cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/d1.224
title: Flow Cytometry files for "An allosteric theory of transcription factor induction"

description: These data correspond to the original flow cytometry standard (.fcs)  files generated from  the experimental measurement of fluorescence on a MiltenyiBiotec MACSQuant flow cytometer. These files were passed through a processing pipeline to quantify the fold-change in gene expression due to action by the Lac repressor. These data are separated by the operator we examined. Eight different strains were measured for each dataset. Please see the main text or the paper website at http://rpgroup-pboc.github.io/mwc_induction for more information.
description: Related Publication:
An allosteric theory of transcription factor induction

Manuel Razo-Mejia Caltech

Stephanie L. Barnes Caltech

Nathan M. Belliveau Caltech

Griffin Chure Caltech

Tal Einav Caltech

Rob Phillips Caltech

https://doi.org/10.1101/111013
eng
DOI: 10.22002/d1.1628
title: Data accompanying "A probabilistic approach to determination of Ceres' average surface composition from Dawn VIR and GRaND data"

description: This dataset zipfile includes the spectra and MATLAB scripts necessary to reproduce the figures in the Journal of Geophysical Research - Planets paper "A probabilistic approach to determination of Ceres' average surface composition from Dawn VIR and GRaND data". See _README.txt
description: Contact person: Bethany Ehlmann ehlmann@caltech.edu
DOI: 10.22002/d1.1385
title: Ncd K401 multi 1

description: Ncd & K401 optogenetic motors activated by light.  % different activation regions
DOI: 10.22002/d1.1108
title: Raw flow cytometry data for mapping DNA sequence with SortSeq

description: Raw flow cytometry data for all data collections in the paper "Mapping DNA sequence to transcription factor binding energy in vivo" in PLOS Computational Biology. Each data file is available in .fcs and .csv formats and are labeled by date taken followed by a descriptor which corresponds to a data point referenced in the paper. 

    The raw data for April 19, 21, and 22 has been lost but processed versions of the data can be found at https://github.com/RPGroup-PBoC/seq_mapping/tree/master/data
description: Contact person: Stephanie Barnes sbarnes@caltech.edu
DOI: 10.22002/d1.942
title: MCMC Samples for channel quantification and logistic regression described in "Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution."

description: This data set contains all samples obtained through Markov chain Monte Carlo  for estimation of the fluorescence calibration factor, the average cell area, and the most-likely channel copy number for a series of cells.
description: Related Publication:
Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution

Griffin Chure Caltech

Heun Jin Lee Caltech

Rob Phillips Caltech

BioRxiv
eng
DOI: 10.22002/d1.941
title: Microscopy images analyzed in "Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution"

description: This data set contains all images, metadata, and marker positions  for the calibration and osmotic shock experiments. This set does not include the growth series from which survivors were identified.
description: Related Publication:
Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution

Griffin Chure Caltech

Heun Jin Lee Caltech

Rob Phillips Caltech

BioRxiv
eng
DOI: 10.22002/d1.8771
title: GOSAT Solar-Induced Chlorophyll Fluorescence Datasets 2009-2020

description: This dataset contains level 2 GOSAT SIF retrievals. The dataset is documented in the following paper. 
Doughty, R., Kurosu, T., Parazoo, N., Köhler, P., Wang, Y., Sun, Y., and Frankenberg, C.: Global GOSAT, OCO-2 and OCO-3 Solar Induced Chlorophyll Fluorescence Datasets, Earth Syst. Sci. Data Discuss. [preprint], https://doi.org/10.5194/essd-2021-237, in review, 2021.
DOI: 10.22002/d1.227
title: Single-Cell Intensity Values Obtained From Microscopy for "An allosteric theory of transcription factor induction"

description: These data correspond to the single-cell mean intensity values obtained from microscopy images used to quantify fluorescence and compute the fold-change in gene expression due to the activity of the Lac repressor molecule in E. coli cells. These data were used to calculate the population mean fluorescence value. This information was then used to compute the fold-change in gene expression.  These data are separated by the operator we examined. Eight different strains were measured for each dataset.  Please see the main text or the paper website at http://rpgroup-pboc.github.io/mwc_induction for more information.
description: Related Publication:
An allosteric theory of transcription factor induction

