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Sample GSM3336653 Query DataSets for GSM3336653
Status Public on Sep 12, 2019
Title B6C
Sample type SRA
 
Source name cell
Organism Homo sapiens
Characteristics cell type: human gingival fibroblasts
individual: donor 1
culture time: 6h
treatment: control
Treatment protocol Cells were treated with F. nucleatum at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and cultured at 2h, 6h, 12h, 24h and 48h
Growth protocol Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.Then we assembled those clean reads into Unigenes, followed with Unigene functional annotation, SSR detection and calculate the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differential expressed genes) between samples and do clustering analysis and functional annotations
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs
 
Submission date Aug 17, 2018
Last update date Sep 12, 2019
Contact name Wenyan Kang
E-mail(s) 202090000024@sdu.edu.cn
Organization name Shandong university
Street address No. 44-1 Wenhua Road West
City Jinan, Shandong
ZIP/Postal code 250012
Country China
 
Platform ID GPL23227
Series (1)
GSE118691 Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival fibroblasts
Relations
BioSample SAMN09847593
SRA SRX4562706

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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