Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
4,725
datasets available to search
ShareScore release 0.9.0
Dataset results
4,725 results for “Normalization”
Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provides both common and discordant biological insights
<p>The datasets generated by <em>Cellranger </em>for all 24 samples (.h5 format).<br><br></p>
Fig. 17 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 17. Cytherid ostracod Minyocythere tuberculata (Luppold, 2012) from Borehole Rodewald WA12, 404.5 m, NW Germany, Lower Bajocian. A. SMF Xe 23754, female left valve in external (A1) and internal (A4) views, micro sieve-type pore canals (StPC-m) (A2), macro sieve-type normal pore canals (StPC-M) A3), hinge, posterior (A5) and anterior (A6) parts. B. SMF Xe 23755, female right valve in external view.
Fig. 10 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 10. Cytherid ostracod Minyocythere sp. cf. M. macroporosa sp. nov. from Borehole Rodewald WA12, 404.5 m (A), 386 m (B–E), 404.5 m (F, G), NW Germany, Witchellia laeviuscula Zone (Braun Jura γ upper), Lower Bajocian. A. SMF Xe 23725, male left valve in external view (A1), antero-dorsal area (A2), macro sieve-type normal pore canals (StPC-M) (A3), and micro sieve-type normal pore canals (StPC-m) (A4). B. SMF Xe 23726, female left valve in external view. C. SMF Xe 23727, female carapace in right (C1) and dorsal (C2) views. D. SMF Xe 23728, female right valve in external view. E. SMF Xe 23729, male carapace in dorsal view. F. SMF Xe 23730, fragment of female right valve in internal view. G. SMF Xe 23731, male left valve, internal view (G1), hinge (G2).
Fig. 16 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 16. Normal pore canals (NPC) on juvenile left valves (A, stage A-2; B, stage A-3; C, stage A-4) in cytherid ostracod Minyocythere maculosa (Bate, 1963) from Borehole Rodewald WA6, 390 m, NW Germany, Lower Bajocian (Braun Jura γ). A. SMF Xe 23751, general view (A1), micro sieve-type pore canals (StPC-m) on the outer side of the valve (A2), macro sieve-type normal pore canals (StPC-M) on the outer side of the valve (A3, A4), StPC-M on the inner side of the valve (A5), and simple NPC on the outer side of the valve (A6). B. SMF Xe 23752, general view (B1), StPC-m on the outer side of the valve (B2), StPC-M on the inner side of the valve (B3). C. SMF Xe 23753, general view (C1), StPC-m on the outer side of the valve (C2), StPC-M on the outer side of the valve (C3).
Fig. 3 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 3. Sieve-type normal pore canals (StPC) in Aphelocythere and Camptocythere spp. A. Aphelocythere perforata Plumhoff, 1963, from Borehole Wesendorf 51a, 1031–1035 m, NW Germany, Upper Aalenian. SMF Xe 5608 (Plumhoff Collection), carapace in external right view (A1), macro StPC (StPC-M) (A2–A4). B, C. Camptocythere praecox Triebel, 1950 from Borehole Hambühren WA 2, 341 m, NW Germany, Leioceras opalinum Zone, Lower Aalenian (Braun Jura α). B. Paratype, SMF Xe 1448, male right valve in external view (B1), mid-anterior area behind marginal rim, ornamentation and pores (large and small) (B2), StPC-M with a peripheral large pore (B3), micro StPC (StPC-m) (B4). C. Paratype, SMF Xe 1448, male right valve in internal view (C1), hinge (C2), StPC-m (C3). D. Camptocythere media Triebel, 1950 from Borehole Altencelle 1014, 212/16 m, NW Germany, Upper Aalenian (Braun Jura β). Paratype, SMF Xe 1513, female left valve in external view (D1), detail, antero-dorsal area, ornamentation and pores (large and small) (D2), round StPC-M (D3), elongate StPC-M (D4), StPC-m (D5).
