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| Status |
Public on Feb 13, 2019 |
| Title |
07T |
| Sample type |
SRA |
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| Source name |
mucosa
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| Organism |
Homo sapiens |
| Characteristics |
tissue: oral
Sex: female
condition: OSCC
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| Treatment protocol |
Fresh tissue specimens of OSCC (n=8), OSF (n=8), and normal oral mucosa (n=2) were obtained at the time of surgical resection at Xiangya Second Hospital and Xiangya Hospital, Central South University (Changsha, China) and Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine (Shanghai, China) from January 2016 to June 2017. The patients’ informed consents had been obtained under a protocol reviewed and approved by the Institutional Review Boards of the Xiangya School of Medicine or Shanghai Jiaotong University School of Medicine. 2 normal specimens were obtained from healthy oral mucosa. OSF is diagnosed excluding OSCC or neoplastic disease.
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| Growth protocol |
Fresh tissue specimens of OSCC (n=8), OSF (n=8), and normal oral mucosa (n=2) were obtained at the time of surgical resection at Xiangya Second Hospital and Xiangya Hospital, Central South University (Changsha, China) and Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine (Shanghai, China) from January 2016 to June 2017. The patients’ informed consents had been obtained under a protocol reviewed and approved by the Institutional Review Boards of the Xiangya School of Medicine or Shanghai Jiaotong University School of Medicine. 2 normal specimens were obtained from healthy oral mucosa. OSF is diagnosed excluding OSCC or neoplastic disease.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (MRI, USA), and then measured by using Nanodrop 2.0.
Epicentre Ribo-ZeroTM kit was used to remove rRNA. Subsequently, the fragmentation buffer was used to break the RNA into short fragments of 150-200 bp, which was used as a template to synthesize cDNA using random hexamers. After purification, the double-stranded cDNA was subjected to terminal repair; a tail was added, and the sequencing linker was ligated, and finally cDNA library of total RNA was obtained by PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
mRNA sequencing approach for library contructions
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| Data processing |
Basecalls performed using CASAVA
RNA reads are removed adaptor sequences and low quality sequences using software SOAPnuke version 1.0.1 with parameters by default aligned to the genome hg19 using hisat version 2.0.12 with default parameters, and Fragments per kilobase of exon per million fragments mapped (FPKM) are caculated.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm files were generated using hisat
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| Submission date |
Jan 29, 2019 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Giles Hu |
| Organization name |
YJY
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| Street address |
Dapeng
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| City |
Shenzhen |
| ZIP/Postal code |
410083 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE125866 |
Long non-coding RNA expression profile associated with malignant progression of oral submucous fibrosis |
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| Relations |
| BioSample |
SAMN10842141 |
| SRA |
SRX5307701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3583678_07T.gene.FPKM.xls.gz |
368.3 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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