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Sample GSM3349835 Query DataSets for GSM3349835
Status Public on Dec 31, 2018
Title Cold_T48_4_Rep B
Sample type SRA
 
Source name Batch Culture - Biological Replicate B - Autorophic - 2xAllen Medium
Organism Galdieria sulphuraria
Characteristics strain: 074W
genotype/variation: wild type
temperature (°c): 28
truseq adapter sequence: CTTGTA
Growth protocol 42°C/28°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions using 2xGS Medium (M. B. Allen (1959). Studies with cyanidium caldarium, an anomalously pigmented chlorophyte. Archiv für Mikrobiologie, vol. 32, no. 3, p. 270–277.)
Extracted molecule total RNA
Extraction protocol RNA was extracted using Roboklon’s Universal RNA Purification Kit by following the “plant tissue samples” protocol (Roboklon, Berlin - Germany). RNA quality and concentration was assessed using a Nanodrop photospectrometer ND-1000 (Peqlab Biotechnologie GmbH, Erlangen -Germany).
The samples were synthetized to Illumina HiSeq2000 compatible RNA-Seq libraries strictly following "Illumina TruSeq RNA Sample Prep v2 LS Protocol" (Illumina, San Diego - USA). All reagents were scaled by 2/3 to the volume proposed in the protocol. The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA).
The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The libraries were sequenced in paired-end mode (2x100bp) on two lanes with an Illumina HiSeq2000 sequencer at the BMFZ (Biologisch-Medizinisches Forschungszentrum, Düsseldorf - Germany).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 11_b_28_48_CTTGTA_L008
04_Cold_T48_B (fpkm)
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,
Mapping with RSEM
Differential Expression Calling with EdgeR
Genome_build: PRJNA13023; ASM34128v1
Supplementary_files_format_and_content: fpkm, logFC, raw counts etc. per gene
 
Submission date Aug 22, 2018
Last update date Dec 31, 2018
Contact name Andreas PM Weber
E-mail(s) aweber@hhu.de
Organization name Heinrich-Heine-University
Department Institute for Plant Biochemistry
Street address Universitätsstr. 1
City Düsseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL22605
Series (1)
GSE118890 Cold acclimation of the thermoacidophilic red alga Galdieria sulphuraria - changes in gene expression and involvement of horizontally acquired genes
Relations
BioSample SAMN09874395
SRA SRX4590961

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

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