cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/d1.1945
title: Packer et al 2019 scRNAseq dataset wrangled into standard WormBase anndata- 89k cells profiled with 10xv2 across multiple timepoints of development

description: This is part of a curated collection of all C. elegans single cell RNA sequencing 
high throughput data wrangled into the anndata format in .h5ad files 
with standard fields, plus any number of optional fields that vary depending 
on the metadata the authors provide.

As possible, we attempt to keep the field names lower case, short, descriptive, 
and only using valid Python variable names so they may be accessed via the syntax 
adata.var.field_name

For the convention used to wrangle the h5ad files see 
https://github.com/WormBase/single-cell/blob/main/data_wrangling_convention.md

Notebook used to wrangle the data: 
https://github.com/WormBase/wormcells-notebooks/blob/main/wormcells_wrangle_packer2019_h5ad.ipynb


Original study:
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

Packer, Jonathan S. and Zhu, Qin and Huynh, Chau and Sivaramakrishnan, 
Priya and Preston, Elicia and Dueck, Hannah and Stefanik, Derek and Tan, 
Kai and Trapnell, Cole and Kim, Junhyong and Waterston, Robert H. and Murray, John I.

Science 20 Sep 2019: Vol. 365, Issue 6459, eaax1971 DOI: 10.1126/science.aax1971 
https://science.sciencemag.org/content/365/6459/eaax1971.editor-summary

Data description:
89,701 cells profiled with 10xv2 across multiple timepoints of development

Data available at:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126954


Fields of the anndata object as printed from Python:

```

print(adata) 

AnnData object with n_obs × n_vars = 20222 × 89701
    obs: 'gene_id', 'gene_name'
    var: 'study', 'batch', 'sample', 'sample_description', 'barcode', 'cell_type', 'n_umi', 'time_point', 'size_factor', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc'

print(adata.var.head(1).T) 

AnnData object with n_obs × n_vars = 20222 × 89701
    obs: 'gene_id', 'gene_name'
    var: 'study', 'batch', 'sample', 'sample_description', 'barcode', 'cell_type', 'n_umi', 'time_point', 'size_factor', 'cell_subtype', 'plot_cell_type', 'raw_embryo_time', 'embryo_time', 'embryo_time_bin', 'raw_embryo_time_bin', 'lineage', 'passed_qc'

print(adata.obs.head(1).T) 

           WBGene00010957
gene_id    WBGene00010957
gene_name          nduo-6
```
DOI: 10.22002/d1.1943
title: Supplementary Data Set for Manuscript "The horizontal slab beneath East Asia..."

description: Grid files of the predicted present-day temperature field in "The Horizontal Slab Beneath East Asia and Its Subdued
Surface Dynamic Response" (Liu,S.,Ma,P.,Zhang,B. and Gurnis,M.).
Grids for each case are organized in a folder, whose name is the name of the case. In the folder, temperature field grids are named according to the section (e.g. section_a.grd).
All the grid files are in the gmt NetCDF format and have two dimensions. For the temperature files , the x direction is the span of the great arc in degrees. The y direction corresponds to the non-dimensional radius of the earth.
description: Related Publication:
The Horizontal Slab Beneath East Asia and Its Subdued Surface Dynamic Response

Liu, S., Ma, P., Zhang, B., & Gurnis, M. CUGB and Caltech

Journal of Geophysical Research: Solid Earth

2021-03-10

https://doi.org/10.1029/2020JB021156
eng
DOI: 10.22002/d1.1942
title: SARS-CoV-2 is detectable using sensitive RNA saliva testing days before viral load reaches detection range of low-sensitivity nasal swab tests

description: This dataset is part of a COVID-19 household transmission study comparing SARS-CoV-2 in saliva and nasal swabs.
DOI: 10.22002/d1.1941
title: SUGARseq_TMG_Opt_Tags_10XLookupTable

description: 10X lookup table to match 10X barcodes on feature tags to 10X barcodes on cDNA.
DOI: 10.22002/d1.1940
title: SUGARseq_TMG_Opt_cDNA_GeneNames_Dict

description: Dictionary to convert ensemble IDs to gene names.
DOI: 10.22002/d1.1939
title: SUGARseq_TMG_Opt_cDNA_GeneIDs

description: Kallisto process gene IDs for cDNA data.
DOI: 10.22002/d1.1938
title: SUGARseq_TMG_Opt_Tags_FeatureIDs

