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| Status |
Public on Sep 12, 2019 |
| Title |
C24F |
| Sample type |
SRA |
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| Source name |
cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human gingival fibroblasts
individual: donor 2
culture time: 24h
treatment: F. nucleatum
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| 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
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| Growth protocol |
Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| 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
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| Submission date |
Aug 17, 2018 |
| Last update date |
Sep 12, 2019 |
| Contact name |
Wenyan Kang |
| E-mail(s) |
[email protected]
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| Organization name |
Shandong university
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| Street address |
No. 44-1 Wenhua Road West
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| City |
Jinan, Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE118691 |
Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival fibroblasts |
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| Relations |
| BioSample |
SAMN09847577 |
| SRA |
SRX4562722 |
| 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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