{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Wengui Shi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15686"],"description":["To identify genes driver resistance of apatinib on human umbilical vein endothelial cells (HUVECs). The CRISPR-Pool SAM human library, containing 70290 sgRNAs targeting 23430 genes were constructed in MS2-P65-HSF1. After the cells were treated with apatinib for another week and their genomic DNA was extracted. The sgRNA fragments were amplified by PCR. After passing quality control, 20–50 ng of DNA fragments are used to construct a high-throughput sequencing library for the Illumina platform through steps such as End Repair, 5' Phosphorylation and dA-Tailing, Adapter Ligation, Clean Up, and PCR Enrichment and Clean Up."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The sgRNA fragments were amplified by PCR. After passing quality control, 20-50 ng of DNA fragments are used to construct a high-throughput sequencing library for the Illumina platform through steps such as End Repair, 5 Phosphorylation and dA-Tailing, Adapter Ligation, Clean Up, and PCR Enrichment and Clean Up.","Sequencing - DNA libraries labeled with different indexes were pooled and subjected to PE150 paired-end sequencing using the Illumina HiSeq Xten/Illumina Novaseq platform according to the manufacturer's instructions. Data analysis was subsequently performed by bioinformatics analysis engineers upon completion of sequencing.","Sample Collection - The CRISPR-Pool SAM human library, containing 70290 sgRNAs targeting 23430 genes were constructed in MS2-P65-HSF1. After the cells were treated with apatinib for another week and their genomic DNA was extracted.","Nucleic Acid Extraction - Total DNA were extracted using NEBNext Ultra II DNA Kit"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The paired-end sequencing data was merged using the FLASH software. Based on the 5-bp overlapping regions of the upstream and downstream reads, target sgRNAs were extracted from both the merged and unmerged R1 and R2 data using an in-house script. The extracted sgRNAs were then subjected to data quantity statistics and quality assessment.  The MAGeCK software was used to align the extracted sgRNAs to the sgRNA library. The alignment data from all samples were aggregated, and the alignment rate, gRNA sequencing depth, as well as gRNA and gene coverage were evaluated.  The read counts for each gRNA in each sample were calculated and annotated to their corresponding target genes, followed by normalization of the count results. Principal component analysis and cluster analysis were performed on the samples to visualize the clustering relationships among them."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","HiSeq X Ten"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["Wengui Shi"],"additional_accession":[]},"is_claimable":false,"name":"sgRNA sequencing of Non-kinase Orchestrated VEGFR2–ERK Hyperactivation as a Dependency and Pharmacological Target in Tumor Angiogenesis","description":"To identify genes driver resistance of apatinib on human umbilical vein endothelial cells (HUVECs). The CRISPR-Pool SAM human library, containing 70290 sgRNAs targeting 23430 genes were constructed in MS2-P65-HSF1. After the cells were treated with apatinib for another week and their genomic DNA was extracted. The sgRNA fragments were amplified by PCR. After passing quality control, 20–50 ng of DNA fragments are used to construct a high-throughput sequencing library for the Illumina platform through steps such as End Repair, 5' Phosphorylation and dA-Tailing, Adapter Ligation, Clean Up, and PCR Enrichment and Clean Up.","dates":{"release":"2025-10-30T00:00:00Z","modification":"2026-05-30T17:15:18.51Z","creation":"2025-10-09T16:21:23.974Z"},"accession":"E-MTAB-15686","cross_references":{"ENA":["ERP181289"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}