Skip to main content
Addgene

Enter a sequence to perform a BLAST-based search of Addgene plasmid sequence databases.

In Category

We narrowed to 271 results for: atic

Showing: 1 - 20 of 271 results

  1. Bioinformatics at Addgene

    Type
    Blog Post
    Published
    July 14, 2022, 1:15 p.m.
    ... series, we will describe the importance of bioinformatics at Addgene and how our search for solutions...Labs.              DNA sequencing drives our bioinformatics needs       Fig. 1: QC'ing data at Addgene...presented with a new challenge: automating the bioinformatics steps needed to transform the raw sequencing... for our QC team to analyze. Criteria for a bioinformatics workflow management system As novices to creating...entire ecosystem Proven performance with other bioinformatics purposes  Integrated user interface, so our... entire pipeline. Benefits of Nextflow for bioinformatics pipelining In many use-cases, including ours... system for scientific pipelines, including bioinformatics. We loved the parallels between Seqera’s mission...

  2. A Case Study of Addgene Bioinformatics

    Type
    Blog Post
    Published
    May 25, 2023, 1:15 p.m.
    ...Last summer, we posted about our bioinformatics quest, which led us to Seqera Labs, a company that provides...

  3. How to Keep a Lab Notebook for Bioinformatic Analyses

    Type
    Blog Post
    Published
    June 2, 2016, 2:30 p.m.
    ...Traditional lab notebooks just won't cut it for bioinformatics. All kinds of biologists are finding themselves...prevent you from getting lost in the wide word of informatics. I am a molecular biologist who began coding ... one way to keep a virtual lab notebook for bioinformatics. In fact, there are endless ways and everyone... bioinformatic... bioinformatic analyses...

  4. Starter Guide to induced Pluripotent Stem Cells (iPSCs) Part 2:  Reprogramming and Transdifferentiation

    Type
    Blog Post
    Published
    Nov. 6, 2018, 1:12 p.m.
    ...transdifferentiated in vivo to pancreatic β-like-cells with the expression of pancreatic and duodenal homoeobox...discuss the two major processes by which an adult somatic cell is converted to a different cell type for ...conversion happens via: ReprogrammingA differentiated somatic cell reverts back to a pluripotent state, which...Transdifferentiation In this process, differentiated adult somatic cells are converted to cells of a different lineage...stages: Dedifferentiation - Conversion of adult somatic cells into the pluripotent state. Redifferentiation...KLF4, and C-MYC - that induce a differentiated somatic cell to revert back to a pluripotent stage (iPSC...factors can be delivered and expressed in multiple somatic cells via various methods. Some of the more common...

  5. Antibodies 101: ChIP

    Type
    Blog Post
    Published
    March 10, 2022, 3:25 p.m.
    ...high-frequency sound waves to break up the DNA, or enzymatic digestion. Sonication provides a truly random ...but is harsher and requires more optimization. Enzymatic digestion, while gentler on the sample, introduces...While sonication is usually the preferred method, enzymatic digestion can be appropriate when your protein...factor or cofactor. In such cases, the gentler enzymatic digestion can preserve more of the protein:DNA... Capture After crosslinking and sonication or enzymatic digestion, you’re ready to incubate the sample...phenol-chloroform extraction.    Fig. 1: Schematic overview of ChIP. Image courtesy of Shengliu via...could affect antibody selection. Sonication (or enzymatic digest) will also have to be optimized for both...

  6. Simple CRISPR-based Epigenetic Editing: dCas9-directed DNA Demethylation

    Type
    Blog Post
    Published
    Dec. 14, 2021, 2:15 p.m.
    ... of Dr. Moshe Szyf at McGill University. Some enzymatic fusions are godsends. Tethering dCas9 to the histone...which where they were absent before. But other enzymatic fusions, such as dCas9-TET, can, like the iron...tool of choice in the field: dCas9 fused to the enzymatic domain of TET1 or TET2 (Morita et al. 2016, Xu... transcriptional consequences (Sprujit 2013). Enzymatic domains tethered to dCas9 often interact with ...proteins affect transcription independent of their enzymatic activity. They interact with transcriptional machinery...counterintuitive: how can a DNA-binding protein with no enzymatic activity cause demethylation?  Dividing cells ...in pluripotent cells at thousands of methylated somatic enhancers. Nat Genet 52, 819–827. https://doi.org...

