Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Streptavidin-HRP | GE Healthcare | Cat#RPN1231; |
| Oct-3/4 (N-19) antibody | Santa Cruz | Cat#sc-8628; RRID: AB_653551 |
| c-Myc antibody | Cell Signaling Technology | Cat#9402; RRID: AB_2151827 |
| H3K4me3 antibody | Abcam | Cat#ab1012; RRID: AB_442796 |
| H3K9ac antibody | Abcam | Cat#ab4441; RRID: AB_2118292 |
| RNA Pol II CTD, phos. Serine 5 [3E8] antibody | Chromotek | Cat#3e8–5; RRID: AB_2631404 |
| RNA Pol II CTD, phos. Serine 2 [3E10] antibody | Chromotek | Cat#3e10–5; RRID: AB_2631403 |
| RNA Pol II CTD, unphosphorylated CTD [1C7] antibody | Chromotek | Cat#1c7–5; RRID: AB_2631402 |
| Bacterial and Virus Strains | ||
| E.cloni 10G ELITE electrocompentent cells | Lucigen | Cat#60052–4 |
| Critical Commercial Assays | ||
| QIAGEN MinElute PCR purification kit | QIAGEN | Cat#28006 |
| APC BrdU Flow Kit | BD | Cat#552598 |
| Vector Red Substrate Kit | Vector Lab | Cat#SK-5100 |
| Agilent Seahorse XF Cell Mito Stress Test Kit | Agilent | Cat#103015–100 |
| iQ SYBR Green Supermix | Bio-Rad | Cat#1708882 |
| iScript cDNA Synthesis Kit | Bio-Rad | Cat#1708891 |
| RNeasy Mini Kit | QIAGEN | Cat#74106 |
| rRNA Depletion Kit | NEB | Cat#E6310L |
| NEBNext Ultra Directional RNA Library Prep Kit | NEB | Cat#E7420L |
| NEBNext ChIP-seq Library Prep Master Mix Set for Illumina | NEB | Cat#6240L |
| NEBNext Ultra DNA Library Prep Kit for Illumina | NEB | Cat#E7370L |
| Dynabeads MyOne Streptavidin T1 beads | Thermo Fisher Scientific | Cat#65601 |
| Dynabeads Protein A | Thermo Fisher Scientific | Cat#10002D |
| Dynabeads Protein G | Thermo Fisher Scientific | Cat#10004D |
| NE-PER reagents | Thermo Fisher Scientific | Cat#78833 |
| Deposited Data | ||
| RNA-seq and ChIP-seq data | This paper | GEO: GSE113335 |
| ChIP-seq data | Das et al., 2014 | GEO: GSE43231 |
| Mendeley dataset | This paper | https://doi.org/10.17632/gkp97zr5zy.1 |
| Experimental Models: Cell Lines | ||
| J1 mouse embryonic stem cells | ATCC | Cat#SCRC-1010, RRID:CVCL_6412 |
| Taf5l, Taf6l, c-Myc KO mESCs | This paper | N/A |
| HEK293T | ATCC | Cat#CRL-3216; RRID: CVCL_0063 |
| Experimental Models: Organisms/Strains | ||
| Mouse embryonic fibroblast isolated from ROSA26-rtTA, Collagen-OKSM, Oct4-GFP mouse embryos | Stadtfeld et al., 2010 | JAX: 011001; 008214; 006965 |
| Recombinant DNA | ||
| Lentiguide-Puro | Sanjana et al., 2014 | Addgene Plasmid # 52963 |
| LentiCRISPR-mCherry V6 | Unpublished | Addgene Plasmid #99154 |
| LentiCas9-Blast | Sanjana et al., 2014 | Addgene Plasmid #52962 |
| Software and Algorithms | ||
| BEDTools (2.26.0) | Quinlan and Hall, 2010 | http://bedtools.readthedocs.io/en/latest/ |
| Bowtie 2 (2.3.2) | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MACS2 (2.1.1.20160309) | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| DeepTools (2.5.3) | Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ |
| STAR (2.5.3a) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Salmon (0.8.2) | Patro et al., 2017 | https://combine-lab.github.io/salmon/ |
| wigToBigWig, Kent tools (v4) | Kent et al., 2010 | http://hgdownload.cse.ucsc.edu/admin/exe/ |
| DESeq2 R package (1.14.1; Bioconductor 3.4) | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| DiffBind R package (2.2.12; Bioconductor 3.4) | Ross-Innes et al., 2012 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| R statistical program (3.3.2) | N/A | https://www.R-project.org/ |
| ggplot2 R package (2.2.1) | N/A | http://ggplot2.tidyverse.org |
| pheatmap R package (1.0.8) | N/A | https://cran.r-project.org/web/packages/pheatmap/index.html |
| NIH DAVID website (6.8) | Dennis et al., 2003 | https://david.ncifcrf.gov/ |
| Mendeley dataset | This paper | https://doi.org/10.17632/gkp97zr5zy.1 |