|
| Status |
Public on Jun 11, 2014 |
| Title |
N252_3 |
| Sample type |
SRA |
| |
|
| Source name |
Healthy_N252, Healthy, Agonist
|
| Organism |
Homo sapiens |
| Characteristics |
patient: Healthy_N252
patient id: H3
gender: F
age: 36-74 mean 51
tissue/treatment id: 3
tissue: Healthy
treatment: Agonist
|
| Treatment protocol |
All lesional and non lesional skin biopsies were quartered and one quarter of each was stored in RNA-later (Life Technologies) at 4oC until further use. The remaining three quarters were cultured with either 0.1% DMSO (vehicle control), the AhR agonist FICZ (250 nM) or the AhR antagonist CH-2233191 (3 μM) in IMDM (Sigma) containing 2% Pen-Strep-Gln solution (Sigma) and 10% knockout Serum replacement factor (Life Technologies) at 37°C in humidified 5% CO2/95% air for 16h. Skin biopsies from healthy donors were processed in the same ways as those of patients.
|
| Growth protocol |
Eight psoriatic patients of European descendent (5 males, 3 females; mean age 52 years, range 30-63 years) not receiving any systemic treatment at the time of visit were recruited at the Psoriasis-Center, University Medical Center Schleswig-Holstein, Kiel (Germany) following an examination by an expert clinician; one 6 mm full-thickness skin biopsy was obtained from the margin of a lesion and one from non lesional skin at least 5 cm apart from any psoriatic lesion at the same anatomical site. Full patient demographics are shown in Supplementary Table 1. Four 5 mm full-thickness skin biopsies were obtained from discarded healthy skin from female donors of European descendent (mean age 51 years, range 36-74 years) undergoing plastic surgery procedures at Guy’s and St. Thomas’ Hospital, London (UK).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human skin was obtained using the Mirvana Kit (Life Technologies) according to the manufacturer’s instructions
cDNA libraries were prepared using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
N252_3
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
Reads pairs were mapped using bowtie version 0.12.7 with parameters "-v 3 -a --best -y -I 0 -X 10000" to the transcriptome of GRCh37
Reads mapping uniquely to a gene were counted, and normalised by the total reads per library.
Genome_build: GRCh37
Supplementary_files_format_and_content: Files ps_tt_gel_raw.txt (text, tab-delimit, read counts per gene) and ps_tt_gel_norm.txt (text, tab-delimit, normalised read counts per gene). Boths files are linked as supplementary files on the Series record.
|
| |
|
| Submission date |
Jun 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gitta Stockinger |
| E-mail(s) |
bstocki@nimr.mrc.ac.uk
|
| Organization name |
National Institute for Medical Research
|
| Department |
Division of Molecular Immunology
|
| Street address |
The Ridgeway
|
| City |
London |
| ZIP/Postal code |
NW7 1AA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE47944 |
Environmental factors transmitted by aryl hydrocarbon receptor influence severity of psoriatic skin inflammation [RNA-Seq] |
| GSE47965 |
Environmental factors transmitted by aryl hydrocarbon receptor influence severity of psoriatic skin inflammation |
|
| Relations |
| BioSample |
SAMN02203793 |
| SRA |
SRX306140 |
