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- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.Lab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.Elements selection method: synthetic elementsLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA of TERT locus in HEK293TElements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
- MPRA of SORT1 locus in HepG2Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT enhancer, using 3' to 5' direction.
- MPRA of SORT1 locus in HepG2Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
- MPRA of SORT1 locus in HepG2Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
- MPRA of MYC locus in HEK293TElements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.
- MPRA of MSMB locus in HEK293TElements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
- MPRA of LDLR locus in HepG2Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
- MPRA of LDLR locus in HepG2Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
- MPRA of HNF4A locus in HEK293TElements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the HNF4A promoter.
- MPRA of FOXE1 locus in HeLaElements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the FOXE1 promoter.
- MPRA of F9 locus in HepG2Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the F9 promoter.
- CRISPRi proliferation screen in HCT116Homo sapiens HCT116, 14 days post-nucleic acid delivery time genetically modified (insertion) using transduction, using CRISPRi (pgRNA)Elements selection method: histone modificationsTiling modality: peak tilingLab: Bing Ren, UCSDProject: ENCODE
- CRISPRi proliferation screen in HCT116Homo sapiens HCT116, 14 days post-nucleic acid delivery time genetically modified (insertion) using transduction, using CRISPRi (pgRNA)Elements selection method: histone modificationsTiling modality: peak tilingLab: Bing Ren, UCSDProject: ENCODE
- CRISPRi proliferation screen in HCT116Homo sapiens HCT116, 0 days post-nucleic acid delivery time genetically modified (insertion) using transduction, using CRISPRi (pgRNA)Elements selection method: histone modificationsTiling modality: peak tilingLab: Bing Ren, UCSDProject: ENCODE
- CRISPRi proliferation screen in HCT116Homo sapiens HCT116, 0 days post-nucleic acid delivery time genetically modified (insertion) using transduction, using CRISPRi (pgRNA)Elements selection method: histone modificationsTiling modality: peak tilingLab: Bing Ren, UCSDProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HCT116Homo sapiens HCT116, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HCT116Homo sapiens HCT116, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: DNase hypersensitive sites, histone modifications, synthetic elementsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: DNase hypersensitive sites, histone modifications, synthetic elementsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in mammary epithelial cellHomo sapiens mammary epithelial cell female genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2 genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HEK293Homo sapiens HEK293 genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HEK293Homo sapiens HEK293 genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- perturbation followed by snATAC-seq in MCF-7CRISPRi perturbation of MCF7sLab: Will Greenleaf, StanfordProject: ENCODE
- MPRA in HepG2Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as ORI, and serves as an internal control to ORI_full.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Elements cloned into the pGL4 vector upstream of a minimal promoter. One of nine methods testing element activity in parallel.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 24 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Homo sapiens HepG2, 48 hours post-nucleic acid delivery time genetically modified (episome) using transient transfectionElements selection method: sequence variantsLab: Ryan Tewhey, JAXProject: ENCODE
- MPRA in HepG2Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.Elements selection method: DNase hypersensitive sitesLab: Nadav Ahituv, UCSFProject: ENCODE
- CRISPRi proliferation screen of multiple loci in DU 145Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- CRISPRi proliferation screen of multiple loci in NCI-H460Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- CRISPRi proliferation screen of multiple loci in MDA-MB-231Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- CRISPRi proliferation screen of multiple loci in MCF-7Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- CRISPRi proliferation screen of multiple loci in HepG2Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- CRISPRi proliferation screen of multiple loci in HCT116Growth-based CRISPR screen targeting genomic regions near MYC and MYB genes.
- STARR-seq in MCF-7Homo sapiens MCF-7 genetically modified (episome) using transient transfectionLab: Kevin White, UChicagoProject: ENCODE
- STARR-seq in HCT116Homo sapiens HCT116 genetically modified (episome) using transient transfectionLab: Kevin White, UChicagoProject: ENCODE
- STARR-seq in SH-SY5YHomo sapiens SH-SY5Y genetically modified (episome) using transient transfectionLab: Kevin White, UChicagoProject: ENCODE
- STARR-seq in HepG2Homo sapiens HepG2 genetically modified (episome) using transient transfectionLab: Kevin White, UChicagoProject: ENCODE