|
| Status |
Public on Jan 22, 2018 |
| Title |
c2 control cell line |
| 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 |
c2
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN03292260 |
| SRA |
SRX850954 |
