Review



cell id 20 plex pd barcoding kit  (fluidigm)


Bioz Verified Symbol fluidigm is a verified supplier
Bioz Manufacturer Symbol fluidigm manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 96
      Buy from Supplier

    Structured Review

    fluidigm cell id 20 plex pd barcoding kit
    Cell Id 20 Plex Pd Barcoding Kit, supplied by fluidigm, used in various techniques. Bioz Stars score: 96/100, based on 650 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/Cell-ID+20-Plex+Pd+Barcoding+Kit/ppr0568348-59-11-16
    Average 96 stars, based on 650 article reviews
    cell id 20 plex pd barcoding kit - by Bioz Stars, 2026-10
    96/100 stars

    Images

    Related Articles

    Staining:

    Article Title: Multiomic analysis of ART-interruption cohorts identifies cell-extrinsic and -intrinsic mechanisms driving lymphocyte-mediated control of HIV rebound.
    Article Snippet: The conjugates were then diluted 1:1 with a PBS-based Antibody Stabilizer (Boca Scientific) supplemented with 0.05% sodium azide, and stored at 4 ◦ C until use. .. CyTOF cell barcoding and staining Cell barcoding was performed using the Cell-ID 20-Plex Pd Barcoding Kit in accordance with manufacturer’s guidelines (Standard BioTools). .. Briefly, for each sample, a total of 1-3 million cells was washed twice with Barcode Perm Buffer (Standard BioTools).

    Article Title: Homoharringtonine exhibits senotherapeutic activity that mitigates diet- and age-associated obesity and insulin resistance and extends lifespan in mice
    Article Snippet: The flow-through was centrifuged for 5 min at 400 x g. After removing the floating adipocyte fraction and supernatant, red blood cell lysis buffer (Sigma-Aldrich, #R7757) was added and incubated at room temperature for 2-3 min. .. The red blood cell lysis buffer is neutralized with DMEM/F12 media (supplemented with 10% FBS) and centrifuged for 5 min at 400 x g. The dissociated cells from adipose tissue or spleen were washed in a cell staining medium (CSM) and each sample was barcoded before staining according to the protocol described in the Cell-ID 20-Plex Pd Barcoding kit (Fluidigm, San Francisco, CA). ..

    Article Title: Mass Cytometry Workflow to Achieve High‐Dimensional Immunophenotyping in Resource‐Limited or Decentralized Environments
    Article Snippet: .. Foxp3/Transcription Factor Staining Buffer Set (eBioscience, cat. no. 00‐5523‐00) Cell‐ID 20‐Plex Pd Barcoding Kit (Standard BioTools, cat. no. 201060) CyTOF antibodies for intracellular targets (see Table ) FACS buffer (see recipe) Maxpar Cell Acquisition Solution (Standard BioTools, cat no. 201240) 5‐ml round‐bottom tubes 15‐ or 50‐ml centrifuge tubes as needed (see step 10) Ultrafree Centrifugal Filter (Millipore, cat. no. UFC30DV25) 2‐ml screw‐cap micro tubes (cryovials), sterile (Sarstedt, cat. no. 72.694.005) CoolCell LX Freezing Container (Corning, cat. no. 432002) −80°C freezer 5‐ml Falcon Round‐Bottom Tubes with Cell Strainer Cap (STEMCELL, cat. no. 38030) EQ Six Element Calibration Beads (100 ml; Standard BioTools, cat. no. 201245) CyTOF instrument: e.g., Helios system with standard equipment and CyTOF software ..

