cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7241180
title: Spectrums Data

description: Spectrums data contained intensity at specific mass-to-charge value in spectrums were packaged. A "Master Mass List" file was also provided as an accompaniment for tsv files of Spectrums Data.
DOI: 10.6084/m9.figshare.7241180.v1
title: Spectrums Data

description: Spectrums data contained intensity at specific mass-to-charge value in spectrums were packaged. A "Master Mass List" file was also provided as an accompaniment for tsv files of Spectrums Data.
DOI: 10.6084/m9.figshare.13532699
title: Additional file 1 of Micro-costing in health and medicine: a critical appraisal

description: Additional file 1.
DOI: 10.6084/m9.figshare.13532699.v1
title: Additional file 1 of Micro-costing in health and medicine: a critical appraisal

description: Additional file 1.
DOI: 10.6084/m9.figshare.13532701
title: Additional file 2 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 2: Table S2. Overlapping genes inTCGA and METABRIC.
DOI: 10.6084/m9.figshare.13532698
title: Additional file 1 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 1: Table S1. The inclusion patient ids.
DOI: 10.6084/m9.figshare.13532701.v1
title: Additional file 2 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 2: Table S2. Overlapping genes inTCGA and METABRIC.
DOI: 10.6084/m9.figshare.13532698.v1
title: Additional file 1 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 1: Table S1. The inclusion patient ids.
DOI: 10.6084/m9.figshare.13532704
title: Additional file 3 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 3: TableS3. Primary filter via univariate Cox regression analysis based on TCGA dataset.
DOI: 10.6084/m9.figshare.13532704.v1
title: Additional file 3 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 3: TableS3. Primary filter via univariate Cox regression analysis based on TCGA dataset.
DOI: 10.6084/m9.figshare.13532716
title: Additional file 7 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 7: TableS5. Spearman correlation in TCGA and METABRIC (R&gt;0.3).
DOI: 10.6084/m9.figshare.13532716.v1
title: Additional file 7 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 7: TableS5. Spearman correlation in TCGA and METABRIC (R&gt;0.3).
DOI: 10.6084/m9.figshare.13532722
title: Additional file 9 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 9: Table S6. The alteration peaks of CNAs in breast cancer with different PPP2R2B expression.
DOI: 10.6084/m9.figshare.13532722.v1
title: Additional file 9 of PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer

description: Additional file 9: Table S6. The alteration peaks of CNAs in breast cancer with different PPP2R2B expression.
DOI: 10.6084/m9.figshare.11959881
title: Additional file 10 of Trend analysis of the role of circular RNA in goat skeletal muscle development

description: Additional file 10: Table S8. Functional analysis of cluster 18.
DOI: 10.6084/m9.figshare.11959881.v1
title: Additional file 10 of Trend analysis of the role of circular RNA in goat skeletal muscle development

description: Additional file 10: Table S8. Functional analysis of cluster 18.
DOI: 10.6084/m9.figshare.13532728.v1
title: Additional file 2 of Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

description: Additional file 2: Supplementary Table 2. The permutation tests of the mean distance matrix (β-diversity).
DOI: 10.6084/m9.figshare.13532734.v1
title: Additional file 4 of Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

description: Additional file 4: Supplementary Table 5. Full bacteria name listed in Fig. 4a in male rats. Supplementary Table 6. Full bacteria name listed in Fig. 4b in female rats.
DOI: 10.6084/m9.figshare.13532743
title: Additional file 7 of Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

description: Additional file 7: Supplementary Figure 1. Schematic diagram of QIIME 2 workflow. Supplementary Figure 2. Correlation of liver triglyceride with signature gut bacteria in CuAF rats. Correlation of liver triglyceride with signature gut bacteria in CuAF rats. Data represent means ± SD (n = 7). Statistical significance was set at p ≤ 0.05. P values displayed are for Spearman correlation test.
DOI: 10.6084/m9.figshare.13532734
title: Additional file 4 of Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

description: Additional file 4: Supplementary Table 5. Full bacteria name listed in Fig. 4a in male rats. Supplementary Table 6. Full bacteria name listed in Fig. 4b in female rats.
DOI: 10.6084/m9.figshare.13532731
title: Additional file 3 of Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

