{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Johannes Gubat"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14135"],"description":["The goal of the project is to identify deubiquitinases (DUBs) networks that could be targetable in cancer. To identify functionally interacting DUBs, we performed a pooled combinatorial knockout screen using a CRISPR/Cas12a system. Here we transduced a custom guide library targeting any 2-gene combination derived from 160 genes (including ~90 DUBs and other genes of interest) into Cas12a-expressing HCT116 cells. While the cells are subjected to puromycin selection, a reference sample (Day 4 post-transduction) was taken and sequenced. Two replicates were derived from this pool that were expanded and sequenced at Day 11 and Day 18 post-transduction."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Genomic DNA was isolated using QIAamp DNA Blood Maxi Kit (Qiagen) as per manufacturer's instructions","Sequencing - The amplicon was sequenced on Illumina NovaSeq, reading 66 cycles Read 1 with custom primer cttgtggaaaggacgaaacaccgAAATTTCTCCTCTTGGAGAT; 10 cycles index read i7 to read the RSL, and six cycles index read i5 for the sample barcode","Library Construction - An amplicon containing guide and UMI sequences was amplified by PCR, also attaching adapter sequences.","Growth Protocol - The cells were grown in a humidified incubator at 37C and 5% CO2 and were regularly passaged at 70-80% confluence. Cell numbers were kept at >100 million cells.","Sample Collection - At the specified time point, the cells were detached with 0.25% trypsin and pelletted"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - NGS data was analyzed with the MaGeCK software, v.0.5.6. Read counts are normalized to median"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["Johannes Gubat","Padraig D'Arcy"],"additional_accession":[]},"is_claimable":false,"name":"Combinatorial CRISPR loss-of-function screen for deubiquitinases and genes related to the ubiquitin proteasome system in HCT116 cells","description":"The goal of the project is to identify deubiquitinases (DUBs) networks that could be targetable in cancer. To identify functionally interacting DUBs, we performed a pooled combinatorial knockout screen using a CRISPR/Cas12a system. Here we transduced a custom guide library targeting any 2-gene combination derived from 160 genes (including ~90 DUBs and other genes of interest) into Cas12a-expressing HCT116 cells. While the cells are subjected to puromycin selection, a reference sample (Day 4 post-transduction) was taken and sequenced. Two replicates were derived from this pool that were expanded and sequenced at Day 11 and Day 18 post-transduction.","dates":{"release":"2026-05-31T00:00:00Z","modification":"2026-05-31T01:01:15.541Z","creation":"2024-05-31T08:03:21.8Z"},"accession":"E-MTAB-14135","cross_references":{"ENA":["ERP160781"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}