|
Antibodies
|
|
Anti-FLAG M2 Magnetic Beads
|
Sigma-Aldrich |
M8823 |
|
Anti-FLAG M2 antibody |
Sigma-Aldrich |
F3165 |
| Alexa Fluor 488 Secondary Antibody |
Thermo Fisher Scientific |
A-11034 |
| Alexa Fluor 594 Secondary Antibody |
Thermo Fisher Scientific |
A-11032 |
| Anti-HNRNPF Antibody |
|
hpa069667 |
| Anti-PKM2 (D78A4) |
Cell Signaling |
4053 |
| Anti-PKM |
Abcam |
ab150377 |
| Anti-RNA polymerase II CTD repeat YSPTSPS antibody - ChIP Grade |
Abcam |
ab26721 |
| Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody |
Abcam |
(ab5095) |
| Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody |
Abcam |
(ab5131) |
| GAPDH |
ProteinTech |
10494-1-AP |
|
|
|
|
|
|
|
|
|
|
Bacterial and virus strains
|
| E. coli BL21 |
NEB |
C2527H |
| E. coli C321.ΔA |
Addgene |
48998 |
| E. coli 5-alpha |
NEB |
C2987H |
|
|
|
|
Chemicals, peptides, and recombinant proteins
|
| 4-Thiouridine |
BIOSYNTH |
NT06186 |
| ATP Solution (100 mM) |
Thermo |
R0441 |
| Blasticidin S |
Gibco |
A1113903 |
| Blasticidin S HCl |
Gibco |
A1113903 |
| Chloroform:Isoamyl alcohol 24:1 |
Sigma |
C0549-1PT |
| cOmplete Protease Inhibitor Cocktail |
Roche |
1.1697E+10 |
| Deoxynucleotide (dNTP) Solution Mix |
NEB |
10966034 |
| DMEM, high glucose |
Gibco |
11965092 |
| Dynabeads Protein G for Immunoprecipitation |
Invitrogen |
10004D |
| EMEM |
ATCC |
30-2003 |
| Fetal Bovine Serum |
GeminiBio |
100-800 |
| FLAG Peptide |
Sigma |
F3290 |
| Gateway BP Clonase II Enzyme mix |
Invitrogen |
11789020 |
| Gateway LR Clonase II Enzyme mix |
Invitrogen |
11791020 |
| GlycoBlue Coprecipitant |
Thermo Fisher Scientific |
AM9515 |
| HisPur™ Ni-NTA Magnetic Beads |
Thermo Scientific |
88831 |
| Hygromycin B |
Gibco |
10687010 |
| Insulin solution from bovine pancreas |
Sigma |
I0516 |
| IPTG |
MP Biomedicals |
02102101-CF |
| Lipofectamine 3000 |
Invitrogen |
L3000001 |
| Lipofectamine RNAiMAX |
Invitrogen |
13778075 |
| Opti-MEM I Reduced Serum Medium |
Gibco |
31985070 |
| PageRuler Plus, Prestained Protein Ladder |
Thermo Fisher Scientific |
26620 |
| Penicillin-Streptomycin |
Gibco |
15140163 |
| Platinum Taq DNA polymerase |
Thermo Fisher Scientific |
10966034 |
| Proteinase K |
Millipore Sigma |
3115879001 |
| Puromycin Dihydrochloride |
Gibco |
A1113803 |
| Quick CIP |
NEB |
M0525S |
| RNase I |
Thermo Fischer Scientific |
AM2294 |
| RNase T1 |
Thermo Fischer Scientific |
EN0542 |
| Rnl1 T4 RNA ligase |
Thermo Fischer Scientific |
EL0021 |
| SUPERase•In RNase inhibitor |
Thermo Fisher Scientific |
AM2694 |
| Superscript IV |
Thermo Fisher Scientific |
18090010 |
| T4 PNK |
NEB |
M0201S |
|
|
|
|
|
|
|
|
|
|
Critical commercial assays
|
| EnzyChrom Pyruvate Kinase Assay Kit |
Bio Assay Systems |
EPRK-100 |
| EnzyLight ATP Assay kit |
Bio Assay Systems |
EATP-100 |
|
|
|
|
|
|
|
|
|
|
Deposited data
|
| RNA-Seq |
This study |
GSE179817 |
| PARCLIP |
This study |
GSE179817 |
| RBNS |
This study |
GSE179817 |
| CHIP-Seq |
This study |
GSE179817 |
| Normalized TCGA expression data |
TCGA |
GSE62944 |
| Hybrid E/M state breast cancer cells |
Kröger et al.76
|
GSE119149 |
|
|
|
|
Experimental models: Cell lines
|
| HEK293 T-Rex Flp-In |
Thermo Fisher Scientific |
R78007 |
| MCF-7 |
ATCC |
HTB-22 |
| MDA-MB-231 |
ATCC |
HTB-26 |
| 293T/17 [HEK 293T/17] |
ATCC |
CRL-11268 |
|
|
|
|
Experimental models: Organisms/strains
|
| NOD scid gamma (NSG) mice |
The Jackson Laboratory |
005557 |
|
|
|
|
Oligonucleotides
|
| DsPKM 3’UTR |
IDT |
hs.Ri.PKM.13.3 |
| DsSCRAMBLE |
IDT |
51-01-14-03 |
|
|
|
|
|
|
|
|
|
|
Plasmids
|
| pOG44 Flp-Recombinase Expression Vector |
Invitrogen |
V600520 |
| pLKO.1 |
Addgene |
8453 |
| pFRT_TO_DESTFLAGHA |
Addgene |
26361 |
| pMDLg/pRRE |
Addgene |
12251 |
| pRSV-Rev |
Addgene |
12253 |
| pMD2.G |
Addgene |
12259 |
| pET-28a-hPKM1 |
Addgene |
44241 |
| pET-28a-hPKM2 |
Addgene |
44242 |
| pCRT7 NT Topo |
Addgene |
73446 |
| SepOTSA |
Addgene |
68292 |
|
|
|
|
|
|
|
Software and algorithms
|
| ImageJ |
Fiji |
SCR_002285 |
| GraphPad Prism |
GraphPad |
https://www.graphpad.com/
|
| ChimeraX |
Petterson et al.95
|
http://plato.cgl.ucsf.edu/chimerax/download.html
|
| Samtools Version: 1.9 |
Li et al.96
|
https://samtools.sourceforge.net/
|
| PyMOL |
Schrödinger |
https://www.pymol.org
|
| Cutadapt v2.4 |
Martin97
|
https://github.com/marcelm/cutadapt
|
| STAR v2.7.2b |
Dobin et al.98
|
https://github.com/alexdobin/STAR
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Other
|
| Slide-A-Lyzer™ Dialysis Cassette, 10K MWCO |
Thermo Fisher Scientific |
66380 |
| Pierce™ Protein Concentrators PES |
Thermo Fisher Scientific |
88513 |
| Ni-charged MagBeads |
GenScript |
L00295 |
|
|
|
|
|
|
