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TranscriptomicsiCLIP of TDP-43
A stable HEK293 FlpIn T-Rex cells expressing TDP-43 with an N-terminal eGFP-tag was generated that allowed inducible physiological expression of the protein (Ling et al. 2010). Duplicate iCLIP experiments were performed using an antibody targeting eGFP (Abcam ab290). Crosslinked RNA-protein complexe...
ORGANISM(S): Homo sapiens 
2017-05-01 | E-MTAB-4733 | biostudies-arrayexpress
Transcriptomicslong-read CAGE for 10 specific loci in cortical neurons
long-read CAGE was design to identify full length capped transcript across 10 specific loci in cortical neurones. Long-read CAGE was based on the Cap-Trapper method with the full length cDNA sequencing using ONT MinION sequencer. After RNA extraction, 10 µg total RNAs from Human iPS (WTC-11) cells, ...
ORGANISM(S): Homo sapiens 
2024-10-08 | E-MTAB-14500 | biostudies-arrayexpress
TranscriptomicsCharacterisation of the AGO2 binding sites in HeLa cell line using eiCLIP
Here we investigate the RNA-binding protein AGO2 in HeLa by using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP). We find that 5’ capped RNAs derived from 3’UTRs likely originate from AGO2-mediated cleavage, and most often occur at lo...
ORGANISM(S): Homo sapiens 
2024-09-19 | E-MTAB-12945 | biostudies-arrayexpress
TranscriptomicsCharacterisation of the AGO2 binding sites in HeLa cell line using eiCLIP
Here we investigate the RNA-binding protein AGO2 in HeLa by using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP). We find that 5’ capped RNAs derived from 3’UTRs likely originate from AGO2-mediated cleavage, and most often occur at lo...
ORGANISM(S): Homo sapiens 
2024-10-07 | E-MTAB-12944 | biostudies-arrayexpress
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
Transcriptomics3'-end targeted sequencing of 6 control and 6 TDP-43 KD samples in HEK293
HEK293 FlpIn T-Rex cells were maintained in Dulbeccos Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS), supplemented with 3 g/ml blasticidine and 50 g/ml zeocin. For the siRNA-induced knockdown of TDP-43, 20 nM of TDP-43 stealth siRNA was mixed with 10 L of RNAiMAX following the manufa...
ORGANISM(S): Homo sapiens 
2017-05-01 | E-MTAB-4732 | biostudies-arrayexpress
TranscriptomicsRNA libraries of sorted CD8+ memory T cells from the spleen and RNA libraries of sorted IELs from the small intestine of C57BL/6J mice
Intraepithelilal lymphocytes (IELs) are located at the intestinal barrier where they can offer swift protection against invading pathogens. However, they are kept in a heightened state of activation resembling effector T cells, but without cytokine production or clonal proliferation. They also posse...
ORGANISM(S): Mus musculus 
2018-07-10 | E-MTAB-6510 | biostudies-arrayexpress
TranscriptomicsAlternative splicing in Mouse E18 brain
Total RNA was extracted from wild-type and FUS -/- mouse E18 brain samples using RNeasy kit, cDNA was synthesized using GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix 900673) and hybridised to Affymetrix mouse high-resolution AltSplice microarrays.
ORGANISM(S): Mus musculus 
2013-07-30 | E-MTAB-1229 | biostudies-arrayexpress
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