Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT
DownloadExperimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
DOI: 10.15490/fairdomhub.1.investigation.162.1
Zenodo URL: None
Created at: 7th Nov 2017 at 14:36
Omics_data_analysis
This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows
RNAseq
RNAseq data for L.ferriphilum samples
LF_RNAseq_TPM_continuous
Normalized counts (tpm) for L.ferriphilum samples from continuous culture.
- LF_continuous_tpm.tsv
LF_omics_combined_Table
Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation
- combined_full_table.tsv
LF_deseq_comparison
Comparison between axenic and planktonic readcounts with deseq2
- LF_deseq2_comparison.tsv
Proteomics
Proteomics data for L.ferriphilum samples (continuous and with mineral)
LF_proteomics_maxquant_perseus_filtered
LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed
- 201708_proteingroups_perseus_filtered.txt
LF_proteomics_maxquant_perseus_unfiltered
LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed
- 201708_proteingroups_perseus_unfiltered.txt
LF_omics_combined_Table
Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation
- combined_full_table.tsv
LF_LFQ_comparison_ttest
Comparison for LFQs with t-test in Perseus
- 13_201708_proteingroups_perseus_filtered2_ttest.txt
Perseus workflow t-test
Filtering of data in Perseus and t-test between conditions
Perseus save file
- t_test_filt2.sps
Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture
Maxquant output.
Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture:
mineral samples:
LNU-LXX9-Si00-14B-P-B-Pr
LNU-LXX9-Si00-14B-P-C-Pr
LNU-LXX9-Si00-14B-P-D-Pr
conitnuous culture samples:
LNU-LXX9-Si00-CnA-P-B2-Pr
LNU-LXX9-Si00-CnA-P-B3-Pr
LNU-LXX9-Si00-CnA-P-B4-Pr
LNU-LXX9-Si00-CnA-P-B5-Pr
LNU-LXX9-Si00-CnA-P-B6-Pr
LNU-LXX9-Si00-CnA-P-B7-Pr
- proteinGroups mineral continuous.xlsx
Genomics
Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation
LF_functional_annotation_gbk
Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta
- lf_chrm.gbk
LF_omics_combined_Table
Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation
- combined_full_table.tsv
Experimental methods
Collection for experimental SOPs
003 Biomolecular Extractions from LAO (Qiagen AllPrep)
Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples.
So far succesfully used for pelleted cells from planktonic cultures.
- 003_BIOMOLECULAR EXTRACTIONS FROM LAO (Qiagen AllPrep).docx
SOP - RNA/Protein sampling for continuous culture
steps conducted to pellet cells for RNA and protein extraction
- SOP_RNA-Prot_sampling.docx
SOP - Bioleaching in flasks (LNU)
Initial configuration and parameters of the Bioleaching
- SOP_bioleaching_in_flasks.docx
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Created: 7th Nov 2017 at 14:36
Last updated: 7th Nov 2017 at 14:37
(Since September 2018)
