cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10848847
title: Supporting data for SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale

description: Supplementary data supporting the SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale publication

 



To showcase the capabilities of SpatialOne, two human lung cancer formalin-fixed, paraffin-embedded (FFPE) samples are analyzed. These samples are prepared following the CG000495 protocol (Figure 1b), sequenced with the 10x Visium CytAssist, and processed using the 10x SpaceRanger version 2. We also present analysis of two adult mouse samples sequenced using 10x Visium samples (one fresh frozen brain tissue section processed using SpaceRanger v2 and one FFPE kidney sample processed using the SpaceRanger v1), and 75 internal samples. 

 For the human lung cancer samples, single-cell data from the the Lung Cancer Atlas (Salcher et al., 2022) is used as reference. This dataset is filtered to include only Chromium-generated data. For the mice samples, the GSE107585 single-cell dataset serves as reference. In the human lung cancer datasets, a pathologist annotated regions of interest corresponding to tumors, blood vessels, and alveolar regions.
DOI: 10.5281/zenodo.10837967
title: Supporting data for SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale

description: Supplementary data supporting the SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale publication

 



To showcase the capabilities of SpatialOne, two human lung cancer formalin-fixed, paraffin-embedded (FFPE) samples are analyzed. These samples are prepared following the CG000495 protocol (Figure 1b), sequenced with the 10x Visium CytAssist, and processed using the 10x SpaceRanger version 2. We also present analysis of two adult mouse samples sequenced using 10x Visium samples (one fresh frozen brain tissue section processed using SpaceRanger v2 and one FFPE kidney sample processed using the SpaceRanger v1), and 75 internal samples. 

 For the human lung cancer samples, single-cell data from the the Lung Cancer Atlas (Salcher et al., 2022) is used as reference. This dataset is filtered to include only Chromium-generated data. For the mice samples, the GSE107585 single-cell dataset serves as reference. In the human lung cancer datasets, a pathologist annotated regions of interest corresponding to tumors, blood vessels, and alveolar regions.


 

Changelog:



Added a README file describing the zip content.
DOI: 10.5281/zenodo.12605154
title: Supporting data for SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale

description: Supplementary data supporting the SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale publication

 



To showcase the capabilities of SpatialOne, two human lung cancer formalin-fixed, paraffin-embedded (FFPE) samples are analyzed. These samples are prepared following the CG000495 protocol (Figure 1b), sequenced with the 10x Visium CytAssist, and processed using the 10x SpaceRanger version 2. We also present analysis of two adult mouse samples sequenced using 10x Visium samples (one fresh frozen brain tissue section processed using SpaceRanger v2 and one FFPE kidney sample processed using the SpaceRanger v1), and 75 internal samples. 

 For the human lung cancer samples, single-cell data from the the Lung Cancer Atlas (Salcher et al., 2022) is used as reference. This dataset is filtered to include only Chromium-generated data. For the mice samples, the GSE107585 single-cell dataset serves as reference. In the human lung cancer datasets, a pathologist annotated regions of interest corresponding to tumors, blood vessels, and alveolar regions.


 

Changelog:



Added a README file describing the zip content.
DOI: 10.15468/dl.k3w388
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus guentheri (Murray, 1884)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006453-240626123714530/datasets/export for details.
DOI: 10.15468/dl.kbp5qt
title: Occurrence Download

description: A dataset containing 864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Elephas maximus maximus, Panthera pardus kotiya Deraniyagala, 1956)"
 ]
}

 The dataset includes 864 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006454-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r6xdh3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus mako Whitley, 1929",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006456-240626123714530/datasets/export for details.
DOI: 10.15468/dl.64dahc
title: Occurrence Download

description: A dataset containing 50211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Observation.org, Nature data from around the World",
 "Geometry POLYGON((77.22874 21.66139,106.30341 21.66139,106.30341 37.41087,77.22874 37.41087,77.22874 21.66139))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 50211 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006455-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zvpfn8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus oxyrhincus Rafinesque, 1810",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006457-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ybmgvu
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teixeirichthys jordani (Rutter, 1897)"
 ]
}

 The dataset includes 210 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006458-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ey2tze
title: Occurrence Download

description: A dataset containing 384507 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus halepensis Mill."
 ]
}

 The dataset includes 384507 records from 535 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006433-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m3rt7g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus spallanzani Rafinesque, 1810",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006459-240626123714530/datasets/export for details.
DOI: 10.15468/dl.wwqkqn
title: Occurrence Download

description: A dataset containing 285 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lethrinus haematopterus Temminck & Schlegel, 1844"
 ]
}

 The dataset includes 285 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006460-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12591092
title: NBSDC "Data Usage and Data Value Evaluation" Survey

description: This file is the questionnaire of "NBSDC 'Data Usage and Data Value Evaluation' Survey".
DOI: 10.5281/zenodo.12591091
title: NBSDC "Data Usage and Data Value Evaluation" Survey

description: This file is the questionnaire of "NBSDC 'Data Usage and Data Value Evaluation' Survey".
DOI: 10.5281/zenodo.12605200
title: NBSDC "Data Usage and Data Value Evaluation" Survey

description: This file is the questionnaire of "NBSDC 'Data Usage and Data Value Evaluation' Survey".
DOI: 10.15468/dl.eg6ay9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus tigris (Atwood, 1869)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006461-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26134870
title: Carbon flux

description: This is carbon flux data.
DOI: 10.5281/zenodo.12593832
title: Multiway Alignment of Twitter networks from 2019 and 2023 Finnish Parliamentary Elections

description: This dataset includes partition identifiers obtained from retweet networks collected before the 2019 Finnish Parliamentary Elections and before the 2023 Finnish Parliamentary Elections from conversation streams related to Finnish political parties (SDP, National Coalition, Finns Party, Green Party, Left Party, Center Party) and salient topics (economic policy, social security, immigration, climate, education).

