Find research datasets worth reusing

Discretized bulk data by the discretization step of rFASTCORMICS used in in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

Bulk data RNAseq data were downloaded from GEO, GTEX, and other sources (see below) and discretized by the discretization step of rFASTCORMICS (Pacheco et al, 2019) used in the optimization step in scFASTCORMICS: CRC bulk RNAseq data were obtained from Lee et al(2020)  CRC control (NM) was downloaded from GSE81861  (GTEX, Healthy colon from) Pancreatic  Human islet bulk RNAseq data was downloaded from EBI Expression Atlas (Pancreatic islet cells) Immune cells in pancreatic carcinoma bulk data were obtained from GEO (GSE156278) liver and breast cancer bulk RNAseq data were obtained from the TCGA (GSE62944)   rFASTCORMICS and tutorial on rFASTCORMICS can be found: https://github.com/sysbiolux

single-cell RNAseq data (data set 5) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset5) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor3 downloaded from the GEO website (GSE114297).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 15) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset15) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from CD8 T-cells in PACA samples downloaded from the GEO website (GSE156728).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 4) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset4) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor2 downloaded from the GEO website  (GSE114297).    see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.

single-cell RNAseq data (data set 3) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data

The present dataset (dataset3) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from normal Pancreas donor1 downloaded from the GEO website (GSE114297).  see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data and github: https://github.com/sysbiolux/scFASTCORMICS For more information, version updates of the scFASTCORMICS.  <pre>  </pre>

opencc-by-4.0Jul 2022View details →

Targeted DNA methylation from cell free DNA using hybrid probe capture

CSV files contain beta value and coverage per base & per region, as indicated in the file name. Columns are samples, rows are CpGs or target region - depending on the file. Files were generated from our bismark/bsseq pipeline as described in the manuscript. Contact: dnbuckle@usc.edu

opencc-zeroNov 2022View details →

Multidimensional control of therapeutic human cell function with synthetic gene circuits

Synthetic gene circuits that precisely control human cell function could expand the capabilities of gene and cell-based therapies. However, platforms for developing circuits in primary human cells that drive robust functional changes in vivo and have compositions suitable for clinical use are lacking. Here, we develop synthetic transcriptional regulators that are compact and based largely on human-derived proteins (synZiFTRs). As a proof of principle, we engineer gene switches and circuits that allow precise, user-defined control over therapeutically-relevant genes in primary T cells using orthogonal, FDA-approved small molecule inducers. Our circuits can instruct T cells to sequentially activate multiple cellular programs, such as proliferation and anti-tumor activity, to drive synergistic therapeutic responses. This platform should accelerate development and clinical translation of synthetic gene circuits in diverse human cell types and contexts.

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis"

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis".

opencc-by-4.0Dec 2021View details →

Non-cell autonomous small RNA silencing in Arabidopsis female gametes

Raw data tables as well as R script

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation PCR) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.

opencc-by-4.0May 2023View details →

[Data S2] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation

Data S2. GLIPH2 hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. For all TCRs within each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), GLIPH2 specificity groups are generated as described in methods.

opencc-by-4.0May 2023View details →

[Data S1] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation

Data S1. ALICE hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. For each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), all ALICE hits generated as described in methods.

Single-cell burst size estimates

Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population, not single-cell, level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different length intracellular accumulation periods by employing E. coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data show that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis), and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation or "noise" in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.

opencc-by-4.0May 2023View details →

[Github Sample Dataset] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation

[Github Sample Dataset]. This is an accompanying data set for the github repository "https://github.com/acyeh-lab/2023/tree/main/tcr-simulation" referred to in "Non-genetic determinants of clonotypic T cell expansion following stem cell transplantation" by Yeh AC et al.

Hyperspectral imaging of exciton confinement within a moiré unit cell with a subnanometer electron probe

Data and processing notebooks for article titled "Hyperspectral imaging of exciton confinement within a moiré unit cell with a subnanometer electron probe" published in Science in Decembner 2022. The `ADF Image.dm4` is the simultaneously acquired annular dark field (ADF-) scanning transmission electron microscopy (STEM) image. This was used to determine the structural reconstruction of the WSe2 / WS2 heterostructure. The `EELS Spectrum Image.dm4` is a spectrum image (one spectra per probe position). This was used to determine the extent of the localization of the exciton peak I. The two `ipynb` jupyter notebooks were used to do the analysis shown in the paper. The output is embedded in the notebooks. Also, each notebook was run and then exported as a static HTML file to retain the code and output together in a generally readable format. Contact Peter Ercius (percius@lbl.gov) regarding the code or data.

