| Antibodies |
| Mouse monoclonal anti-ILF2 |
Santa-Cruz |
Cat# sc-365068 |
| Rabbit polyclonal anti-ILF3 |
Abcam |
Cat# ab50832 |
| Rabbit monoclonal anti-ILF3 |
Origene |
Cat# TA307124 |
| Mouse monoclonal anti-γH2AX |
Millipore |
Cat# 05636 |
| Rabbit monoclonal anti-γH2AX |
Cell Signaling |
Cat# 9718 |
| Rabbit monoclonal anti-phospho-ATM |
Cell Signaling |
Cat# 5883 |
| Rabbit polyclonal anti-phospho-Chk2 |
Cell Signaling |
Cat# 2661 |
| Rabbit monoclonal anti-cleaved Caspase3 |
Cell Signaling |
Cat#96645 |
| Rabbit polyclonal anti-cleaved Parp |
Cell Signaling |
Cat# 9541 |
| Mouse monoclonal anti-TP53 |
Santa-Cruz |
Cat# sc-126 |
| Rabbit monoclonal anti-β-actin |
Cell Signaling |
Cat# 49705 |
| Rabbit polyclonal anti-hnRNPC-like 2 |
Millipore |
Cat# AB12226 |
| Mouse monoclonal anti-Adar1 |
Santa Cruz |
Cat# sc-73408 |
| Goat Polyclonal anti-hnRNPC1/C2 |
Santa Cruz |
Cat# sc-10037 |
| Goat Polyclonal anti-hnRNPG |
Santa Cruz |
Cat# sc-14581 |
| Rabbit polyclonal anti-vinculin |
Sigma-Aldrich |
Cat# V9131 |
| Rabbit polyclonal anti-phospho-ATR |
Cell Signaling |
Cat# 2853 |
| Rabbit polyclonal anti-phospho-DNAPK |
Cell Signaling |
Cat# 4215 |
| Mouse monoclonal anti-NPM |
Invitrogen |
Cat# 325200 |
| Rabbit polyclonal anti-YB1 |
Abcam |
Cat# ab12148 |
| Rabbit polyclonal anti-Sam68 |
Santa Cruz |
Cat# sc-333 |
| Rabbit polyclonal anti-nucleolin |
Santa Cruz |
Cat# sc-13057 |
| Rabbit polyclonal anti-DHX9 |
Abcam |
Cat# ab26271 |
| Goat Polyclonal anti-DHX15 |
Santa Cruz |
Cat# sc-67550 |
| Mouse monoclonal anti-hnRNPF/H |
Santa Cruz |
Cat# sc-32310 |
| Mouse monoclonal anti-hnRNPA1 |
Santa Cruz |
Cat# sc-32301 |
| Mouse monoclonal anti-hnRNPK |
Santa Cruz |
Cat# sc-28380 |
| Rabbit polyclonal anti-hnRNPU-like 2 |
Abcam |
Cat# ab104042 |
| Rabbit polyclonal anti-U2AF65 |
Abcam |
Cat# ab37483 |
| Rabbit polyclonal anti-Fancd2 |
Novus Biologicals |
Cat# NB100-182 |
| Mouse monoclonalanti-U2AF65 (immunoprecipitation) |
Santa Cruz |
Cat# sc-53942 |
| Rabbit polyclonal anti-ILF2 (immunoprecipitation) |
Abcam |
Cat# ab113205 |
| Mouse monoclonal anti-phospho-ATM (immunofluorescence) |
Active Motif |
Cat# 39529 |
| Mouse monoclonal anti-CD138 |
Abcam |
Cat# ab34164 |
| Anti-F actin |
Thermo Fisher |
Cat# A34055 |
| Mouse monoclonal anti-phospho-DNAPK |
Abcam |
Cat# ab18356 |
| Ant-rabbit/mouse immunoglobulin G |
Santa Cruz |
Cat# sc-2027/2025 |
| Bacterial and Virus Strains |
| pCMVR8.74 packaging vector |
Didier Trono's lab |
AddgeneCat# 22036 |
| PMD2.G packaging vector |
Didier Trono's lab |
AddgeneCat# 12259 |
| Biological Samples |
|
|
| aCGH and microarray data |
Multiple Myeloma Research Consortium collection |
http://www.broadinstitute.org/mmgp/data |
| FISH and microarray data |
Zhan et al, 2006 |
GSE2658 |
| Microarray and survival data |
Shaughnessy et al, 2003 |
GSE2658 |
| 15 primary MM samples from 14 patients |
This paper |
University of Parma (Italy) |
| Chemicals, Peptides, and Recombinant Proteins |
| Melphalan |
Sigma-Aldrich |
Cat# M2011 |
| Critical Commercial Assays |
| Anti-Annexin V-APC |
