Singh 2019, ChIP-seq against several targets in cell lines, patient-derived tumors and biopsies.

The samples from this study demonstrate the merits of an optimized ChIP-seq procedure that facilitates epigenomic profiling of human tumors and core needle biopsies. The following molecular targets, cells and tissue samples were used:

ChIP-seq targets: histone modifications H3K4me3 and H3K27ac, transcription factors AR, ESR1 and FOXA1
Cell lines: LNCAP, MCF7.
Patient-derived tumors: prostate, breast and endometrial cancer.
Core needle biopsies: prostate cancer.

Two cross-linking protocols were compared:

• Formaldehyde (FA): single cross-linking.
• Disuccinimidyl glutarate (DSG): double cross-linking.

• Raw data was downloaded from SRA, bioprojects: PRJNA472620
• Input file format: FASTQ
• Download date: 06-12-2021

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	LNCAP_AR_FA.sga	LNCAP|AR|FA|	AR	GSM3149022
2	LNCAP_AR_DSG.sga	LNCAP|AR|DSG|	AR	GSM3149023
3	LNCAP_FOXA1_FA.sga	LNCAP|FOXA1|FA|	FOXA1	GSM3149024
4	LNCAP_FOXA1_DSG.sga	LNCAP|FOXA1|DSG|	FOXA1	GSM3149025
5	LNCAP_H3K4me3_FA.sga	LNCAP|H3K4me3|FA|	H3K4me3	GSM3149026
6	LNCAP_H3K4me3_DSG.sga	LNCAP|H3K4me3|DSG|	H3K4me3	GSM3149027
7	LNCAP_H3K27ac_FA.sga	LNCAP|H3K27ac|FA|	H3K27ac	GSM3149028
8	LNCAP_H3K27ac_DSG.sga	LNCAP|H3K27ac|DSG|	H3K27ac	GSM3149029
9	MCF7_ER_FA.sga	MCF7|ESR1|FA|	ESR1	GSM3149030
10	MCF7_ER_DSG.sga	MCF7|ESR1|DSG|	ESR1	GSM3149031
11	MCF7_FOXA1_FA.sga	MCF7|FOXA1|FA|	FOXA1	GSM3149032
12	MCF7_FOXA1_DSG.sga	MCF7|FOXA1|DSG|	FOXA1	GSM3149033
13	MCF7_H3K4me3_FA.sga	MCF7|H3K4me3|FA|	H3K4me3	GSM3149034
14	MCF7_H3K4me3_DSG.sga	MCF7|H3K4me3|DSG|	H3K4me3	GSM3149035
15	MCF7_H3K27ac_FA.sga	MCF7|H3K27ac|FA|	H3K27ac	GSM3149036
16	MCF7_H3K27ac_DSG.sga	MCF7|H3K27ac|DSG|	H3K27ac	GSM3149037
17	P1_AR_FA.sga	PC T1|AR|FA|	AR	GSM3149038
18	P1_AR_DSG.sga	PC T1|AR|DSG|	AR	GSM3149039
19	P1_FOXA1_FA.sga	PC T1|FOXA1|FA|	FOXA1	GSM3149040
20	P1_FOXA1_DSG.sga	PC T1|FOXA1|DSG|	FOXA1	GSM3149041
21	P1_H3K27ac_FA.sga	PC T1|H3K27ac|FA|	H3K27ac	GSM3149042
22	P1_H3K27ac_DSG.sga	PC T1|H3K27ac|DSG|	H3K27ac	GSM3149043
23	P2_AR_FA.sga	PC T2|AR|FA|	AR	GSM3149044
24	P2_AR_DSG.sga	PC T2|AR|DSG|	AR	GSM3149045
25	P2_FOXA1_FA.sga	PC T2|FOXA1|FA|	FOXA1	GSM3149046
26	P2_FOXA1_DSG.sga	PC T2|FOXA1|DSG|	FOXA1	GSM3149047
27	P2_H3K27ac_FA.sga	PC T2|H3K27ac|FA|	H3K27ac	GSM3149048
28	P2_H3K27ac_DSG.sga	PC T2|H3K27ac|DSG|	H3K27ac	GSM3149049
29	P3_AR_FA.sga	PC T3|AR|FA|	AR	GSM3149050
30	P3_AR_DSG.sga	PC T3|AR|DSG|	AR	GSM3149051
