Last updated: 2022-04-26

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Knit directory: diamantopoulou-ctc-dynamics/

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Publication

Diamantopoulou, Z., Castro-Giner, F., Schwab F.D., Foerster C., Saini, M., Budinjas, S., Strittmatter, K., Krol, I., Seifert, B., Heinzelmann-Schwarz, V., Kurzeder, C., Rochlitz, C., Vetter, M., Weber, W.P., & Aceto N. The metastatic spread of breast cancer is accomplished during sleep time. (2022)

Abstract

We isolated live circulating tumor cells (CTCs) from a breast cancer patient (number of CTCs = 36) and two breast cancer xenografts, NSG-CDX-BR16 (number of CTCs = 138) and NSG-LM2 (number of CTCs = 108) at different time points. Isolated CTCs were categorized into three different types : single CTC, CTC clusters and CTC-white blood cells (CTC-WBC) clusters. Amplified cDNA was prepared according to the Smart-seq2 protocol. Libraries were prepared using with Nextera XT (Illumina) and sequenced on Illumina NextSeq500 instrument in 75-bp single-read mode.

Data pre-processing

Raw data is available at Gene Expression Omnibus (GEO, NCBI; accession number GSE180097). Data processing is computationally expensive and is not covered in this repository. We provide description of the data pre-processing workflow together with software version in the original publication. Processed data, large result files, additional functions, references and metadata are were archived at https://doi.org/10.5281/zenodo.6358987 .

Data and code availability

To reproduce our analysis, first clone source code from the GitHub repository

git clone https://github.com/TheAcetoLab/diamantopoulou-ctc-dynamics.git

Next, download processed data deposited in Zenodo into the cloned project folder ./data directory and untar the files.

for file in *.tar.gz; do tar xzvf "${file}" && rm "${file}"; done

Reproducibility

The results form our analyses are listed below in webpage format. They were generated from R Markdown documents deposited in the GitHub repository. The workflow of the analysis was created using the workflowr R package and can be reproduced in its totality using workflowr wflow_build command after the installation of the proper R-packages. Session info, including R and package versions, was automatically included at the end of each analysis file.

Some files containing results from differential expression or gene-set enrichment analyses were deposited in Zenodo. In order to generate those files again change the option eval = FALSE to eval = TRUE in the specific code chunk from the R Markdown file.