Table 1.

Detailed sample information and experimental design of the eight illustrative BS-seq samples in this protocol

Index	Accession number	Cell line	Condition	Sample title	Download file name	R object
1	GSM1084238	A549	normal	A0R_d0_rep1	GSM1084238_A0R_d0_rep1.cpgs.txt	dat1
2	GSM1084239	A549	metastatic	A3R_d0_rep1	GSM1084239_A3R_d0_rep1.cpgs.txt	dat2
3	GSM1084244	HTB56	normal	H0R_d0_rep1	GSM1084244_H0R_d0_rep1.cpgs.txt	dat3
4	GSM1084245	HTB56	metastatic	H3R_d0_rep1	GSM1084245_H3R_d0_rep1.cpgs.txt	dat4
5	GSM1251236	A549	normal	A0R_d0_rep2	GSM1251236_A0R_d0_rep2.cpgs.txt	dat5
6	GSM1251237	A549	metastatic	A3R_d0_rep2	GSM1251237_A3R_d0_rep2.cpgs.txt	dat6
7	GSM1251238	HTB56	normal	H0R_d0_rep2	GSM1251238_H0R_d0_rep2.cpgs.txt	dat7
8	GSM1251239	HTB56	metastatic	H3R_d0_rep2	GSM1251239_H3R_d0_rep2.cpgs.txt	dat8

Here in sample names, “A” stands for A549 cells, “H” stands for HTB56 cells, “0” stands for normal cells, “3” stands for metastatic cells, “rep1” and “rep2” stand for first and second replicate, respectively. Their corresponding R objects are shown in the last column.