 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 06, 2020 |
| Title |
glycinelowCO2_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells
|
| Organism |
Cupriavidus necator |
| Characteristics |
strain: H16
condition: glycinelowCO2
replicate: 2
|
| Growth protocol |
Pre-cultures of Cupriavidus necator were inoculated at a starting OD600 of 0.01 on 10 mL minimal medium supplemented with 40 mM glycine (JMM medium, Li et al., Science, 2012 doi: 10.1126/science.1217643) in 50 mL erlenmeyer flasks. Cultures were incubated at 30C while shaking at 180 rpm with ambient air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted after stabilization of 1 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| 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).
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)
|
| |
|
| Submission date |
Jun 05, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
Nico J Claassens |
| E-mail(s) |
nico.claassens@wur.nl
|
| Phone |
0317483740
|
| Organization name |
Wageningen University
|
| Department |
Laboratory of Microbiology
|
| Street address |
Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
6708 WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL27909 |
| Series (1) |
| GSE151887 |
Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator |
|
| Relations |
| BioSample |
SAMN15146831 |
| SRA |
SRX8480127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4592997_4142_C_ReadsPerGene.out.tab.gz |
42.3 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
