cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/6rpek-ac710
title: Legionella_JV9246

description: Legionella_JV9246: DotF-sfGFP fusion to the wild-type gene on the chromosome (thyA) and ΔdotO.
description: <strong>Tilt Series Date:</strong> 2019-05-28</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected by Debnath Ghosal and Yuxi Liu.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-28-39/rawdata/</p>JV9246_area1_tomo0068.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-28-39/rawdata/JV9246_area1_tomo0068.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9246_area1_tomo0068_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-28-39/3dimage_103456/JV9246_area1_tomo0068_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.65myp3
title: Occurrence Download

description: A dataset containing 13262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Eucalyptus albens"
 ]
}

 The dataset includes 13262 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048122-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/zb3cx-ypb21
title: bio13-4_lam4_ts5

description: IT 1s
description: <strong>Tilt Series Date:</strong> 2019-02-21</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Gluconacetobacter hansenii</p>
<strong>Strain:</strong> ATCC 23769</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 60.0°), step: 1°, constant angular increment, dosage: 58.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Little Petri dishes were inoculateed with 1mL of Ghansenii cultures with a gold grid layed at the bottom. Incubated at 30C for 6 hours</p>
<strong>Sample Preparation:</strong> BC 0% 22C - BT5s BF15 DT2s +1uL on each side (Frontblotted more than it backblotted) - Thick biofilm</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-02-21-3/rawdata/</p>lam4_ts5_orig.st,  Tilt Series (Pixel Size 0.54 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-02-21-3/rawdata/lam4_ts5_orig.st"
        > <i class="download icon"></i> Download </a></p>

        lam4_ts5.rec,  Reconstruction (Pixel Size 2.164 nm), 139.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-02-21-3/3dimage_101739/lam4_ts5.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.uddmwm
title: Occurrence Download

description: A dataset containing 2317 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galinsoga quadriradiata",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2317 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048124-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/6rn3w-gwk84
title: Pseudomonas aeruginoas_JT2944

description: Raw data files of Pseudomonas aeruginoas_JT2944
description: <strong>Tilt Series Date:</strong> 2018-08-16</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> Cells produced by Jonida Toska from Melakanos lab.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown overnight in LB at 37 C.</p>
<strong>Sample Preparation:</strong> Cells from overnight culture were added to thick carbon grids and blotted using the vitrobot in BI. Blot force 6, blot time 3 s, drain time 1s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-16-73/rawdata/</p>Pseudomonas_JT2944Tilt418.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-16-73/rawdata/Pseudomonas_JT2944Tilt418.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_JT2944Tilt418_full.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-16-73/3dimage_94496/Pseudomonas_JT2944Tilt418_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/449e6-vwv92
title: Ecoli_EPEC_8609

description: EPEC cells strain 8609 (has the conjugation pilus, the bundle-forming pilus but lack the core  .  complex). The aim is to see whether these cells make similar membrane tubes as to those .  observed in EPEC 8612
description: <strong>Tilt Series Date:</strong> 2020-02-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8609, EPEC ΔLEE ΔflhBA ΔfliOPQR ΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 115.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Samples prepared with Ritesh and Amit (from Ilan Rosenshine and Sigal ben Yehuda labs at the . Hebrew university).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were prepared as EPEC 8612 (see these tomograms).</p>
<strong>Sample Preparation:</strong> Similar to what is described for EPEC 8612 tomograms.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-25-19/rawdata/</p>EPEC_8609_012_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-25-19/rawdata/EPEC_8609_012_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8609_012_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-25-19/3dimage_111699/EPEC_8609_012_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/acywn-2ws67
title: Pseudomonas aeruinosa

description: This is from the transposon mutant library of Pseudomonas aeruginosa PAO1. The aim is to check for the presence of PL sub complexes in the absence of FliF protein.
description: <strong>Tilt Series Date:</strong> 2018-10-01</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -9.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Serial EM</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newmann lab (Shannon Park)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown overnight at 37 C in LB with 100 ug/ml gentamicin</p>
<strong>Sample Preparation:</strong> Samples from the overnight culture were used to prepare the grids.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-10-01-32/rawdata/</p>Test_Pseudomonas_dfliF_32_fix.mrc,  Tilt Series (Pixel Size 0.37 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-10-01-32/rawdata/Test_Pseudomonas_dfliF_32_fix.mrc"
        > <i class="download icon"></i> Download </a></p>

        Test_Pseudomonas_dfliF_32_fix_full.rec,  Reconstruction (Pixel Size 1.48 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-10-01-32/3dimage_97336/Test_Pseudomonas_dfliF_32_fix_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.neersf
title: Occurrence Download

description: A dataset containing 291000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos, Arthurdendyus triangulatus, Cabomba caroliniana, Callosciurus finlaysonii, Cherax destructor, Corvus splendens, Crassula helmsii, Elodea densa, Eriocheir sinensis, Erythranthe guttata, Faxonius immunis, Faxonius juvenilis, Faxonius rusticus, Faxonius virilis, Gambusia affinis, Heracleum mantegazzianum, Heracleum persicum, Heracleum pubescens, Houttuynia cordata, , Impatiens glandulifera, Koenigia polystachya, Lagarosiphon major, Lepomis gibbosus, Limnoperna fortunei, Ludwigia grandiflora, Ludwigia peploides, Lysichiton americanus, Morone americana, Muntiacus reevesi, Myriophyllum aquaticum, Myriophyllum heterophyllum, Pacifastacus leniusculus, Petasites japonicus, Pontederia cordata, Procambarus acutus, Procambarus clarkii, Procambarus virginalis, Pseudorasbora parva, Pycnonotus cafer, Saururus cernuus, Sciurus carolinensis, Sciurus niger, Solenopsis invicta, Solenopsis richteri, Threskiornis aethiopicus, Vespa velutina, Zizania latifolia)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 291000 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048078-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/sh0f9-5cs38
title: Xanthomonas WT

