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anti claudin 1  (Thermo Fisher)


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    Thermo Fisher anti claudin 1
    Anti Claudin 1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/Racks+for+Matrix+2D+Barcoded+Storage+Tubes/pm41902480-263-15-16
    Average 95 stars, based on 1 article reviews
    anti claudin 1 - by Bioz Stars, 2026-11
    95/100 stars

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    Related Articles

    Staining:

    Article Title: Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells.
    Article Snippet: Non-specific antibody binding was blocked for 30 min by incubation with 5% normal goat serum in PBS (Invitrogen, Cat No. 50062Z). .. Tissue was stained using the following primary antibodies; anti-ZO-1 (Invitrogen, Cat No. 33–9100, 1:250 dilution), anti-Claudin-1 (Invitrogen, Cat No. 37–4900, 1:250 dilution), anti-Muc-2 (Santacruz, Cat No. sc-15334, 1:200 dilution), anti-Total OXPHOS (Abcam, Cat No. ab317270, 1:500 dilution) which targets key five complexes of the electron transport chain often known as complexes I –V involved in oxidative phosphorylation (OXPHOS), anti-Olfm4 (Cell Signaling, Cat No. 39141, 1:250 dilution), diluted in 1% of blocking buffer and incubated overnight at 4◦C in a dark humidified chamber. .. Sections were washed with 0.1% TBST and incubated with secondary antibody, such as donkey anti-Rabbit IgG conjugated with Alexa Fluor 647 (Invitrogen, Cat. No. A32795), Goat anti-rabbit IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. R37117), Goat anti-Mouse IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. A-11005), 1:1000 diluted in 1% of blocking buffer and incubated in dark humidified chamber for 1 h. After being washed with 0.1% TBST, the sections were mounted in Vectashield Dapi-containing mounting medium (Vector Labs., Cat. No. H1200) and Fluorescence images were acquired using a confocal microscope (Nikon A1RMP).

    Article Title: Altered distribution of tissue galectins correlates with mucosal dysregulation in SIV infection
    Article Snippet: .. Fc receptors were blocked with Human TruStain FcX blocking antibody (Biolegend, San Diego, California, USA) diluted in blocking buffer (1xPBS, 2% donkey or goat serum, 2% fetal bovine serum) for 1 h. Slides were stained with primary antibodies diluted in blocking buffer (1:300) for 1 h. Primary antibodies include those targeting human galectin-9 (Cat. AF2045; R&D Systems) and galectin-3 (Cat. AF1197; R&D Systems), galectin-1 (Cat. Ab108389 ; Abcam), and ZO-1 (Cat. 61-7300; ThermoFisher), Occludin (Cat. 33-1500; ThermoFisher), Claudin-1 (Cat. 37-4900; ThermoFisher), and Claudin-5 (Cat. PA5-99415; ThermoFisher). .. Slides were washed and then stained with Donkey anti-Goat 488 (Cat. A-11055; ThermoFisher), Donkey anti-Rabbit 555 (Cat. A-31572; ThermoFisher), and Donkey anti-Mouse 647 (Cat. A-31571; ThermoFisher) secondary antibodies (1:400) in blocking buffer for 1 h. Slides were washed and stained with nuclear marker Hoechst 33342 (ThermoFisher) for 10 min.

    Article Title: Transplantation of hPSC‐Derived Pericyte‐Enriched Vascular Assemblies Restores Cerebral Perfusion in the Context of Permanent Brain Ischemia
    Article Snippet: Despite advancements in vascular reconstruction techniques, insufficient distal perfusion following ischemic stroke continues to cause irreversible neurological damage, and effective strategies for reconstructing functional microvascular networks remain inadequate.. While vascular organoids have shown potential, their clinical translation is limited by the need for invasive surgical resection to accommodate large 3D grafts.. This study improves the vascular organoid technology pipeline by developing hPSCderived Pericyte-Enriched Vascular Assemblies.

