|
| Status |
Public on Dec 01, 2021 |
| Title |
db-db-3 |
| Sample type |
SRA |
| |
|
| Source name |
male leptin receptor-deficient db/db mice
|
| Organism |
Mus musculus |
| Characteristics |
age: 16-week-old male
strain: C57BL/6
tissue: submandibular gland
|
| Growth protocol |
The submandibular glands of mice are preserved at -80 degrees Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.
When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value).
Genome_build: MmiRBase v21
|
| |
|
| Submission date |
Dec 03, 2019 |
| Last update date |
Dec 01, 2021 |
| Contact name |
huimin liu |
| E-mail(s) |
1811210002@pku.edu.cn
|
| Phone |
13146619655
|
| Organization name |
Peking University
|
| Department |
Peking University Health Science Center
|
| Lab |
Department of Physiology and Pathophysiology
|
| Street address |
38 Xueyuan Rd , Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE141393 |
MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice [seq] |
| GSE141412 |
MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice |
|
| Relations |
| BioSample |
SAMN13474153 |
| SRA |
SRX7262871 |
