10 Chromium Services

HudsonAlpha Discovery offers long range genomic sequencing on the Chromium platform from 10X Genomics. Applications for this technology include generating phased genomic data, finding structural variants in human genome and exome samples, and assembly of genomes for novel organisms. Analysis of Chromium data is handled by several different software packages provided by 10X Genomics. First, a bclprocessor is used to generate specially formatted fastq files. Human samples may then be analyzed using Long Ranger to yield high-quality hapotype phasing and structural variant calls. Finally, results can be visualized using Loupe, a desktop genome browser. Supernova, an assembly tool for Chromium data, is available for de novo assemblies. If you are providing non-standard organism for Chromium library preparation, please include the estimated genome size in the Special Instructions. This information is required to titrate the input DNA. Software downloads are available on the 10X website.

Sample Requirements and Considerations

Upon arrival to the HudsonAlpha Discovery, all DNA samples are evaluated for concentration and integrity. DNA samples intended for the Chromium platform are evaluated with PicoGreen or Qubit and a 0.4% agarose gel with EtBr, or a pulsed field gel. A DNA sample intended for Chromium WGS or Exome protocol must be high molecular weight, which requires a specialized isolation procedure. If you are providing non-standard organism for Chromium library preparation, please include the estimated genome size in the Special Instructions. This information is required to titrate the input DNA.

10X Genomics has approved specific HMW isolation protocols for the Chromium platform. There are many other methods and kits which produce RNA-free HMW DNA, but less variation in performance is seen with 10X-approved methods. There are other factors besides size of the gDNA that determine the performance of the Chromium platform and many of these cannot be measured (DNA damage, nicking, etc). In addition, size of the gDNA as measured during QC does not always predict the "analyzed" size of the DNA when measured through the Chromium platform analysis software. There are very clear effects seen in anlayzed output data when gDNA sizes drop from the highest molecular weights possible/preferred (i.e. 80% at 100kb or larger). Given the inability to measure all contributing factors (both known and unknown) needed for success with the Chromium platform, no guarantees of performance with respect to analysis metrics or assembly efforts are offered. All Chromium work is considered at the customer's risk and projects must be pre-paid.

Ideally, DNA should be above 50kb with greater than 80% of the DNA at 100kb or larger. After isolation, the DNA should be handled very gently (minimal pipetting, use of wide-bore tips, avoid freeze/thaw, etc). Ship HMW DNA on dry ice for stability, but once it arrives at HudsonAlpha Discovery it will be stored at 4C. Though the protocol uses 1ng of HMW DNA as input, a minimum of 500ng of DNA in 20ul of water or Tris should be submitted to allow for QC and visualization of the HMW DNA on a gel. HudsonAlpha Discovery can perform the HMW isolation if needed, and leftover DNA may be returned at the completion of the project.

Special note regarding isolation of HMW DNA from blood: a CPT blood collection tube with sodium citrate must be used for blood submissions (do not use the CPT tube containing heparin). After blood collection, follow the instructions provided with the tube for centrifugation to separate the blood into layers. Pull off the mononuclear cells and platelets and transfer to a new microfuge tube. The DNA from the cells can then isolated in your lab. If HudsonAlpha Discovery will perform the HMW isolation, spin the cells down into a pellet and remove as much buffer as possible. Freeze the pellet and ship it to us on dry ice.

Chromium Service Options

HudsonAlpha Discovery currently offers:

Chromium Data and Sequencing

Chromium libraries have a unique structure that require special sequencing considerations. Each DNA sample is indexed with four i7 barcodes sequenced as a standard i7 index read of 8bp in length. No i5 index read is sequenced for Chromium libraries. Instead, the unique barcode used to link reads is found at the beginning of read 1 and is 16bp in length. HudsonAlpha Discovery typically sequences Chromium libraries on the NovaSeq 6000.

If Chromium libraries are returned to the customer for sequencing, the following information may be helpful for clustering. Chromium libraries are QC'd using qubit, bioanalysis, and kapa qPCR. For accurate nM determination by qPCR, HudsonAlpha Discovery adjusts the input fragment size and concentration (from flourmetric assays) by decreasing it 10-15%. In other words, reduce the fragment size by 10-15% (as determined by bioanalysis), reduce the concentration from Qubit by 10-15%, and use those values for the kapa qPCR calculation. This provides a more accurate nM concentration, prevents overclustering, and allows the samples to fall in the standard curve. This approach has been tested/validated within HudsonAlpha Discovery but your results and experiences may vary.