Project description:Type VI CRISPR enzymes are RNA-targeting proteins with nuclease activity that enable specific and robust target gene knockdown without altering the genome. To define rules for the design of Cas13d guide RNAs, we conducted massively parallel screens targeting messenger RNAs of a green fluorescent protein transgene, and CD46, CD55 and CD71 cell-surface proteins in human cells. In total, we measured the activity of 24,460 gRNAs with and without mismatches relative to the target sequences. Knockdown efficacy is driven by gRNA-specific features and target site context. Single mismatches generally reduce knockdown to a modest degree, but spacer nucleotides 15–21 are largely intolerant of target site mismatches. We developed a computational model to identify optimal gRNAs and confirm their generalizability testing 3,979 guides targeting mRNAs of 48 endogenous genes. We show that Cas13 can be used in forward transcriptomic pooled screens and, using our model, predict optimized Cas13 gRNAs for all protein-coding transcripts in the human genome.

2020-01-30 | GSE142675 | GEO

HNSCC samples vs. normal tonsil samples: self-self hybridization design

Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a self-self hybridization experimental design on two-color arrays. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the reference design experimental setting. Keywords: tumor/normal comparison 8 HNSCC tumor samples and 8 normal tonsil samples. Each was profiled using a self-self hybridization design, where two aliquots of the same sample were labeled with two different dyes (cy3 and cy5) and hybridize to the same array.

2010-05-06 | E-GEOD-13397 | biostudies-arrayexpress

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians.

Project description: Not available

| S-EPMC6041728 | biostudies-literature

A comprehensive guide to conduct a systematic review and meta-analysis in medical research.

Project description: Not available

| S-EPMC12366998 | biostudies-literature

HNSCC samples vs. normal tonsil samples: self-self hybridization design

2009-01-22 | GSE13397 | GEO