    Phospho-proteomics:

    Article Title: Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells.
    Article Snippet: Non-specific antibody binding was blocked for 30 min by incubation with 5% normal goat serum in PBS (Invitrogen, Cat No. 50062Z). .. Tissue was stained using the following primary antibodies; anti-ZO-1 (Invitrogen, Cat No. 33–9100, 1:250 dilution), anti-Claudin-1 (Invitrogen, Cat No. 37–4900, 1:250 dilution), anti-Muc-2 (Santacruz, Cat No. sc-15334, 1:200 dilution), anti-Total OXPHOS (Abcam, Cat No. ab317270, 1:500 dilution) which targets key five complexes of the electron transport chain often known as complexes I –V involved in oxidative phosphorylation (OXPHOS), anti-Olfm4 (Cell Signaling, Cat No. 39141, 1:250 dilution), diluted in 1% of blocking buffer and incubated overnight at 4◦C in a dark humidified chamber. .. Sections were washed with 0.1% TBST and incubated with secondary antibody, such as donkey anti-Rabbit IgG conjugated with Alexa Fluor 647 (Invitrogen, Cat. No. A32795), Goat anti-rabbit IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. R37117), Goat anti-Mouse IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. A-11005), 1:1000 diluted in 1% of blocking buffer and incubated in dark humidified chamber for 1 h. After being washed with 0.1% TBST, the sections were mounted in Vectashield Dapi-containing mounting medium (Vector Labs., Cat. No. H1200) and Fluorescence images were acquired using a confocal microscope (Nikon A1RMP).

    Blocking Assay:

    Article Title: Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells.
    Article Snippet: Non-specific antibody binding was blocked for 30 min by incubation with 5% normal goat serum in PBS (Invitrogen, Cat No. 50062Z). .. Tissue was stained using the following primary antibodies; anti-ZO-1 (Invitrogen, Cat No. 33–9100, 1:250 dilution), anti-Claudin-1 (Invitrogen, Cat No. 37–4900, 1:250 dilution), anti-Muc-2 (Santacruz, Cat No. sc-15334, 1:200 dilution), anti-Total OXPHOS (Abcam, Cat No. ab317270, 1:500 dilution) which targets key five complexes of the electron transport chain often known as complexes I –V involved in oxidative phosphorylation (OXPHOS), anti-Olfm4 (Cell Signaling, Cat No. 39141, 1:250 dilution), diluted in 1% of blocking buffer and incubated overnight at 4◦C in a dark humidified chamber. .. Sections were washed with 0.1% TBST and incubated with secondary antibody, such as donkey anti-Rabbit IgG conjugated with Alexa Fluor 647 (Invitrogen, Cat. No. A32795), Goat anti-rabbit IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. R37117), Goat anti-Mouse IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. A-11005), 1:1000 diluted in 1% of blocking buffer and incubated in dark humidified chamber for 1 h. After being washed with 0.1% TBST, the sections were mounted in Vectashield Dapi-containing mounting medium (Vector Labs., Cat. No. H1200) and Fluorescence images were acquired using a confocal microscope (Nikon A1RMP).

    Article Title: Altered distribution of tissue galectins correlates with mucosal dysregulation in SIV infection
    Article Snippet: .. Fc receptors were blocked with Human TruStain FcX blocking antibody (Biolegend, San Diego, California, USA) diluted in blocking buffer (1xPBS, 2% donkey or goat serum, 2% fetal bovine serum) for 1 h. Slides were stained with primary antibodies diluted in blocking buffer (1:300) for 1 h. Primary antibodies include those targeting human galectin-9 (Cat. AF2045; R&D Systems) and galectin-3 (Cat. AF1197; R&D Systems), galectin-1 (Cat. Ab108389 ; Abcam), and ZO-1 (Cat. 61-7300; ThermoFisher), Occludin (Cat. 33-1500; ThermoFisher), Claudin-1 (Cat. 37-4900; ThermoFisher), and Claudin-5 (Cat. PA5-99415; ThermoFisher). .. Slides were washed and then stained with Donkey anti-Goat 488 (Cat. A-11055; ThermoFisher), Donkey anti-Rabbit 555 (Cat. A-31572; ThermoFisher), and Donkey anti-Mouse 647 (Cat. A-31571; ThermoFisher) secondary antibodies (1:400) in blocking buffer for 1 h. Slides were washed and stained with nuclear marker Hoechst 33342 (ThermoFisher) for 10 min.

