The stratum corneum transcriptome in atopic dermatitis can be assessed by tape stripping
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA673403 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12952919.fastq.gz | Fastqsanger.gz | |||
| SRR12952920.fastq.gz | Fastqsanger.gz | |||
| SRR12952921.fastq.gz | Fastqsanger.gz | |||
| SRR12952922.fastq.gz | Fastqsanger.gz | |||
| SRR12952923.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 42 |
Similar Datasets
Project description:Background: Skin biopsies represent a gold standard in skin immunology and pathology but can cause pain and induce scarring. Non-invasive techniques will facilitate study recruitment of e.g. patients with pediatric atopic dermatitis (AD), hand eczema or facial dermatitis. Objective: By RNA sequencing, we examined whether the stratum corneum transcriptome in AD skin can be assessed by tape stripping, as compared to the epidermal transcriptome of AD in skin biopsies. To make the procedure clinically relevant tape strips were stored and shipped at room temperature for up to 3 days. Methods: Nine adult Caucasian AD patients and three healthy volunteers were included. Tape samples were collected from non-lesional and lesional skin. Biopsies were collected from lesional skin and were split into epidermis and dermis. Total RNA was extracted, and shotgun sequencing was performed. Results: Shotgun sequencing could be performed on skin cells obtained from two consecutive tape strips which had been stored and shipped at room temperature for up to three days. The most prominent differences between the tape strip and biopsy derived transcriptome were due to structural genes, while established molecular markers of AD, including CCL17, CCL22, IL17A and S100A7-S100A9, were also identified in tape strip samples. Furthermore, the tape strip derived transcriptome showed promise in also analysing the skin microbiome. Conclusion: Our study shows that the stratum corneum (SC) transcriptome of AD can be assessed by tape stripping the skin, supporting that this method may be central in future skin biomarker research.
2020-10-31 | GSE160501 | GEO
Project description:Hand eczema (HE) is a prevalent skin disease. However, classification of HE into different subtypes remains challenging. Limited number of prior studies have employed invasive biopsy-based strategies; yet, studies of the HE proteome using non-invasive tape stripping methodology have not been reported. In this study, we wanted to assess whether global proteomic analysis of skin tape strip samples can be used for sub-classification of HE patients. Tape strips were collected from patients with HE and healthy skin. Liquid chromatography–mass spectrometry (LC/MS) proteomics was performed, and the global protein expression was analyzed. We identified 2,919 proteins in stratum corneum-derived skin cells from tape strip samples. Compared to healthy skin, the lesional samples from HE patients exhibited increased expression of immune-related markers and a decreased expression of structural barrier proteins. The difference between HE subtypes was restricted to the lesional skin areas, and included an increased expression of skin barrier-related proteins independently of the concurrent AD. In conclusion we found, that the non-invasive tape strip method used in combination with LC/MS proteomics can be used for analysis of skin protein expression in HE patients. Thus, the method shows potential for assessing the proteomic differences between subtypes of HE, and biomarker discovery.
2023-04-26 | PXD039665 | Pride
Project description:This project aims to evaluates Tape Stripping (TS) of stratum corneum (SC) for non-invasive proteomic analysis of AK using mass spectrometry approach.
2018-10-01 | PXD011000 | Pride
Project description:Use of tape stripping for the collection of stratum corneum is a versatile and reliable procedure for the evaluation of the human skin health, including assessments of the skin barrier function, microbial content, and disease biomarkers. The tape stripping procedure is widely referenced; however, the number and type of tapes required for sample collection vary considerably, and the lack of standardized sampling, processing and normalization protocols complicate data comparison and interpretation. We have compared the performances of two commonly used non-invasive skin sampling platforms by collecting skin tissue from 34 healthy volunteers and applying standardization throughout the workflow, from sampling to data analysis. Our results showed significant differences in the amounts of tissue collected per tape, erythema levels, RNA and protein yields. RNA extracts from both platforms were suitable for sequencing; comparable input and quality of reads were produced for both test groups, however significant differences were found in the percentage of uniquely mapped reads and detected genes. This data highlights processing optimization as an important step in maximizing the efficiency of biomolecule extraction from tape strips and further presents a tape stripping method suitable for fast, efficient, and non-invasive epidermal tissue collection applicable to skin biomarker discovery.
2024-04-24 | GSE262827 | GEO
Project description:Tape stripping has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq (a low cost, multiplex-based, transcriptomic profiling technique) to study the epidermal transcriptome of AD patients and healthy controls from tape stripped skin samples.
2022-05-31 | GSE199046 | GEO
Project description:The objective of this study was to provide a comprehensive evaluation of how well tape-stripping paired with high resolution RNA-sequencing captures the global transcriptomic changes in psoriasis.
2022-01-20 | GSE178197 | GEO
Project description:Profilig the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq
| PRJNA818188 | ENA
Project description:Decreased levels of antimicrobial peptides (AMPs) in atopic dermatitis (AD) have previously been reported and have been linked to the increased susceptibility to skin infections found in AD patients. This study intents to identify AMPs: hBD-2, hBD-3, RNase7, psoriasin and LL-37 in AD patients and healthy controls, and determine concentrations in consecutive depths of the outer most skin layers. Tape stripping was used on lesional and non-lesional skin. From each skin site, 35 consecutive tape strips were collected and pooled in groups of 5. Commercially available ELISA kits were used to determine AMP concentration in stratum corneum samples. hBD-2, hBD-3, RNase7 and psoriasin were identified in stratum corneum samples. hBD-3-level was markedly higher in AD non-lesional skin compared to healthy controls, and a similar trend was observed for RNase7. Most AMPs were distributed evenly through 35 tape strips, implying a homogeneous distribution of antimicrobial defense in the outer most skin layers. The findings indicate that AD patients may not suffer from a general baseline deficiency in AMPs, and that the innate immune defense is present throughout the stratum corneum, both insights of importance for understanding the role of AMPs in AD.
| S-EPMC5786105 | biostudies-literature
Project description:Non-invasive tape-stripping of psoriatic skin with high-resolution RNA profiling
| PRJNA737647 | ENA
Project description:The aim of this study was to investigate the amount of protein in stratum corneum in atopic dermatitis (AD) patients and healthy controls, using tape stripping technique. Furthermore, to compare two different methods for protein assessment. Tape stripping was performed in AD patients and healthy controls to collect stratum corneum samples and subsequently analysed with two different methods: Squame Scan, which gives an estimate of total protein (soluble and insoluble) and Micro BCA protein determination kit which measures soluble protein. Significant differences in cumulative protein content between AD lesional, AD non-lesional and healthy control skin was found using the Squame Scan as well as the Micro BCA protein determination kit. AD patients had significantly lower amount of protein, both total protein and soluble protein compared to healthy controls. Furthermore, soluble protein formed 82% of total protein in AD lesional skin, compared to 17-24% for AD non-lesional skin and healthy control. A decreasing amount of total protein with increasing stratum corneum depth was found for all skin types. Significant differences in stratum corneum protein content between AD lesional, AD non-lesional and healthy control skin were revealed, independent of method used.
| S-EPMC4730153 | biostudies-literature