cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18686750
title: Datasets from Multi-omic characterization of the ILC Cell Line Encyclopedia (ICLE)

description: This repository contains the processed multi-omic datasets and supplementary material for the ILC Cell Line Encyclopedia (ICLE).

Dataset Overview The ICLE provides a comprehensive molecular characterization of Invasive Lobular Carcinoma (ILC) and ILC-like breast cancer cell lines. This deposition includes processed data files supporting the manuscript: "Multi-omic characterization of the ILC cell line encyclopedia (ICLE) defines new models for biomarkers discovery and therapeutic exploration."

1. ICLE Datasets (Internal) This section contains processed data generated specifically for this study, organized by platform:





Optical Genome Mapping (Bionano): Contains structural variation (SV) calls, gene fusion candidates, and ShatterSeek output for chromothripsis analysis.




SNP Arrays (CytoSNP): Includes raw IDAT files, processed genotyping data, and copy number segmentation files. Analyses include GISTIC2.0 output, chromosomal instability (CIN) metrics, and CNTools logRR matrices.




DNA Methylation (DNAm): Processed beta-value matrices derived from Illumina arrays (processed via SeSAMe), including differential methylation results (Limma) comparing ILC vs. NST subtypes.




Transcriptomics (RNA-seq): Gene expression data including raw counts, normalized log2CPM values, and PAM50 molecular subtyping scores. Differential expression analysis results (DESeq2) comparing ILC vs. NST subtypes.




Proteomics (RPPA): Normalized protein expression matrices from Reverse Phase Protein Arrays (RPPA), including batch-corrected data (COMBAT) and antibody mapping files.




Whole Exome Sequencing (WES): Variant calling files (VCF), filtered Mutation Annotation Files (MAF), Tumor Mutational Burden (TMB) calculations, and specific read pileups of CDH1 exons to identify exonic deletions.




Note: Raw RNAseq and WES sequencing files are available at BioProject PRJNA1406296.



2. External Datasets (Benchmarking & Integration) We integrated and analyzed public datasets from the following sources:





BRCA Cell Lines Cohorts: CCLE, Sanger, and Marcotte et al. datasets.




BRCA Patient Cohorts: TCGA, MSK-IMPACT, and FMI (Foundation Medicine) datasets.



Analysis Code: All scripts for figure generation and processing are available on GitHub. To reproduce the study analyses, clone GitHub repository and download the ICLE and external datasets from Zenodo. Extract the contents of these .tar.gz files directly into the repository's 1-Dataset folder.

cBioPortal Instance: cBioPortal instances were setup for ICLE and Integrated BRCA cell line datasets for visualization and analysis.

Authors Osama Shiraz Shah, Fangyuan Chen, Abdalla Wedn, Anokhi Kashiparekh, Beth A. Knapick, Jian Chen, Laura Savariau, Ben Clifford, Matthias Christgen, Ethan Sokol, Jagmohan Hooda, Jennifer M. Atkinson, Steffi Oesterreich*, Adrian V. Lee* *Equal contribution, corresponding authors
DOI: 10.5281/zenodo.18686819
title: Linked collectors and determiners for: FBIP:IZIKO-UCT:Historical Survey (1930-1980).

description: Natural history specimen data linked to collectors and determiners held within, "FBIP:IZIKO-UCT:Historical Survey (1930-1980)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2429f28c-dc43-40e7-92f6-49206e0729fb using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2429f28c-dc43-40e7-92f6-49206e0729fb. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583352
title: Linked collectors and determiners for: FBIP:IZIKO-UCT:Historical Survey (1930-1980).

description: Natural history specimen data linked to collectors and determiners held within, "FBIP:IZIKO-UCT:Historical Survey (1930-1980)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2429f28c-dc43-40e7-92f6-49206e0729fb using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2429f28c-dc43-40e7-92f6-49206e0729fb. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686820
title: Linked collectors and determiners for: Some Plant Specimens from KUN, IBSC, NAS  Herbarium in China from 1900 to 1950.

