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Sample GSM3583672 Query DataSets for GSM3583672
Status Public on Feb 13, 2019
Title 025N
Sample type SRA
 
Source name mucosa
Organism Homo sapiens
Characteristics tissue: oral
Sex: female
condition: OSF
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description mRNA sequencing approach for library contructions
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
 
Submission date Jan 29, 2019
Last update date Feb 14, 2019
Contact name Giles Hu
Organization name YJY
Street address Dapeng
City Shenzhen
ZIP/Postal code 410083
Country China
 
Platform ID GPL20795
Series (1)
GSE125866 Long non-coding RNA expression profile associated with malignant progression of oral submucous fibrosis
Relations
BioSample SAMN10842151
SRA SRX5307695

Supplementary file Size Download File type/resource
GSM3583672_025N.gene.FPKM.xls.gz 356.4 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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