    Red Blood Cell Lysis:

    Article Title: Homoharringtonine exhibits senotherapeutic activity that mitigates diet- and age-associated obesity and insulin resistance and extends lifespan in mice
    Article Snippet: The flow-through was centrifuged for 5 min at 400 x g. After removing the floating adipocyte fraction and supernatant, red blood cell lysis buffer (Sigma-Aldrich, #R7757) was added and incubated at room temperature for 2-3 min. .. The red blood cell lysis buffer is neutralized with DMEM/F12 media (supplemented with 10% FBS) and centrifuged for 5 min at 400 x g. The dissociated cells from adipose tissue or spleen were washed in a cell staining medium (CSM) and each sample was barcoded before staining according to the protocol described in the Cell-ID 20-Plex Pd Barcoding kit (Fluidigm, San Francisco, CA). ..

    FACS:

    Article Title: Mass Cytometry Workflow to Achieve High‐Dimensional Immunophenotyping in Resource‐Limited or Decentralized Environments
    Article Snippet: .. Foxp3/Transcription Factor Staining Buffer Set (eBioscience, cat. no. 00‐5523‐00) Cell‐ID 20‐Plex Pd Barcoding Kit (Standard BioTools, cat. no. 201060) CyTOF antibodies for intracellular targets (see Table ) FACS buffer (see recipe) Maxpar Cell Acquisition Solution (Standard BioTools, cat no. 201240) 5‐ml round‐bottom tubes 15‐ or 50‐ml centrifuge tubes as needed (see step 10) Ultrafree Centrifugal Filter (Millipore, cat. no. UFC30DV25) 2‐ml screw‐cap micro tubes (cryovials), sterile (Sarstedt, cat. no. 72.694.005) CoolCell LX Freezing Container (Corning, cat. no. 432002) −80°C freezer 5‐ml Falcon Round‐Bottom Tubes with Cell Strainer Cap (STEMCELL, cat. no. 38030) EQ Six Element Calibration Beads (100 ml; Standard BioTools, cat. no. 201245) CyTOF instrument: e.g., Helios system with standard equipment and CyTOF software ..

    Sterility:

    Article Title: Mass Cytometry Workflow to Achieve High‐Dimensional Immunophenotyping in Resource‐Limited or Decentralized Environments
    Article Snippet: .. Foxp3/Transcription Factor Staining Buffer Set (eBioscience, cat. no. 00‐5523‐00) Cell‐ID 20‐Plex Pd Barcoding Kit (Standard BioTools, cat. no. 201060) CyTOF antibodies for intracellular targets (see Table ) FACS buffer (see recipe) Maxpar Cell Acquisition Solution (Standard BioTools, cat no. 201240) 5‐ml round‐bottom tubes 15‐ or 50‐ml centrifuge tubes as needed (see step 10) Ultrafree Centrifugal Filter (Millipore, cat. no. UFC30DV25) 2‐ml screw‐cap micro tubes (cryovials), sterile (Sarstedt, cat. no. 72.694.005) CoolCell LX Freezing Container (Corning, cat. no. 432002) −80°C freezer 5‐ml Falcon Round‐Bottom Tubes with Cell Strainer Cap (STEMCELL, cat. no. 38030) EQ Six Element Calibration Beads (100 ml; Standard BioTools, cat. no. 201245) CyTOF instrument: e.g., Helios system with standard equipment and CyTOF software ..

    Software:

    Article Title: Mass Cytometry Workflow to Achieve High‐Dimensional Immunophenotyping in Resource‐Limited or Decentralized Environments
    Article Snippet: .. Foxp3/Transcription Factor Staining Buffer Set (eBioscience, cat. no. 00‐5523‐00) Cell‐ID 20‐Plex Pd Barcoding Kit (Standard BioTools, cat. no. 201060) CyTOF antibodies for intracellular targets (see Table ) FACS buffer (see recipe) Maxpar Cell Acquisition Solution (Standard BioTools, cat no. 201240) 5‐ml round‐bottom tubes 15‐ or 50‐ml centrifuge tubes as needed (see step 10) Ultrafree Centrifugal Filter (Millipore, cat. no. UFC30DV25) 2‐ml screw‐cap micro tubes (cryovials), sterile (Sarstedt, cat. no. 72.694.005) CoolCell LX Freezing Container (Corning, cat. no. 432002) −80°C freezer 5‐ml Falcon Round‐Bottom Tubes with Cell Strainer Cap (STEMCELL, cat. no. 38030) EQ Six Element Calibration Beads (100 ml; Standard BioTools, cat. no. 201245) CyTOF instrument: e.g., Helios system with standard equipment and CyTOF software ..

