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Dataset results
15 results for “OMAP”
OMAP-23: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of vermiform appendix (FFPE) with MICS on MACSima
<p><strong>Description</strong></p> <p> OMAP-23 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human vermiform appendix sample. Tissue fixation and antigen retrieval is described in (<a href="https://www.biorxiv.org/content/biorxiv/early/2023/11/07/2023.10.27.564191.full.pdf">Spatial protein and RNA analysis on the same tissue section using MICS technology</a>). The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors</a>). All, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region, removing Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding. The use of human IgG1 recombinant antibodies allows for the addition of uncoupled monoclonal antibodies from other species followed by a fluorescence labelled secondary reagent specific for the species of the monoclonal antibody. The multiplex system has been described already for OMAP-10 and OMAP-21. A new dye VioB515 is used for one reagents. The fluorescence is removed by cleavage. The panel contains 28 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for six anatomical structures and most cell types present in the vermiform appendix (link to ASCT+B table added). OMAP-23 follows OMAP-21, with fewer antibodies but adding antibodies for non-immune cells.</p> <p>All reagents are from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The MACSima system is continuously evolving, this is the third OMAP for the MACSima system. A representative dataset created using OMAP-23 can be found here 10.5281/zenodo.14008816 .The AVRs for the dataset can be found here (to be added).</p>
OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0
<p> </p> <p>OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of <em>paraformaldehyde</em> (PFA)-fixed human tonsil samples. The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the ASCT+B tonsil table, v1.0 (submitted for review). OMAP-10 follows closely OMAP-1 described for human lymph nodes (<a href="https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html">https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html</a>). The initial dataset associated with OMAP-10 can be found in this dataset. All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in the table below. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The plan was to also include the data analysis in the uploaded dataset. However mixing the original data with analyses data would lead to confusion. Therefore only the original image files are included here. This is in brief the image analysis pipeline: the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, and this is the first OMAP dataset generated by using the MACSima system (Instrument, Reagents and Software).</p> <p>The images enclosed are in OME-tif format (16 bit depth). The optical resolution is 0.17 micron/pixel. The imaged area size is 1.6 mm x 1.3 mm. This Data is currently under review by the OMAP community and changes are still possible in the follow up version. The image contains stichted images of 9 fields of view. The complete runtime on the MACSima for this image dataset was about 12 hours on the instrument. The OMAP description also links to the ASCT+B table for the palatine tonsil.</p> <p><strong>Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Palatine Tonsil v1.0</strong></p> <p><strong>Description</strong></p> <p><a href="https://hubmapconsortium.github.io/ccf/pages/ccf-anatomical-structures.html">Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables</a> aim to capture the nested <em>part of</em> structure of anatomical human body parts, the typology of cells, and biomarkers used to identify cell types. The tables are authored and reviewed by an international team of experts. The Palatine Tonsil ASCT+B table is derived from published literature, public datasets, and unpublished studies from table authors. The Palatine Tonsil is part of the tonsiluar ring of Waldeyer network. In comparison to other Tonsils the Palatine Tonsil has an enlarged lymphoid tissue.</p> <p>The gene biomarkers are primarily derived from a preprint on an Atlas of Cells of the human tonsil (<a href="https://www.biorxiv.org/content/10.1101/2022.06.24.497299v1">Ramon Massoni-Badosa et al 2022</a>). The tonsil azimuth data set can be explored <a href="https://azimuth.hubmapconsortium.org/references/human_tonsil/">here</a> .Cell phenotypes, especially for antibody-based assays like the MACSima are very complex and in its first version, only the basic cell types are listed with many more to be included in the next iteration of the ASCT+B table. The correlation between protein detection and RNA expression data at the single cell level needs to be established. In total, this table reports 13 anatomical structures, 17 cell types, and 30 biomarkers. </p> <p>The following list contains the file name and the target name of the antibody used in a given staining:</p> <p>ACTIN_REAL650/ACTA2</p> <p>Bcl2_REA872/BCL2</p> <p>CD11c_REAL235/ITGAX</p> <p>CD138_REA929/SDC1</p> <p>CD15_VIMC6/FUT4</p> <p>CD19_REAL106/CD19</p> <p>CD1c_REA694/CD1C</p> <p>CD209_REAL1087/CD209</p> <p>CD20_REA1087/MS4A1</p> <p>CD21_REA940/CR2</p> <p>CD274_PDL1/CD274</p> <p>CD279_REAL531/PDCD1</p> <p>CD27_REA499/CD27</p> <p>CD39_REA739/ENTPD1</p> <p>CD3_REAL1097/CD3E</p> <p>CD44_REA690/CD44</p> <p>CD4_REA1307/CD4</p> <p>CD68_REA1306/CD68</p> <p>CD79a_REA1142/CD79A</p> <p>CD8_REA734/CD8A</p> <p>CollagenIV_REAL1212/COL4A1</p> <p>Cytokeratin_CK36H5/KRT7,KRT8,KRT18,KRT19</p> <p>FoxP3_REA1253/FOXP3</p> <p>HLADR_REAL550/HLA-DRA</p> <p>IgD_REA740/IGHD</p> <p>IgM_REAL689/IGHM</p> <p>Ki67_REA183/MKI67</p> <p>PlasmaCell_REA908/CKAP4</p> <p>Vimentin_REA409/VIM</p>
