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Supplementary Material: Decoding sequence determinants of gene expression in diverse cellular and disease states
<p>Supplementary material for the following publication:</p> <p><strong>Decoding sequence determinants of gene expression in diverse cellular and disease states</strong></p> <p>Avantika Lal*,1, Alexander Karollus*,1,2,3, Laura Gunsalus1, David Garfield4, Surag Nair1, Alex M Tseng1, M Grace Gordon5, John Blischak6, Bryce van de Geijn6, Tushar Bhangale6, Jenna L Collier1, Nathaniel Diamant1, Tommaso Biancalani1, Hector Corrada Bravo1, Gabriele Scalia1, Gokcen Eraslan1</p> <p>*Equal contributions</p> <p>1Biology Research | AI Development, gRED Computational Sciences, Genentech, South San Francisco, CA 94080, USA</p> <p>2School of Computation, Information and Technology, Technical University of Munich, Germany</p> <p>3Munich Center for Machine Learning </p> <p>4OMNI Bioinformatics and Department of Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA</p> <p>5 Department of Cellular and Tissue Genomics, Genentech Research and Early Development, Genentech, South San Francisco, CA 94080, USA</p> <p>6 Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA</p> <p><strong><br></strong>Correspondence: Avantika Lal (<a href="mailto:lal.avantika@gene.com">lal.avantika@gene.com</a>), Gokcen Eraslan (<a href="mailto:eraslan.gokcen@gene.com">eraslan.gokcen@gene.com</a>)</p>
Supplementary material 1 from: Foster R, Peeler E, Bojko J, Clark PF, Morritt D, Roy HE, Stebbing P, Tidbury HJ, Wood LE, Bass D (2021) Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation. NeoBiota 69: 79-102. https://doi.org/10.3897/neobiota.69.71358
Table S1
Supplementary material 2 from: Foster R, Peeler E, Bojko J, Clark PF, Morritt D, Roy HE, Stebbing P, Tidbury HJ, Wood LE, Bass D (2021) Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation. NeoBiota 69: 79-102. https://doi.org/10.3897/neobiota.69.71358
Table S2
Supplementary material 1 from: Armijos-Ojeda D, Székely D, Székely P, Cogălniceanu D, Cisneros-Heredia DF, Ordóñez-Delgado L, Escudero A, Espinosa CI (2021) Amphibians of the equatorial seasonally dry forests of Ecuador and Peru. ZooKeys 1063: 23-48. https://doi.org/10.3897/zookeys.1063.69580
Tables S1, S2
Supplementary material 3 from: Armijos-Ojeda D, Székely D, Székely P, Cogălniceanu D, Cisneros-Heredia DF, Ordóñez-Delgado L, Escudero A, Espinosa CI (2021) Amphibians of the equatorial seasonally dry forests of Ecuador and Peru. ZooKeys 1063: 23-48. https://doi.org/10.3897/zookeys.1063.69580
Dataset including amphibian species occurence information, museum specimen numbers, source of data
Supplementary material 3 from: Foster R, Peeler E, Bojko J, Clark PF, Morritt D, Roy HE, Stebbing P, Tidbury HJ, Wood LE, Bass D (2021) Pathogens co-transported with invasive non-native aquatic species: implications for risk analysis and legislation. NeoBiota 69: 79-102. https://doi.org/10.3897/neobiota.69.71358
Table S3
Supplementary material 1 from: Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
Table S1
Engineered Osteoclasts as Living Treatment Materials for Heterotopic Ossification Therapy
<p>All data generated in this study are provided in the Supplementary materials and raw data. The data that support the findings of this study are available from the corresponding authors in reasonable request.</p>
Supplementary material 1 from: Mühlenhaupt M, Baxter-Gilbert J, Makhubo BG, Riley JL, Measey J (2021) Growing up in a new world: trait divergence between rural, urban, and invasive populations of an amphibian urban invader. NeoBiota 69: 103-132. https://doi.org/10.3897/neobiota.69.67995
Supporting information
