|
| Status |
Public on Mar 14, 2018 |
| Title |
UVA-1 |
| Sample type |
SRA |
| |
|
| Source name |
Normal Human Epidermal Keratinocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: epidermis
age: adult
|
| Treatment protocol |
NHEKs were washed 2X in PBS, supplemented with Dulbecco's modified PBS (DPBS, 1X), then treated with sham or UVA irradiation (20J/cm2).
|
| Growth protocol |
Adult normal human epidermal keratinocytes (NHEKs) obtained from Lonza (cat. #: 192627) were grown in KGM-Gold BulletKit medium (Lonza) according to manufacturer's protocol. Cells were cultured at 37°C and in 95% air/5% CO2 (vol/vol). Cells were passaged 3 times.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NHEKs were purified 6h after radiation using Qiagen Rneasy Plus kit according to manufacturer's instructions. RNA quality was assessed using Agilent Bioanalyzer.
An oligo dT-selected library was prepared and sequencing was performed on an Illumina HiSeq2000 platform with 50 bp single-end reads by the Functional Genomics Facility at the University of Chicago using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
UVA-irradiated keratinocytes (20J/cm2)
|
| Data processing |
Quality control analysis of raw data using FastQ Groomer v1.0.4
Read alignment using Tophat2
Transcript assembly using Cufflinks v2.2.1
Assemblies merged using CuffMerge v1.0.0
Differential gene expression analysis using CuffDiff v2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample from Cufflinks
|
| |
|
| Submission date |
Mar 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu-Ying He |
| E-mail(s) |
yyhe@medicine.bsd.uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Medicine
|
| Street address |
5841 S Maryland Ave, AMB N011
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE96596 |
RNA-Sequencing Analysis of the Effects of UVA Radiation on Keratinocytes |
|
| Relations |
| BioSample |
SAMN06600793 |
| SRA |
SRX2639325 |
