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| Status |
Public on Jan 31, 2020 |
| Title |
SHR5-mRNAseq |
| Sample type |
SRA |
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| Source name |
heart tissue
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
group: Hypertension
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| 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. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:： Check the sample for contamination and, if there is pollution, remove it If the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window; Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed; if the truncated read length is less than 50 bp, the entire read is removed Remove unmatched reads Q30，Q20 explanation： Q30 indicates that the sequencing error rate of the base is 0.1%. Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
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 FPKM values for each Sample
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| Submission date |
Jan 30, 2020 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Jun Peng |
| E-mail(s) |
pjunlab@hotmail.com
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| Organization name |
Fujian University of Traditional Chinese Medicine
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| Department |
Academy of Integrative Medicine
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| Street address |
1 Qiuyang Road, Minhou Shangjie
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| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350122 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE144548 |
Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (mRNA-seq dataset) |
| GSE144550 |
Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling |
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| Relations |
| BioSample |
SAMN13946271 |
| SRA |
SRX7651981 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4290708_SHR5.txt.gz |
261.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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