|
| Status |
Public on Dec 12, 2022 |
| Title |
epidermis_32h_subject111 |
| Sample type |
RNA |
| |
|
| Source name |
Skin biopsy from upper back, epidermis, subject P111, taken at 8:00h day after
|
| Organism |
Homo sapiens |
| Characteristics |
subject: P111
tissue: Skin – epidermis
time of collection: 8:00h day after
Sex: female
age: 28
|
| Treatment protocol |
Skin biopsies were subsequently incubated in PBS at 55oC for 3 min to separate epidermis and dermis. Tissue samples were then frozen in liquid nitrogen and stored at -80oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 mm biopsies were obtained from the upper back for seven time points over a period of 24 h (8:00, 12:00, 16:00, 20:00, 00:00, 04:00 and 8:00 the following day).
RNA extraction and quality control was performed with TRIzol following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
For each of the samples, RNA was amplified and 1.2–1.65 μg of RNA were labelled with Cyanine 3-CTP according to the manufacturer's instruction (Miltenyi Biotec).
|
| |
|
| Hybridization protocol |
Samples were hybridized to Agilent Whole Genome Oligo Microarrays 4x44k (Agilent Technologies).
|
| Scan protocol |
Agilent protocol
|
| Description |
Gene expression at 8:00h the day after in human epidermis
|
| Data processing |
The RMA algorithm was used to preprocess and extract expression profiles from the raw CEL files. Genes were annotated with ENSEMBL and ENTREZ IDs using Agilent “Human Genome, Whole” annotation data (hgug4112a.db, v3.2). Background correction was performed with the “normexp” function from R package “limma”; normalization between the different arrays was done with the “quantile” function from the same package. Non-annotated probes as well as control probes were filtered out. Genes were considered to be expressed if the signal across the 7 time points was well above the background signal in at least 50% of the samples. Averaged values of probes that mapped to the same gene were used for further analysis.
|
| |
|
| Submission date |
May 31, 2022 |
| Last update date |
Dec 12, 2022 |
| Contact name |
Bharath Ananthasubramaniam |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin
|
| Street address |
Philippstr. 13, House 20, R. 209
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE205155 |
Inter-layer and inter-subject variability of circadian gene expression in human skin |
|
