| Antibodies |
| Monoclonal Anti-FLAG M2 Antibody |
Merck |
F3165 |
| Histone-H3 |
Abcam |
ab1791 |
| Secondary anti mouse HRP |
Sigma-Aldrich |
12-349 |
| Secondary anti rabbit HRP |
Sigma-Aldrich |
12-348 |
| Bacterial and virus strains |
| MegaX DH10B T1R Electrocomp™ Cells |
Thermo Fisher |
C640003 |
| Experimental models: Cell lines |
|
|
| D. melanogaster Schneider S2 cells |
Thermo Fisher |
R69007 |
| HCT-116 |
ATCC |
CCL-247 |
| S2OsTir1
|
This Paper |
N/A |
| S2OsTir1-Snr1-AID
|
This Paper |
N/A |
| S2OsTir1-Iswi-AID
|
This Paper |
N/A |
| S2OsTir1-Ino80-AID
|
This Paper |
N/A |
| S2OsTir1-Chd1-AID
|
This Paper |
N/A |
| S2OsTir1-Brd7-AID
|
This Paper |
N/A |
| Chemicals, peptides, and recombinant proteins |
| Puromycin |
Invivogen |
ant-pr-1 |
| FastDigest MluI |
ThermoFisher |
FD0564 |
| BspQI |
NEB |
R0712S |
| Blasticidin S HCl |
ThermoFisher |
R21001 |
| 3-Indoleacetic acid |
Merck |
I3750 |
| QuickExtract™ DNA Extraction Solution |
Lucigen |
QE9059 |
| 2x Laemmli Sample Buffer |
BioRad |
1610737 |
| EGTA |
Merck |
E4378 |
| Biotin-11-CTP |
PerkinElmer |
NEL542001EA |
| Trizol |
ThermoFisher |
15596026 |
| Trizol-LS |
ThermoFisher |
10296010 |
| GlycoBlue™ Coprecipitant |
ThermoFisher |
AM9515 |
| NTP Set, 100 mM Solution |
ThermoFisher |
R0481 |
| N-Lauroylsarcosine sodium salt |
Merck |
L5125 |
| Dynabeads™ M-280 Streptavidin |
ThermoFisher |
11205D |
| Cap-CLIP |
BioZym |
C-CC15011H |
| T4 Polynucleotide Kinase |
NEB |
M0201S |
| Murine RNAse Inhibitor |
NEB |
M0314L |
| T4 RNA Ligase |
NEB |
M0204L |
| SuperScript™ III Reverse Transcriptase |
ThermoFisher |
18080093 |
| KAPA HiFi HotStart Real-Time Library Amp Kit |
Roche |
7959028001 |
| AMPure XP beads |
Beckman Coulter |
A63882 |
| Anti-FLAG® M2 Magnetic Beads |
Merck |
M8823 |
| Nuclease micrococcal from Staphylococcus aureus |
Merck |
N3755 |
| Proteinase K, recombinant, PCR Grade |
Merck |
3115828001 |
| TissueRuptor Disposable Probes |
Qiagen |
990890 |
| ROTI® Phenol/ Chloroform/ Isoamylalkohol, 500 ml |
Roth |
A156.2 |
| Turbo DNase |
Thermo |
AM2239 |
| RNase A (17,500 U) |
Qiagen |
19101 |
| Digitonin |
Merck |
D141 |
| Spermidine trihydrochloride |
Merck |
85580 |
| Lysyl endopeptidase |
Wako Chemicals |
Cat#7041 |
| Ammoniumbicarbonate |
Sigma-Aldrich |
Cat#09830 |
| Tris-(2-carboxyethyl)-phosphin-hydrochloride (TCEP) |
Sigma-Aldrich |
Cat#646547 |
| S-Methyl-thiomethanesulfonate (MMTS) |
Sigma-Aldrich |
Cat#64306 |
| Trifluoroacetic acid |
Sigma-Aldrich |
Cat#T6508 |
| oComplete mini protease inhibitors |
Sigma-Aldrich |
Cat# 11836170001 |
| Axygen 1.5mL MaxyClear tube |
