cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26537529
title: Yampi Peninsula felsic Hart Dolerite: re-evaluating the Nellie Tonalite using evidence from whole rock, petrography and geochronology

description: The Nellie Tonalite forms a discontinuous 20 km elongate northwest-trending felsic intrusion at the far-western end of the Western Zone of the Lamboo Province, in the Wunaamin Miliwundi Orogen, Western Australia. This intrusion is poorly understood with previous interpretations assigning it to the <i>ca</i> 1860 Ma Paperbark Supersuite. We present the first geochronological results for the Nellie Tonalite, which have a weighted mean laser ablation, inductively coupled plasma, mass spectrometry (LA-ICP-MS) U–Pb zircon age of 1794 ± 4 Ma. This date is coincident with the age for felsic granophyres of the Hart Dolerite, which have previously been described from the Kimberley Basin overlying the Halls Creek Orogen and central parts of the Wunaamin Miliwundi Orogen. Other similarities of the Nellie Tonalite with the felsic Hart Dolerite are micrographic and granophyric intergrowths of quartz and K-feldspar, and a distinct geochemical depletion of V. This V depletion is interpreted to be the result of closed-system, <i>in situ</i> fractional crystallisation of titanomagnetite from a basaltic composition. The fractional residue from this process can be found at several locations across the Halls Creek Orogen and Wunaamin Miliwundi Orogen and at Speewah Dome in the east Kimberley where magnetite gabbros within the Hart Dolerite also host a large Ti–V mineral resource. It is proposed that the Nellie Tonalite is a western correlate of the felsic Hart Dolerite. This demonstrates that the magmatic processes required for Speewah-style Ti–V mineralisation are extensive across the entire Lamboo Province. Additionally, the scale, constancy of the composition, texture and age of the felsic Hart Dolerite encompassing the entire inland margin of the Kimberley Region, and the rapid emplacement time of &lt;3 m.y., support the interpretation of a mantle plume model for the emplacement of the Hart Dolerite. The Nellie Tonalite is redefined as a granophyric granite, has been dated to 1794 ± 4 Ma and is coeval with the <i>ca</i> 1800 Ma Hart Dolerite. Petrographic, geochemical and geochronological evidence suggests that the Nellie Tonalite is a product of <i>in situ</i> fractional crystallisation of the Hart Dolerite (felsic Hart Dolerite). Plots of Ti/Nb <i>vs</i> V/Sc are ideal in identifying the distinctive V-depletion associated with the felsic Hart Dolerite, which marks a valuable stratigraphic horizon for identifying potential Speewah-style Ti–V mineralisation.
DOI: 10.6084/m9.figshare.26537529.v1
title: Yampi Peninsula felsic Hart Dolerite: re-evaluating the Nellie Tonalite using evidence from whole rock, petrography and geochronology

description: The Nellie Tonalite forms a discontinuous 20 km elongate northwest-trending felsic intrusion at the far-western end of the Western Zone of the Lamboo Province, in the Wunaamin Miliwundi Orogen, Western Australia. This intrusion is poorly understood with previous interpretations assigning it to the <i>ca</i> 1860 Ma Paperbark Supersuite. We present the first geochronological results for the Nellie Tonalite, which have a weighted mean laser ablation, inductively coupled plasma, mass spectrometry (LA-ICP-MS) U–Pb zircon age of 1794 ± 4 Ma. This date is coincident with the age for felsic granophyres of the Hart Dolerite, which have previously been described from the Kimberley Basin overlying the Halls Creek Orogen and central parts of the Wunaamin Miliwundi Orogen. Other similarities of the Nellie Tonalite with the felsic Hart Dolerite are micrographic and granophyric intergrowths of quartz and K-feldspar, and a distinct geochemical depletion of V. This V depletion is interpreted to be the result of closed-system, <i>in situ</i> fractional crystallisation of titanomagnetite from a basaltic composition. The fractional residue from this process can be found at several locations across the Halls Creek Orogen and Wunaamin Miliwundi Orogen and at Speewah Dome in the east Kimberley where magnetite gabbros within the Hart Dolerite also host a large Ti–V mineral resource. It is proposed that the Nellie Tonalite is a western correlate of the felsic Hart Dolerite. This demonstrates that the magmatic processes required for Speewah-style Ti–V mineralisation are extensive across the entire Lamboo Province. Additionally, the scale, constancy of the composition, texture and age of the felsic Hart Dolerite encompassing the entire inland margin of the Kimberley Region, and the rapid emplacement time of &lt;3 m.y., support the interpretation of a mantle plume model for the emplacement of the Hart Dolerite. The Nellie Tonalite is redefined as a granophyric granite, has been dated to 1794 ± 4 Ma and is coeval with the <i>ca</i> 1800 Ma Hart Dolerite. Petrographic, geochemical and geochronological evidence suggests that the Nellie Tonalite is a product of <i>in situ</i> fractional crystallisation of the Hart Dolerite (felsic Hart Dolerite). Plots of Ti/Nb <i>vs</i> V/Sc are ideal in identifying the distinctive V-depletion associated with the felsic Hart Dolerite, which marks a valuable stratigraphic horizon for identifying potential Speewah-style Ti–V mineralisation.
DOI: 10.6084/m9.figshare.26839940
title: Response of Permian sediment provenance conversion in Hainan Island to the closure of the Eastern Paleo-Tethys Ocean

