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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
Transcriptomics3' sequencing following arginine methylation inhibition in a panel of cancer cell lines
Numerous RNA-binding proteins involved in alternative polyadenylation are arginine methylation substrates. Therefore we aimed to study how alternative polyadenylation is impacted by preventing arginine methylation, and assess how conserved this phenotype is across a panel of cancer lines with differ...
ORGANISM(S): Homo sapiens 
2026-10-19 | E-MTAB-14932 | biostudies-arrayexpress
Transcriptomics3' mRNA-seq of protrusions and cell bodies of BJ, PC-3M, RPE-1, U-87 and WM-266.4 cells
3' mRNA-seq of protrusions and cell bodies of a panel of normal and malignant cell lines. These data show that Ribosomal protein (RP) -mRNAs localization to cell protrusions is a conserved phenomenon.
ORGANISM(S): Homo sapiens 
2020-10-30 | E-MTAB-8470 | biostudies-arrayexpress
Transcriptomics3' sequencing of activated murine T cells + / - inhibition of arginine methylation
Activation of naive T cells stimulates increased proliferation coupled with a global switch to usage of proximal poly(A) sites. We wanted to investigate how this polyadenylation switch would be impacted by inhibition of arginine methylation. Therefore, we activated naive murine T cells with anti-CD3...
ORGANISM(S): Mus musculus 
2026-10-19 | E-MTAB-14990 | biostudies-arrayexpress
TranscriptomicsGLORI mapping of m⁶A sites in human primary CD8⁺ T cells under activation and METTL3 inhibition
Glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) was applied to human primary CD8⁺ T cells subjected to in vitro activation with αCD3/αCD28 beads. To identify N⁶-methyladenosine (m⁶A) sites at single-nucleotide resolution and to test their dependence on METTL3, we generate...
ORGANISM(S): Homo sapiens 
2025-10-15 | E-MTAB-15649 | biostudies-arrayexpress
TranscriptomicsmiCLIP profiling of m6A sites in human CD8⁺ T cells during activation, with Input and noUV controls
Methylation individual-nucleotide-resolution crosslinking and immunoprecipitation (miCLIP) was performed in human primary CD8⁺ T cells subjected to in vitro activation with αCD3/αCD28 beads. To map m⁶A sites and assess their dynamic signatures during T cell activation, we applied an improved iCLIP (...
ORGANISM(S): Homo sapiens 
2025-11-01 | E-MTAB-15643 | biostudies-arrayexpress
Transcriptomicsmodified iCLIP experiment with the addition of a 5'marker to identify read-through reads
We added an oligonucleotide to the 5′ end of RNA fragments —5′ marker— to differentiate between truncated and read–through cDNAs. By applying the protocol to PTBP1 and eIF4A3 iCLIP, we determined that the start sites of read–through cDNAs are enriched in adenosines, while the truncated cDNAs prefere...
ORGANISM(S): Homo sapiens 
2018-06-15 | E-MTAB-6927 | biostudies-arrayexpress
TranscriptomicsSLAM-seq analysis of mRNA half-lives in human CD8⁺ T cells during activation
SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) was applied to human primary CD8⁺ T cells subjected to in vitro activation with αCD3/αCD28 beads. To quantify mRNA half-lives and their dynamic changes during CD8⁺ T cell activation, we implemented a pulse-chase design with 2...
ORGANISM(S): Homo sapiens 
2025-10-15 | E-MTAB-15648 | biostudies-arrayexpress
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