KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD34 PE-Cy7 | BD Biosciences | Cat. 348791; CLONE 8G12 |
| CD38 PE-Cy5 | BD Biosciences | Cat. 555461; CLONE HIT2 |
| CD90 PE | BD Biosciences | Cat. 555596; CLONE 5E10 |
| CD45RA FITC | BioLegend | Cat. 304105; CLONE HI100 |
| DAPI solution | BD Biosciences | Cat. 564907 |
| CD45RA V450 | BD Biosciences | Cat. 560362; CLONE HI100 |
| CD133/1 APC | Miltenyi Biotec | Cat. 130-090-826; CLONE AC133 |
| CD19 PE | BD Biosciences | Cat. 349209; CLONE 4G7 |
| CD45 PE-Cy5 | Coulter | CLONE Immu19.2 |
| CD33 APC | BD Biosciences | Cat. 340474; CLONE P67.6 |
| CD45 APC-Cy7 | BD Biosciences | Cat. 561863; CLONE 2D1 |
| V5 | MBL | Cat. M167-3 |
| H3K4me2 | Diagenode | Cat. 035-050 |
| Biological Samples | ||
| Cord Blood CD34+ Cells | Lonza | Cat. 2C-101 |
| Cord Blood CD34+ Cells | AllCells | Cat. CB008F |
| Fetal Liver CD34+ Cells | AllCells | Cat. FL-CD34-002F |
| Bone Marrow CD34+ Cells | AllCells | Cat. ABM017F |
| Bone Marrow CD34+ Cells | Lonza | Cat. 2M-101C |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Actinomycin D | Sigma-Aldrich | Cat. A1410 |
| Doxycycline Hyclate | Sigma-Aldrich | Cat. D9891 |
| Protamine Sulfate | Sigma-Aldrich | Cat. P4020 |
| Recombinant Human SCF | Peprotech | Cat. 300-07 |
| Recombinant Human FLT3L | Peprotech | Cat. 300-19 |
| Recombinant Human TPO | Peprotech | Cat. 300-18 |
| Recombinant Human IL6 | Peprotech | Cat. 200-06 |
| Retronectin | Clontech | Cat. T100A |
| DOTAP Liposomal Transfection Reagent | Sigma-Aldrich | Cat. 11202375001 |
| DharmaFECT Duo Transfection Reagent | Dharmacon | Cat. T-2010-03 |
| Critical Commercial Assays | ||
| Dual-Luciferase Reporter Assay System | Promega | Cat. E1910 |
| TruSeq RNA Library Prep Kit v2 | Illumina | Cat. RS-122-2001 |
| SMART-Seq v4 Ultra Low Input RNA Kit | Clontech | Cat. 634888 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat. FC-131-1024 |
| nCounter Human v2 miRNA Expression Assay | NanoString Technologies | Cat. GXA-MIR2-24 |
| ChiP-Seq Assay | Broad Institute Epigenomics Program | n/a |
| Experimental Models: Cell Lines | ||
| PC-3 | ATCC | Cat. CRL-1435 |
| K562 | ATCC | Cat. CCL-243 |
| HPC-5F | Doulatov et al. 2013 | n/a |
| DGCR8 knockout MEF | Novus Biologicals | Cat. NBP2-25171 |
| Experimental Models: Organisms/Strains | ||
| NOD/LtSz-scidIL2Rgnull (NSG) | Jackson Laboratory | n/a |
| Recombinant DNA | ||
| pLVX_HMGA2-L_ORF_V5_PURO | In this paper | n/a |
| pLVX_HMGA2-S_ORF_V5_PURO | In this paper | n/a |
| pLVX_CTRL_V5_PURO | In this paper | n/a |
| pSMAL_HMGA2-L_ORF_BFP (RNAi resistant) | In this paper | n/a |
| pSMAL_HMGA2-S_ORF_BFP (RNAi resistant) | In this paper | n/a |
| pSMAL_CTRL_BFP | In this paper | n/a |
| pSMAL_HMGA2-L_GFP | In this paper | n/a |
| pSMAL_HMGA2-S_GFP | In this paper | n/a |
| pSMAL_HMGA2-L+3′UTRwt_GFP | In this paper | n/a |
| pSMAL_HMGA2-L+3′UTRmt_GFP | In this paper | n/a |
| pSMAL_HMGA2-S+3′UTRwt_GFP | In this paper | n/a |
| pSMAL_CLK3_GFP | In this paper | n/a |
| pSMAL_CTRL_GFP | In this paper | n/a |
| pLKO.1_shRNA_HMGA2-L_1 | In this paper | n/a |
| pLKO.1_shRNA_HMGA2-L_2 | In this paper | n/a |
| pLKO.1_shRNA_HMGA2-S_1 | In this paper | n/a |
| pLKO.1_shRNA_HMGA2-S_2 | In this paper | n/a |
| pLKO.1_shRNA_BOTH | In this paper | n/a |
| pLKO.1_CLK3_1 | Sigma-Aldrich | TRCN0000196926 |
