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ELL datasets

Here you have a descriptive list of the datasets available in ell-vault:

HPA v24

  • Description: FOV and single cell published images of HPA v24
  • Modality: Immunoflurescence
  • Contact person: Frederic Ballllosera
  • Vault location: HPA/Subcellular
  • Other location:
  • Comments: Images from the HPA subcellular resources as of version V24. Not including specialized data sets like sperm, cilia, stem cells, cell cycle.
  • Full documentation: HPASubcellularDatasetInfo.md

IRF3OPS

  • Description: Copy of pooled optical CRISPR screening images from Blainey Lab
  • Modality: Immunoflurescence; fluorescent reporter (IRF3)
  • Contact person: Noorsher Ahmed
  • Vault location: IRF3OpticalPooledScreen
  • Other location: /scratch/groups/emmalu/noor/IRF3_OPS_Blainey
  • Comments: Protein Localization DAPI, MT, ER, IRF3 (Protein) https://www.pnas.org/doi/10.1073/pnas.2210623120
  • Full documentation: TBW

JUMP1 Cell Painting

  • Description: 16 plate subset of JUMP Pilot data. Chemical and CRISPR perturbations
  • Modality: Immunofluoresence
  • Contact person: Zoe Wefers
  • Vault location: JUMP
  • Other location:
  • Comments: Cell Morphology, Perturbation screen Mitochondria, AGP, NucleoiliRNA, ER, Nucleus Also have sc crops of some plates, and CellProfiler features

Seq2Loc

COMAS

Bridge2AI

  • Description: Breast cancer cells treated with paclitaxel or vorinostat. Stem cells as well as differentiated into neurons and cardiomyocytes. HPA-style imaging.
  • Modality: Immunofluoresence
  • Contact person: Jan Hansen
  • Vault location: B2AI
  • Other location:
  • Comments: Perturbations, Differentiation, Breast cancer cells, Vorinostat, Paclitaxel, Neurons, Cardiomyocytes, KOLF2.1J, MDA-MB-468, HPA-style mapping.
  • Full documentation: Bridge2AIDatasetInfo.md

Cell cycle

  • Description: Different cell lines and tissues stained with structural and cell cycle markers. HPA-style imaging as well as other imaging modalities applied on the same samples.
  • Modality: Immunofluoresence
  • Contact person: Jan Hansen, Will Leineweber
  • Vault location: cellcycle
  • Other location:
  • Comments: Cell Morphology, Cell cycle, Cell types, 3D images, different microscopes and resolutions (10x, 20x, 40x, 63x). Channels: Nucleus, MT, GMNN, CDT1, (+ER marker for some datasets). Maximum intensity projections available for which segmentations and single-cell crops have been made. Cell crops in 3D based on 2D segmentation will be available soon. SubCell features will be available soon, too.
  • Full documentation: CellcycleDatasetInfo.md

HPA cilia

  • Description: Deep 3D image-based screen for protein localization in three different ciliated cell types. HPA-style imaging but with cilia markers. In Proteinatlas from V24 on.
  • Modality: Immunofluoresence
  • Contact person: Jan Hansen
  • Vault location: hpa_cilia
  • Other location:
  • Comments: 2000 proteins, three cell lines (hTERT/RPE1 serum starved, ASC52telo, RPTEC/TERT1), 3D confocal image stacks, channels (DNA, Protein of Interest, Cilia (ARL13B), Basal bodies (PCNT))/
  • Full documentation HPACiliaDatasetInfo.md

HPA sperm

  • Description: 3D image-based screen for protein localization in human sperm.
  • Modality: Immunofluoresence
  • Contact person: Jan Hansen
  • Vault location: hpa_sperm
  • Other location:
  • Comments: Many proteins stained in human sperm cells received from a collaborator (Timo Strünker lab, University of Münster, Germany). Markers are DNA, flagellum/axoneme (acetylated tubulin), mitochondria. One protein of interest at a time is stained.
  • Full documentation HPASpermDatasetInfo.md

Pfizer Macrophages

  • Description:
  • Modality:
  • Contact person:
  • Vault location:
  • Other location:
  • Comments:
  • Full documentation:

Danaher Beacon

  • Description:
  • Modality:
  • Contact person:
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  • Comments:
  • Full documentation:

HPA TMA

  • Description: Whole body tissue TMA from HPA Tissue Atlas stained with a multiplexed tissue imaging panel (Akoya Phenocycler Fusion)
  • Modality: Highly-multiplexed immunofluorescence
  • Contact person: Anna Martinez Casals
  • Vault location: HPA_TMA_PCF
  • Other location:
  • Comments:
  • Full documentation:

Your data set here?

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