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Sample GSM6541950

Query DataSets for GSM6541950

Status

Public on Apr 22, 2024

Title

S. pombe, WT, rep3

Sample type

SRA

Source name

Schizosaccharomyces strains

Organism

Schizosaccharomyces pombe

Characteristics

genotype: WT

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Using the STRING protein interaction database (http://string-db.org).
Assembly: Ensembl_release45
Supplementary files format and content: Each txt file corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

Submission date

Sep 02, 2022

Last update date

Apr 22, 2024

Contact name

冯刚

E-mail(s)

fengg@njnu.edu.cn

Organization name

南京师范大学

Street address

江苏省南京市仙林街道南京师范大学