Manuel Razo-Mejia Caltech

Stephanie L. Barnes Caltech

Nathan M. Belliveau Caltech

Griffin Chure Caltech

Tal Einav Caltech

Rob Phillips Caltech

https://doi.org/10.1101/111013
eng
DOI: 10.22002/d1.2202
title: Data for "Topological Dissipation in a Time-Multiplexed Photonic Resonator Network"

description: This dataset contains the code and data used to generate the figures in the main text of the paper "Topological Dissipation in a Time-Multiplexed Photonic Resonator Network."
DOI: 10.22002/d1.2125
title: List of LIN-41 protein-expressing neurons

description: List of LIN-41 protein-expressing neurons.
description: Related Publication:
Brain-wide identification of LIN-41 (TRIM71) protein-expressing neurons by NeuroPAL

Mushaine Shih Department of Biological Sciences, University of Illinois at Chicago

Chieh Chang Department of Biological Sciences, University of Illinois at Chicago

microPublication Biology

https://doi.org/10.17912/micropub.biology.000472
eng
description: Contact person: Chieh Chang chieh.chang1@gmail.com
DOI: 10.22002/d1.2115
title: Extended dataset -   Comprehensive profile of the CaORC protein sequences on comparison with the publicly available yeast databases.

description: Comprehensive profile of the CaORC protein sequences on comparison with the publicly available yeast databases. To determine the sequence identity of CaORC across 86 diverse publicly available yeast databases, a TBLASTN was performed in the Sequenceserver (http://blast.wei.wisc.edu/) with CaORC proteins as the query sequence. All the fields are mentioned individually for CaORC1-6 proteins individually: query id, query gi, query acc., subject id, subject ids, subject gi, subject gis, subject accession, subject accessions., query start, query end, sequene start, sequence end, query sequence, subject sequence, evalue, bit score, score, alignment length, % identity, identical a.a., mismatches, positives, gap opens, gaps, % positives, query/subject frames, query frame, BTOP, subject tax ids, subject scientific names, subject common names, subject blast names, subject super kingdoms, subject title, subject titles, subject strand, % query coverage per subject, % query coverage per hsp. N/A means Not applicable/Not available.
description: Related Publication:
Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans

Padmanabhan, Sreedevi Molecular Biology Laboratory, Veer Bahadur Singh Purvanchal University, Jaunpur- 222003, Uttar Pradesh, India.

microPublication Biology

2021-09-13

https://doi.org/10.17912/micropub.biology.000465
eng
description: Contact person: Sreedevi Padmanabhan sreepbc@gmail.com
DOI: 10.22002/d1.2109
title: Cohen2021_N2_Ascr_Extended

description: N2 Extended Data
description: Related Publication:
Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans

Sarah M Cohen Caltech

Jessica J Sun Caltech

Frank C Schroeder Boyce Thompson Institute; Cornell University

Paul W Sternberg Caltech

microPublication Biology

2021-05-12

https://doi.org/10.17912/micropub.biology.000397
eng
description: Contact person: Paul Sternberg pws@caltech.edu
DOI: 10.22002/d1.2110
title: Cohen2021_daf-22_Ascr_Extended

description: daf-22 Extended Data
description: Related Publication:
Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans

Sarah M Cohen Caltech

Jessica J Sun Caltech

Frank C Schroeder Boyce Thompson Institute; Cornell University

Paul W Sternberg Caltech

microPublication Biology

2021-05-12

https://doi.org/10.17912/micropub.biology.000397
eng
description: Contact person: Paul W Sternberg pws@caltech.edu
DOI: 10.22002/d1.2080
title: gpa-4 expressing cells identified through Cao et al., 2017 sci-RNA Seq

description: Cell types with endogenous gpa-4 transcript expression during development from single-cell RNA-seq datasets from Cao et al., 2017.
description: Related Publication:
Widespread gpa-4 promoter-driven expression during Caenorhabditis elegans development

