 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 25, 2019 |
| Title |
High-throughput transcriptome analysis of clinical psoriasis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The present study is aiming to understand transcriptome changes during psoriatic changes using high-throughput sequencing and thereby comprehensively assess the diseases and guide future research directions.
Methods: Clinical psoriatic samples, including psoriatic lesions and their adjacent normal skin samples, and the surgical derived skins from healthy individuals as comparative controls were collected and analysed of their RNA expression profile using Illumina HiSeq 4000. raw sequencing reads were processed and pre-qualified using Trimmomatic and Fragments Per kb Per Million Reads (FPKM) method was used to calculate the abundance of each transcript followed by Negative Binomial Distribution tests to identify significant differences in each comparison.
Results: Total reads for mRNAs, lncRNAs and miRNAs was 108,552, 105,136 and 2762, respectively, including 649 novel lncRNAs and 905 novel miRNAs. 5383 DE_mRNAs, 1201 DE_lncRNAs and 80 DE_miRNAs were identified in the comparison of the psoriasis lesions-adjacent normal group (PN) vs. healthy control-derived normal skin group (NN; PN vs. NN). A total of 9513 DE_mRNAs, 1940 DE_lncRNAs and 251 DE_miRNAs were identified in the psoriasis lesion group (PS) vs. NN comparison (PS vs. NN), and 4946 DE_mRNAs, 1559 DE_lncRNAs and 92 DE_miRNAs were identified in the PS vs. PN comparison.
Conclusions: We identified numerous differentially expressed RNAs, including mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). Our results reveal transcriptomic changes, expand our mechanistic understanding of psoriasis, and may lead to new directions for psoriasis research.
|
| |
|
| Overall design |
Five adult psoriasis patients were recruited in this study, none of which had received systematic treatment and all were free from medical treatment within the 3 months before recruitment. Psoriatic plaque tissue (PS) and adjacent normal skin tissue (PN) was taken from each patient, and five control skin samples were obtained from surgical discard specimens of healthy people (NN). Total RNA was isolated and sequencing was conducted with a HiSeq 4000 (Illumina).
|
| |
|
| Contributor(s) |
Yu Z, Shi Y |
| Citation(s) |
32381429 |
| |
| Submission date |
Dec 24, 2019 |
| Last update date |
Nov 01, 2020 |
| Contact name |
Zengyang Yu |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Tenth People's Hospital, Tongji University School of Medicine
|
| Street address |
301 Yanchang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200072 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (15)
|
|
| Relations |
| BioProject |
PRJNA597533 |
| SRA |
SRP238713 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142582_lncRNA_counts.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE142582_mRNA_counts.txt.gz |
19.6 Mb |
(ftp)(http) |
TXT |
| GSE142582_miRNA_counts.txt.gz |
67.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...