[3dem] New Large-Scale CryoET Dataset: ~13, 700 Tilt Series of Affinity-Captured Lysosomes

[Utz Ermel]

Dear colleagues,

We are pleased to announce the release of a large-scale cryo-electron
tomography dataset on the CryoET Data Portal. This deposition comprises
13,694 tilt series yielding 27,388 tomograms and 25,210 semantic
segmentations of organelles affinity-captured from HEK293T cell lysates.

The dataset features lysosomes, late endosomes, and microsomes isolated
using EM grids functionalized with anti-GFP nanobodies to capture GFP-LAMP1
or GFP-TMEM192-tagged organelles. Four physiological states are
represented: untreated cells, bafilomycin A1-treated cells, amino
acid-starved cells, and amino acid-starved cells with amino acid
reintroduction. All data were acquired on a Titan Krios G4 with a Falcon 4i
detector and Selectris X energy filter at 1.54 Å pixel spacing, processed
using the AreTomo3 pipeline, and include organelle segmentations generated
using SABER (https://urldefense.com/v3/__https://virtualcellmodels.cziscience.com/model/saber__;!!Mih3wA!HhBTn1Qc7aYm0ksYfTPAg6NDdZHe4WkgDWSZ_jofZ9DAMnFw3Kw_Pqx0ceM7RAU5CHmvzQRaEizOlaSfJira$ ) and
Membrain-Seg (https://urldefense.com/v3/__https://github.com/CellArchLab/MemBrain-v2__;!!Mih3wA!HhBTn1Qc7aYm0ksYfTPAg6NDdZHe4WkgDWSZ_jofZ9DAMnFw3Kw_Pqx0ceM7RAU5CHmvzQRaEizOlcD0oITm$ ).

The complete dataset, including raw movies, alignments, tomograms, and
annotations, is openly available for download and reuse at:
https://urldefense.com/v3/__https://cryoetdataportal.czscience.com/depositions/10318__;!!Mih3wA!HhBTn1Qc7aYm0ksYfTPAg6NDdZHe4WkgDWSZ_jofZ9DAMnFw3Kw_Pqx0ceM7RAU5CHmvzQRaEizOlbJbPCnx$ 

We hope this resource will be valuable for methods development, machine
learning applications, and biological discovery.

Best regards,
Dynamic Structural Biology Team @ Biohub
-- 

Utz Heinrich Ermel

[image: image.png]

utz.ermel at biohub.org <utz.ermel at czbiohub.org>

https://urldefense.com/v3/__http://www.biohub.org__;!!Mih3wA!HhBTn1Qc7aYm0ksYfTPAg6NDdZHe4WkgDWSZ_jofZ9DAMnFw3Kw_Pqx0ceM7RAU5CHmvzQRaEizOlXoMyPil$ 
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