    Incubation:

    Article Title: Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells.
    Article Snippet: Non-specific antibody binding was blocked for 30 min by incubation with 5% normal goat serum in PBS (Invitrogen, Cat No. 50062Z). .. Tissue was stained using the following primary antibodies; anti-ZO-1 (Invitrogen, Cat No. 33–9100, 1:250 dilution), anti-Claudin-1 (Invitrogen, Cat No. 37–4900, 1:250 dilution), anti-Muc-2 (Santacruz, Cat No. sc-15334, 1:200 dilution), anti-Total OXPHOS (Abcam, Cat No. ab317270, 1:500 dilution) which targets key five complexes of the electron transport chain often known as complexes I –V involved in oxidative phosphorylation (OXPHOS), anti-Olfm4 (Cell Signaling, Cat No. 39141, 1:250 dilution), diluted in 1% of blocking buffer and incubated overnight at 4◦C in a dark humidified chamber. .. Sections were washed with 0.1% TBST and incubated with secondary antibody, such as donkey anti-Rabbit IgG conjugated with Alexa Fluor 647 (Invitrogen, Cat. No. A32795), Goat anti-rabbit IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. R37117), Goat anti-Mouse IgG conjugated with Alexa Fluor 594 (Invitrogen, Cat. No. A-11005), 1:1000 diluted in 1% of blocking buffer and incubated in dark humidified chamber for 1 h. After being washed with 0.1% TBST, the sections were mounted in Vectashield Dapi-containing mounting medium (Vector Labs., Cat. No. H1200) and Fluorescence images were acquired using a confocal microscope (Nikon A1RMP).

    Concentration Assay:

    Article Title: African-ancestry-specific variant IKKβ p.Glu502Lys confers high lupus risk
    Article Snippet: .. DNA samples from NashBio were received on dry-ice in two-dimensional barcoded Matrix tubes (Thermo Scientific) in 96-well racks in a volume of 70 μl and a target concentration of >20 ng μl − 1 . .. Samples and plates were registered in our inhouse database and stored at −20 °C in an automated Hamilton Verso freezer until use.

    Immunostaining:

    Article Title: Transplantation of hPSC‐Derived Pericyte‐Enriched Vascular Assemblies Restores Cerebral Perfusion in the Context of Permanent Brain Ischemia
    Article Snippet: Despite advancements in vascular reconstruction techniques, insufficient distal perfusion following ischemic stroke continues to cause irreversible neurological damage, and effective strategies for reconstructing functional microvascular networks remain inadequate.. While vascular organoids have shown potential, their clinical translation is limited by the need for invasive surgical resection to accommodate large 3D grafts.. This study improves the vascular organoid technology pipeline by developing hPSCderived Pericyte-Enriched Vascular Assemblies.

    Fluorescence:

    Article Title: Transplantation of hPSC‐Derived Pericyte‐Enriched Vascular Assemblies Restores Cerebral Perfusion in the Context of Permanent Brain Ischemia
    Article Snippet: Despite advancements in vascular reconstruction techniques, insufficient distal perfusion following ischemic stroke continues to cause irreversible neurological damage, and effective strategies for reconstructing functional microvascular networks remain inadequate.. While vascular organoids have shown potential, their clinical translation is limited by the need for invasive surgical resection to accommodate large 3D grafts.. This study improves the vascular organoid technology pipeline by developing hPSCderived Pericyte-Enriched Vascular Assemblies.

