|
| Status |
Public on Dec 20, 2013 |
| Title |
Skin sample from young subjects |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Homo sapiens |
| Characteristics |
subjects: 10 healthy female volunteers
age of subjects: about 25 years
tissue: skin (epidermal suction blister samples)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Epidermal suction blister samples were collected according to the current version of the Declaration of Helsinki and the guideline of the International Conference on Harmonization Good Clinical Practice (ICH GCP) was observed as applicable to a non-drug study. All volunteers provided written, informed consent. Suction blister samples were obtained at the study center of Beiersdorf AG and approved by the Beiersdorf AG Legal Review Board. Briefly, epidermis samples were detached from the forearms of 10 healthy female volunteers by applying a negative pressure of 150–250 mmHg for 2 h. Subsequently, suction blister roofs were taken and immediately stored at -20 °C. Before RNA isolation, suction blister samples were homogenized using a TissueLyser (Retsch). Total RNA from suction blister samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturer’s instructions. The Poly(A)Purist™ MAG Kit (Ambion) was used for mRNA selection.
Sequencing libraries were prepared using 1µg of DNAse-treated human total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Young
|
| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Transcriptome-mapping: tophat 2.0
Evaluation of differential expression: DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE46486 |
Age-related methylation changes are associated with altered transcriptional circuitry [RNA-seq] |
| GSE46487 |
Age-related methylation changes are associated with altered transcriptional circuitry |
|
| Relations |
| BioSample |
SAMN02086417 |
| SRA |
SRX272490 |
