RNA_seq analysis for N. salina CCMP1776 v2 under N starvation, RNA-seq, N-starvation, averaged by 3 replicates


Overview
Analysis NameRNA_seq analysis for N. salina CCMP1776 v2 under N starvation
Organism NameNannochloropsis salina (N. salina CCMP1776)
MethodTuxedo (Tuxedo)
SourceRNA-seq, N-starvation, averaged by 3 replicates
Date performed2019-10-10

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N starvation, 3 replicates averaged

Transcriptomic data for N. salina CCMP 1776 that had not been previously published, were based on four independent repeats of RNA-seq for normal, nitrogen (N) limitation and high salt stress conditions. The quality of raw reads was evaluated by SolexaQA software v3.1.5 (http://solexaqa.sourceforge.net/) (Cox et al., 2010) and cleaned reads were extracted by removing low-quality (phred < 20) reads from the dataset. The cleaned reads were mapped to the transcripts with the bowtie2 (v2.1.0) software (Langmead et al., 2009). The number of mapped reads for each transcript was calculated and normalized with DESeq package in R (Anders and Huber, 2010). The read counts of all genes were published through the expression menu and genome browse menu on "Nannochloropsis WebDB" (http://web.seeders.co.kr/NSK2019/), and now incorporated into NanDeSyn (http://nandesyn.single-cell.cn/organism/5).

Biomaterial Browser
The following browser provides a list of biomaterials associated with this analysis.
Biomaterial NameOrganismBiomaterial ProviderTreatment
WTNannochloropsis salina (N. salina CCMP1776)KAIST, CoreITControl
NdepNannochloropsis salina (N. salina CCMP1776)KAIST, CoreITNdep

Feature Expression

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