description: Kallisto processed feature IDs for tags data.
DOI: 10.22002/d1.1937
title: SUGARseq_TMG_Opt_Tags_CellBarcodes

description: 10X cell barcode IDs for tags data.
DOI: 10.22002/d1.1935
title: SUGARseq_TMG_Opt_Tags_FASTQ

description: FASTQ Files for tags
DOI: 10.22002/d1.1933
title: SUGARseq_TMG_Opt_SupplementalFiles_CellCycleGenes

description: CSV files of cell cycle associated genes from the literature.
DOI: 10.22002/d1.1932
title: SUGARseq_TMG_Opt_Tags_Mtxfile

description: Kallisto processed cell by gene matrix for tags.
DOI: 10.22002/d1.1931
title: SUGARseq_TMG_Opt_cDNA_CellBarcodes

description: Kallisto processed 10X cell barcode for cDNA data.
DOI: 10.22002/d1.1929
title: SUGARseq_TMG_Opt_cDNA_Mtxfile

description: Kallisto processed cell by gene matrix for CDNA.
DOI: 10.22002/d1.1921
title: Data for "An Internal Energy-dependent model for the Grüneisen parameter of silicate liquids"

description: Pressure-volume-energy for all simulations, from which Grüneisen parameters can be extracted.
description: Contact person: Goddard, William A. wag@caltech.edu
DOI: 10.22002/d1.1920
title: Measurements of atmospheric HDO/H2O in southern California from CLARS-FTS

description: These are data for the paper Zeng et al. 2021, JGR-A, under review, preprint at: https://www.essoar.org/doi/10.1002/essoar.10506339.1
Brief Intro: we retrieved HDO and H2O columns from observations by the California Laboratory for Atmospheric Remote Sensing Fourier Transform Spectrometer (CLARS-FTS), a mountaintop observatory on Mt. Wilson (1.67 km above sea level) overlooking the Los Angeles (LA) basin in southern California. CLARS-FTS observations are highly sensitive to the lower atmosphere due to the long light path along the PBL. Retrievals were conducted using spectral windows centered in the range of 6000-7000 cm -1. The entire spectral record of CLARS-FTS from 2011-2019 was processed. The isotopological abundance δD, which represents the relative difference of the HDO/H2O ratio to a standard abundance ratio, is also calculated.
description: Related Publication:
Measurements of atmospheric HDO/H2O in southern California from CLARS-FTS

https://doi.org/10.1002/essoar.10506339.1
eng
DOI: 10.22002/d1.1891
title: Constraining Fault Friction and Stability with Fluid-Injection Field Experiments

description: We provide model outputs of the simulations presented in the study as well as data from the field experiment detailed in Guglielmi et al. (2015)

The headings for the model output  temporal evolution files are:
time, time step, slip, slip rate, shear stress, effective normal stress, state variable term (ln(V*\theta/D_RS)), pore pressure
The headings for the model output spatial and temporal evolution files are: 
x, slip, slip rate, shear stress, state variable term, temperature (constant here), effective normal stress, pore pressure
DOI: 10.22002/d1.1878
title: Optical absorption of metal oxides and results of machine learning predictions

description: CSV files that collectively contain optical absorption data from metal oxides with different cation elements compositions.
The optical properties for each metal oxide composition are the 10-dimensional unitless absorption coefficient where the 10 dimensions correspond to equally-spaced ranges of photon energy spanning 1.39 eV to 3.11 eV.
These data also include test-train splits for benchmarking machine learning models that predict the optical absorption, along with results obtained to-date with various machine learning models. For each test-train split, data are normalized to 0 mean, unit variance.
DOI: 10.22002/d1.1874
title: Enceladus ocean overturning circulation simulations

description: Model output used to create figures.
DOI: 10.22002/d1.1862
title: CRISPRcruncher: A tool for engineering restriction sites into coding regions

description: Extended data of RE sites identified by CRISPRcruncher, a computational tool that analyzes an input coding sequence and produces a complete list of all possible changes that could be made that will create new RE sites while preserving the original peptide sequence.
description: Related Publication:
CRISPRcruncher: A tool for engineering restriction sites into coding regions