    Immunohistochemical staining:

    Article Title: Transplantation of hPSC‐Derived Pericyte‐Enriched Vascular Assemblies Restores Cerebral Perfusion in the Context of Permanent Brain Ischemia
    Article Snippet: Despite advancements in vascular reconstruction techniques, insufficient distal perfusion following ischemic stroke continues to cause irreversible neurological damage, and effective strategies for reconstructing functional microvascular networks remain inadequate.. While vascular organoids have shown potential, their clinical translation is limited by the need for invasive surgical resection to accommodate large 3D grafts.. This study improves the vascular organoid technology pipeline by developing hPSCderived Pericyte-Enriched Vascular Assemblies.

    other:

    Article Title: Microbial metabolite Enterobactin impairs mitochondrial respiration and alleviates colitis
    Article Snippet: Antibodies to OXPHOS (Catalog # 45-8099) were from Thermo Fischer, and antibodies to occludin (Catalog #40-4700) and claudin-1 (Catalog #37-4900) from Invitrogen and UCP1 (Catalog #MAB6158) from R&D Systems.

    Labeling:

    Article Title: A switch from α5β1 to αvβ3 integrin activity contributes to the development of a profibrotic mesenchymal phenotype in trabecular meshwork cells
    Article Snippet: .. Briefly, TM cells were lifted with Cell Dissociation Solution Non-enzymatic (Sigma-Aldrich Corp.), blocked for 30 min on ice with 1% BSA in PBS and labeled for 1 h on ice with 10 μg/mL α5 (P1D6, ThermoFisher Scientific, #12-4900-42, RRID:AB_10717080), total αvβ3 (LM609, Sigma-Millipore, mAb 1976, RRID:AB_2296419), and active αvβ3 (LIBS2, Millipore Sigma, MABT27, RRID:AB_10806476) integrin antibodies in 1% BSA/PBS. .. This was followed by a secondary Alexa 647-conjugated rabbit anti-mouse IgG (Thermo Fisher Scientific) diluted 1:400 in 1% BSA/PBS for 45 min on ice.



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    86
    Exosome Diagnostics multicolor barcode array
    A. Schematic of the <t>Swap-seq</t> workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a <t>barcode</t> cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.
    Multicolor Barcode Array, supplied by Exosome Diagnostics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/array+barcode+multicolor/pm42321851-2520-19-25
    Average 86 stars, based on 1 article reviews
    multicolor barcode array - by Bioz Stars, 2026-11
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    feature barcode technology  (10X Genomics)
    86
    10X Genomics feature barcode technology
    A. Schematic of the <t>Swap-seq</t> workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a <t>barcode</t> cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.
    Feature Barcode Technology, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/cellranger/pm42320984-60-38-41
    Average 86 stars, based on 1 article reviews
    feature barcode technology - by Bioz Stars, 2026-11
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    feature barcode kit  (10X Genomics)
    86
    10X Genomics feature barcode kit
    A. Schematic of the <t>Swap-seq</t> workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a <t>barcode</t> cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.
    Feature Barcode Kit, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/3%CA%B9+barcode+feature+kit/pm42321208-228-27-34
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    barcode r  (Sangon Biotech)
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    Sangon Biotech barcode r
    A. Schematic of the <t>Swap-seq</t> workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a <t>barcode</t> cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.
    Barcode R, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/barcode+f+linker/pmc13142104-76-0-5
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    Image Search Results


    A. Schematic of the Swap-seq workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a barcode cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.

