Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 1. Addgene CRISPR distribution and deposits. (A) Cumulative CRISPR plasmids shipped by year (top) and CRISPR plasmids shipped each year from 2012 to 2022 (bottom). (B) Cumulative CRISPR plasmids deposited with Addgene by year (top) and CRISPR plasmids deposited each year from 2012 to 2022 (bottom). (C) Cumulative number of laboratories that have deposited CRISPR plasmids by year (top) and new depositing CRISPR laboratories each year from 2012 to 2022 (bottom). (D) Cumulative CRISPR pooled libraries shipped by year (top) and number of CRISPR libraries shipped each year from 2014 to 2022 (bottom).

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: CRISPR

Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 3. Percentage of requests per year for CRISPR plasmids categorized by year of deposit. Outlines show a representative proportion of CRISPR plasmids requested, categorized by year of deposit, for each year from 2012 to 2022.

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: CRISPR

Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 2. Addgene CRISPR deposit and distribution by function and expression type. (A) Cumulative number of deposited CRISPR items, categorized by CRISPR function, by year. (B) Number of requests per month for each CRISPR function from 2012 to 2022; data are smoothed using locally estimated scatterplot smoothing. (C) Number of requests per year for pooled libraries, categorized by function, from 2014 to 2022.

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: CRISPR, Expressing

Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 4. Addgene deposits and distribution by country. (A) Total CRISPR plasmids deposited by country; square size is proportional to number of plasmids deposited by each country. Countries shown are top 10 depositing countries. (B) Total CRISPR plasmids requested by country; square size is proportional to the number of plasmids requested by each country. Countries shown are the top 10 requesting countries. (C) Percentage of orders by country each year that include CRISPR materials.

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: CRISPR

Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 5. Addgene distribution and deposits by country and expression type. (A) Percentage of mammalian, bacterial, plant, and other (yeast, insect, worm) CRISPR items requested by year for each UN geographical region, from 2012 to 2022. Percentages are presented in decreasing value for each given year. (B) Percentage of mammalian, bacterial, plant, and other (yeast, insect, worm) CRISPR materials deposited by year for each UN geographical region from 2012 to 2022. Percentages are presented in decreasing value for each given year. UN, United Nations.

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: Expressing, CRISPR

Journal: The CRISPR journal

Article Title: The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene.

doi: 10.1089/crispr.2023.0059

Figure Lengend Snippet: FIG. 6. Change in Addgene deposits post-COVID-19. Percentage change in CRISPR plasmids deposited during 2020–2022 compared with that during 2017–2019 by country. The color intensity is proportional to number of CRISPR items deposited by the indicated country. Countries with >200% increase in number of CRISPR deposits are not shown.

Article Snippet: CRISPR-Cas effectors have revolutionized and democratized genome editing since its utility as a molecular tool was first realized in 2012.1 Plasmids encoding CRISPR components were quickly deposited at Addgene, a nonprofit repository whose mission is to accelerate research and discovery by providing access to useful research materials and information.2 Unlike zinc-finger nucleases and transcription activator-like effector nucleases that required new protein sequences for each target, CRISPR-Cas systems required cloning oligos for the guide RNA (gRNA) into the nuclease expression plasmids.

Techniques: CRISPR

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: Map of LV DNA in the LV shuttle plasmids. pLV.Tbx20 ( a ), pLV.Ctrl ( b ). 5′ LTR chimeric 5′ long terminal repeat including the Rous sarcoma virus U3 region as well as the HIV1 R and U5 regions. Ψ HIV1 packaging signal, RRE HIV1 Rev-responsive element, cPPT HIV1 central polypurine tract and termination site, hCMV-IE human cytomegalovirus immediate early gene promoter, Tbx20 coding sequence of desired gene, EMCV IRES encephalomyocarditis virus internal ribosomal entry site, EGFP enhanced green fluorescent coding sequence, hHBVPRE human hepatitis B virus posttranscriptional regulatory element, 3′ LTR 3′ HIV1 long terminal repeat involving a deletion in the U3 region to render the LV self-inactivating

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques: Virus, Sequencing

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: RT-qPCR primers

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques:

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: Fluoromicrographs ( a1 , a2 ) and brightfield images ( b1 , b2 ) of LV-Ctrl ( a1 , b1 )- or LV- Tbx20 ( a2 , b2 )-transduced Ad-MSCs that were maintained in osteogenic differentiation medium for 21 days. c Expression of Tbx20 (murine) in transduced cells, 14 days after transduction. RT-qPCR demonstrated that the Tbx20 expression in LV- Tbx20 transduced cells was around 20 times higher than its expression in LV-Ctrl transduced cells.***Indicates significant differences ( p < 0.001) between LV-Ctrl and LV- Tbx20

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques: Expressing, Transduction, Quantitative RT-PCR

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: Enhanced expression of Tbx20 in Ad-MSCs reduced osteogenesis. Cells were infected with control viral vector (LV-Ctrl) or LV- Tbx20 and allowed to differentiate in osteogenic medium. a After 21 days, mineral nodules deposition was stained with Alizarin Red S (ARS). b The stained cells were extracted using 10% acetic acid and its absorbance was read at 405 nm to quantify the mineralization level. c After 21 days, induced cells were stained with BCIP/NBT to detect secreted alkaline phosphatase. d After 7 and 14 days ALP activity was conducted using pNPP liquid substrate system. All data are presented as mean ± SD. ****Shows significant differences ( p < 0.0001) between negative control (cells grown in normal medium) and infected groups; ***Indicates significant differences ( p < 0.001) between LV-Ctrl and LV- Tbx20 . Experiments were performed in triplicate and repeated three times

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques: Expressing, Infection, Control, Plasmid Preparation, Staining, Activity Assay, Negative Control

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: Increased expression of Tbx20 decreased ALP and ColI expression. Representative micrograph of 14 days incubation of Ad-MSCs exposed to LV-Ctrl or LV- Tbx20 with EGFP-positive, ALP and ColI expressions ( a – d ). Ad-MSCs overexpressed Tbx20 demonstrated two- and threefolds reduction in ALP and ColI expression respectively compared to LV-Ctrl ( e , f ). ****Shows significant differences ( p < 0.0001) between LV-Ctrl and LV- Tbx20 . Experiments were performed in triplicate and repeated three times

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques: Expressing, Incubation

Journal: Journal of Biological Research

Article Title: T - Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T - Box20 on osteogenesis

doi: 10.1186/s40709-019-0099-5

Figure Lengend Snippet: Analysis, by RT-qPCR, of the expression of the osteoblast marker genes ALPL ( a ), COL1A1 ( b ), RUNX2 ( c ), OPN ( d ), and human Tbx20 ( e ) in LV-Ctrl- and LV-Tbx20-transduced Ad-MSCs that were maintained in osteogenic differentiation medium for 7 or 14 days. Expression levels were normalized to those in untreated cells (i.e. cells cultured in normal growth medium) as mean ± SD. The GAPDH gene served as internal control. **** p < 0.0001. *** p < 0.001. ** p < 0.01. ns not significant. Experiments were performed in triplicate and repeated three times

Article Snippet: The murine Tbx20 -coding sequence was excised from plasmid pCRII Topo- Tbx20 (Addgene, Cambridge, MA; plasmid number: 24715) with Eco RV and Spe I and inserted into the polylinker of the lentiviral vector shuttle construct pLV.hCMV-IE.IRES.EGFP.hHBVPRE that was previously known as pLV-CMV-IRES-EGFP [ ] digested with the same enzymes.

Techniques: Quantitative RT-PCR, Expressing, Marker, Cell Culture, Control