Fig. 2 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 2. Sieve-type normal pore canals (StPC) in Phraterfabanella spp. A, B. Phraterfabanella tridentinensis Whatley and Boomer in Boomer et al., 2001, from Rotzo Member, Calcari Grigi Formation, Trento Platform, Venetian Prealps, NE Italy, Upper Sinemurian, Lower Jurassic. A. SMF Xe 23715, female left valve, in external view (A1). Detail of antero-dorsal area (A2), macro StPC (StPC-M) (A3), micro StPC (StPC-m) (A4), and large StPC (A5). B. SMF Xe 23716, male? fragment of right valve, in internal view (B1), StPC-M in general view (B2) and details (B3, B4). C. Phraterfabanella boomeri Cabral and Colin, 2015, from Praia da Concha, Coimbra Formation, sample PCR-318, Portugal, Upper Sinemurian, Lower Jurassic. SMF Xe 23717, male carapace, in external left view (C1), StPC-M in general view (C3) and details (C2, C4, C5).
Fig. 13 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 13. Length versus height plots for Minyocythere angulata sp. nov. A-1, A-2, A-4, estimated growth (moult) stages.
Fig. 21 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 21. Stratigraphic distribution of Minyocythere angulata sp. nov., Minyocythere sp. cf. M. macroporosa sp. nov., Minyocythere macroporosa sp. nov., Minyocythere maculosa (Bate, 1963), and Minyocythere tuberculata (Luppold, 2012) in Borehole Hambühren WA2, NW Germany.
Fig. 6 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 6. Distribution of sieve-type normal pore canals (StPC) and simple normal pore canals (NPC) on the outer side of left valves of cytherid ostracod Minyocythere gen. et spp. nov. A. Minyocythere macroporosa sp. nov. from Borehole Hambühren WA2, 166 m, NW Germany, Witchellia laeviuscula Zone (Braun Jura γ), Lower Bajocian. Holotype, SMF Xe 23721, male left valve (A), detail (A), total area of A, c. 45 μm2. B. Minyocythere angulata 1 2 2 sp. nov. from Borehole Hambühren WA2, 203 m, NW Germany, Upper Aalenian (Braun Jura β). Holotype, SMF Xe 23737, male left valve (B1), detail (B), total area of B, c. 44 μm2. C. Minyocythere sp. cf. M. macroporosa sp. nov. from Borehole Rodewald WA12, 404.5 m, NW Germany, Witchellia 2 2 laeviuscula Zone (Braun Jura γ upper), Lower Bajocian. SMF Xe 23725, male left valve (C1), detail (C2). D. Minyocythere maculosa (Bate, 1963) from Hambühren WA2, 171–174 m, NW Germany, Upper Aalenian (Braun Jura β). SMF Xe 23750, male left valve. E. Minyocythere tuberculata (Luppold, 2012) from Borehole Rodewald WA12, 404.5 m, NW Germany, Witchellia laeviuscula Zone (Braun Jura γ upper), Lower Bajocian. SMF Xe 23754, female left valve. Black dots refer to macro StPC (StPC-M); white arrows point to micro StPC (StPC-m); simple NPC underlined; black arrows indicate position of the two StPC-M characteristic of Minyocythere species. Scale bars 100 μm.
Fig. 9 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 9. Marginal pore canals of cytherid ostracods Minyocythere macroporosa sp. nov. and Minyocythere angulata sp. nov. A, B. Minyocythere angulata sp. nov. from Borehole Hambühren WA2, 203 m, NW Germany, Upper Aalenian (Braun Jura β). A. SMF Xe 23742 (specimen broken), female right valve in internal view. B. Unnumbered (specimen missing), male right valve in internal view. C, D. Minyocythere macroporosa sp. nov. from Hambühren WA2, 166 m, NW Germany, Upper Aalenian (Braun Jura β). C. Holotype, SMF Xe 23721, male left valve in external view. D. Paratype, SMF Xe 23722, female right valve in external view. Light micrographs by Erich Triebel. Scale bars 100 μm.
