Feeder-free culture of human embryonic stem cells in conditioned medium for efficient genetic modification.

Abstract:

:Realizing the potential of human embryonic stem cells (hESCs) in research and commercial applications requires generic protocols for culture, expansion and genetic modification that function between multiple lines. Here we describe a feeder-free hESC culture protocol that was tested in 13 independent hESC lines derived in five different laboratories. The procedure is based on Matrigel adaptation in mouse embryonic fibroblast conditioned medium (CM) followed by monolayer culture of hESC. When combined, these techniques provide a robust hESC culture platform, suitable for high-efficiency genetic modification via plasmid transfection (using lipofection or electroporation), siRNA knockdown and viral transduction. In contrast to other available protocols, it does not require optimization for individual lines. hESC transiently expressing ectopic genes are obtained within 9 d and stable transgenic lines within 3 weeks.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Braam SR,Denning C,Matsa E,Young LE,Passier R,Mummery CL

doi

10.1038/nprot.2008.140

subject

Has Abstract

pub_date

2008-01-01 00:00:00

pages

1435-43

issue

9

eissn

1754-2189

issn

1750-2799

pii

nprot.2008.140

journal_volume

3

pub_type

杂志文章
  • Fast, efficient and reproducible genetic transformation of Phaseolus spp. by Agrobacterium rhizogenes.

    abstract::This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.259

    authors: Estrada-Navarrete G,Alvarado-Affantranger X,Olivares JE,Guillén G,Díaz-Camino C,Campos F,Quinto C,Gresshoff PM,Sanchez F

    更新日期:2007-01-01 00:00:00

  • Reverse transfection on cell arrays for high content screening microscopy.

    abstract::Here, we describe a robust protocol for the reverse transfection of cells on small interfering (siRNA) arrays, which, in combination with multi-channel immunofluorescence or time-lapse microscopy, is suitable for genome-wide RNA interference (RNAi) screens in intact human cells. The automatic production of 48 'transfe...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2006.483

    authors: Erfle H,Neumann B,Liebel U,Rogers P,Held M,Walter T,Ellenberg J,Pepperkok R

    更新日期:2007-01-01 00:00:00

  • Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.

    abstract::PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantit...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.133

    authors: Carvalho PC,Lima DB,Leprevost FV,Santos MD,Fischer JS,Aquino PF,Moresco JJ,Yates JR 3rd,Barbosa VC

    更新日期:2016-01-01 00:00:00

  • Video tracking and analysis of sleep in Drosophila melanogaster.

    abstract::In the past decade, Drosophila has emerged as an ideal model organism for studying the genetic components of sleep as well as its regulation and functions. In fruit flies, sleep can be conveniently estimated by measuring the locomotor activity of the flies using techniques and instruments adapted from the field of cir...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.041

    authors: Gilestro GF

    更新日期:2012-04-26 00:00:00

  • Preparation, functionalization and characterization of engineered carbon nanodots.

    abstract::Carbon-based dots (CDs) and their functionalized (nano)composites have recently attracted attention due to their seemingly easy preparation and numerous potential applications, ranging from those in the biomedical field (i.e., imaging and drug delivery) to those in (opto)electronics (i.e., solar cells and LEDs). This ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0207-x

    authors: Ðorđević L,Arcudi F,Prato M

    更新日期:2019-10-01 00:00:00

  • Deubiquitinase-based analysis of ubiquitin chain architecture using Ubiquitin Chain Restriction (UbiCRest).

    abstract::Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (m...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2015.018

    authors: Hospenthal MK,Mevissen TET,Komander D

    更新日期:2015-02-01 00:00:00

  • Intravascular staining for discrimination of vascular and tissue leukocytes.

    abstract::Characterization of the cellular participants in tissue immune responses is crucial to understanding infection, cancer, autoimmunity, allergy, graft rejection and other immunological processes. Previous reports indicate that leukocytes in lung vasculature fail to be completely removed by perfusion. Several studies sug...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2014.005

    authors: Anderson KG,Mayer-Barber K,Sung H,Beura L,James BR,Taylor JJ,Qunaj L,Griffith TS,Vezys V,Barber DL,Masopust D

    更新日期:2014-01-01 00:00:00

  • Synthesis and use of an amphiphilic dendrimer for siRNA delivery into primary immune cells.

    abstract::Using siRNAs to genetically manipulate immune cells is important to both basic immunological studies and therapeutic applications. However, siRNA delivery is challenging because primary immune cells are often sensitive to the delivery materials and generate immune responses. We have recently developed an amphiphilic d...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-020-00418-9

    authors: Chen J,Ellert-Miklaszewska A,Garofalo S,Dey AK,Tang J,Jiang Y,Clément F,Marche PN,Liu X,Kaminska B,Santoni A,Limatola C,Rossi JJ,Zhou J,Peng L