    Journal: bioRxiv

    Article Title: Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

    doi: 10.64898/2026.10.08.756856

    Figure Lengend Snippet: A. Schematic of the Swap-seq workflow for measuring the effects of DNA sequence deletions on gene expression. Each Swap-seq edit uses a pair of pegRNAs to delete a 50- to 250-bp target sequence and replace it with a barcode cassette containing an edit-specific 8-bp barcode together with sequences common to all edits, including PCR primer-binding sites (yellow) and a 3′ overlap sequence (purple). In a Swap-seq screen, hundreds of such edits are designed to perturb sequences surrounding a gene of interest. Cells are infected with a lentiviral pegRNA-pair library at low multiplicity of infection (MOI); after 14 days of editing, cells are cultured without doxycycline for 7 days before undergoing FlowFISH sorting and quantification of changes in gene expression. B. Individual Swap-seq editing test in three regions: the PPIF promoter, a candidate enhancer with high accessibility and H3K27ac signal (enhancer e2 in G ), and a region with low accessibility (hg19: chr10:81,069,000-81,069,517). Error bars: 95% CI for the mean. C. Correlation of effect sizes between two biological replicates, after removing edits that did not pass the 0.001% frequency threshold. Effects for each edit are averaged among barcodes. (Pearson’s r = 0.97, n = 117 edits). D. Editing efficiency and number of cells assayed for each barcode. A barcode passed the threshold in a given technical replicate if aligned reads exceeded 0.001% of all reads. Bottom axis, mean allele frequency calculated as the percent of reads aligned to the barcode averaged across replicates; y-axis, number of barcodes; top axis, number of cells assayed. E. Volcano plot of Swap-seq edits passing the frequency threshold. Edits were considered significant at BH-corrected p < 0.001 (horizontal dashed line). Error bars: 95% CI for the mean. F. Swap-seq screen candidate elements at the PPIF locus. In total, 24 candidate regulatory elements were targeted and the PPIF promoter was included as a positive control. *Two elements with no edits above the frequency threshold of 0.001%. G. Swap-seq effects on PPIF expression. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits. H. Swap-seq edits spanning the promoter, splice junction, and enhancer g1. Red, significant edits (BH-corrected p < 0.001, one-sample t-test); gray, non-significant edits.

    Article Snippet: Following extraction, we split genomic DNA into PCR replicates and amplified the Swap-seq barcode cassettes with Q5 High-Fidelity 2X Master Mix (New England Biolabs #M0492L) and 0.5 uM of each amplification primer ( table S1 ) with the following program: 98°C for 1 minute and then 26 cycles of 98°C for 10 seconds, 69°C for 20 seconds, 72°C for 20 seconds, followed by a final 72°C extension for 2 minutes.

    Techniques: Sequencing, Gene Expression, Binding Assay, Infection, Cell Culture, Positive Control, Expressing, Polymerase Chain Reaction, ChIP-sequencing

    A. Comparison of regulatory elements identified by Swap-seq and CRISPRi. An element was classified as significant in Swap-seq if at least one edit within the element was significant (one-sample t-test, BH-corrected p < 0.001). CRISPRi used the average effects of all gRNAs targeting the same region (one-sample t-test, BH-corrected p < 0.05). Elements were grouped according to the hypothesized mechanisms based on their candidate element categories and effects on PPIF gene expression. B. Correlation between Swap-seq and CRISPRi effect sizes. Elements within the PPIF gene body, which are not testable by CRISPRi, were excluded from this analysis; when an element contains several significant edits, the one with the strongest effect was used for comparison with CRISPRi (Pearson’s r = 0.75, n = 18 elements). Error bars: 95% CI for the mean. C. Swap-seq edits overlap key transcription factor binding sites (TFBS) within regulatory elements. Close-up views of four elements with significant effects on PPIF expression (left to right: e2, a PPIF enhancer with high H3K27ac; e5, a low-H3K27ac enhancer; g1, an enhancer in intron 1 of PPIF ; c2, a CTCF binding site). ChromBPNet attribution scores are plotted together with TF-MoDISco motif annotations. All edits that passed the frequency threshold are plotted with width corresponding to the deleted region. Significance determined by one-sample t-test: red, significant edits (BH-corrected p < 0.001); gray, non-significant edits. Error bars: 95% CI for the mean. D. Schematic of the downstream lentiMPRA. Candidate regulatory elements were cloned downstream of the promoter and an ORF–barcode–poly(A) cassette (ORF-BC-pA). Cells were infected with the lentiviral library at high MOI, and barcodes were sequenced from both DNA and RNA; CRE activity was calculated as the ratio of RNA to DNA barcode abundance. E. LentiMPRA validation of candidate enhancers. Each dot represents a barcode from two biological replicates. A sequence lacking predicted TFBS (noTFBS) served as a negative control for basal promoter strength. Significance determined by two-sample t-test: *p < 0.05, **p < 0.01, ***p < 0.001. Error bars: 95% CI for the mean. F. CTCF deletion alters 3D genome contacts at the PPIF locus. Contact frequencies were averaged across region-capture Micro-C (RCMC) measurements from three independent clones, and log2 fold-change was calculated as log2(c2-deleted clones / WT clones) at 1.6 kb bin sizes. G. Quantification of contact changes associated with CTCF deletion, with the viewpoint on the PPIF promoter. Bars show changes in contact frequency between the PPIF promoter and each regulatory element, averaged across three clonal lines at 1.6 kb binsize. Significance determined by two-sample t-test: *p < 0.05, **p < 0.01, ***p < 0.001. Error bars: 95% CI for the mean.

