|
Status |
Public on Feb 08, 2020 |
Title |
Melanocyte2 control |
Sample type |
SRA |
|
|
Source name |
Human Neonatal Foreskin
|
Organism |
Homo sapiens |
Characteristics |
cell type: Melanocyte uvb treatment: none
|
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 |
SAMN08502481 |
SRA |
SRX3671084 |