- Repository of code and pipelines of the lab: https://github.com/seruggialab
- Design of sgRNA libraries for tiling experiments: http://crispor.tefor.net/crispor.py?batchId=ozJbN0W08qlgEBn3RvZK
- Count sgRNA from NGS, analyze CRISPR tiling screens: https://crisprsurf.pinellolab.partners.org/
- Detect/quantify genome editing by NGS/amplicon sequencing: http://crispresso2.pinellolab.org/submission
- Is gene X expressed in cell type Y?: http://biogps.org/#goto=welcome or https://cellxgene.cziscience.com/gene-expression?utm_source=twitter&utm_medium=social&utm_campaign=ge_fmg_2023&utm_content=2023_twitter_1
- Database of ChIP-seq experiments: http://cistrome.org/db/#/
- Database of PROTACs: http://cadd.zju.edu.cn/protacdb/about
- Existing KO mouse lines & phenotype: https://www.mousephenotype.org/
- Protein sequence to molecular weight: https://web.expasy.org/compute_pi/
- Make KOs with base editors by targeting splicing acceptor or donor sites: https://moriaritylab.shinyapps.io/splicer/
- Find protein partners of your favorite protein: https://thebiogrid.org/ and https://opencell.czbiohub.org/ (also: resource for C-term GFP tagging)
- sgRNA design tool for SpG and SpRY nucleases: https://www.crisprscan.org/
- Find a sequence in the genome: https://genome.ucsc.edu/cgi-bin/hgBlat?hgsid=1547504093_Lp2XvM5n043oBeMBZ82YvqbWSmKL&command=start
- Computational tools for ChIP-seq etc: https://ihec-epigenomes.org/research/tools/
- Design sgRNAs for Base Editing: https://deepcrispr.info/DeepBE/
- Design sgRNA libraries for Base Editing: https://pypi.org/project/beditor/
- Library of sgRNA targeting start codons and splice sites: https://www.addgene.org/pooled-library/barbeko-sgrna-library/?utm_term=&utm_campaign=Primary+Ad+Group:+Website,+blog,+collections.&utm_source=adwords&utm_medium=ppc&hsa_acc=3245806047&hsa_cam=112133441&hsa_grp=7318542161&hsa_ad=523677385436&hsa_src=g&hsa_tgt=dsa-19959388920&hsa_kw=&hsa_mt=&hsa_net=adwords&hsa_ver=3&gad_source=1&gclid=CjwKCAjwt-OwBhBnEiwAgwzrUkfeFpdToBL0cXZpxwqdiWqNdx-2VJNumegJ3FE3aCMnee58gFjTcxoCho8QAvD_BwE
- ABC looping model in different cell types: https://flekschas.github.io/enhancer-gene-vis/?daet=Uz1_tEABQf-uzktblvBKSQ%3Arg%3ADNA%20Accessibility&dals=indicator&darn=true&dasi=true&dasp=false&e=chr10.81269256&egce=max-score&egi=true&egp=false&erc=solid&erhu=false&eri=true&erso=0d05&ert=e3lpYv5LSIiik7CFtuAMTw%3Arg%3A1%3A4%3A4%3A0%3A3%3A5%3AEnhancer%20regions&f=rs1250566&g=ARID5B&s=chr10.63438208&vs=pValue&vt=VF5-RDXWTxidGMJU7FeaxA%3Arg%3A7%3A8&w=0
Seruggia lab 