| Cell line (Homo sapiens) |
CaSki (HPV16+) |
ATCC |
CRL-1550 |
Cervical cancer cell line |
| Cell line (Homo sapiens) |
C4II (HPV18+) |
ATCC |
CRL-1595 |
Cervical cancer cell line |
| Cell line (Homo sapiens) |
SiHa (HPV16+) |
ATCC |
HTB-35 |
Cervical cancer cell line |
| Cell line (Homo sapiens) |
HeLa (HPV18+) |
ATCC |
CCL-2 |
Cervical cancer cell line |
| Cell line (Homo sapiens) |
C33A (HPV-) |
ATCC |
HTB-31 |
Cervical cancer cell line |
| Cell line (Homo sapiens) |
HEK293 |
ATCC |
CRL-1573 |
Kidney epithelial-like cell |
| Cell line (Homo sapiens) |
HCT116 |
Dr. Bert Vogelstein (Johns Hopkins University) |
N/A |
Colorectal cancer cell line |
| Cell line (Homo sapiens) |
W12 subclones (20861, 20863) |
Dr. Paul Lambert (University of Wisconsin) |
N/A |
HPV16+ (integrated/episomal) |
| Cell line (Homo sapiens) |
BCBL-1 (KSHV+) |
NIH AIDS Reagent Program |
N/A |
Body cavity B lymphoma |
| Cell line (Homo sapiens) |
HaCaT |
Dr. Carl C Baker (NIH) |
N/A |
Skin keratinocyte |
| Antibody |
Anti-MCAM (Rabbit polyclonal) |
ProteinTech |
Cat# 17564-1-AP |
Rabbit polyclonal; WB (1:1000), IF (1:200) |
| Antibody |
Anti-E2F1 (Rabbit polyclonal) |
ProteinTech |
Cat# 12171-1-AP |
Rabbit polyclonal; WB (1:1000) |
| Antibody |
Anti-MAP4K4 (Rabbit polyclonal) |
ProteinTech |
Cat# 55247-1-AP |
Rabbit polyclonal; WB (1:1000) |
| Antibody |
Anti-p53 (Rabbit polyclonal) |
ProteinTech |
Cat# 10442-1-AP |
Rabbit polyclonal; WB (1:1000) |
| Antibody |
Anti-α-Tubulin (Mouse monoclonal) |
Sigma-Aldrich |
Cat# T5201 |
Mouse monoclonal; WB (1:5000) |
| Antibody |
Anti-hnRNP C1/C2 (Mouse monoclonal) |
Abcam |
Cat# Ab10294 |
Mouse monoclonal; WB (1:1000) |
| Antibody |
Anti-RAC3 (Rabbit monoclonal) |
Abcam |
Cat# ab129062 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-CCND2 (Cyclin D2) (Rabbit monoclonal) |
Cell Signaling Technology |
Cat# 3741 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-Akt (Rabbit polyclonal) |
Cell Signaling Technology |
Cat# 9272 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-phospho-Akt (Ser473) (Rabbit polyclonal) |
Cell Signaling Technology |
Cat# 9271 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-Erk1/2 (p44/42 MAPK) (Rabbit monoclonal) |
Cell Signaling Technology |
Cat# 4695 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-phospho-Erk1/2 (Thr202/Tyr204) (Rabbit monoclonal) |
Cell Signaling Technology |
Cat# 4370 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-IGFBP3 (D1U9C) (Rabbit monoclonal) |
Cell Signaling Technology |
Cat# 25864 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-Vimentin (VIM) (Mouse monoclonal) |
Thermo Fisher Scientific |
Cat# MA5-11883 |
Mouse monoclonal; WB (1:1000), IF (1:200) |
| Antibody |
Anti-PODXL2 (Goat polyclonal) |
R&D Systems |
Cat# AF1524 |
Goat polyclonal; WB (1:500) |
| Antibody |
Anti-ECM1 (Mouse monoclonal) |
R&D Systems |
Cat# MAB39371 |
Mouse monoclonal; WB (1:500) |
| Antibody |
Anti-TIMP2 (Goat polyclonal) |
R&D Systems |
Cat# AF971 |
Goat polyclonal; WB (1:500) |
| Antibody |
Anti-ADAM8 (Goat polyclonal) |
R&D Systems |
Cat# AF1031 |
Goat polyclonal; WB (1:500) |
| Antibody |
Anti-SRSF3 (Rabbit monoclonal) |
Novus Biologicals |
Cat# NBP2-76892 |
Rabbit monoclonal; WB (1:1000) |
| Antibody |
Anti-HPV16 E7 (Rabbit polyclonal) |
GeneTex |
Cat# GTX133411 |
Rabbit polyclonal; IF (1:500) |
| Sequence-based reagent |
lnc-FANCI-2 siRNA |
Custom (see Supplementary file 5) |
N/A |
Double-stranded, target-specific siRNA |
| Sequence-based reagent |
MAP4K4 siRNA |
Dharmacon, Inc |
#M-003971 |
Human MAP4K4 targeting siRNA |
| Sequence-based reagent |
IGFBP3 siRNA |
Dharmacon, Inc |
#M-004777 |
Human IGFBP3 targeting siRNA |
| Sequence-based reagent |
Non-targeting control siRNA |
Dharmacon, Inc |
#D-001210-01 |
Negative control siRNA |
| Chemical compound, drug |
LY294002 (PI3K inhibitor) |
Cell Signaling Technology |
#9901 |
20 µM treatment |
| Chemical compound, drug |
U0126 (MEK inhibitor) |
Cell Signaling Technology |
#9903 |
10 µM treatment |
| Commercial assay, kit |
RAS GTPase Chemi ELISA Kit |
Active Motif |
#52097 |
RAS activity measurement |
| Sequence-based reagent |
lnc-FANCI-2 siRNA |
Dharmacon |
Custom (Supplementary file 5) |
Target: lnc-FANCI-2 |
| Sequence-based reagent |
lnc-FANCI-2 gRNAs |
Zhang Lab CRISPR Designer |
Custom (Supplementary file 5) |
CRISPR knockout |
| Software, algorithm |
CCBR Pipeliner |
GitHub |
CCBR/Pipeliner |
RNA-seq analysis |
| Software, algorithm |
ZEN 2.3 |
Zeiss |
N/A |
Confocal microscopy |
| Commercial assay, kit |
Nuclei EZ Prep Kit |
Sigma-Aldrich |
#NUC-101 |
Nuclear/cytoplasmic fractionation |
| Commercial assay, kit |
Superscript First-Strand Synthesis kit |
Thermo Fisher Scientific |
#11904018 |
cDNA synthesis |
| Commercial assay, kit |
TaqMan gene expression Master Mix |
Applied Biosystems |
#4369016 |
qPCR amplification |
| Commercial assay, kit |
TaqMan Gene Expression Assay (GAPDH) |
Applied Biosystems |
Hs02758991_g1 |
Internal control for qPCR |
| Commercial assay, kit |
RNAscope Multiplex Fluorescent V2 Assay |
Advanced Cell Diagnostics |
#323100 |
RNA in situ hybridization |
| Sequence-based reagent |
lnc-FANCI-2 custom probe |
Advanced Cell Diagnostics |
Custom (nt 359–1713 of MT669800.1) |
Targets lnc-FANCI-2a-PA2 transcript |
| Sequence-based reagent |
IGFBP3 probe |
Advanced Cell Diagnostics |
#310351 |
Channel 1 probe |
| Sequence-based reagent |
lnc-FANCI-2 probe |
Advanced Cell Diagnostics |
#509061-C3 |
Channel 3 probe |
