chimera embryo RNAseq
LIN28AGFP vs LIN28ANLSGFP e7.5 tetraploid embryos
SDMA iCLIP
Protein Arginine Methyltransferase-5 (PRMT5) is an arginine methyltransferase that catalyses the symmetric dimethylation of arginine (SDMA) residues on both histone and non-histone proteins. This collection contains iCLIP datasets of SDMA-modified RNA-binding proteins obtained from cells treated with different PRMT5 inhibitors or vehicle-control (DMSO).
miCLIP_genecounts_PG
Tardbp Q331K knock-in mouse
RBM7_iCLIP
Decipering the role of RBM7 in DDR. iCLIP experiments were performed using an MS2 antibody targeting FLAG (Sigma). FLAG tag protein induced with doxycycline. Cell lines treated with DMSO or 4NQ0 as indicated
RNA-Seq Analysis (auto-generated)
This collection has been auto-generated as part of work in progress in the Analyze module. It has been given a temporary name and description. Deleting this collection will reset the work in progress in the Analyze module.
TDP-43 iCLIP in mESC
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expres- sion, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment ‘‘paraspeckles’’, are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR- 21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
TDP-43 iCLIP in hESC
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expres- sion, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment ‘‘paraspeckles’’, are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR- 21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
RNA-Seq Analysis (auto-generated)
This collection has been auto-generated as part of work in progress in the Analyze module. It has been given a temporary name and description. Deleting this collection will reset the work in progress in the Analyze module.
RNA-Seq Analysis (auto-generated)
This collection has been auto-generated as part of work in progress in the Analyze module. It has been given a temporary name and description. Deleting this collection will reset the work in progress in the Analyze module.
STAU1-TARBP2-PACT hiCLIP
SDMA-iCLIP_RNAseq
These RNAseq fastq files are the matched to the SDMA-iCLIP samples upon PRMT5 inhibition in HCT116 cells: treatment with DMSO, GSK_500nM or Lilly_100nM (biological triplicates)
DENR_3T3
Sm iCLIP in SMA mouse
Sm iCLIP in SMA mice. These are knockouts of mouse Smn and knockin of human SMN2, which partially rescues Smn loss. For preparing the Sm iCLIP libraries brain and spinal cord were used from wildtype (Smn+/+;SMN2), heterozygotes (Smn+/-;SMN2) and knockout (Smn-/-;SMN2) mice, each as triplicate.
TIRR and 53BP1 iCLIP
PKR-TARBP2 rRNA tRNA
TIA1-TIAL iCLIPs
Old TIA1-TIAL iCLIPs 2009
PTBP1 iCLIPs
PTBP1 iCLIPs from 2011
Dyskerin_Chiara
DKC1_and_GAR1_iCLIP
PRPF8 iCLIP with 4A3 KD
Recursive splicing (RS) starts by defining an “RS-exon,” which is then spliced to the preceding exon, thus creating a recursive 5′ splice site (RS-5ss). Previous studies focused on cryptic RS-exons, and now we find that the exon junction complex (EJC) represses RS of hundreds of annotated, mainly constitutive RS-exons. The core EJC factors, and the peripheral factors PNN and RNPS1, maintain RS-exon inclusion by repressing spliceosomal assembly on RS-5ss. The EJC also blocks 5ss located near exon-exon junctions, thus repressing inclusion of cryptic microexons. The prevalence of annotated RS-exons is high in deuterostomes, while the cryptic RS-exons are more prevalent in Drosophila, where EJC appears less capable of repressing RS. Notably, incomplete repression of RS also contributes to physiological alternative splicing of several human RS-exons. Finally, haploinsufficiency of the EJC factor Magoh in mice is associated with skipping of RS-exons in the brain, with relevance to the microcephaly phenotype and human diseases.
Neuroblastoma m6A miCLIP
HEK293 miCLIP RNA modification comparison
miCLIP to test the protocol across different RNA modifications in HEK 293 cells
iCLIP Sm testing
Spliceosome iCLIP testing various conditions and two antibodies.