Index Catalog // Deep Blue Data

Data from "A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications"

Creator:: Walker, Logan A, Li, Ye, McGlothlin, Maggie, and Cai, Dawen
Description:: These are datasets released from our manuscript "A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications". Included in this data release are: `noise16.tif`: a file containing background noise collected from a 1000-frame acquisition of a ORCA-Fusion camera; `noise8.tif`: a file containing the 16-bit data collective above converted into a 8-bit form; `brainbow.tif`: This is a mouse Brainbow image originally published and described in Roossien, et al. Bioinformatics 2019; `bead.tif`: This is a 3D image of 100nm Invitrogen TetraSpeck fluorescent microspheres imaged in a blue channel using a custom microscope; `fly.tif`: This is a 3D image of a fly Bitbow brain collected as described in Li, et al. Front. Neural Circuits 2021; and `neurite.tif`: This is a 3D image of DiD-labeled mouse V1 tissue, collected using a custom microscope.
Keyword:: neuroscience, microscopy, and Bitbow
Discipline:: Health Sciences

Untargeted lipidomics and targeted metabolomics analysis of Cardiolipin synthase deficient murine macrophages

Creator:: Reynolds, Mack B., Hong, Hanna S., Zhang, Li, Lyssiotis, Costas A., and O'Riordan, Mary X.
Description:: Untargeted lipidomics (Data S1) and targeted metabolomics (Data S2) analysis from in vitro culture of a murine macrophage cell line expressing shRNA targeted to Cardiolipin synthase (CRLS1), referred to as CRLS1 knockdown (KD), or a paired non-target shRNA-expressing (NT-Control). CRLS1 KD and NT-Control macrophages were either directly analyzed (untargeted lipidomics) or stimulated with lipopolysaccharide for a variety of timepoints and then analyzed (targeted metabolomics). Datasets are available as .csv files.
Keyword:: Lipidomics, Metabolomics, Cardiolipin, Macrophage, CRLS1, lipopolysaccharide, and LPS
Citation to related publication:: Reynolds M.B. et al. (2023). Cardiolipin coordinates inflammatory metabolic reprogramming through regulation of Complex II disassembly and degradation. Science Advances, 9(5). DOI: 10.1126/sciadv.ade8701
Discipline:: Health Sciences

Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy - Code & Data

Creator:: Szuromi, Matthew P. and Stacey, William C.
Description:: The data and scripts are meant to show how burster dynamics determine response to a single biphasic stimulus. The files include data which show trends in the propensity of termination for different burster types and the MATLAB scripts used to generate this data. The MATLAB scripts also allow the user to generate their own data sets for alternative bursting paths and stimulus parameter combinations. Furthermore, they allow the user to visually examine the effects of single stimuli in the voltage timeseries and in state space. How the user can access these features of the script is described in the file "ReadMe.pdf."
Keyword:: Epilepsy, Stimulation, Modelling, Dynamics, Seizure, and Dynamotype
Citation to related publication:: (PROVISIONAL) Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy
Discipline:: Health Sciences, Engineering, and Science

Epileptic High Frequency Oscillation EEG with Network Analysis Dataset

Creator:: Lin, Jack and Stacey, William C.
Description:: The characterization of HFO networks through functional connectivity analysis and network centrality. Details of the code repository can be found in the README.txt file.
Keyword:: Epilepsy, High Frequency Oscillation, HFO, Network, and EEG
Citation to related publication:: Pending
Discipline:: Health Sciences

Literature search files for "Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease: A Meta-Analysis and Systematic Review"

Creator:: Saylor, Kate M., McCormick, Amanda D., Wilde, Megan M., Charpie, Christine E., Yu, Sunkyung, and Cousino, Melissa K.
Description:: The search data supports a literature review project on Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease. The data included are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). Both the original search files and updated search files have been included in the deposit.
Keyword:: pediatrics, univent, Single Ventricle Congenital Heart Disease, and psychological
Discipline:: Health Sciences

