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA] |
| GSE190224 |
Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation |
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| Relations |
| BioSample |
SAMN23673035 |
| SRA |
SRX13323377 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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