EMPIAR-12104 - Cryo-electron tomography data acquired on S. cerevisiae (BY4741) cryo-FIB lamellae [multiple data sets in TIFF and MRC formats]

EMPIAR-12104

Cryo-electron tomography data acquired on S. cerevisiae (BY4741) cryo-FIB lamellae [multiple data sets in TIFF and MRC formats]

Publication:

Polysome collapse and RNA condensation fluidize the cytoplasm

Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ

Molecular cell 84 (2024) 2698-2716.e9

PMID: 39059370

DOI: 10.1016/j.molcel.2024.06.024

Related EMDB entry:

EMD-50415 EMD-50409

Deposited:

2024-05-25

Released:

2025-02-04

Last modified:

2025-02-04

Imageset size:

165.38 GB

Imageset DOI:

10.6019/EMPIAR-12104

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
reconstructed volumes
tilt series

Image Sets

1. Raw unaligned multi-frame micrographs for each tilt in 4 tilt-series on native S. cerevisiae cryo-FIB lamellae

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

203

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, None)

Details:

Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using AreTomo. Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017. Original metadata files (mdocs_ori) and the count ref file (dm4 file) are provided in the frames folder.

Files:

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2. Reconstructed cryo-electron tomograms acquired on native S. cerevisiae cryo-FIB lamellae

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Tomograms (4-times binned reconstructions, original unbinned pixel size 3.425Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder). Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017. For each of the 4 tomograms, cleaned particle lists are provided in the labels folder. Ribosome particle coordinates (star files) are provided in the corresponding particle_lists folder.

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.

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3. Tilt series stacks and metadata of cryo-electron tomograms acquired on native S. cerevisae cryo-FIB lamellae

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

Tilt series stacks (st files from Warp) from aligned frame stacks (in frames folder), tilt series alignment files (xf files) and acquisition metadata files modified to exclude bad tilts (in mdocs_modified) required to reconstruct tomograms (in tomograms folder). Naming for tomograms of control cells: TS_006, TS_007, TS_008, TS_017.

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)

4. Raw unaligned multi-frame micrographs for each tilt in 10 tilt-series acquired on S. cerevisiae cryo-FIB lamellae under acute glucose starvation

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

565

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.425, 3.425)

Details:

Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using AreTomo. Naming for tomograms of cells under glucose starvation: TS_001, TS_002, TS_003, TS_004, TS_007, TS_008, TS_010, TS_014, TS_017, TS_018. Original metadata files (mdocs_ori) provided in the frames folder.

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)

5. Reconstructed cryo-electron tomograms acquired on S. cerevisiae cryo-FIB lamellae under acute glucose starvation

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Tomograms (4-times binned reconstructions, original unbinned pixel size 3.425Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder). Naming for tomograms of cells under glucose starvation: TS_001, TS_002, TS_003, TS_004, TS_007, TS_008, TS_010, TS_014, TS_017, TS_018. For each of the 10 tomograms, cleaned particle lists are provided in the labels folder. Ribosome particle coordinates (starfiles) are provided in the corresponding particle_lists folder.

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)

6. Tilt series stacks and metadata of cryo-electron tomograms acquired on S. cerevisae cryo-FIB lamellae under acute glucose starvation

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

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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