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3421 Data files visible to you, out of a total of 5622
No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Submitter: Maja Rey

No description specified

Creators: Maja Rey, Ulrike Wittig

Submitter: Maja Rey

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 tertiary mixture, planktonic cells, proteomics

Creator: Malte Herold

Submitter: Malte Herold

Main page at NCBI for the salmon genome. Contains download links to annotation GFF, genome sequence FASTA, etc.

Creator: Jon Olav Vik

Submitter: Jon Olav Vik

The file contains the GC-MS raw data as cdf files, a sample list and an excel sheet with the results of metabolome analysis.

This Excel file lists the samples uploaded in PRIDE. The table “Table Sorted PP and Replicates” in the Excel file has all the relevant annotation.

There are more than the expected 168 samples in the PRIDE upload for the following reasons:

First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of problems during the MS run. These samples are not annotated in the table. Second, we had included 4 Gold Standard samples (2 ...

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

Data file for PLaSMo accesssion ID PLM_12, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Information on samples submitted for RNAseq

Rows are individual samples

Columns are: ID Sample Name Date sampled Species Sex Tissue Geographic location Date extracted Extracted by Nanodrop Conc. (ng/µl) 260/280 260/230 RIN Plate ID Position Index name Index Seq Qubit BR kit Conc. (ng/ul) BioAnalyzer Conc. (ng/ul) BioAnalyzer bp (region 200-1200) Submission reference Date submitted Conc. (nM) Volume provided PE/SE Number of reads Read length

No description specified

Batch sample publishing

Batch sample publishing

Batch sample publishing

No description specified

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

Batch sample publishing

No description specified

Raw proteomics data for St + Ac planktonic cells

Creator: Malte Herold

Submitter: Malte Herold

No description specified

Creators: Dorothee Houry, Arne Raasakka, Petri Kursula

Submitter: Dorothee Houry

Data file for PLaSMo accesssion ID PLM_71, version 2

Validation of the sc-SynO model for the first use case of cardiac glial cell annotation. UMAP representation of the manually clustered Bl6 dataset of Wolfien et al. (2020) Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. UMAP representation of the manually clustered dataset of Vidal (2019). Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. Average expression of the respective top five cardiac glial cell marker genes for both validation ...

Validation of the sc-SynO model for the second use case of proliferative cardiomyocytes annotation. a) UMAP representation of the manually clustered single-nuclei dataset of Linscheid et al. (2019) Precicted cells of sc-SynO are highlighted in blue (based on top 20 selected features in the training model), red (based on top 100 selected features in the training model) cells not chosen are grey. b) UMAP representation of the manually clustered dataset of Vidal et al. (2020). PPrecicted cells of ...

Visualization of the workflow demonstrating a step-by-step explanation for a sc-SynO analysis. a) Several or one snRNA-Seq or scRNA-Seq fastq datasets can be used as an input. Here, we identify our cell population of interest and provide raw or normalized read counts of this specific population to sc-SynO for training. b) Further information for cluster annotation and processed count data are serving as input for the core algorithm. c) Based on the data input, we utilize the LoRAS synthetic ...

No description specified

Creators: Jay Moore, David Hodgson

Submitter: Jay Moore

No description specified

Creators: Jay Moore, David Hodgson

Submitter: Jay Moore

Data file for PLaSMo accesssion ID PLM_1, version 1

Data file for PLaSMo accesssion ID PLM_3, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_22, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

_p_RNAinVAL/_I_01_LabTrials/_S_01_TargetSelect/_A_02_UlrichTop100-BLAST/

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_02_metagenome_resp/_A_05_extr_reads-rcf/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-newG-DE/_A_06_SxPv1-0_Illumina-Centrifuge/

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_CoExpNetViz/_A_02_Nb_datasets-CoExp/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-newG-DE/_A_07_NbAUSv1-0-InterPro/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-newG-DE/_A_07_NbAUSv1-0-InterPro/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Creator: Marko Petek

Submitter: Marko Petek

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_07_allReads_meta-assembly/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_CoExpNetViz/_A_02_Nb_datasets-CoExp/

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_06_splitter_BLAST-dry/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_CoExpNetViz/_A_02_Nb_datasets-CoExp/

Creator: Marko Petek

Submitter: Marko Petek

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-oldG-DE/_A_03a_mapping2-STAR/

Creator: Marko Petek

Submitter: Marko Petek

Zip archive of N1 protonated reference and newly synthesized pteridines (series 1-5) in SDF format.

after shankra, saving the images that could not be analysed earlier. here they are simply treated by imagej change in brightness/contrast. the same can also be done with imagemagic.

Note: "FigSM.A.1_Model-A.cps" corresponds to "SM-A-no design FigSM.A.1_Model-A.cps" in Suppl. Inform.

Concentrations of metals, PAHs and PCBs in sediment samples from Kollevåg and reference site.

