Antibodies |
|
KDM1A/LSD1 |
Abcam |
Cat#ab17721; RRID: AB_443964 |
GR-H300 |
Santa Cruz |
Cat#sc-8992; RRID: AB_2155784 |
H3K4me1 |
Abcam |
Cat#ab8895; RRID: AB_306847 |
H3K4me2 |
Millipore |
Cat#07–030; RRID: AB_310342 |
H3K4me3 |
Millipore |
Cat#07–473; RRID: AB_1977252 |
H3K9me2 |
Abcam |
Cat#ab1220; RRID: AB_449854 |
H3K27ac |
Millipore |
Cat#17–683; RRID: AB_1977529 |
H3 |
Abcam |
Cat#ab1791; RRID: AB_302613 |
|
Bacterial and Virus Strains |
|
KDM1A shRNA (L-sh1) |
Sigma |
TRCN0000046071 |
KDM1A shRNA (L-sh2) |
Sigma |
TRCN0000046072 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
GR protein |
This paper |
N/A |
KDM1A protein |
This paper |
N/A |
Dexamethasone |
Sigma |
Cat#D1756 |
Tranylcypromine |
Sigma |
Cat#P8511 |
|
Deposited Data |
|
RNA-seq and ChIP-seq |
This paper |
GEO: GSE108588
|
|
Experimental Models: Cell Lines |
|
A549 |
ATCC |
ATCC CCL-185; RRID: CVCL_0023 |
|
Recombinant DNA |
|
GR-pGEX-4T-1 |
This paper |
available upon request |
|
Software and Algorithms |
|
Salmon |
Patro et al., 2017 |
https://combine-lab.github.io/salmon/ |
DESeq2 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
Bowtie (v0.12.7) |
Langmead et al., 2009 |
http://bowtie-bio.sourceforge.net/index.shtml |
MACS v1.4 |
Zhang et al., 2008 |
http://liulab.dfci.harvard.edu/MACS/ |
Samtools |
|
http://samtools.sourceforge.net |
DeepTools |
Ramírez et al., 2016 |
https://deeptools.readthedocs.io/en/develop/ |
KentUtils |
Kent et al., 2010 |
https://github.com/ENCODE-DCC/kentUtils |
BEDtools |
Quinlan and Hall, 2010 |
https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html |
GenomicRanges |
Lawrence et al., 2013 |
https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html |
HOMER (v4.10) |
Heinz et al., 2010 |
http://homer.ucsd.edu/homer/motif/ |
MEME Suit |
Bailey et al., 2009 |
http://homer.ucsd.edu/homer/motif/ |
ggplot2 |
Wickham, 2009 |
https://ggplot2.tidyverse.org |
ComplexHeatmap |
Gu et al., 2016 |
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |