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Status |
Public on Oct 12, 2019 |
Title |
U5(UVB 40mJ/cm2) |
Sample type |
SRA |
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Source name |
Epidermis
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Organism |
Homo sapiens |
Characteristics |
cell line: HaCaT tissue: Epidermis passages: Less than 30 passages
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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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
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Submission date |
Oct 11, 2019 |
Last update date |
Oct 15, 2019 |
Contact name |
lidan Xiong |
E-mail(s) |
beardan0505@sina.com
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Organization name |
West China Hospital
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Street address |
No. 5, Gong Xing Road
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City |
Chengdu |
ZIP/Postal code |
610000 |
Country |
China |
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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 |
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Relations |
BioSample |
SAMN13020532 |
SRA |
SRX6983390 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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