Find research datasets worth reusing

opencc-bySep 2023View details →

Transcriptome Analysis of Cisplatin, Cannabidiol, and Intermittent Serum Starvation Alone and in Various Combinations on Colorectal Cancer Cells

* See README file for the description of data files available in this repository 1. Study Description: Platinum-derived chemotherapy medications are often combined with other conventional therapies for treating different tumours, including colorectal cancer. However, the development of drug resistance and multiple adverse effects remain common in clinical settings. Thus, there is a necessity to find novel treatments and drug combinations that could effectively target colorectal cancer cells and lower the probability of disease relapse. To find potential synergistic interaction, we designed multiple different combinations between cisplatin, cannabidiol, and intermittent serum starvation on colorectal cancer cell lines. Based on the cell viability assay, we found that combinations between cannabidiol and intermittent serum starvation, cisplatin, and intermittent serum starvation, as well as cisplatin, cannabidiol and intermittent serum starvation can work in a synergistic fashion on different colorectal cancer cell lines. Furthermore, we analyzed differentially expressed genes and affected pathways in colorectal cancer cell lines to understand further the potential molecular mechanisms behind the treatments and their interactions. We found that synergistic interaction between cannabidiol and intermittent serum starvation can be related to changes in the transcription of genes responsible for cell metabolism and cancer’s stress pathways. Moreover, when we added cisplatin to the treatments, there was a strong enrichment of genes taking part in G2/M cell cycle arrest and apoptosis.   2. Bioinformatics workflow: Initial quality control was conducted using FastQC v0.11.9 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Sequencing reads were trimmed of adapter sequences and low-quality bases using Trimmomatic. Trimmed sequence files were examined with FastQC to verify the trimming results. Trimmed sequencing reads were mapped to Human genome (GRCh37, Ensembl) downloaded from Illumina iGenome website (<a href="https://support.illumina.com/sequencing/sequencing_software/igenome.html">https://support.illumina.com/sequencing/sequencing_software/igenome.html</a>). Mapping was done using splice aware aligner HISAT2 2.1.0. Alignment files in SAM format were converted to BAM, sorted and indexed with samtools v.1.3.1. Mapping quality and statistics were collected with QualiMap software package v.2.2.2 <a href="http://qualimap.conesalab.org/">http://qualimap.conesalab.org/</a> The counts if reads mapping to features (genes) were counted using FeatureCounts v.2.0.1 software. Data exploration, visualization and statistical comparisons were conducted using R language version 4.2.2. Pair-wise comparisons between experimental groups were done with DESeq2 v.2.1.36 as described in the package manual. To decrease computational time, only the genes with at least 5 reads across 3 samples were kept in the analysis. In addition to hard threshold filtering mentioned above, DESeq2 implements independent filtering based on mean of normalized count as a filter statistic. We used hierarchical clustering (HC) and principal components analysis (PCA) to investigate the relationship between samples and detect potential outliers. Prior to HC and PCA analysis, DESeq2 normalized values underwent variance stabilizing transformation with using vst() function from DESeq2. HC was done using hclust() function implemented in R, with the clustering method set as “complete” for the matrices of sample-to-sample distances, and “Ward.D2” in case of the sample and gene clustering based on top 500 most variable genes. The distance measure in HC analysis was set to “euclidean”. Principal components analysis (PCA), applied to top 500 highly variable genes, was conducted using prcomp() function implemented in R with default options. Differentially expressed genes (DEGs) were detected with DESeq2 function results() with default options. DESeq2 uses Wald test to determine significantly changed genes between groups. The independent filtering option was set to TRUE with alpha threshold (adjusted p-value) kept at 0.1. Multiple comparison adjustment was done using Bejamini-Hochberg procedure.

dryad40/100

A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

Teleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon: the seat of plastic behavior, learning, and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly conserved goldfish homologs. We further suggest different elements of a hippocampal formation across the goldfish pallium. Finally, aiding study of the teleostan everted telencephalon, we describe substantial molecular similarities between the goldfish and zebrafish neuronal taxonomies. Together, our atlas provides new insights into organization and evolution of vertebrate forebrains and may serve as a resource for the functional study underlying cognition in teleost fish.

opencc-zeroSep 2023View details →

Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries

Upload of relevant sequencing data for the paper "Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries"

Cell membrane buckling governs early-stage ridge formation in butterfly wing scales: data

This repository contains the raw data for: JF Totz, AD McDougal, L Wagner, S Kang, PTC So, J Dunkel, BD Wilts, and M Kolle, Cell membrane buckling governs early-stage ridge formation in butterfly wing scales, (forthcoming). The raw data is of a volumetric time series of scales growing on the wing of an individual Vanessa cardui pupa, collected with quantitative phase imaging. Additional details may be found in the Materials and Methods, as well as the SI, of the above publication.   The companion code repository may be found on Zenodo: JF Totz, AD McDougal, L Wagner, S Kang, PTC So, J Dunkel, BD Wilts, and M Kolle. (Forthcoming). "Cell membrane buckling governs early-stage ridge formation in butterfly wing scales:code" (v1.0) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.8369163">https://doi.org/10.5281/zenodo.8369163</a>   Note that file A-40-01_11_04_34_set_115.mat was previously released in: AD McDougal, S Kang, Z Yaqoob, PTC So, and M Kolle, Data and analysis codes for “In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui.” Zenodo. https://doi.org/10.5281/zenodo.5532941. We include it here for completeness of this time series.