| pLKO.1_CLK3_2 | Sigma-Aldrich | TRCN0000000749 |
| pLKO.1_shRNA_LUC | In this paper | n/a |
| pLX_TRC304/317_splicing_regulators_ORFs | Broad Institute GPP | n/a |
| psiCHECK2_Rluc-3’UTRwt_HMGA2-L | In this paper | n/a |
| psiCHECK2_Rluc-3’UTRmt_HMGA2-L | In this paper | n/a |
| psiCHECK2_Rluc-3’UTRwt_HMGA2-S | In this paper | n/a |
| pcDNA3.1_Luc-exon-4-WT (HMGA2-L) | In this paper | n/a |
| pcDNA3.1_Luc-exon-4-mut (HMGA2-L) | In this paper | n/a |
| Oligonucleotides | ||
| HMGA2 detection primers (full ORF cDNA) | ||
| HMGA2-common_FW | AGCGCCTCAGAAGAGAGGAC | n/a |
| HMGA2-L_RV | TGAGGATGTCTCTTCAGTTTCC | n/a |
| HMGA2-S_RV | TGGAAGAAAGGCTTCTAAGCTG | n/a |
| HMGA2-RI_RV | AGGCTCCTGTAGTCAGTCATTG | n/a |
| HMGA2-S”_RV | TGAAGACACTTTCCTTGGATCC | n/a |
| HMGA2 detection primers (partial ORF cDNA) | ||
| HMGA2-L-ORF_FW | AGACCTAGGAAATGGCCACA | n/a |
| HMGA2-L-ORF_RV | GTCCTCTTCGGCAGACTCTT | n/a |
| HMGA2-S-ORF_FW | AGTCCCTCTAAAGCAGCTCA | n/a |
| HMGA2-S-ORF_RV | TGAACACCACATGACACCAA | n/a |
| HMGA2-ex2-ORF_FW | GAACCAACCGGTGAGCCCT | n/a |
| HMGA2-ex2-ORF_RV | CTTTTGAGCTGCTTTAGAGGG | n/a |
| PROM1 detection primers | ||
| CAGAAGGCATATGAATCCAAA | n/a | |
| PROM1_FW | A | |
| PROM1_RV | GGTGCATTTCTCCACCACAT | n/a |
| Commercial detection primers | ||
| QuantiTect Primer Assay Hs_CLK3_1_SG | Qiagen | Cat. QT00197428 Prod. 249900 |
| QuantiTect Primer Assay Hs_SRSF1_1_SG | Qiagen | Cat. QT00203056 Prod. 249900 |
| QuantiTect Primer Assay Hs_HPRT1_1_SG | Qiagen | Cat. QT00059066 Prod. 249900 |
| miScript Primer Assay (miRNAs in this paper) | Qiagen | Cat. MS000XXXXX Prod. 218300 |
| miScript Primer Assay Hs_RNU6-2_11 | Qiagen | Cat. MS00033740 Prod.218300 |
| siRNA, miRNA inhibitors and mimics | ||
| ON-TARGETplus Human SRSF1 (6426) siRNA pool | Dharmacon | Cat. L-018672-01-0005 |
| ON-TARGETplus Non-targeting pool | Dharmacon | Cat. D-001810-10-05 |
| miRIDIAN Hairpin Inhibitor (miRNAs in this paper) | Dharmacon | Cat. IH-HMR-XX-0002 |
| miRIDIAN Hairpin Inhibitor Negative Control #1 | Dharmacon | Cat. IN-001005-01-05 |
| miRIDIAN Hairpin Inhibitor Negative Control #2 | Dharmacon | Cat. IN-002005-01-05 |
| miRIDIAN Mimic (miRNAs in this paper) | Dharmacon | Cat. C-HMR-XX-0002 |
| miRIDIAN Mimic Negative Control #1 | Dharmacon | Cat. CN-001000-01-05 |
| Deposited Data | ||
| RNA-seq, ChIP-seq, miRNA nanostring data | In this paper | NCBI GEO: GSE109093 |
| TargetScan | Agarwal et al., 2015 | v7 |
| MSigDb | Subramanian et al., 2005 | v6.1 |
| Blueprint Epigenome dataset | Stunnenberg et al., 2016 | 7th data release |
| Gencode gene annotations | Harrow et al., 2012 | v17, v19 |
| Human reference genome, hg19 | UCSC Genome Browser | hg19 |
| SRSF1 motifs | Wang et al., 2011 | n/a |
| Software and Algorithms | ||
| BEDTools | Quinlan and Hall. 2010 | v2.2.6 |
| Cufflinks | Trapnell et al., 2012 | v2.2.1 |
| TopHat | Trapnell et al., 2012 | v2.0.14 |
| cummeRbund | Trapnell et al., 2012 | v2.20.0 |
| Bowtie2 | Langmead and Salzberg. 2012 | v2.2.1 |
| GSEA | Subramanian et al., 2015 | v2.0 |
| BubbleGUM | Spinelli et al., 2015 | v1.3.19 |
| IGV | Robinson et al., 2011 | v2.3 |
| SUPPA | Alamancos et al., 2015 | v2.2.1 |
| rMAPS | Park et al., 2016 | v1.0.6 |
| HOMER | Heinz et al., 2010. | v4.9 |
| R | The R Project | v3.1 |
| Python | Python | v2.7 |
n/a: does not apply