Samuel F. Fay Wyoming INBRE Bioinformatics Core, University of Wyoming

David S. Fay Dept. of Molecular Biology, University of Wyoming

Vikram E. Chhatre Dept. of Molecular Biology, University of Wyoming

microPublication Biology

https://doi.org/10.17912/micropub.biology.000343
eng
description: Contact person: David S. Fay davidfay@uwyo.edu
DOI: 10.22002/d1.1858
title: Active matter driven fluid flows

description: Biological systems achieve precise control over ambient fluids through the self-organization of active protein structures including flagella, cilia, and cytoskeletal networks. In such active structures individual proteins consume chemical energy to generate force and motion at molecular length scales. Self-organization of protein components enables the control and modulation of fluid flow fields on micron scales. The physical principles underlying the organization and control of active-matter-driven fluid flows are poorly understood. Here, we apply an optically-controlled active-matter system composed of microtubule filaments and light-switchable kinesin motor proteins to analyze the emergence of persistent flow fields in a model active matter system. Using light, we form contractile microtubule networks of varying size and shape and explain the resulting flow fields within a simple and unified theoretical framework. We specifically demonstrate that the geometry of microtubule flux at the corners of contracting microtubule networks predicts the architecture of fluid flow fields across network geometries through a simple point force model. Our work provides a foundation for programming microscopic fluid flows with controllable active matter and could enable the engineering of versatile and dynamic microfluidic devices.
DOI: 10.22002/d1.1856
title: ClickTag Fastqs for Clytia Starvation Dataset

description: MiSeq fastq files from ClickTag sequencing of fed and starved Clytia medusae
DOI: 10.22002/d1.1853
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_07

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_07 from HiSeq 4000
DOI: 10.22002/d1.1852
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_07

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_07 from HiSeq 4000
DOI: 10.22002/d1.1848
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_05

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_05 from HiSeq 4000
DOI: 10.22002/d1.1846
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_04

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1 for HiSeq 4000
DOI: 10.22002/d1.1845
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_03

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2 from HiSeq 4000
DOI: 10.22002/d1.1844
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_03

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1 from HiSeq 4000
DOI: 10.22002/d1.1835
title: Estimation of C. elegans cell- and tissue volumes

description: Cell- and Tissue Volumes, including Syncytia and Ploidy. This table provides all the primary data obtained from measuring cell and tissue volumes of the Virtual Worm and the information collected from the literature on ploidy and syncytia.
description: Related Publication:
Estimation of C. elegans cell- and tissue volumes

Jonathan J Froehlich Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany

Nikolaus Rajewsky Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany

Collin Y Ewald Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, 8603 Schwerzenbach-Zürich, Switzerland

microPublication Biology

2020-12-31

https://doi.org/10.17912/micropub.biology.000345
eng
DOI: 10.22002/d1.1831
title: Sequences of ClickTag Barcodes for Clytia Multiplexed Experimentation

description: fasta file of ClickTag sequences used in multiplexed Clytia experiments
DOI: 10.22002/d1.1830
title: Clytia Medusa Cufflinks Transcriptome

description: gff3 file for original Clytia transcriptome (from Cufflinks assembly)
DOI: 10.22002/d1.1829
title: Clytia Medusa Cufflinks Transcripts

description: fasta file for transcripts from original Clytia transcriptome (Cufflinks assembly)
DOI: 10.22002/d1.1828
title: Clytia Genome

description: fasta file for Clytia genome assembly
DOI: 10.22002/d1.1827
title: Clytia Peptide Sequences from TRINITY Annotation

description: .pep file for peptide sequences of Clytia transcripts from TRINITY assembly
DOI: 10.22002/d1.1826
title: Clytia Peptide Sequences from XLOC Annotation

description: .pep file for protein sequences from original Clytia transcriptome (XLOC annotations)
DOI: 10.22002/d1.1825
title: Clytia Medusa TRINITY Transcripts

description: Fasta file for transcript sequences from TRINITY-assembled Clytia transcriptome
DOI: 10.22002/d1.1824
title: Clytia Medusa TRINITY Transcriptome

description: TRINITY-assembled transcriptome for Clytia medusae
DOI: 10.22002/d1.1822
title: GO Terms for Clytia Hemisphaerica

description: txt file for GO Terms associated with Clytia genes
DOI: 10.22002/d1.1820
title: Panther Annotations for Clytia Hemisphaerica

description: txt file for Panther annotations of Clytia genes
DOI: 10.22002/d1.1819
title: Clytia Hemisphaerica Orthologs

