Data files
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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.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Data for Raman microspectroscopy in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Creator: Jennifer Zehner
Submitter: Jennifer Zehner
Metabolite profiles after 24h incubation with different ratios of HSD11B1 and AKR1C3 transfected HEK293 cells.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Creator: Margrete Solheim
Submitter: Margrete Solheim
Samples underwent size exclusion chromoatography
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Creator: Natalia Gebara
Submitter: Natalia Gebara
Raw MS data files of the comparison of Sulfolobus solfataricus grown on either caseinhydrolysate or D-glucose. The numbers represents the fractions collected from the HPLC run (e.g. 22 indicates that this sample was collected from 21 min to 22 min). For MS analysis every two fractions were combined, indicated by double numbers (e.g. 80-81: combined fractions 80 and 81). Furhter all combined fractions were run twice on the MS. Zip archive. Requires the supplementary .z01, .z02 and .z03 files for ...
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Umbrella study for all RNAseq rawdata Separate projects can be accessed under "component projects"
Creator: Malte Herold
Submitter: Malte Herold
Raw data of Figure 5, main text
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
Raw data of Figure 3, main text
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
Raw data of Figure 4, main text
Creator: Lorenzo Tagliazucchi
Submitter: Lorenzo Tagliazucchi
Creator: Sebastian Curth
Submitter: Sebastian Curth
Data file for PLaSMo accesssion ID PLM_24, version 1
Creators: BioData SynthSys, Jonathan Massheder
Submitter: BioData SynthSys
Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria
Creators: Natalie Stanford, Katy Wolstencroft, Olga Krebs, Stuart Owen, Carole Goble, Wolfgang Müller
Submitter: Natalie Stanford
Supplementary material for "Mass spectrometry proteomic and network enrichment analysis to track FOLFOX response in drug resistant ovarian carcinoma"
_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_07_MergeEvi-dry/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_02_FieldTrials/_S_02_2020/_A_01_jun20-wet/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv1TransientExp/_A_TransientSPv11andSPv12-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv1TransientExp/_A_SPv10EaDActAnalysis-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_03-Centrifuge/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_02_CLC-RNASeq/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_02_FieldTrials/_S_01_2019/_A_01_jun19-wet/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_02_FieldTrials/_S_02_2020/_A_01_jun20-wet/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_03_dec2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_03_jun2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_03_dec2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_01_ns-dsRNA_trans/_A_02_CLC-RNASeq/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv10T0andT1/_A_SP10T0Analysis-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv10T0andT1/_A_SP10T1Analysis-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv10T2andT3/_A_SPv10T2Analysis-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SPv10T2andT3/_A_SPv10T3Analysis-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-oldG-DE/_A_00_SxP_photos-phenotyping/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-oldG-DE/_A_00_SxP_photos-phenotyping/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_03_jun2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_06_splitter_BLAST-dry/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_06_oct2016/_A_01_oct2016-phenotyping/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_08_SelTargetsA-dry/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_03-Centrifuge/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_03_dsRNAprod/_A_04_prod-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_03_dsRNAprod/_A_04_prod-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_03_dsRNAprod/_A_04_prod-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_04_stages-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_03_jun2017-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_05_extr_reads-rcf/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/reports/RNAseq_reports/
Creators: None
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/
Creator: Marko Petek
Submitter: Marko Petek
Repository for code used in data analysis (mainly for RNAseq) and for generating summary tables and overviews.
Creator: Malte Herold
Submitter: Malte Herold
Files for the reference genomes utilized in the analysis are summarised in this repository.
Creator: Malte Herold
Submitter: Malte Herold
Tutorial given at the Reproducible and Citable Data and Models Workshop, Warnemunde September 14th-16th 2015.
Creators: Natalie Stanford, Stuart Owen
Submitter: Natalie Stanford
One example of a ReStoRunT sheet.
Creators: None
Submitter: Wolfgang Müller
Creators: None
Submitter: Sarah Kirstein
Creator: Katrin Ripken
Submitter: Sarah Kirstein
Resulting data from the modelling workflow, see associated publication.
Creators: Gudrun Gygli, Xinmeng Xu, Juergen Pleiss
Submitter: Gudrun Gygli
Columnwise datamatrix of reactions, gene identifiers, substrates and products. The direction of reactions is not given.
Creator: Sebastian Curth
Submitter: Sebastian Curth
Creators: Franco du Preez, Jacky Snoep
Submitter: Franco du Preez
RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the ...
Creators: None
Submitter: Leif Steil
Creator: Theresa Kouril
Submitter: Theresa Kouril
See wild type sample.
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
RNA-Seq mapping results (part1): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
RNA-Seq mapping results (part2): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
Creator: Fekadu Yadetie
Submitter: Fekadu Yadetie
The aim of the exposure was to study the effects of activation of peroxisome proliferator-activated receptors (PPARs) in Atlantic cod (Gadus morhua), by injecting the fish with the compounds WY-14,643 and GW501516. Using luciferase reporter assay in vitro, we have shown that WY-14,643 activate Atlantic cod Ppara1 and Ppara2, while GW501516 activate Ppara1, Ppara2, and Pparb. The experimental set-up was as follows: Immature cod were injected at day 0 and day 4 with either high dose (40 mg/kg ...
Creators: None
Submitter: Marta Eide
RNA-Seq raw data: Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose.
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
WT 110901_SN865_B_L006_R1_GQC-28- ATCACG.fastq.gz 100 19.624.852 1,29
llumina fastq format 4 lines for each sequence: 1- Unique identifier, with the following format: @::::#/ 2- Sequence (A, T, C ,G or N (undetermined) only) 3- Orientation (always forward without mapping) 4- Quality value for each base, corresponding to a Phred-like score encoded in ASCII format, with an offset of of 33 (e.g. “J” gives a value of 41) and is in accordance with sanger FASTQ format. The sequence file is compressed ...
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Creator: Federico Rojas
Submitter: Federico Rojas
RNAseq data file, Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/splicing/elovl2.splicing.txt
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
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.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
TRK1 and TRK2
Creator: Clara Navarrete
Submitter: The JERM Harvester