description: From the late Permian to Early Triassic, the eastern part of the Paleo-Tethys Ocean was closed, and the Jinshajiang–Ailaoshan–Songma suture belt formed between the Yangtze Craton and the Indochina Block. The structural belt extends eastward to Hainan Island as the Changjiang–Qionghai fault, which controls the closure of the southern and northern parts of Hainan Island and the transformation of the sedimentary environment. This study focuses on the late Permian Nanlong Formation in Nanlong village, Dongfang County, western Hainan Island. Detrital zircon U–Pb ages from the Permian strata in southern and northern Hainan Island are used to discuss the provenance and sedimentary environment during the early and late Permian. The detrital zircon U–Pb ages from the upper Permian Nanlong Formation are 2800–900, 700–500, 500–400 and 400–320 Ma, with the majority falling into the 500–400 Ma range. The sedimentary environment on Hainan Island transitioned from early Permian semi-deep to deep-sea to late Permian coastal and shallow sea. The sediment provenance changed from a recycled orogen belt during the early Permian to a combination of recycled and arc orogen belt (Devonian–Carboniferous) during the late Permian. This reflects the closure of the east Paleo-Tethys Ocean during the late Permian that resulted in the collision and assembly of south and north Hainan Island and its relative uplift in the central part, which controlled the transition in sedimentary provenance and environment during the late Permian on Hainan Island. The sedimentary environment of Hainan Island changed from the early to late Permian. The sediment provenance of Hainan Island also changed from the early to late Permian. The closure of the east Paleo-Tethys Ocean during the late Permian led to the collision and assembly of north and south of Hainan Island.
DOI: 10.6084/m9.figshare.26839940.v1
title: Response of Permian sediment provenance conversion in Hainan Island to the closure of the Eastern Paleo-Tethys Ocean

description: From the late Permian to Early Triassic, the eastern part of the Paleo-Tethys Ocean was closed, and the Jinshajiang–Ailaoshan–Songma suture belt formed between the Yangtze Craton and the Indochina Block. The structural belt extends eastward to Hainan Island as the Changjiang–Qionghai fault, which controls the closure of the southern and northern parts of Hainan Island and the transformation of the sedimentary environment. This study focuses on the late Permian Nanlong Formation in Nanlong village, Dongfang County, western Hainan Island. Detrital zircon U–Pb ages from the Permian strata in southern and northern Hainan Island are used to discuss the provenance and sedimentary environment during the early and late Permian. The detrital zircon U–Pb ages from the upper Permian Nanlong Formation are 2800–900, 700–500, 500–400 and 400–320 Ma, with the majority falling into the 500–400 Ma range. The sedimentary environment on Hainan Island transitioned from early Permian semi-deep to deep-sea to late Permian coastal and shallow sea. The sediment provenance changed from a recycled orogen belt during the early Permian to a combination of recycled and arc orogen belt (Devonian–Carboniferous) during the late Permian. This reflects the closure of the east Paleo-Tethys Ocean during the late Permian that resulted in the collision and assembly of south and north Hainan Island and its relative uplift in the central part, which controlled the transition in sedimentary provenance and environment during the late Permian on Hainan Island. The sedimentary environment of Hainan Island changed from the early to late Permian. The sediment provenance of Hainan Island also changed from the early to late Permian. The closure of the east Paleo-Tethys Ocean during the late Permian led to the collision and assembly of north and south of Hainan Island.
DOI: 10.48539/hbm493.djfq.925
title: OMAP-15 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Intestines with CODEX, v1.1

