Data files

_p_stRT/_I_STRT/_S_04_stPanTr/_A_01_GC_content-count

This file contains the top 100 transcripts for the identified cell types in the integrated dataset.

Supplementary Table S5 Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal.

Supplementary Table S3 Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée.

Supplementary Table S4 PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363.

File contains the detailed cluster names for each data set, number of nuclei per cluster, average reads per nucleus, and average reads per cluster.

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.

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

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

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

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

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

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 proteomics data for L. ferriphilum planktonic samples

Raw proteomics data for S. thermosulfidooxidans samples

Raw data for tertiary mixture, planktonic cells, proteomics

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