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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Amplicon DNA-sequencing of time series of pooled-CRISPR knock-out screens of Osimertinib and DMSO-treated cell lines

ABSTRACT: This project is a drug-gene interaction CRISPR screen to compare a 3-guide and a 6-guide library.

INSTRUMENT(S): NA, Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-13979 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP159128

REPOSITORIES: biostudies-arrayexpress

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Amplicon DNA-sequencing of time series of pooled-CRISPR knock-out screens of Osimertinib and DMSO-treated cell lines using a dual-guide CRISPR library

Project description:This project is a drug-gene interaction dual-guide CRISPR screen using a 3-guide pairs per gene library design.

2025-02-12 | E-MTAB-13980 | biostudies-arrayexpress

Genome-wide CRISPR Knock-out screen of LIMD1-/- isogenic and parental A549 cell line

Project description:LIMD1 is a tumour suppressor commonly found to have loss-of-function mutations in lung adenocarcinoma patients. Here we explore potential vulnerabilities of a lung cancer cell line specific to LIMD1 loss.

2026-02-01 | E-MTAB-15655 | biostudies-arrayexpress

Amplicon DNA-sequencing of time series of pooled-CRISPR knock-out screens of colon cancer cell lines

Project description:This project aims to compare gRNA design algorithms using a benchmark CRISPR-knockout library composed of gRNAs targeting essential and non-essential genes.

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Amplicon DNA-sequencing of time series of pooled-CRISPR knock-out screens of the HT29 colon cancer cell line

Project description:This project also aims to compare gRNA design algorithms using a benchmark CRISPR-knockout library composed of gRNAs targeting essential and non-essential genes.

2025-02-12 | E-MTAB-13977 | biostudies-arrayexpress

Amplicon DNA-sequencing of time series of pooled-CRISPR knock-out screens of cell lines using a dual-guide CRISPR library

Project description:This project aims to compare gRNA design algorithms and single- versus dual-targeting using a benchmark CRISPR-knockout library composed of gRNAs targeting essential and non-essential genes.

2025-02-12 | E-MTAB-13981 | biostudies-arrayexpress

CRISPR screen exploring resistance to AKTi (Capivasertib) in ER+ Breast Cancer in MCF7, T47D and CAMA-1 cell lines

Project description:A genome-wide CRISPR-Cas9 knockout screen was performed in the breast cancer cell lines T47D, MCF7, and CAMA-1 to identify genes modulating sensitivity and resistance to capivasertib, a selective AKT inhibitor. Cells were transduced with a CRISPR library, followed by treatment with capivasertib or vehicle control (DMSO). Guide RNA (sgRNA) enrichment and depletion were assessed via next-generation sequencing to determine gene-level effects on cell viability and drug response. Gene-level data are provided for the initial plasmid library, baseline, DMSO-treated controls, and post-capivasertib treatment across replicates.

2026-05-25 | E-MTAB-16438 | biostudies-arrayexpress

Combinatorial CRISPR loss-of-function screen for deubiquitinases and genes related to the ubiquitin proteasome system in HCT116 cells

Project 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.

2026-05-31 | E-MTAB-14135 | biostudies-arrayexpress

shRNA Sensor Analysis of 5' U converted shRNAs reveals 3' target bias exists in addition to 5' guide bias

Project description:shRNAs selected with the shERWOOD algorithm were converted to have a U at the 5' end of their guide. When endogenous 1U shRNAs were compared to artificial shRNA via the sensor algorithm, the endogenous shRNAs were found to be more efficacious. Purpose: Structural studies have hinted that the 5' end of shRNA guides is engulfed in the RISC complex. It has also been reported that shRNAs with a 5' U are more efficacious than those with other 5' caps. We wished to determine whether replacement of shRNA guide 5' nucleotides with a U, regardless of the corresponding target base, would increase their efficacy. Method: For each gene in the "druggable genome" 10 shRNAs were selected with the shERWOOD algorithm. In each case the score was assessed as if the guide had a 5' U. Sensor constructs were designed pairing 1U-guide shRNAs with their endogenous target. shRNAs were assessed for efficacy via the shRNA sensor assay (Fellmann et al. Mol Cell 2011). Results: shRNAs with artificial 5' Us were found to be less efficacious than those with an endogenous 5' U,

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Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

Amplicon Sequencing of gRNAs from Druggable Genome CRISPR mutagenized Huh7.5.1 cells after live/dead selection with DENV2

Project description:Huh7.5.1 cells were stably transduced with lentiCas9-Blast (Addgene, #52962) and subsequently selected using Blasticidin. Then, Huh7.5.1 cells that constitutively express Cas9 were transduced with lentiGuide-Puro from the druggable genome library at MOI 0.3. Cells were then selected with puromycin, expanded, and then pooled together and cryofrozen in aliquots. Cells were thawed constituting over 1000× genome coverage worth of mutagenized library. The cells were infecting with DENV2_429557 and DENV-2_16681_Hap1-adapted at MOI of 0.1. Virus-resistant colonies were harvested. The uninfected reference used was the unselected starting population. The unselected and selected cells were both processed with QIAamp DNA columns to purify the gDNA. A first round of PCR was used to amplify the guide RNA sequences encoded in the gDNA, followed by a second round of PCR to add the barcodes/adapters for amplicon sequencing. 2% agarose gels and a QIAquick gel extraction kit were used to purify the amplicons. The amplicons were then subjected to next-generation sequencing on a HiSeq instrument lane (Illumina) via Novogene.

2024-12-29 | E-MTAB-14693 | biostudies-arrayexpress

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