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/
|