Yu 2015, NFAT1 and H3K4me3 in D1 dendritic cells.

ChIP-seq against the transcription factor NFATc2 target sites and H3K4me3 in the long-term murine splenic dendritic cells (D1). For details see "Notes on samples" below.

• Raw data was downloaded from GEO series: GSE59998
• Input file format: SRA

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	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

ChIP-seq peaks files:

	Filename	Description	Feature	GEO-ID
1	GSM1463320_NFAT1_peaks.sga	D1 dendritic cells|NFAT1 peaks|curdlan	NFAT1_P	GSM1463320

Notes on samples :

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.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the mm9 genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• 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 Res. 2015 Jan;43(2):836-47. doi: 10.1093/nar/gku1369. Epub 2014 Dec 30. 25550437
• GEO series GSE59998: Genome wide mapping of NFAT1 binding sites in dendritic cells and of chromatin state in steady and dectin-1 activated dendritic cell line D1