The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website. GTH or HGH pseudopotentials are used to remove the core electrons. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). Homepage: URL: Keyword:physĭescription: BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Jack Deslippe, Georgy Samsonidze, David A. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Lastly, practice single-cell/ single-nuclei preps are encouraged and can be brought to the Single Cell Genomics Core to be examined by a Core member upon a scheduled request.Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. The Core will advise on the condition of the prep upon sample submission. If poor sample preps are provided, poor-quality data will be generated. It is best to submit a sample using optimal sample conditions to receive high quality data. Suspension media: (should be in an approved media/buffer) Specific for assay type selected.Viability >90% preferred (unless working with nuclei or fixed cells).Concentration: Specific for assay type selected.
The following checklist has been provided to illustrate what is expected of the sample upon delivery to the Single Cell Genomics Core. The investigator is responsible for generating a high-quality single cell or single nuclei suspension that meets the needs of the Chromium system and the assay type selected. Chromium Single Cell V(D)J Enrichment Kit, Mouse B CellĬhromium Single Cell ATAC Library & Gel Bead Kit v1 Chromium Sample Requirements.Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell.Chromium™ Single Cell V(D)J Enrichment Kit, Human B Cell.Chromium™ Single Cell V(D)J Enrichment Kit, Human T Cell.Feature Barcoding technology for Cell Surface ProteinĬhromium™ Single Cell 5’ Library & Gel Bead Kit v1.The following are currently offered through the Single Cell Genomics Core.Ĭhromium Single Cell 3’ Library & Gel Bead Kit v3 Chromium Assaysġ0X Genomics offers several kits to be used with the Single Cell Chromium Controller. Upon completion, the library can be sequenced on an Illumina platform.
In preparation for library construction, the cDNA is subjected to enzymatic fragmentation, size selection, end repair A-tailing, adaptor ligation and PCR. Once brought together, thousands of Gel Bead-In-Emulsions (GEMs) are generated where all the cDNA from a single cell share the same 10x™ barcodes.Īfter the initial cDNA synthesis, cDNA is amplified to generate enough product for cDNA library construction. The system utilizes this microfluidics platform to bring together single cells or nuclei and 10x™ barcoded beads at a nanoliter scale. Up to eight suspensions can be run simultaneously on one microfluidics chip for any assay selected. The scATAC-Seq assay can provide data for 500 – 10,000 individual nuclei per single-nuclei suspension. 10X Genomics also offers scATAC-Seq (Assay for Transposase Accessible Chromatin) for use with the Chromium instrument. There are 3’ or 5’ gene expression assays that provide data for 500 – 10,000 individual cells or nuclei per single-cell or single-nuclei suspension (scRNA-Seq or snRNA-Seq). The 10X Genomics, Chromium instrument can perform several assays from which investigators may select. Single Cell Gene Expression Assays – 10X Genomic Chromium
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