cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16676233
title: Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss - All datasets

description: This repository contains supplementary data for the article: Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss.

Transcriptomic data were deposited in .csv files. For the App NL-F/NL-F mouse model, the 18-month data are in the norm_Quant_18_GeoMX.csv file and the 10-month data are in the norm_Quant_10_GeoMX.csv file. The quality control (QC) analysis for Next Generation Sequencing (NGS) and Biological Probe QC was conducted using the default GeoMX DSP parameters (GeoMX NGS Pipeline version 2.3.4). All subsequent analyses were performed in R [R Core Team, Vienna, Austria; https://www.R-project.org/]. Probes were excluded from the analysis if their counts were too low or if they failed the Grubbs outlier test according to NanoString guidelines. In the 10-month-old group, nine regions of interest (ROIs) were excluded due to ambiguous spot morphology, the presence of more than one plaque, or very low intensity in the MALDI results. Similarly, six ROIs from the 18-month-old group were excluded for the same reason. After filtering the data, the geometric mean was calculated for each target within the areas of interest (AOIs). The QC results were then compared with those obtained from the standard NanoString pipeline, revealing generally consistent outcomes in terms of outlier detection. Any minor discrepancies observed are likely attributable to slight differences in the test parameters used. Finally, quantile normalization was applied using the `normalize:quantiles` function provided by the `preprocessCore` R package.

The zip files titled spectra_10mo_csv.zip and spectra_18mo_csv.zip contain MALDI MSI data with a linear positive mode. Nitrogen index LP (linear positive mode): Extracts the target m/z region (e.g. amyloid Aβ₁₋₄₂), performs normalisation, smoothing, ALS baseline correction, FWHM peak analysis and exports annotated results. More details and code are available on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker. Under the ‘SPECTRA VIEWER’ tab, all MALDI spectra from 18-month and 10-month groups can be viewed and downloaded on https://maciejdulewiczgu.shinyapps.io/MALDI_GEOMX_VOLCANO/

The zip file titled RP_Mode_MALDI_MSI.zip contains the reflector mode data that was used to calculate the RP Nitrogen Index. More details and how to analyse the data can be found on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker.
DOI: 10.5281/zenodo.16676234
title: Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss - All datasets

description: This repository contains supplementary data for the article: Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss.

Transcriptomic data were deposited in .csv files. For the App NL-F/NL-F mouse model, the 18-month data are in the norm_Quant_18_GeoMX.csv file and the 10-month data are in the norm_Quant_10_GeoMX.csv file. The quality control (QC) analysis for Next Generation Sequencing (NGS) and Biological Probe QC was conducted using the default GeoMX DSP parameters (GeoMX NGS Pipeline version 2.3.4). All subsequent analyses were performed in R [R Core Team, Vienna, Austria; https://www.R-project.org/]. Probes were excluded from the analysis if their counts were too low or if they failed the Grubbs outlier test according to NanoString guidelines. In the 10-month-old group, nine regions of interest (ROIs) were excluded due to ambiguous spot morphology, the presence of more than one plaque, or very low intensity in the MALDI results. Similarly, six ROIs from the 18-month-old group were excluded for the same reason. After filtering the data, the geometric mean was calculated for each target within the areas of interest (AOIs). The QC results were then compared with those obtained from the standard NanoString pipeline, revealing generally consistent outcomes in terms of outlier detection. Any minor discrepancies observed are likely attributable to slight differences in the test parameters used. Finally, quantile normalization was applied using the `normalize:quantiles` function provided by the `preprocessCore` R package.

The zip files titled spectra_10mo_csv.zip and spectra_18mo_csv.zip contain MALDI MSI data with a linear positive mode. Nitrogen index LP (linear positive mode): Extracts the target m/z region (e.g. amyloid Aβ₁₋₄₂), performs normalisation, smoothing, ALS baseline correction, FWHM peak analysis and exports annotated results. More details and code are available on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker. Under the ‘SPECTRA VIEWER’ tab, all MALDI spectra from 18-month and 10-month groups can be viewed and downloaded on https://maciejdulewiczgu.shinyapps.io/MALDI_GEOMX_VOLCANO/

The zip file titled RP_Mode_MALDI_MSI.zip contains the reflector mode data that was used to calculate the RP Nitrogen Index. More details and how to analyse the data can be found on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker.
DOI: 10.15468/dl.x38gx8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orconectes limosus",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000224-250802193616735/datasets/export for details.
DOI: 10.15468/dl.v886qh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orconectes limosus",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000223-250802193616735/datasets/export for details.
DOI: 10.15468/dl.d7tkev
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Thryssa baelama)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 124 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000225-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j39hgy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micropterus salmoides",
 "Country is Slovenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000226-250802193616735/datasets/export for details.
DOI: 10.15468/dl.d6mjbu
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Persicaria capitata",
 "Country is Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000228-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zzf59
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micropterus salmoides",
 "Country is Viet Nam",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000227-250802193616735/datasets/export for details.
DOI: 10.15468/dl.5pzbxk
title: Occurrence Download

description: A dataset containing 457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Persicaria capitata",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 457 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000229-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mey8ky
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Persicaria capitata",
 "Country is Malaysia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 63 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000230-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfq7ba
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acanthochaenus luetkenii"
 ]
}

