Transcriptomic Profiling of Splenic Red Pulp Macrophages in Response to Dietary Iron Deficiency

This study investigates how dietary iron deficiency affects the transcriptional profile of spleen-derived red pulp macrophages (RPMs) in mice. Female C57BL/6J mice were divided into two groups: Iron-deficient (ID) group: fed a low-iron diet (<5 ppm Fe) from 4 to 9 weeks of age. Iron-balanced (IB) group: maintained on a standard iron-sufficient diet (200 ppm Fe) over the same period. At 9 weeks of age, mice were sacrificed, and spleens were harvested. RPMs were FACS-sorted using F4/80 and TREML4 markers, approx. 100 000 RPMs were sorted/sample. Sorting was performed to TRIzol, and RNA was isolated using Direct-zol columns. For all samples RIN was at least 7. Sequencing was conducted on the Illumina NextSeq 500 platform at the EMBL Genomics Core Facility (Heidelberg, Germany) using 75 bp single-end reads. The dataset consists of 8 samples: 4 from iron-deficient mice (S1_DEF to S4_DEF) and 4 from control mice (S5_BAL to S8_BAL). This RNA-seq dataset enables comparison of gene expression changes in red pulp macrophages under conditions of iron deficiency, contributing to our understanding of iron homeostasis and macrophage adaptation. The dataset was obtained with the support of the National Science Centre Sonata Bis grant (UMO-2020/38/E/NZ4/00511).