|
| Status |
Public on Apr 01, 2021 |
| Title |
G2_miRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
femur bone of hyperlipidemic rats
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
gender: male
tissue: femur bone
developmental stage: 12-13 weeks after birth
|
| Treatment protocol |
Titanium root-form implants was inserted into both femoral shafts of each rat.
|
| Growth protocol |
Wistar rats in the experimental group and the control group were fed a high-fat diet and a normal diet for eight weeks, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The bone around the implant was dissected with a margin of 1 mm and the surrounding muscle tissues were thoroughly removed.Then the remaining bone specimens were grinded into powder while submerged in liquid nitrogen and total RNA was isolated with QIAGEN miRNeasy Mini Kit (QIAGEN, USA).
Small RNA sequencing libraries were prepared from the abovementioned total RNA using TruSeq Small RNA Sample Prep Kit (Illumina, USA). Briefly, the RNA fragments were ligated to 5'- and 3’-adapters using T4 RNA Ligase 1 and 2, respectively, before being reverse-transcribed with miScriptII RT-Kit (Qiagen, Germany) and then amplified. The resultant cDNA fragments were electrophoresized on a 4% agarose gel. Bands between 140 and 160 bp were excised and the DNA was extracted by MinElute Gel Extraction Kit (Qiagen, Germany). Library constructs were then sequenced on the HiSeq4000 Illumina platform (Illumina, USA) to generate 50-bp single-end reads.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then detected miRNA using miRDeep2 v2_0_0_8; mapper.pl with parameters -d -c -i -j -l 18 -m,miRDeep2.pl with default parameter
miRNA expression were calcuated using quantifier.pl from miRDeep2 v2_0_0_8 with parameters, then differential analysis using R package Ballgown
Genome_build: Rnor_6.0
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Chen Jishuang |
| E-mail(s) |
biochenjs@njtech.edu.cn
|
| Organization name |
Nanjing Tech University
|
| Department |
College of Biotechnology and Pharmaceutical Engineering
|
| Street address |
NO.30 Puzhu Road(S)
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
211800 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE113521 |
Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (miRNA-seq data sets) |
| GSE113523 |
Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats |
|
| Relations |
| BioSample |
SAMN08970578 |
| SRA |
SRX3987908 |
