Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT (snapshot 1)

Experimental 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

Created at: 7th Nov 2017 at 15:36

Contents

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_rawdata

Raw read files for samples

  • PRJEB21842

LF_RNAseq_TPM_mineral

Normalized counts (tpm) for LF samples with mineral

  • LF_mineral_tpm.tsv

LF_RNAseq_TPM_continuous

Normalized counts (tpm) for L.ferriphilum samples from continuous culture.

  • LF_continuous_tpm.tsv

LF_omics_analysis

Repository for omics data analysis

  • LF_omics_analysis

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_proteomics_LFQs_mineral

No description specified

  • LFQs_mineral_filt2.tsv

LF_proteomics_LFQs_continuous

No description specified

  • LFQs_continuous_filt2.tsv

LF_proteomics_continuous_scaled

No description specified

  • LFQs_continuous_scaled_filt2.tsv

LF_proteomics_LFQs_mineral_scaled

No description specified

  • LFQs_mineral_scaled_filt2.tsv

LF_omics_analysis

Repository for omics data analysis

  • LF_omics_analysis

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_sequencing_data

Raw data and assembly for pacbio sequencing of L.ferriphilum.

  • PRJEB21703

LF_functional_annotation_gbk

Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta

  • lf_chrm.gbk

Functional_annotation_repository

Link to the repository for functional annotation

  • LF_annotation_new

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
Fingerprints

These checksums allow you to check a Snapshot you have downloaded hasn't been modified. For details on how to use these please visit this guide

MD5: fa141d6c131d94e6ab265df6913b0065

SHA1: e59c5932c7a83c726c3059dfed460f4c85fa4ea3

Citation
Herold, M. (2017). Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT. FAIRDOMHub. http://doi.org/10.15490/fairdomhub.1.investigation.162.1
Snapshots
Snapshot 1 (7th Nov 2017) DOI
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