description: txt file with ortholog matches for Clytia genes
DOI: 10.22002/d1.1816
title: CellRanger ClickTag Data for Clytia Starvation 2

description: Bam files for ClickTags sequenced on MiSeq for Clytia starvation (lane 2)
DOI: 10.22002/d1.1815
title: CellRanger ClickTag Data for Clytia Starvation 1

description: Bam files for ClickTags sequenced on MiSeq for Clytia starvation
DOI: 10.22002/d1.1812
title: Filtered Gene Expression for Clytia Starvation

description: h5ad file for Scanpy analysis with metadata information on cells selected by ClickTag filtering
DOI: 10.22002/d1.1811
title: Filtered Cell Barcodes for Clytia Starvation Dataset

description: csv of cell barcodes selected by ClickTag demultiplexing
DOI: 10.22002/d1.1803
title: CellRanger Metadata (Features) for Clytia Starvation Data

description: Features tsv output from standard cellRanger pipeline on starved Clytia cDNA
DOI: 10.22002/d1.1802
title: CellRanger Output for Clytia Starvation Data

description: Matrix output from standard cellRanger pipeline on starved Clytia cDNA
DOI: 10.22002/d1.1801
title: CellRanger Barcode Metadata for Clytia Starvation Data

description: Barcode tsv output from standard cellRanger pipeline on starved Clytia cDNA
DOI: 10.22002/d1.1800
title: Clytia Starvation ClickTag Counts 2

description: CSV of ClickTag-by-cell counts from MiSeq (2nd lane) sequencing on starved medusae
DOI: 10.22002/d1.1799
title: Clytia Starvation ClickTag Counts 1

description: CSV of ClickTag-by-cell counts from MiSeq sequencing on starved medusae
DOI: 10.22002/d1.1798
title: CellRanger-processed Clytia Starvation Data

description: h5ad for Scanpy analysis of initial cellRanger processing of starved Clytia medusae cDNA
DOI: 10.22002/d1.1793
title: ClickTag Fastqs for Clytia Stimulation Dataset

description: Concatenated fastqs from HiSeq/MiSeq sequencing of ClickTags for DI, KCl, and seawater treated Clytia medusae
DOI: 10.22002/d1.1702
title: SARS-CoV-2 Viral Load Data In A Household with Observed Transmission

description: Please see Data Annotation file for a full description of the variables in this dataset. 

This dataset is part of a COVID-19 household transmission study run by the Ismagilov lab and Pasadena Public Health Department, and approved by the Caltech Institutional Review Board (protocol #20-1026). All participants provided written informed consent prior to participation.
DOI: 10.22002/d1.1701
title: Quantitative sequencing clarifies the role of disruptor taxa, the oral microbiome, and strict anaerobes in the human small-intestine microbiome

description: Raw data and processing scripts for manuscript. All processing scripts are python jupyter notebooks. Unzip data file folders and keep the folder hierarchy as is or alter path locations in jupyter notebooks.
DOI: 10.22002/d1.1693
title: The context-dependent, combinatorial logic of BMP signaling

description: Cell-cell communication systems typically comprise families of ligand and receptor variants that function together in combinations. Pathway activation depends in a complex way on which ligands are present and what receptors are expressed by the signal-receiving cell. To understand the combinatorial logic of such a system, we systematically measured pairwise Bone Morphogenetic Protein (BMP) ligand interactions in cells with varying receptor expression. Ligands could be classified into equivalence groups based on their profile of positive and negative synergies with other ligands. These groups varied with receptor expression, explaining how ligands can functionally replace each other in one context but not another. Context-dependent combinatorial interactions could be explained by a biochemical model based on competitive formation of alternative signaling complexes with distinct activities. Together, these results provide insights into the roles of BMP combinations in developmental and therapeutic contexts and establish a framework for analyzing other combinatorial, context-dependent signaling systems.
description: This deposit contains the data, code, and analysis to recreate the results in the manuscript, 'The combinatorial logic of BMP signaling across contexts.' The processed data and analysis are organized by figures, and the raw data are organized by data type. The code and analysis are written for Matlab 2019a and Python 3. Please see the related publication for more details, and contact the corresponding authors for any questions.
description: Klumpe, H., Langley, M.A., Linton, J.M., Su, C.J. Antebi, Y.E., Elowitz, M.B. (2020). The combinatorial logic of BMP signaling across contexts (Version 1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.1693
or choose a different citation style.
DOI: 10.22002/d1.1672
title: IHN Hydrolysis 1D Model Results