  7. QC Sequencing Technologies at Addgene

    Type
    Blog Post
    Published
    July 15, 2025, 1:15 p.m.
    ...-to-sequence plasmids, other sequencing and bioinformatic technologies are used.  Improvements to sequencing...sequencing technologies and bioinformatic analysis are occurring every year. At Addgene, we want to maintain...cassettes of the same gene multiple times.  Bioinformatics at Addgene After a run on our Illumina MiSeq...sequences submitted by depositors. A sample will automatically pass through our QC process if there is a 100%... of emerging technologies in sequencing and bioinformatic analysis. At Addgene, we use a mix-and-match... F. (2021). Nanopore sequencing technology, bioinformatics and applications. Nature Biotechnology, 39(...Addgene Blog A Look at Addgene’s QC Process Bioinformatics at Addgene The Power Behind NGS Plasmid Validation...

  8. pCXLE toolkit: Efficient episomal plasmid-based method to reprogram peripheral blood cells to iPSCs

    Type
    Blog Post
    Published
    Dec. 14, 2017, 2:08 p.m.
    ...opportunity to develop and use patient-specific somatic cells that are otherwise difficult to obtain. These...cell plasmids at Addgene Many sources of adult somatic cells have been probed for their suitability in...These advantages make PBMCs the ideal source of somatic cells for reprogramming purposes. In this post,...reprogramming often depends on the source of the somatic cells, the common goal of all reprogramming methods... only 0.001% when using PBMCs as the source of somatic cells. This translates to only about 16 hiPSC colonies... major hindrance in using PBMCs as a source of somatic cells for reprogramming. Enhancing PBMC reprogramming...

  9. Plasmids 101: Antibiotic Resistance Genes

    Type
    Blog Post
    Published
    Jan. 30, 2014, 3:29 p.m.
    ...bactericidal) or slow growth/prevent cell division (bacteriostatic); however, the distinction between the two ...categories may be a bit of a gray area as some bacteriostatic reagents can kill bacteria when used at high...subunit; inhibits aminoacyl translocation Bacteriostatic 50-100 ug/mL in EtOH Polymyxin B polypeptide...inhibits protein synthesis (elongation step) Bacteriostatic 10 ug/mL Chloramphenicol   Binds 50S ribosomal...ribosomal subunit; inhibits peptidyl translocation Bacteriostatic 5-25 ug/mL in EtOH *In prokaryotes.     ...

  10. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

    Type
    Blog Post
    Published
    May 11, 2017, 2:30 p.m.
    ... variants across a large number of genes as systematically as possible. In developing these assays, we...to demonstrate how gene expression profiling, systematic tumorigenesis assays, drug epistasis assays, ...genes: High-throughput Phenotyping of Lung Cancer Somatic Mutations. Berger AH, Brooks AN, Wu X, et al. Cancer...mutant collection is described in this paper. Systematic Functional Interrogation of Rare Cancer Variants...reference collections are described in this paper Systematic morphological profiling of human gene and allele...

  11. Plasmids 101: Biotinylation

    Type
    Blog Post
    Published
    Nov. 15, 2018, 1:50 p.m.
    ...macromolecule. Biotin can be added enzymatically or chemically. Enzymatic biotinylation occurs naturally ...using a biotinylated primer. Biotin can also be enzymatically incorporated during PCR using a biotin labelled...sometimes easier and less expensive than other enzymatic methods. Scientists have commonly used this method...10064313. 2. Chapman-Smith, A., & Cronan, J. E. “The enzymatic biotinylation of proteins: A post-translational...

  12. A new platform for fast functional characterization of potentially cancerous mutations

    Type
    Blog Post
    Published
    May 7, 2019, 12:39 p.m.
    ... Patrick Kwok-Shing, et al. "Systematic functional annotation of somatic mutations in cancer." Cancer ...Plasmid Collection for “Functional Annotation of Somatic Mutations in Cancer.” Of all the mutations and ...annotation of rare gene aberration drivers of pancreatic cancer." Nature communications 7 (2016): 10500...