Supplementary material 1 from: Weber D, Brad T, Stoch F, Flot J-F (2021) Rediscovery and redescription of Niphargus enslini Karaman, 1932 (Amphipoda, Niphargidae) in southern Germany. Subterranean Biology 40: 65-89. https://doi.org/10.3897/subtbiol.40.73017
Tables S1–S4, Figure S1
Supplementary material 1 from: J. Hribar L (2021) Dataset for Mosquitoes (Diptera: Culicidae) from Cross Key, Monroe County, Florida, USA. Research Ideas and Outcomes 7: e73768. https://doi.org/10.3897/rio.7.e73768
Cross Key
Large-scale statistical learning for mass transport prediction in porous materials using 90,000 artificially generated microstructures
<p>Dataset and code used in B Prifling, et al, "Large-scale statistical learning for mass transport prediction in porous materials using 90,000 artificially generated microstructures", published in Frontiers in Materials. In this work, we investigate relationships between 3D microstructure and effective diffusivity and permeability, based on a dataset of 90,000 structures and using analytical formulas, artificial neural networks (ANNs), and convolutional neural networks (CNNs). Herein, the codes in Matlab and Python/Tensorflow necessary to investigate the prediction models and reproduce the results of the paper are supplied. Also, microstructures together with their computed geometrical descriptors and effective properties are included.</p>
Supplementary material 1 from: Heinrich S, Gomez L (2021) India's use of CITES Appendix III. Nature Conservation 44: 163-176. https://doi.org/10.3897/natureconservation.44.63688
Table S1
Supplementary material 1 from: Wu Y, Shi S, Zhang H, Chen W, Cai B, Hoang VC, Wu J, Wang B (2021) A new species of the genus Rana sensu lato Linnaeus, 1758 (Anura, Ranidae) from Wuyi Mountain, Fujian Province, China. ZooKeys 1065: 101-124. https://doi.org/10.3897/zookeys.1065.67005
Table S1
Supplementary material 2 from: Bălăcenoiu F, Japelj A, Bernardinelli I, Castagneyrol B, Csóka G, Glavendekić M, Hoch G, Hrašovec B, Krajter Ostoic S, Paulin M, Williams D, Witters J, de Groot M (2021) Corythucha arcuata (Say, 1832) (Hemiptera, Tingidae) in its invasive range in Europe: perception, knowledge and willingness to act in foresters and citizens. NeoBiota 69: 133-153. https://doi.org/10.3897/neobiota.69.71851
Appendix 2
Supplementary material 1 from: Bălăcenoiu F, Japelj A, Bernardinelli I, Castagneyrol B, Csóka G, Glavendekić M, Hoch G, Hrašovec B, Krajter Ostoic S, Paulin M, Williams D, Witters J, de Groot M (2021) Corythucha arcuata (Say, 1832) (Hemiptera, Tingidae) in its invasive range in Europe: perception, knowledge and willingness to act in foresters and citizens. NeoBiota 69: 133-153. https://doi.org/10.3897/neobiota.69.71851
Annex 1. The questionnaire
Supplementary material 1 from: Ahmed MZ, Moore MR, Rohrig EA, McKenzie CL, Liu D, Feng J, Normark BB, Miller DR (2021) Taxonomic and identification review of adventive Fiorinia Targioni Tozzetti (Hemiptera, Coccomorpha, Diaspididae) of the United States. ZooKeys 1065: 141-203. https://doi.org/10.3897/zookeys.1065.69171
Figures S1–S4
Supplementary material 3 from: Ahmed MZ, Moore MR, Rohrig EA, McKenzie CL, Liu D, Feng J, Normark BB, Miller DR (2021) Taxonomic and identification review of adventive Fiorinia Targioni Tozzetti (Hemiptera, Coccomorpha, Diaspididae) of the United States. ZooKeys 1065: 141-203. https://doi.org/10.3897/zookeys.1065.69171
Table S2. PCR primers and thermocycling conditions.
Supplementary material 2 from: Ahmed MZ, Moore MR, Rohrig EA, McKenzie CL, Liu D, Feng J, Normark BB, Miller DR (2021) Taxonomic and identification review of adventive Fiorinia Targioni Tozzetti (Hemiptera, Coccomorpha, Diaspididae) of the United States. ZooKeys 1065: 141-203. https://doi.org/10.3897/zookeys.1065.69171
Table S1
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.