description: Output of one-dimensional model that incorporated the condensed-phase hydrolysis of the isoprene hydroxynitrates
DOI: 10.22002/d1.1671
title: GC Chromatograms from 2017 Caltech Roof Study

description: Chromatograms of isoprene hydroxynitrates (m/z 232) collected with the GC-HR-ToF-CIMS during a 2017 field study located on the Caltech Library rooftop
DOI: 10.22002/d1.1670
title: LAS1 wave velocity model for the central Los Angeles Basin

description: LAS1 wave velocity model for the central Los Angeles Basin presented in Jia and Clayton (2020).
DOI: 10.22002/d1.1667
title: Dynamic rupture initiation and propagation in a fluid-injection laboratory setup with diagnostics across multiple temporal scales

description: Fluids are known to trigger a broad range of slip events, from
slow, creeping transients to dynamic earthquake ruptures. Yet, the
detailed mechanics underlying these processes and the conditions
leading to different rupture behaviors are not well understood.
Here, we use a laboratory earthquake setup, capable of injecting
pressurized fluids, to compare the rupture behavior for different
rates of fluid injection, slow (megapascals per hour) versus fast
(megapascals per second). We find that for the fast injection
rates, dynamic ruptures are triggered at lower pressure levels and
over spatial scales much smaller than the quasistatic theoretical
estimates of nucleation sizes, suggesting that such fast injection
rates constitute dynamic loading. In contrast, the relatively slow
injection rates result in gradual nucleation processes, with the
fluid spreading along the interface and causing stress changes
consistent with gradually accelerating slow slip. The resulting
dynamic ruptures propagating over wetted interfaces exhibit dynamic
stress drops almost twice as large as those over the dry
interfaces. These results suggest the need to take into account the
rate of the pore-pressure increase when considering nucleation
processes and motivate further investigation on how friction
properties depend on the presence of fluids.
DOI: 10.22002/d1.1666
title: Data for "Assessing the influence of COVID-19 on the radiative balance over the East Asian Marginal Seas"

description: This datasets provides AM4 data required to produce results in the paper "Assessing the influence of COVID-19 on the radiative balance over the East Asian Marginal Seas".
DOI: 10.22002/d1.1662
title: Supplemental Tables for Deuterium Isotope Model

description: Data for all deuterium measurements used in moiety model for thesis Chapter 5 (Laura Chimiak). Includes measurement data, references, moiety assignments, and predictions. Table S1 presents data for organic mater in the Murchison meteorite and Table S2 presents data for organic mater in Murchison and other meteorites.
DOI: 10.22002/d1.1661
title: Supplemental Information Tables for Carbon Isotope SOM Model for Meteorites

description: These are the carbon isotope ratio in delta space (d13C) for measurements and predictions the soluble organic material on meteorites assuming production by the integrated aldehyde network (Strecker synthesis, aldehyde oxidation, and reductive amination), Fischer Tropsch type synthesis, and Formose type chemistry.
DOI: 10.22002/d1.1660
title: Data set for: Understanding dynamic friction through spontaneously evolving laboratory earthquakes

description: The data set includes the time histories of friction, slip and slip rate associated with the propagation of spontaneously evolving dynamic ruptures.
description: Related Publication:
Understanding dynamic friction through spontaneously evolving laboratory earthquakes

Vito Rubino California Institute of Technology

Ares J Rosakis California Institute of Technology

Nadia Lapusta California Institute of Technology

Nature Communications

2017-06-29

https://doi.org/10.1038/ncomms15991
eng
DOI: 10.22002/d1.1659
title: GWML/GWSkyNet: GWSkyNet_v1

description: GWSkyNet is a binary CNN classifier for gravitational-wave candidates. This repository contains the published model together with instructions on how to use the classifier. The input is a sky map FITS file from BAYESTAR, which can be found on GraceDB for real gravitational-wave candidates.
description: Related Publication:
GWSkyNet: a real-time classifier for public gravitational-wave candidates

Miriam Cabero The University of British Columbia

Ashish Mahabal Caltech

Jess McIver The University of British Columbia

The Astrophysical Journal Letters

https://doi.org/10.3847/2041-8213/abc5b5
eng
description: Contact person: Miriam Cabero micamu@phas.ubc.ca