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Sample GSM1589102 Query DataSets for GSM1589102
Status Public on Jan 22, 2018
Title c+b3 control cell line add bFGF treatment
Sample type SRA
Source name human dermis fibroblast
Organism Homo sapiens
Characteristics tissue: dermis fibroblast
genotype: wild type
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately.The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description b3
Data processing Mapping of single-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to human genome (version: GRCH38) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied DEseq algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) Fold Change>1.5 or <0.667; ii) FDR<0.05. [3] Volcano Plot was drawn by the R based on the differentially gene analysis and the color was determined by the filtering criteria.
Genome_build: GRCH38
Supplementary_files_format_and_content: RPKM for each sample
Submission date Jan 22, 2015
Last update date May 15, 2019
Contact name Yuanhu Xuan
Organization name wenzhou medical university
Department Medical School
Street address Chashan High School District
City Wenzhou
ZIP/Postal code 325035
Country China
Platform ID GPL17303
Series (1)
GSE65193 The activation of the NF-κB-JNK pathway is independent of the PI3K-Rac1-JNK pathway involved in the bFGF-regulated human fibroblast cell migration
BioSample SAMN03292257
SRA SRX850952

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

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