EMPIAR-10624 - Cryo Soft X-ray data for tetraspeck correlation [multiple data sets in MRC format]

EMPIAR-10624

Cryo Soft X-ray data for tetraspeck correlation [multiple data sets in MRC format]

Publication:

Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures

Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M

Nature protocols 16 (2021) 2851-2885

PMID: 33990802

DOI: 10.1038/s41596-021-00522-4

Related EMDB entry:

Deposited:

2021-01-15

Released:

2021-02-12

Last modified:

2022-02-25

Imageset size:

6.78 GB

Imageset DOI:

10.6019/EMPIAR-10624

Experimental metadata:

Download xml json

Contains:

tilt series

Image Sets

1. Cryo soft X-ray tomography reconstruction of NIH-3T3 cells

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(984, 974)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(100.0, 100.0)

Details:

Data name :20200311_tomo04_3DS30_man.mrc
Collection date: 11/03/2020
Location: Mistral Beamline, Alba Synchrotron (Spain)
Sample: NIH-3T3 (CRL-1658)
Fluorophore: Mitotracker Red (CMXRos) exogenous administration
Fiducials: 100 nm Au Fiducial (BBI Solutions)
Support: Quantifoil on Au Finder grid (3 mm F2/2)

520 eV; 25 nm Zoneplate; 984 * 974 Pixel; 10 * 10 * 10 nm Voxel size
-65 to 65 degree rotation with steps of 1 degree (131 images).

Data is already normalized and deconvolved using the standard Mistral prep-processing pipeline
Alignment of the Raw data done using IMOD, reconstruction done using tomo3D with 30 iterations of SIRT

Files:

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2. Cryo Soft X-ray tomography of NIH-3T3 cells with Tetraspeck as correlative fiducial markers

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(984, 974)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(100.0, 100.0)

Details:

Data name :20200312_tomo23_3DS30_man.mrc
Collection date: 12/03/2020
Location: Mistral Beamline, Alba Synchrotron (Spain)
Sample: NIH-3T3 (CRL-1658)
Fluorophore: Mitotracker Red (CMXRos) exogenous administration
Fiducials: 100 nm Au Fiducial (BBI Solutions) and 200 nm Tetraspeck
Support: Quantifoil on Au Finder grid (3 mm F2/2)

520 eV; 25 nm Zoneplate; 984 * 974 Pixel; 10 * 10 * 10 nm Voxel size
-65 to 65 degree rotation with steps of 1 degree (131 images).

Data is already normalized and deconvolved using the standard Mistral prep-processing pipeline
Alignment of the Raw data done using IMOD, reconstruction done using tomo3D with 30 iterations of SIRT

Files:

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)

3. Cryo Soft X-ray tomography of Tetraspeck on Quantifoil

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(984, 974)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(100.0, 100.0)

Details:

Data name :20200311_tomo03_3DS30_man.mrc
Collection date: 11/03/2020
Location: Mistral Beamline, Alba Synchrotron (Spain)
Sample: Tetraspeck on quantifoil
Fiducials: 100 nm Au Fiducial (BBI Solutions)
Support: Quantifoil on Au Finder grid (3 mm F2/2)

520 eV; 25 nm Zoneplate; 984 * 974 Pixel; 10 * 10 * 10 nm Voxel size
-65 to 65 degree rotation with steps of 1 degree (131 images).

Data is already normalized and deconvolved using the standard Mistral prep-processing pipeline
Alignment of the Raw data done using IMOD, reconstruction done using tomo3D with 30 iterations of SIRT

Files:

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)

Browse All Files

Files:

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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