description: Additional file 3: Supplementary Table 3. Mean abundance of gut microbiome taxa in male rats. Supplementary Table 4. Mean abundance of gut microbiome taxa in female rats. Numbers listed under study groups are percentages. Data are expressed as means ± SD (n = 7–8) and analyzed by two-way ANOVA testing factors of copper (Cu), fructose (F), and interactions (Cu × F), followed by Tukey’s multiple comparison test. Statistical significance was set to p ≤ 0.05. P values are displayed for the factors Cu, F, and Cu × F. NS, p &gt; 0.05. CuA, adequate copper diet; CuM, marginal copper diet; CuAF, adequate copper diet +10% fructose drinking; CuMF, marginal copper deficient diet + 10% fructose drinking. * versus CuA; # versus CuAF; $ versus CuM. p_Phyla, f_Families, and s_species with average abundance greater than 1% in any of the groups are listed. Unknown, 16S rRNA sequence distinct from any known genera in this family/species.
DOI: 10.15468/dl.7y2zbm
title: Occurrence Download

description: A dataset containing 2334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Triuridaceae"
 ]
}

 The dataset includes 2334 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047554-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0ahy5u
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Strix dakota Miller, 1944"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023354-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wpjyq9
title: Occurrence Download

description: A dataset containing 428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micrathene whitneyi (J.G.Cooper, 1861)",
 "Country is Mexico"
 ]
}

 The dataset includes 428 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004521-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.plw1sv
title: Occurrence Download

description: A dataset containing 5076 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sakesphorus canadensis (Linnaeus, 1766)"
 ]
}

 The dataset includes 5076 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004521-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s4qmax
title: Occurrence Download

description: A dataset containing 283489 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Bombus Latreille, 1802",
 "Year 1000-2022"
 ]
}

 The dataset includes 283489 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055477-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5ixex
title: Occurrence Download

description: A dataset containing 4026006 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anura"
 ]
}

 The dataset includes 4026006 records from 1646 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014932-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2g8aj9
title: Occurrence Download

description: A dataset containing 4968 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Amaranthus dubius Mart.",
 "TaxonKey is Urena lobata L.",
 "TaxonKey is Musa acuminata Colla",
 "TaxonKey is Hibiscus cannabinus L.",
 "TaxonKey is Boesenbergia rotunda (L.) Mansf.",
 "TaxonKey is Hodgsonia heteroclita (Roxb.) Hook.fil. & Thomson",
 "TaxonKey is Triticum urartu Thumanjan ex Gandilyan",
 "TaxonKey is Aegilops tauschii Coss.",
 "TaxonKey is Triticum boeoticum Boiss.",
 "TaxonKey is Triticum dicoccoides (Körnicke) G.Schweinfurth",
 "TaxonKey is Eleusine africana Kenn.-O'Byrne"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4968 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013464-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnw3sc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crocidura eisentrauti Heim de Balsac, 1957"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001921-171020152545675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lrl0wr
title: Occurrence Download

description: A dataset containing 126031 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mosquito Occurrence Dataset"
 ]
}

 The dataset includes 126031 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006969-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3c6w34
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Diclidurus scutatus Peters, 1869"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0272795-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4buzr
title: Occurrence Download

description: A dataset containing 826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alopecurus aequalis Sobol.",
 "MediaType is Image",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 826 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000490-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mztzgj
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nereis callaona Grube, 1857"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001922-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8xdk9j
title: Occurrence Download

description: A dataset containing 1145 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhinella icterica (Spix, 1824)"
 ]
}

 The dataset includes 1145 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065343-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wz8v3f
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "DatasetKey is FloraCAT: Banco de datos de los cormófitos de Cataluña",
 "DatasetKey is CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España",
 "DatasetKey is Institut Botanic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), BC-Plantae"
 ]
 },
 "TaxonKey is Armeria muelleri A.Huet"
 ]
}

 The dataset includes 63 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013466-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6pja47
title: Occurrence Download

description: A dataset listing the 38 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lopadostomataceae"
 ]
}

 The dataset's 38 records were derived from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278072-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m3tz8t
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2024",
 "Geometry POLYGON ((-130.7383528944533 -59.46314024951374, -130.7383528944533 32.71876227804215, -26.26729810228821 32.71876227804215, -26.26729810228821 -59.46314024951374, -130.7383528944533 -59.46314024951374))",
 "OccurrenceStatus is Present",
 "TaxonKey is Pithys castaneus Berlioz, 1938"
 ]
}

