GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1921148 Query DataSets for GSM1921148
Status Public on Feb 22, 2017
Title H2L_0h_1-6-5
Sample type SRA
Source name CCAP 19/3 algae culture cells
Organism Dunaliella salina
Characteristics condition: low-salt to high-salt
time point: 0h
strain: CCAP 19/3
Extracted molecule total RNA
Extraction protocol Total RNA from Dunaliella salina cells was isolated using RNeasy Plant Mini Kit (Qiagen, Netherlands) according to the manufacturer’s instructions. RNA integrity number (RIN) was measured using RNA 6000 Pico Kit (Agilent, USA) on an Agilent 2100 Bioanalyzer (Schroeder et al., 2006).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Using FastQC to check the qualities of sequenced reads
De novo assembly using Trinity with processed reads (ALL biosamples) (--SS_lib_type FR --CPU 60 --min_contig_length 300 --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7, length of homology to subject/ full length> 25%) (-max_target_seqs 1 -num_threads 60 -outfmt 6 -evalue 1e-7)
Expression levels of annotated EST were determined using Trinity-bundled perl script which utilizes RSEM to calculate FPKM values (--est_method RSEM --aln_method bowtie2 --SS_lib_type FR --thread_count 60 --trinity_mode)
Differentially expressed ESTs were identified using Trinity-bundled perl script based on the ESTs counts Matrix
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Supplementary_files_format_and_content: Non-redundant assembly of D.salina: D.salina_43236.fasta
Supplementary_files_format_and_content: FASTA sequences with annotation in this study: D.salina_annotated_6815.fasta
Submission date Oct 29, 2015
Last update date May 15, 2019
Contact name Jianhua Liu
Organization name Zhejiang University
Department Ocean Research Centre of Zhoushan
Street address 10 Tiyu Road, Room 502
City Zhoushan
State/province Zhejiang
ZIP/Postal code 316021
Country China
Platform ID GPL21086
Series (1)
GSE74466 De novo transcriptomic profiling of halotolerant microalga Dunaliella salina (Chlorophyta) in response to reciprocal alteration of salinities.
SRA SRX1252492
BioSample SAMN04092666

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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