| Antibodies |
| Anti-H4K16ac, rabbit polyclonal |
Millipore |
Cat# 07-329, RRID:AB_310525 |
| Anti-H3K4me3, rabbit monoclonal |
Millipore |
Cat# 04-745, RRID:AB_1163444 |
| Anti-H3K27ac, rabbit monoclonal |
RevMab |
Cat# 31-1056, RRID:AB_2716381 |
| Anti-H3K9ac, rabbit monoclonal |
RevMab |
Cat# 31-1054, RRID:AB_2716379 |
| Anti-H3K9me2, mouse monoclonal |
Abcam |
Cat# ab1220, RRID:AB_449854 |
| Anti-H3K36me2, rabbit polyclonal |
Abcam |
Cat# ab9049, RRID:AB_1280939 |
| Anti-H3, rabbit polyclonal |
Abcam |
Cat# ab1791, RRID:AB_302613 |
| Anti-H4, rabbit polyclonal |
Abcam |
Cat# ab7311, RRID:AB_305837 |
| Anti-H4K5/8/12ac, rabbit monoclonal |
Millipore |
Cat# 04-557, RRID:AB_870989 |
| Anti-Oct4, rabbit polyclonal (Western Blot) |
Santa Cruz Biotechnology |
Cat# sc-9081, RRID:AB_2167703 |
| Anti-Oct4, mouse monoclonal (IF) |
Santa Cruz Biotechnology |
Cat# sc-5279, RRID:AB_628051 |
| Anti-Nanog, rabbit monoclonal |
Cell Signaling Technology |
Cat# 4903, RRID:AB_10559205 |
| Anti-RNA Polymerase II, mouse monoclonal |
Abcam |
Cat# ab817, RRID:AB_306327 |
| Anti-RNA Polymerase II phospho-S2 (Pol II S2p), rabbit polyclonal |
Abcam |
Cat# ab5095, RRID:AB_304749 |
| Anti-EGFP, rabbit polyclonal |
Thermo Fisher Scientific |
Cat# A-11122, RRID:AB_221569 |
| Anti-Topors |
Santa Cruz Biotechnology |
Cat# sc-292009, RRID:AB_10852342 |
| Anti-Chd1, rabbit monoclonal |
Cell Signaling Technology |
Cat# 4351S, RRID:AB_11179073 |
| Anti-Tip60, rabbit |
GeneTex |
Cat# GTX112197, RRID:AB_1950610 |
| Anti-Brd1, mouse monoclonal |
Developmental Studies Hybridoma Bank |
Cat# PCRP-BRD1-2H2, RRID:AB_2618449 |
| Anti-Btf3, goat polyclonal |
R and D Systems |
Cat# AF5747, RRID:AB_2067525 |
| Anti-Gapdh, mouse monoclonal |
Millipore |
Cat# MAB374, RRID:AB_2107445 |
| Anti-beta-actin, rabbit polyclonal |
Abcam |
Cat# ab8227, RRID:AB_2305186 |
| Anti-Hp1alpha, mouse monoclonal |
Millipore |
Cat# 05-689, RRID:AB_11213599 |
| Anti-Ezh2, rabbit monoclonal |
Cell Signaling Technology |
Cat# #5246, RRID:AB_10694683 |
| Anti-G9a, mouse monoclonal |
Thermo Fisher Scientific |
Cat# 435200, RRID:AB_2532211 |
| Anti-IgG, rabbit |
Abcam |
Cat# ab46540, RRID:AB_2614925 |
| Anti-rabbit IgG HRP |
Jackson ImmunoResearch Labs |
Cat# 111-035-144, RRID:AB_2307391 |
| Anti-mouse IgG HRP |
Jackson ImmunoResearch Labs |
Cat# 115-035-062, RRID:AB_2338504 |
| Anti-goat IgG HRP |
Santa Cruz Biotechnology |
Cat# sc-2768, RRID:AB_656964 |
|
|
|
| Bacterial and Virus Strains |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Biological Samples |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Chemicals, Peptides, and Recombinant Proteins |
| Cycloheximide, translation inhibitor |
Amresco |
Cat# 94271 |
| INK128, mTor inhibitor |
Medchem |
Cat# HY13328 |
| 10058-F4, Myc inhibitor |
Sigma |
Cat# F3680 |
| Homoherringtonine, translation inhibitor |
Sigma |
Cat# SML1091 |
| AZD8055, mTor inhibitor |
Selleckchem |
Cat# S1555 |
| a-amanitin, Pol II inhibitor |
