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Sample GSM4119639 Query DataSets for GSM4119639
Status Public on Oct 12, 2019
Title U5(UVB 40mJ/cm2)
Sample type SRA
 
Source name Epidermis
Organism Homo sapiens
Characteristics cell line: HaCaT
tissue: Epidermis
passages: Less than 30 passages
Extracted molecule total RNA
Extraction protocol RNA was extracted from tissues or cells by standard extraction method, followed by strict quality control of RNA samples, which mainly included the following three aspects. Agarose gel electrophoresis: analysis of RNA integrity and presence of DNA contamination. NanoPhotometer spectrophotometer: RNA purity was determined (OD260/280 and OD260/230 ratios). Agilent 2100 bioanalyzer: accurate detection of RNA integrity.
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
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome whole genome using featureCounts 1.5.0-p3 with parameters -Q 10 -B -C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Garber M et al., Nature methods, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human genome
Supplementary_files_format_and_content: table-delimited text files include RPKM values for each Sample
 
Submission date Oct 11, 2019
Last update date Oct 15, 2019
Contact name lidan Xiong
E-mail(s) beardan0505@sina.com
Organization name West China Hospital
Street address No. 5, Gong Xing Road
City Chengdu
ZIP/Postal code 610000
Country China
 
Platform ID GPL20795
Series (1)
GSE138800 Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes
Relations
BioSample SAMN13020532
SRA SRX6983390

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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