description: OMAP-15 was designed for CODEX (CO-Detection by indEXing) imaging of formalin-fixed paraffin-embedded (FFPE) human<br>intestine samples using the Akoya Biosciences PhenoCycler system (Black et al. 2021; Kennedy‐Darling et al. 2021). The<br>panel consists of 54 antibodies and DAPI for nuclear segmentation. This OMAP provides spatial context for anatomical<br>structures and cell types listed in ASCT+B Large Intestine v1.3 (Longacre, Hickey, and Lin 2022) and Small Intestine<br>v1.1 (Longacre 2022). It builds upon OMAP-2 (Radtke et al. 2023) by adapting marker panels from frozen to FFPE tissue.<br>Nineteen markers from OMAP-2 were excluded, and 22 new markers were included: ATP1A1, CD206, COL1A1, CTNNB1, FN1,<br>FOXP3, GP2, HLA-DRA, IGHA1, IGHM, ITGAM, KRT4/5/6a/6b/6c/8/10/13/18, MS4A1, MUC6, PDGFRA/B, POSTN, RORC, SIGLEC8,<br>SPIB, TNC, TPSAB1, and UCHL1. Markers for tuft cells and naive intestinal stem cells (LGR5+, ASCL2+) are not included.<br>Carrier-free antibodies were used whenever possible; if carrier-containing antibodies were standard, custom<br>carrier-free alternatives were ordered. All antibodies were oligo-conjugated using protocols detailed in Wei and Bi<br>(2024a). Protocols for sample preparation and antigen retrieval are described in Wei and Bi (2023), and a<br>representative dataset for this OMAP is available (Wei and Bi 2024b).<br><br>**Bibliography:**<br><br>* Black, Sarah, Darci Phillips, John W. Hickey, Julia Kennedy-Darling, Vishal G. Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M. Schürch, and Garry P. Nolan. 2021. “CODEX Multiplexed Tissue Imaging with DNA-Conjugated Antibodies.” *Nature Protocols* 16 (8): 3802–35. https://doi.org/10.1038/s41596-021-00556-8.<br>* Kennedy‐Darling, Julia, Salil S. Bhate, John W. Hickey, Sarah Black, Graham L. Barlow, Gustavo Vazquez, Vishal G. Venkataraaman, et al. 2021. “Highly Multiplexed Tissue Imaging Using Repeated Oligonucleotide Exchange Reaction.” *European Journal of Immunology* 51 (5): 1262–77. https://doi.org/10.1002/eji.202048891.<br>* Longacre, Teri. 2022. “Small-Intestine (v1.1) Graph Data, v1.1.” 2022. https://lod.humanatlas.io/asct-b/small-intestine/v1.1/.<br>* Longacre, Teri, John Hickey, and Yiing Lin. 2022. “Large-Intestine (v1.3) Graph Data, v1.3.” 2022. https://lod.humanatlas.io/asct-b/large-intestine/v1.3/.<br>* Radtke, Andrea J., Katy Börner, Neil Kelleher, and Ronald N. Germain. 2023. “2-Intestine-Codex (v1.3) Graph Data, v1.3.” 2023. https://lod.humanatlas.io/omap/2-intestine-codex/v1.3/.<br>* Wei, Bei, and Joanna Bi. 2023. “CODEX FFPE Staining and Fixation,” December. https://www.protocols.io/view/codex-ffpe-staining-and-fixation-c6atzaen.<br>* Wei, Bei, and Joanna Bi. 2024a. “CODEX Antibody Conjugation Protocol,” April. https://www.protocols.io/view/codex-antibody-conjugation-protocol-db2j2qcn.<br>* Wei, Bei, and Joanna Bi. 2024b. “OMAP-15 Human Intestine with CODEX.” Zenodo. https://zenodo.org/records/10963121.
DOI: 10.48539/hbm925.jgnd.963
title: OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima, v1.2

description: OMAP-10 was designed for MICS (MACSima imaging cyclic staining) imaging of paraformaldehyde (PFA)-fixed human tonsil<br>samples. The MICS technology is described in detail in Kinkhabwala et al. (2022). Most antibodies in this panel are<br>recombinant antibodies with a mutated human IgG1 constant region that eliminates Fc receptor binding, reducing<br>non-specific binding and removing the need for blocking steps. Highly multiplexed imaging is achieved through cycles<br>of immunolabeling with FITC, PE, and APC conjugated antibodies followed by photobleaching between cycles. The panel<br>contains 30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides<br>spatial context for all anatomical structures and most cell types in the human palatine tonsil. It follows closely the<br>antibody panel and methodology described in OMAP-1 for human lymph nodes. All reagents were obtained from Miltenyi<br>Biotec and were quality controlled internally; lot numbers are not provided. Image processing and downstream analysis<br>were conducted using the MACSIQ View Analysis software described in Kinkhabwala et al. (2022), which supports<br>segmentation, gating, normalization, dimensionality reduction (tSNE, UMAP), clustering, and spatial analyses with<br>interactive visualization. This is the first OMAP generated using the MACSima platform. A representative dataset is<br>available via Müller, Rüberg, and Bosio (2023).<br><br>**Bibliography:**<br><br>* Kinkhabwala, Ali, Christoph Herbel, Jennifer Pankratz, Dmytro A. Yushchenko, Silvia Rüberg, Paurush Praveen, Sandy Reiß, et al. 2022. “MACSima Imaging Cyclic Staining (MICS) Technology Reveals Combinatorial Target Pairs for CAR T Cell Treatment of Solid Tumors.” *Scientific Reports* 12 (1): 1911. https://doi.org/10.1038/s41598-022-05841-4.<br>* Müller, Werner, Silvia Rüberg, and Andreas Bosio. 2023. “OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0.” Zenodo. https://zenodo.org/records/7875938.
DOI: 10.48539/hbm754.bhvr.258
title: OMAP-13: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0

