Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA269685 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1698140.fastq.gz | Fastqsanger.gz | |||
| SRR1698150.fastq.gz | Fastqsanger.gz | |||
| SRR1698160.fastq.gz | Fastqsanger.gz | |||
| SRR1698170.fastq.gz | Fastqsanger.gz | |||
| SRR1698141.fastq.gz | Fastqsanger.gz |
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Project description:In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. The combined reference had 67,157 lncRNA transcripts with no overlaps. We identified differential expression of 971 lncRNAs between PP and NN, 157 between PP and PT, and 377 between PT and NN. Based on differentially expressed (DE) lncRNAs between PP and NN, we identified a molecular lncRNA signature that distinguishes psoriatic skin from healthy skin .
2015-11-17 | GSE74697 | GEO
Project description:Psoriasis is a chronic inflammatory immune-mediated disorder affecting the skin and other organs including joints. Over 1,300 transcripts are altered in psoriatic involved skin compared to normal skin. Global epigenetic profiles of psoriatic skin have not been described. Here we describe the first genome-wide study of altered CpG methylation in psoriatic skin. We determined the methylation levels at 27,578 CpG sites in skin samples from individuals with psoriasis (12 involved, 8 uninvolved) and 10 unaffected individuals. CpG methylation of involved skin differed from normal skin at 1,108 sites. Twelve mapped to the epidermal differentiation complex, upstream or within genes that are highly up-regulated in psoriasis. Hierarchical clustering of 50 of the top differentially methylated (DM) sites separated psoriatic from normal skin samples. CpG sites where methylation was correlated with gene expression are reported. Sites with inverse correlations between methylation and nearby gene expression include those of KYNU, OAS2, S100A12, and SERPINB3, whose strong transcriptional up-regulation are important discriminators of psoriasis. We observed intrinsic epigenetic differences in uninvolved skin. Pyrosequencing of bisulfite-treated DNA from skin biopsies at three DM loci confirmed earlier findings and revealed a reversion of methylation levels towards the non-psoriatic state after one month of anti-TNF-a therapy.
2011-11-11 | GSE31835 | GEO
Project description:Psoriasis is a chronic inflammatory immune-mediated disorder affecting the skin and other organs including joints. Over 1,300 transcripts are altered in psoriatic involved skin compared to normal skin. Global epigenetic profiles of psoriatic skin have not been described. Here we describe the first genome-wide study of altered CpG methylation in psoriatic skin. We determined the methylation levels at 27,578 CpG sites in skin samples from individuals with psoriasis (12 involved, 8 uninvolved) and 10 unaffected individuals. CpG methylation of involved skin differed from normal skin at 1,108 sites. Twelve mapped to the epidermal differentiation complex, upstream or within genes that are highly up-regulated in psoriasis. Hierarchical clustering of 50 of the top differentially methylated (DM) sites separated psoriatic from normal skin samples. CpG sites where methylation was correlated with gene expression are reported. Sites with inverse correlations between methylation and nearby gene expression include those of KYNU, OAS2, S100A12, and SERPINB3, whose strong transcriptional up-regulation are important discriminators of psoriasis. We observed intrinsic epigenetic differences in uninvolved skin. Pyrosequencing of bisulfite-treated DNA from skin biopsies at three DM loci confirmed earlier findings and revealed a reversion of methylation levels towards the non-psoriatic state after one month of anti-TNF-a therapy. Control n=8 (NN), psoriasis involved n = 19 (PP), psoriasis uninvolved n=8 (PN). Hybridized to Illumina Human 27k methylation array. Paired samples are as follows: PN1 and PP1 PN2 and PP2 PN3 and PP3 PN4 and PP4 PN5 and PP5 PN6 and PP6 PN7 and PP7 PN8 and PP8
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Project description: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.
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