KEY RESOURCES TABLE
REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Living Colors A.v. Monoclonal GFP Antibody (JL-8) | Clontech Laboratories | Cat # 632381; RRID:AB_2313808 |
c-Myc (D84C12) Rabbit mAb | Cell Signaling Technology | Cat # 5605S; RRID:AB_1903938 |
GAPDH rabbit polyclonal Antibody (FL-335) | Santa Cruz Biotecnology | Cat # sc-25778; RRID:AB_10167668 |
Mouse monoclonal anti-vinculin Antibody | Sigma-Aldrich | Cat # V9131; RRID:AB_477629 |
anti-p53 ser15 rabbit antibody #9284 | Cell Signaling Technology | Cat # 9284s |
anti-p21 antibody | Calbiochem/EMD | Cat # OP64 |
E2F1 antibody | Cell Signaling Technology | Cat # #3742 |
Chemicals, Peptides, and Recombinant Proteins | ||
Clontech Labs Doxycycline (5g) | Fisher Scientific | Cat # NC0424034 |
Critical Commercial Assays | ||
GeneJET Genomic DNA Purification Kit | Thermo Fisher Scientific | Cat # K0722 |
NEBNext Ultra RNA Library Prep Kit for Illumina | NEB | E7530S |
RNeasy Plus Mini Kit | QIAGEN | 74134 |
NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) | NEB | E7335S |
NEBNext Poly(A) mRNA Magnetic Isolation Module | NEB | E7490S |
Deposited Data | ||
Human cancer gene expression data | TCGA | https://tcga-data.nci.nih.gov/docs/publications/tcga |
CCLE cancer gene expression data | Cancer Cell Line Encyclopedia | Barretina et al., 2012 |
SCNA data | TCGA | https://tcga-data.nci.nih.gov/docs/publications/tcga? |
RNA-seq | This paper | GSE109326 |
Experimental Models: Cell Lines | ||
rtTA-HMEC clone 1-9 | This paper | N/A |
rtTA-HPNE clone 5-12 | This paper | N/A |
rtTA-IMR90 cells | This paper | N/A |
rtTA-MCF7 cells | This paper | N/A |
rtTA-HMEC 1-9 p53−/− | This paper | N/A |
hTERT-HMECs | Solimini et al., 2012 | N/A |
hTERT-IMR90s | This paper | N/A |
hTERT-HPNEs | Campbell lab | N/A |
MCF7s | Polyak lab | N/A |
Experimental Models: Organisms/Strains | ||
NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) | The Jackson Laboratory | Cat # 005557; RRID:IMSR_JAX:005557 |
Recombinant DNA | ||
Human genome-scale ORF Libraries 1 and 2 | This paper | N/A |
HMEC ORF sublibrary | This paper | N/A |
pInducer-rtTA-Neo | This paper | N/A |
pHAGE-TRE-ORF-BC-3′ | This paper | N/A |
pInducer20-EGFP | This paper | N/A |
pX330-U6-Chimeric_BB-CBh-hSpCas9 | Cong et al., 2013; Addgene | Plasmid #42230 |
lentiCRISPR V2 puro vector | Addgene | Plasmid #52961 |
psPax2 | Addgene | Plasmid #12260 |
pMD2.G | This paper | Plasmid #12259 |
E2F1sh-1 GGAGTTCATCAGCCTTTCCCCA | This paper | N/A |
E2F1sh-2 TAAGAGCAAACAAGGCCCGATC | This paper | N/A |
E2F1sh-3 GTGGACTCTTCGGAGAACTTT | This paper | N/A |
E2F1sh-4 ATGAGACCTCACTGAATCTGAC | This paper | N/A |
OR11L1 -sh (control sh, ctr-sh) ACCACCTGTTGCCTGAAATCAAT | This DaDer | N/A |
Sequence-Based Reagents | ||
PCR Primer ORF.BC1.For: CCAGTAGGTCCACTATGAGT | This paper | N/A |
PCR Primer ORF.BC1.Rev: CTAGTTCCGCTTACACAGCT | This paper | N/A |
PCR Primer ISP-ORF.BC1 .For: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAGTAGGTCCACTATGAGT | This paper | N/A |
PCR Primer P5-ORF.BC1.Rev: AATGATACGGC GACCACCGACTAGTT CCGCTTACACAGCT | This paper | N/A |
PCR Primer P7-Index-ISP: CAAGCAGAAGACGGCATACGAGATxxxxxxxGTGACTGGAGTT CAGACGTGT | Meyer and Kircher, 2010 | N/A |
Sequencing Primer heyME19: GCGACCACCGACTAGTTCCGCTTACACAGCT | This paper | N/A |
TP53 sgRNA: GTTGCAAACCAGACCTCAGG | This paper | N/A |
Software and Algorithms | ||
edgeR | Robinson et al., 2010 | http://www.bioconductor.org/packages/release/bioc/html/edgeR.html; RRID:SCR_012802 |
GSEA | Mootha et al., 2003; Subramanian et al., 2005 | http://software.broadinstitute.org/gsea/index.jsp; RRID:SCR_003199 |
Bowtie 2 | Langmead et al., 2009; Langmead and Salzberg 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
limma | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
Mageck | Li etal., 2014 | https://sourceforge.net/projects/mageck/ |
GISTIC2 | Mermel et al., 2011 | http://archive.broadinstitute.org/cancer/cga/gistic |