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Sample GSM1306055 Query DataSets for GSM1306055
Status Public on Jun 04, 2015
Title PS1
Sample type SRA
Source name hepatic fibrosis tissue
Organism Rattus norvegicus
Characteristics tissue: hepatic fibrosis tissue
Treatment protocol Liver tissues were fixed in 10% formaldehyde in NaCl⁄Pi buffer, dehydrated in alcohol, and embedded in paraffin. Sections were prepared and stained with hematoxylin-eosin (HE) and Masson trichrome (MT) stain.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from liver tissues with TRIZOL (Invitrogen, Carlsbad, CA, US). The concentration and quality of the purified RNAs were evaluated on a Bioanalyzer 2100 (Agilent Technologies,PaloAlto,CA). Libraries were constructed using the Illumina Small RNA Sample Prep Kit V1.0.
RNA libraries were prepared for sequencing using standard Illumina protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
Data processing Basecalls performed using CASAVA version 1.4
After trimming the low quality sequences and removing the adapters, the remaining reads were aligned to rat genome sequence (Rattus norvegucus assembly, rn5) using SOAP2. BLAST was adopted to identify known miRNAs (miRBase 20) and other type RNAs (rRNA, tRNA, snRNA, snoRNA; GenBank&Rfam).
We normalized all miRNA reads as transcripts per million clean tags (TPM).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample replicates.
Submission date Jan 13, 2014
Last update date May 15, 2019
Contact name Wang Xiaowei
Organization name BGI-Tianjin Techonology Co., Ltd.
Street address Business park of Tianjin airport economic zone
City Tianjin
ZIP/Postal code 300308
Country China
Platform ID GPL14844
Series (1)
GSE54028 Next Generation Sequencing Facilitates Quantitative Analysis of miRNAs in hepatic fibrosis and normal tissues.
BioSample SAMN02582747
SRA SRX425998

Supplementary file Size Download File type/resource
GSM1306055_PS1.txt.gz 2.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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