BioMicroCenter:Element Sequencing

Element Sequencing

The Center currently hosts an AVITI24 platform from Element Biosciences. AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.

Service Element Sequencing SUBMISSION Illumina OR Element libraries MIN VOLUME 15 uL MIN CONCENTRATION 2 nM INCLUDED SERVICES Quality Control:Fragment Analyzer and qPCR Element Sequencing Demultiplexing ADDITIONAL SERVICES Quality Control Element library preperation DATA FORMATS FASTQ (stored 1 year) QUALITY CONTROL FASTQC Basic run metrics (alignment rate, complexity) Basic RNAseq metrics (where applicable) Basic paired end metrics (where applicable) Contamination checks PRICING LINK SUBMISSION MIT - ilabs

ANCHORS Element supports both Illumina anchors (P5/P7) using 'Freestyle' chemistry and and Element Anchors (SP5/SP27) for 'Adept' chemistry. For runs in the BMC, P5/P7 anchored library (Illumina) are preferred. Element Adept libraries (SP5/SP27) require a 5'-phosphate on the forward end in order to circularize and sequence. INDEXING Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers to the forward and reverse reads with the P7 side read first (index 1). Indexes are therefore antisense to the ordered oligos in traditional chemistry. Index sequences should be provided AS READ and not as ordered. Custom primer submission: 70 uL at 100 uM for Read 1, all other reads require 40 uL at 100 uM. Custom primers must be compatible with TruSeq, Nextera, TruSeq, smRNA and Element sequencing primers SINGLE LANE Each lane of the AVITI24 can be loaded independently. Flowcells require both lanes to be filled to be run. Custom primers must be designed to not interfere with other user's samples. All other requests require a full flowcell. 300PE kits only have a single lane. MINIMUM READS Minimum reads per lane are guaranteed if: the BMC has performed quality control, the samples have high diversity, especially within the first 5 bases of read 1, and submitted libraries are at least 2 nM.

The AVITI24 Platform

	AVITI24	NOTES
SEQUENCER
READS/FLOWCELL Low number is minimum per lane for standard P5/P7 libraries.	250M HQ read pairs (150 for PE300)
RUN TIME	75 PE 24 hours 150 PE 38 hours 300 PE 60 hours
KITS AVAILABLE	2x75 Cloudbreak FS High 2x150 Cloudbreak FS High 2x300 Cloudbreak FS High	- Single end supported - each kit comes with 34 additional cycles
KEY NOTES	4-color chemistry Random flow cell 2-lanes per flow cell (1 for 300PE) Q40+ > 80% Low-binding surface chemistry
THANKS TO	Element Biosciences / Scott Ritterbush

The AVITI24 can run 2 flow cells per run, each hosting 2 independently-addressable lanes. Both lanes are washed with the same reagents. Element currently offers kits with 150 and 300 cycles, both supporting 2 lanes, as well as a 600 cycle kit that supports a single lane. Index hopping rates are similar to non-patterned Illumina, limiting the need for UDI's. The AVITI24 can also perform direct in sample sequencing which includes spatial imaging of RNA, proteins, phospho-proteins, and cell morphology using Teton chemistry for cytoprofiling.