Sigma |
Cat# A2263 |
| CX-5461, Pol I inhibitor |
Selleckchem |
Cat# S2684 |
| MG132, proteasome inhibitor |
Selleckchem |
Cat# S2619 |
| LIF |
Millipore |
Cat# ESG1107 |
| PD0325901 |
Stemgent |
Cat# 04-0006 |
| CHIR99021 |
Selleckchem |
Cat# S2924 |
| 2-phospho ascorbic acid |
Sigma |
Cat#A8960 |
| Retinoic acid |
Sigma |
Cat#R2625 |
| B27 supplement 50x |
Life Technologies |
Cat# 17504044 |
| N2 supplement 100x |
Life Technologies |
Cat# 17502048 |
| Fetal bovine serum |
Atlanta Biologicals |
Cat# S 11150 |
| GlutaMAX |
Gibco |
Cat# 3505-061 |
| DMEM with high glucose, GlutaMAX, Na pyruvate |
Gibco |
Cat# 10569044 |
| Neurobasal |
Gibco |
Cat# 21103-049 |
| DMEM/F-12 |
Gibco |
Cat# 10565-018 |
| EmbryoMax 2-Mercaptoethanol 100X |
Millipore |
Cat# ES-007-E |
| Penicillin-Streptomycin (10,000 U/ml) |
UCSF Cell Culture Facility |
Cat# 15140122 |
| Non-essential amino acids solution (100X) |
UCSF Cell Culture Facility |
Cat# 11140050 |
| Gelatin solution, type B, 2% |
Sigma |
Cat# G1393 |
| EGF |
PeproTech |
Cat# AF-100-15 |
| BFGF |
PeproTech |
Cat# 100-18B |
| Heparin sodium salt |
Sigma |
Cat# H3149 |
| Fraction V BSA, 7.5% solution |
Gibco |
Cat# 15260-037 |
| Poly-D-Lysine |
Millipore |
Cat# A-003-E |
| Laminin |
Sigma |
Cat# L2020 |
| KSOMaa Evolve |
Zenith Biotech |
Cat# ZEKS-050 |
| M2 |
Zenith Biotech |
Cat# ZFM2-100 |
| DMSO |
Sigma |
Cat# D2650 |
| DMEM high glucose, - Met/Cys |
Gibco |
Cat# 21013-024 |
| DMEM minus L-Lysine, L-Arginine |
Cambridge Isotope Laboratories |
Cat# DMEM-500 |
| Dialyzed fetal bovine serum |
Cambridge Isotope Laboratories |
Cat# FBS-50 |
| L-Lysine:2HCL unlabeled |
Cambridge Isotope Laboratories |
Cat# ULM-8766 |
| L-Arginine:HCL unlabeled |
Cambridge Isotope Laboratories |
Cat# ULM-8347 |
| L-Lysine:2HCL (4,4,5,5-D4, 96–98%) |
Cambridge Isotope Laboratories |
Cat# DLM-2640-PK |
| L-Arginine:HCL (13C6, 99%) |
Cambridge Isotope Laboratories |
Cat# CLM-2265-H |
| L-Lysine:2HCL (13C6, 99%; 15N2, 99%) |
Cambridge Isotope Laboratories |
Cat# CNLM-291-H |
|
|
|
| Critical Commercial Assays |
|
|
| Protein A Dynabeads |
Invitrogen |
Cat# 10002 |
| Diagenode Low Cell ChIP kit |
Diagenode |
Cat# C01010070 |
| NEBNext ChIP-seq Library Prep for Illumina kit |
NEB |
Cat# E6200 |
| NEBNext Multiplex Oligos for Illumina (Index Primers set 1) |
NEB |
Cat# E7335S |
| Agilent High Sensitivity DNA kit |
Agilent |
Cat# 5067-4626 |
| RNeasy Mini/Micro kits |
Qiagen |
Cat# 74104/4 |
| Click-iT Nascent RNA Capture kit |
Life Technologies |
Cat# C10365
|
| Click-iT RNA Alexa Fluor 488 or 594 HCS Assay kits |
Life Technologies |
Cat# C10327/8 |
| Click-iT HPG Alexa Fluor 488 Protein Synthesis Assay kit |
Life Technologies |
Cat# C10428
|
| Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit |
Life Technologies |
Cat# C10420
|
| Nextera DNA Library Prep kit |
Illumina |
Cat# FC-121-1030 |
| KAPA Library Quantification kit |
KAPA Biosystems |
Cat# 07960204001 |