Jaime Osuna-Luque University of Bern/ ETH Zurich

Collin Ewald ETH Zurich

Peter Meister University of Bern

microPublication Biology

https://doi.org/10.17912/micropub.biology.000443
eng
description: Contact person: Peter Meister peter.meister@izb.unibe.ch
DOI: 10.22002/d1.2061
title: Specious Art Pseudotime Lineage Cell Metadata

description: Cell metadata csv for Packer and Zhu et al dataset used for pseudotime analysis
DOI: 10.22002/d1.2060
title: Specious Art Pseudotime Lineage Counts

description: Raw count matrix for Packer and Zhu et al dataset used for pseudotime analysis
DOI: 10.22002/d1.2033
title: Mineral Luminescence Mask Derived from TROPOMI & OCO-2 SIF data

description: Mineral luminescence mask on a 0.05° x 0.05° spatial resolution derived from TROPOMI & OCO-2 SIF data.
DOI: 10.22002/d1.20271
title: Dataset: Enteroendocrine cell expression of split-GAL4 drivers bearing regulatory sequences associated with panneuronally expressed genes in Drosophila melanogaster

description: This table provides detailed midgut and brain scoring data for each split-GAL4 pair examined in this study
description: Related Publication:
DOI: 10.22002/d1.20265
title: Dataset: Enteroendocrine cell expression of split-GAL4 drivers bearing regulatory sequences associated with panneuronally expressed genes in Drosophila melanogaster

description: This table provides detailed midgut and brain scoring data for each split-GAL4 pair examined in this study.
description: Related Publication:
DOI: 10.22002/d1.20258
title: Bedrock Topography and Sections Across Raymond Basin

description: Geologic Map and Sections across the Raymond Basin. Consulting geologist, John P. Buwalda produced a report entitled Geology of the Raymond Basin for the Pasadena Water Department. Here, we report the bedrock topography (plate 2) and the cross-sections (plate 3) from the Geology of the Raymond Basin report by John P. Buwalda.
DOI: 10.22002/d1.20251
title: Dataset: Photo Phenosizer, a rapid machine learning-based method to measure cell dimensions in fission yeast

description: Descriptive and Summary Statistics
description: Related Publication:
DOI: 10.22002/d1.20235
title: Isotope and XRD dataset for Scheller et al. GCA 2022

description: The zip folder contains data from table 1 and table 2 csv format. It also contains the all of the XRD patterns arranged in folders according to samples from the dry experiment, wet experiment, Mono Lake samples, and one measurement of unheated monohydrocalcite.
DOI: 10.22002/d1.20239
title: Dataset: Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily

description: ConSurf sequence conservation results for A0A1U8MGX4
description: Related Publication:
DOI: 10.6084/m9.figshare.19382156.v1
title: Update Request Comments in Stack Overflow Answer Posts

description: Comments play an important role in updating Stack Overflow (SO) posts. They are used to point out a problem (e.g., obsolete answer and buggy code) in a SO answer or ask for more details about a proposed answer. We refer to this type of comment as update request comments (URCs), which may trigger an update to the answer post and thus improve its quality. We manually analyzed a set of 384 sampled SO answer posts and their associated 1,221 comments to investigate the prevalence of URCs and how URCs are addressed. We have provided three level of annotation: 1- If it is a URC, 2- For URCs, where is it addressed, i.e., in the next comments, in the post body, or both. 3- For URCs that are addressed by the following comments, which comment addresses it.
DOI: 10.22002/d1.20233
title: Dataset: WormRuler: A software to track body length used to characterize a super red-shifted channelrhodopsin in Caenorhabditis elegans

description: Original videos and WormRuler analysis of the animals which are depicted in figure 1
description: Related Publication:
DOI: 10.22002/d1.20241
title: Dataset: Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily

description: ClustalOmega MSA of PhyloGenes phylogenetic tree
description: Related Publication:
DOI: 10.22002/d1.20244
title: Dataset: Engineered device in E. coli lyses S. aureus at physiological fever temperatures

description: Plate Lysis Assay Raw Data
description: Related Publication:
DOI: 10.6084/m9.figshare.19382156
title: Update Request Comments in Stack Overflow Answer Posts

description: Comments play an important role in updating Stack Overflow (SO) posts. They are used to point out a problem (e.g., obsolete answer and buggy code) in a SO answer or ask for more details about a proposed answer. We refer to this type of comment as update request comments (URCs), which may trigger an update to the answer post and thus improve its quality. We manually analyzed a set of 384 sampled SO answer posts and their associated 1,221 comments to investigate the prevalence of URCs and how URCs are addressed. We have provided three level of annotation: 1- If it is a URC, 2- For URCs, where is it addressed, i.e., in the next comments, in the post body, or both. 3- For URCs that are addressed by the following comments, which comment addresses it.
DOI: 10.22002/d1.20231
title: Dataset: Exact breakpoints of the In(1)wm4 rearrangement