description: OMAP-13 was designed for imaging of 4% PFA-fixed, cryopreserved human pancreas samples by CO-Detection by indEXing<br>(CODEX) (https://doi.org/10.1038/s41596-021-00556-8). Containing 27 antibodies and nuclear marker DAPI, this OMAP<br>provides spatial context for 13 anatomical structures and 21 cell types in the ASCT+B Pancreas table v1.2<br>(https://doi.org/10.48539/HBM975.BBTF.393) and shares 8 markers with OMAP-6<br>(https://doi.org/10.48539/HBM868.XLTM.922). It also facilitates identification of gamma and epsilon cells, lymphatic<br>endothelial cells, pericytes, resident immune cells, neuronal structures, and some stromal cells and the extracellular<br>matrix (ECM). Due to the inclusion of biomarkers PPY, GHRL, PTPRC (CD45), CD19, ITGAX (CD11c), AIF1 (IBA1), and CD14,<br>this panel is suitable for all regions of the human pancreas (including the uncinate process, UBERON:0010373) from<br>birth to adulthood and can detect inflammatory cells present in diabetes. Panel design and validation was performed on<br>the PhenoCycler Open and Fusion systems (Akoya Biosciences). Carrier free aliquots for antibodies directed against<br>targets GHRL, PPY, and LYVE1 were ordered directly from R&D Biosciences to allow custom conjugation; antibody<br>metadata reflect the catalog versions. The GP2 antibody, which was purified and conjugated by Leinco Technologies,<br>Inc., is best used in conjunction with another acinar cell marker. Application of this CODEX panel to early-stage T2D<br>samples (Walker et al. 2021; https://doi.org/10.1101/2021.12.16.466282) included cellular segmentation by DAPI using<br>the Highplex FL module of HALO image analysis software (Indica Labs). Details on sample preparation and antibody<br>screening can be found at https://doi.org/10.17504/protocols.io.36wgq7dryvk5/v1 and a representative dataset is<br>uploaded at https://doi.org/10.5281/zenodo.7916784. Interactive image browsing is available on Pancreatlas<br>(RRID:SCR_01856).
DOI: 10.48539/hbm494.rrld.598
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Large Intestine, v1.2

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm538.gcjj.874
title: OMAP-20: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of kidney with cyclic multiplexed immunofluorescence, v1.1

description: OMAP-20 was developed for cyclic multiplexed immunofluorescence (MxIF) microscopy of fresh frozen human kidney tissues<br>(Brewer et al. 2023). This panel includes 10 antibodies and the nuclear marker Hoechst for image alignment and<br>segmentation. It offers spatial context for key renal structures and cell types associated with proximal tubules,<br>glomeruli, and vasculature—components represented in the ASCT+B kidney table v1.4. Other functional tissue units of<br>the kidney, such as distal tubules or collecting ducts, are not captured in this OMAP. The antibody against tensin<br>(RRID: AB_10796111) is noted to perform optimally in cycle 1 of imaging, and placement in later cycles may lead to<br>reduced signal fidelity. Antibody validation and sample preparation protocols, including tissue handling and staining<br>workflows, are detailed by the VU Biomolecular Multimodal Imaging Center / Spraggins Research Group (2025).<br>Representative imaging datasets utilizing this OMAP are presented in the work by Esselman et al. (2024), which<br>integrates imaging mass spectrometry and MxIF microscopy to characterize glomerular substructures.<br><br>**Bibliography:**<br><br>* Brewer, Maya, Liz McDonough, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, and Mark De Caestecker. 2023. “Multiplex Cyclical Immunofluorescence on Fresh Frozen Tissue-V3.” September 8, 2023. https://www.protocols.io/view/multiplex-cyclical-immunofluorescence-on-fresh-fro-czsax6ae.<br>* Esselman, Allison B., Felipe A. Moser, Léonore Tideman, Lukasz G. Migas, Katerina V. Djambazova, Madeline E. Colley, Ellie L. Pingry, et al. 2024. “Revealing In Situ Molecular Profiles of Glomerular Cell Types and Substructures with Integrated Imaging Mass Spectrometry and Multiplexed Immunofluorescence Microscopy.” bioRxiv. https://doi.org/10.1101/2024.02.21.581450.<br>* VU Biomolecular Multimodal Imaging Center / Spraggins Research Group. 2025. “VU Biomolecular Multimodal Imaging Center / Spraggins Research Group - Research Workspace on Protocols.Io.” Protocols.Io. 2025. https://www.protocols.io/workspaces/BIOMIC.
DOI: 10.48539/hbm989.wtjw.393
title: OMAP-3 Organ Mapping Antibody Panel (OMAP)  for Multiplexed Antibody-Based Imaging of Kidney with CODEX, v1.4

