|
| 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 |
