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opencc-by-4.0Sep 2023View details →

Zip archive containing datasets described in the manuscript entitled "Distribution-agnostic Deep Learning Enables Accurate Single‐Cell Data Recovery and Transcriptional Regulation Interpretation"

The datasets used in the manuscript entitled "Distribution-agnostic Deep Learning Enables Accurate Single‐Cell Data Recovery and Transcriptional Regulation Interpretation". These datasets encompass all the experiments conducted in the manuscript, including simulation experiments, downsampling experiments, clustering, differential expression analysis, enrichment analysis, trajectory inference, batch correction, and clinical case discovery. The open-source software is available at https://github.com/XuYuanchi/Bis.

Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment

These are 3D live-cell imaging datasets of gastric tumor organoids in co-culture with primary human Natural Killer (NK) cells. The datasets were analyzed by a new, deep learning-based 3D image analysis software tool, SiQ-3D, which we developed and presented in the paper titled "Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment". Interested users can download the SiQ-3D software code from GitHub (https://github.com/simonlbd1/SiQ-3D) or Code Ocean (https://codeocean.com/capsule/6676007/tree/v2), analyze the 3D image datasets locally, and cross-check the results with the SiQ-3D quantified results that we provided here.

Fragment-sequencing unveils local tissue microenvironments at single-cell resolution

This dataset contains the Resolve dataset that was used in the publication. Other data set can be found in GEO with the accession number GSE216189. The code that was used during the analysis can be found on our GitHub repository: https://github.com/Moors-Code/Fragment-sequencing

Data from: Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight

3-dimensional super-resolution microscopy volumes of human PBMCs recorded on a Zeiss LSM980 Airyscan2 laser scanning confocal microscope. Sample preparation and image capture: Live PBMCs were stained with 60 nM MitoTracker Red-CMX-Ros (ThermoFisher, Waltham, MA) either in 6-well plates or in the microgravity chambers for the last 2 hr of the microgravity simulation. At the end of the microgravity simulation cells were immediately fixed by 1:1 mixing the cell suspensions with 2× concentrated fixative (10% Sucrose (w/v) 120 mM KCl, 1% (w/v) glutaraldehyde, 8% (w/v) PFA pH 7.4) and incubated for 15 minutes at room temperature followed by 15 minutes on ice. Fixed cells were washed and stored in PBS until further staining for up to a week at 4 °C. 1 million fixed cells were resuspended in 1 mL of permeabilization solution (0.1% TritonX-100 in PBS) for 5 minutes. After twice washing in PBS, pellets were resuspended in 0.5 mL 1% BSA PBS containing Phalloidin-iFluor-488 (cat# ab176753, Abcam plc., Cambridge, UK) at the manufacturer’s recommended dilution, and were incubated for 90 minutes with gentle agitation. After washing in PBS, cells were stained with Hoechst 33342 (1 µg/mL in PBS) for 10 minutes. The fixed-stained cells were immobilized at 3 × 105 cells per well density in glass-bottom 96-well microplates (Greiner Bio-One, Monroe, NC), which were pre-coated with polyethyleneimine (1:15,000 (w/v)) for 16 hours in a 37 °C incubator, and washed twice with PBS. Microplates with the cell suspensions were centrifuged in a swing plate rotor centrifuge (Eppendorf 5810 R) at 400 × g and for 10 min and then fixed on the surface by adding an equal volume of 8% (w/v) PFA for 5 min. Finally, the fixative was replaced with 100 µL of antifade reagent (Vector Prolong Gold (ThermoFisher)). Samples were imaged immediately after this procedure on a Zeiss LSM980 Airyscan2 laser scanning confocal microscope (Carl Zeiss Microscopy, White Plains, NY). Single PBMCs were manually selected for recording based on low-resolution preview scans showing only nuclei. All singlet cells were selected in a small neighborhood to avoid biases. In each microscopy session, 24-40 cells were selected for recording in one well for each condition. This was performed in an interleaved manner, capturing 6-8 cells at a time, and then moving to the next well and then repeating this multiple times using the Experiment Designer module for automation. Super-resolution volumes of (358 × 358 × 70 pixels, 0.035 × 0.035 × 0.13 µm/voxel resolution) were recorded in the above-determined positions using Definite Focus autofocusing. A Plan-Apochromat 63 × 1.40 Oil lens, Airyscan2 SR (super-resolution) mode with optimal sampling and frame switching between 3 fluorescence channels to minimize spectral cross-bleed were used. MitoTracker Red, iFluor488, and Hoechs33342 were excited with 561, 488, and 405 nm solid-state lasers, respectively, using the optimal emission filter for each channel. 3D Airyscan2 processing was performed with standard filtering settings. File naming: Four zip files were deposited named as <Donor#id>.zip, where id goes from 1 to 4. Each zip file contains the following Zeiss Microscopy format image files: <Condition>_<Donor#id>_<Stain#batch>_<Cell>.czi <Condition>: <ul> <li>1G – Control culturing in 6-well plates for 25h</li> <li>uG – simulated microgravity culturing for 25h in NASA Rotating Wall Vessels</li> <li>1G+TLR – as above, with TLR 7/8 agonist (1 μM R848)</li> <li>uG+TLR– as above, with TLR 7/8 agonist (1 μM R848)</li> <li>1G+CyD– as above, with cytochalasin D</li> <li>uG+CyD– as above, with cytochalasin D</li> <li>1G+Q – as above, with quercetin 50µM</li> <li>uG+Q – as above, with quercetin 50µM</li> </ul> <Donor#id>: 1-4 indicates biological replicates <Stain#batch>: 1-2 indicates experimental replicates of phalloidin staining and imaging session <Cell>: arbitrary number to distinguish images within the same condition/donor/stain set. See image analysis pipelines used with these data at: https://github.com/gerencserlab/Superresolution-actin-and-mitochondria-analysis

