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. 2017 Jul 5;8:16067. doi: 10.1038/ncomms16067

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Copyright © 2017, The Author(s)

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/

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RNA-seq analysis was performed in triplicates from hCD2⁺ sorted B cells from CTCF^fl/fl and CTCF^fl/+ mice after 48 h stimulation in the presence of CD3/CD28 T or LPS/IL4. Differentially expressed genes (adjusted P<0.05) were subject to further analysis. (a) Number of differentially transcribed genes between CTCF^fl/fl and CTCF^fl/+ B cells stimulated LPS/IL4 (50 differentially expressed genes) or CD3/CD28 stimulation (2,229 differentially expressed genes) conditions. Red: upregulated genes; green: downregulated genes. Adjusted P<0.05. See Supplementary Data 1 and Supplementary Data 2 for complete list of genes. (b) Heatmap analysis of the 20% most differentially expressed genes between CTCF^fl/fl and CTCF^fl/+ B cells after CD3/CD28 T stimulation. Z-scores values are represented. Clustering was performed using the average linkage method based on Pearson correlation distance. Each column represents an independent replicate. (c) Overlap between genes differentially expressed in GC reaction (wild-type GC B cells versus wild-type-resting B cells, grey circle) and genes differentially expressed upon CTCF depletion in CD3/CD28 T-stimulated B cells (CTCF^fl/fl versus CTCF^fl/+ hCD2⁺ sorted B cells, red circle). (d) Two-dimension expression plot. X axis, log2 fold values of significantly changed genes upon CTCF deficiency (CTCF^fl/fl versus CTCF^fl/+, CD3/CD28-stimulated B cells). Y axis, log2 fold values of significantly changed genes in GC versus resting B cells. Percentage of genes in each quadrant is shown. (e) KEGG pathway enrichment analysis of genes differentially expressed in CTCF^fl/fl versus CTCF^fl/+ CD3/CD28-stimulated B cells. (f) Log fold change (LogFC) representation of the genes included in the KEGG pathways analysed in (e). Black, GC versus resting B cells fold change. Orange, CTCF^fl/fl versus CTCF^fl/+ CD3/CD28 T-stimulated splenic B cells fold change.