Data for Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina

Data from the publication "Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina" published in Nature Communications (2022) https://doi.org/10.1038/s41467-022-32762-7. Code for working with this dataset may be found at https://github.com/eulerlab/bc-motion

Malaria drives unique regulatory responses across multiple immune cells during human infection

To investigate malaria driven transcriptional changes in specific immune cell subsets, we sorted live PBMCs from 6 malaria infected donors (day 0), and two subsequent time points after drug treatment (day 7 and 28), along with PBMCs from 2 healthy controls. We performed scRNAseq of these cells, and used clustering and sub-clustering to identify specific immune cell subsets. Differential gene analysis between day 0 and day 28 was performed for each cell cluster and sub-cluster. Key transcriptional changes were confirmed at the protein level with additional donor samples.

opencc-by-4.0Feb 2023View details →

Image stacks for full-body transcription factor expression atlas with completely resolved cell identities in C. elegans

Each image stack presented as zip file. Once decompressed, each folder contain '.ano' linker file, straightening C. elegans L1 images file, the segmentation mask image file and the cell annotation file. The image files are stored in Peng Hanchuan RAW/TIFF format, and the cell annotation file is stored in simple comma separated values format. To visualize the image stack data, drag the '.ano' linker file to VANO interface.  vano_win32_1.741.zip contains VANO for worm visualization.

opencc-by-4.0Oct 2023View details →

Code repository for: Base editing mutagenesis maps functional alleles to tune human T cell activity

Jupyter notebook and supplemental datasets required to created critical figures for the publication.

opencc-by-4.0Oct 2023View details →

CyTOF and Flow Cytometry dataset assocaited with "Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females"

This dataset contains all the raw mass cytometry (CyTOF) and flow cytometry fcs files associated with Capelle et al. 'Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females', Nature Communications, 2023, In Press.The dataset contains the following information:1, The folder " CoPImmunoPD Flow Zenodo V2.zip " contains all the raw fcs files of flow cytometry analysis and the excel table with marker information of five staining panels in the initial discovery analysis using fresh blood samples. The folder also includes the fcs files of analyzing cytotoxicity potential within CD8 T cells and of validation analyses using cryopreserved samples. Single-color/fluorochrome staining files have also been provided for the relevant experiments in the given subfolders for compensation.2, The folder "<a href="https://zenodo.org/api/files/75c910aa-3615-4eff-a201-9d2d46e33ea0/CoPImmunoPD_CyTOF_Zenodo.zip">CoPImmunoPD_CyTOF_Zenodo.zip</a>" contains all the raw fcs files generated from the CyTOF measurements in the initial discovery analysis.To reproduce our published Figures, please be assure to first read all the accompanied readme/excel information annotation files deposited in the corresponding folders within the zip files, all the Source Data files of different main and supplementary Figure subpanels, Methods and/or any other relevant sections in our manuscript.

dryad40/100

Single-cell RNA sequencing of sclerotome-derived fibroblasts in zebrafish

Despite their importance in tissue maintenance and repair, fibroblast diversity and plasticity remain poorly understood. Using single-cell RNA sequencing, we uncover distinct sclerotome-derived fibroblast populations in zebrafish, including progenitor-like perivascular/interstitial fibroblasts, and specialized fibroblasts such as tenocytes. To determine fibroblast plasticity in vivo, we develop a laser-induced tendon ablation and regeneration model. Lineage tracing reveals that laser-ablated tenocytes are quickly regenerated by preexisting fibroblasts. By combining single-cell clonal analysis and live imaging, we demonstrate that perivascular/interstitial fibroblasts actively migrate to the injury site, where they proliferate and give rise to new tenocytes. By contrast, perivascular fibroblast-derived pericytes or specialized fibroblasts, including tenocytes, exhibit no regenerative plasticity. Interestingly, active Hedgehog (Hh) signaling is required for the proliferation of activated fibroblasts to ensure efficient tenocyte regeneration. Together, our work highlights the functional diversity of fibroblasts and establishes perivascular/interstitial fibroblasts as tenocyte progenitors that promote tendon regeneration in a Hh signaling-dependent manner.

opencc-zeroOct 2023View details →

opencc-by-4.0Oct 2023View details →

Data from: Characterisation of GFAP-Expressing Glial Cells in the Dorsal Root Ganglion after Spared Nerve Injury

