Data and Code Access — Swarbrick Lab

We proudly make all data publicly available following its publication

Processed Data access

Processed data for each study is generally available on GEO or Zenodo, or as indicated in each study below. Please contact j.reeves(at)garvan.org.au if clarification is required.

scRNA-seq data is generally available from the Broad Institute's Single Cell Portal (https://singlecell.broadinstitute.org/single_cell) together with relevant meta data and, in some cases, multi-modal data such as CITE-seq.

Please use GitHub "issues" to raise questions about data files.

Article access here
1. Single-cell RNA-Seq
a. Raw data: EGA.
b. Processed data: From 26 early breast cancers. Data can be explored in a web browser or downloaded for further analysis, without restriction access here or at CellXGene.
2. Bulk RNA-Seq
a. Raw data:
b. Processed data: access here
3. Spatial
a. Images: Down-sampled images on Zenodo, raw images available on request
b. Raw data: On request (only for samples generated in-house)
c. Processed data: Zenodo
Article access here
1. Single-Cell RNA-Seq
a. Raw data: EGA. See section below for details on how to access raw data
b. Processed data: access here
Article access here
1. Single-Cell RNA-Seq:
a. Raw data: EGA.
b. Processed data: From 5 breast cancer cases. Data can be explored in a web browser or downloaded for further analysis, without restriction access here
Article access here
a. All raw data, intermediary files and resulting analysis files can be accessed here
b. The remaining data were available within the manuscript, supplementary information or source data file. Mm10 (GRCm38.p4) reference genome was used for alignment and can be accessed here. Source data are provided with this paper.
Article access here
All data analysed in this study are included in this article and its supplementary information files. The raw sequencing data supporting these findings are available at European Genome Archive (accession number EGAS00001006285) or through this link.

Code Availability

Code for lab publications are hosted on GitHub. Click the icon below to access.

These repositories also include annotations and other meta data. Please use GitHub "issues" to raise questions about code or data files referred to in the code.

For additional queries regarding data access, please contact John Reeves (j.reeves(at)garvan.org.au)

We proudly make all data publicly available following its publication

Wu, S.Z., Al-Eryani, G., Roden, D.L. et al. A single-cell and spatially resolved atlas of human breast cancers. Nat Genet 53, 1334–1347 (2021)

Wu, S.Z., Roden, D.L., Al-Eryani, G. et al. Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis. Genome Med 13, 81 (2021)

Wu, Sunny Z., et al. "Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer." The EMBO Journal 39.19 (2020)

Baldwin, Louise A., et al. "DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and immunotherapy response." Nature Communications 13.1 (2022)

Deng, Niantao, et al. "Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models." Breast Cancer Research 24.1 (2022)