Table 1. Reagents and resources.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Antibodies | |||
| anti-p-ERK | Cell Signaling | Cat# 4695 | |
| anti-ERα | Santa Cruz | Cat# sc-543 | |
| anti-p-ER | Cell Signaling | Cat# 2511 | |
| Chemicals, Peptides, and Recombinant Proteins | |||
| (Z)-4-Hydroxytamoxifen (4-OHT) | Sigma-Aldrich | Cat# H7904 | |
| Recombinant human GDNF | PeproTech | Cat# 450–10 | |
| SUPERase In RNase Inhibitor (20 U/L) | Life Technologies | Cat# AM2694 | |
| Protease Inhibitor Cocktail | Roche | Cat# 11836153001 | |
| Biotin-11-ATP | PerkinElmer | Cat# NEL544001EA | |
| Biotin-11-GTP | PerkinElmer | Cat# NEL545001EA | |
| Biotin-11-CTP | PerkinElmer | Cat# NEL542001EA | |
| Biotin-11-UTP | PerkinElmer | Cat# NEL543001EA | |
| Sarkosyl | Fisher Scientific | Cat# AC612075000 | |
| Trizol | Life Technologies | Cat# 15596–026 | |
| Trizol LS | Life Technologies | Cat# 10296–010 | |
| GlycoBlue | Ambion | Cat# AM9515 | |
| Hydrophilic streptavidin magnetic beads | NEB | Cat# S1421S | |
| RppH | NEB | Cat# M0356S | |
| T4 RNA Ligase 1 | NEB | Cat# M0204L | |
| Critical Commercial Assays | |||
| RNeasy Kit | Qiagen | Cat# 74104 | |
| High Capacity RNA-to-cDNA | Applied Biosystems | Cat# 4387406 | |
| Power SYBR Green PCR Master Mix | Applied Biosystems | Cat# 4367659 | |
| Deposited Data | |||
| All genomic data was deposited in GEO and the sequence read archive | Herein | GSE93229 | |
| Experimental Models: Cell Lines | |||
| MCF7-B7TamS | (Gonzalez-Malerva et al., 2011) | N/A | |
| MCF7-C11TamS | (Gonzalez-Malerva et al., 2011) | N/A | |
| MCF7-G11TamR | (Gonzalez-Malerva et al., 2011) | N/A | |
| MCF7-H9TamR | (Gonzalez-Malerva et al., 2011) | N/A | |
| Sequence-Based Reagents | |||
| Primers for ACTB, see STAR Methods | This paper | N/A | |
| Primers for ESR1, see STAR Methods | This paper | N/A | |
| Primers for GDNF, see STAR Methods | Boulay et al., 2008 | N/A | |
| Primers for EGR1, see STAR Methods | Fang et al., 2016 | N/A | |
| Software and Algorithms | |||
| cutadapt | Martin, 2011 | ||
| dREG | Danko et al., 2015 | https://github.com/Danko-Lab/dREG | |
| dREG-HD | Manuscript in preparation; This paper | https://github.com/Danko-Lab/dREG.HD; | |
| bigWig software package | https://github.com/andrelmartins/bigWig | ||
| Visualization using R | Team, 2010 | ||
| BedTools | Quinlan and Hall, 2010 | ||
| bedGraphToBigWig program in the Kent Source software package | Kuhn et al., 2013 | ||
| DEseq2 | Love et al., 2014 | ||
| RTFBSDB | Wang et al., 2016 | ||
| Cytoscape software package | Shannon et al., 2003 | ||
| GraphPad Prism | |||
The following reagents and resources were used in this study.