Fig. 20 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 20. Cytherid ostracod Dolocythere amphistiela sp. nov. from Borehole Rodewald WA4, 187 m, NW Germany Leymeriella tardefurcata Zone, Lower Albian. A. Paratype, SMF Xe 23760, male right valve in external view. B. Holotype, SMF Xe 23761, male left valve in external view (B1), dorsal-posterior area (B2), ornamentation (B3). C. Paratype, SMF Xe 23762, female left valve in external view. D. Paratype, SMF Xe 23763, female right valve in external view (D1), small StPC (cf. micro sieve-type normal pore canals StPC-m) (D2, D3), simple pore (D4). E. Paratype, SMF Xe 23764, female right valve in internal view. F. Paratype, SMF Xe 23765, male left valve in internal view (F1), small StPC (cf. StPC-m) (F2), muscle scars (F3). G. Paratype, SMF Xe 23766, male left valve in internal view (G1), hinge (G2).
Fig. 1 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 1. Schematic cross-sections of ostracod valves, exterior to top, interior to bottom. A. NPC classification of Puri and Dickau (1969). B. StPC with sieve plate flush with external surface (1) and sieve plate in funnel-shaped depression (2).
Fig. 15 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 15. Length versus height plots for Minyocythere maculosa (Bate, 1963) from UK (A) and Germany (B).
Fig. 4 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 4. Comparison of muscle scars of Dolocythere Mertens, 1956 and Minyocythere gen. nov. A. Dolocythere rara Mertens, 1956 from Borehole Lingen 196, 697–704 m, NW Germany, Lower Albian. Paratype, BGR T.-K. 1300 (Mertens Collection, Hannover), female left valve in internal view. B. Minyocythere angulata sp. nov. from Borehole Hambühren WA2, 203 m, NW Germany, Upper Aalenian (Braun Jura β). Paratype, SMF Xe 23738, female left valve in internal view. A1, B1, photographs; A2, B2, explanatory drawings.
Fig. 7 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 7. Cytherid ostracod Minyocythere macroporosa sp. nov. from Borehole Hambühren WA2, 166–167 m (A–C), 166 m (D, E), 168–169 m (F), NW Germany, Witchellia laeviuscula Zone (Braun Jura γ), Lower Bajocian. A. Paratype, SMF Xe 23718, female carapace in right view. B. Paratype, SMF Xe 23719, male carapace in right (B1) and dorsal (B2) views, antero-dorsal margin (B3). C. Paratype, SMF Xe 23720, female carapace in dorsal (C1) and ventral (C6) views, pores (large and small) (C2), macro sieve-type normal pore canals (StPC-M) (C3), antero-dorsal margin (C4), and micro sieve-type →
Fig. 12 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 12. Cytherid ostracod Minyocythere angulata sp. nov. from Borehole Hambühren WA2, 177–180 m (A, H), 203–206 m (B–E), 203 m (F, G), NW Germany, Upper Aalenian (Braun Jura β). A. Paratype, SMF Xe 23732, female carapace in right view. B. Paratype, SMF Xe 23733, female right valve in external view (B1), micro sieve-type pore canals (StPC-m) (B2), and round macro sieve-type normal pore canals (StPC-M) (B3). C. Paratype, SMF Xe 23734, female left valve in external view (C1), elongate StPC-M (C2). D. Paratype, SMF Xe 23735, female carapace in dorsal view. E. Paratype, SMF Xe 23736, female carapace in ventral view. F. Holotype, SMF Xe 23737, male left valve in external (F1) and internal (F4) views, ornamentation and StPC-M and StPC-m (F2), StPC-m (F3), hinge (F5). G. Paratype, SMF Xe 23738, female left valve in internal view (G1), muscle scars (G2), StPC-m (G3). H. Paratype, SMF Xe 23740, male carapace in right view. I. Paratype, SMF Xe 23739, A-2? juvenile right valve in external view.