Dataset of Clinical Consent Forms

Creator:: Umberfield, Elizabeth, Ford, Kathleen, Stansbury, Cooper, and Harris, Marcelline R.
Description:: Research Overview: This dataset is clinical consent forms, collected as part of Dr. Elizabeth Umberfield's dissertation research of at the University of Michigan. 134 consent forms are used in the analysis, 102 of which are shared here (not all are shared due to data protection agreements with participating sites). The research aimed to enable representation of clinical consent forms and their permissions within the Informed Consent Ontology. These efforts were supported by the Rackham Graduate Student Research Grant, and Dr. Umberfield's doctoral training was supported by the Robert Wood Johnson Foundation Future of Nursing Scholars Program.
Keyword:: Consent, Consent Form, Informed Consent, Health Care, and Healthcare
Citation to related publication:: Umberfield, E., Jiang, Y., Fenton, S., Stansbury, C., Ford, K., Crist, K., Kardia, S., Thomer, A., & Harris, M. R. (In Press). Lessons Learned for Identifying and Annotating Permissions in Clinical Consents. Applied Clinical Informatics. and Umberfield, E., Stansbury, C., Ford, K., Jiang, Y., Kardia, S. L. R., Thomer, A., & Harris, M. R. (Under Review). Evaluating and Extending the Informed Consent Ontology for Representing Permissions from the Clinical Domain.
Discipline:: Health Sciences

Pharmacometabolomics of L-carnitine-Kaplan-Meier survival data: numbers at risk

Creator:: Stringer, Kathleen A.
Description:: These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
Keyword:: sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
Citation to related publication:: Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687
Discipline:: Health Sciences

FGFR2-C342Y/+ and FGFR2+/+ Treated with/without Tissue Nonspecific Alkaline Phosphatase (TNAP) Mouse Skulls: C57B:6 strain 3 weeks postnatal

Creator:: Hatch, Nan E.
Description:: Crouzon FGFR2-C342Y/+ and wild type littermate pups on a C57BL/6 congenic background were injected with lentivirus expressing recombinant TNAP enzyme or phosphate buffered saline shortly after birth. Mice were euthanized 3 weeks after birth for analyses.
Keyword:: craniofacial, bone, craniosynotosis, FGFR2, TNAP tissue nonspecific alkaline phosphatase, mouse model, and development
Citation to related publication:: Nam, H. K., Vesela, I., Schutte, S. D., & Hatch, N. E. (2020). Viral delivery of tissue nonspecific alkaline phosphatase diminishes craniosynostosis in one of two FGFR2C342Y/+ mouse models of Crouzon syndrome. PLOS ONE, 15(5), e0234073. https://doi.org/10.1371/journal.pone.0234073
Discipline:: Health Sciences

Supplemental Data for "Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge"

Creator:: Tronson, Natalie C and Tchessalova, Daria
Description:: The main goal of this research was to identify potential molecular pathways that contribute to memory dysregulation and decline that persists long after illness or inflammation. We have previously established a subchronic immune challenge model that results in memory impairments months after the inflammatory challenge. This project aimed to determine whether memory impairments were accompanied by transcriptional dysregulation in memory related brain region (the hippocampus). These data show the differential gene expression as log2fold change (and p-value) in males and females 3 months after immune challenge (Supp Tables 1 and 2); after a subsequent immune challenge (Supp Tables 3 and 4); the differential regulation of genes in males and females (Supp Table 5); genes differentially expressed in the hippocampus of males and females at baseline (Supp Table 6) and the differential regulation of those genes in males and females after immune challenge (Supp Tables 7,8).
Keyword:: hippocampus, lipopolysaccharide, differential gene expression, RNA sequencing, neuroimmune, sex differences, learning and memory, and inflammation
Citation to related publication:: Tchessalova, D., & Tronson, N. C. (2019). Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge. BioRxiv, 566570. https://doi.org/10.1101/566570
Discipline:: Science and Health Sciences

Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data

Creator:: Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
Description:: The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/r6vg-9658
Keyword:: evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
Citation to related publication:: Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
Discipline:: Science, Engineering, and Health Sciences

Data from "A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications"

Untargeted lipidomics and targeted metabolomics analysis of Cardiolipin synthase deficient murine macrophages

Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy - Code & Data

Epileptic High Frequency Oscillation EEG with Network Analysis Dataset

Literature search files for "Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease: A Meta-Analysis and Systematic Review"

Dataset of Clinical Consent Forms

Pharmacometabolomics of L-carnitine-Kaplan-Meier survival data: numbers at risk

FGFR2-C342Y/+ and FGFR2+/+ Treated with/without Tissue Nonspecific Alkaline Phosphatase (TNAP) Mouse Skulls: C57B:6 strain 3 weeks postnatal

Supplemental Data for "Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge"

Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data

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