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69 Immunoprecipitation is performed under stringent conditions with an antibody against the RBP of interest, the unbound portion of RNA is digested, and the resulting RBP-protected RNA fragments are analyzed by high-throughput sequencing (the entire procedure is often abbreviated as HITS-CLIP or CLIP-seq).
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Residual RNA was digested with RNAase.
RNA was digested using RNase A, DNA precipitated and quantified using a NanoDrop.
After that, the isolated RNA was digested with TURBO DNase™ (Ambion) to discard the DNA contaminants.
RNA was digested with DNAseI (Invitrogen) and reverse transcribed to cDNA using Superscript III reverse transcriptase (Invitrogen).
RNA was digested with RNase and then propidium di-iodide was added at a final concentration of 50 µg/ml.
The unbound RNA was digested by addition of 3 units of RNase T1 and incubation at 25°C for 10 minutes.
For RT-PCR, 5 µg RNA was digested with DNAseI, followed by reverse transcription and quantitative PCR.
Twenty µg of total RNA from each sample was hybridized with antisense, radiolabeled probes, after which free probe and remaining single-stranded RNA were digested with RNase A/T1.
The isolated RNA was digested with TURBO DNase™ (Ambion, Austin, TX, USA) to discard the DNA contaminant, according to the manufacturer's protocol.
For the PCR array, cells were processed as above and total RNA was digested with DNase I to eliminate chromosomal DNA contamination (Qiagen, Valencia, CA) and purified using the Qiagen RNeasy Mini Kit per the manufacturer's instructions.
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