FLASH-seq Low-Amplification protocol (V1) v1

2021 ◽  
Author(s):  
Simone Picelli ◽  
Vincent Hahaut
Keyword(s):  
Full Length ◽  
Amplification Protocol ◽  
Hands On ◽  
Number Of Genes

Building upon the existing Smart-seq2/3 workflows, we developed FLASH-seq (FS), a new full-length scRNA-seq method capable of detecting a significantly higher number of genes than both previous versions, requiring limited hands-on time and with a great potential for customization. FLASH-seq Low-Amplification (FS-LA), represents FS quickest iteration, generating sequencing-ready libraries in 4.5 hours by removing intermediate cleanups and QC steps and without sacrificing performance. FS-LA is the best choice when a large number of plates need to be processed in parallel.

FLASH-seq protocol (V1) v1

2021 ◽  
Author(s):  
Simone Picelli ◽  
Vincent Hahaut
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Full Length ◽  
Terminal Portion ◽  
Emulsion Droplets ◽  
Hands On ◽  
Single Cell Rna Sequencing ◽  
Number Of Genes ◽  
Reproducible Analysis ◽  
And Performance

The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased over a very short timespan. However, it was not until the introduction of emulsion droplets methods, that the robust and reproducible analysis of thousands of cells became feasible. Despite generating data at a speed and a cost per cell that remains unmatched by full-length protocols like Smart-seq, scRNA-seq in droplets still comes with the drawback of addressing only the terminal portion of the transcripts, thus lacking the required sensitivity for comprehensively analyzing the transcriptome of individual cells. Building upon the existing Smart-seq2/3 workflows, we developed FLASH-seq (FS), a new full-length scRNA-seq method capable of detecting a significantly higher number of genes than both previous versions, requiring limited hands-on time and with a great potential for customization.

scholarly journals Allosteric alterations in the androgen receptor and activity in prostate cancer

2017 ◽  
Vol 24 (9) ◽  
pp. R335-R348 ◽  
Author(s):  
Takuma Uo ◽  
Stephen R Plymate ◽  
Cynthia C Sprenger
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Full Length ◽  
Constitutive Activity ◽  
The Novel ◽  
Functional Interaction ◽  
Successful Development ◽  
Novel Variants ◽  
Number Of Genes ◽  
Androgen Receptor Variants

Organisms have evolved to generate biological complexity in their proteome and transcriptome from a limited number of genes. This concept holds true for the androgen receptor, which displays a diversity of inclusion/exclusion events in its structural motifs as a mechanism of resistance to the most forefront anti-androgen therapies. More than 20 androgen receptor variants that lack various portions of ligand-binding domain have been identified in human prostate cancer (PCa) samples. Most of the variants are inactive on their own, with a few exceptions displaying constitutive activity. The full-length receptor and one or more variants can be co-expressed in the same cell under many circumstances, which raises the question of how these variants physically and functionally interact with the full-length receptor or one another in the course of PCa progression. To address this issue, in this review, we will characterize and discuss androgen receptor variants, including the novel variants discovered in the last couple of years (i) individually, (ii) with respect to their physical and functional interaction with one another and (iii) in clinical relevance. Here, we also introduce the very recent understanding of AR-Vs obtained through successful development of some AR-V-specific antibodies as well as identification of novel AR-Vs by data mining approaches.

In Situ Localization of PPAR Gamma and Uncoupling Protein in Mouse Embryo Sections Using Digoxigenin-Labeled Riboprobes

1996 ◽  
Vol 54 ◽  
pp. 32-33
Author(s):  
C. Jennermann ◽  
S. A. Kliewer ◽  
D. C. Morris
Keyword(s):  
Alkaline Phosphatase ◽  
Room Temperature ◽  
Uncoupling Protein ◽  
Ppar Gamma ◽  
Nuclear Hormone Receptor ◽  
Full Length ◽  
Northern Analysis ◽  
Peroxisome Proliferator

Peroxisome proliferator-activated receptor gamma (PPARg) is a member of the nuclear hormone receptor superfamily and has been shown in vitro to regulate genes involved in lipid metabolism and adipocyte differentiation. By Northern analysis, we and other researchers have shown that expression of this receptor predominates in adipose tissue in adult mice, and appears first in whole-embryo mRNA at 13.5 days postconception. In situ hybridization was used to find out in which developing tissues PPARg is specifically expressed.Digoxigenin-labeled riboprobes were generated using the Genius™ 4 RNA Labeling Kit from Boehringer Mannheim. Full length PPAR gamma, obtained by PCR from mouse liver cDNA, was inserted into pBluescript SK and used as template for the transcription reaction. Probes of average size 200 base pairs were made by partial alkaline hydrolysis of the full length transcripts. The in situ hybridization assays were performed as described previously with some modifications. Frozen sections (10 μm thick) of day 18 mouse embryos were cut, fixed with 4% paraformaldehyde and acetylated with 0.25% acetic anhydride in 1.0M triethanolamine buffer. The sections were incubated for 2 hours at room temperature in pre-hybridization buffer, and were then hybridized with a probe concentration of 200μg per ml at 70° C, overnight in a humidified chamber. Following stringent washes in SSC buffers, the immunological detection steps were performed at room temperature. The alkaline phosphatase labeled, anti-digoxigenin antibody and detection buffers were purchased from Boehringer Mannheim. The sections were treated with a blocking buffer for one hour and incubated with antibody solution at a 1:5000 dilution for 2 hours, both at room temperature. Colored precipitate was formed by exposure to the alkaline phosphatase substrate nitrobluetetrazoliumchloride/ bromo-chloroindlylphosphate.

