Editing BioMicroCenter:SingleCell (section)

== 10x CHROMIUM X ==
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  !scRNA
  !snATACseq
  !multiome
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  !INPUT 
  |colspan="3"| ~500-10,000 Cells or Nuclei Per Sample (CNPS) for NextGEM <BR> ~500-20,000 CNPS for GEM-X <BR> HT ~2,000-60,000 Cells or Nuclei Per Channel for HT <BR> FRP or probe based available for some assays, otherwise freshly counted cells preferred
  |-
  !RECOMMENDED SEQUENCING 
  |NextSeq - 75nt kit <BR>2-4 samples/flowcell
  |NextSeq - 150nt kit <BR> 2-4 samples/flowcell
  |NextSeq - 150nt kit <BR> 1-2 samples/flowcell
  |-
  !SUBMISSION 
  |colspan="3"| ASSISTED - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=12903 ilabs] <BR> WALKUP - [https://mit.ilabsolutions.com/equipment/380963 Calendar]
  |-
  !DELIVERY 
  |colspan="3"| FASTQ, SAM, BAM, 10X QC, loupe file
  |-
  !UNIT 
  |colspan="3"| PER SAMPLE or PER USAGE
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  !DONATED BY 
  |colspan="3"| [http://mit.edu/manoli/ Prof. Manolis Kellis]
  |-
  !EXAMPLE DATA
  |colspan="3"| [[image:BMC_10X_data.jpg|thumb|left|600px|Example of QC Data from a 10x 3' v4 GEM-X assay.]]
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[[image:10xX.jpg|thumb|right|500px|10x Chromium X]]
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The BioMicro Center provides access to 10x Genomics library preparation as an assisted or a walk-up service. Added in 2023, The 10x Chromium X can handle a broad variety of methodologies now including [https://www.10xgenomics.com/solutions/single-cell/ 3' and 5' RNA sequencing], [https://www.10xgenomics.com/solutions/single-cell-atac/ ATACseq] and [https://www.10xgenomics.com/solutions/single-cell-cnv/ CNV]. Dropoff for assisted service is coordinated with Center staff with at least one week's lead time. Users should bring their single cell/nuclei suspension(s) in 1.5 mL microfuge tubes in the standard buffer at or around that time. Staff works with the user to intake the initial samples and proceed through the protocol with quality control checks at the appropriate steps. 
<BR><BR>
This is also offered as a walkup service. Usage may be scheduled on the ilabs calendar after training by BMC staff. You will not have permission to schedule the equipment until you have been approved by BMC staff. Reagents are stocked in the BioMicro Center and we ask that you use our reagents. This allows us to get larger bulk discounts we can pass on to our users. Please note that we do include a fraction of the instrument usage cost in the cost of the chips and will charge this cost if you use your own chips.
<BR><BR>
The full 10x suite of software is installed on LURIA and is integrated into our analysis package. <BR><BR>

FAQs for Users <BR>
'''1) What buffers in the final suspension are compatible with 10X applications?''' 
<br>
[https://kb.10xgenomics.com/hc/en-us/articles/115001937123-What-buffers-can-be-used-for-washing-and-cell-resuspension Buffers/media] for the submitted single cell/nuclei suspension should not contain excessive amounts of EDTA (>0.1 mM) or magnesium (>3 mM) and should be free of surfactants (i.e. Tween-20, SDS etc) and any RNases or DNases.
*1xPBS (calcium free and magnesium free) containing 0.04%  weight/volume BSA (400 µg/ml) is recommended for most general protocols and is considered the standard buffer
*Cell culture media with up to 1% BSA or up to 10% FBS if cells are not viable in standard buffer
*1xPBS (calcium free and magnesium free) containing up to 10% FBS for CMO labelling
*Nuclei also require addition of RNase Inhibitor along with 10X Genomics 1X nuclei buffer before chip loading, instructions for which are included in 10x user guides. If needed, users can collect buffer aliquots from the BMC after submitting a project. Please coordinate with BMC staff for pick-up. <br>
'''2) How many cells are captured in the Assay?'''
<br>Up to 10,000 cells for NextGEM and 20,000 cells for GEM-X can be uniquely barcoded, but this highly depends on cell counts and viability. Dying cells will leak RNA, hence may not be captured efficiently leading to sample failures. We recommend to count cells at the BMC to avoid discrepancies, but can work with users' counts as well. <BR>
'''3) What are the best practices for flow sorting cells? <br> 
10x provides guidance with their tested protocols about pre-sort buffer, collection buffer and FACS best practices [https://kb.10xgenomics.com/hc/en-us/articles/360048826911-What-are-the-best-practices-for-flow-sorting-cells-for-10x-Genomics-assays here.] <br>
'''4) What is the expected size distribution for cDNA?''' <br>
cDNA for 3' and 5' libraries will span between 400 to 9000 base pairs, depending on sample type.
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For more resources, please visit https://kb.10xgenomics.com/hc/en-us
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