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Sample GSM4189684

Query DataSets for GSM4189684

Status

Public on Oct 13, 2020

Title

miRNA_GF3

Sample type

SRA

Source name

germ-free mice

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

ZIP/Postal code