Data files

Umbrella study for all RNAseq rawdata
Separate projects can be accessed under "component projects"

An example of a JERM-compliant template for RT-PCR data

This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

Excel sheet template : concentrations of intracellular metabolites

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

The causal interactions service provides the extracted data of causality from Reactome database.

This dot-plot represents only the most significant genes per identified cell type cluster.

This file contains the top markers for the identified cell types.

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

This file contains the R-script to analyse single nuclei data previously processed with kallisto and bustools. The analyses utilizes the Seurat, harmony and RNAvelocity package.

This file contains the detailed UNIX commands for mm10 index file creation (suitable for RNAvelocity) for kallisto as well as the commands used for the alignment with kallisto and the subsequent quantification with bustools.

Overivew of RNAseq and proteomics samples with respective accessions to access the raw data on ENA or PRIDE respectively.

Overview for quality control of mapping statistics, after mapping processed reads to reference genomes

Overview of the quality control for the RNAseq short read data after quality filtering of the reads

Files for the reference genomes utilized in the analysis are summarised in this repository.

Repository for code used in data analysis (mainly for RNAseq) and for generating summary tables and overviews.

Raw proteomics data for S. thermosulfidooxidans samples

Overview of the quality control for the RNAseq short read data before quality filtering of the reads

Parameters used in maxQuant analysis

Raw proteomics data for St + Ac planktonic cells

Raw data for tertiary mixture, planktonic cells, proteomics

Raw proteomics data for L. ferriphilum planktonic samples

Pride project for raw and search data for AXX-Cn samples:
LNU-AXX-Si00-CnB-P-B6ST-Pr_180min
LNU-AXX-Si00-CnB-P-B7ST-Pr_180min
LNU-AXX-Si00-CnB-P-B8ST-Pr_180min

Raw data for , Ac + St or Lf + St planktonic cells from leaching experiments

Raw data for Ac+St planktonic cells, leaching experiments with St 10x incoulum sizing

Raw data for Ac + St leaching experiments proteomics data, with Ac 10x inoculum sizing

Raw data for mixed cultures of S. thermosulfidooxidans and L.ferriphilum

Raw data for mixed culture biofilm proteomics

Samples:
UDE-SAL8-7O-M-B-Pr-2
UDE-SAL8-7O-M-B-Pr
UDE-SAL7-Pc20-7M-P-B-Pr_2uL
UDE-SAL7-A7-M-B-Pr
UDE-SAL7-7C-M-B-Pr
UDE-SAL7-7A-M-B-Pr

Raw data for L.ferriphilum biofilm proteomics data

Microscopy images of A.Caldus (A), L.ferriphilum (L), S.thermosulfidooxidans (S) biofilms on chalcopyrite particles. (individual,e.g. SXX or mixed, e.g. SAL, cultures)

Timepoints: Day1, Day3, Day7, Day14, Day21