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TranscriptomicsPTBP1 - Modified iCLIP
This experiments was performed in HeLa cells according to the iCLIP protocol with the following modifications: no antiRNase was used and the concentration of RNase I was 0.5 U/ml. In iCLIP4, the dephosphorylation step was omitted from the standard protocol. The rest of the protocol was identical to...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5026 | biostudies-arrayexpress
TranscriptomicsModified iCLIP sequencing of HEK293 cells with antibody PTBP1
For modified iCLIP experiment, 4SU was used for crosslinking as described in published protocol (citation is bellow) and the RNase conditions were optimised to ensure efficient RNase I-dependent fragmentation. In detail, HEK293T cells were grown on 10 cm 2 dishes, incubated for 8 h with 100 M 4SU an...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5027 | biostudies-arrayexpress
TranscriptomicseIF4A3 - Modified iCLIP
The modified iCLIP protocol is based on the previously described protocol (Huppertz et al., 2014) with modifications that enable the definition of readthrough cDNAs. HeLa cells were crosslinked with 0.15mJ/cm2 254nm UV light. Protein G Dynabeads were used for immunoprecipitations (IP). For each IP, ...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-4000 | biostudies-arrayexpress
ProteomicsMeta-unstable mRNAs in activated CD8+ T cells are defined by interlinked AU-rich elements and m6A mRNA methylation
CD8 ⁺ T cells can rapidly produce effector molecules following activation. This activation triggers fast changes in gene expression that rely on control of mRNA levels via multiple transcriptional and post-transcriptional mechanisms, including RNA modifications. N ⁶ -methyladenosine (m ⁶ A) is an ab...
ORGANISM(S): Homo sapiens (Human) 
2025-11-24 | PXD059083 | Pride
ProteomicsProteins co-localized with RNA Pol2 in ALS patient-derived neural precursors
Deficiency of proteostasis and RNA metabolism are increasingly recognized as critical drivers of neurodegenerative diseases. In this study, we focused on RNA polymerase II (Pol2) as the converging point of these two elements to understand how transcriptional machinery is affected by ALS-associated V...
ORGANISM(S): Homo Sapiens (human) 
2023-03-02 | PXD034483 | JPOST Repository
Genomicsena-DATASET-UKBEC-12-03-2015-16:21:20:556-32 - samples
Brain samples for this dataset were provided by the Medical Research Council Sudden Death Brain and Tissue Bank (Edinburgh, UK). All four individuals sampled were of European descent, neurologically normal during life and confirmed to be neuropathologically normal by a consultant neuropathologist...
EGAD00001001274 | EGA
GenomicsRecursive splicing in long vertebrate genes
Recent studies have shown that expression of many genes with exceptionally long introns in the mammalian brain can be perturbed by regulatory factors linked to neurodevelopmental or neurodegenerative disorders1-3, suggesting unique regulatory mechanisms. Here we identify functional recursive splice ...
EGAS00001001170 | EGA
GenomicsThis DAC is the list of persons that, on behalf of the UKBEC consortium, manage the access to the UKBEC data.
Data Access Committee EGAC00001000314
EGAC00001000314 | EGA
ProteomicsSubcytoplasmic location of translation controls protein output
Supporting raw data of HEK293T cells proteomics analysis. (related to Horste et al 2023 - DOI: 10.1016/j.molcel.2023.11.025). TMTpro channel used for analysis 132c and 133n.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-06-15 | MSV000092176 | MassIVE
TranscriptomicsTranscriptional profiling upon knockdown of the RNA-binding protein Unkempt
RNAseq to assess changes in transcript abundance upon knockdown of the RNA-binding protein Unkempt in human SH-SY5Y cell lines.
ORGANISM(S): Homo sapiens 
2015-01-15 | E-MTAB-2277 | biostudies-arrayexpress
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