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| Status |
Public on Jan 31, 2020 |
| Title |
H2lowCO2_2 |
| Sample type |
SRA |
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| Source name |
Bacterial cells
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| Organism |
Cupriavidus necator |
| Characteristics |
strain: H16
condition: H2, low CO2
replicate: 2
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| Growth protocol |
Pre-cultures of Cupriavidus necator were inoculated at a starting OD600 of 0.05 on 10 mL minimal medium (JMM medium, Li et al., Science, 2012 doi: 10.1126/science.1217643) in 50 mL erlenmeyer flasks. For the heterotrophic growth 40 mM sodium pyruvate. Autotrophic were incubated inside a dessicator filled with 4% H2 and either ambient or 10% CO2. Cultures were incubated at 30C while shaking at 180 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted after stabilization of 2 mL samples using RNA Protect Bacteria Kit (Qiagen). Total RNA was isolated using RNeasy mini-kit QIAGEN, including enzymatic (15 mg/mL lysozyme) and phsyical lysis (Retschmill, 5 min, 30Hz). An on-column DNAase step was performed to digest all DNA (RNase-Free DNAse Set Qiagen).
cDNA libraties were made at after rRNA depletion using the Ribozero Bacteria kit (Illumina ) at the Max Planck-Genome-centre Cologne, Germany , sequencing was performed using 150 bp single read sequencing in Illuminqa HiSeq3000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Sequence data of all samples were mapped with STAR v2.5.4b using default parameters. Ensembl version 38 genome reference in FASTA format and Ensembl version 38 cDNA Annotation in GTF format were used for genome indexing with adapted parameters for genome size (--genomeSAindexNbases 10) and read length (--sjdbOverhang 150).
Anti-strand read counts from the ReadsPerGene files of all 6 samples were merged in order to perform a differential expression analysis with DESeq2 as guided by the rnaseqGene Bioconductor workflow. Briefly, samples were grouped by their single parameter condition, read count data were then loaded with DESeqDataSetFromMatrix to create a DeSeqDataSet ct to subsequently run the standard analysis consisting of the functions DESeq and Results. Transcript abundance data were expressed as log2-transformed fold changes (log2fc).
Genome_build: Bacteria ensembl version 38 of Ralstonia eutropha H16 (synonymous species name)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)
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| Submission date |
Dec 13, 2019 |
| Last update date |
Jan 31, 2020 |
| Contact name |
Nico J Claassens |
| E-mail(s) |
nico.claassens@wur.nl
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| Phone |
0317483740
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| Organization name |
Wageningen University
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| Department |
Laboratory of Microbiology
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| Street address |
Stippeneng 4
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| City |
Wageningen |
| ZIP/Postal code |
6708 WE |
| Country |
Netherlands |
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| Platform ID |
GPL27909 |
| Series (1) |
| GSE141999 |
Elucidating photorespiration pathways in a chemolithoautotroph |
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| Relations |
| BioSample |
SAMN13559142 |
| SRA |
SRX7367580 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4217513_3840_B_ReadsPerGene.out.tab.gz |
41.9 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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