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Status |
Public on Oct 02, 2024 |
Title |
HaCaT cells, Control 2 |
Sample type |
SRA |
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Source name |
HaCaT
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Organism |
Homo sapiens |
Characteristics |
cell line: HaCaT cell type: human keratinocytes genotype: WT treatment: sham irradiated
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol. Ribosomal RNA was depleted from total RNA using RNase R.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
TPM
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Data processing |
Used the standard base calling software provided by Illumina HiSeq2500 to generate raw sequence reads in FASTQ format. Circular RNAs were identified and quantified using find_circ and CIRCexplorer2. Data filtering (Removed low quality reads, Removed reads with >10% N bases, Removed reads with adapter contamination, Removed reads <18 nt). Used find_circ (version 1.2) to identify candidate circRNAs, Used CIRCexplorer2 (version 2.3.3) to further identify circRNAs. Assembly: The human reference genome build/assembly used for read alignment was hg38/GRCh38. Supplementary files format and content: Tab-delimited text files include expected counts and TPMs.
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Submission date |
Oct 23, 2023 |
Last update date |
Oct 02, 2024 |
Contact name |
yi peng |
E-mail(s) |
yipengswmu@gmail.com
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Phone |
18180092445
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Organization name |
西南医科大学
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Street address |
xianglinlu
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City |
luzhou |
ZIP/Postal code |
646000 |
Country |
China |
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Platform ID |
GPL16791 |
Series (1) |
GSE246068 |
Circular RNA expression profiling in UVA-treated HaCaT cells |
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Relations |
BioSample |
SAMN37932657 |
SRA |
SRX22184581 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7855044_C2.tpm.txt.gz |
34.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
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