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Dataset results
623 results for “Cell Identity”
A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity
<p> </p> <p>In our manuscript, we utilized scRNA-seq libraries we generated from:</p> <p>-8 human psoriatic skin samples and 7 healthy control skin samples (ZIST.rds)</p> <p>-3 human psoriatic skin samples before and after tildrakizumab treatment (three_tildra_Trm1.rds) </p> <p>These *rds files are the Seurat objects for these data sets post-filtering and integration. For raw sequencing data corresponding to these samples, access can be found under accession number EGA: S00001005271.</p> <p>We also utilized bulk RNAseq data generated from CRISPR-Cas9 knockout of ZFP36L2 in human CD4 T cells from 3 different donors. The count matrices for each of these individual samples is uploaded here alongside a key explaining what each of the samples are with filenames that also correspond to the raw fastq files submitted at the European Genome-Phenome Archive (EGA), under accession number EGA: S00001005271. There are two replicates for each sample.</p> <p>All methods underlying the generation and analysis of these datasets can be found in the original manuscript: </p> <p>Cook CP, Taylor M, Liu Y, et al. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. <em>Cell Rep Med</em>. 2022;3(8):100715. doi:10.1016/j.xcrm.2022.100715</p> <p><br> Any additional questions or information requests can be addressed to Jeffrey.cheng@ucsf.edu or cook.675@berkeley.edu</p> <p> </p>
Image stacks for full-body transcription factor expression atlas with completely resolved cell identities in C. elegans
<p>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. </p> <p>vano_win32_1.741.zip contains VANO for worm visualization.</p>
Resolving Organoid Brain Region Identities by Mapping Single-Cell Genomic Data to Reference Atlases
<p>Data underlying the figures in the publication “Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases”, published in <em>Cell Stem Cell, </em><strong>2021</strong><em>, </em>28, 1148–1159.</p> <p><a href="https://www.sciencedirect.com/science/article/pii/S1934590921000655">https://www.sciencedirect.com/science/article/pii/S1934590921000655</a></p> <p>Table of contents:</p> <p><strong>1. patscreen_srt.rds</strong>; Numerical data for <em>Figure 7</em>: RNA-seq data of a patterning screen in organoids with an array of small molecules. The dataset is in the rds data format, which can be opened in the R programming language using the function `readRDS()`. Once opened, the dataset is a Seurat object (https://satijalab.org/seurat/) and contains both the transcript counts and the metadata for all samples in the screen. The raw data used in figure 7 was also deposited in ArrayExpress (<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10037/">https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10037/</a>)</p>
H3K36 methylation maintains cell identity by regulating opposing lineage programs
<p>This upload contains cellranger count outputs and RDS objects of preprocessed scRNAseq data from the publication "H3K36 Methylation Maintains Cell Identity by Regulating Opposing Lineage Programs" for new data published with the paper.</p> <p>These RDS objects are produced by code available here <a href="https://github.com/Michorlab/H3K36_methylation_scRNAseq">https://github.com/Michorlab/H3K36_methylation_scRNAseq</a>. The same GitHub repo contains plots and tables generated from data in these objects.</p>
Hematopoietic Stem Cell Transplantation for the Treatment of Patients With Fanconi Anemia Lacking a Genotypically Identical Donor, Using a Chemotherapy Only Cytoreduction With Busulfan, Cyclophosphami
ClinicalTrials.gov study NCT00987480. IPD Sharing: Not stated. Countries: 1. Publications: 2.
IPA Targeted Adoptive Immunotherapy vs Adult Haplo-identical Cell Infusion During Induction of High Risk Leukemia
ClinicalTrials.gov study NCT02508324. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Caspar specifies primordial germ cell count and identity in Drosophila melanogaster
Open the record for dataset details and reuse information.
Zoledronic Acid in Combination With Interleukin-2 to Expand Vγ9Vδ2 T Cells After T-replete Haplo-identical Allotransplant
ClinicalTrials.gov study NCT03862833. IPD Sharing: NO. Countries: 1. Publications: 1.
Minimizing Toxicity in HLA-identical Sibling Donor Transplantation for Children With Sickle Cell Disease
ClinicalTrials.gov study NCT03587272. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Chronic Graft-versus-host Disease (cGvHD) Prophylaxis With or Without ATG Prior to Stem Cell Transplantation (SCT) From HLA-identical Siblings in Patients With Acute Leukemia
ClinicalTrials.gov study NCT00678275. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Study of Non-Myeloablative Haplo-identical Haematopoietic Stem Cell Transplantation in Patients With Haematological Malignancies or Acquired Aplastic Anaemia
ClinicalTrials.gov study NCT01719341. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Safety and Survival of Genetically Modified White Blood Cells in HIV-Infected Persons - A Study in Identical Twin Pairs
ClinicalTrials.gov study NCT00001353. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Stem Cell Transplantation With Identical Donors for Patients With Sickle Cell Disease
ClinicalTrials.gov study NCT00186810. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Plants use identical inhibitors to protect their cell wall pectin against microbes and insects
Open the record for dataset details and reuse information.
Data from: Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling
Background: Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although the field of transcriptomics and functional genomics has quickly grown in the last decade, a deep comparative analysis of human MSCs expression profiles in a meaningful cellular context has not been yet performed. There is also a need to find a well-defined MSCs gene-signature because many recent biomedical studies show that key cellular interaction processes (i.e. inmuno-modulation, cellular cross-talk, cellular maintenance, differentiation, epithelial-mesenchymal transition) are dependent on the mesenchymal stem cells within the stromal niche. Results: In this work we define a core mesenchymal lineage signature of 489 genes based on a deep comparative analysis of multiple transcriptomic expression data series that comprise: (i) MSCs of different tissue origins; (ii) MSCs in different states of commitment; (iii) other related non-mesenchymal human cell types. The work integrates several public datasets, as well as de-novo produced microarray and RNA-Seq datasets. The results present tissue-specific signatures for adipose tissue, chorionic placenta, and bone marrow MSCs, as well as for dermal fibroblasts; providing a better definition of the relationship between fibroblasts and MSCs. Finally, novel CD marker patterns and cytokine-receptor profiles are unravelled, especially for BM-MSCs; with MCAM (CD146) revealed as a prevalent marker in this subtype of MSCs. Conclusions: The improved biomolecular characterization and the released genome-wide expression signatures of human MSCs provide a comprehensive new resource that can drive further functional studies and redesigned cell therapy applications.
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
<p>This dataset contains gene expression values, i. e. transcript counts, of 278 intestinal epithelial cells.</p>
Cord Blood With T-Cell Depleted Haplo-identical Peripheral Blood Stem Cell Transplantation for Hematological Malignancies
ClinicalTrials.gov study NCT01682226. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Unrelated Cord Blood Transplant Plus a Haplo-Identical (Half-Matched), T-Cell Depleted Stem Transplant From a Related Donor for Subjects With High Risk Malignancies
ClinicalTrials.gov study NCT00673114. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Hematopoietic Stem Cell Transplantation for Treatment of Patients With Fanconi Anemia Lacking a Genotypically Identical Donor, Using Total Body Irradiation, Cyclophosphamide and Fludarabine
ClinicalTrials.gov study NCT00595127. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Haplo-identical Viral-Specific T-cells for Treatment of Cytomegalovirus and Adenovirus Infections After Hematopoietic Cell Transplantation
ClinicalTrials.gov study NCT05664126. IPD Sharing: YES. Countries: 1. Publications: 0.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.