Matches in Nanopublications for { ?s ?p ?o <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU/assertion>. }
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- data-analysis type Thing assertion.
- protocol type Thing assertion.
- step-isolation type Thing assertion.
- step-library-prep type Thing assertion.
- step-rnase-treatment type Thing assertion.
- step-sequencing type Thing assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU type AIDA-Sentence assertion.
- step-isolation comment "Optional isopycnic centrifugation in sucrose gradient for enhanced purity" assertion.
- step-library-prep comment "Excludes RNase-cleaved transcripts (5'-OH and 3'-PO4 incompatible with ligation)" assertion.
- step-rnase-treatment comment "Parallel Mock CoLoC-seq with detergent-permeabilized membranes as control" assertion.
- step-isolation description "Differential centrifugation of crude mitochondria" assertion.
- step-library-prep description "Selective sequencing of intact (non-RNase-cleaved) transcripts" assertion.
- step-rnase-treatment duration "10 minutes at 25°C" assertion.
- data-analysis has_function operation_3680 assertion.
- protocol has_function operation_3207 assertion.
- protocol has_function operation_3801 assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU has_function operation_3207 assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU has_function operation_3801 assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU text "The CoLoC-seq experimental protocol integrates organellar isolation, RNase gradient treatment, custom library preparation with selective sequencing of intact transcripts, and kinetics model-based bioinformatic analysis." assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU relatesTo RAMVUimnATifJYJw0VP2zAesw4OK_Gw30p9NgcEU4oVW8 assertion.
- step-rnase-treatment range "0 - 3 μg/ml RNase A" assertion.
- step-rnase-treatment numberOfSamples "9-10 samples per gradient" assertion.
- step-sequencing platform "Illumina NextSeq 500" assertion.
- data-analysis qualityControl "30-read cut-off for untreated samples; exclusion of cross-mapped sequences; parameter dependency <0.3" assertion.
- step-sequencing readLength "75 nt" assertion.
- step-sequencing readType "single-end" assertion.
- protocol step step-isolation assertion.
- protocol step step-library-prep assertion.
- protocol step step-rnase-treatment assertion.
- protocol step step-sequencing assertion.
- step-library-prep substep "First-strand cDNA synthesis (M-MLV reverse transcriptase)" assertion.
- step-library-prep substep "3'-adapter ligation to hydroxyl ends" assertion.
- step-library-prep substep "5'-adapter ligation to phosphorylated ends" assertion.
- step-library-prep substep "Cap removal (RNA 5'-pyrophosphohydrolase)" assertion.
- step-library-prep substep "PCR amplification (15 cycles, high-fidelity polymerase)" assertion.
- step-library-prep substep "Size selection: 10-220 nt on agarose gel" assertion.
- data-analysis tool "Origin 2021b (v9.8.5.212)" assertion.
- data-analysis tool "READemption (v0.4.3)" assertion.
- data-analysis tool "cutadapt (v2.8)" assertion.
- data-analysis tool "segemehl (v0.2.0-418)" assertion.
- data-analysis workExample "Adapter trimming; read alignment to GRCh38.p13; kinetics model fitting" assertion.
- step-isolation workExample "14,000 g for 20 min at 4°C to pellet mitochondria" assertion.
- RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU about gkac1205 assertion.
- data-analysis name "Bioinformatic Analysis Pipeline" assertion.
- protocol name "CoLoC-seq Experimental Protocol" assertion.
- step-isolation name "Organelle Isolation" assertion.
- step-library-prep name "Custom Library Preparation" assertion.
- step-rnase-treatment name "RNase A Gradient Treatment" assertion.
- step-sequencing name "High-Throughput Sequencing" assertion.