Ebioscience |
Cat# 88-8007-74 |
| High Capacity cDNA Reverse Transcription Kit |
Thermo Fisher |
Cat# 4368814 |
| RNeasyMinikit |
Qiagen |
Cat# 74104 |
| CompoZr Target Integration Kit |
Sigma-Aldrich |
Cat# CTI1-1KT |
| Magna RIP RNA-binding protein immunoprecipitation kit |
Millipore |
Cat# 17-700 |
| TruSeq® Stranded Total RNA LT - (with Ribo-Zero TM Gold) - Set A |
Illumina |
Cat# RS-122-2301 |
| Nuclear/Cytosol Fractionation Kit |
Biovision |
Cat# K266-100 |
| Ovation RNA-Seq System V2 |
Nugen |
Cat # 7102-32 |
| QuikChange site-directed mutagenesis kit |
Agilent |
Cat# 200523 |
| Deposited Data |
| Raw data (RNA-sequencing, H929 cell line) |
This paper |
GSE97323 |
| Raw data (RNA-sequencing, JJN3 cell line) |
This paper |
GSE83712 |
| Raw data (RIP-sequencing, H929 and JJN3 cell lines) |
This paper |
GSE83665 |
| Experimental Models: Cell Lines |
| Human JJN3 cell line |
DSMZ |
Cat# ACC541 |
| Human NCIH929 cell line |
ATCC |
Cat# CRL-9068 |
| Human OCI-MY5 cell line |
Dr. Kuehl (NIH) |
NA |
| Human L-363 cell line |
DSMZ |
Cat# ACC49 |
| Human OPM-2 cell line |
DSMZ |
Cat# ACC40 |
| Human NCUMM1 cell line |
Dr. Hanamura (Aichi Medical University) |
NA |
| Human XG-6 cell line |
Dr. Kuehl (NIH) |
NA |
| Experimental Models: Organisms/Strains |
| Mouse: NOD/MrkBomTac-Prkdcscid
|
Taconic |
NODSC-F |
| Oligonucleotides |
| ILF2-shRNA |
Dharmacon |
V3LHS_410035 |
| ILF2-shRNA |
Dharmacon |
V2LHS_48795 |
| MCL1-shRNA |
Dharmacon |
V3LHS_413586 |
| MCL1-shRNA |
Dharmacon |
V2LHS_72721 |
| KRTCAP2-shRNA |
Dharmacon |
V3LHS_354655 |
| KRTCAP2-shRNA |
Dharmacon |
V3LHS_354652 |
| INT3-shRNA |
Dharmacon |
V3LHS_335830 |
| INT3-shRNA |
Dharmacon |
V3LHS_637486 |
| LASS2-shRNA |
Dharmacon |
V3LHS_334041 |
| LASS2-shRNA |
Dharmacon |
V3LHS_334038 |
| UBAPL2-shRNA |
Dharmacon |
V3LHS_381632 |
| UBAPL2-shRNA |
Dharmacon |
V3LHS_381634 |
| YB-1-shRNA |
Dharmacon |
V3LHS_316625 |
| YB-1-shRNA |
Dharmacon |
V2LHS_232997 |
| ILF2-shRNA |
Sigma-Aldrich |
TRCN0000014557 |
| ILF2-shRNA |
Sigma-Aldrich |
TRCN0000329784 |
| FANCD2 primers |
This paper |
NA |
| Recombinant DNA |
| pHAGE-ILF2-GFP |
This paper |
NA |
| pGFP-Pem1-Ad2 |
Shamanna et al, 2011 |
NA |
| Software and Algorithms |
| GraphPad Prism 6 |
GraphPad Software |
www.graphpad.com |
| ImageJ |
NIH |
http://rsbweb.nih.gov/ij/) |
| Gistic2 |
Mermel et al, 2011 |
http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=216&p=t |
| Mascot |
Matrix Science |
http://www.matrixscience.com/daemon_support_v2_3.html |
| FastQC |
Simon Andrews |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Tophat2 |
Kim et Al, 2013 |
http://ccb.jhu.edu/software/tophat. |
| Pathway Studio |
Elsevier Inc |
http://www.pathwaystudio.com/ |
| STAR |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR/releases |
| Cufflinks |
Trapnell et al, 2012 |
http://cole-trapnell-lab.github.io/cufflinks/ |
| HTSeq |
Anders et al, 2015 |
http://www-huber.embl.de/HTSeq/doc/overview.html |
| rMATS (version rMATS 3.2.5) |
Shen et al, 2014 |
http://rnaseq-mats.sourceforge.net/ |
| Other |
