|
| Status |
Public on May 31, 2018 |
| Title |
skin control 2 |
| Sample type |
SRA |
| |
|
| Source name |
skin tissues of healthy individuals
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
diagnosis: healthy
|
| Treatment protocol |
This study was performed according to the principles of the Declaration of Helsinki. Written informed consent was provided by all the individuals participating in the experiments.Skin biopsies of AI patients with NCSTN mutations were obtained from surgical excision.Control skin tissues were obtained from healthy individuals undergoing cosmetic surgery procedures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals
sample name:
8
|
| Data processing |
The NGS (Next Generation Sequencing) technology uses to sequence cDNA. The original image file firstly obtained is then base-recognized and error-filtered to finally obtain the original sequencing fragments that can be used for analysis. We call them Reads. The results are stored in fastq format
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Seqtk [1]
Using the spliced mapping algorithm of TopHat(version:2.0.9)[2] to perform Genome mapping on preprocessed reads.
HTSeq [4] was used to count the number of Fragments of each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) [5] method. Finally, the perl script was used to calculate the FPKM value of each gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count and RPKM values for each Sample
|
| |
|
| Submission date |
May 30, 2018 |
| Last update date |
May 31, 2018 |
| Contact name |
Yanyan He |
| E-mail(s) |
[email protected]
|
| Organization name |
hinese Academy of Medical Sciences and Peking Union Medical College
|
| Department |
Institute of Dermatology
|
| Street address |
Jiangwangmiao Street
|
| City |
Nanjing |
| ZIP/Postal code |
210042 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE115099 |
Transcriptome sequencing of differentially expressed genes in acne inversa (AI) patients with NCSTN mutation and healthy individuals |
| GSE115101 |
Transcriptome sequencing of differentially expressed genes in mouse and human skin with and without NCSTN mutation |
|
| Relations |
| BioSample |
SAMN09282821 |
| SRA |
SRX4141452 |