31	P3_FOXA1_FA.sga	PC T3|FOXA1|FA|	FOXA1	GSM3149052
32	P3_FOXA1_DSG.sga	PC T3|FOXA1|DSG|	FOXA1	GSM3149053
33	P3_H3K27ac_FA.sga	PC T3|H3K27ac|FA|	H3K27ac	GSM3149054
34	P3_H3K27ac_DSG.sga	PC T3|H3K27ac|DSG|	H3K27ac	GSM3149055
35	P4_AR_FA.sga	PC T4|AR|FA|	AR	GSM3149056
36	P4_AR_DSG.sga	PC T4|AR|DSG|	AR	GSM3149057
37	P4_FOXA1_FA.sga	PC T4|FOXA1|FA|	FOXA1	GSM3149058
38	P4_FOXA1_DSG.sga	PC T4|FOXA1|DSG|	FOXA1	GSM3149059
39	P4_H3K27ac_FA.sga	PC T4|H3K27ac|FA|	H3K27ac	GSM3149060
40	P4_H3K27ac_DSG.sga	PC T4|H3K27ac|DSG|	H3K27ac	GSM3149061
41	B1_ER_FA.sga	BC T1|ESR1|FA|	ESR1	GSM3149062
42	B1_ER_DSG.sga	BC T1|ESR1|DSG|	ESR1	GSM3149063
43	B1_FOXA1_FA.sga	BC T1|FOXA1|FA|	FOXA1	GSM3149064
44	B1_FOXA1_DSG.sga	BC T1|FOXA1|DSG|	FOXA1	GSM3149065
45	B1_H3K4me3_FA.sga	BC T1|H3K4me3|FA|	H3K4me3	GSM3149066
46	B1_H3K4me3_DSG.sga	BC T1|H3K4me3|DSG|	H3K4me3	GSM3149067
47	B1_H3K27ac_FA.sga	BC T1|H3K27ac|FA|	H3K27ac	GSM3149068
48	B1_H3K27ac_DSG.sga	BC T1|H3K27ac|DSG|	H3K27ac	GSM3149069
49	B2_ER_FA.sga	BC T2|ESR1|FA|	ESR1	GSM3149070
50	B2_ER_DSG.sga	BC T2|ESR1|DSG|	ESR1	GSM3149071
51	B2_FOXA1_FA.sga	BC T2|FOXA1|FA|	FOXA1	GSM3149072
52	B2_FOXA1_DSG.sga	BC T2|FOXA1|DSG|	FOXA1	GSM3149073
53	B2_H3K4me3_FA.sga	BC T2|H3K4me3|FA|	H3K4me3	GSM3149074
54	B2_H3K4me3_DSG.sga	BC T2|H3K4me3|DSG|	H3K4me3	GSM3149075
55	B2_H3K27ac_FA.sga	BC T2|H3K27ac|FA|	H3K27ac	GSM3149076
56	B2_H3K27ac_DSG.sga	BC T2|H3K27ac|DSG|	H3K27ac	GSM3149077
57	B3_ER_FA.sga	BC T3|ESR1|FA|	ESR1	GSM3149078
58	B3_ER_DSG.sga	BC T3|ESR1|DSG|	ESR1	GSM3149079
59	B3_FOXA1_FA.sga	BC T3|FOXA1|FA|	FOXA1	GSM3149080
60	B3_FOXA1_DSG.sga	BC T3|FOXA1|DSG|	FOXA1	GSM3149081
61	B3_H3K4me3_FA.sga	BC T3|H3K4me3|FA|	H3K4me3	GSM3149082
62	B3_H3K4me3_DSG.sga	BC T3|H3K4me3|DSG|	H3K4me3	GSM3149083
63	B3_H3K27ac_FA.sga	BC T3|H3K27ac|FA|	H3K27ac	GSM3149084
64	B3_H3K27ac_DSG.sga	BC T3|H3K27ac|DSG|	H3K27ac	GSM3149085
65	B4_ER_FA.sga	BC T4|ESR1|FA|	ESR1	GSM3149086
66	B4_ER_DSG.sga	BC T4|ESR1|DSG|	ESR1	GSM3149087
67	B4_FOXA1_FA.sga	BC T4|FOXA1|FA|	FOXA1	GSM3149088
68	B4_FOXA1_DSG.sga	BC T4|FOXA1|DSG|	FOXA1	GSM3149089
69	B4_H3K4me3_FA.sga	BC T4|H3K4me3|FA|	H3K4me3	GSM3149090
70	B4_H3K4me3_DSG.sga	BC T4|H3K4me3|DSG|	H3K4me3	GSM3149091
71	B4_H3K27ac_FA.sga	BC T4|H3K27ac|FA|	H3K27ac	GSM3149092
72	B4_H3K27ac_DSG.sga	BC T4|H3K27ac|DSG|	H3K27ac	GSM3149093
73	E1_ER_FA.sga	EC T1|ESR1|FA|	ESR1	GSM3149094
74	E1_ER_DSG.sga	EC T1|ESR1|DSG|	ESR1	GSM3149095
75	E1_H3K27ac_FA.sga	EC T1|H3K27ac|FA|	H3K27ac	GSM3149096