Multiplexed Staining Dataset - OMAP 5 - Liver-Lanthanides-conjugated antibodies and C60-secondary ion mass spectrometry imaging
<p>This dataset contains images of multiplexed antibody panel on a human pediatric liver section including the nuclear marker and antibodies conjugated with lanthanides tags. The dataset is one example of serial experiments of multiplexed antibody staining and imaging. The antibody panel targets the major cell types and tissue structures in the liver tissue. Data acquisition was performed using single multiplexing imaging by C60-secondary ion mass spectrometry.</p> <p> </p>
OMAP-8: Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0
<p>OMAP-8 was designed for Imaging Mass Cytometry (IMC) (<a href="https://pubmed.ncbi.nlm.nih.gov/24584193/">https://pubmed.ncbi.nlm.nih.gov/24584193/</a>) of formalin-fixed paraffin-embedded (FFPE) human term-placenta samples. The tissue slides were prepared with a two-step antigen retrieval process (pH 6 and pH 9, as described <a href="https://dx.doi.org/10.17504/protocols.io.bpwumpew">https://dx.doi.org/10.17504/protocols.io.bpwumpew</a>). OMAP antibodies validated by immunohistochemistry and IMC were conjugated to polymers containing metal isotopes. Conjugated antibodies were used to stain processed human term-placenta tissue simultaneously. Regions of the processed tissue were then acquired on the imaging mass cytometer (Hyperion; Standard BioTools) by laser ablation and visualized. The panel contains 26 antibodies conjugated to unique metal isotopes and iridium marks the DNA. This OMAP provides a spatial context for key placenta cell types in the <a href="https://doi.org/10.48539/HBM446.WGLG.755">ASCT+B v.1.0 table</a>. Single-cell RNA sequencing data were used to guide marker selection for multiplexed tissue imaging. For example, ASCL2, HLA-G, PD-L1, CD68 and LYVE1 allow functionally specialized cell types to be visualized and quantified in the placenta. Note that one of our core antibodies is to LYVE1 but, unlike in other tissues where it is used to mark lymphatic vasculature, here we use it to mark the macrophage of the placenta (Hofbauer cells) – there should be no lymphatics in the placenta.</p>
OMAP-21: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MICS on MACSima 1.5
<p>OMAP-21 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human tonsil samples. Tissue fixation and antigen retrieval is described in (<a href="https://www.biorxiv.org/content/biorxiv/early/2023/11/07/2023.10.27.564191.full.pdf">Spatial protein and RNA analysis on the same tissue section using MICS technology</a>). The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 47 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the human palatine tonsil. OMAP-21 follows closely OMAP-1 described for human lymph nodes (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-1-human-lymph-node-ibex.html">omap-1-human-lymph-node-ibex</a>) and OMAP-10 (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-10-palatine-tonsil-macsima.html">omap-10-palatine-tonsil-macsima</a>).</p> <p>All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The result of the analysis is included in the uploaded dataset. In brief, the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, this is the second OMAP for the MACSima system. A representative dataset created using OMAP-21 can be found here:<a href="https://doi.org/10.5281/zenodo.7875937"> </a><strong> 10.5281/zenodo.11281609 .</strong></p>
Multiplexed Immunofluorescence Staining Dataset - OMAP 7 - Lung, Cell DIVE
<p>This dataset contains an exemplary multiplexed immunofluorescence (MxIF) dataset for the antibody markers captured in Cell DIVE Lung OMAP (OMAP #7). The slide type is a TMA of FFPE tissue, and it contains a range of human lung tissue.</p> <p> </p> <p> </p>
OMAP Kidney-3
<p>Data was acquired using the CODEX Phenocycler, a multiplexed immunoflourescence profiling platform. All images available as .tiff. The targets here are fundamental markers for identification of human kidney functional tissue units. </p> <p> </p><p> </p> <p></p>
OMAP-15 Human Intestine with CODEX
<p>Datasets are CODEX experiments performed on TMA ffpe sections (composed of human duodenum, proximal jejunum, 3 mid jejunum samples, ileum, ascending colon, and sigmoid colon samples) labeled with nuclear marker DAPI and anitbodies directed against the indicated markers in OMAP-15. Images were acquired with the Akoya Phenocycler. </p> <p>Markers not included in OMAP-15 are not representative images.</p> <p>See "S16-0513-B13-TMA_Scan1.qptiff" for all markers except SPIB. See "S7-B017-011624_Scan1.qptiff" for SPIB.</p>
