EMPIAR-10806 - electron cryo-tomograms of axons from human cerebral organoids, expressing membrane-targeted GFP [multiple data sets in MRC and MRCS formats]

EMPIAR-10806

electron cryo-tomograms of axons from human cerebral organoids, expressing membrane-targeted GFP [multiple data sets in MRC and MRCS formats]

Publication:

Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids

Hoffmann P, Giandomenico S, Ganeva I, Wozny M, Sutcliffe M, Lancaster M, Kukulski W

eLife 10 (2021)

DOI: 10.7554/eLife.70269

Related EMDB entry:

EMD-13195

Deposited:

2021-07-13

Released:

2021-11-01

Last modified:

2021-11-01

Imageset size:

181.43 GB

Imageset DOI:

10.6019/EMPIAR-10806

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
micrographs - multiframe

Image Sets

1. reconstructed electron tomographic volumes of axons from human cerebral organoids expressing membrane-targeted GFP

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1920, 1854)

Pixel type:

SIGNED BYTE

Pixel spacing:

(None, None)

Details:

Tomograms were reconstructed with IMOD using back projection with a SIRT-like filter from stacks aligned by patch tracking, binning 2. Pixel sizes are 7.1 or 7.4 Å (check header).

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. raw image frames of tilt series acquired on axons from human cerebral organoids expressing membrane-targeted GFP

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.5, 3.5)

Details:

22 folders, each corresponding to one tilt series and containing raw image frames as well as metadata in an .mdoc file. Image frames are not aligned. Image files contained in folders named starting with g4 are gain-corrected .mrcs files. Image files contained in folders named starting with g7 and g9 are not gain-corrected .tiff files. Two additional folders contain the respective gain reference and defect files. Tilt images in folders starting with g7 were acquired as 3 frames per image, all other tilt images were acquired as 4 frames per image. Pixel sizes are 3.5 Å for images in folders starting with g4, and 3.7 Å for all other images.

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

[2024-11-20]

224 new PDB entries have been released on 2024-11-20.

[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