Find research datasets worth reusing

opencc-by-4.0Dec 2020View details →

Genome wide Illumina 450K array in AML patients with or without CEBPA mutation

<ul> <li>Num: Row Number</li> <li>Hybridization REF: CpG Reference ID</li> <li>Position: Position in hg19</li> <li>Gene: Entrez Gene Symbol</li> <li>Chrome: Chromosome Number</li> <li>p_vals: P value for t-test between patients with CEBPA and without CEBPA mutation</li> <li>mean_cebpa_mut: mean methylation score for patients with CEBPA mutation</li> <li>mean_no_cebpa_mut: mean methylation score for patients with CEBPA mutation </li> <li> site_status: prediction status for CEBPA sites  </li> <li> fdr: fdr p_value  </li> </ul>

opencc-by-4.0Oct 2021View details →

Alignment files for coverage benchmarks: Illumina and Nanopore sequencing datasets

<ul> <li>cpara-illumina-noseq.bam and cpara-ont-noseq.bam: BAM files produced aligning the raw reads produced respectively by Illumina NextSeq and ONT Nanopore sequencing of an isolate of C. parapsilosis to evaluate the coverage calculations using real datasets.*</li> <li>HG00258.bam: Exome sequencing from the 1000 Genomes Project (Clarke et al 2016 <a href="https://doi.org/10.1093/nar/gkw829">https://doi.org/10.1093/nar/gkw829</a>).</li> <li>panel_01.bam: targeted sequencing of a Human gene panel of 16 genes.*</li> </ul> * Sequences and qualities have been removed

SARS-Cov-2 illumina sequencing training course

Dataset with two samples of SARS-Cov-2 sequenced with Illumina using Artic v3 amplicon enrichment protocol.

Improved genome annotation of Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions

Improved genome annotation of the Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions. The short reads used for the annotation are available at <a href="https://doi.org/10.5281/zenodo.5729968">https://doi.org/10.5281/zenodo.5729968</a> and <a href="https://doi.org/10.5281/zenodo.5729863">https://doi.org/10.5281/zenodo.5729863</a>.To create the gene models, we used tophat v. 2.0.14 to align short reads to the UK7 reference genome (Trapnell et al., 2009). The Intron splice site hints were generated using bam2hints, included in the AUGUSTUS v. 3.2.1 software (Stanke et al., 2006). Due to the very high RNA-sequencing depth available, intron splice hints were filtered for a minimum coverage of 20 reads to avoid an impact of spurious splice signals on gene prediction. To produce ab initio gene models, the BRAKER v. 1.0 pipeline (Hoff et al., 2016) combining GeneMark-ET ab initio gene model predictions and AUGUSTUS v. 3.2.1. GeneMark-ET was trained using the RNA-seq-based splice information as hints. AUGUSTUS was automatically trained using ab initio gene models that were fully supported by splice information. Finally, AUGUSTUS was used to predict gene models using both RNA-seq splice information and coding sequence hints based on exonerate protein alignments as extrinsic evidence.

opencc-by-4.0Apr 2022View details →

Illumina sequencing data of Agro-mediated gene-edited apple lines

FastaQ pair-end Illumina sequencing data of the Dipm1/4, Hipm1, and Mlo19 genes from the different apple Agro-edited lines obtained in the project. GA = Gala; GD = Golden Delicious Lines included are: GA1, GA3, GA4, GA5, and GA WT GD1, 2, 6, 10, 11, 12, 15, 17, 18, 19, 20, 21, 23, 24, 26, 27, 29, 31, 33, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, and WT

opencc-by-4.0Aug 2022View details →

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip, supplementary table 3

Supplementary table 3: Summary statistics from an EWAS assessing the relationship between variance in DNA methylation value and DNA input level.

opencc-zeroJun 2024View details →

Dataset: Illumina, Inc. (ILMN) Stock Performance

This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.

opencc-by-4.0Jul 2024View details →

Illumina Sequencing Data for "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes"

Illumina Sequencing Data for Sulaiman et al., "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes".

opencc-by-sa-4.0Apr 2018View details →

Reduced size Illumina NovaSeq runfolder

This dataset is a reduced size version of an Illumina NovaSeq run of PhiX, where all but the first four cycles have been removed. All metadata associated with the run has been kept intact. This dataset is e.g. useful in testing workflows which require raw Illumina data (i.e. bcl files rather than fastq files). To demultiplex this data with Illumina bclfastq (https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html) it is recommended that the following options are used: <pre><code>--ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --use-bases-mask y4n*,n*</code></pre> This work was supported by the R&D group at the SNP&SEQ Technology Platform in Uppsala. This facility is part of the National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory. The SNP&SEQ Platform is also supported by the Swedish Research Council and the Knut and Alice Wallenberg Foundation.

opencc-by-4.0Jun 2019View details →

Draft genome assemblies of killifish from the Fundulus genus with ONT and Illumina sequencing platforms

Four species from the genus Fundulus were selected for genome sequencing to study the physiological and genetic mechanisms that diverge between euryhaline and stenohaline freshwater species within this cyprinodontiform order of ray-finned fishes.

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Development of Illumina oligos for fungal ITS sequencing

New PCR primers were designed with the following objectives: 1) targetting the ITS2 region to minimize bias due to introns at the 3' end of the SSU, 2) have the broadest possible coverage of Fungi, 3) minimize amplification of plant, protist and other Eukaryote sequences, 4) compatibility with Illumina sequencing adaptors and GOLAY barcodes. Primer regions were selected by eye from sequence alignments then further analyzed using PrimerProspector. At present, several mock communities and hundreds of soil DNA extracts have been successfully sequenced on the Illumina MiSeq platform using the oligos that were developed.

openOpenAug 2014View details →

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Garfagnina goats with Illumina CaprineSNP50 BeadChip

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG), Bionda dell'Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. For GRF, an excess of ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of excess ROH was also present in DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRFshared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

opencc-zeroSep 2020View details →

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.bam alignment files of Illumina and ONT sequencing of pREF plasmid

The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides the first universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.

opencc-zeroFeb 2024View details →

opencc-by-4.0Dec 2024View details →

Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"

Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"

Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in plantae

Transcription profiles were generated from the Rhynchosporium commune isolate UK7. RNA-seq experiments were conducted in plantae on the barley cultivar Beatrix (Viskosa 9 Pasadena, Saaten Union, breeders’ Reference NS01/2449). Leaves were collected at 9 and at 13 days post infection (dpi). All experiments were conducted in triplicates. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.

Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in vitro

Transcription profiles were generated from the Rhynchosporium commune isolate UK7. Cultures were grown either on Luria-Bertani (LBA) or Potato Dextrose Broth (PDB) media. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. Experiments were conducted in triplicates. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.

opencc-by-4.0Jul 2022View details →

Illumina HD genotypes for 3,092 cattle from Burkina Faso, Ghana, Nigeria and Tanzania for: "Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle"

Raw HD data for Riggio et al. 2022: Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle This repository contains the raw Illumina HD genotypes (i.e., 777,962 SNPs) mapped to the bovine UMD3.1 genome assembly for 3,092 animals from four African countries (namely Burkina Faso, Ghana, Nigeria and Tanzania).