The column headers in the two files are the same and indicate the topic of the retweet network. Each row in one file represents all the memberships of one particular Twitter account for the corresponding networks. Memberships are obtained by partitioning each retweet network with METIS algorithm into two similar-sized groups with minimal retweet activity between them. For each column, one partition includes all users marked with 0, whereas the other partition includes all users marked with 1. The order of the numbering is random. Missing values mean that the account was not found in the corresponding network.

The dataset does not contain any identifying information or original raw data from the Twitter platform. Anonymization was achieved by randomly shuffling the order of the users so that, within each file, a row index identifies a user. Importantly, there no correspondence can be implied between users in 2019 and users in 2023: in general, the user at row 1 in the 2019 dataset is not the same as the user at row 1 in the 2023 dataset.
DOI: 10.5281/zenodo.12593833
title: Multiway Alignment of Twitter networks from 2019 and 2023 Finnish Parliamentary Elections

description: This dataset includes partition identifiers obtained from retweet networks collected before the 2019 Finnish Parliamentary Elections and before the 2023 Finnish Parliamentary Elections from conversation streams related to Finnish political parties (SDP, National Coalition, Finns Party, Green Party, Left Party, Center Party) and salient topics (economic policy, social security, immigration, climate, education).

The column headers in the two files are the same and indicate the topic of the retweet network. Each row in one file represents all the memberships of one particular Twitter account for the corresponding networks. Memberships are obtained by partitioning each retweet network with METIS algorithm into two similar-sized groups with minimal retweet activity between them. For each column, one partition includes all users marked with 0, whereas the other partition includes all users marked with 1. The order of the numbering is random. Missing values mean that the account was not found in the corresponding network.

The dataset does not contain any identifying information or original raw data from the Twitter platform. Anonymization was achieved by randomly shuffling the order of the users so that, within each file, a row index identifies a user. Importantly, there no correspondence can be implied between users in 2019 and users in 2023: in general, the user at row 1 in the 2019 dataset is not the same as the user at row 1 in the 2023 dataset.
DOI: 10.15468/dl.cfx6xq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isurus tigris africanus Smith, 1957",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006462-240626123714530/datasets/export for details.
DOI: 10.15468/dl.hfxm6d
title: Occurrence Download

description: A dataset containing 14143 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Selaroides leptolepis (Cuvier, 1833)"
 ]
}

 The dataset includes 14143 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006463-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.olm1i6
title: Occurrence Download

description: A dataset containing 11013 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Micropterus dolomieu Lacepède, 1802"
 ]
}

 The dataset includes 11013 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029787-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmgm9t
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alocasia puteri A.Hay"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002270-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lexnuw
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus ayacahuite Ehrend."
 ]
}

 The dataset includes 80 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007121-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rax7gs
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leontodon laciniatus (Bertol.) Widder, 1967"
 ]
}

 The dataset includes 44 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029791-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.guqmc8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus turkmenensis Dural, Tugay & Ertugrul"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038384-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xvuecp
title: Occurrence Download

description: A dataset containing 10054 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma opacum (Gravenhorst, 1807)"
 ]
}

 The dataset includes 10054 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002191-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mu9iou
title: Occurrence Download

description: A dataset containing 379 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lotus collinus (Boiss.) Heldr."
 ]
}

 The dataset includes 379 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029793-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ngs67c
title: Occurrence Download

description: A dataset containing 134520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ailanthus altissima (Mill.) Swingle"
 ]
}

 The dataset includes 134520 records from 960 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020504-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tezksv
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Byasa impediens (Seitz, 1907)"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002192-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfajpu
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliconia gracilis G.S.Daniels & F.G.Stiles"
 ]
}

 The dataset includes 45 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053290-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yf9hax
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aulandra longifolia H.J.Lam"
 ]
}

 The dataset includes 39 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038393-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zexsml
title: Occurrence Download

description: A dataset containing 1720 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spartina alterniflora Loisel."
 ]
}

 The dataset includes 1720 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029814-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lelkh0
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fucus spiralis L.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "DatasetKey is Marine Records from Pembrokeshire Marine Species Atlas"
 ]
}

 The dataset includes 110 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002194-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.32zw2b
title: Occurrence Download

description: A dataset containing 366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Doricha eliza (R.Lesson & Delattre, 1839)"
 ]
}

 The dataset includes 366 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010503-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwtrqc
title: Occurrence Download

description: A dataset containing 1738 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myrtaceae",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 1738 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029795-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cnubqx
title: Occurrence Download

description: A dataset containing 1085 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ptychoramphus aleuticus (Pallas, 1811)",
 "Country is Mexico"
 ]
}

 The dataset includes 1085 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002194-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pacbsa
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alocasia robusta M.Hotta"
 ]
}

 The dataset includes 47 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002315-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cyk9j1
title: Occurrence Download

description: A dataset containing 1070 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crotalus atrox Baird & Girard, 1853",
 "Country is Mexico"
 ]
}

 The dataset includes 1070 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029796-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eejqb0
title: Occurrence Download

description: A dataset containing 2103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyroderus scutatus (Shaw, 1792)"
 ]
}

 The dataset includes 2103 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002194-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iqosv3
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliconia librata Griggs"
 ]
}

 The dataset includes 190 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053292-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.