 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 04, 2015 |
| Title |
NS2 |
| Sample type |
SRA |
| |
|
| Source name |
hepatic normal tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: hepatic normal 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 |
| E-mail(s) |
wangxiaowei1@genomics.cn
|
| 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. |
|
| Relations |
| BioSample |
SAMN02582748 |
| SRA |
SRX426001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1306058_NS2.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