description: The sequence of the In(1)wm4 heterochromatin breakpoint region. Breakpoint position is 19978.
description: Related Publication:
DOI: 10.22002/d1.2022
title: Pasadena Traffic data as monitored by Distributed Acoustic Sensing

description: Traffic data in Pasadena as monitored by the Pasadena Distributed Acoustic Sensing array. A MATLAB script is provided to read the data.
description: Related Publication:
Ground vibrations recorded by fiber-optic cables reveal traffic response to COVID-19 lockdown measures in Pasadena, California

Xin Wang, Zhongwen Zhan, Ethan Williams, Miguel Gonzalez Herraez, Hugo Fidalgo Martins, and Martin Karrenbach

2021-08-11

https://doi.org/10.1038/s43247-021-00234-3
eng
DOI: 10.22002/d1.20210
title: Dataset: Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult flies

description: Pb Extended Data
description: Related Publication:
DOI: 10.22002/d1.20192
title: Dataset: Live imaging and quantification of circulating potentially metastatic tumor cells in early pupal stage of Drosophila melanogaster.

description: Movie 3. 2-Dimensional confocal projections showing circulatory tumors cells (CTCs) during early Drosophila pupal leg and wing development. 2D projections (A-B) showing the movement of CTCs during morphogenesis. Panel A shows only the green channel, where invasive tumor cells (RasV12; scrib1) are marked with GFP. Panel C shows a composite of the green and DIC channel. CTCs are labelled within circles of various colors. Arrows indicate the direction of CTC movement.
description: Related Publication:
DOI: 10.22002/d1.20209
title: Dataset: Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult flies

description: Cu Extended Data
description: Related Publication:
DOI: 10.22002/d1.20191
title: Dataset: Live imaging and quantification of circulating potentially metastatic tumor cells in early pupal stage of Drosophila melanogaster.

description: Movie 2. 2-Dimensional confocal projections showing circulatory tumors cells (CTCs) during early Drosophila pupal leg and wing development. 2D projections (A-B) showing the movement of CTCs during morphogenesis. Panel A shows only the green channel, where invasive tumor cells (RasV12; scrib1) are marked with GFP. Panel C shows a composite of the green and DIC channel. CTCs are labelled within circles of various colors. Arrows indicate the direction of CTC movement.
description: Related Publication:
DOI: 10.22002/d1.20208
title: Dataset: Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult flies

description: Cd Extended Data
description: Related Publication:
DOI: 10.22002/d1.20190
title: Dataset: Live imaging and quantification of circulating potentially metastatic tumor cells in early pupal stage of Drosophila melanogaster.

description: Movie 1. 2-Dimensional confocal projections showing circulatory tumors cells (CTCs) during early Drosophila pupal leg and wing development. Schematic (A) and 2D projections (B-D) show the movement of CTCs during morphogenesis. Panel A shows schematically the region imaged (dotted line). Panel B shows only the green channel, where invasive tumor cells (RasV12; scrib1) are marked with GFP. Panel C shows a composite of the green and DIC channels. This panel, in addition to showing tumor cells, also allows for observing the developing legs and wings. Panel D shows the composite of the green and DIC as well as various labels that allow for the direction of CTCs to be observed. CTCs are labelled within circles of various colors. Arrows indicate the direction of CTC movement. Sections of developing leg are labelled with blue lines. The distal boundaries of leg and wing imaginal discs are labelled with yellow lines.
description: Related Publication:
DOI: 10.22002/d1.20174
title: Caltech Football Numbers (CaltechFN)

description: Digit datasets are widely used as compact, generalizable benchmarks for novel computer vision models. However, modern deep learning architectures have surpassed the human performance benchmark on the current state-of-the-art digit datasets. These datasets largely contain images of digits that are smooth and fully visible, which limits the variability between the digits. On the other hand, the digits on American football jerseys are highly variable due to the propensity of jerseys to be wrinkled, stretched, twisted, and otherwise distorted in live action. Given that American football is a fast-paced sport, the digits on a jersey will likely be distorted in a different way from moment to moment, making it harder for artificial vision systems to differentiate between distinct digits. Furthermore, the digits on American football jerseys will often be partially occluded in a live-action capture due to the presence of other players and props. While the human brain is able to infer the identity of partially occluded digits by "filling in" visual gaps, artificial vision systems struggle to do this. To catalyze the improvement of computer vision models in these areas, we introduce CaltechFN, an image dataset of American football numbers that will serve as a new state-of-the-art benchmark for classification, detection, and localization tasks.
description: The dataset is presented through four tar.gz files. We describe each: 

