Yu 2015, NFAT1 and H3K4Me3 in D1 dendritic cells


ChIP-seq characterization of NFATc2 (NFAT1) regulatory targets and H3K4me3 landscape in mouse spleen dendritic D1 cells. NFAT1 was isolated from cells stably expressing NFAT1-V5 using a mouse anti-V5 antibody. Isolated DNA fragments were sequenced using Illumina HiSeq 2000 technology. D1 cells were cultured and treated with or without the dectin-1 ligand curdlan and with or without the NFAT1 inhibitor Fk506. The curdlan treated cells were rested 2 hours for H3K4me3 samples and 30 minutes otherwise (sample treatment is 30 minutes if nothing is specified in the sample description below). FK506 treatment was 2 hours. Samples which were not treated at all bear 'none', in their descriptions.


Files downloaded from GEO series : GSE59998
Input file format : sra


Filename Description Feature GEO-ID
1 GSM1463320_NFAT1.sga D1 dendritic cells|NFAT1|curdlan NFAT1 GSM1463320
2 GSM1463321_Input.sga D1 dendritic cells|Input|curdlan Input GSM1463321
3 GSM1463322_H3K4me3.sga D1 dendritic cells|H3K4me3|none H3K4me3 GSM1463322
4 GSM1463323_Input.sga D1 dendritic cells|Input|none Input GSM1463323
5 GSM1463324_H3K4me3.sga D1 dendritic cells|H3K4me3|curdlan2h H3K4me3 GSM1463324
6 GSM1463325_Input.sga D1 dendritic cells|Input|curdlan Input GSM1463325
7 GSM1463326_H3K4me3.sga D1 dendritic cells|H3K4me3|curdlan2h+Fk506 H3K4me3 GSM1463326
8 GSM1463327_Input.sga D1 dendritic cells|Input|curdlan+Fk506 Input GSM1463327
9 GSM1463320_NFAT1_peaks.sga D1 dendritic cells|NFAT1 peaks|curdlan NFAT1_P GSM1463320

Technical Notes

The sga files were generated from the original data available on GEO. Read mapping was done using bowtie, using 28bp seed length as described by the authors.


  1. Yu HB, Yurieva M, Balachander A, Foo I, Leong X, Zelante T, Zolezzi F, Poidinger M, Ricciardi-Castagnoli P. NFATc2 mediates epigenetic modification of dendritic cell cytokine and chemokine responses to dectin-1 stimulation. Nucleic Acids Research 2015, 43 (2): 836-847. PMID: 25550437

Genome browser viewable files