 The dataset includes 130 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052614-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aikwkd
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Valeriana johannae Weberling"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013472-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n8ae2m
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.8201 16.94229,-89.897 16.87637,-89.85855 16.74454,-89.32022 16.7775,-89.16367 16.84341,-89.13895 17.04666,-89.20761 17.04391,-89.54819 17.01096,-89.8201 16.94229))",
 "TaxonKey is Reptilia",
 "Year 2000-2020"
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049601-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4drz8
title: Occurrence Download

description: A dataset containing 587 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Siluriformes",
 "Geometry POLYGON((-48.603515 -0.395504,-48.603515 -10.271681,-41.660156 -10.271681,-41.660156 -0.395504,-48.603515 -0.395504))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 587 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001922-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11355186
title: Tonsil Atlas: CellRanger outputs

description: This repository contains all the expression and accessibility matrices for each of the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) associated with the article "An Atlas of Cells in The Human Tonsil," published in Immunity in 2024. In particular, each modality was produced with different platforms from 10X Genomics and processed with different versions of CellRanger. This repository contains the most important outputs from each CellRanger run of each library. In addition, it also includes de expression and accessiblity matrices for the two mantle cell lymphoma (MCL) patients analyzed in the paper.

Version 3.0 of this repository corrects the error with the scATAC-seq.zip folder as reported in an issue in the TonsilAtlas GitHub repo.
description: Structure

For each modality, the first folders represent a "subproject", which you can view as one run of the 10X Chromium. Inside it, you will find all the gel-bead-in-emulsion ids (GEM ids), which correspond to the output from a single 10X Chip Channel (see Cellranger glossary for more information). Inside each GEM-specific folder, you can find the most relevant files from the "outs" folder produced by CR. This include the expression/accessibility matrices, fragment files, web summaries (html with QC reports), and more. Here you can find a more detailed explanation of every output.To access processed data in the form of Seurat objects please check this other Zenodo repository. To access the data, documentation and reasoning behind each annotation in the tonsil atlas, please check the HCATonsilData package. Finally, to annotate cells from secondary lymphoid organs using the tonsil atlas as reference, check the Azimuth reference.

Metadata

We provide two levels of metadata:- Donor-level metadata: file "tonsil_atlas_donor_metadata.csv". For each of the 17 donors, this file specifies the hospital in which the tonsil was sampled (Clinic, CIMA or Newcastle), the sex, age, age group (child, young adult or old adult), the reason for tonsillectomy (tonsillitis, sleep apnea, or surgery for another condition), and the cohort type (discovery or validation). Note that for the four tonsils sampled in Newcastle we include the link between the original ids and the ones specific for this article (e.g. BCLL-20-T / TIP01)- Library-specific metadata: for each sequencing library, this metadata documents the subproject, GEM well (10X Chip Channel, see above), library name, library id, library type, and donor id. The donor_id column allows to link this table with the previous one (donor-level), and the gem_id column is important to understand which libraries were derived from the same GEM well. For instance, multiome GEM wells contain two library_ids per GEM well (RNA+ATAC).
DOI: 10.15468/dl.jdk5g9
title: Occurrence Download

description: A dataset containing 3819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena lapponica Zetterstedt, 1838)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 3819 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278050-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gvfwfk
title: Occurrence Download

description: A dataset containing 13105 species occurrences available in GBIF matching the query:
{
 "PublishingOrg" : [
 "is 8feb568b-f026-4d58-93b7-a2b56dc946f8"
 ]
}

 The dataset includes 13105 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013472-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57rafx
title: Occurrence Download

description: A dataset containing 508 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Telmatobius culeus (Garman, 1876)"
 ]
}

 The dataset includes 508 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0397358-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ceoqan
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus ciliaris L.",
 "Country is Colombia"
 ]
}

 The dataset includes 44 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001922-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3ahaj
title: Occurrence Download

description: A dataset containing 420 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anthophora villosula Smith, 1854)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 420 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278140-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0pqkar
title: Occurrence Download

description: A dataset containing 510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carpinus caroliniana Walter",
 "Country is Mexico"
 ]
}

 The dataset includes 510 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013474-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.