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TranscriptomicsiiCLIP protocol benchmarking with PTBP1
We describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions with 1...
ORGANISM(S): Homo sapiens 
2022-08-01 | E-MTAB-10881 | biostudies-arrayexpress
TranscriptomicsConcordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study
Background: Genome-wide transcriptome profiling generated by microarray and RNA-Seq often provides deregulated genes or pathways applicable only to larger cohort. On the other hand, individualized interpretation of transcriptomes is increasely pursued to improve diagnosis, prognosis, and patient tre...
ORGANISM(S): Homo sapiens 
2013-11-20 | E-GEOD-52493 | biostudies-arrayexpress
TranscriptomicsAn Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates
Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects ...
ORGANISM(S): Homo sapiens 
2015-09-01 | E-GEOD-69656 | biostudies-arrayexpress
ProteomicsPolypyrimidine Tract Binding Proteins PTBP1 and PTBP2 Interact with Distinct Proteins Under Splicing Conditions
RNA binding proteins play an important role in regulating alternative pre-mRNA splicing and in turn cellular gene expression. Polypyrimidine tract binding proteins, PTBP1 and PTBP2, are paralogous RNA binding proteins that play a critical role in the process of neuronal differentiation and maturatio...
ORGANISM(S): Homo sapiens (Human) 
2022-01-20 | PXD029899 | Pride
Nptb Ptbp1 Ptbp2 Splicing Ptbp Ptb Lc-ms/ms 
TranscriptomicsRegulation of co-transcriptional splicing by RNA-binding protein PTBP1
We examined the role of PTBP1 in regulation of co-transcriptional splicing process by depleting this RNA-binding protein from embryonic stem cells using the auxin-inducible degron technology and analysing the total and chromatin-associated RNA fractions by RNA-seq. We also performed mNET-seq and ChI...
ORGANISM(S): Mus musculus 
2023-01-08 | E-MTAB-11544 | biostudies-arrayexpress
TranscriptomicsRNA-seq of human MCF10A EditR breast epithelial cells expressing Cas9, with PTBP1 mutation as compared to control
RNA-seq to determine alterations in gene expression and in alternative splicing events in cells where the PTBP1 gene was mutated by CRISPR/Cas9 technology causing resistance to CDC7 kinase inhibitor.
ORGANISM(S): Homo sapiens 
2023-05-22 | E-MTAB-12578 | biostudies-arrayexpress
TranscriptomicsCoordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention
Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the unde...
ORGANISM(S): Mus musculus 
2012-07-12 | E-GEOD-37933 | biostudies-arrayexpress
Transcriptomics4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion
The aim of the experiment was to compare binding of PTBP1 in presence and absence of MATR3. HEK293T cells were transfected with siRNA targeting MATR3 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).
ORGANISM(S): Homo sapiens 
2018-05-01 | E-MTAB-6286 | biostudies-arrayexpress
ProteomicsPTBP1 and PTBP2 associate with distinct proteins and have distinct post-translational modifications in nuclear neuronal extract.
PTBP1 and PTBP2 are highly conserved paralogs, yet exhibit distinct splicing patterns. Here we use mass spectrometry to show that PTBP1 and PTBP2 interact with distinct proteins and undergo distinct post translational modifications under splicing conditions in neuronal nuclear extract.
ORGANISM(S): Homo sapiens (Human) 
2026-02-09 | PXD058740 | Pride
Post-translational modificantions Ptbp1 Mass spectrometry Splicing Ptbp2 Protein-protein interactions 
GenomicsiiCLIP protocol benchmarking with PTBP1
iiCLIP protocol benchmarking with PTBP1
PRJEB47097 | ENA
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