DATASETS

We believe strongly in open science and, to the extent feasible, release all datasets for public analysis through EMPIAR (for cryo-EM and cryo-ET raw data), Zenodo, or locally hosted for other datatypes. Some such examples are linked. PL-qMS datasets are at the bottom of this page.

Cryo-EM and Cryo-ET source data, metadata, and analysis scripts

EMPIAR-10076: Assembling Ribosomal Subunit

A highly cited "benchmarking" dataset that I collected as a post-doc and our lab has used extensively. Read more about the original work here. Download here.

ZENODO-4355284: CRYODRGN BENCHMARKING DATASETS

Simulated datasets, curated particle stacks, and trained models used in the Zhong 2021 (Nature Methods) manuscript. Download here.

ZENODO-5164127: CRYODRGN PROTOCOLS DATASETS

Simulated datasets, curated particle stacks, and trained models used in the Kinman 2022 CryoDRGN deep analysis and protocols manuscript published in Nature Protocols. Download here.

EMPIAR-11526, EMPIAR-11528-9, ZENODO-7884215: KSGA treated small ribosomal subunits

Three EMPIAR entries related to our Sun 2023 Nature Structural and Molecular Biology manuscript, where we apply cryoDRGN to understand the impact of KsgA on assembly of the small ribosomal subunit. Please also note the Zenodo depositions that include additional metadata.

EMPIAR-11349: SspB delivering an ssrA-tagged substrate to ClpXP

Raw data we collected for our Ghanbarpour 2023 PNAS manuscript describing the first structure of the SspB adapter delivering a substrate to ClpXP. Download here.

EMPIAR-11706: A substrate free ClpXP

Raw data we collected for our Ghanbarpour 2023 Nature Communications manuscript describing the structures of substrate-free ClpXP. Download here.

EMPIAR-11843, Zenodo-10076628, Zenodo-10093310: Datasets used in development and early applications of tomoDRGN

Source datasets, including extracted image series and volume series data we used to analyze EMPIAR-10499 in our Powell 2024 Nature Methods manuscript, were we describe the development and application of tomoDRGN.

EMPIAR-11983, Zenodo-10841632: Datasets and scripts used in rapid analysis of E. coli tomograms

Source datasets collected and analysis scripts applied in our Powell 2024 bioRxiv manuscript describing the rapid analysis of cryo-electron tomograms collected from E. coli that resulted in generation of a ~6Å structure within 10 days of culturing cells. Read more in the preprint here.