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| Status |
Public on Aug 31, 2017 |
| Title |
Ms_pH4.84 2 |
| Sample type |
SRA |
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| Source name |
bacterial culture
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| Organism |
Metallibacterium scheffleri |
| Characteristics |
strain: DKE6
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| Growth protocol |
Cells were grown at 30°C and 150 rpm in 21 mL medium, containing 132 mg/L (NH4)2SO4, 53 mg/L MgCl2 x 6 H2O, 27 mg/L KH2PO4, 147 mg/L CaCl2 x 2 H2O, 0.5 mg/L VOSO4 x 5 H2O, 10 mg/L FeSO4 x 7 H2O, 10 mg/L casitone, 1 mL/L Wolfe's mineral elixier (DSMZ medium 792) and 10 mL/L vitamin solution (DSMZ medium 141), buffered with 50 mL 0.2 M Na2HPO4 and 47 mL 0.1 M citrate to pH 4.5.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested in exponential growth phase and samples were pooled in triplicates, resulting in two independent replicates that were used for RNA extraction. Cell suspension were immediately treated with RNA protect (Qiagen) and RNA was isolated using the RNeasy Mini Kit (Qiagen). Genomic DNA was depleted using the DNA-free kit (Ambion, life technologies) and rRNA was depleted using the MICROBExpress kit (Ambion, life technologies)
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al, 2009, doi: 10.1093/nar/gkp596). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina).
The two RNA-seq data sets were mapped to the 5 contigs that were assembled from the genomic sequencing data using bowtie2 (Langmead & Salzberg, 2012, doi: 10.1038/nmeth.1923).
The mapped sequence reads were processed with samtools (Li, 2011, doi: 10.1093/bioinformatics/btr509) and sequence reads overlapping the annotated genes were counted using HTSeq (Anders et al, 2015, doi: 10.1093/bioinformatics/btu638) with the ‘intersection-nonempty’ option.
Average gene expression was determined as the arithmetic mean value of both samples using read counts that were normalized using DESeq2 (Love et al., 2014, doi: 10.1186/s13059-014-0550-8) and divided by the gene length (in kilobasepairs, kbp), yielding RPK values (normalized reads per kilobase).
Genome_build: LDOS01000000
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the genomic contigs and corresponding annotation prepared in this study.
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| Submission date |
Sep 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas Doetsch |
| E-mail(s) |
andreas.doetsch@mri.bund.de
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| Phone |
+497216625443
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| Organization name |
Max Rubner-Institute
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| Department |
Physiology and Biochemistry of Nutrition
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| Street address |
Haid-und-Neu-Str. 9
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| City |
Karlsruhe |
| ZIP/Postal code |
76131 |
| Country |
Germany |
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| Platform ID |
GPL22480 |
| Series (1) |
| GSE87349 |
Metallibacterium scheffleri: Genetic data reveal a versatile metabolism |
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| Relations |
| BioSample |
SAMN05824339 |
| SRA |
SRX2191361 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2328662_MsII.rpg.txt.gz |
31.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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