76	E1_H3K27ac_DSG.sga	EC T1|H3K27ac|DSG|	H3K27ac	GSM3149097
77	E2_ER_FA.sga	EC T2|ESR1|FA|	ESR1	GSM3149098
78	E2_ER_DSG.sga	EC T2|ESR1|DSG|	ESR1	GSM3149099
79	E2_H3K27ac_FA.sga	EC T2|H3K27ac|FA|	H3K27ac	GSM3149100
80	E2_H3K27ac_DSG.sga	EC T2|H3K27ac|DSG|	H3K27ac	GSM3149101
81	E3_ER_FA.sga	EC T3|ESR1|FA|	ESR1	GSM3149102
82	E3_ER_DSG.sga	EC T3|ESR1|DSG|	ESR1	GSM3149103
83	E3_H3K27ac_FA.sga	EC T3|H3K27ac|FA|	H3K27ac	GSM3149104
84	E3_H3K27ac_DSG.sga	EC T3|H3K27ac|DSG|	H3K27ac	GSM3149105
85	G1_AR_DSG.sga	PC biopsy 1|AR|DSG|	AR	GSM3149106
86	G1_FOXA1_DSG.sga	PC biopsy 1|FOXA1|DSG|	FOXA1	GSM3149107
87	G1_H3K27ac_DSG.sga	PC biopsy 1|H3K27ac|DSG|	H3K27ac	GSM3149108
88	G2_AR_DSG.sga	PC biopsy 2|AR|DSG|	AR	GSM3149109
89	G2_FOXA1_DSG.sga	PC biopsy 2|FOXA1|DSG|	FOXA1	GSM3149110
90	G2_H3K27ac_DSG.sga	PC biopsy 2|H3K27ac|DSG|	H3K27ac	GSM3149111
91	LNCAP_Input.sga	LNCAP|Input||	Input	GSM3149112
92	MCF7_Input.sga	MCF7|Input||	Input	GSM3149113
93	P_Input_DSG.sga	PC tumors mixed|Input|DSG|	Input	GSM3149114
94	P_Input_FA.sga	PC tumors mixed|Input|FA|	Input	GSM3149115
95	B_Input_DSG.sga	BC tumors mixed|Input|DSG|	Input	GSM3149116
96	B_Input_FA.sga	BC tumors mixed|Input|FA|	Input	GSM3149117
97	E_Input_DSG.sga	EC tumors mixed|Input|DSG|	Input	GSM3149118
98	E_Input_FA.sga	EC tumors mixed|Input|FA|	Input	GSM3149119
99	G_Input.sga	PC biopsies mixed|Input||	Input	GSM3149120

Notes on samples nomenclature (abbreviations):

BC: primary breast cancer
EC: primary endometrium cancer
PC: primary prostate cancer
FA: formalehyde (single cross-linking)
DSG: disuccinimidyl glutarate (double cross-linking)

• Strand correlation plots: singh19_strand_cor.pdf
• ChIP-seq tag enrichment around bound AR, ESR1 and FOXA1. singh19_motif_enr.pdf

The scripts for generating the QC and analysis plots can be found here: singh19_analysis.tar.gz

FASTQ files were downloaded from SRA using fastq-dump (SRA toolkit v2.10.8) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

For reproducibility purposes, the scripts used for generating the SGA files are posted here: singh19_scripts.tar.gz

• Singh AA, Schuurman K, Nevedomskaya E, Stelloo S, Linder S, Droog M, Kim Y, Sanders J, van der Poel H, Bergman AM, Wessels LF, Zwart W.
  Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. Life Sci Alliance. 2018 Dec 28;2(1):e201800115. doi: 10.26508/lsa.201800115. 30620009
• GEO series GSE114737: Optimized ChIP-seq procedure facilitates hormone receptor profiling in human tumors.