Ben-Ami 2013, AML1 (Kazumi -1) cells, ChIP Seq for RUNX1, AML1-ETO, AP4.

CHIP-seq against RUNX1, AML1-ETO and AP4 in Kazumi-1 cells (a cell line derived from AML cells from a patient with translocation t(8,21)). The translocation creates a fusion gene between RUNX1 and ETO called AML1-ETO (A-E). Two antibodies against RUNX1 were used, recognizing the N-terminus (present in wild-type RUNX1 and AML-ETO) and the other one the C-terminus (present only in the wild-type).

• Raw data was downloaded from GEO series: GSE45738
• Input file format: SRA

From H. sapiens (March 2006 NCBI36/hg18).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1113427.sga	Kasumi RUNX1 C-term rep1	RUNX1_CT	GSM1113427
2	GSM1113428.sga	Kasumi RUNX1 C-term rep2	RUNX1_CT	GSM1113428
3	GSM1113429.sga	Kasumi AML1-ETO rep1	AML1_ETO	GSM1113429
4	GSM1113430.sga	Kasumi AML1-ETO rep2	AML1_ETO	GSM1113430
5	GSM1113431.sga	Kasumi control(RUNX1) rep1	NIS	GSM1113431
6	GSM1113432.sga	Kasumi control(RUNX1) rep2	NIS	GSM1113432
7	GSM1113433.sga	Kasumi AP4 rep1	AP4	GSM1113433
8	GSM1113434.sga	Kasumi AP4 rep2	AP4	GSM1113434
9	GSM1113435.sga	Kasumi control(AP4) rep1	NIS	GSM1113435
10	GSM1113436.sga	Kasumi control(AP4) rep2	NIS	GSM1113436
11	GSM1113437.sga	Kasumi RUNX1 N-term rep1	RUNX1_NT	GSM1113437
12	GSM1113438.sga	Kasumi RUNX1 N-term rep2	RUNX1_NT	GSM1113438

Notes on samples nomenclature:

Control samples were generated by CHIP-seq using a non immune serum (NIS) instead of a specific antibody. _1 _2 are duplicates.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg18 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. 1.5.2).

• Ben-Ami O, Friedman D, Leshkowitz D, Goldenberg D, Orlovsky K, Pencovich N, Lotem J, Tanay A, Groner Y
  Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1. Cell Rep. 2013 Sep 26;4(6):1131-43. doi: 10.1016/j.celrep.2013.08.020. Epub 2013 Sep 19. 24055056
• GEO series GSE45738: Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]