Creators: None

Submitter: Karina Dale

Data file for PLaSMo accesssion ID PLM_52, version 1

Data file for PLaSMo accesssion ID PLM_66, version 1

Data file for PLaSMo accesssion ID PLM_51, version 1

No description specified

Creators: Maja Rey, Ulrike Wittig

Submitter: Maja Rey

This report gives an overview of the sessions and outcomes from the recent SEEK Users meeting in Berlin. Please see related 'Presentation' entries for related slides and supplementary material.

Creator: Katy Wolstencroft

Submitter: Katy Wolstencroft

Calculated by using R package GOSemSim.

Semi-targeted Mass Spectrometry proteomics study to detect 12 selected proteins of two serum samples belonging to the FOLFOX-4 study on heavly-pretreated ovarian cancer patients. The two samples, F10 and F12, are basal samples collected at before the first FOLFOX-4 treatment cycle (T0) and were selected for this study because they show a different proteome profile.

This .csv file contains growth parameters measured from chemostat runs of the Sheffield Infors chemostats. The runs were carried out for acetate calibration purposes and for sampling for the steady-state transcriptional profiles.

Columns: Date O2_input (% total) Aerobiosis level (%AAU) OD600 Redox (mV) pO2 (μM) DCW (g/L) Viable cell counts (CFU/ml) RespRate (mmol/h/gDCW) RespRate STDEV [Acetate] (mM) Qacet (mmoles/h/gDCW)

This .pdf file shows a graphical representation of the physiological measurements from the Sheffield Infors chemostat which were made during acetate calibration and also when sampling for the steady-state transcriptional profiles.

No description specified

Creator: Matthew Rolfe

Submitter: The JERM Harvester

No description specified

Creator: Matthew Rolfe

Submitter: The JERM Harvester

Prorocentrum cordatum was subjected to whole cell shotgun analyses (in-solution digest) unsing nanoLC ESI-intrap MS/MS

No description specified

Creators: None

Submitter: Lars Wöhlbrand

Data file for PLaSMo accesssion ID PLM_11, version 1

Data file for PLaSMo accesssion ID PLM_2, version 1

Data file for PLaSMo accesssion ID PLM_22, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_23, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_11, version 1

Data file for PLaSMo accesssion ID PLM_11, version 2

Data file for PLaSMo accesssion ID PLM_23, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_24, version 1

Creators: BioData SynthSys, Jonathan Massheder

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_23, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_22, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_30, version 1

Data file for PLaSMo accesssion ID PLM_3, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_3, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_41, version 1

Data file for PLaSMo accesssion ID PLM_1, version 1

Data file for PLaSMo accesssion ID PLM_3, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_33, version 1

Data file for PLaSMo accesssion ID PLM_38, version 1

Data file for PLaSMo accesssion ID PLM_76, version 1

Data file for PLaSMo accesssion ID PLM_2, version 1

Data file for PLaSMo accesssion ID PLM_32, version 1

Data file for PLaSMo accesssion ID PLM_34, version 1

Data file for PLaSMo accesssion ID PLM_35, version 1

Data file for PLaSMo accesssion ID PLM_36, version 1

Data file for PLaSMo accesssion ID PLM_37, version 1

Data file for PLaSMo accesssion ID PLM_39, version 1

Data file for PLaSMo accesssion ID PLM_40, version 1

Data file for PLaSMo accesssion ID PLM_41, version 1

Data file for PLaSMo accesssion ID PLM_6, version 1

Creators: BioData SynthSys, Alexandra Pokhilko, Andrew Millar

Submitter: BioData SynthSys

Simulation results of experimental data of the reconstituted gluconeogenic system

The file contains simulated data of the electron transport chain model (EcoliETC1) for varying parameter values, i.e. a local sensitivity analysis.

Data file for PLaSMo accesssion ID PLM_66, version 1

Small set of values for entering into NetLogo simulation

Small set of values for entering into NetLogo Simulation

Creator: Hannah O'Keefe

Submitter: Hannah O'Keefe

Owner: Nils Gehlenborg (nils@hms.harvard.edu)

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

Compound SMILES of resynthesized or newly designed pteridine compounds 1b, 1c, 2a-e, 3a-e, 4a-j and 5a-f used for ligand preparation within Maestro (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Maestro.). SMILES strings and compound identifiers are comma-separated and can be readily imported in Maestro.

See 'Figure 3 legend' and 'Materials and methods - Time course experiments, cell lysis and quantitative immunoblotting' for details.

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.

Specific activity of Gre2p was measured after different treatments (none, on ice, at room temperature, in the ITC, stirred, shaken). These data are used to perform a Selwyn Test to determine if enzyme inactivation or slow-onset inhibition occurs. This is a file that can be opened with the Origin Software for analysis and contains data copied in manually from the xlsx.

Specific activity of Gre2p was measured after different treatments (none, on ice, at room temperature, in the ITC, stirred, shaken). These data are used to perform a Selwyn Test to determine if enzyme inactivation or slow-onset inhibition occurs. These are the raw data obtained directly from the Synergy UV-Vis Spectrophotometer.