train.tar.gz:
This file contains a folder, 'images', and a .json file, 'train.json'. 'images' contains 49,383 full-sized images of various dimensions. 'train.json' contains their bounding box digit annotations in COCO format.
 
test.tar.gz:
This file also contains a folder, 'images', and a .json file, 'test.json'. 'images' contains 12,345 full-sized images of various dimensions. 'test.json' contains their bounding box digit annotations in COCO format.

train_cropped.tar.gz:
This file contains a folder, 'images', and a .mat file, 'train.mat'. 'images' contains 211,661 images of various dimensions, but much smaller than the images in the previous two formats. 'train.mat' contains two arrays: 'names', which is a list of the image names, and 'y', which contains the ground-truth labels of the images, matching 'names'.

test_cropped.tar.gz:
This file contains a folder, 'images', and a .mat file, 'test.mat'. 'images' contains 52,911 images of various dimensions, but much smaller than the images in the previous two formats. 'test.mat' contains two arrays: 'names', which is a list of the image names, and 'y', which contains the ground-truth labels of the images, matching 'names'.
description: We have benchmarked our dataset with the methods provided in this repository: https://github.com/snigdhasaha7/caltechfn_eval
DOI: 10.22002/d1.20176
title: Paleogeographic evolution of an ocean margin on Mars - data

description: Shapefiles, code, and spreadsheets used in the associated publication.
DOI: 10.22002/d1.20161
title: Dataset: Systematic identification of tRNA genes in Drosophila melanogaster

description: Cytosolic tRNA genes
description: Related Publication:
DOI: 10.22002/d1.20175
title: Dataset: Gene conversion restores selfing in experimentally evolving C. elegans populations with fog-2 loss-of-function mutation

description: This is a fasta file including the sequences presented in Figure 1 B:  newly obtained sequence of fog-2 fragment converted with ftr-1. The sequence is in the file aligned to fog-2(wt), fog-2(q71) and ftr-1 for reference.
description: Related Publication:
DOI: 10.22002/d1.20158
title: Dataset: Long-read sequencing infers a mechanism for copy number variation of template for alternative lengthening of telomeres in a wild C. elegans strain

description: Extended data 2: Six raw reads covering the 6-copy TALT array of DL226
description: Related Publication:
DOI: 10.22002/d1.20162
title: Dataset: Systematic identification of tRNA genes in Drosophila melanogaster

description: Mitochondrial tRNA genes
description: Related Publication:
DOI: 10.22002/d1.20101
title: Murray-Stimson Contact

description: Shapefile containing a trace of the Murray-Stimson contact in Gale crater, Mars based on images from the Mars Science Laboratory (MSL) rover and HiRISE.
description: Related Publication:
Burial and exhumation of sedimentary rocks revealed by the base Stimson erosional unconformity, Gale crater, Mars

Jessica Watkins California Institute of Technology

JGR-Planets
eng
description: Contact person: Nathaniel Stein nstein@caltech.edu
DOI: 10.22002/d1.20053
title: Clytia Medusa TRINITY Transcriptome GTF Converted

description: GTF version of the Clytia TRINITY assembled transcriptome (converted from the gff3 file)
DOI: 10.22002/d1.20080
title: Dataset: Estimation of C. elegans cell- and tissue volumes

description: Updated File: 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:
DOI: 10.22002/d1.20050
title: Idealized simulations of Earth-like planets

description: Aquaplanet simulations for Lobo and Bordoni (2022). For simulation details, also see methods section in Lobo and Bordoni (2020) at https://doi.org/10.1016/j.icarus.2019.113592
DOI: 10.22002/d1.1997
title: Gehring et al 2019 Multiplexed Data h5ad

description: h5ad file containing labeled cells from Gehring et al 2019 multiplexed dataset. Used for validation l1 metric analysis in Clytia single-cell experimentation