 The dataset includes 73 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000232-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r6xptu
title: Occurrence Download

description: A dataset containing 363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eriocnemis nigrivestis)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 363 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000231-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8u7kwg
title: Occurrence Download

description: A dataset containing 248606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Buddleja davidii"
 ]
}

 The dataset includes 248606 records from 1586 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000141-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc92h1w
title: CCDC 270507: Experimental Crystal Structure Determination

description: Related Article: B.Twamley|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m619|doi:10.1107/S1600536805005441
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc8rgwb
title: CCDC 260892: Experimental Crystal Structure Determination

description: Related Article: Hong-Ji Chen|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m616|doi:10.1107/S1600536805005866
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92h2x
title: CCDC 270508: Experimental Crystal Structure Determination

description: Related Article: G.Labat, C.Boscovic, H.U.Gudel|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m611|doi:10.1107/S160053680500557X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92h3y
title: CCDC 270509: Experimental Crystal Structure Determination

description: Related Article: Yu-Guang Li, Meng Wang, Ling-Bin Zeng, Zhong-Lu You, Hai-Liang Zhu|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m667|doi:10.1107/S1600536805007026
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92h61
title: CCDC 270512: Experimental Crystal Structure Determination

description: Related Article: Ping Zhong, Zhiping Yang, Qian Shi|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o841|doi:10.1107/S1600536805006112
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.bjjx6h
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphenisciformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((50 -10,60 -10,60 0,50 0,50 -10))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022475-251009101135966/datasets/export for details.
DOI: 10.5517/cc92h72
title: CCDC 270513: Experimental Crystal Structure Determination

description: Related Article: Xiaohong Zhang, Zhiping Yang, Ping Zhong, Maolin Hu|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o908|doi:10.1107/S1600536805006707
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92h83
title: CCDC 270514: Experimental Crystal Structure Determination

description: Related Article: Du-Xia Cao, Guo-Zhong Li, Gang Xue, Wen-Tao Yu, Zhi-Qiang Liu|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o977|doi:10.1107/S1600536805006987
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.hqduja
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphenisciformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((40 -10,50 -10,50 0,40 0,40 -10))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022476-251009101135966/datasets/export for details.
DOI: 10.5517/cc92h94
title: CCDC 270515: Experimental Crystal Structure Determination

description: Related Article: G.R.Clark, C.L.Flowers, M.A.Brimble|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o910|doi:10.1107/S1600536805006938
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hb5
title: CCDC 270516: Experimental Crystal Structure Determination

description: Related Article: E.B.Miminoshvili, K.E.Miminoshvili, A.N.Sobolev|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m775|doi:10.1107/S1600536805009050
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hc6
title: CCDC 270517: Experimental Crystal Structure Determination

description: Related Article: Kui Cheng, Zhong-Lu You, Yu-Guang Li, Hai-Liang Zhu|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o1137|doi:10.1107/S1600536805008986
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hd7
title: CCDC 270518: Experimental Crystal Structure Determination

description: Related Article: Hai-Liang Zhu, Kui Cheng, Zhong-Lu You, Yu-Guang Li|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m755|doi:10.1107/S1600536805009025
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hf8
title: CCDC 270519: Experimental Crystal Structure Determination

description: Related Article: M.Gdaniec|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o1187|doi:10.1107/S1600536805009347
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.9jy3bs
title: Occurrence Download

description: A dataset containing 1017 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gruiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((40 10,50 10,50 20,40 20,40 10))"
 ]
}

 The dataset includes 1017 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022477-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc92hg9
title: CCDC 270520: Experimental Crystal Structure Determination

description: Related Article: C.Muthamizhchelvan, K.Saminathan, J.Fraanje, R.Peschar, K.Sivakumar|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o1153|doi:10.1107/S1600536805009189
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hjc
title: CCDC 270522: Experimental Crystal Structure Determination

description: Related Article: Xue-Yi Chen, J.R.Dias, D.R.Powell, J.D.Van Horn, T.C.Sandreczki|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o941|doi:10.1107/S1600536805006811
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hkd
title: CCDC 270523: Experimental Crystal Structure Determination

description: Related Article: Xue-Yi Chen, J.R.Dias, D.R.Powell, J.D.Van Horn, T.C.Sandreczki|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o944|doi:10.1107/S1600536805006823
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92hlf
title: CCDC 270524: Experimental Crystal Structure Determination

description: Related Article: E.V.Savinkina, Y.F.Al Ansari, I.A.Zamilatskov, D.V.Albov, A.Yu.Tsivadze|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m664|doi:10.1107/S1600536805006781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92j73
title: CCDC 270544: Experimental Crystal Structure Determination

description: Related Article: T.Akitsu, Y.Takeuchi, Y.Einaga|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|m772|doi:10.1107/S1600536805009062
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc92j84
title: CCDC 270545: Experimental Crystal Structure Determination

description: Related Article: Hui Wu, Zhou Xu, Jun Zhou, Yongmin Liang|2005|Acta Crystallogr.,Sect.E:Struct.Rep.Online|61|o1095|doi:10.1107/S160053680500838X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.