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Sample GSM1174930 Query DataSets for GSM1174930
Status Public on May 10, 2014
Title SK-HEP-1, 2U, miRNA (SOLiD 5500xl)
Sample type SRA
 
Source name Liver cell line SK-HEP-1, control, 2 hours
Organism Homo sapiens
Characteristics cell line: SK-HEP-1
treatment: DMSO control
time: 2 hours
Treatment protocol Treated with 0.5 mg/ml Antrodia cinnamomea fruiting body ethanol extracts or 0.5 mg/ml DMSO.
Growth protocol Cells were cultured in DMEM medium with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using Trizol reagent. mRNA were isolated from total RNA samples by Poly(A) Purist-MAG kit.
SOLiD™ total RNA-seq kit for whole transcriptome libraries and small RNA libraries kits were used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard SOLiD™protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB 5500xl Genetic Analyzer
 
Description microRNA; small RNA-Seq
2U
Processed data file: miRNA_solid5500.txt
Data processing miRNA data utilized in-house built miRNA pipeline combined with publicly available tools such as bowtie and cutadapt for pre data processing.
Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity or reads shorter than 16 bp and longer than 30 bp, then mapped to mm9 for the CL2 samples and hg19 for the human sample whole genome using bowtie v0.12.7 with perfect match for known miRNA detection. Transcripts Per Million (TPM) were calculated.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.
 
Submission date Jun 26, 2013
Last update date May 15, 2019
Contact name mike thang
Organization name Academia Sinica
Department Genome Research Center
Lab 2L11
Street address 128 Academia Road, Section 2, Nankang
City Taipei
State/province Taipei
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL16288
Series (1)
GSE48327 Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells
Relations
SRA SRX315251
BioSample SAMN02214070

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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