I have never done any CRISPR experiment before and my tutor asked me to use CRISPR KI to induce a mCherry tag for a gene in U2OS, I decided to follow the protocol described in Article Generation and validation of homozygous fluorescent knock-in...
.It tells that 'The fluorescent marker replaces either the start or the stop codon and is in-frame with the GOI and the endogenous promoter.' I put the gene sequence in benchling to pick gRNA and found that there's simply no DSBs at the start codon(ATG) of the gene, and since the start codon is in the very 5' of exon2, there's also no DSBs in that part of exon2(I tried stop codon and found nearly no difference). I have some questions below:(1,2 urgent)
1. Should I take a proper pair of gRNA in exon1 or just in the intron at 5' of exon2?
2. Is it possible to replace the ATG of my gene when there's no DSB at ATG? How do I design my donor DNA?
3. Is there any other simple way to add fluorescent label in endogenous gene of U2OS?
4. Should I use human gene sequence in NCBI since U2OS is kind of a cancer cell line?
5. How do I find the endogenous promoter of the gene?