Find research datasets worth reusing

openJul 2024View details →

Datasets collected for benchmarking in spatial transcriptomics

Datasets collected for benchmarking in spatial transcriptomics. In addition, the code for benchmarking (March 2025 version, svg-benchmark-main.zip) is also located here and can be accessed on the GitHub website <a href="https://github.com/XiDsLab/svg-benchmark">https://github.com/XiDsLab/svg-benchmark</a>.

opencc-by-4.0Jul 2024View details →

Imaging spatial transcriptomics in a transgenic mouse model of α-synucleinopathy

Open the record for dataset details and reuse information.

opencc-zeroDec 2019View details →

Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison

Petal size determines the value of ornamental plants, and thus their economic worth. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes regulating petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 17 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with extreme differences in petal size identified 11 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, BnaA05.RAP2.2 homologous to RAP2.2 in rapeseed may be a critical gene negatively influencing petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two extreme accessions were determined mainly by cell number differences. Finally, we propose a preliminary model for the control of petal size in rapeseed. Our results provide insights into the genetic mechanisms regulating petal size, and also lay the foundation for a better understanding of petal development in plants.

opencc-by-4.0Sep 2021View details →

10X Genomics Human Visium Spatial Transcriptomics Demo Dataset for Cellxgene VIP

4 Visium Spatial Transcriptomics datasets downloaded 10X Genomics data site ,and organized in the way to be used for Cellxgene VIP input. 10X_demo_data_Breast_Cancer_Block_A_Section_1 10X_demo_data_Breast_Cancer_Block_A_Section_2 10X_demo_data_Human_Heart 10X_demo_data_Human_Lymph_Node

opencc-by-4.0Jan 2022View details →

Results of matrix factorization decompositions for a set of 14 colon cancer transcriptomic datasets using different methods

These are the results of application of several matrix factorization methods (ICA, StabilizedICA, NMF, PCA) for a set of 14 independent colon cancer transcriptomics datasets. The analysis was done to compare the methods in terms of their reproducibility (ability to generalize).  The results of this analysis was published in  <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821374/pdf/btz225.pdf">Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinformatics. 2019 Nov 1;35(21):4307-4313. doi: 10.1093/bioinformatics/btz225. </a>

opencc-zeroJan 2022View details →

Transcriptome for: MYB42 inhibits hypocotyl cell elongation by coordinating brassinosteroid homeostasis and signaling in Arabidopsis

The precise control of brassinosteroids (BRs) homeostasis and signaling is a prerequisite for hypocotyl cell elongation in plants. Little is known, however, of such regulators of BR homeostasis and signaling. Here, we have demonstrated that MYB42 negatively regulates hypocotyl elongation through partial inhibition of BRASSINAZOLE-RESISTANT 1 (BZR1) signaling and promotion of BR inactivation. Transgenic Arabidopsis plants repressing the expression of MYB42 and its paralog MYB85 (MYB85 RNAi;myb42) exhibited longer hypocotyls than wild-type (WT) plants in darkness, while MYB42 or MYB85 overexpression inhibits hypocotyl elongation. Hypocotyl length of MYB85 RNAi;myb42 plants can be resorted into WT level by MYB42 overexpression. MYB42 inhibits hypocotyl elongation by mediating BR signaling, because MYB42 expression is repressed with BR treatment and in the dominant BR mutant bzr1-1D, and mutation of both MYB42 and MYB85 enhances the dwarf phenotype of the BR receptor mutant bri1-5. BZR1 directly represses MYB42 expression in response to BR, and the hypocotyl length of bzr1-1D is reduced in MYB42 overexpression plants but increased in MYB85 RNAi;myb42 plants. These results show MYB42 is a negative target of BZR1. Transcriptome data revealed that a number of BZR1-induced genes associated with cell elongation are down-regulated by MYB42, suggesting that MYB42 may partially inhibit BZR1 signaling. In addition, MYB42 enlarges its action in BR signaling through feedback activation of the BR-inactivating enzyme DOGT1. The present study shows a MYB42-mediated multilevel system that contributes to fine regulation of BR-induced hypocotyl elongation.

tomato tissue transcriptome -2

tomato tissue transcriptome

tomato tissue transcriptome -4

tomato tissue transcriptome

tomato tissue transcriptome -7

tomato tissue transcriptome

tomato tissue transcriptome -6

tomato tissue transcriptome

tomato tissue transcriptome -3

tomato tissue transcriptome

tomato tissue transcriptome -5

tomato tissue transcriptome

tomato tissue transcriptome -8

tomato tissue transcriptome

tomato tissue transcriptome

tomato tissue transcriptome

tomato tissue transcriptome -9

tomato tissue transcriptome

tomato RNAi, OE and WT fruit transcriptome at MG, Br and pink fruit stages-2

tomato RNAi, OE and WT fruit transcriptome at MG, Br and pink fruit stages-2

tomato RNAi, OE and WT fruit transcriptome at MG, Br and pink fruit stages-1

tomato RNAi, OE and WT fruit transcriptome at MG, Br and pink fruit stages

opencc-zeroDec 2021View details →

Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003. Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

opencc-zeroJan 2022View details →

Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation

Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.