NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2563525 Query DataSets for GSM2563525
Status Public on Feb 23, 2019
Title Dunaliella salina RNA-seq
Sample type SRA
 
Source name Dunaliella salina cells under nitrogen deprivation condition
Organism Dunaliella salina
Characteristics tissue: nitrogen-depleted Dunaliella salina
Treatment protocol Dunaliella salina cells cultured under nitrogen deprivation conditions were harvested for Illumina HiseqTM2000 RNA-sequencing
Growth protocol KNO3 in culture media was replaced by equimolar KCl, The algae were grown at 30°C in 0.5-L Erlenmeyer flasks containing 250 mL of medium under continuous illumination (60 μmol m-2 s-1, fluorescent lamp, 400-700 nm). The cultures were shaken manually on a day-to-day basis. Cells were inoculated at 2.0× 105/ml. All the cells were cultured for two 16/8 hour light/dark cycles to synchronize the growth phases before inoculation and transfer to continuous light conditions.
Extracted molecule total RNA
Extraction protocol Trizol reagent (Invitrogen, CA, USA) was used to extract total RNA as manufacturer's instructions. RNA quantity and purity were determined by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA for each sample was used to isolate mRNA by magnetic beads with poly-T oligo attached (Invitrogen). The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature.
The cDNA library was prepared by reverse-transcription in accordance with instructions of the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). The paired-end sequencing was performed on an Illumina HiseqTM2000 platform (LC Sciences, USA) following the vendor's instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Sequencing reads were de novo assembled by using Trinity (2013-02-25) under default parameters choice. Assembly quality was assessed by length distribution analysis by common perl scripts.
BLASTX 2.2.22 with an E-value threshold of 10-5 was used for annotation.
RSEM (1.2.3) was used for caculating RPKM of gene expression level
Supplementary_files_format_and_content: Transcripts sequencs of Dunaliella salina under nitrogen deprivation condition in fasta format. Transcrition levels and function annotations of of Dunaliella salina under nitrogen deprivation condition in table format.
 
Submission date Apr 04, 2017
Last update date May 15, 2019
Contact name Hexin Lv
E-mail(s) lvhexin@yeah.net
Organization name Tianjin University of Science and Technology
Street address 29 13th street
City TEDA
State/province Tianjin
ZIP/Postal code 300457
Country China
 
Platform ID GPL21086
Series (1)
GSE97378 Transcriptome of nitrogen depleted Dunaliella salina
Relations
BioSample SAMN06680603
SRA SRX2704961

Supplementary file Size Download File type/resource
GSM2563525_1_NNG_Trinity_transcript.fasta.gz 17.7 Mb (ftp)(http) FASTA
GSM2563525_Transcription_Level.xlsx 4.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap