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| Status |
Public on Jul 01, 2014 |
| Title |
Dshibae, first run, day 2, 4 h light |
| Sample type |
SRA |
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| Source name |
D. shibae cultivated in a chemostat under light/dark cycles
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| Organism |
Dinoroseobacter shibae DFL 12 = DSM 16493 |
| Characteristics |
chemostat run: 1
light/dark-cycle: 1
time in light or darkness: 4
light(l)/dark(d): l
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| Extracted molecule |
total RNA |
| Extraction protocol |
For isolation and purification the RNeasy-kit (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cells lysis was performed enzymatically using 15 mg/mL lysozyme in Tris-EDTA-buffer (ph 8.0) and mechanically by vortexing for 3 min with acid washed glass beads. A first digestion of genomic DNA was performed on the column, using RNase-free DNase I (Qiagen) according to the manufacturer’s protocol. Total RNA was eluted in 88 µL RNase-free H2O and a second DNase I-digestion of genomic DNA was performed in solution, followed by a second RNeasy purification step. In this second purification an additional washing step with 80 % ethanol was performed prior to elution with 30µl RNase-free water. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). Ribosomal RNA depletion: The Ribo-Zero (gram-negative) kit (Madison, Wisconsin, USA) to remove the prokaryotic rRNA, according to the manufacturer’s instructions.
Libraries of 300 bp for RNA sequencing were prepared using the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) according the manufacturer’s instructions. Quality control of the prepared libraries was validated using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA). Cluster generation was performed using the Illumina cluster station.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Sequencing was done on the Genome Analyzer IIx (Illumina, San Diego, CA, USA) following a standard protocol. The fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina, San Diego, CA, USA).
The sequencing output (50 bp single end short reads) of the Genome Analyzer IIx was controlled for general quality features using the fastq-mcf tool of ea-utils (http://code.google.com/p/ea-utils) and was mapped against the genome sequence of D.shibae (NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1) using BWA v 0.5.9-r16.
Genome_build: NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1
Supplementary_files_format_and_content: tab-delimited text files include unique and total mapped reads and RPKM values for each gene of one sample
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| Submission date |
Apr 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jürgen Tomasch |
| E-mail(s) |
tomasch@alga.cz
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| Organization name |
Center Algatech, Institute of Microbiology of the Czech Academy of Science
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| Lab |
Anoxygenic Phototrophs
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| Street address |
Novohradská 237
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| City |
Třeboň |
| ZIP/Postal code |
37901 |
| Country |
Czech Republic |
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| Platform ID |
GPL18337 |
| Series (2) |
| GSE53967 |
Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum |
| GSE57164 |
Transcriptome of Dinoroseobacter shibae under changeing light regimes |
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| Relations |
| BioSample |
SAMN02767144 |
| SRA |
SRX535005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1376594_h.clipped_RNA-Seq.txt.gz |
102.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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