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
|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|
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.