Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA558785 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:With the recent advancements in genome editing, next generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop novel algorithms for target identi fication and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for Sequencing-based Target Ascertainment and Modular Perturbation Screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
2021-08-14 | GSE182088 | GEO
Project description:CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. Most previous CRISPR-based screens were implemented in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. A survival-based screen revealed neuron-specific essential genes and a small number of genes that improved neuronal survival upon knockdown. A screen with a single-cell transcriptomic readout uncovered several examples for genes knockdown of which had dramatically different cell-type specific consequences. A longitudinal imaging screen detected distinct consequences of gene knockdown on neuronal morphology. Our results highlight the potential of interrogating cell biology in iPSC-derived differentiated cell types and provide a platform for the systematic dissection of normal and disease states of neurons.
2019-01-07 | GSE124703 | GEO
Project description:Genetic heterogeneity is an important feature of solid tumors, however it is often assumed that most cancer cell lines are genetically homogeneous. A disparity in genetic complexity between cell lines and the disease they model could result in problems such as in vitro preclinical experiments overstating the effectiveness of putative therapeutics. We therefore derived clonal sublines by single cell cloning of in house derived early passage melanoma cell lines (LM-MEL-series), and compared their genomes to each other and the parental cell line using Illumina 610-Quad SNP arrays.
2013-09-08 | E-MTAB-1753 | biostudies-arrayexpress
Project description:Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity, rendering a decline in cloning. To test this possibility, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning. Our plan included the control hybridizations (self to self) of 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency. Results We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cloning efficiency cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). Conclusions Our findings reveal that large copy number genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline. 9 custom 2.1M high density aCGH were performed to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning, accommodating the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency.
2011-05-23 | E-GEOD-26132 | biostudies-arrayexpress
Project description:Single-cell CRISPR screens allow for the exploration of mammalian gene function and genetic regulatory networks, but their utility has been limited in part by their reliance on indirect sgRNA indexing. Here, we present direct capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct capture Perturb-seq enables the detection of multiple distinct sgRNAs expressed from a single vector within individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries. We demonstrate that this approach allows high-throughput investigations of genetic interactions, and we leverage this ability to dissect epistatic interactions between cholesterol biogenesis and DNA repair. We also show that targeting individual genes with multiple sgRNAs per cell improves the efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Lastly, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
2020-03-03 | GSE146194 | GEO
Project description:Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity, rendering a decline in cloning. To test this possibility, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning. Our plan included the control hybridizations (self to self) of 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency. Results We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cloning efficiency cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). Conclusions Our findings reveal that large copy number genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline.
2011-05-23 | GSE26132 | GEO
Project description:RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines
| PRJNA278161 | ENA
Project description:Two sets of wheat lines near-isogenic to Lr34 were used to compare gene expression profiles of wheat: 1. with and without Lr34 gene; 2. rust and mock inoculation; 3. distal and basal portion of the flag leaves. The two sets of wheat near-isogenic lines were used to subtract genetic background variations and to enrich Lr34-regulated gene expression profiles. The study is aimed to better understand the mechanisms of the well-known durable leaf rust resistance gene, Lr34, mediated resistance at the transcriptome level. Keywords: Distal and basal leaf halves of near-isogenic lines
2007-02-01 | GSE6227 | GEO