|
| Status |
Public on Feb 08, 2020 |
| Title |
Melanocyte2 10J UVB |
| Sample type |
SRA |
| |
|
| Source name |
Human Neonatal Foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Melanocyte
uvb treatment: 10J
|
| Treatment protocol |
4 X 105 melanocytes were plated in 6 well dishes for UVB exposure. 12h-24h post-plating, the cells were exposed to mock, 10mJ/cm2 or 30mJ/cm2 UVB integrated over 10s using a Daavlin Research Irradiator (Daavlin Company, Bryan, OH).
|
| Growth protocol |
Matched melanocytes, keratinocytes and fibroblasts were obtained from 3 individual donors and cultured in M254, M154 and DMEM with 10% FBS respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested in QiaZol Lysis reagent (Qiagen, Redwood City, CA) at 0h and 24h post-irradiation. RNA was isolated using miRNEasy Isolation kit (Qiagen, Cat. No. 217004) for all melanocyte, fibroblast and keratinocyte samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. RSEM was used to map the reads to transcripts from human genome version hg19 and call isoform level expression.
Genome_build: hg19
Supplementary_files_format_and_content: Excel File: contains information on reads per million.
|
| |
|
| Submission date |
Feb 08, 2018 |
| Last update date |
Feb 08, 2020 |
| Contact name |
Vijayasaradhi Setaluri |
| E-mail(s) |
setaluri@wisc.edu
|
| Phone |
608-263-5362
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Dermatology
|
| Street address |
1300 University Avenue
|
| City |
MADISON |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE110375 |
Next Generation Sequencing Facilitated Differential Transcriptome Study of melanocytes treated with UVB radiation compared to matched fibroblasts and keratinocytes |
|
| Relations |
| BioSample |
SAMN08502480 |
| SRA |
SRX3671085 |
