|
| Status |
Public on Aug 01, 2018 |
| Title |
Non-SCC1 |
| Sample type |
SRA |
| |
|
| Source name |
RDEB1
|
| Organism |
Homo sapiens |
| Characteristics |
tag: Normal RDEB Skin
diagnosis: recessive dystrophic epidermolysis bullosa (RDEB)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen Rneasy protocols from fresh forzen tumors where tumor cellularity was determined to be >85% using immunohistochemistry for SCC cases and whole skin used for non-SCC.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Non-SCC1
|
| Data processing |
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample
|
| |
|
| Submission date |
Mar 08, 2018 |
| Last update date |
Aug 01, 2018 |
| Contact name |
Andrew South |
| E-mail(s) |
[email protected]
|
| Organization name |
Thomas Jefferson University
|
| Department |
Dermatology and Cutaneous Biology
|
| Lab |
BLSB 406
|
| Street address |
233 S 10th Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE111582 |
APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa |
|
| Relations |
| BioSample |
SAMN08663013 |
| SRA |
SRX3775951 |