description: Xac WT pBRaφ pBRR
description: <strong>Tilt Series Date:</strong> 2019-12-06</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 19500x. </p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Carvalho and Farah lab sent the strain. Debnath Ghosal collected data</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in 2xTY with apt antibiotics, freeze cells next day after about 14 hour when they are in stationary phase.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 5 sec. ** Use 7 sec for next sessions.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-06-9/rawdata/</p>Xac_No1_TS42.mrc,  Tilt Series (Pixel Size 0.353 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-06-9/rawdata/Xac_No1_TS42.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_No1_TS42_full.rec,  Reconstruction (Pixel Size 1.412 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-06-9/3dimage_112343/Xac_No1_TS42_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4awzg-0ej62
title: Legionella_delta-lspGHIJK

description: Legionella pneumophila Philadelphia-1_Lp02. Lacks all the T2SS major and minor pseudopilins.
description: <strong>Tilt Series Date:</strong> 2019-05-18</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-45.0°, 45.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent by Nicholas Cianciotto, Northwestern University. Data collected and processed by Debnath Ghosal.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain (2x concentrated culture, OD~4.8); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-18-30/rawdata/</p>DG8_201905180070.mrc,  Tilt Series (Pixel Size 0.26 nm), 882.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-18-30/rawdata/DG8_201905180070.mrc"
        > <i class="download icon"></i> Download </a></p>

        DG8_201905180070_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-18-30/3dimage_102945/DG8_201905180070_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.26208/6mnw-yk31
title: Predicting energetic and entropic driving forces with coarse-grained models

description: Low resolution coarse-grained (CG) models provide exceptional computational efficiency for simulating soft materials. Consequently, many studies employ CG models to determine free energy surfaces along order parameters or reaction coordinates of interest. However, because CG models average over atomic details, it is challenging to determine the energetic and entropic contributions to the resulting free energy surfaces. In this work, we present a rigorous and predictive CG framework for computing these energetic and entropic driving forces based upon simulations at a single temperature. This dual approach employs distinct variational principles to independently approximate the exact CG interaction potential, W(R), and its energetic component, E_W(R). This dual approach determines the free energy surface, a_φ(x), along an order parameter, φ(x), via simulations with W(R). The dual approach then determines the energetic driving force, u_φ(x), by evaluating E_W(R) for the sampled configurations. The entropic driving force, s_φ(x), is indirectly inferred, s_φ(x) = (u_φ(x)−a_φ(x)) /T. Importantly, this entropic contribution reflects both the CG configuration distribution and the atomic details that have been eliminated from the CG model. We demonstrate that the dual approach reasonably describes the energetic and entropic driving forces between a pair of nonpolar solutes in a polar solvent. In contrast, naıvely estimating energetics with the CG interaction potential provides a qualitatively incorrect description for these driving forces.
DOI: 10.22002/xrr0g-z2875
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-368/rawdata/</p>JV9298_PD-1-3_344.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-368/rawdata/JV9298_PD-1-3_344.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_344_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/r39c6-nm574
title: Legionella_delta-lspHIJK

description: Legionella pneumophila Philadelphia-1_Lp02. Lacks all the T2SS minor pseudopilins.
description: <strong>Tilt Series Date:</strong> 2019-05-16</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-45.0°, 45.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent by Nicholas Cianciotto, Northwestern University. Data collected and processed by Debnath Ghosal.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-16-79/rawdata/</p>DG7_20190516_tomo0040.mrc,  Tilt Series (Pixel Size 0.26 nm), 882.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-16-79/rawdata/DG7_20190516_tomo0040.mrc"
        > <i class="download icon"></i> Download </a></p>

        DG7_20190516_tomo0040_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-16-79/3dimage_102795/DG7_20190516_tomo0040_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29992147
title: Expanding canonical cortical cell type markers in the era of single-cell transcriptomics

description: The manuscript "Expanding canonical cortical cell type markers in the era of single-cell transcriptomics" is an investigation into the performance of canonical cell type markers, examining their variability, expression trends across 16 unique regions (scRNA-Seq datasets) of the human cortex, particularly for 6 of the major cortical cell types. We further make use of these datasets to discover new generalizable cell type specific markers with high gene expression fidelity and minimum background expression to further the list of known canonical cell type markers. We demonstrate their performance in clustering and classifying our 488,397 nuclei dataset and further show how we can extend this to the sublayer cell types in the dorsolateral prefrontal cortex. We further provide an application to replicate our analysis and for the community to design marker sets in an evidence based manner for the human cortex.
DOI: 10.6084/m9.figshare.29992147.v1
title: Expanding canonical cortical cell type markers in the era of single-cell transcriptomics

description: The manuscript "Expanding canonical cortical cell type markers in the era of single-cell transcriptomics" is an investigation into the performance of canonical cell type markers, examining their variability, expression trends across 16 unique regions (scRNA-Seq datasets) of the human cortex, particularly for 6 of the major cortical cell types. We further make use of these datasets to discover new generalizable cell type specific markers with high gene expression fidelity and minimum background expression to further the list of known canonical cell type markers. We demonstrate their performance in clustering and classifying our 488,397 nuclei dataset and further show how we can extend this to the sublayer cell types in the dorsolateral prefrontal cortex. We further provide an application to replicate our analysis and for the community to design marker sets in an evidence based manner for the human cortex.