Martinez 2015, Transription Factor NFAT1 in CD8+ T cells

Description

ChIP-seq analysis of NFAT1 transcription factor in CD*+ T cells. There are two version of it, the wild type (WT NFAT1) and a constitutively nuclear and therefore constitutively active (CA) and also unable to interact with AP-1 (RIT) (CA-RIT-NFAT1) present in a KO NFAT background. Some samples are also treated for 1 h with PMA and ionomycin.

Source

Files downloaded from GEO

Input file format: SRA

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly

Filename Description Feature GEO-ID
1 GSM1570756.sga WT NFAT1|None NFAT1 GSM1570756
2 GSM1570759.sga WT NFAT1|PMA+Ionomycin 1h NFAT1 GSM1570759
3 GSM1570757.sga NFAT1-KO|None NFAT1 GSM1570757
4 GSM1570760.sga NFAT1-KO|PMA+Inomycin 1h NFAT1 GSM1570760
5 GSM1570758.sga NFAT1-KO CA-RIT-NFAT1|None NFAT1 GSM1570758
6 GSM1570761.sga NFAT1-KO CA-RIT-NFAT1|PMA+Ionomycin 1h NFAT1 GSM1570761
7 GSM1570755.sga Input NFAT1-KO CA-RIT-NFAT1|PMA+Ionomycin input GSM1570755
8 GSM1570754.sga Input NFAT1-KO|PMA+Inomycin 1h input input GSM1570754
9 GSM1570753.sga Input WT NFAT1|PMA+Ionomycin input input GSM1570753
10 GSM1570752.sga Input NFAT1-KO CA-RIT-NFAT1|None input input GSM1570752
11 GSM1570751.sga Input NFAT1-KO|None input input GSM1570751
12 GSM1570750.sga Input WT NFAT1|None input input GSM1570750

Technical Notes

Raw sequences were mapped to mouse genome using bowtie and converted into SGA file format using samtools (download from http://samtools.sourceforge.net/ ) and ChIP-Seq tools (download from http://sourceforge.net/projects/chip-seq/ )

References

  1. Martinez GJ, Pereira RM, Äijö T, Kim EY et al. The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells. Immunity 2015 Feb 17;42(2):265-78. PMID: 25680272