description: Natural history specimen data linked to collectors and determiners held within, "Some Plant Specimens from KUN, IBSC, NAS  Herbarium in China from 1900 to 1950". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/246ad1f8-e75c-419d-b97e-16dde697ae30 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/246ad1f8-e75c-419d-b97e-16dde697ae30. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583358
title: Linked collectors and determiners for: Some Plant Specimens from KUN, IBSC, NAS  Herbarium in China from 1900 to 1950.

description: Natural history specimen data linked to collectors and determiners held within, "Some Plant Specimens from KUN, IBSC, NAS  Herbarium in China from 1900 to 1950". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/246ad1f8-e75c-419d-b97e-16dde697ae30 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/246ad1f8-e75c-419d-b97e-16dde697ae30. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686821
title: Linked collectors and determiners for: Taxonomic revision of the Afrotropical species of Pachyanthidium Friese (Hymenoptera: Megachilidae: Anthidiini).

description: Natural history specimen data linked to collectors and determiners held within, "Taxonomic revision of the Afrotropical species of Pachyanthidium Friese (Hymenoptera: Megachilidae: Anthidiini)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/247eb149-de99-4046-ae9e-b44b817fe8b9 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/247eb149-de99-4046-ae9e-b44b817fe8b9. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583360
title: Linked collectors and determiners for: Taxonomic revision of the Afrotropical species of Pachyanthidium Friese (Hymenoptera: Megachilidae: Anthidiini).

description: Natural history specimen data linked to collectors and determiners held within, "Taxonomic revision of the Afrotropical species of Pachyanthidium Friese (Hymenoptera: Megachilidae: Anthidiini)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/247eb149-de99-4046-ae9e-b44b817fe8b9 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/247eb149-de99-4046-ae9e-b44b817fe8b9. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686824
title: Linked collectors and determiners for: Plant Specimen from Herbarium (CDBI) in China, Chengdu Institute of Botany, Chinese Academy of Sciences.

description: Natural history specimen data linked to collectors and determiners held within, "Plant Specimen from Herbarium (CDBI) in China, Chengdu Institute of Botany, Chinese Academy of Sciences". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/249ec6d9-ce13-4096-baf5-42130fc3d0b1 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/249ec6d9-ce13-4096-baf5-42130fc3d0b1. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583366
title: Linked collectors and determiners for: Plant Specimen from Herbarium (CDBI) in China, Chengdu Institute of Botany, Chinese Academy of Sciences.

description: Natural history specimen data linked to collectors and determiners held within, "Plant Specimen from Herbarium (CDBI) in China, Chengdu Institute of Botany, Chinese Academy of Sciences". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/249ec6d9-ce13-4096-baf5-42130fc3d0b1 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/249ec6d9-ce13-4096-baf5-42130fc3d0b1. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583368
title: Linked collectors and determiners for: A revision of the Neotropical ant-like genus Cardiacephala Macquart, including Plocoscelus Enderlein syn. nov. (Diptera: Micropezidae, Taeniapterinae).

description: Natural history specimen data linked to collectors and determiners held within, "A revision of the Neotropical ant-like genus Cardiacephala Macquart, including Plocoscelus Enderlein syn. nov. (Diptera: Micropezidae, Taeniapterinae)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/249faa66-1f6a-44a0-b7f2-f12acaf62e5b using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/249faa66-1f6a-44a0-b7f2-f12acaf62e5b. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686827
title: Linked collectors and determiners for: A revision of the Neotropical ant-like genus Cardiacephala Macquart, including Plocoscelus Enderlein syn. nov. (Diptera: Micropezidae, Taeniapterinae).

description: Natural history specimen data linked to collectors and determiners held within, "A revision of the Neotropical ant-like genus Cardiacephala Macquart, including Plocoscelus Enderlein syn. nov. (Diptera: Micropezidae, Taeniapterinae)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/249faa66-1f6a-44a0-b7f2-f12acaf62e5b using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/249faa66-1f6a-44a0-b7f2-f12acaf62e5b. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686830
title: Linked collectors and determiners for: UWIZM Mammals.

description: Natural history specimen data linked to collectors and determiners held within, "UWIZM Mammals". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/24a25949-4531-428d-885d-ae402177440c using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/24a25949-4531-428d-885d-ae402177440c. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583371
title: Linked collectors and determiners for: UWIZM Mammals.