Specific activity of Gre2p was measured after incubation with different Tween-20 concentrations (none, 0.01, 0.1, 1.0%). These data are also used to perform a Selwyn Test to determine if enzyme inactivation or slow-onset inhibition occurs. This is a file that can be opened with the Origin Software for analysis and contains data copied in manually from the xlsx.

Specific activity of Gre2p was measured after incubation with different Tween-20 concentrations (none, 0.01, 0.1, 1.0%). These data are also used to perform a Selwyn Test to determine if enzyme inactivation or slow-onset inhibition occurs. These are the raw data obtained directly from the Synergy UV-Vis Spectrophotometer.

Reference genome of Sulfolobus solfataricus P2 used for mapping of RNA-seq results. Based on NCBI genome of Sulfolobus solfataricus.

Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)

Submitter: Stefan Albaum

No description specified
No description specified
No description specified

metabolite quantification via enzymatic analysis

Incorporate research data

Creator: Runyu Liang

Submitter: Runyu Liang

Transcriptional profiles of steady-state chemostat cultures were measured at a range of oxygen levels using microarrays. Oxygen levels were defined by the aerobiosis scale of Alexeeva et al. (2002).

Concentrations of E2 and T in cod plasma of female cod caged in Kollevåg measured by enzyme immunoassay.

Creators: None

Submitter: Karina Dale

The stressosome is composed of three proteins that assemble in the form of an icosahedron. Icosahedra can be modelled in different ways with different abstraction levels regarding the original stressosome structure. The pdf-figure introduces geometric modelling of the stressosome using origami and particle dynamics simulations.

NMN formation by NamPT was measured using LC-MS as described in supplementary information

Data file for PLaSMo accesssion ID PLM_24, version 1

Creators: BioData SynthSys, Jonathan Massheder

Submitter: BioData SynthSys

Summary table of identified pigment binding proteins with relative shares in % and calculations of total amount of pigment binding proteins in the different data sets.

Creators: None

Submitter: Jana Kalvelage

Summary of identified ribosomal proteins of P. cordatum.

Creators: None

Submitter: Jana Kalvelage

Content:

  • Nuclear protein fractions: NSP, NMP and NTP R1-R3 (Peptide counts)
  • Summary nuclear proteins geLC
  • Cellular protein fractions: CSP, CMP R1-R3 (Peptide counts)
  • Summary cellular proteins geLC
  • Summary nuclear protein fractions NSP R1-R3 (iBAQs)
  • Summary cellular protein fractions CSP R1-R3 (iBAQs)
  • 15 columns annotation
  • Final summary of protein data
  • Prediction results
  • Annotation (biological processes and categories)

Tab color: raw data, green; summarized data, orange; final ...

Creators: None

Submitter: Jana Kalvelage

No description specified

Parameters used in maxQuant analysis

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

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

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

A list of the search terms used for identifying SARS-CoV2 studies involving enrichment analysis. A random sample of 100 papers were used as input to the experiment.

This file provides a full list of the PubMed IDs used as input to our survey of SARS-CoV2 enrichment analysis results

This file contains description of all model parameters and corresponding references

Supplementary information file from Chew et al. PNAS 2014, including full model description for Arabidopsis Framework Model v1, model simulations and experimental validations.

Supplementary File 1 - Merged ITAG/PGSC Phureja DM gene models. Archive containing GTF, CDS and peptide fasta files for merged ITAG and PGSC gene models for S. tuberosum Group Phureja DM genome v4.04

1 file with legends 4 files with figures 2 files with tables

Data file for PLaSMo accesssion ID PLM_32, version 1

No description specified

Liver samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Columns: Compound 8.60_759.5784n Compound ID GPCho(12:0/22:1) Accepted? Adducts M+H, M+Na Formula C42H82NO8P Score 51,1 Fragmentation Score 62,1 Mass Error (ppm) 0,808672852 Isotope Similarity 94,59106017 Theoretical Isotope Distribution 100 - 47 - 12.5 - 2.39 - 0.367 Link http://nonlinear.com/redirect/outbound?p=lipidblast¶m=GPCho%2812%3A0%2F22%3A1%29 Description GPCho(12:0/22:1) Neutral mass (Da) ...

Muscle samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Columns: Compound 8.60_759.5784n Compound ID GPCho(12:0/22:1) Accepted? Adducts M+H, M+Na Formula C42H82NO8P Score 51,1 Fragmentation Score 62,1 Mass Error (ppm) 0,808672852 Isotope Similarity 94,59106017 Theoretical Isotope Distribution 100 - 47 - 12.5 - 2.39 - 0.367 Link http://nonlinear.com/redirect/outbound?p=lipidblast&param=GPCho%2812%3A0%2F22%3A1%29 Description GPCho(12:0/22:1) Neutral ...

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP1012-finalG/

Creator: Marko Petek

Submitter: Marko Petek

Raw proteomics data for S. thermosulfidooxidans samples

Creator: Malte Herold

Submitter: Malte Herold

Symmetric mean absolute percentage error per sample graph for the 40 independent samples

The file contains complete agenda of the SEEK users meeting , 26-27 March 2012 in Berlin

Creator: Olga Krebs

Submitter: Olga Krebs

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