Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Application: bulk placenta gene expression dataset and CIBERSORTx deconvolution

KC Kyle A. Campbell
JC Justin A. Colacino
MP Muraly Puttabyatappa
JD John F. Dou
EE Elana R. Elkin
SH Saher S. Hammoud
SD Steven E. Domino
DD Dana C. Dolinoy
JG Jaclyn M. Goodrich
RL Rita Loch-Caruso
VP Vasantha Padmanabhan
KB Kelly M. Bakulski
ask Ask a question
Favorite

Bulk placental tissue microarray gene expression (previously batch-corrected and normalized) from eight preeclampsia case–control studies was downloaded from the NCBI Gene Expression Omnibus (accession number GSE75010) for deconvolution33. We used the CIBERSORTx Docker container (accessed December 7, 2021) to create a signature gene expression matrix for deconvolution from the counts of the single-cell RNA-sequencing data with the following default parameters: differential expression q value < 0.01, no minimum gene expression cutoff, and a 300 gene feature selection floor and a 500 gene feature selection ceiling99. We used the signature matrix to estimate constituent cell type proportions in GSE75010 using CIBERSORTx with cross-platform S-mode batch correction and 50 permutations to evaluate imputation goodness-of-fit.

Copyright and License information: The Author(s) ©2023
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A