EMPIAR-11063 - Cryo-EM data and 2DTM results of entire sections of differentiated ER-HoxB8 cells [multiple data sets in TIFF and MRC formats]

EMPIAR-11063

Cryo-EM data and 2DTM results of entire sections of differentiated ER-HoxB8 cells [multiple data sets in TIFF and MRC formats]

Publication:

Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections

Elferich J, Schiroli G, Scadden DT, Grigorieff N

eLife 11 (2022)

PMID: 36382886

DOI: 10.7554/elife.80980

Related EMDB entry:

Deposited:

2022-06-01

Released:

2023-02-01

Last modified:

2023-02-13

Imageset size:

1.26 TB

Imageset DOI:

10.6019/EMPIAR-11063

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
stitched maps

Image Sets

1. Unaligned multi-frame micrographs of ER-HoxB8 lamella

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4647

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.6667, 0.6667)

Details:

For each lamella a cisTEM project is provided. Raw movies are under /data/???_Lamella?/Assets/Movies/*.tif. The SerialEM metadata and gain references are in the same folder.

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. Aligned micrographs of ER-HoxB8 lamella

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

4647

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.5, 1.5)

Details:

For each lamella a cisTEM project is provided. Aligned micrographs are under /data/???_Lamella?/Assets/Images/*_0.mrc. Since each micrographs is cropped to the beam, the dimensions are different for every micrograph. A mask that indicated the illuminated area is provided for each micropgraph under *_mask.mrc

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. 2DTM results of micrographs of ER-HoxB8 lamella

Category:

stitched maps

Image format:

MRC

No. of images or tilt series:

4647

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.5, 1.5)

Details:

2DTM results can be found in the /data/???_Lamella?/Assets/TemplateMatching/ folder. For each image there are several mrc files that encode SNR, defocus, psi, theta, and phi at each pixel. To reduce file size pixels where the scaled SNR was below 6.5 (substantially below detection threshold) were set to 0 and the files were compressed using zstd.

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. Stitched maps of lamellae imaged using DeCo-LACE - Overview

Category:

stitched maps

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(75.0, 75.0)

Details:

Stitched maps of lamellae made from individual DeCo-LACE exposures. The files ???_Lamella?_montage_t2_tophat.tif were resampled to 75A pixel size and the exposure was flattened using a top-hat filter.

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. Stitched maps of lamellae imaged using DeCo-LACE - High resolution

Category:

stitched maps

Image format:

TIFF

No. of images or tilt series:

Image size:

(14010, 17082)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(7.5, 7.5)

Details:

Stitched maps of lamellae made from individual DeCo-LACE exposures. The files ???_Lamella?_montage_t2_highres.tif were resampled to 7.5A pixel size.

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

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

See all citations

Protein Data Bank Japan News

[2024-11-27]

374 new PDB entries have been released on 2024-11-27.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024