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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
ProteomicsTMT quantitative proteomics of a) protrusions and cells bodies of a panel of cell lines, b) protrusions and cells bodies of MDA-MB231 cells collected after 1 h, 2 h, 4 h, 8 h post- induction of protrusions, c) non-transfected (nt) or LARP6 siRNAs MDA-MB231 cells grown on either close or open collagen coated transwells and d) protrusions and cells bodies of a panel of breast cell lines.
Translation of Ribosomal Protein coding mRNAs (RP-mRNAs) constitutes a key step in regulation of ribosome biogenesis in human cells, but the exact mechanisms which modulate RP-mRNAs translation under various cellular and environmental conditions remain poorly understood. Here we show that the subcel...
ORGANISM(S): Homo sapiens (Human) 
2021-09-08 | PXD015808 | Pride
Human Malignant and non-malignant cell lines Lc-ms/ms 
ProteomicsPulsed-SILAC analysis of protein translation rate changes upon protrusion formation
To assess the impact of protrusion formation on protein synthesis rates on a global scale, we carried out a pulsed-SILAC (pSILAC) analysis in MDA-MB231 cells grown with or without protrusions for 1, 2, 4, and 8 hrs. Briefly, light SILAC labelled cells were seeded on top of 2x 3 micron transwell filt...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021203 | Pride
Pulsed-silac  psilac Mda-mb231  protrusions translation  orbitrap 
ProteomicsAssessment of nascent protein accumulation in different subcellular fractions following protrusion induction
To assess if newly synthesised ribosomal proteins participate in canonical ribosome biogenesis in the nucleus, following their enhanced translation upon protrusion induction, Light (L) SILAC labelled MDA-MB231 breast cancer cells were seeded on top of collagen-I coated 3 micron transwell filters (co...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021205 | Pride
Pulsed-silac  psilac  ibaq  protrusions  mda-mb231  orbitrap 
TranscriptomicsiCLIP Analysis of WT, phospho-defective, and phospho-mimicking mutants of mouse Nucleolin in iKras PDAC cells
This experiment aimed to identify Nucleolin (Ncl) binding sites on a transcriptome-wide scale, by performing iCLIP in mouse iKras PDAC cells (Ying et al., 2012) transiently transfected with a mammalian expression construct encoding a wild-type (WT) myc-Ncl, a phospho-defective mutant in which S28, S...
ORGANISM(S): Mus musculus 
2023-03-01 | E-MTAB-12481 | biostudies-arrayexpress
TranscriptomicsQUANTSEQ 3' sequencing of protrusions and cell bodies of control (NT) or LARP6 siRNA (LARP6 KD) transfected MDA-MB231 breast cancer cells
To assess how LARP6 affects mRNA localisation to cell-protrusions, we transfected MDA-MB231 cells with either non-targeting control siRNA or LARP6 siRNA for 72 hrs, before fractionating the cells into protrusion and cell-bodies, and analysed total RNA from each fraction via Lexogen QUANTSEQ FWD 3' m...
ORGANISM(S): Homo sapiens 
2020-10-30 | E-MTAB-9520 | biostudies-arrayexpress
ProteomicsAnalysis of LARP6 depletion impact on the proteome of MDA-MB231 breast cancer cells
We analysed the impact of LARP6 depletion on the proteome of actively growing MDA-MB231 breast cancer cells by SILAC. For this purpose, Light (L) SILAC-labelled MDA-MB231 cells were treated with non-targeting control (NT) or two independent LARP6 siRNA (18i & 97i) for 72 hrs, before lysis in 4% SDS,...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021204 | Pride
Larp6  silac  mda-mb231  breast cancer  orbitrap 
ProteomicsTMT analysis of LARP6 knockdown impact on protrusion induced changes in the proteome of MDA-MB231 cells
To assess if LARP6 is required for upregulation of ribosomal proteins upon protrusion induction, MDA-MB231 breast cancer cells were treated with non-targeting (NT) or LARP6 siRNA for 48 hrs, before being seeded on top of collagen-I coated 3 micron transwell filters (corning). No media was added to t...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021180 | Pride
Mda-mb231  larp6  tmt  protrusions  orbitrap 
ProteomicsQuantitative proteomics analysis of actin-rich protrusions and cell-bodies in migratory cells
This upload concerns 2 independent but related experiments that were searched together: a) To reveal proteins that consistently localise to actin-rich protrusions across different human migratory cell-lines, we profiled the distribution of cellular proteins between protrusions and cell-bodies in a...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021239 | Pride
Protrusion  cell-body  spatial proteomics  tmt  mesenchymal-like migration  orbitrap 
ProteomicsAssessing the short and long-term impacts of protrusion induction on the proteome of MDA-MB231 cells
To assess the impact of protrusion induction on the proteome of mesenchymal-like migratory cells, MDA-MB231 breast cancer cells were seeded on top of collagen-I coated 3 micron transwell filters (corning). No media was added to the bottom chamber and cells were allowed to adhere to filter overnight....
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021206 | Pride
Tmt  protrusion  mda-mb231  orbitrap 
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