Spatial Transcriptomics Protocol v1

2021 ◽  
Author(s):  
Michael Eadon ◽  
Ricardo Melo Ferreira ◽  
Ying-Hua Cheng ◽  
Tarek Ashkar
Keyword(s):  
Cdna Synthesis

The tissue in OCT undergoes cryosectioning, affixment to the cDNA capture slide, H+E staining, 20x Keyence imaging, tissue permeabilization, RNA capture, and cDNA synthesis. Data is analyzed in Loupe browser and in R prior to uploading to the KPMP Data Lake.

scholarly journals Arginase 1 (Arg1) as an Up-Regulated Gene in COVID-19 Patients: A Promising Marker in COVID-19 Immunopathy

2021 ◽  
Vol 10 (5) ◽  
pp. 1051 ◽  
Author(s):  
Afshin Derakhshani ◽  
Nima Hemmat ◽  
Zahra Asadzadeh ◽  
Moslem Ghaseminia ◽  
Mahdi Abdoli Shadbad ◽  
...  
Keyword(s):  
Immune Responses ◽  
Whole Blood ◽  
Roc Analysis ◽  
Operating Characteristic ◽  
Rna Extraction ◽  
Diagnostic Value ◽  
Healthy Individuals ◽  
Cdna Synthesis ◽  
Arginase 1 ◽  
Global Pandemic

Background: The coronavirus disease 2019 (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic. It is well-established that SARS-CoV-2 infection can lead to dysregulated immune responses. Arginase-1 (Arg1), which has a pivotal role in immune cells, can be expressed in most of the myeloid cells, e.g., neutrophils and macrophages. Arg1 has been associated with the suppression of antiviral immune responses. Methods: Whole blood was taken from 21 COVID-19 patients and 21 healthy individuals, and after RNA extraction and complementary DNA (cDNA) synthesis, gene expression of Arg1 was measured by real-time PCR. Results: The qPCR results showed that the expression of Arg1 was significantly increased in COVID-19 patients compared to healthy individuals (p < 0.01). The relative expression analysis demonstrated there were approximately 2.3 times increased Arg1 expression in the whole blood of COVID-19 patients. Furthermore, the receiver operating characteristic (ROC) analysis showed a considerable diagnostic value for Arg1 expression in COVID-19 (p = 0.0002 and AUC = 0.8401). Conclusion: Arg1 might be a promising marker in the pathogenesis of the disease, and it could be a valuable diagnostic tool.

Efficient Second-Strand cDNA Synthesis Using T7 DNA Polymerase

1994 ◽  
Vol 13 (9) ◽  
pp. 977-985 ◽  
Author(s):  
MYRIAM BODESCOT ◽  
OLIVIER BRISON
Keyword(s):  
Dna Polymerase ◽  
Cdna Synthesis

The Mauriceville plasmid of Neurospora crassa: characterization of a novel reverse transcriptase that begins cDNA synthesis at the 3' end of template RNA

1992 ◽  
Vol 12 (11) ◽  
pp. 5131-5144
Author(s):  
H Wang ◽  
J C Kennell ◽  
M T Kuiper ◽  
J R Sabourin ◽  
R Saldanha ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Reverse Transcription ◽  
Full Length ◽  
Minus Strand ◽  
Ribonucleoprotein Particle ◽  
Cdna Synthesis ◽  
Reverse Transcriptases ◽  
In Vitro Transcripts

The Mauriceville and Varkud plasmids are retroid elements that propagate in the mitochondria of some Neurospora spp. strains. Previous studies of endogenous reactions in ribonucleoprotein particle preparations suggested that the plasmids use a novel mechanism of reverse transcription that involves synthesis of a full-length minus-strand DNA beginning at the 3' end of the plasmid transcript, which has a 3' tRNA-like structure (M. T. R. Kuiper and A. M. Lambowitz, Cell 55:693-704, 1988). In this study, we developed procedures for releasing the Mauriceville plasmid reverse transcriptase from mitochondrial ribonucleoprotein particles and partially purifying it by heparin-Sepharose chromatography. By using these soluble preparations, we show directly that the Mauriceville plasmid reverse transcriptase synthesizes full-length cDNA copies of in vitro transcripts beginning at the 3' end and has a preference for transcripts having the 3' tRNA-like structure. Further, unlike retroviral reverse transcriptases, the Mauriceville plasmid reverse transcriptase begins cDNA synthesis directly opposite the 3'-terminal nucleotide of the template RNA. The ability to initiate cDNA synthesis directly at the 3' end of template RNAs may also be relevant to the mechanisms of reverse transcription used by LINEs, group II introns, and other non-long terminal repeat retroid elements.

