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

Description

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.

Source

Samples

From Human Mar. 2006 (GRCh36/hg18) Assembly.

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

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: 18 May 2016