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

Description

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).

Source

Samples

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.

Technical Notes

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).

References

Last update: 30 Jan 2017