Deposition

In situ cryo-electron tomography of NIH/3T3 mouse fibroblast nuclei

Deposition ID:CZCDP-10364

Release Date: 2026-08-31

Last Modified: 2026-08-31

key visualization for In situ cryo-electron tomography of NIH/3T3 mouse fibroblast nuclei

Photo Caption: Central slab of 4 representative tomograms with selected sets of annotations.

Deposition Overview

Cryo-electron tomograms of cryo-FIB-milled lamellae through intact, plunge-frozen NIH/3T3 mouse fibroblasts, collected across three acquisition sessions and targeting the nucleus and nuclear periphery. The tomograms resolve the nuclear envelope, ribosomes and densely packed native chromatin, and supported the determination of in-cell nucleosome structure and the mapping of higher-order nucleosome interaction networks.

Authors

Deposition Data

Annotations:228

Tomograms:456

Publications

DOI:10.1073/pnas.2426449122
DOI:10.1101/2024.12.01.626131

Related Databases

EMDB ID:EMD-53275
EMDB ID:EMD-49929

Methods Summary

Annotations	Method Type	Method Details	Method Links
114	Automated	A mesh marking the valid sample region of each lamella. A sample/vacuum boundary was predicted with octopi on a downsampled reconstruction, and a spline slab was fitted to that boundary and intersected with the tomogram's valid-area box to give the enclosing surface.	Source Code:copick +2 more
114	Automated	Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt	Source Code:copick +4 more

Deposited Data

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Data Contents

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FramesAvailable

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228 of 228 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
101sample Annotation ID: AN-182040	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L8_ts_002
100membrane Annotation ID: AN-182039	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L8_ts_002
101sample Annotation ID: AN-182038	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_007
100membrane Annotation ID: AN-182037	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_007
101sample Annotation ID: AN-182036	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_003
100membrane Annotation ID: AN-182035	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_003
101sample Annotation ID: AN-182034	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_002
100membrane Annotation ID: AN-182033	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L7_ts_002
101sample Annotation ID: AN-182032	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L6_ts_006
100membrane Annotation ID: AN-182031	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L6_ts_006
101sample Annotation ID: AN-182030	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L6_ts_002
100membrane Annotation ID: AN-182029	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L6_ts_002
101sample Annotation ID: AN-182028	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L5_ts_003
100membrane Annotation ID: AN-182027	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L5_ts_003
101sample Annotation ID: AN-182026	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L1_ts_003
100membrane Annotation ID: AN-182025	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L1_ts_003
101sample Annotation ID: AN-182024	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L1_ts_002
100membrane Annotation ID: AN-182023	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L1_ts_002
101sample Annotation ID: AN-182022	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L10_ts_010
100membrane Annotation ID: AN-182021	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 3)Run: L10_ts_010