 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 14, 2017 |
| Title |
24_NL |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
skin phenotype: Non-lesional psoriatic skin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TissueLyser LT homogenizer (Qiagen, USA) was used to homogenize biopsy specimens. Total RNA was extracted with ExtractRNA reagent (Evrogen, Russia) according to the manufacturer’s protocol. Isolated RNA was dissolved in RNase free water, rRNA was depleted using RiboMinus™ Eukaryote Kit for RNA-Seq (Life Technologies, USA), and the samples were stored at -80C°. The quality of total RNA was evaluated with RNA 6000 Pico Chip Kit and Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA) and with Quant-iT™ RNA Assay Kit and Qubit Fluorometer (Life Technologies, USA). The average RNA integrity number (RIN) of samples was ≥7.
Library preparation and sequencing were performed using SOLiD 4 System platform and sequencing chemistry according to the manufacturer’s instructions (Life Technologies, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
4 mm punch biopsy specimens were taken from nonlesional (NL sample) skin 3-4 cm apart from the lesion, so as the area doesn’t have any visual signs of psoriasis
|
| Data processing |
Raw pair-end reads (50+25 bp) were obtained from SOLID4 System (Applied Biosystems) in color space format (*.csfasta)
*.csfasta were filtered for quality, the adaptor sequences were trimmed and the reads were aligned to the UCSC human reference genome (hg19) using the Applied Biosystems’s Bioscope software to obtain reads in the BAM format.
Mapping to multiple locations was permitted. The aligned read BAM files were assembled into transcripts, their abundance was estimated and tests for differential expression were processed by Bioconductor DESeq package
FDR correction for multiple testing was performed according to Benjamini et al.
Using the cutoffs of fold change (FC) > 1.5 and false discovery rate of (FDR) <0.05, only genes that had read counts at all samples were listed
Genome_build: UCSC human reference genome (hg19)
Supplementary_files_format_and_content: tab-delimited text file includes ensembl_gene_id, hgnc_symbol, baseMean, foldChange, log FoldChange, p-values and normalized counts produced by DESeq for each sample
|
| |
|
| Submission date |
Feb 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Evgeny Chekalin |
| E-mail(s) |
eygen.chekalin@gmail.com
|
| Organization name |
Vavilov Institute of General Genetics
|
| Lab |
Functional Genomics
|
| Street address |
Gubkina, 3
|
| City |
Moscow |
| ZIP/Postal code |
119991 |
| Country |
Russia |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE78023 |
Transcriptional regulatory networks of psoriasis |
|
| Relations |
| SRA |
SRX1590497 |
| BioSample |
SAMN04502596 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