The Instructional SEM Laboratory at Iowa State University

1996 ◽  
Vol 54 ◽  
pp. 396-397
Author(s):  
L. S. Chumbley ◽  
M. Meyer ◽  
K. Fredrickson ◽  
F.C. Laabs
Keyword(s):  
Materials Science ◽  
Computer Network ◽  
Energy Dispersive Spectrometer ◽  
Computer Control ◽  
State University ◽  
Iowa State University ◽  
Internet Server ◽  
Schematic Layout ◽  
Hands On ◽  
Improve Instruction

The Materials Science Department at Iowa State University has developed a laboratory designed to improve instruction in the use of the scanning electron microscope (SEM). The laboratory makes use of a computer network and a series of remote workstations in a classroom setting to provide students with increased hands-on access to the SEM. The laboratory has also been equipped such that distance learning via the internet can be achieved.A view of the laboratory is shown in Figure 1. The laboratory consists of a JEOL 6100 SEM, a Macintosh Quadra computer that acts as a server for the network and controls the energy dispersive spectrometer (EDS), four Macintosh computers that act as remote workstations, and a fifth Macintosh that acts as an internet server. A schematic layout of the classroom is shown in Figure 2. The workstations are connected directly to the SEM to allow joystick and computer control of the microscope. An ethernet connection between the Quadra and the workstations allows students seated there to operate the EDS. Control of the microscope and joystick is passed between the workstations by a switch-box assembly that resides at the microscope console. When the switch-box assembly is activated a direct serial line is established between the specified workstation and the microscope via the SEM’s RS-232.

Students Involvement in Multilingual and Multicultural Community Services

2015 ◽  
Vol 22 (2) ◽  
pp. 77-89 ◽  
Author(s):  
Ying-Chiao Tsao
Keyword(s):  
Service Learning ◽  
Cultural Competence ◽  
Linguistically Diverse ◽  
Community Services ◽  
Cultural Humility ◽  
Self Assessment ◽  
Multicultural Community ◽  
Raising Awareness ◽  
Hands On ◽  
Teaching Learning

Promoting cultural competence in serving diverse clients has become critically important across disciplines. Yet, progress has been limited in raising awareness and sensitivity. Tervalon and Murray-Garcia (1998) believed that cultural competence can only be truly achieved through critical self-assessment, recognition of limits, and ongoing acquisition of knowledge (known as “cultural humility”). Teaching cultural humility, and the value associated with it remains a challenging task for many educators. Challenges inherent in such instruction stem from lack of resources/known strategies as well as learner and instructor readiness. Kirk (2007) further indicates that providing feedback on one's integrity could be threatening. In current study, both traditional classroom-based teaching pedagogy and hands-on community engagement were reviewed. To bridge a gap between academic teaching/learning and real world situations, the author proposed service learning as a means to teach cultural humility and empower students with confidence in serving clients from culturally/linguistically diverse backgrounds. To provide a class of 51 students with multicultural and multilingual community service experience, the author partnered with the Tzu-Chi Foundation (an international nonprofit organization). In this article, the results, strengths, and limitations of this service learning project are discussed.

A ’Hands-On’ Approach

ASHA Leader ◽  
2012 ◽  
Vol 17 (9) ◽  
pp. 55-55
Author(s):  
Kimberly Abts
Keyword(s):  
Hands On

Telepractice: A Survey of AuD Students Pre- and Post-Telepractice

2017 ◽  
Vol 2 (18) ◽  
pp. 28-41
Author(s):  
Kelli M. Watts ◽  
Laura B. Willis
Keyword(s):  
Doctoral Students ◽  
Graduate School ◽  
Professional Services ◽  
Hands On ◽  
Before And After ◽  
Lack Of Knowledge

Telepractice, defined by the American Speech-Language-Hearing Association (ASHA, n.d.) as “the application of telecommunications technology to the delivery of professional services at a distance by linking clinician to client, or clinician to clinician, for assessment, intervention, and/or consultation,” is a quickly growing aspect of practicing audiology. However, only 12% of audiologists are involved in providing services via telepractice (REDA International, Inc., 2002). Lack of knowledge regarding telepractice has been cited as one of the reasons many audiologists do not use telepractice to provide audiology services. This study surveyed audiology doctoral students regarding their opinions about the use of telepractice both before and after their opportunity to provide services via telepractice sessions. The authors expected that by providing students the opportunity to have hands-on training in telepractice with supervision, they would be more open to using telepractice after becoming licensed audiologists. Overall, the data indicates benefits of exposing students to telepractice while they are in graduate school.

University Dropout

2008 ◽  
Vol 29 (3) ◽  
pp. 134-147 ◽  
Author(s):  
Manuel C. Voelkle ◽  
Nicolas Sander
Keyword(s):  
Grade Point Average ◽  
Structural Equation ◽  
Unobserved Heterogeneity ◽  
School Grade ◽  
Grade Point ◽  
High School Grade ◽  
Hands On ◽  
University Dropout ◽  
The Individual ◽  
A Prospective Study

University dropout is a politically and economically important factor. While a number of studies address this issue cross-sectionally by analyzing different cohorts, or retrospectively via questionnaires, few of them are truly longitudinal and focus on the individual as the unit of interest. In contrast to these studies, an individual differences perspective is adopted in the present paper. For this purpose, a hands-on introduction to a recently proposed structural equation (SEM) approach to discrete-time survival analysis is provided ( Muthén & Masyn, 2005 ). In a next step, a prospective study with N = 1096 students, observed across four semesters, is introduced. As expected, average university grade proved to be an important predictor of future dropout, while high-school grade-point average (GPA) yielded no incremental predictive validity but was completely mediated by university grade. Accounting for unobserved heterogeneity, three latent classes could be identified with differential predictor-criterion relations, suggesting the need to pay closer attention to the composition of the student population.

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