Cell-type specific responses to associative learning in the primary motor cortex

The primary motor cortex (M1) is known to be a critical site for movement initiation and motor learning. Surprisingly, it has also been shown to possess reward-related activity, presumably to facilitate reward-based learning of new movements. However, whether reward-related signals are represented among different cell types in M1, and whether their response properties change after cue-reward conditioning remains unclear. Here, we performed longitudinal in vivo two-photon Ca2+ imaging to monitor the activity of different neuronal cell types in M1 while mice engaged in a classical conditioning task. Our results demonstrate that most of the major neuronal cell types in M1 showed robust but differential responses to both cue and reward stimuli, and their response properties undergo cell-type specific modifications after associative learning. PV-INs' responses became more reliable to the cue stimulus, while VIP-INs' responses became more reliable to the reward stimulus. PNs only showed robust response to the novel reward stimulus, and they habituated to it after associative learning. Lastly, SOM-IN responses emerged and became more reliable to both conditioned cue and reward stimuli after conditioning. These observations suggest that cue- and reward-related signals are represented among different neuronal cell types in M1, and the distinct modifications they undergo during associative learning could be essential in triggering different aspects of local circuit reorganization in M1 during reward-based motor skill learning.

Soluble T-cadherin promotes pancreatic β-cell proliferation by upregulating Notch signaling

Endogenous humoral factors that link systemic and/or local insulin demand to pancreatic β-cells have not been identified. Here, we demonstrated that T-cadherin, a unique glycosylphosphatidylinositol-anchored cadherin primarily expressed in vascular endothelial cells and cardiac and skeletal muscle cells, but not in pancreatic β-cells, was secreted as soluble forms and was important for β-cell proliferation. Cdh13 (T-cadherin) knockout mice exhibited impaired glucose handling due to attenuated β-cell proliferation under high-fat diet conditions. The gene expression analyses indicated the impairment in cell cycle and Notch signaling in the islets of T-cadherin knockout mice under high-fat diet conditions. In streptozotocin-induced diabetes, the replacement of soluble T-cadherin improved β-cell mass and blood glucose levels in T-cadherin knockout mice. Recombinant soluble T-cadherin upregulated Notch signaling in cultured murine islets. We concluded that soluble T-cadherin could work as an endogenous humoral factor whose signaling pathways including Notch signaling regulate β-cell proliferation under diabetic conditions in mice.

Supplementary Figures -B Cell Epitopes Mapping of the Vibrio cholera Toxins A, B, and P and an ELISA assay

Figure S1- List of Vibrio cholerae [toxin A (P01555), B (P01556), and P (P29485)] synthetic peptides and position in the cellulose membrane of Spot synthesis. Figure S2- Purification of the peptide B (Vc/TxB-11) by HPLC using an XBridge BEH C18 (2.7 μ, 5 cm x 4.6 mm) column coupled to a Water HPLC system at a flow rate of 1.2 ml min-1 using mobile phases A [0.05% formic acid in water (18 MΩ × cm)] and B [(0.05% formic acid in ACN (acetonitrile acid)] (v/v) in water. Detection at 200-300 nm using a diode array. Figure S3- Mass spectrometry. The peptide B (Vc/TxB-11) was solubilized in deionized water to a final concentration of 10 µg/ml and then added formic acid to a final concentration of 0.1%. The mass spectrometer used was the Water UPLC model Acquity-I Class. The samples were electronically injected by the equipment at 1 µl/min. The range used for ion detection ranged from 1000-11500 m/z.

Data sets for "Automated cell segmentation for reproducibility in bioimage analysis"

This is the raw data sets used in "Automated cell segmentation for reproducibility in bioimage analysis", published in Synthetic Biology (Oxford Academic)

Dataset: Carbonate Regeneration Using a Membrane Electrochemical Cell for Efficient CO2 Capture

Dataset for journal publication "Carbonate Regeneration Using a Membrane Electrochemical Cell for Efficient CO2 Capture," published in ACS Sustainable Chemistry & Engineering (DOI: 10.1021/acssuschemeng.2c04175). Data are organized according to figure number.