    更新日期:2021-01-01 00:00:00

  • Six alternative proteases for mass spectrometry-based proteomics beyond trypsin.

    abstract::Protein digestion using a dedicated protease represents a key element in a typical mass spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been predominantly performed with trypsin, mainly because of its high specificity, widespread availability and ease of use. Lately, it has become appar...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2016.057

    authors: Giansanti P,Tsiatsiani L,Low TY,Heck AJ

    更新日期:2016-05-01 00:00:00

  • Site-specific protein labeling using PRIME and chelation-assisted click chemistry.

    abstract::This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: probe incorporation mediated by enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.096

    authors: Uttamapinant C,Sanchez MI,Liu DS,Yao JZ,Ting AY

    更新日期:2013-08-01 00:00:00

  • Production of highly potent recombinant siRNAs in Escherichia coli.

    abstract::We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro-siRNAs for prokaryotic siRNAs. We present a detailed protocol d...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.149

    authors: Huang L,Lieberman J

    更新日期:2013-12-01 00:00:00

  • CRISPR-Cas9-mediated genome editing in apple and grapevine.

    abstract::The CRISPR-Cas9 genome-editing tool and the availability of whole-genome sequences from plant species have revolutionized our ability to introduce targeted mutations into important crop plants, both to explore genetic changes and to introduce new functionalities. Here, we describe protocols adapting the CRISPR-Cas9 sy...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0067-9

    authors: Osakabe Y,Liang Z,Ren C,Nishitani C,Osakabe K,Wada M,Komori S,Malnoy M,Velasco R,Poli M,Jung MH,Koo OJ,Viola R,Nagamangala Kanchiswamy C

    更新日期:2018-12-01 00:00:00

  • Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing.

    abstract::The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has bec...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.396

    authors: Harakalova M,Mokry M,Hrdlickova B,Renkens I,Duran K,van Roekel H,Lansu N,van Roosmalen M,de Bruijn E,Nijman IJ,Kloosterman WP,Cuppen E

    更新日期:2011-11-03 00:00:00

  • Expander: from expression microarrays to networks and functions.

    abstract::A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.230

    authors: Ulitsky I,Maron-Katz A,Shavit S,Sagir D,Linhart C,Elkon R,Tanay A,Sharan R,Shiloh Y,Shamir R

    更新日期:2010-02-01 00:00:00

  • Fabrication and practical applications of molybdenum disulfide nanopores.

    abstract::Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-019-0131-0

    authors: Graf M,Lihter M,Thakur M,Georgiou V,Topolancik J,Ilic BR,Liu K,Feng J,Astier Y,Radenovic A

    更新日期:2019-04-01 00:00:00

  • In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons.

    abstract::Neurons in cortical sensory regions receive modality-specific information through synapses that are located on their dendrites. Recently, the use of two-photon microscopy combined with whole-cell recordings has helped to identify visually evoked dendritic calcium signals in mouse visual cortical neurons in vivo. The c...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2010.169

    authors: Jia H,Rochefort NL,Chen X,Konnerth A

    更新日期:2011-01-01 00:00:00

  • Transient expression and analysis of fluorescent reporter proteins in plant pollen tubes.

    abstract::The pollen tube is an excellent single-cell model system for studying cellular processes in plant cell biology. This protocol describes a detailed step-by-step procedure with optimized conditions for introducing various fluorescent reporter proteins into lily, tobacco and Arabidopsis pollen grains by means of biolisti...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2011.309

    authors: Wang H,Jiang L

    更新日期:2011-04-01 00:00:00

  • Footprinting protein-DNA complexes using the hydroxyl radical.

    abstract::Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA-protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent probe for high-resolution footprinting of DNA-protein complexes; this technique can provide structural detail th...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.72

    authors: Jain SS,Tullius TD

    更新日期:2008-01-01 00:00:00

  • Orthotopic mouse lung transplantation as experimental methodology to study transplant and tumor biology.

    abstract::Unlike transplantation of other solid organs, vascularized mouse lung transplantation has only recently been developed. In this protocol, we describe a detailed method for performing a vascularized and aerated mouse orthotopic lung transplant, which to date represents the most physiological mouse model of lung transpl...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.218

    authors: Krupnick AS,Lin X,Li W,Okazaki M,Lai J,Sugimoto S,Richardson SB,Kornfeld CG,Garbow JR,Patterson GA,Gelman AE,Kreisel D

    更新日期:2009-01-01 00:00:00

  • Using the rat forced swim test to assess antidepressant-like activity in rodents.

