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| Status |
Public on Jan 10, 2023 |
| Title |
buccal pouch,coated with DMBA (squamous cell carcinoma), rep 3 |
| Sample type |
SRA |
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| Source name |
hamster buccal pouch
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| Organism |
Cricetulus griseus |
| Characteristics |
tissue: hamster buccal pouch
genotype: WT
treatment: coated with DMBA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Gradually extract total RNA from tissues according to the experimental instruction manual in Trizol kit
A total of 18–30 nt RNA fragments were excised, purified from a PAGE gel, and ligated with 5' and 3' adaptors using T4RNA ligase. Reverse transcription followed by PCR was used to create cDNA based on the small RNA ligated with 3' and 5' adapters. Subsequently, the amplified cDNA constructs were purified from agarose gel, in preparationfor sequencing analysis using the Illumina HiSeq 2500 Analyzer (Illumina, CA, USA) according to the manufacturer’sinstructions
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
s21E23
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| Data processing |
After base recognition by CASAVA software, it is converted into original sequencing sequence
After the basic analysis, the qualified sequenceswere mapped onto the reference sequence using the genome alignment analysis softwareBowtie2 (http://computing.bio.cam.ac.uk/local/doc/bowtie2.html)
The mappable sequences were then folded into a secondary structureusing RNAfold software with default parameters. Only the non-coding sequences could form a perfect stem-loopstructure and meet the criteria for miRNAs prediction were then considered to be a novel miRNA candidate.
Quantification of known miRNAs was performed using the present species known miRNA sequences from the mirdeep2 software (v1.1.2) miRBase database (release 22), counting the number of clean reads that match a known miRNA, and normalizing the rpm values
Assembly: hg19
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| Submission date |
Jan 09, 2023 |
| Last update date |
Jan 10, 2023 |
| Contact name |
Guohua Song |
| E-mail(s) |
ykdsgh@sxmu.edu.cn
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| Organization name |
Shanxi Medical University
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| Department |
Laboratory Animal Center
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| Lab |
Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model
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| Street address |
Road Xinjian 56, Taiyuan 030001, China
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| City |
Taiyuan |
| State/province |
Shanxi |
| ZIP/Postal code |
030001 |
| Country |
China |
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| Platform ID |
GPL20904 |
| Series (1) |
| GSE222429 |
Screening and identification of miR-181a-5p in oral squamous cell carcinoma and functional verification in vivo and in vitro |
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| Relations |
| BioSample |
SAMN32641629 |
| SRA |
SRX18978934 |
| 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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