OMAP-19 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Tonsil with IBEX
<p>Representative dataset acquired using the Iterative Bleaching Extends multi-pleXity (IBEX) imaging method described in:</p> <ol> <li>“IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues“, A. Radtke et al., <em>Proc. Natl. Acad. Sci. USA,</em> 2020, <a href="https://doi.org/10.1073/pnas.2018488117">doi.org/10.1073/pnas.2018488117</a>.</li> <li>"IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues", A. J. Radtke, et al., <em>Nat Protoc</em>, 2022, <a href="https://doi.org/10.1038/s41596-021-00644-9">doi.org/10.1038/s41596-021-00644-9</a>.</li> </ol> <p>This dataset accompanies the <a href="https://www.nature.com/articles/s41592-023-01846-7">Organ Mapping Antibody Panel (OMAP) effort</a> led by the <a href="https://commonfund.nih.gov/HuBMAP">Human BioMolecular Atlas Program</a> detailed <a href="https://humanatlas.io/omap">here</a>.</p> <p>OMAP-19 was designed for IBEX imaging of human FFPE tonsil samples sectioned onto glass slides. The panel consists of 6 cycles of 20 primary antibodies, 5 secondary antibodies, and the nuclear label Hoechst for image alignment and nuclear segmentation. This OMAP provides a spatial context for 10 anatomical structures and at least 16 cell types present in the <a href="https://cdn.humanatlas.io/hra-releases/v2.0/docs/asct-b/asct-b-vh-palatine-tonsil.copy.html">ASCT+B tonsil table</a>. OMAP-19 was designed to examine myeloid subsets (CD11b, CD11c, CD14, CD15, HLA-DR) and angiogenesis (VEGF-A and VEGF-C) in human ovarian cancer biopsies. The human tonsil was used as a positive control for antibody validation and panel development. Antigen retrieval was performed using a pressure cooker (Borg Decloaker BD1000, 110°C for 15 minutes) and a tris-based buffer (pH 9.5). Several custom antibodies were created using commercial labeling kits as indicated in the associated RRID entries for these antibodies. More details on the antigen retrieval protocol and step-by-step application of antibodies can be found on the <a href="https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/">IBEX Imaging Community knowlege-base</a> (current version) and on <a href="../records/7693279">Zenodo</a> (last official version).</p> <p>Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as a 405 nm laser. All images were captured at an 16-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.379 µm), y (0.379 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software.</p> <p>Image supplied as a .ims Imaris Format file and can be opened with the <strong>free</strong> <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer</a> software or <a href="https://imagej.net/software/fiji/">ImageJ/Fiji</a>. Image channel and antibody meta-data supplied as an xlsx file.</p>
OMAP-8: Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0
<p>OMAP-8 was designed for Imaging Mass Cytometry (IMC) (<a href="https://pubmed.ncbi.nlm.nih.gov/24584193/">https://pubmed.ncbi.nlm.nih.gov/24584193/</a>) of formalin-fixed paraffin-embedded (FFPE) human term-placenta samples. The tissue slides were prepared with a two-step antigen retrieval process (pH 6 and pH 9, as described <a href="https://dx.doi.org/10.17504/protocols.io.bpwumpew">https://dx.doi.org/10.17504/protocols.io.bpwumpew</a>). OMAP antibodies validated by immunohistochemistry and IMC were conjugated to polymers containing metal isotopes. Conjugated antibodies were used to stain processed human term-placenta tissue simultaneously. Regions of the processed tissue were then acquired on the imaging mass cytometer (Hyperion; Standard BioTools) by laser ablation and visualized. The panel contains 26 antibodies conjugated to unique metal isotopes and iridium marks the DNA. This OMAP provides a spatial context for key placenta cell types in the <a href="https://doi.org/10.48539/HBM446.WGLG.755">ASCT+B v.1.0 table</a>. Single-cell RNA sequencing data were used to guide marker selection for multiplexed tissue imaging. For example, ASCL2, HLA-G, PD-L1, CD68 and LYVE1 allow functionally specialized cell types to be visualized and quantified in the placenta. Note that one of our core antibodies is to LYVE1 but, unlike in other tissues where it is used to mark lymphatic vasculature, here we use it to mark the macrophage of the placenta (Hofbauer cells) – there should be no lymphatics in the placenta.</p>
Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX
<p>Representative dataset using OMAP-13: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0. See https://humanatlas.io/omap.</p>
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP RIP]
GEO Series GSE217563. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [Xist OMAP RIP]
GEO Series GSE217565. Mus musculus x Mus spretus. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP ChIP]
GEO Series GSE217562. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [Xist OMAP ChIP]
GEO Series GSE217564. Mus musculus x Mus spretus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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