Martens 2010, PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia.

ChIP-seq against PML, RAR alpha, RXR, DNAme, RNA polymerase II (RNApolII), H3K9K14ac, H3K27me3, and H3K9me3 in NB4, MR4, and APL cells, before and after ATRA treatment and in the PML-RAR alpha zinc-inducible cell line UPR9. Includes total genomic DNA sample as control.

• Raw data was downloaded from: FTP site
• Input file format: SRA

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM468195-H3K27me3_ChIP-seq_APL164_48hoursATRA_JM16.sga	APL164|H3K27me3|48hoursATRA	H3K27me3	GSM468195
2	GSM468193-H3K27me3_ChIP-seq_APL164_noATRA_JM14.sga	APL164|H3K27me3|noATRA	H3K27me3	GSM468193
3	GSM468194-H3K9K14ac_ChIP-seq_APL164_48hoursATRA_JM15.sga	APL164|H3K9K14ac|48hoursATRA	H3K9K14ac	GSM468194
4	GSM468192-H3K9K14ac_ChIP-seq_APL164_noATRA_JM13.sga	APL164|H3K9K14ac|noATRA	H3K9K14ac	GSM468192
5	GSM468183-PML_ChIP-seq_APL164_noATRA.sga	APL164|PML|noATRA	PML	GSM468183
6	GSM468184-RXR_ChIP-seq_APL164_noATRA.sga	APL164|RXR|noATRA	RXR	GSM468184
7	GSM468203-PML_ChIP-seq_APL74_noATRA_JM24.sga	APL74|PML|noATRA	PML	GSM468203
8	GSM468204-RXR_ChIP-seq_APL74_noATRA_JM25.sga	APL74|RXR|noATRA	RXR	GSM468204
9	GSM468208-H3K9K14ac_ChIPseq_MR4_24hrATRA_JM29.sga	MR4|H3K9K14ac|24hrATRA	H3K9K14ac	GSM468208
10	GSM468207-H3K9me3_ChIPseq_MR4_noATRA_JM28.sga	MR4|H3K9me3|noATRA	H3K9me3	GSM468207
11	GSM468206-PML_ChIP-seq_MR4_24hoursATRA_JM27.sga	MR4|PML|24hoursATRA	PML	GSM468206
12	GSM468205-PML_ChIP-seq_MR4_noATRA_JM26.sga	MR4|PML|noATRA	PML	GSM468205
13	GSM468188-H3K27me3_ChIP-seq_NB4_24hoursATRA.sga	NB4|H3K27me3|24hoursATRA	H3K27me3	GSM468188
14	GSM468186-H3K27me3_ChIP-seq_NB4_noATRA.sga	NB4|H3K27me3|noATRA	H3K27me3	GSM468186
15	GSM468187-H3K9K14ac_ChIP-seq_NB4_24hoursATRA.sga	NB4|H3K9K14ac|24hoursATRA	H3K9K14ac	GSM468187
16	GSM468185-H3K9K14ac_ChIP-seq_NB4_noATRA.sga	NB4|H3K9K14ac|noATRA	H3K9K14ac	GSM468185
17	GSM468202-H3K9me3_ChIPseq_NB4_24hrATRA_JM23.sga	NB4|H3K9me3|24hrATRA	H3K9me3	GSM468202
18	GSM468201-H3K9me3_ChIPseq_NB4_noATRA_JM22.sga	NB4|H3K9me3|noATRA	H3K9me3	GSM468201
19	GSM468198-PML_ChIP-seq_NB4_24hoursATRA_JM19.sga	NB4|PML|24hoursATRA	PML	GSM468198
20	GSM468180-PML_ChIP-seq_NB4_noATRA.sga	NB4|PML|noATRA	PML	GSM468180
21	GSM468200-RAR_ChIPseq_NB4_24hoursATRA_JM21.sga	NB4|RAR|24hoursATRA	RAR	GSM468200
22	GSM468182-RAR_ChIP-seq_NB4_noATRA.sga	NB4|RAR|noATRA	RAR	GSM468182
23	GSM468190-RNApolII_ChIP-seq_NB4_24hoursATRA_JM11.sga	NB4|RNApolII|24hoursATRA	RNApolII	GSM468190
24	GSM468191-RNApolII_ChIP-seq_NB4_48hoursATRA_JM12.sga	NB4|RNApolII|48hoursATRA	RNApolII	GSM468191
25	GSM468189-RNApolII_ChIP-seq_NB4_noATRA_JM10.sga	NB4|RNApolII|noATRA	RNApolII	GSM468189
26	GSM468199-RXR_ChIP-seq_NB4_24hoursATRA_JM20.sga	NB4|RXR|24hoursATRA	RXR	GSM468199
27	GSM468181-RXR_ChIP-seq_NB4_noATRA.sga	NB4|RXR|noATRA	RXR	GSM468181
28	GSM468216-H3K9K14ac_ChIPseq_UPR9_5hrZinc_JM37.sga	UPR9H3K9K14ac|5hrZinc	H3K9K14ac	GSM468216
29	GSM468218-H3K27me3_ChIPseq_UPR9_5hrZinc_JM39.sga	UPR9|H3K27me3|5hrZinc	H3K27me3	GSM468218
30	GSM468217-H3K27me3_ChIPseq_UPR9_noZinc_JM38.sga	UPR9|H3K27me3|noZinc	H3K27me3	GSM468217
31	GSM468215-H3K9K14ac_ChIPseq_UPR9_noZinc_JM36.sga	UPR9|H3K9K14ac|noZinc	H3K9K14ac	GSM468215
32	GSM468210-PML_ChIPseq_UPR9_5hrZinc_JM31.sga	UPR9|PML|5hrZinc	PML	GSM468210
33	GSM468209-PML_ChIPseq_UPR9_noZinc_JM30.sga	UPR9|PML|noZinc	PML	GSM468209
34	GSM468212-RAR_ChIPseq_UPR9_5hrZinc_JM33.sga	UPR9|RAR|5hrZinc	RAR	GSM468212
35	GSM468211-RAR_ChIPseq_UPR9_noZinc_JM32.sga	UPR9|RAR|noZinc	RAR	GSM468211
36	GSM468214-RXR_ChIPseq_UPR9_5hrZinc_JM35.sga	UPR9|RXR|5hrZinc	RXR	GSM468214
37	GSM468213-RXR_ChIPseq_UPR9_noZinc_JM34.sga	UPR9|RXR|noZinc	RXR	GSM468213

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM468219-GenomicDNA_NB4_noATRA_JM40.sga	JM40|GenomicDNA|noATRA	GenomicDNA	GSM468219
2	GSM468197-DNAme_MeCap-seq_NB4_48hoursATRA_JM18.sga	NB4|DNAme|48hoursATRA	DNAme	GSM468197

• Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG
  PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia. Cancer Cell. 2010 Feb 17;17(2):173-85. doi: 10.1016/j.ccr.2009.12.042. 20159609
• GEO series GSE18886: PML-RARa/RXR alters the epigenetic landscape in Acute Promyelocytic Leukemia