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Sample GSM5326840

Query DataSets for GSM5326840

Status

Public on Oct 31, 2021

Title

ML_10009200157986

Sample type

SRA

Source name

Skin

Organism

Homo sapiens

Characteristics

tissue: Skin
disease state: Unaffected

Extracted molecule

total RNA

Extraction protocol

Participants were adults of European descent. Cases had psoriasis vulgaris and underwent a wash-out period without any topical or systemic-/phototherapy for two and four weeks prior to participation, respectively. Controls did not have psoriasis or any other inflammatory skin disease, nor any first-degree relatives with psoriasis. Participants were excluded if they had used tanning beds four weeks prior to participation. From cases, two 4mm skin biopsies were collected; one PP and one PN. PP was collected from the outer rim of a plaque, in the area which appeared most inflamed macroscopically. From controls, one 4mm skin biopsy NN was collected. When possible, the PN and NN samples were taken from a sun-protected area on the buttock and PN was taken at least 10 cm away from any visible plaque. Biopsies were snap frozen in liquid nitrogen bedside and later stored at -80 °C. Skin biopsies were homogenized using Precellys homogenizer (Bertin Technologies, Rockville, MD USA) and RNA was extracted using mirVana Isolation Kit (Applied Biosystems, Foster City, CA, USA).
Sequencing libraries were prepared using the NEXTflex small RNA-seq kit v3 (Bioo Scientific/PerkinElmer, Austin, TX, USA). Fragments/libraries were run on a Labchip GX (Caliper/PerkinElmer, Hopkinton, MA, USA), for quality control and quantitation. Individual libraries were normalized and pooled. The library pool was later purified with the QIAquick PCR Purification Kit (Qiagen AB, Sweden) and evaluated on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to instructions.
Single-end read sequencing was performed on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA, USA). The reads were mapped to human miRNAs in the miRBase database v22.1 with the miraligner tool.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 4000

Data processing

Adpater were removed with cutadapt and reads with quality score lower than 33 were filtered out with fastx_collapser
The reads were mapped to human miRNAs in the miRBase database v22.1 through miraligner tool.
Counts from each sample were combined to form the combined matrix
The count matrices were transformed using the voom algorithm from the limma package of Bioconductor.
MicroRNAs with an average count per million across all samples, of less than one, were filtered out.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with cpm normalized gene counts for 526 expressed miRNAs and every sample

Submission date

May 20, 2021

Last update date

Oct 31, 2021

Contact name

Mari Løset

E-mail(s)

mari.loset@ntnu.no

Phone

+4790799117

Organization name

NTNU