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Open app program

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The Open App™ program is a software platform developed by Standard BioTools. It provides a flexible and customizable interface for users to access and control various laboratory instruments and applications. The program enables users to integrate and automate multiple workflows, streamlining the overall laboratory operations.

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Lab products found in correlation

C1 single cell auto prep system, by Standard BioTools (3 mentions) Ctr 6000 microscope, by Leica (2 mentions) C1 dna seq cell wash buffer, by Standard BioTools (2 mentions) C1 ifc microfluidic chips, by Standard BioTools (2 mentions) C1 script builder software, by Standard BioTools (2 mentions)

3 protocols using open app program

1

Single-Cell T-ATAC-Seq Using Fluidigm C1

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We adapted the C1 Single-Cell Auto Prep System with its Open App™ program (Fluidigm, Inc.) to perform T-ATAC-seq. Single T cells were captured using the C1 IFC microfluidic chips (small; 5–10micron) and custom-built T-ATAC-seq scripts generated using the C1™ Script Builder Software (scripts available from Fluidigm and upon request). Jurkat cells or peripheral blood T cells were first isolated by FACS sorting and then washed three times in C1 DNA Seq Cell Wash Buffer (Fluidigm). Cells were resuspended in DNA Seq Cell Wash Buffer at a concentration of 300 cells/μL and mixed with C1 Cell Suspension Reagent at a ratio of 3:2. 15μL of this cell mix was loaded onto the IFC. After cell loading, captured cells were visualized by imaging on a Leica CTR 6000 microscope.
Satpathy A.T., Saligrama N., Buenrostro J.D., Wei Y., Wu B., Rubin A.J., Granja J.M., Lareau C.A., Li R., Qi Y., Parker K.R., Mumbach M.R., Serratelli W.S., Gennert D.G., Schep A.N., Corces M.R., Khodadoust M.S., Kim Y.H., Khavari P.A., Greenleaf W.J., Davis M.M, & Chang H.Y. (2018). Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine, 24(5), 580-590.
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2

Single-Cell T-ATAC-Seq Using Fluidigm C1

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We adapted the C1 Single-Cell Auto Prep System with its Open App™ program (Fluidigm, Inc.) to perform T-ATAC-seq. Single T cells were captured using the C1 IFC microfluidic chips (small; 5–10micron) and custom-built T-ATAC-seq scripts generated using the C1™ Script Builder Software (scripts available from Fluidigm and upon request). Jurkat cells or peripheral blood T cells were first isolated by FACS sorting and then washed three times in C1 DNA Seq Cell Wash Buffer (Fluidigm). Cells were resuspended in DNA Seq Cell Wash Buffer at a concentration of 300 cells/μL and mixed with C1 Cell Suspension Reagent at a ratio of 3:2. 15μL of this cell mix was loaded onto the IFC. After cell loading, captured cells were visualized by imaging on a Leica CTR 6000 microscope.
Satpathy A.T., Saligrama N., Buenrostro J.D., Wei Y., Wu B., Rubin A.J., Granja J.M., Lareau C.A., Li R., Qi Y., Parker K.R., Mumbach M.R., Serratelli W.S., Gennert D.G., Schep A.N., Corces M.R., Khodadoust M.S., Kim Y.H., Khavari P.A., Greenleaf W.J., Davis M.M, & Chang H.Y. (2018). Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine, 24(5), 580-590.
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3

Single-cell ATAC-seq Profiling Protocol

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Single-cell ATAC-seq was performed as previously described (Buenrostro et al., 2015 (link)). In brief, cells were sorted by flow cytometry for viability and to remove cell aggregates. The C1 Single-Cell Auto Prep System was used with the Open App™ program (Fluidigm, Inc.). The Open App scripts from the “ATAC Seq” collection from Fluidigm were used to prime the C1 IFC microfluidic chip, load cells, and run the ATAC sample prep protocol. Fluidigm scripts are available from Fluidigm Script Hub, https://www.fluidigm.com/c1openapp/scripthub.
Rubin A.J., Parker K.R., Satpathy A.T., Qi Y., Wu B., Ong A.J., Mumbach M.R., Ji A.L., Kim D.S., Cho S.W., Zarnegar B.J., Greenleaf W.J., Chang H.Y, & Khavari P.A. (2018). Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks. Cell, 176(1-2), 361-376.e17.
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