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Sample GSM2536371 Query DataSets for GSM2536371
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
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
BioSample SAMN06600793
SRA SRX2639325

Supplementary file Size Download File type/resource
GSM2536371_UVA-1-cufflinks.txt.gz 782.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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