Editing BioMicroCenter:SingleCell (section)

== AVITI24 IN SITU SEQUENCING ==
 *** coming in early 2026 ***

The AVITI24 enables direct in situ sequencing of samples, allowing for very rapid characterization of single cells. Cells can be grown or placed on the AVITI24 flowcell and processed. Runs are predicted to produce a few thousand reads plus cytostaining and antibody labeling, all within a day. More information will be released soon. 


<!-- commenting out Seq-Well 
== SEQ-WELL ==
{|
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  !   
  !SEQ-WELL 
  |-
  |INPUT
  |
* FULL PREP: <BR>50,000 single free cells. 90% viability
* EXO1 and AMP <BR> Tubes with cDNA attached to beads
* LIBRARY ONLY <BR> Amplified cDNA
  |-
  |THROUGHPUT 
  |
* FULL PREP/EXO: 4 samples/day
* LIBRARY: 24 samples/day
  |-
  |INCLUDED || QC at cDNA stage, library generation.
  |-
  |RECOMMENDED SEQUENCING || NextSeq500 - 75nt kit - 2-4 samples/flowcell
  |-
  |SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=12903 ilabs] <BR> External contact biomicro@mit.edu
  |-
  |DELIVERY || FASTQ, SAM, BAM, Cell:Gene matrix
  |-
  |UNIT || PER ARRAY
 |}
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The BioMicro Center collaborates closely with the Nanowell Core in the Koch Institute to provide support for the [https://shaleklab.com/resources/seq-well/ Seq-Well] protocol developed by Drs. Alex Shalek and Chris Love's groups. Seq-Well is based on the isolation of individual cells into microwells where cells are lysed and the associated mRNA is attached to polydT containing beads.  <BR><BR>
Seq-Well projects can be brought in two ways. For full service, please use the ilabs form linked on the left. At the end of the form it asks you to select several days on which the experiment can be done. The Nanowell Core will review the possible dates with you to fit it in the schedule. On that date, the core will confirm the quality of your cells prior to beginning the experiment. While 10,000 cells are typically used in a Seq-Well experiment, the core requests you plan to bring more cells - often counts from flow cytometers and other instruments are incorrect. Planning to bring more cells ensures you have the 10,000 desired. The BioMicro Center becomes involved in these projects at the exonuclease treatment step, where we take over the preparation of the library and quality control, as well as sequencing and analysis.<BR><BR>
Many laboratories are also using reagents from the Nanowell core to begin doing Seq-Well on their own. For these labs, we strongly recommend at least confirming the quality of the cDNA on our Advanced Analytical before continuing through library preparation. The library preparation can also be done in the BioMicro Center. Please use the standard Illumina library preparation form and note that the samples are Seq-Well. We do have all the custom primers needed for preparation and the pricing is identical to other NexteraXT preps. 
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