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Sample GSM7306536

Query DataSets for GSM7306536

Status

Public on May 04, 2024

Title

normal eyeball

Sample type

SRA

Source name

eyeball

Organism

Myodes rufocanus

Characteristics

tissue: eyeball

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Qubit RNA HS test kit. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Quality assessment of sequenced raw data by FastQC v 0.11.2,Mass shearing by Trimmomatic to obtain relatively accurate and valid data
Mixing and splicing of sample valid data using Trinity
NCBI Blast+ was used to compare the transcripts with several databases such as CDD, KOG, COG, NR, NT and PFAM to obtain to obtain their functional annotation information. KAAS was used to obtain KEGG annotation information of transcripts. CDS prediction was performed using TransDecoder.
The valid data of the samples were matched to the spliced transcripts using Bowtie2, and the Mapping information was counted.
SSR analysis was performed using MISA based on the sequence information of the transcripts obtained by splicing. The expression of genes was calculated using Salmon. Gene co-expression analysis was performed using WGCNA. Multi-directional statistical analysis and exploration such as sample comparison analysis based on the expression matrix of the samples. Gene expression differential analysis using DESeq2 to visualize the results of expression differential analysis. Based on the results of differential analysis, Venn diagram and heat map were drawn and cluster analysis was performed. Perform GO enrichment analysis using topGO and plot the significant GO directed acyclic graph. KEGG pathway and KOG classification enrichment analysis was performed using clusterProfiler.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

Submission date

May 08, 2023

Last update date

May 04, 2024

Contact name

Shengnan Han

E-mail(s)

hansn22@mails.jlu.edu.cn

Organization name

Jilin University

Street address

Xi'an road No.5333