|
| Status |
Public on Apr 24, 2015 |
| Title |
R13M |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Homo sapiens |
| Characteristics |
subject: 17
disease: C
gender: M
age: 39
tissue: skin
|
| Treatment protocol |
Psoriasis patients and controls, skin biopsies from lesional and non-lesional site
|
| Growth protocol |
tissue sample from the lesional, non-lesional skin and healthy control skin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNALater and mirVana miRNA Isolation Kit
RNA was amplified with Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) and the output double stranded DNA was used to prepare SOLiD 5500 W System DNA fragment library according to manufacturer’s protocols (Thermo Fisher Scientific Inc, Waltham, MA, USA). The barcoding primers in library preparation and fragment sequencing chemistry was applied (75 bp in forward directions). In case of 12 samples per flowchip lane approximately 33 million mappable reads were expected per one sample, which would be enough for successful whole transcriptome expression pattern analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data
|
| |
|
| Submission date |
Mar 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sulev Koks |
| E-mail(s) |
sulev.koks@murdoch.edu.au
|
| Phone |
+61864570313
|
| Organization name |
Murdoch University
|
| Department |
Centre for Molecular Medicine and Innovative Therapeutics
|
| Street address |
90 South Street
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6150 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE66511 |
Transcriptional Landscape of Psoriasis Identifies the Involvement of IL36 and IL36RN |
|
| Relations |
| BioSample |
SAMN03387129 |
| SRA |
SRX897359 |