    abstract::The forced swim test (FST) is one of the most commonly used animal models for assessing antidepressant-like behavior. This protocol details using the FST in rats, which takes place over 48 h and is followed by the video analysis of the behavior. The swim test involves the scoring of active (swimming and climbing) or p...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2012.044

    authors: Slattery DA,Cryan JF

    更新日期:2012-05-03 00:00:00

  • Generation of a transgenic ORFeome library in Drosophila.

    abstract::Overexpression screens can be used to explore gene function in Drosophila melanogaster, but to demonstrate their full potential, comprehensive and systematic collections of fly strains are required. Here we provide a protocol for high-throughput cloning of Drosophila open-reading frames (ORFs) that are regulated by up...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2014.105

    authors: Bischof J,Sheils EM,Björklund M,Basler K

    更新日期:2014-07-01 00:00:00

  • Cryopreservation and banking of mammalian cell lines.

    abstract::This protocol describes the principles and methods used for the preparation of cryopreserved cell stocks. Following these procedures will ensure the availability of reproducible cultures for use within a single laboratory at different times and for different collaborating laboratories. Although the basic principle is ...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.190

    authors: Stacey GN,Masters JR

    更新日期:2008-01-01 00:00:00

  • Detection of protein SUMOylation in vivo.

    abstract::The small ubiquitin-like modifiers (SUMOs) are posttranslationally conjugated to eukaryotic cellular proteins with generally unpredictable consequences. SUMO substrates are found in many cellular systems, and functional analysis has revealed that substrate SUMOylation often has an important role in their regulation. H...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2009.128

    authors: Tatham MH,Rodriguez MS,Xirodimas DP,Hay RT

    更新日期:2009-01-01 00:00:00

  • Generation of lung organoids from human pluripotent stem cells in vitro.

    abstract::The lung epithelium is derived from the endodermal germ layer, which undergoes a complex series of endoderm-mesoderm-mediated signaling events to generate the final arborized network of conducting airways (bronchi, bronchioles) and gas-exchanging units (alveoli). These stages include endoderm induction, anterior-poste...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/s41596-018-0104-8

    authors: Miller AJ,Dye BR,Ferrer-Torres D,Hill DR,Overeem AW,Shea LD,Spence JR

    更新日期:2019-02-01 00:00:00

  • The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins.

    abstract::The Strep-tag II is an eight-residue minimal peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) that exhibits intrinsic affinity toward streptavidin and can be fused to recombinant proteins in various fashions. We describe a protocol that enables quick and mild purification of corresponding Strep-tag II fusion protein...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.209

    authors: Schmidt TG,Skerra A

    更新日期:2007-01-01 00:00:00

  • Direct ester condensation catalyzed by bulky diarylammonium pentafluorobenzenesulfonates.

    abstract::A protocol for ester condensation between equimolar amounts of carboxylic acids and alcohols catalyzed by bulky diarylammonium pentafluorobenzenesulfonate is described. We also present procedures for the synthesis of N-(2,6-diisopropylphenyl)-N-mesitylammonium pentafluorobenzenesulfonate. The present ester condensatio...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.254

    authors: Sakakura A,Nakagawa S,Ishihara K

    更新日期:2007-01-01 00:00:00

  • Silver staining DNA in polyacrylamide gels.

    abstract::This protocol describes a simple silver staining method used to visualize DNA fragments and other organic molecules with unsurpassed detail following traditional polyacrylamide gel electrophoresis (PAGE). Sensitivity rivals radioisotopic methods and DNA in the picogram range can be reliably detected. The described pro...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2007.330

    authors: Bassam BJ,Gresshoff PM

    更新日期:2007-01-01 00:00:00

  • Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates.

    abstract::In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also as trabectedin or E-743) a...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.182

    authors: Ebada SS,Edrada RA,Lin W,Proksch P

    更新日期:2008-01-01 00:00:00

  • Ambient molecular imaging by desorption electrospray ionization mass spectrometry.

    abstract::Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or pre-processed samples under ambient conditions. Among other applications, DESI is used to identify and record spatial distributions of lipids and drug molecules in biological tissue sections. This technique does not require sam...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2008.11

    authors: Wiseman JM,Ifa DR,Venter A,Cooks RG

    更新日期:2008-01-01 00:00:00

  • Real-time single-molecule coimmunoprecipitation of weak protein-protein interactions.

    abstract::Coimmunoprecipitation (co-IP) analysis is a useful method for studying protein-protein interactions. It currently involves electrophoresis and western blotting, which are not optimized for detecting weak and transient interactions. In this protocol we describe an advanced version of co-IP analysis that uses real-time,...

    journal_title:Nature protocols

    pub_type: 杂志文章

    doi:10.1038/nprot.2013.116

    authors: Lee HW,Ryu JY,Yoo J,Choi B,Kim K,Yoon TY

    更新日期:2013-10-01 00:00:00