|
| Status |
Public on Oct 13, 2020 |
| Title |
miRNA_SPF-ABT-4 |
| Sample type |
SRA |
| |
|
| Source name |
specific pathogen free (SPF) mice with broad-spectrum antibiotics (ABX) treatment
|
| Organism |
Mus musculus |
| Characteristics |
tissue: plasma
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
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 ligation3) cDNA synthesis;4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
These mice were not injected with LLC cells and thus do not have xenografted tumors.
processed data 2.txt
|
| Data processing |
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
the trimmed reads were aligned to merged pre-miRNA databases,using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression
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.
Genome_build: miRBase v21
Supplementary_files_format_and_content: text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 22, 2019 |
| Last update date |
Oct 13, 2020 |
| Contact name |
X XX |
| Organization name |
university
|
| Street address |
Road 89
|
| City |
X |
| ZIP/Postal code |
11 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE140886 |
Gut microbiota regulates tumor via circRNA/miRNA networks IV |
| GSE140887 |
Gut microbiota regulates tumor via circRNA/miRNA networks |
|
| Relations |
| BioSample |
SAMN13353993 |
| SRA |
SRX7202826 |