Corning |
Cat#MCT-150-A |
| Critical commercial assays |
| Direct-zol RNA Microprep |
Zymo |
R2061 |
| Micro Bio-spin P-30 gel columns |
Bio-rad |
7326251 |
| NEBNext® Ultra™ II DNA Library Prep Kit for Illumina |
NEB |
E7645 |
| CUTANA pAG-MNAse |
Epicypher |
15-1016 |
| CUTANA Concanavalin A Conjugated Paramagnetic Beads |
Epicypher |
21-1401 |
| Power Blotter Station |
ThermoFisher |
PB0010 |
| MaxCyte STX Scalable Transfection System |
Maxcyte |
NA |
| 4–20% Mini-PROTEAN® TGX™ Precast Protein Gels, 15-well, 15 μl |
Bio-Rad |
#34561096 |
| Mini-PROTEAN Tetra Vertical Electrophoresis Cell |
Bio-Rad |
1658004 |
| Monarch Gel Extraction |
NEB |
T1020L |
| Deposited data |
| Raw and analyzed sequencing data |
This paper |
GEO: GSE184187
|
| Brd7 IP-MS |
This paper |
PRIDE: PXD036007 |
| Mendeley Dataset |
This paper |
DOI: 10.17632/zj2f34rwff.1
|
| STAP-seq cofactor recruitment data |
Haberle et al. 2019
|
GEO: GSE116197
|
| S2 dCP and hkCP STARR-seq |
Zabidi et al., 2015
|
GEO: GSE57876
|
| BG3 STARRseq |
Yanez Cuna et al., 2014 |
GEO: GSE49809
|
| Drosophila CAGE data |
modEncode |
http://www.modencode.org/publications/fly_2010pubs/index.shtml
|
| Nucleosome Occupancy Prediction score |
Segal Lab |
https://genie.weizmann.ac.il/pubs/nucleosomes08/. |
| Oligonucleotides |
| Primers for AID tagging |
This Paper |
Table S1
|
| 5’- /5Phos/rNrNrN rNrNrN rNrNrG rArUrC rGrUrC rGrGrA rCrUrG rUrArG rArArC rUrCrU rGrArA rC/3InvdT/ -3’ |
IDT |
N/A |
| 5- rCrCrU rUrGrG rCrArC rCrCrG rArGrA rArUrU rCrCrA rNrNrN rN -3 (5’ RNA linker) |
IDT |
N/A |
| Recombinant DNA |
| pBabe Puro osTIR1-9Myc |
Addgene |
plasmid #80074 |
| pAc-sgRNA-Cas9 |
Addgene |
plasmid #49330 |
| pCRIS-PITChv2-FBL |
Addgene |
plasmid #63672 |
| Software and algorithms |
| Benchling |
N/A |
https://benchling.com
|
| R version 3.5.3 |
R Development Core Team, 2019 |
https://www.r-project.org
|
| Cutadapt |
Martin et al. 2011 |
https://bioweb.pasteur.fr/packages/pack@cutadapt@1.18
|
| Samtools version 1.9 |
Li et al. 2009 |
http://www.htslib.org/
|
| bowtie version 1.2.2 |
Langmead et al., 2009 |
https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.2/
|
| GenomicRanges 1.34.0 |
Lawrence et al. 2013 |
https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
|
| bigBedtoBed |
Kent et al. 2010 |
https://github.com/ENCODE-DCC/kentUtils/blob/master/src/utils/bigBedToBed/bigBedToBed.c
|
| bedtools 2.27.1 |
Quinlan & Hall 2010 |
https://github.com/arq5x/bedtools2/releases/tag/v2.30.0
|
| DESeq2 package v.1.30.1 |
Love et al. 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
