Data files

Archive contains python scripts for image analysis

Link to the repository for functional annotation

Images used for training and validation of deep learning algorithm to determine biofilm composition of mixed species biofilms on mineral grains

LFQ intensities derived from proteomics measurements

Comparison for LFQs with t-test in Perseus

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

Normalized counts (tpm) for LF samples with mineral

Raw read files for samples

Comparison between axenic and planktonic readcounts with deseq2

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

Repository for omics data analysis

Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation

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LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed

LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed

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

Filtering of data in Perseus and t-test between conditions
Perseus save file

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

Information for RNA and protein samples and cultures they were derived from.

TPM counts for protein coding genes, alongside functional annotations

Source code for running simulations

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