scholarly journals NPY and sbGnRH gene expression in juvenile and adult male Brazilian flounder Paralichthys orbignyanus

2011 ◽  
Vol 41 (11) ◽  
pp. 1927-1930 ◽  
Author(s):  
Vinicius Farias Campos ◽  
Tiago Veiras Collares ◽  
Fabiana Kömmling Seixas ◽  
João Carlos Deschamps ◽  
Luis Fernando Fernandes Marins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Extraction ◽  
Sea Bream ◽  
Mrna Levels ◽  
Adult Males ◽  
Adult Fish ◽  
Cdna Synthesis ◽  
Hypothalamic Regulation ◽  
Measure Gene Expression ◽  
Paralichthys Orbignyanus

The objective of this study was to evaluate neuropeptide Y (NPY) and sea bream gonadotropin-release hormone (sbGnRH) gene expression in juvenile and adult males of Brazilian flounder. Hypothalamuses from fish were sampled for total RNA extraction. After cDNA synthesis, real-time PCR was used to measure gene expression. NPY showed approximately 2-fold increases in their mRNA levels while sbGnRH showed 3-fold increases in adult fish. These results suggest that these peptides could be involved on hypothalamic regulation of Brazilian flounder sexual maturation.

scholarly journals A Carboxy-Terminally Truncated Human CPSF6 Lacking Residues Encoded by Exon 6 Inhibits HIV-1 cDNA Synthesis and Promotes Capsid Disassembly

2013 ◽  
Vol 87 (13) ◽  
pp. 7726-7736 ◽  
Author(s):  
T. Hori ◽  
H. Takeuchi ◽  
H. Saito ◽  
R. Sakuma ◽  
Y. Inagaki ◽  
...  
Keyword(s):  
Cdna Synthesis ◽  
Hiv 1 ◽  
Capsid Disassembly

scholarly journals Aptamer-dependent full-length cDNA synthesis by overlap extension PCR

BioTechniques ◽  
2004 ◽  
Vol 37 (1) ◽  
pp. 124-129 ◽  
Author(s):  
Yasumasa Mitani ◽  
Takayuki Nakayama ◽  
Matthias Harbers ◽  
Yoshihide Hayashizaki
Keyword(s):  
Full Length ◽  
Cdna Synthesis ◽  
Full Length Cdna ◽  
Overlap Extension Pcr ◽  
Overlap Extension

Evaluation of miR-222 Expression in HBV Infected Patients in Comparison with HDV and HBV Co-infected Patients

2021 ◽  
Author(s):  
Zahra Sokhanvar ◽  
Ameneh Elikaei ◽  
Zohreh Sharifi
Keyword(s):  
Gene Expression ◽  
Liver Disease ◽  
Quantitative Pcr ◽  
Internal Control ◽  
Liver Diseases ◽  
Cdna Synthesis ◽  
Severe Liver ◽  
Serum Samples ◽  
Complementary Dna ◽  
Expression Of Genes

Background: Liver disease is more severe in HDV+HBV co-infected patients than HBV infected patients which seems to be related to differences in the expression of genes and other factors such as MicroRNAs (miRNAs). The aim of this study was to investigate miR-222 expression in HBV infected patients in comparison with HDV+HBV co-infected patients. Methods: First, total RNA was extracted from the serum samples and then, complementary DNA (cDNA) was produced using cDNA synthesis kit. Finally, miR-222 gene expression was measured using U6 as the internal control by quantitative PCR (qPCR). Results: The level of miR-222 expression in HDV+HBV co-infected samples was significantly up regulated. The fold change of the miR-222 expression between two groups was 3.3 (95% CI; 0.011- 17.63) with p<0.001. Conclusion: The expression of miR-222 was higher in HBV+HDV co-infected patients than HBV infected patients. Further studies should be conducted to confirm whether miR-222 can be a biomarker for prognosis of severe liver diseases.

Sign in / Sign up

Export Citation Format

Share Document