|
| Status |
Public on Mar 18, 2019 |
| Title |
Patient 10 Posttreatment |
| Sample type |
SRA |
| |
|
| Source name |
Epidermis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Epidermis
treatment stage: Glucocorticoid treatment
|
| Treatment protocol |
All patients had not been treated systemically for at least 4 weeks or topical treatment for at least 2 weeks prior to the study entry. Patients were treated with topical halomethasone monohydrate 0.05% cream daily for 2 weeks. Skin lesion severity was evaluated by PASI (psoriasis area and severity index) score. Typical lesions that represented the overall skin condition before and after treatment as well as relapse (4 weeks after treatment) were taken.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated using a Qiagen RNeasy kit according to the manufacturer’s instructions (Qiagen) or TRIzol (Invitrogen). After total RNA extraction, magnetic beads with oligo dT were used to isolate polyA enriched mRNA.
Libraries were constructed by BGI using their standard RNA transcriptome sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Sample name:
26
Glucocorticoid treatment
|
| Data processing |
QA/QC of raw fastq files was performed using FastQC v 0.10.1
Raw fastq sequences were aligned to the hg38 genome using tophat2 v2.0.13 using the Ensembl gtf
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_geneMatrix_NORMALIZED.txt represents normalized FPKM values using cuffnorm v2.2.1
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
Mar 18, 2019 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE114729 |
Transcriptome analysis of Psoriasis |
|
| Relations |
| BioSample |
SAMN09233545 |
| SRA |
SRX4108721 |
