| Strain, strain background (Homo sapiens) |
FOXA1 |
K562 |
Cat# CCL-243 (ATCC); RRID:CVCL_0004
|
Infected with pINDUCER21 lentiviral vector (Meerbrey et al., 2011) (Addgene#46948) carrying FOXA1 ORF (Addgene#120438) |
| Strain, strain background (H. sapiens) |
HNF4A |
K562 |
Cat# CCL-243 (ATCC); RRID:CVCL_0004
|
Infected with pINDUCER21 lentiviral vector (Meerbrey et al., 2011) (Addgene#46948) carrying HNF4A ORF (Addgene#120450) |
| Strain, strain background (H. sapiens) |
FOXA1-HNF4A |
K562 |
Cat# CCL-243 (ATCC); RRID:CVCL_0004
|
Infected with pINDUCER21 lentiviral vector (Meerbrey et al., 2011) (Addgene#46948) carrying FOXA1 ORF and then HNF4A ORF |
| Chemical compound, drug |
Doxycycline |
Sigma |
Cat# D9891-1G |
Treated at 0.5 and 0.05 µg/ml |
| Chemical compound, drug |
Polybrene |
Sigma |
Cat# TR1003G |
Treated at 10 µg/ml |
| Commercial assay or kit |
PureLink RNA Mini |
Invitrogen |
Cat# 12183020 |
|
| Commercial assay or kit |
PureLink DNase |
Invitrogen |
Cat# 12185010 |
|
| Commercial assay or kit |
ReadyScript cDNA Synthesis Mix |
Sigma |
Cat# RDRT-100RXN |
|
| Commercial assay or kit |
SYBR Green PCR Master Mix |
Applied Biosystems |
Cat# 4301955 |
|
| Commercial assay or kit |
NEBNext Ultra II Directional RNA Library Prep Kit |
NEB |
Cat# E7765S |
|
| Commercial assay or kit |
AMPure XP beads |
Beckman Coulter |
Cat# A63880 |
|
| Commercial assay or kit |
pAG-TN5 |
EpiCypher |
Cat# 15-1017 |
|
| Commercial assay or kit |
Concanavalin A paramagnetic beads |
EpiCypher |
Cat# 21-1401 |
|
| Commercial assay or kit |
HiFi DNA assembly |
NEB |
Cat# E2621L |
|
| Antibody |
Anti-FOXA1 (Rabbit monoclonal) |
Cell Signaling |
Cat# 53528; RRID:AB_2799438
|
(1:100) |
| Antibody |
Anti-HNF4A (mouse monoclonal) |
Invitrogen |
Cat# MA1-199; RRID:AB_2633309
|
(1:100) |
| Antibody |
Anti-H3K4me3 (Rabbit polyclonal) |
EpiCypher |
Cat# 13-0041 |
(1:50) |
| Antibody |
Anti-rabbit (goat polyclonal) |
EpiCypher |
Cat# 13-0047 |
(1:100) |
| Antibody |
Anti-mouse (goat polyclonal) |
EpiCypher |
Cat# 13-0048 |
(1:100) |
| Software, algorithm |
Salmon |
https://combine-lab.github.io/salmon/getting_started/
|
https://doi.org/10.1038/nmeth.4197; RRID:SCR_017036
|
|
| Software, algorithm |
DESeq2 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
https://doi.org/10.1186/s13059-014-0550-8; RRID:SCR_015687
|
|
| Software, algorithm |
deepTools2 |
https://deeptools.readthedocs.io/en/develop/
|
https://doi.org/10.1093/nar/gkw257; RRID:SCR_016366
|
|
| Software, algorithm |
bowtie2 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
https://doi.org/10.1038/nmeth.1923; RRID:SCR_016368
|
|
| Software, algorithm |
MACS2 |
https://pypi.org/project/MACS2/
|
https://doi.org/10.1186/gb-2008-9-9-r137; RRID:SCR_013291
|
|
| Software, algorithm |
featureCounts |
https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts
|
https://doi.org/10.1093/bioinformatics/btt656; RRID:SCR_012919
|
|
| Software, algorithm |
IDR |
https://www.encodeproject.org/software/idr/
|
https://doi.org/10.1214/11-AOAS466; RRID:SCR_017237
|
|
| Software, algorithm |
DiffBind |
https://bioconductor.org/packages/release/bioc/html/DiffBind.html
|
https://doi.org/10.18129/B9.bioc.DiffBind; RRID:SCR_012918
|
|
| Software, algorithm |
BEDTools |
https://bedtools.readthedocs.io/en/latest/
|
https://doi.org/10.1093/bioinformatics/btq033; RRID:SCR_006646
|
|
| Software, algorithm |
STREME |
https://meme-suite.org/meme/tools/streme
|
https://doi.org/10.1093/bioinformatics/btab203; RRID:SCR_001783
|
|
| Software, algorithm |
FIMO |
https://meme-suite.org/meme/tools/fimo
|
https://doi.org/10.1093/bioinformatics/btr064; RRID:SCR_001783
|
|