description: Natural history specimen data linked to collectors and determiners held within, "UWIZM Mammals". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/24a25949-4531-428d-885d-ae402177440c using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/24a25949-4531-428d-885d-ae402177440c. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686831
title: Linked collectors and determiners for: Caenotropus schizodon, a new chilodontid fish from the Rio Tapajos drainage, Brazil (Ostariophysi: Characiformes: Chilodontidae)..

description: Natural history specimen data linked to collectors and determiners held within, "Caenotropus schizodon, a new chilodontid fish from the Rio Tapajos drainage, Brazil (Ostariophysi: Characiformes: Chilodontidae).". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/24b74b65-a402-4387-b73b-bb4664bb0fa6 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/24b74b65-a402-4387-b73b-bb4664bb0fa6. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583385
title: Linked collectors and determiners for: Solanum_baretiae.

description: Natural history specimen data linked to collectors and determiners held within, "Solanum_baretiae". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2528643b-e86e-49c2-b1e0-f56c7c986818 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2528643b-e86e-49c2-b1e0-f56c7c986818. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583373
title: Linked collectors and determiners for: Caenotropus schizodon, a new chilodontid fish from the Rio Tapajos drainage, Brazil (Ostariophysi: Characiformes: Chilodontidae)..

description: Natural history specimen data linked to collectors and determiners held within, "Caenotropus schizodon, a new chilodontid fish from the Rio Tapajos drainage, Brazil (Ostariophysi: Characiformes: Chilodontidae).". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/24b74b65-a402-4387-b73b-bb4664bb0fa6 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/24b74b65-a402-4387-b73b-bb4664bb0fa6. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686832
title: Linked collectors and determiners for: Solanum_baretiae.

description: Natural history specimen data linked to collectors and determiners held within, "Solanum_baretiae". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2528643b-e86e-49c2-b1e0-f56c7c986818 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2528643b-e86e-49c2-b1e0-f56c7c986818. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583391
title: Linked collectors and determiners for: COA Mammal Collection (Arctos).

description: Natural history specimen data linked to collectors and determiners held within, "COA Mammal Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25685aee-445d-4e82-94c8-815ee2169644 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25685aee-445d-4e82-94c8-815ee2169644. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686835
title: Linked collectors and determiners for: COA Mammal Collection (Arctos).

description: Natural history specimen data linked to collectors and determiners held within, "COA Mammal Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25685aee-445d-4e82-94c8-815ee2169644 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25685aee-445d-4e82-94c8-815ee2169644. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686834
title: Linked collectors and determiners for: Revision of Australian species of the dung beetle genus Lepanus (Coleoptera: Scarabaeidae: Scarabaeinae): description of 10 new species from the L. australis, L. monteithi, and L. villosus species groups.

description: Natural history specimen data linked to collectors and determiners held within, "Revision of Australian species of the dung beetle genus Lepanus (Coleoptera: Scarabaeidae: Scarabaeinae): description of 10 new species from the L. australis, L. monteithi, and L. villosus species groups". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/256591b2-6d7b-465d-a818-9a158017ca09 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/256591b2-6d7b-465d-a818-9a158017ca09. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583389
title: Linked collectors and determiners for: Revision of Australian species of the dung beetle genus Lepanus (Coleoptera: Scarabaeidae: Scarabaeinae): description of 10 new species from the L. australis, L. monteithi, and L. villosus species groups.

description: Natural history specimen data linked to collectors and determiners held within, "Revision of Australian species of the dung beetle genus Lepanus (Coleoptera: Scarabaeidae: Scarabaeinae): description of 10 new species from the L. australis, L. monteithi, and L. villosus species groups". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/256591b2-6d7b-465d-a818-9a158017ca09 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/256591b2-6d7b-465d-a818-9a158017ca09. Formatted as a Frictionless Data package.
DOI: 10.26030/vf2f-v411
title: Impact of spaceflight and artificial gravity on sulfur metabolism in mouse liver: sulfur metabolomic and transcriptomic analysis

