|
| Status |
Public on Jan 31, 2017 |
| Title |
CL1-0_S100A7A+ |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CL1-0
genotype/variation: S100A7A knock-in
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA will be isolated from liver tissues using TRIzol® reagent (Invitrogen). Total RNA (15 μg) for each sample will be used for purifying the poly(A)-containing mRNA molecules, RNA amplification, and synthesis of double stranded cDNAs that will be ligated to adapters, following the Illumina (San Diego, California, USA) TruSeq RNA Sample Prep guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Illumina Miseq reporter software 2.1 used for basecalling.
The Strand NGS software (version 2.1) was performed using default parameters for pre-alignment and post-alignment quality control analysis.
Differentially expressed genes (DEGs) from 4 groups of cultured samples were calculated from the raw reads using the DESeq method.
The significance was determined by MannWhitney un-paired test or 2-way ANOVA and a Benjamini and Hochberg false discovery rate (FDR) multiple gene correction was applied.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample
|
| |
|
| Submission date |
Sep 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kuang-Den Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Kaohsiung Chang Gung Memorial Hospital
|
| Department |
Translational Research Center in Biomedical Sicences
|
| Lab |
Liver transplantation lab
|
| Street address |
123, Ta-Pei Rd., Niao-Sung Dist.
|
| City |
Kaohsiung |
| ZIP/Postal code |
83342 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE86344 |
RNA-Seq analysis facilitates quantitative analysis to identify DEGs in lung cancer cell lines regulated by S100A7A introduction in comparison with Cl1-0 control and S100A7A knockdown in comparison with CL1-5 control. |
|
| Relations |
| BioSample |
SAMN05725321 |
| SRA |
SRX2093818 |
