Table 1 Characteristics of the selected ER-ChIP-seq datasets and their experimental design
Accession number | Cell lines | Dose (nM) of E2 | Inputs | Samples treated with vehicles as controls | Samples treated with E2 | chip antibody | Type of vehicle treatment | Experiment |
|---|---|---|---|---|---|---|---|---|
GSE94023 | MCF7 | 10 | - | GSM2467220 | GSM2467224 | F3A6 (to ERalpha, Gronemeyer) | mock | Dzida,…et al. [7] |
GSE99626 | GSM2125164 (Vehicle_Input) GSM2125165 (E2_Input) | GSM2648921 | GSM2648922 | anti-ER (SC biotech HC-20, cat# SC-543, lot# L1911) | ETOH | Singhal,…et al. [17] | ||
GSE67295 | - | GSM1643946 (rep1) GSM1643947 (rep2) | GSM1643948 (rep1) GSM1643949 (rep2) | ERa (Vendor: Santa Cruz, cat# sc-543, lot# C2114) | DMSO | Stender,…et al. [8] | ||
GSE115607 | GSM3184881 | GSM3184871 | GSM3184880 | ERa (Santa Cruz, sc-543, lot F1716) | DMSO | Puyang,…et al. [6] | ||
GSE80367 | T47D | GSM2112811 (Vehicle_Input) GSM2112812 (E2_Input) | GSM2112796 | GSM2112798 | anti-ER (SC biotech HC-20) | ETOH | Singhal,…et al. [18] | |
GSE23893 | T47D | 100 | GSM589247 | GSM589238 | GSM589239 | ERα (sc-543, Santa-Cruz) | ETOH | Kong,…et al. [19] |
GSE23893 | MCF7 | GSM589244 | GSM589236 | GSM589237 | ERα (sc-543, Santa-Cruz) | ETOH | Kong,…et al. [19] | |
GSE54855 | GSM1325252 | GSM1325246 | GSM1325250 | ER (Santa Cruz, sc-542) | mock | Guertin,…et al. [20] | ||
GSE59530 | GSM1534712 (Vehicle_Input_rep1) GSM1534713 (Vehicle_Input_rep2) GSM1534714 (E2_Input_rep1) GSM1534715 (E2_Input_rep2) | GSM1534720 (rep1) GSM1534721 (rep2) | GSM1534722 (rep1) GSM1534723 (rep2) | ER alpha (rabbit polyclonal generated in the Kraus Lab) | unknown | Franco,…et al. [21] |