  13. Deep Dive: qPCR

    Type
    Blog Post
    Published
    Sept. 29, 2022, 1:15 p.m.
    ...sets and most machines have a protocol that automatically performs the normalization step.  Machines Most...and sets.   🔥Hot Tip🔥 The ABI machines automatically record fluorescent data on all channels - helpful... of PCR products in a rich web application, Bioinformatics, Volume 27, Issue 7, 1 April 2011, Pages 1019...1019–1020, https://doi.org/10.1093/bioinformatics/btr065Freeman WM; Walker SJ; Vrana KE. 1999. Quantitative...Statistical analysis of real-time PCR data. BMC Bioinformatics 7, 85 (2006). https://doi.org/10.1186/1471-...

  14. Starter guide to induced pluripotent stem cells (iPSCs) part 1:  A renaissance in regenerative medicine

    Type
    Blog Post
    Published
    Oct. 30, 2018, 1:04 p.m.
    ...donor [7]. Adult stem cells (ASCs) Also known as somatic stem cells, these multipotent stem cells are located...we’ll discuss the two widely used approaches of somatic cell conversion: conversion via iPSC formation,... reprogramming and, direct conversion from one somatic cell type to another, also known as transdifferentiation...pluripotent stem cell lines derived from human somatic cells. Science, 2007. 318(5858): p. 1917-20. PubMed...

  15. MXS Chaining

    Type
    Blog Post
    Published
    Feb. 7, 2017, 3:30 p.m.
    ...High-throughput cloning, in a nutshell, is the systematic combination of different genetic sequences into...L, Chuang RY, Venter JC, Hutchison CA, Smith HO.Enzymatic assembly of DNA molecules up to several hundred... 19363495. 4. Josse J, Kaiser AD, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies...PMC4409215. 7. Swartz MN, Trautner TA, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. XI. Further...

  16. Antibodies 101: Multiplex Immunofluorescence

    Type
    Blog Post
    Published
    May 23, 2023, 1:15 p.m.
    ...conjugate with an enzymatic label such as horseradish peroxidase (HRP). Experiments using enzymatic labeling can...2019; McLaughlin, 2019).    Figure 1: Schematic of multiplex immunofluorescence approaches. A)...yourself stuck with red-green images generated automatically from the microscope software, you can always...

  17. Which Fluorescence Microscopy Technique is Best for Me?

    Type
    Blog Post
    Published
    Oct. 10, 2017, 1:57 p.m.
    ...asking two questions: 1) Is the sample dynamic or static? 2) Is the sample thin (< 15 μm) or thick? These... effects of high light doses to the cells. Thin static samples Ex: Fixed monolayers of cells or thin (...microscopy can be combined with deconvolution, a mathematical software post-processing step that reassigns...in light penetration mentioned above (5). Thick static samples Ex: Fixed tissue sections (> 15 um), 3D...

  18. Who Gives a Tweet? 9 Facts About Scientists on Twitter

    Type
    Blog Post
    Published
    June 26, 2017, 1:31 p.m.
    ... FOMO  but mostly because of this article: “A systematic identification and analysis of scientists on ...computer scientists are overrepresented on Twitter Mathematical, life, and physical scientists are underrepresented... Ke, Q., Ahn, Y., & Sugimoto, C. R. (2017). A systematic identification and analysis of scientists on ...

  19. Hot Plasmids and Viral Preps - July 2021

    Type
    Blog Post
    Published
    July 27, 2021, 1:15 p.m.
    ...Sun, et al. 2021).  Figure 1: Example schematic from the Organoid EasyTag system, showing the ...fluorescent protein or cpGFP) to the petunia SL enzymatic receptor DAD2. SLs induce a conformational change... that when tested in tobacco protoplasts, the enzymatic biosensor retains its catalytic activity.  As ...

  20. Cellosaurus: A Cell Line Information Database

    Type
    Blog Post
    Published
    Feb. 21, 2023, 2:15 p.m.
    ...when Amos Bairoch from the Swiss Institute of Bioinformatics reached out to us to tell us about a resource...collections. Importantly, Cellosaurus also identifies problematic cell lines: ones either suspected to be contaminate....  For those wanting to access Cellosaurus programatically, their API allows fine grained query and retrieval...
Showing: 1 - 20 of 271 results