Yu 2015, NFAT1 and H3K4me3 in D1 dendritic cells.

Description

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.

Source

Samples

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.

Technical Notes

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).

References

Last update: 2 Oct 2017