EMPIAR-13420 - SBF-SEM and FIB-SEM datasets and models of human macrophage and A431 cells [multiple data sets in TIFF format]

EMPIAR-13420

SBF-SEM and FIB-SEM datasets and models of human macrophage and A431 cells [multiple data sets in TIFF format]

Publication:

Nuclear envelope-associated lipid droplets are enriched in cholesteryl esters and increase during inflammatory signaling

Szkalisity Á, Vanharanta L, Saito H, Vörös C, Li S, Isomäki A, Tomberg T, Strachan C, Belevich I, Jokitalo E, Ikonen E

The EMBO journal 44 (2025) 2774-2802

PMID: 40195500

DOI: 10.1038/s44318-025-00423-2

Related EMDB entry:

Deposited:

2026-03-25

Released:

2026-06-01

Last modified:

2026-06-01

Imageset size:

37.87 GB

Imageset DOI:

10.6019/EMPIAR-13420

Experimental metadata:

Download xml json

Contains:

reconstructed volumes

Image Sets

1. Focused ion beam scanning electron microscopy dataset of a differentiated primary human macrophage treated with tumor necrosis factor alpha (TNFa) for 1 h.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

2719

Image size:

(4927, 785)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(60.0, 60.0)

Details:

Voxels: 0.006x0.006x0.012 um
Dwell time: 2us x2 line average
1.6kV, 1nA, EsB detector

Files:

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2. Focused ion beam scanning electron microscopy dataset of A primary human macrophage grown in control differentiation medium.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

2888

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(60.0, 60.0)

Details:

Voxels: 0.006x0.006x0.012 um
Dwell time: 2us x2 line average
1.6kV, 1nA, EsB detector

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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3. Serial block face scanning electron microscopy dataset of An A431 cell grown in complete medium

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

162

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(150.0, 150.0)

Details:

Voxels: 0.015x0.015x0.030 um
Dwell time: 10 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.7 mm

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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4. Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

143

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(150.0, 150.0)

Details:

Voxels: 0.015x0.015x0.030 um
Dwell time: 10 us
2.5kV, spot size 3, Pressure: 0.30 Torr, WD = 5.7 mm

Files:

This entry cannot be downloaded from PDBj.

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5. Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

154

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Voxels: 0.010x0.010x0.030 um
Dwell time: 5 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.7 mm

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

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6. Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

207

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(150.0, 150.0)

Details:

Voxels: 0.015x0.015x0.030 um
Dwell time: 8 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.64 mm

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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7. Serial block face scanning electron microscopy dataset of A primary human macrophage grown in control differentiation medium.

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

257

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Voxels: 0.010x0.010x0.030 um
Dwell time: 5 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.64 mm

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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