    other:

    Article Title: Evaluation of nanobodies engineered with extra-cysteines for site-specific functionalization.
    Article Snippet: Each barcode was resuspended in MaxPar Fix & Perm Buffer (201067, Standard Biotools) and transferred to the corresponding sample, followed by incubation for 30 min at room temperature and three washes with CSB at 800 x g for 5 min. Barcoded cells were then pooled together and incubated with Cell-ID Intercalator-Ir (201192 A, Standard Biotools) diluted in MaxPar Fix & Perm Buffer at a final concentration of 50 nM and stored at 4◦C overnight.

    Article Title: Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops.
    Article Snippet: Subsequently, cells were first stained and fixed 785 with Fix-I buffer (Catalog No. 201061, Fluidigm); then, they were secondarily stained 786 using the Cell-ID 20-Plex Pd Barcoding Kit (Catalog No. 201060, Fluidigm) to 787 reduce sample cross-reactivity.



    Similar Products

    swap seq barcode cassettes  (New England Biolabs)
    99
    New England Biolabs swap seq barcode cassettes
    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.
    Swap Seq Barcode Cassettes, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/Q5+High-Fidelity+Master+Mix/bio_rxiv__64898__2026__10__08__756856-260-12-21
    Average 99 stars, based on 1 article reviews
    swap seq barcode cassettes - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    barcode tf pairs  (New England Biolabs)
    99
    New England Biolabs barcode tf pairs
    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 Tf Pairs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/HindIII/bio_rxiv__64898__2026__10__08__757551-332-10-15
    Average 99 stars, based on 1 article reviews
    barcode tf pairs - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    barcode shrna oligonucleotide  (Qiagen)
    99
    Qiagen barcode shrna oligonucleotide
    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 Shrna Oligonucleotide, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/QIAquick+PCR+Purification+Kit/pm42842673-239-3-14
    Average 99 stars, based on 1 article reviews
    barcode shrna oligonucleotide - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    m0367 native barcoding kit 24 v14 ont  (New England Biolabs)
    99
    New England Biolabs m0367 native barcoding kit 24 v14 ont
    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.
    M0367 Native Barcoding Kit 24 V14 Ont, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/Blunt%2FTA+Ligase+Master+Mix/pm42826104-56-172-170
    Average 99 stars, based on 1 article reviews
    m0367 native barcoding kit 24 v14 ont - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    feature barcode libraries  (Complete Genomics Inc)
    99
    Complete Genomics Inc feature barcode libraries
    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 Libraries, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/DNBSEQ-G400/pmc13634803-31-7-15
    Average 99 stars, based on 1 article reviews
    feature barcode libraries - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    barcode mixture a  (New England Biolabs)
    99
    New England Biolabs barcode mixture a
    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 Mixture A, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding/T4+DNA+Ligase/pm42045467-680-15-23
    Average 99 stars, based on 1 article reviews
    barcode mixture a - by Bioz Stars, 2026-10
    99/100 stars
    		  Buy from Supplier
    multicolor barcode array  (Exosome Diagnostics)
    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, 2026-10
    86/100 stars
    		  Buy from Supplier
    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, 2026-10
    86/100 stars
    		  Buy from Supplier
    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
    Average 86 stars, based on 1 article reviews
    feature barcode kit - by Bioz Stars, 2026-10
    86/100 stars
    		  Buy from Supplier
    barcode r  (Sangon Biotech)
    86
    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
    Average 86 stars, based on 1 article reviews
    barcode r - by Bioz Stars, 2026-10
    86/100 stars
    		  Buy from Supplier

    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