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Sample GSM5621397

Query DataSets for GSM5621397

Status

Public on Oct 15, 2021

Title

1D-2

Sample type

SRA

Source name

Goat kid

Organism

Capra hircus

Characteristics

age: 1 day of age
tissue: liver

Extracted molecule

total RNA

Extraction protocol

Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeqTM stranded total RNA Kit(San Diego, CA) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Casava1.8 software used for basecalling.
Remove the 3' linker sequence in the reads, and remove the reads without inserts due to the connector self-ligation. Remove the reads with low-quality sequence and reads containing the unknown base N, too short(<18nt) or too long(> 32 nt).
Useing fastx_tool 0.04 to ffilter the low quality data , and using bowtie version 1.1.1 for genome mapping.
The expression level of each transcript was calculated according to the (TPM) method. miRDeep2 was used to quantify gene abundances
Differential miRNA expression analysis was done using R package DEGseq
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

Submission date

Oct 11, 2021

Last update date

Oct 15, 2021

Contact name

Chao Tianle

E-mail(s)

chaotianle@sdau.edu.cn

Phone

15153876133

Organization name

6/5000 Shandong Agricultural University