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. Author manuscript; available in PMC: 2017 Aug 25.
Published in final edited form as: Cell. 2016 Aug 25;166(5):1269–1281.e19. doi: 10.1016/j.cell.2016.07.049
KEY RESOURCES TABLE
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-GR antibody, rabbit polyclonal Santa Cruz Biotechnology sc-1003
Sheep anti-rabbit antibody beads Life Technologies M-280
Chemicals, Peptides, and Recombinant Proteins
Dexamethasone Sigma-Aldrich D4902
Critical Commercial Assays
PrepX mRNA seq kit Wafergen 400039
PrepX ILM 32i DNA Library Wafergen 400044
Dual-Glo Luciferase Assay Promega E2940
Fugene HD Promega E2312
Oligo-dT Dynabeads ThermoFisher Sci. 61005
Superscript III reverse transcriptase ThermoFisher Sci. 18080044
Q5 DNA Polymerase New England Biolabs M0491L
Turbo DNase ThermoFisher Sci. AM2238
In-Fusion HD Cloning Plus Clonetech 638911
Deposited Data
Raw and analyzed data This study GEO: GSE79432 and GSE77869
Experimental Models: Cell Lines
A549 cells ATCC/Duke Cancer Center Cell Culture Facility CCL-185
Experimental Models: Organisms/Strains
E.coli MegaX DH10B Electrocomp cells ThermoFisher Sci. C640003
Recombinant DNA
pGL4.24 Lucferase Vector Promega E8421
pRL-TK Promega E2241
pRL-SV40 Promega E2231
pSTARR-seq_human Addgene Plasmid #71509
Sequence-Based Reagents
PCR primers: Luciferase assay validation sequences, See Table S3 This study (IDT) N/A
Gene block sequences: Luciferase assay AP-1-GRE spacing expts. See Table S3 This study (IDT) N/A
Gene block sequences: Luciferase assay AP-1-GRE combination expts. See Table S3 This study (IDT) N/A
PCR primer sequences: Sequencing library prep. See Table S3 This study (IDT) N/A
STARR-seq adapter primers Arnold et al., 2013 N/A
Nextera STARR-seq adapter primers, See Table S3 This study (IDT) N/A
Software and Algorithms
MACS Zhang et al. 2008 http://liulab.dfci.harvard.edu/MACS/
PeakSplitter Salmon-Divon et al. 2010 http://www.bioinformatics.org/peakanalyzer/
BEDTools Quinlan 2014 http://code.google.com/p/bedtools/
Bowtie/Bowtie2 Langmead et al. 2009; Langmead and Salzberg 2012 http://bowtie-bio.sourceforge.net/
SAMtools Li et al. 2009 http://samtools.sourceforge.net
GraphPad Prism GraphPad Inc. http://www.graphpad.com/scientific-software/prism/
DEseq2 Love et al. 2014 http://www.bioconductor.org/packages/release/bioc/html/DESeq2
R R Development Core Team, 2016 https://www.r-project.org/
MEME Suite Bailey and Gribskov 1998 http://meme-suite.org/
pROC Robin et al. 2011 http://web.expasy.org/pROC/
uShuffle Jiang et al. 2008 http://digital.cs.usu.edu/~mjiang/ushuffle/