|
| Status |
Public on Dec 31, 2018 |
| Title |
Cold_T48_4_Rep A |
| Sample type |
SRA |
| |
|
| Source name |
Batch Culture - Biological Replicate A - Autorophic - 2xAllen Medium
|
| Organism |
Galdieria sulphuraria |
| Characteristics |
strain: 074W
genotype/variation: wild type
temperature (°c): 28
truseq adapter sequence: GTGGCC
|
| 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 |
10_a_28_48_CTTGTA_L007
04_Cold_T48_A (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 |
SAMN09874396 |
| SRA |
SRX4590960 |
