Find research datasets worth reusing

VC40429 Million Mutation Project strain | 2016-02-16T15:46:54+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=bvXuuZiocig</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-16T15:46:54+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : anticlockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food R_2016_02_16__15_46_54___4___4</li> <li>total time (s) : 898.967</li> <li>frames per second : 30.03</li> <li>video micrometers per pixel : 6.21293</li> <li>number of segmented skeletons : 25569</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-19T15:33:16+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=QaUW0a1su2Q</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-19T15:33:16+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food L_2016_02_19__15_33_16___4___4</li> <li>total time (s) : 898.967</li> <li>frames per second : 30.03</li> <li>video micrometers per pixel : 6.21293</li> <li>number of segmented skeletons : 26299</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-09T15:35:37+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=VpeSZXxEoos</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-09T15:35:37+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : anticlockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food R_2016_02_09__15_35_37___4___4</li> <li>total time (s) : 899.0</li> <li>frames per second : 30.03</li> <li>video micrometers per pixel : 6.21293</li> <li>number of segmented skeletons : 26138</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-03T12:30:04+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=dPWc539ldB8</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-03T12:30:04+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food L_2016_02_03__12_30_04___4___5</li> <li>total time (s) : 899.0</li> <li>frames per second : 30.03</li> <li>video micrometers per pixel : 6.21293</li> <li>number of segmented skeletons : 26719</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-24T16:20:58+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=m_72gXApJTM</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-24T16:20:58+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food L_2016_02_24__16_20_58___3___3</li> <li>total time (s) : 899.3</li> <li>frames per second : 20.0</li> <li>video micrometers per pixel : 4.61106</li> <li>number of segmented skeletons : 17702</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-19T14:29:32+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=uqPq5hMZIA8</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-19T14:29:32+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : anticlockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food R_2016_02_19__14_29_32___3___1</li> <li>total time (s) : 899.3</li> <li>frames per second : 20.0</li> <li>video micrometers per pixel : 4.61106</li> <li>number of segmented skeletons : 17987</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-16T15:25:25+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=WbNoR4n50FI</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-16T15:25:25+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : anticlockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food R_2016_02_16__15_25_25___3___3</li> <li>total time (s) : 899.3</li> <li>frames per second : 20.0</li> <li>video micrometers per pixel : 4.61106</li> <li>number of segmented skeletons : 16977</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-10T14:37:21+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=PgegsZlC57Y</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-10T14:37:21+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food L_2016_02_10__14_37_21___3___2</li> <li>total time (s) : 899.3</li> <li>frames per second : 20.0</li> <li>video micrometers per pixel : 4.61106</li> <li>number of segmented skeletons : 17220</li> </ul>

VC40429 Million Mutation Project strain | 2016-02-03T12:10:35+00:00

<blockquote> This experiment is part of the C.elegans behavioural database. For more information and the complete collection of experiments visit http://movement.openworm.org </blockquote> <ul> <li>preview link : https://www.youtube.com/watch?v=MnyrifF0DNc</li> <li>strain : VC40429</li> <li>timestamp : 2016-02-03T12:10:35+00:00</li> <li>gene : -N/A-</li> <li>chromosome : -N/A-</li> <li>allele : -N/A-</li> <li>strain_description : Million Mutation Project strain</li> <li>sex : hermaphrodite</li> <li>stage : adult</li> <li>ventral_side : clockwise</li> <li>media : NGM agar low peptone</li> <li>arena : <ul> <li>style : petri</li> <li>size : 35</li> <li>orientation : away</li> </ul> </li> <li>food : OP50</li> <li>habituation : 30m wait</li> <li>who : Laura Grundy</li> <li>protocol : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li>lab : <ul> <li>name : William R Schafer</li> <li>location : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li>software : <ul> <li>name : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li>version : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li>featureID : @OMG</li> </ul> </li> <li>base_name : VC40429 on food L_2016_02_03__12_10_35___3___4</li> <li>total time (s) : 899.35</li> <li>frames per second : 20.0</li> <li>video micrometers per pixel : 4.61106</li> <li>number of segmented skeletons : 17491</li> </ul>

opencc-by-4.0Dec 2018View details →

Photoluminescence study of interband transitions in few-layer, pseudomorphic, and strain-unbalanced Ge/GeSi multiple quantum wells - Dataset