This data pertain to the paper titled "Characterisation of GFAP-Expressing Glial Cells in the Dorsal Root Ganglion after Spared Nerve Injury " by Elena A. Konnova, Alexandru-Florian Deftu, Paul Chu Sin Chung, Marie Pertin, Guylène Kirschmann, Isabelle Decosterd and Marc R. Suter. The name of the data files correspond to the for each figure in the study. The data file in .csv format are organized so that they can easily be opened in R or other analysis language. To understand them and how they are labelled, it is advised to open the figure next to them and find the appropriate panel.Here are included:<ul><li>the representative images of immunohistochemistry for GFAP, IBA1, Ki67, NeuN, ATF3, FABP7, GS, Cx43, Kir4.1, MBP, L1CAM in the dorsal root ganglia (DRG) of hGFAP-CFP mice after spared nerve injury (SNI).</li><li>the western blot images of DRG samples and FACS sorted CFP+ cells from the DRG of hGFAP-CFP mice after SNI</li><li>the voltage clamp data of GFAP+ cells from DRG of hGFAP-CFP mice after SNI</li></ul>

opencc-by-4.0Apr 2023View details →

Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia

Transcriptome analysis by single cell sequencing provides valuable information on intratumor heterogeneity and developmental stages of acute myeloid leukemia (AML) as well as interactions of tumor cells with the microenvironment. However, it has been hardly applied to the subgroup of cases with translocations of the mixed lineage leukemia (MLL) gene for which the enhancer of mRNA decapping 4 (EDC4) gene was recently identified as a novel fusion partner (MLL-EDC4). In our study published in Blood Advances (Schuster et al., 2023; https://doi.org/10.1182/bloodadvances.2022009096), we compared different MLL translocations by single cell RNA sequencing of cells derived from peripheral blood or bone marrow. The MLL-EDC4 positive cells almost exclusively showed a transcriptional profile of hematopoietic progenitor cells while leukemic cells of MLL-MLLT3 and MLL-ELL fusions exhibited a more differentiated phenotype. The MLL-EDC4 progenitor state was characterized by the upregulation of key transcriptional regulators in AML (RUNX1, SOX4, HOPX), target genes of MYC and interferon signaling as well as other genes known to play a critical role in hematopoiesis or leukemic stem cell activation (CDK6, FLT3, NPM1). Here, the scRNA-seq dataset of our study is provided. It contains six scRNA-seq read count matrices of the AML samples with MLL fusions as described in the table scRNA-seq_samples.xlsx. Further details are given in the publication associated with this dataset.

opencc-by-4.0Aug 2024View details →

scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues

All analysis results for the spatial proteomics imaging techniques in the scProAtlas database are stored in compressed files named accordingly. Within each compressed file, the folders are organized in a fixed storage structure in the following order: Analysis module > Imaging Technique > Dataset > Tissue > ROI. Each folder contains the corresponding metadata (including original sample information, cell type annotations, and neighborhood annotations) stored in a file named <code>cells.tsv</code>. Additionally, the module used to identify spatial pattern genes includes an <code>anndata</code> format file, named <code>adata_moran.h5ad</code>, which stores the integrated results of scRNA-seq and spatial proteomics. scProAtlas_analysis_code.tar.gz contains example codes for all analysis modules in scProAtlas. Here, we provide the example using SCP_CODEX1 - Large intestine. The codes include all the scripts used for the entire workflow, from image segmentation to scRNA-spatial proteomics integration, and spatial analysis. We have also uploaded the raw protein channel matrices with AnnData format in version 3 and 4.

Study of Two Doses of Crizanlizumab Versus Placebo in Adolescent and Adult Sickle Cell Disease Patients

ClinicalTrials.gov study NCT03814746. IPD Sharing: YES. Countries: 21. Publications: 2.

A Study of Oral Ixazomib Maintenance Therapy in Participants With Newly Diagnosed Multiple Myeloma (NDMM) Not Treated With Stem Cell Transplantation (SCT)

ClinicalTrials.gov study NCT02312258. IPD Sharing: YES. Countries: 35. Publications: 2.

ALTA-1L Study: A Study of Brigatinib Versus Crizotinib in Anaplastic Lymphoma Kinase Positive (ALK+) Advanced Non-small Cell Lung Cancer (NSCLC) Participants

ClinicalTrials.gov study NCT02737501. IPD Sharing: YES. Countries: 19. Publications: 5.

Pazopanib Versus Sunitinib in the Treatment of Locally Advanced and/or Metastatic Renal Cell Carcinoma

ClinicalTrials.gov study NCT00720941. IPD Sharing: YES. Countries: 14. Publications: 10.

Study of DS-1062a in Advanced or Metastatic Non-small Cell Lung Cancer With Actionable Genomic Alterations (TROPION-Lung05)

ClinicalTrials.gov study NCT04484142. IPD Sharing: YES. Countries: 10. Publications: 1.

Study of Dose Confirmation and Safety of Crizanlizumab in Pediatric Sickle Cell Disease Patients

ClinicalTrials.gov study NCT03474965. IPD Sharing: YES. Countries: 14. Publications: 1.

Brentuximab Vedotin in Chinese Participants With Relapsed/Refractory CD30-Positive Hodgkin Lymphoma (HL) or Systemic Anaplastic Large Cell Lymphoma (sALCL)

ClinicalTrials.gov study NCT02939014. IPD Sharing: YES. Countries: 1. Publications: 1.