Fig. 18. Cytherid ostracod Dolocythere rara Mertens, 1956 from Borehole Lingen 196, 697–704 m in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 18. Cytherid ostracod Dolocythere rara Mertens, 1956 from Borehole Lingen 196, 697–704 m (A, B), Borehole Rodewald WA6, 206 m (C), WA7, 383.7 m (E), Borehole ZW Losser 1, 256.4–258.4 m (F) from NW Germany, Lower Albian and Ziegelei Bekum (D) from NW Germany, Upper Aptian. A. Paratype, BGR T.-K. 1300 (Mertens Collection, Hannover), female left valve in external (A1) and internal (A5) views, ornamentation (A2–A4), muscle scars (A6), hinge (A7), small sieve-type pore canals (StPC) (cf. micro sieve-type normal pore canals StPC-m) (A8). B. Paratype, BGR T.-K. 1300 (Mertens →
Fig. 11 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 11. Distribution of macro sieve-type normal pore canals (StPC-M), micro sieve-type normal pore canals (StPC-m), and simple normal pore canals NPC) on the inner side of cytherid ostracods Minyocythere gen. nov. and Dolocythere Mertens, 1956. A. Minyocythere macroporosa sp. nov., holotype, SMF Xe 23721 from Borehole Hambühren WA2, 166 m, NW Germany, Witchellia laeviuscula Zone (Braun Jura γ), Lower Bajocian; male left valve. B. Dolocythere rara Mertens, 1956, SMF Xe 23756 from Borehole Rodewald WA6, 206 m, NW Germany, Lower Albian; male left valve (B1), detail (B2). C. Minyocythere sp. cf. M. macroporosa sp. nov., SMF Xe 23724 from Borehole Rodewald WA12, 386 m, NW Germany, Upper Aalenian (Braun Jura β upper); male right valve. D. Dolocythere amphistiela sp. nov., paratype, SMF Xe 23765 from Borehole Rodewald WA4, 187 m, NW Germany, Leymeriella tradefurcata Zone, Lower Albian; male left valve. In A and C, black dots refer to StPC-M, white arrows point to StPC-m; in B1, B2, D white arrows point to NPC; black arrows in B1, B2 indicate the peculiar pores of D. rara (which do not exist in D. amphistiela). Scale bars 100 μm.
Fig. 14 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 14. Cytherid ostracod Minyocythere maculosa (Bate, 1963) from Everthorpe Quarry, South Cave, UK, Basement Beds, Bajocian (A, B) and Borehole Rodewald WA12, 395 m (C, D), 390 m (E), NW Germany, Witchellia laeviuscula Zone (Braun Jura γ), Lower Bajocian. A. Topotype, SMF Xe 23744, male left valve in external view (A1), macro sieve-type pore canals (StPC-M) (A2), micro sieve-type normal pore canals (StPC-m) (A3), and simple pore (A4). B. Topotype, SMF Xe 23745, female right valve in internal view (B1), muscle scars (B2), hinge (B3). C. SMF Xe 23746, male left valve in external view (C1), StPC-M (C2, C3), StPC-m (C4). D. SMF Xe 23747, female right valve in external (D1) and internal (D3) views, simple pore (D2), StPC-M (D4), StPC-m (D5), hinge, posterior part (D6), muscle scars (D7). E. SMF Xe 23748, interior of StPC-M (E1), fragment of a left valve in internal view (E2).
