|
| Status |
Public on Mar 01, 2021 |
| Title |
RDEBSCC70_untreated1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line derived from cutaneous squamous cell carcinoma tumor in patient with recessive dystrophic epidermolysis bullosa
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cell line derived from cutaneous squamous cell carcinoma tumor in patient with recessive dystrophic epidermolysis bullosa
cell line number: 70
treatment: untreated
|
| Treatment protocol |
EpiLife Medium with 1% EpiLife Defined Growth Supplement (EDGS) and 0.2% Gentamicin/Amphotericin solution (Gibco/Thermo Fisher Scientific)
|
| Growth protocol |
500,000 cells plated in 10cm dishes with EpiLife media (see above for specific experimental treatments) for 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested after 24 hours in culture using the RNeasy Micro Kit (Qiagen). RNA concentration and quality were determined using RiboGreen quantitation and Agilent 2100 Bioanalyzer
Libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit. Libraries were analyzed using PicoGreen, DNA Agilent, and KAPA to determine concentration, size, and functionality
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RDEBSCC70_1_1
|
| Data processing |
FastQC v0.11.8 - generates sequence quality plots
Trimmomatic v0.39 - removes sequence adapters and low quality bases
FastQC v0.11.8 - generates sequence quality plots for filtered fastq files
HISAT2 v2.1.0 - aligns reads to the genome, creating a bam file that is then sorted and indexed
Picard v2.18.10 - calculates insert size metrics
SubRead v1.6.2 - featureCounts program in SubRead package is used to generate a transcript abundance file
Cufflinks v2.2.1 - Cuffquant program in the Cufflinks package is used to generate a .cxb transcript abundance file
Cufflinks v2.2.1 - Cuffnorm program in the Cufflinks package is used to generate FPKM data
Genome_build: hg38
Supplementary_files_format_and_content: xlsx spreadsheet in matrix form, where each row corresponds to a gene, each column corresponds to a sample, with raw read counts in the individual cells
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Jakub Tolar |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota - Twin Cities
|
| Department |
Pediatrics
|
| Lab |
Stem Cell Institute
|
| Street address |
2001 6th St SE
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE134395 |
Role of Transforming Growth Factor-β1 in Recessive Dystrophic Epidermolysis Bullosa Squamous Cell Carcinoma |
|
| Relations |
| SRA |
SRX6455460 |
| BioSample |
SAMN12306412 |
