High throughput phenotype screening pipeline for functional genomics in Magnaporthe oryzae

2007 ◽  
Author(s):  
Sook-Young Park ◽  
Myoung-Hwan Chi ◽  
Junhyun Jeon ◽  
Yong-Hwan Lee
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Magnaporthe Oryzae ◽  
Phenotype Screening

scholarly journals Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

2016 ◽  
Vol 17 (6) ◽  
pp. 460-475 ◽  
Author(s):  
Anis Ben-Amar ◽  
Samia Daldoul ◽  
Götz M. Reustle ◽  
Gabriele Krczal ◽  
Ahmed Mliki
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Reverse Genetics ◽  
High Throughput Sequencing

scholarly journals A genome-wide screen in the mouse liver reveals sex-specific and cell non-autonomous regulation of cell fitness

2021 ◽  
Author(s):  
Heather R. Keys ◽  
Kristin A. Knouse
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Mouse Liver ◽  
Ex Vivo ◽  
Screening Method ◽  
Living Organism ◽  
Cellular Processes ◽  
Autonomous Regulation ◽  
Genome Wide ◽  
A Genome

ABSTRACTOur ability to understand and modulate mammalian physiology and disease requires knowing how all genes contribute to any given phenotype in the organism. Genome-wide screening using CRISPR-Cas9 has emerged as a powerful method for the genetic dissection of cellular processes1,2, but the need to stably deliver single guide RNAs to millions of cells has restricted its implementation to ex vivo systems. These ex vivo systems cannot reproduce all of the cellular phenotypes observed in vivo nor can they recapitulate all of the factors that influence these phenotypes. There thus remains a pressing need for high-throughput functional genomics in a living organism. Here, we establish accessible genome-wide screening in the mouse liver and use this approach to uncover the complete regulation of cellular fitness in a living organism. We discover novel sex-specific and cell non-autonomous regulation of cell growth and viability. In particular, we find that the class I major histocompatibility complex is essential for preventing immune-mediated clearance of hepatocytes. Our approach provides the first comprehensive picture of cell fitness in a living organism and highlights the importance of investigating cellular phenomena in their native context. Our screening method is robust, scalable, and easily adapted to examine diverse cellular processes using any CRISPR application. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling unprecedented insight into mammalian physiology and disease.

scholarly journals High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea

2016 ◽  
Vol 131 ◽  
pp. 113-121 ◽  
Author(s):  
Mary E. Walter ◽  
Alicia Ortiz ◽  
Casey Sondgeroth ◽  
Nathan M. Sindt ◽  
Nikolas Duszenko ◽  
...  
Keyword(s):  
High Throughput ◽  
Methanogenic Archaea ◽  
Phenotype Screening

Functional Analysis of the Differential Gene Expression Profile of Human HSC Using a Functional Genomics Screen in the Zebrafish.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 136-136
Author(s):  
Craig E. Eckfeldt ◽  
Eric M. Mendenhall ◽  
Stephen C. Ekker ◽  
Catherine M. Verfaillie
Keyword(s):  
Gene Expression ◽  
Fluorescence Microscopy ◽  
Functional Genomics ◽  
Differentially Expressed Genes ◽  
High Throughput ◽  
Hla Antigens ◽  
Differentially Expressed ◽  
Sequence Information ◽  
Hematopoietic Stem

Abstract Self-renewal and lineage differentiation of hematopoietic stem cells (HSC) is likely regulated by a combination of intrinsic and extrinsic signals. At present these signals are poorly understood. Recently, numerous groups have identified the expressed gene profile of HSC in an attempt to identify novel genes that regulate HSC fate decisions. Likewise, our group compared the expressed gene profiles of CD34+CD33−CD38−Rholoc-kit+ (Rholo) cells, enriched in primitive progenitors and presumed human HSC, compared to CD34+CD33−CD38−Rhohi (Rhohi) cells, depleted of such cells, from umbilical cord blood (UCB) and bone marrow (BM) to identify conserved signaling pathways active in these ontogenically distinct populations using the Afftymetrix™ HG-U133 GeneChip® set. We identified a putative molecular signature for human HSC containing 286 genes, expressed more highly in Rholo or Rhohi cells from both cell sources using a p<0.05 and fold change of 1.5 cutoff. To assess the role of this series of genes in a high-throughput fashion, we developed an in vivo functional genomics screen in the zebrafish that allows for the determination of hematopoietic function of the differentially expressed genes. Candidate gene expression was knocked down by injecting morpholino antisense oligonucleotides (MO) into 1–4 cell embryos from GATA1:DsRed transgenic zebrafish that have red fluorescent GATA1+ blood cells and blood production was scored by fluorescence microscopy at 30 and 48 hours post-fertilization. Of the 286 differentially expressed genes, 128 were deemed too universal or likely non-specific for hematopoiesis, and were not targeted. These included histones, HLA-antigens, hemoglobin genes, and genes encoding proteins involved in general cellular metabolism. Of the remaining 158, MO were designed for 70 (44%), no zebrafish ortholog could be identified for 72 (46%), inadequate sequence information was available to design morpholinos for 9 (6%) and multiple zebrafish orthologs were identified for 7 (4%). Fluorescence microscopy of GATA1:DsRed fish has revealed a reproducible reduction in GATA1+ blood cell number for 13 of 55 MO-targeted genes analyzed to date, giving a 24% frequency for hematopoietic phenotypes in the screen, that compares very favorably with the noted 0.5–1% frequency of hematopoietic genes identified in ENU mutagenesis screens that mutate genes in a near random fashion. The functionally-validated genes identified thus far include known genes that lack a known hematopoietic function such as SPRY1, CRTAP, IRAK3 and UCP2, as well as genes that currently lack a functional annotation such as C12orf2, DKFZp564D137, MGC15875 and FLJ21269. Hematopoietic phenotypes are being further characterized by whole-mount in situ hybridization for hematopoietic genes and rescue of hematopoietic phenotypes by co-injection of overexpression vectors in the zebrafish. In addition, we are confirming the role of the genes in mammalian hematopoiesis using overexpression and knockdown studies in murine and human repopulating HSC. This is the first description of a high-throughput functional genomics screen in the zebrafish to functionally validate differentially expressed genes, an essential step in obtaining meaningful functional data from global gene profiling studies.

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

Nature ◽  
2014 ◽  
Vol 509 (7501) ◽  
pp. 487-491 ◽  
Author(s):  
Yuexin Zhou ◽  
Shiyou Zhu ◽  
Changzu Cai ◽  
Pengfei Yuan ◽  
Chunmei Li ◽  
...  
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
High Throughput Screening ◽  
Human Cells

scholarly journals High-Throughput Cryopreservation of Plant Cell Cultures for Functional Genomics

2012 ◽  
Vol 53 (5) ◽  
pp. 943-952 ◽  
Author(s):  
Yoichi Ogawa ◽  
Nozomu Sakurai ◽  
Akira Oikawa ◽  
Kosuke Kai ◽  
Yoshihiko Morishita ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Plant Cell ◽  
Cell Cultures ◽  
High Throughput ◽  
Plant Cell Cultures
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