Data CitationsMonzn-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CJ, Turner M. 2015. HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response. NCBI Gene Expression Omnibus. GSE62129Ling JP, Chhabra R, Merran JD, Schaughency PM, Wheelan SJ, Corden JL, Wong PC. 2016. PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons. NCBI BioProject. PRJNA309732Supplementary MaterialsFigure 4source data 1: Changes in mRNA abundance. DESeq2 results shown in Figure 4A. Separate tabs show genes with significant differential (padj? 0.05) mRNA abundance with a |log2 fold change|? ?0.5 for the different pairwise comparisons carried out and also all the results obtained with DESeq2. Additional tabs show genes whose transcripts were bound by PTBP1 clusters at their 3UTR. elife-53557-fig4-data1.xls (29M) GUID:?8549C00F-0684-4D8A-9C4C-F337CA6E46ED Figure 4source GPR40 Activator 2 data 2: Changes in AS. Different tabs show inclusion level differences (IncLevelDifference) shown in Figure 4B for the three pairwise comparisons carried out. The first three tabs show significant (FDR? ?0.05) Rabbit Polyclonal to CaMK2-beta/gamma/delta alternative splicing events with an absolute inclusion level difference? 0.1. allresults tabs show all the results from rMATS. PTBP1 bound tabs show those significantly differential splicing events that were bound in their vicinity by PTBP1 clusters. elife-53557-fig4-data2.xls (57M) GUID:?600269BF-9156-4D16-9C6B-761FD6F79D6F Figure 5source data 1: Gene ontology enrichment analysis. Results from gene ontology enrichment analysis carried out with the groups of genes identified in Figure 4D and Figure 4E. elife-53557-fig5-data1.xls (1.1M) GUID:?AB3263B1-2D62-4F4C-8C3C-C042054FA751 Figure 8source data 1: DESeq2 results for genes shown to have high mRNA expression levels in S or G2/M phases?(Giotti et al., 2019) in the three pair-wise comparisons shown in Figure 8A. elife-53557-fig8-data1.xls (6.0M) GUID:?14853FBF-F03A-45CA-8853-DFEB02599F42 Supplementary file 1: PTBP1 binding sites (xlinks). elife-53557-supp1.csv.zip (13M) GUID:?87033835-E716-46EF-939D-E45F15D83F08 Supplementary file 2: PTBP1 binding sites (clusters). elife-53557-supp2.csv (7.3M) GUID:?F6938E98-E45C-44F2-8E87-1C65052C5909 Supplementary file 3: Key resources table. elife-53557-supp3.docx (30K) GUID:?CF9E9F31-3D66-492C-BED5-3B59B57D341E Transparent reporting form. elife-53557-transrepform.docx (246K) GUID:?124CB939-FEC3-4077-A606-4D001EEF209F Data Availability StatementmRNAseq libraries and iCLIP analysis generated in this study have been deposited in GEO and can be accessed with the “type”:”entrez-geo”,”attrs”:”text”:”GSE136882″,”term_id”:”136882″GSE136882 accession code at GEO. Mitogen-activated primary GPR40 Activator 2 B cell mRNAseq libraries were previously reported and can be accessed with the “type”:”entrez-geo”,”attrs”:”text”:”GSM1520115″,”term_id”:”1520115″GSM1520115, “type”:”entrez-geo”,”attrs”:”text”:”GSM1520116″,”term_id”:”1520116″GSM1520116, “type”:”entrez-geo”,”attrs”:”text”:”GSM1520117″,”term_id”:”1520117″GSM1520117 and “type”:”entrez-geo”,”attrs”:”text”:”GSM1520118″,”term_id”:”1520118″GSM1520118 accession codes in GEO. The following dataset was generated: Monzn-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CJ, Turner M. 2020. Polypyrimidine tract binding proteins are essential for B cell development. NCBI Gene Expression Omnibus. GSE136882 The following previously published datasets were used: Diaz-Mu?oz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, GPR40 Activator 2 Curk T, Kontoyiannis DL, Ule J, Turner M. 2015. WT_LPS4. NCBI Gene Expression Omnibus. GSM1520118 Diaz-Mu?oz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Kontoyiannis DL, Ule J, Turner M. 2015. WT_LPS1. NCBI Gene Expression Omnibus. GSM1520115 Diaz-Mu?oz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Kontoyiannis DL, Ule J, Turner M. 2015. WT_LPS2. NCBI Gene Expression Omnibus. GSM1520116 Diaz-Mu?oz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Kontoyiannis DL, Ule J, Turner M. 2015. WT_LPS3. NCBI Gene Expression Omnibus. GSM1520117 Diaz-Mu?oz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Kontoyiannis DL, Ule J, Turner M. 2015. HuR- dependent regulation of mRNA GPR40 Activator 2 splicing is essential for the B cell antibody response. NCBI Gene Expression Omnibus. GSE62129 Ling JP, Chhabra R, Merran JD, Schaughency PM, Wheelan SJ, Corden JL, Wong PC. 2016. PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons. NCBI BioProject. PRJNA309732 Abstract Polypyrimidine tract-binding protein 1 (PTBP1) is a RNA-binding protein (RBP) expressed throughout B cell development. Deletion of in mouse pro-B cells results in upregulation of PTBP2 and normal B cell development. We show that PTBP2 compensates for PTBP1 in B cell ontogeny as deletion of both and results in a complete block at the pro-B cell stage and a lack of mature B cells. In pro-B cells PTBP1 ensures precise synchronisation of the.