|
| Status |
Public on Jan 31, 2020 |
| Title |
QDG5-smallRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
heart tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
group: QDG Treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEB Next®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The sequencing quality of raw data of fastq format was assessed with FastQC and then low quality data were filtered using NGSQC. The clean reads with high quality were then aligned to the reference genome using Tophat2 with default parameters. The rat genome version of RGSC6.0/RN6 (UCSC) was used as the reference.
miRNA reads were normalized with TPM（Transcripts Reads Number Per Million）
Differential expression analyses were performed using the limma package.
Genome_build: RGSC6.0/RN6 (UCSC)
Supplementary_files_format_and_content: tab_delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Jan 30, 2020 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Jun Peng |
| E-mail(s) |
pjunlab@hotmail.com
|
| Organization name |
Fujian University of Traditional Chinese Medicine
|
| Department |
Academy of Integrative Medicine
|
| Street address |
1 Qiuyang Road, Minhou Shangjie
|
| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350122 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (2) |
| GSE144549 |
Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (miRNA-seq dataset) |
| GSE144550 |
Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling |
|
| Relations |
| BioSample |
SAMN13946248 |
| SRA |
SRX7652049 |