Data used in paper "Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON"

This directory contains the data resources of the following paper: "Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON"

Single-cell and spatially resolved transcriptomic data of mouse regenerative livers under normal and fibrotic conditions

A single-cell spatial-temporal transcriptomic atlas of liver regeneration under normal and fibrotic condition, including a total of 30 mouse liver samples obtained from 15 normal and 15 fibrotic mice at timepoints Day 0, 1, 2, 3, and 7 after a partial hepatectomy (PHx) procedure with three replicates for each time point, followed by the scRNA-seq and SRT sequencing for each sample using the Stereo-seq platform.

A Study of Atezolizumab Compared With a Single-Agent Chemotherapy in Treatment Naïve Participants With Locally Advanced or Recurrent or Metastatic Non-Small Cell Lung Cancer Who Are Deemed Unsuitable

ClinicalTrials.gov study NCT03191786. IPD Sharing: Not stated. Countries: 24. Publications: 4.

controlledIPD-YESFeb 2026View details →

Effects of Single Agent Niraparib and Niraparib Plus Programmed Cell Death-1 (PD-1) Inhibitors in Non-Small Cell Lung Cancer Participants

ClinicalTrials.gov study NCT03308942. IPD Sharing: YES. Countries: 1. Publications: 1.

Single Agent Ofatumumab Vs. Single Agent Rituximab in Indolent B-Cell Non Hodgkin Lymphoma Relapsed After Rituximab-Containing Therapy

ClinicalTrials.gov study NCT01200589. IPD Sharing: Not stated. Countries: 16. Publications: 1.

closedIPD-NOFeb 2026View details →

Safety of a Single, Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Retinitis Pigmentosa

ClinicalTrials.gov study NCT02320812. IPD Sharing: NO. Countries: 1. Publications: 1.

LUX-Lung 5: Afatinib Plus Weekly Paclitaxel Versus Investigator's Choice of Single Agent Chemotherapy Following Afatinib Monotherapy in Non-small Cell Lung Cancer Patients Failing Erlotinib or Gefitin

ClinicalTrials.gov study NCT01085136. IPD Sharing: Not stated. Countries: 23. Publications: 1.

controlledIPD-YESFeb 2026View details →

PF-00299804 As A Single Agent, In Patients With Advanced Non-Small Cell Lung Cancer Who Have Failed Chemotherapy And Erlotinib

ClinicalTrials.gov study NCT00548093. IPD Sharing: YES. Countries: 1. Publications: 1.

SMaRT Blood: Single-unit Versus Multiple-unit Packed Red Blood Cell Transfusion in Non-acute Postpartum Anemia

ClinicalTrials.gov study NCT03419780. IPD Sharing: Not stated. Countries: 1. Publications: 2.

Study of Tazemetostat as Single Agent in Solid Tumors or B-cell Lymphomas and in Combination With Prednisolone in DLBCL

ClinicalTrials.gov study NCT01897571. IPD Sharing: Not stated. Countries: 10. Publications: 4.

Single-cell CBD Biomarkers of Inflammation Reduction in People Living With HIV

ClinicalTrials.gov study NCT05209867. IPD Sharing: Not stated. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Study to Evaluate Effect of a Single Dose of Sotatercept (ACE-011) on Red Blood Cell Mass and Plasma Volume in Participants With Solid Tumors

ClinicalTrials.gov study NCT01190644. IPD Sharing: YES. Countries: 1. Publications: 1.

A Single Agent Phase II Study of Romidepsin (Depsipeptide, FK228) in the Treatment of Cutaneous T-cell Lymphoma (CTCL)

ClinicalTrials.gov study NCT00106431. IPD Sharing: Not stated. Countries: 6. Publications: 4.

closedIPD-NOFeb 2026View details →

Haploidentical CD34+ Selected Cells Combined With Single Unit Umbilical Cord Blood Transplant for Treatment of High-risk Hematologic Disorders

ClinicalTrials.gov study NCT03093844. IPD Sharing: NO. Countries: 1. Publications: 4.

A Phase II Study of Single-Agent Lenalidomide in Subjects With Relapsed Or Refractory T-Cell Non-Hodgkin's Lymphoma

ClinicalTrials.gov study NCT00655668. IPD Sharing: Not stated. Countries: 4. Publications: 1.

Transcoronary Infusion of Cardiac Progenitor Cells in Patients With Single Ventricle Physiology

ClinicalTrials.gov study NCT01273857. IPD Sharing: Not stated. Countries: 1. Publications: 8.