Source data are included for Figures 1,3,4,5,6. of macrophage and erythroid markers and Piperidolate hydrochloride their expression levels in each cell type. elife-61070-fig1-data3.xlsx (11K) GUID:?9637932E-E4F8-478D-8894-0769BD85B4FD Physique 1source data 4: Log2 FPKM values of all expressed genes in the cell types shown in Physique 1. elife-61070-fig1-data4.csv.zip (517K) GUID:?7D44DB26-F784-486D-A310-7D66578A9201 Physique 1figure supplement 1source data 1: Quantification of cells isolated by FACS sorting F4/80+ macrophages from E13.5 fetal?liver after cytospin. elife-61070-fig1-figsupp1-data1.csv.zip (277 bytes) GUID:?611CBA7D-033A-4274-954E-28E2A088E280 Physique 3source data 1: Differential expression test results obtained from DESeq2 using the RNA-Seq data from EKLF+/+ and EKLF-/- fetal liver?F4/80+?macrophages. elife-61070-fig3-data1.csv.zip (136K) GUID:?09604F4A-07CF-4DAC-A695-9CC8F5969C00 Figure 4source data 1: Coordinates of principal components 1 and 2 corresponding to each replicate of EKLF/GFP+ and EKLF/GFP- RNA-Seq data. elife-61070-fig4-data1.csv.zip (393 bytes) GUID:?89FCA806-3DF5-4B62-B4B4-0684F4189161 Physique 4source data 2: Differential gene expression results obtained using DESeq2 from your EKLF/GFP RNA-Seq dataset. elife-61070-fig4-data2.csv.zip (969K) GUID:?54CAB006-775B-4FE8-930D-5BA07F7CFF59 Figure 4figure supplement 1source data 1: Scaled Z-scores of FPKM values of the top 10,000 highly Piperidolate hydrochloride expressed genes in the EKLF/GFP+ F4/80+ RNA-Seq dataset. elife-61070-fig4-figsupp1-data1.csv.zip (280K) GUID:?A4E6BFB5-981D-4D8F-95EC-DEF727FEC683 Figure 5source data 1: Expression values of differentially expressed genes in EKLF-/-?cells vs WT?cells compared with their expression in the EKLF/GFP+ dataset. elife-61070-fig5-data1.csv.zip (42K) GUID:?66DAAECA-90EE-4502-988A-325C446BA057 Figure 5source data 2: FASTA sequences of the promoters of EKLF-dependent genes. elife-61070-fig5-data2.fa.zip (51K) GUID:?3F0E36D6-1717-4D0F-AB54-BFF31951F64A Physique 5source data 3: FASTA sequences of the promoters of all genes not included in the EKLF-dependent gene set. elife-61070-fig5-data3.fa.zip (2.5M) GUID:?E115567D-F6F8-43DF-AC53-2C4ED706E490 Figure 5figure product 1source data 1: Expression values of EKLF-dependent genes. elife-61070-fig5-figsupp1-data1.csv.zip (8.3K) GUID:?443C4B24-2D55-4532-B2C5-DD254619AF39 Physique 5figure supplement 2source data 1: Expression values of signature genes from Physique 1E that are significantly enriched in EKLF/GFP+?cells. elife-61070-fig5-figsupp2-data1.csv.zip (650 bytes) GUID:?DE62476E-8735-4510-B962-3C646D43DD5C Physique 5figure supplement 2source data 2: Expression of signature genes from Physique 1E that are significantly downregulated in EKLF-/-?cells compared to WT. elife-61070-fig5-figsupp2-data2.csv.zip (1.1K) GUID:?D2DDE413-5FF8-4ECD-87D5-72A1ED7046A0 Figure 6source data 1: Differentially expressed genes associated with each cluster of the single-cell RNA-Seq dataset. elife-61070-fig6-data1.csv.zip (248K) GUID:?944C929B-64AF-40D8-979C-83544A0E3F53 Supplementary file 1: Revigo analysis of the functions of fetal liver F4/80+ signature genes. elife-61070-supp1.xlsx (11K) GUID:?540FE4F9-B31D-4155-A4E7-FDE2455CEC72 Supplementary file 2: DESeq2 results of significantly downregulated genes in EKLF-/-?cells. elife-61070-supp2.xlsx (151K) GUID:?C3569643-A73F-4794-A3D4-4D4ECF580A26 Supplementary file 3: DESeq2 results of significantly enriched genes in EKLF/GFP+?cells. elife-61070-supp3.xlsx (266K) GUID:?5063AF38-B5B7-4618-BAF0-4A4783CCA7C8 Supplementary file 4: Complete results of Centrimo analysis of the promoters of EKLF-dependent genes in F4/80+ macrophages. elife-61070-supp4.xlsx (28K) GUID:?C8E462F5-D548-44EB-B51F-747B29B36B9F Supplementary file 5: GO analysis of the top 100 differentially enriched genes in clusters 0, 1, 2, and 3 of the single-cell sequencing data. elife-61070-supp5.xlsx (17K) GUID:?8BE62014-DA9C-4999-81DB-AB7BABB7A461 Supplementary file 6: GO analysis of the top 100 differentially enriched genes in clusters 4, 5, 7, and 8 of the single-cell sequencing data. elife-61070-supp6.xlsx (12K) GUID:?C16DCB94-0EF2-4B40-B559-4B51DE348F93 Transparent reporting form. elife-61070-transrepform.docx (247K) GUID:?0C7C44B4-3EB0-4A80-9D0D-A3589F66BB08 Data Availability StatementData were deposited in GEO, accession number: GSE156153. Source data are included for Figures 1,3,4,5,6. R and Python code is usually deposited in https://github.com/mkaustav84/biekerlab-f480_macrophage; copy archived at https://archive.softwareheritage.org/swh:1:rev:907b15e74d998c5dd2a3106bce30af812c2b60b4/. The following dataset was generated: Mukherjee K, Planutis A, Xue L, Bieker JJ. 2021. EKLF/Klf1 expression specifies a unique macrophage subset during mouse erythropoiesis. NCBI Gene Expression Omnibus. GSE156153 The following previously published dataset was used: Lavin Y, Winter D, Blecher-Gonen R, David E, Keren-Shaul H, Merad M, Jung Piperidolate hydrochloride S, Amit I. 2014. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. NCBI Gene Expression Omnibus. GSE63340 Abstract Erythroblastic islands are a specialized niche that contain a central macrophage surrounded by erythroid cells at numerous stages of maturation. However, identifying the precise genetic and transcriptional control mechanisms in the island macrophage remains hard due to macrophage heterogeneity. Using unbiased global sequencing and directed genetic approaches focused on early mammalian development, we SIGLEC1 find that fetal liver macrophages exhibit a unique expression signature that differentiates them from erythroid and adult macrophage cells. The importance of erythroid Krppel-like factor (EKLF)/KLF1 in this identity is shown by expression analyses in EKLF-/-.