description: OMAP-3 was designed for CODEX (CO Detection by indEXing) of fresh frozen human kidney samples (Black et al. 2021;<br>2021). The panel contains 24 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation.<br>Additional details on tissue preparation, panel design, image analysis, and representative images can be found in<br>accompanying publications (Neumann et al. 2022; 2021). This OMAP provides a spatial context for all anatomical<br>structures and most cell types present in the ASCT+B kidney table v1.1 (Jain, Valerius, and He 2021). Additionally,<br>the inclusion of tryptase and MARCKS allow profiling of different regions in the glomeruli that are often affected by<br>disease. Several cell types are identified by their morphology, location in the kidney, and expression of Cytokeratin<br>7. The panel was designed to provide a survey of the cell types found in the kidney and does not allow for granular<br>phenotyping of immune cell populations. However, mast cells, NK cells, T cells, and B cells are broadly classified by<br>several markers included in this OMAP. The core and essential protein biomarkers detailed here overlap (>40%) with a<br>panel developed for multiplexed imaging of kidney samples using imaging mass cytometry (IMC) (Singh et al. 2019). A<br>representative dataset can be found here: (Neumann and Farrow 2023).<br><br>**Bibliography:**<br><br>* Black, Sarah, Darci Phillips, John W. Hickey, Julia Kennedy-Darling, Vishal G. Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M. Schürch, and Garry P. Nolan. 2021. “CODEX Multiplexed Tissue Imaging with DNA-Conjugated Antibodies.” *Nature Protocols* 16 (8): 3802–35. https://doi.org/10.1038/s41596-021-00556-8.<br>* Jain, Sanjey, M. Todd Valerius, and Yongqun He. 2021. “Kidney (v1.1) Graph Data, v1.1.” https://lod.humanatlas.io/asct-b/kidney/v1.1/.<br>* Neumann, Elizabeth K., and Melissa Farrow. 2023. “OMAP Kidney-3.” Zenodo. https://zenodo.org/records/8082943.<br>* Neumann, Elizabeth K., Nathan Heath Patterson, Jamie L. Allen, Lukasz G. Migas, Haichun Yang, Maya Brewer, David M. Anderson, et al. 2021. “Protocol for Multimodal Analysis of Human Kidney Tissue by Imaging Mass Spectrometry and CODEX Multiplexed Immunofluorescence.” *STAR Protocols* 2 (3): 100747. https://doi.org/10.1016/j.xpro.2021.100747.<br>* Neumann, Elizabeth K., Nathan Heath Patterson, Emilio S. Rivera, Jamie L. Allen, Maya Brewer, Mark P. deCaestecker, Richard M. Caprioli, Agnes B. Fogo, and Jeffrey M. Spraggins. 2022. “Highly Multiplexed Immunofluorescence of the Human Kidney Using Co-Detection by Indexing.” *Kidney International* 101 (1): 137–43. https://doi.org/10.1016/j.kint.2021.08.033.<br>* Singh, Nikhil, Zachary M. Avigan, Judith A. Kliegel, Brian M. Shuch, Ruth R. Montgomery, Gilbert W. Moeckel, and Lloyd G. Cantley. 2019. “Development of a 2-Dimensional Atlas of the Human Kidney with Imaging Mass Cytometry.” *JCI Insight* 4 (12). https://doi.org/10.1172/jci.insight.129477.
DOI: 10.48539/hbm557.xhhv.557
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Pancreas, v1.1

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.