Normalized and batch-corrected concentration of 43 immune markers from 248 subjects with stress-related mental disorders and 36 healthy controls
<h1>Abstract</h1> <p>In a subset of patients with mental disorders, such as depression, low-grade inflammation and altered immune marker concentrations are observed. However, these immune alterations are often assessed by only one data type and small markers panels. Here, we used a transdiagnostic approach and combined data from two cohorts to define subgroups of depression symptoms across the diagnostic spectrum through a large-scale multi-omics clustering approach in 237 individuals. The method incorporated age, body mass index (BMI), 43 plasma immune markers and RNA-seq data from peripheral mononuclear blood cells (PBMCs). Our initial clustering revealed four clusters, including two immune-related depression symptom clusters characterized by elevated BMI, higher depression severity and elevated levels of immune markers such as interleukin-1 receptor antagonist (IL-1RA), C-reactive protein (CRP) and C-C motif chemokine 2 (CCL2 or MCP-1). In contrast, the RNA-seq data mostly differentiated a cluster with low depression severity, enriched in brain related gene sets. This cluster was also distinguished by electrocardiography data, while structural imaging data revealed differences in ventricle volumes across the clusters. Incorporating predicted cell type proportions into the clustering resulted in three clusters, with one showing elevated immune marker concentrations. The cell type proportion and genes related to cell types were most pronounced in an intermediate depression symptoms cluster, suggesting that RNA-seq and immune markers measure different aspects of immune dysregulation. Lastly, we found a dysregulation of the SERPINF1/VEGF-A pathway that was specific to dendritic cells by integrating immune marker and RNA-seq data. This shows the advantages of combining different data modalities and highlights possible markers for further stratification research of depression symptoms.</p> <h1>Methods</h1> <p>The normalized and batch-corrected concentration of 43 immune markers from 237 subjects with stress-related mental disorders and 36 healthy controls was determined in plasma. This data was used in the initial analysis. Additionally, the same measurements are provided for 11 subjects with stress-related mental disorders used in a replication analysis.</p> <p>- blood was collected in the morning under fasted conditions and plasma stored at -80°C until further processing<br>- samples were randomized into 96 well plates<br>- immune marker concentration was measured with the Meso Scale Diagnostics V-PLEX Human Biomarker 54-Plex Kit and the MESO QuickPlex SQ 120 imager according to the manufacturer's instructions<br>- additionally, high-sensitivity C-reactive protein (Tecan Group Ltd.), cortisol (Tecan Group Ltd.), interleukin (IL)-6 (Thermo Fisher Scientific), IL-6 soluble receptor (Thermo Fisher Scientific) and IL-13 (Thermo Fisher Scientific) was measured via ELISA according to the manufacturer's instructions<br>- values below the detection limit in markers measured with ELISA were set to zero and values above the detection limit to the upper limit<br>- the data was quantile-normalized (values were ranked and mapped to the quantiles of a standard normal distribution)<br>- the normalized concentration was corrected for the biobank storage position (batch_variable) via a linear model and the residuals reported as the concentration</p> <p>The following markers were measured:<br>fibroblast growth factor 2 (FGF2 or bFGF), cortisol, C-C motif chemokine 11 (CCL11 or eotaxin), CCL26 (eotaxin-3), vascular endothelial growth factor receptor 1 (VEGFR1 or Flt-1), hsCRP, intercellular adhesion molecule (ICAM)-1, interferon (IFN)-gamma, IL-1alpha, IL-1 receptor antagonist (IL-1RA), IL-10, IL-12/IL-23p40, IL-12p70, IL-13, IL-15, IL-16, IL-17A, IL-17B, IL-2, IL-27, IL-31, IL-5, IL-6 high sensitivity (IL-6HS), IL-7, IL-8HS, C-X-C motif chemokine 10 (CXCL10 or IP-10), CCL2 (MCP-1), CCL13 (MCP-4), CCL22 (MDC), CCL3 (MIP-1alpha), CCL4 (MIP-1beta), placental growth factor (PlGF), serum amyloid A (SAA), sIL-6R, CCL17 (TARC), angiopoietin-1 receptor (Tie-2), tumor necrosis factor (TNF or TNF-alpha), lymphotoxin-alpha (LT-alpha or TNF-beta), thymic stromal lymphopoietin (TSLP), vascular cell adhesion protein 1 (VCAM-1), vascular endothelial growth factor (VEGF)-A-HS, VEGF-C, VEGF-D</p> <p>The data is provided as a tab separated file.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.