description: Spaceflight induces hepatic damage, partially owing to oxidative stress caused by the space environment such as microgravity and space radiation. We examined the roles of anti-oxidative sulfur-containing compounds on hepatic damage after spaceflight. We analyzed the livers of mice on board the International Space Station for 30 days. During spaceflight, half of the mice were exposed to artificial earth gravity (1 g) using centrifugation cages. Sulfur-metabolomics of the livers of mice after spaceflight revealed a decrease in sulfur antioxidants (ergothioneine, glutathione, cysteine, taurine, thiamine, etc.) and their intermediates (cysteine sulfonic acid, hercynine, N-acethylserine, serine, etc.) compared to the controls on the ground. Furthermore, RNA-sequencing showed upregulation of gene sets related to oxidative stress and sulfur metabolism, and downregulation of gene sets related to glutathione reducibility in the livers of mice after spaceflight, compared to controls on the ground. These changes were partially mitigated by exposure to 1 g centrifugation. For the first time, we observed a decrease in sulfur antioxidants based on a comprehensive analysis of the livers of mice after spaceflight. Our data suggest that a decrease in sulfur-containing compounds owing to both microgravity and other spaceflight environments (radiation and stressors) contributes to liver damage after spaceflight.
DOI: 10.5281/zenodo.10583397
title: Linked collectors and determiners for: Collection of myxomycetes of Young Naturalists Circle of Zoological Museum of Moscow State University.

description: Natural history specimen data linked to collectors and determiners held within, "Collection of myxomycetes of Young Naturalists Circle of Zoological Museum of Moscow State University". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25a7f866-6262-41f9-a5e5-c44829ea7c3e using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25a7f866-6262-41f9-a5e5-c44829ea7c3e. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686836
title: Linked collectors and determiners for: Collection of myxomycetes of Young Naturalists Circle of Zoological Museum of Moscow State University.

description: Natural history specimen data linked to collectors and determiners held within, "Collection of myxomycetes of Young Naturalists Circle of Zoological Museum of Moscow State University". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25a7f866-6262-41f9-a5e5-c44829ea7c3e using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25a7f866-6262-41f9-a5e5-c44829ea7c3e. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686837
title: Linked collectors and determiners for: Malawi-Histeridae-Biodiversity-Data.

description: Natural history specimen data linked to collectors and determiners held within, "Malawi-Histeridae-Biodiversity-Data". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25cf9b9b-4bf8-46c4-b85c-7a08933b1577 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25cf9b9b-4bf8-46c4-b85c-7a08933b1577. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583403
title: Linked collectors and determiners for: Malawi-Histeridae-Biodiversity-Data.

description: Natural history specimen data linked to collectors and determiners held within, "Malawi-Histeridae-Biodiversity-Data". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/25cf9b9b-4bf8-46c4-b85c-7a08933b1577 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/25cf9b9b-4bf8-46c4-b85c-7a08933b1577. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686839
title: Linked collectors and determiners for: Colección de Reptiles del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-R).

description: Natural history specimen data linked to collectors and determiners held within, "Colección de Reptiles del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-R)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2618e878-7e19-412d-99e3-f12a8aa23ebb using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2618e878-7e19-412d-99e3-f12a8aa23ebb. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583411
title: Linked collectors and determiners for: Colección de Reptiles del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-R).

description: Natural history specimen data linked to collectors and determiners held within, "Colección de Reptiles del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-R)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/2618e878-7e19-412d-99e3-f12a8aa23ebb using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/2618e878-7e19-412d-99e3-f12a8aa23ebb. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686840
title: Linked collectors and determiners for: Inventario de ofiuroideos del Pacífico mexicano.

description: Natural history specimen data linked to collectors and determiners held within, "Inventario de ofiuroideos del Pacífico mexicano". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/261f3489-e820-40d0-8245-094aede04672 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/261f3489-e820-40d0-8245-094aede04672. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583413
title: Linked collectors and determiners for: Inventario de ofiuroideos del Pacífico mexicano.

description: Natural history specimen data linked to collectors and determiners held within, "Inventario de ofiuroideos del Pacífico mexicano". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/261f3489-e820-40d0-8245-094aede04672 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/261f3489-e820-40d0-8245-094aede04672. Formatted as a Frictionless Data package.
DOI: 10.15468/dl.2atukk
title: Occurrence Download

description: A dataset containing 433060736 species occurrences available in GBIF matching the query:
{
 "and" : [
 "License is CC0 1.0",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 433060736 records from 34682 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028168-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.