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Sample GSM4910343

Query DataSets for GSM4910343

Status

Public on Dec 21, 2022

Title

Control_2

Sample type

SRA

Source name

whole body

Organism

Plutella xylostella

Characteristics

developmental stage: 2th instar larva

Treatment protocol

2th instar larva after DMNT treatment at 12h

Growth protocol

2th instar larva

Extracted molecule

total RNA

Extraction protocol

Total RNA of P. xylostalla larva was extracted with TRIzol RNA preparation method (Invitrogen, CA, USA),and then construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Novaseq™ 6000
A cDNA library constructed by technology from the pooled RNA from brain samples of pig was sequenced run with Illumina Novaseq™ 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: GCA_000330985.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

Submission date

Nov 16, 2020

Last update date

Dec 21, 2022

Contact name

Chen Hongyi

E-mail(s)

Peijin.li@ahau.edu.cn

Phone

13696779037

Organization name

Anhui Agricultural University