Relevant PL data (as txt files) for the publication  <a href="https://arxiv.org/ct?url=https%3A%2F%2Fdx.doi.org%2F10.1103%252FPhysRevB.98.195310&v=88200607">10.1103/PhysRevB.98.195310</a>

opencc-by-4.0Sep 2022View details →

Dataset for "Micromechanics and Strain Localization in Sand in the Ductile Regime"

This dataset contains tomography images and stress-strain curves used in the publication titled "Micromechanics and Strain Localization in Sand in the Ductile Regime" in the Journal of Geophysical Research: Solid Earth

NTUH Reference strain

<a href="https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/484021">Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044</a>, reference strain used in ALPPACA

Functional annotation of the reference transcriptome of Mesodinium rubrum strain JAMR

Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.

Functional annotation of the reference transcriptome of Dinophysis acuminata strain DAVA01

Functional annotation of the reference transcriptome of Mesodinium rubrum strain MBL-DK2009

Functional annotation of the reference transcriptome of Dinophysis ovum strain DoSS3195

opencc-by-4.0Dec 2022View details →

Dataset - Campylomics, strain-typing metagenomics data

Raw data files for submission: "Metagenomic Strain-Typing Combined with Isolate   Sequencing Provides Increased Resolution of the Genetic   Diversity of Campylobacter jejuni Carriage in Wild Birds" strainestDB.tar.xz files expand to rather large file sizes 6-12Gb Code for workflow and additional description: https://git.list.lu/malte.herold/campylomics_pipeline   contained: <ul> <li>additional tables (e.g. list of reference genomes, metadata), multiqc data</li> <li>3 Cjejuni strainEST databases</li> <li>Results of the workflow for the 3 databases: strainest_results</li> <li>KMA results (the same for all 3 runs)</li> <li>KMA database</li> <li>sourmash distances of references genomes used for the strainest DBs</li> </ul> some files might still hold references to a 4th database CJC_CGC, not included here.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES

Appendix 1 Table showing the Mycobacterium bovis genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others. Appendix 2 Table showing the Mycobacterium bovis genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022). Appendix 3 Table showing the Mycobacterium bovis genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample"). Appendix 4 Position of IS6110 insertion sites in the panel of Mycobacterium bovis strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS6110 are determined with the ISMapper tool and the reference genome AF2122/97. Appendix 5 Position of IS6110 insertion sites in the Mycobacterium bovis strain panel of SB0120-DHV. Position of the start and end of IS6110 are determined with the ISMapper tool and the Mb3601 reference genome. Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES

Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric. Annex S2: Pan-genomic study performed on 12 M. bovis complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence. Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS6110 is marked in green. "Indel distribution" sheet shows the indel distribution on the M. bovis genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found. Annex S4: WgSNP analysis performed on 98 M. bovis. SNPs were annotated and selected according to their specificity to an M. bovis group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position. Annex S5: Alignments of the 12 M. bovis complete genomes.

Neutron Bragg edge imaging for strain characterization in powder bed additive manufacturing environments

The paper describes an approach to disentangle the recorded transmission spectrum obtained from Bragg edge imaging. The transmission spectrum of the samples embedded in their corresponding powder was successfully extracted, proven by the coinciding strain maps produced. The horizontal profiles from the maps were plotted together with neutron diffraction results and they agree very well. The uploaded data were the raw data obtained from Bragg edge imaging and neutron diffraction experiments used to construct the strain maps and plots shown in the paper.