| DharmaFECT 1 Transfection Reagent |
Dharmacon |
Cat# T-2001-03 |
| Custom siRNA library, Cherry-pick Library 0.1 nmol |
Dharmacon |
Cat# G-CUSTOM-177075 |
|
|
|
| Deposited Data |
|
|
| Raw and processed sequencing data |
NCBI Gene Expression Omnibus |
GEO: GSE98358
|
|
|
|
| Experimental Models: Cell Lines |
|
|
| E14TG2a ES cells |
Bill Skarnes, Sanger Institute |
(Hooper et al., 1987) |
| Mouse embryonic fibroblasts |
This study |
|
| Neural stem/progenitor cells |
Daniel Lim, UCSF |
(Hudlebusch et al., 2011) |
| FUCCI cells |
Benoit Bruneau, UCSF |
(Nora et al., 2017) |
|
|
|
| Experimental Models: Organisms/Strains |
|
|
| Swiss Webster |
Charles River |
Strain # 024 |
|
|
|
| Oligonucleotides |
|
|
|
|
|
|
|
|
| Recombinant DNA |
|
|
| pCAGGS-Chd1chr-EGFP-IRES-Puro |
This study |
N/A |
| pCAGGS-Hp1α-EGFP-IRES-Puro |
(Bulut-Karslioglu et al., 2014) |
N/A |
|
|
|
| Software and Algorithms |
|
|
| FlowJo, v10 |
FlowJo LLC |
https://www.flowjo.com/ |
| Prism, 7.0a |
GraphPad |
https://www.graphpad.com/scientific-software/prism/ |
| Cell Profiler |
(Carpenter et al., 2006) |
http://cellprofiler.org/ |
| GNU Image Manipulation Program (GIMP) 2.8.22 |
GPLv3 |
https://www.gimp.org/ |
| GREAT |
(McLean et al., 2010) |
http://great.stanford.edu/public/html/ |
| Bowtie2, v2.2.4 |
(Langmead and Salzberg, 2012) |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools |
(Li et al., 2009) |
http://www.htslib.org/ |
| R |
R core team |
http://www.R-project.org/ |
| Rsubread package, version 1.24.1 |
(Liao et al., 2013) |
https://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| R Bioconductor |
(Huber et al., 2015) |
https://www.bioconductor.org/ |
| Macs14, version 1.4.2 20120305 |
(Zhang et al., 2008) |
http://liulab.dfci.harvard.edu/MACS/index.html |
| DeepTools |
(Ramirez et al., 2016) |
https://deeptools.readthedocs.io/en/latest/# |
| Galaxy |
(Afgan et al., 2016) |
https://usegalaxy.org/ |
| Homer, version 4.7 |
(Heinz et al., 2010) |
http://homer.ucsd.edu/homer/motif/ |
| PAVA in-house software |
(Guan et al., 2011) |
N/A |
| ProteinProspector, version 5.10.10 |
UCSF Mass Spectrometry Facility |
http://prospector.ucsf.edu |
|
|
|
| Other: Datasets reanalyzed |
|
|
| H3K4me1 ChIP-seq |
GSM1003750 |
(ENCODE Project Consortium, 2012) |
| H3K4me3 ChIP-seq |
GSM1003756 |
(ENCODE Project Consortium, 2012) |
| H3K27ac ChIP-seq |
GSM1000126 |
(ENCODE Project Consortium, 2012) |
| H3K27me3 ChIP-seq |
GSM1000089 |
(ENCODE Project Consortium, 2012) |
| H3K9me3 ChIP-seq |
GSM1003751 |
(ENCODE Project Consortium, 2012) |
| DNaseI-seq |
GSM1014154 |
(ENCODE Project Consortium, 2012) |
| p300 ChIP-seq |
GSM918750 |
(ENCODE Project Consortium, 2012) |
| H2A.Z ChIP-seq |
GSM958501 |
(Ku et al., 2012) |
| Acetylated H2A.Z ChIP-seq |
GSM958502 |
(Ku et al., 2012) |
| H3.3 ChIP-seq |
GSM423355 |
(Goldberg et al., 2010) |
| Mappability track |
UCSC Table Browser |
(Karolchik et al., 2004) |
|
|
|
|
|
|
|
|
|
|
|
|
