| Antibodies |
| CDK4 |
Cell Signaling |
Cat#12790, RRID:AB_2631166 |
| CDK6 |
Santa Cruz |
Cat#sc-7961, RRID:AB_627242 |
| Histone 3 |
Abcam |
Cat#ab1791, RRID:AB_302613 |
| β-actin |
Sigma-Aldrich |
Cat#A5441, RRID:AB_476744 |
| p-Rb S780 |
Cell Signaling |
Cat#8180, RRID:AB_10950972 |
| Rb |
Cell Signaling |
Cat#9309, RRID:AB_823629 |
| Peroxidase-conjugated AffiniPure Goat Anti-Mouse IgG |
Jackson Immuno Research |
Cat#115–035-003, RRID:AB_10015289 |
| Peroxidase-conjugated AffiniPure Goat Anti-Rabbit IgG |
Jackson Immuno Research |
Cat#111–035-003, RRID:AB_2313567 |
| Chemicals, Peptides, and Recombinant Proteins |
| BSJ-03–123 |
This study |
N/A |
| BSJ-bump |
This study |
N/A |
| YKL-06–102 |
This study |
N/A |
| Palbociclib |
Selleckchem |
Cat#S1116 |
| Critical Commercial Assays |
| Caspase-Glo 3/7 |
Promega |
Cat#G8090 |
| NanoBiT |
Promega |
Cat#N2011 |
| Deposited Data |
| Project Achilles: CRISPR-Cas9 Avana |
Meyers et al., 2017 |
https://portals.broadinstitute.org/achilles/datasets/18/download |
| Gene expression data of 675 cell lines |
Klijn et al., 2015 |
https://www.nature.com/articles/nbt.3080#supplementary-information |
| ENCODE transcription factor targets |
ENCODE Consortium |
http://amp.pharm.mssm.edu/Harmonizome/dataset/ENCODE+Transcription+Factor+Targets |
| Human protein-protein interaction network |
Alanis-Lobato et al., 2016 |
http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/ |
| Human reference genome NCBI build 38, GRCh38 |
|
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/ |
| RNA sequencing upon CDK6 degradation |
This study |
GEO: GSE116187
|
| CDK4/6 targets |
Anders et al., 2011 |
https://doi.org/10.1016/j.ccr.2011.10.001 |
| Experimental Models: Cell Lines |
| MV4–11 |
ATCC |
RRID:CVCL_0064 |
| THP-1 |
ATCC |
RRID:CVCL_0006 |
| MOLM13 |
DMSZ |
RRID:CVCL_2119 |
| P31/FUJ |
CCLE/Broad Institute |
RRID:CVCL_1632 |
| MOLT4 |
ATCC |
RRID:CVCL_0013 |
| NCI-H358 |
ATCC |
RRID:CVCL_1559 |
| HT29 |
ATCC |
RRID:CVCL_0320 |
| HEK293T |
ATCC |
RRID:CVCL_0063 |
| Hs578T |
ATCC |
RRID:CVCL_0332 |
| Oligonucleotides |
| sgCDK4 sense (5’- CACCGAGCCACTGGCTCATATCGAG-3’) |
Sigma-Aldrich |
N/A |
| sgCDK4 antisense (5’- AAACCTCGATATGAGCCAGTGGCTC-3’) |
Sigma-Aldrich |
N/A |
| sgCRBN sense (5’- CACCGTAAACAGACATGGCCGGCGA-3’) |
Sigma-Aldrich |
N/A |
| sgCRBN antisense (5’- AAACTCGCCGGCCATGTCTGTTTAC-3’) |
Sigma-Aldrich |
N/A |
| Recombinant DNA |
| Lenti_sgRNA_EFS_GFP |
Addgene |
https://www.addgene.org/65656 |
| pBit1.1-C [TK/LgBiT] |
Promega |
Cat#N2014 |
| pBit2.1-N [TK/SmBiT] |
Promega |
Cat#N2014 |
| Software and Algorithms |
| Cytoscape |
Institute for Systems Biology |
http://cytoscape.org;RRID:SCR_003032 |
| GraphPad Prism |
|
https://www.graphpad.com/scientific-software/prism/ |
| Proteome Discoverer |
Thermo Fisher Scientific |
https://www.thermofisher.com/order/catalog/product/OPTON-30795 |
| KSEA App |
|
https://casecpb.shinyapps.io/ksea |
| STAR Aligner |
|
https://github.com/alexdobin/STAR |
| limma |
|
https://bioconductor.org/packages/release/bioc/html/limma.html |
| GOrilla |
|
http://cbl-gorilla.cs.technion.ac.il/ |
| networkx |
|
https://networkx.github.io/ |