    Journal: bioRxiv

    Article Title: Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

    doi: 10.64898/2026.10.08.756856

    Figure Lengend Snippet: A. Comparison of regulatory elements identified by Swap-seq and CRISPRi. An element was classified as significant in Swap-seq if at least one edit within the element was significant (one-sample t-test, BH-corrected p < 0.001). CRISPRi used the average effects of all gRNAs targeting the same region (one-sample t-test, BH-corrected p < 0.05). Elements were grouped according to the hypothesized mechanisms based on their candidate element categories and effects on PPIF gene expression. B. Correlation between Swap-seq and CRISPRi effect sizes. Elements within the PPIF gene body, which are not testable by CRISPRi, were excluded from this analysis; when an element contains several significant edits, the one with the strongest effect was used for comparison with CRISPRi (Pearson’s r = 0.75, n = 18 elements). Error bars: 95% CI for the mean. C. Swap-seq edits overlap key transcription factor binding sites (TFBS) within regulatory elements. Close-up views of four elements with significant effects on PPIF expression (left to right: e2, a PPIF enhancer with high H3K27ac; e5, a low-H3K27ac enhancer; g1, an enhancer in intron 1 of PPIF ; c2, a CTCF binding site). ChromBPNet attribution scores are plotted together with TF-MoDISco motif annotations. All edits that passed the frequency threshold are plotted with width corresponding to the deleted region. Significance determined by one-sample t-test: red, significant edits (BH-corrected p < 0.001); gray, non-significant edits. Error bars: 95% CI for the mean. D. Schematic of the downstream lentiMPRA. Candidate regulatory elements were cloned downstream of the promoter and an ORF–barcode–poly(A) cassette (ORF-BC-pA). Cells were infected with the lentiviral library at high MOI, and barcodes were sequenced from both DNA and RNA; CRE activity was calculated as the ratio of RNA to DNA barcode abundance. E. LentiMPRA validation of candidate enhancers. Each dot represents a barcode from two biological replicates. A sequence lacking predicted TFBS (noTFBS) served as a negative control for basal promoter strength. Significance determined by two-sample t-test: *p < 0.05, **p < 0.01, ***p < 0.001. Error bars: 95% CI for the mean. F. CTCF deletion alters 3D genome contacts at the PPIF locus. Contact frequencies were averaged across region-capture Micro-C (RCMC) measurements from three independent clones, and log2 fold-change was calculated as log2(c2-deleted clones / WT clones) at 1.6 kb bin sizes. G. Quantification of contact changes associated with CTCF deletion, with the viewpoint on the PPIF promoter. Bars show changes in contact frequency between the PPIF promoter and each regulatory element, averaged across three clonal lines at 1.6 kb binsize. Significance determined by two-sample t-test: *p < 0.05, **p < 0.01, ***p < 0.001. Error bars: 95% CI for the mean.

    Article Snippet: Following extraction, we split genomic DNA into PCR replicates and amplified the Swap-seq barcode cassettes with Q5 High-Fidelity 2X Master Mix (New England Biolabs #M0492L) and 0.5 uM of each amplification primer ( table S1 ) with the following program: 98°C for 1 minute and then 26 cycles of 98°C for 10 seconds, 69°C for 20 seconds, 72°C for 20 seconds, followed by a final 72°C extension for 2 minutes.

    Techniques: Comparison, Gene Expression, Analysis, Binding Assay, Expressing, Clone Assay, Infection, Activity Assay, Biomarker Discovery, Sequencing, Negative Control