BioMicroCenter:ShortRead - Revision history

Asoberan: Revise platform detail sections: add manufacturer intros, run times, custom oligo requirements, external links

2026-04-21T00:00:00Z

Revise platform detail sections: add manufacturer intros, run times, custom oligo requirements, external links

← Older revision		Revision as of 00:00, 21 April 2026
Line 54:		Line 54:
	== Illumina ==		== Illumina ==
	<span id="ILLUMINA"></span>		<span id="ILLUMINA"></span>

			The BioMicro Center operates the [https://www.illumina.com/systems/sequencing-platforms/miseq-i100.html MiSeq i100] and provides access to [https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html NovaSeqX Plus] through collaboration with nearby academic core facilities. Both instruments use Illumina's two-color XLEAP-SBS chemistry (G bases are inferred from signal absence) and are best suited to high-complexity libraries. UDIs are strongly recommended on both platforms.

	=== NovaSeqX Plus ===		=== NovaSeqX Plus ===
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	* See [[MIT:Pricing\|Pricing]] for rates.		* See [[MIT:Pricing\|Pricing]] for rates.
	* Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.		* Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.
			* Minimum 2 nM; 110 µL per lane.
			* Custom sequencing primers: at least 30 µL at 100 µM of each primer type per flowcell. Contact [mailto:biomicro@mit.edu biomicro@mit.edu] before planning a custom library prep.

	=== MiSeq i100 ===		=== MiSeq i100 ===
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	\|		\|

	The MiSeq i100 uses ~~Illumina's~~ XLEAP-SBS chemistry on a patterned (CMOS nanowell) flowcell~~. It~~ is the BMC's walkup-capable instrument, ~~suited to~~ amplicon panels, 16S rRNA surveys, validation runs, and applications ~~requiring long reads (up to 1000 nt)~~.		The MiSeq i100 uses XLEAP-SBS chemistry on a patterned (CMOS nanowell) flowcell and is the BMC's walkup-capable instrument. It supports the longest read lengths of any instrument in the center (up to 1000 nt), making it ideal for amplicon panels, 16S rRNA surveys, validation runs, and other applications where read length matters more than throughput.

	'''Kits available:''' 100 nt (25M, 100M), 300 nt (5M, 25M, 100M), 600 nt (5M, 25M, 50M), 1000 nt (25M).<BR><BR>		'''Kits available:''' 100 nt (25M, 100M), 300 nt (5M, 25M, 100M), 600 nt (5M, 25M, 50M), 1000 nt (25M). Run times range from under 4 hours (25M 100 nt) to ~24 hours (100M 300 nt).<BR><BR>

	'''Walkup service''' is not available to external users. Runs must be scheduled in the [https://mit.ilabsolutions.com/schedules/555535#/schedule/ iLabs calendar].		'''Walkup service''' is not available to external users. Runs must be scheduled in the [https://mit.ilabsolutions.com/schedules/555535#/schedule/ iLabs calendar]. Server training and storage access on BMC servers is required.<BR><BR>

			'''Custom sequencing primers:''' At least 15 µL of each primer type at 100 µM must be provided per flowcell. Contact [mailto:biomicro@mit.edu biomicro@mit.edu] before planning a custom library prep.

	'''Thanks to:''' MIT VPR, Drs. Gene Li, Michael Birnbaum, Dept. of Biology, Scott Ritterbush '89 SM '92		'''Thanks to:''' MIT VPR, Drs. Gene Li, Michael Birnbaum, Dept. of Biology, Scott Ritterbush '89 SM '92
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	\|}		\|}

	See [[MIT:Pricing]] · [[BioMicroCenter:Pricing]] for kit pricing.		See [[MIT:Pricing]] · [[BioMicroCenter:Pricing]] for kit pricing. Custom sequencing primers follow the same submission guidelines as the MiSeq i100: at least 15 µL at 100 µM per primer type.

	<!-- Donor information for MiSeq classic is not recorded in current source pages. Please update if known. -->		<!-- Donor information for MiSeq classic is not recorded in current source pages. Please update if known. -->
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	== Element Biosciences ==		== Element Biosciences ==
	<span id="ELEMENT"></span>		<span id="ELEMENT"></span>

			The BioMicro Center operates an [https://www.elementbiosciences.com/products/aviti24 AVITI24] from Element Biosciences. The AVITI24 uses Element's proprietary [https://www.elementbiosciences.com/resources/avidity-sequencing Avidity Base Chemistry (ABC)], a 4-color sequencing approach that achieves high base-call accuracy (>80% of reads Q40+) by leveraging multivalent binding of avidites rather than single-nucleotide incorporation. The random flowcell and rolling-circle amplification approach produce low levels of index hopping and optical duplicates compared to patterned-flowcell instruments. Beyond standard NGS, the AVITI24 supports [https://www.elementbiosciences.com/products/aviti24/cytoprofiling Teton CytoProfiling] for direct in-cell co-detection of RNA, protein, and morphology — see [[BioMicroCenter:Spatial\|Spatial Services]] for details.

	=== AVITI24 ===		=== AVITI24 ===
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	\|}		\|}
	\|		\|
	~~=== ANCHORS ===~~
	Element supports both Illumina anchors (P5/P7) using Freestyle chemistry and Element anchors (SP5/SP27) for Adept chemistry. For standard runs at the BMC, P5/P7-anchored (Illumina) libraries are preferred. Element Adept libraries (SP5/SP27) require a 5′-phosphate on the forward end to circularize.<BR><BR>

	~~=== INDEXING ===~~		'''Kits and run times:'''
	~~Compared to Illumina, AVITI24 read direction is similar to Illumina~~'~~s Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers — P7 side first (index 1). Index sequences should be provided~~ ''~~'as read~~''', ~~not as ordered.<BR>~~		* 75 PE (150 nt total): ~24 hours, ~400M reads/lane
	* ~~Custom primer submission~~: ~~70 µL at 100 µM for Read 1; all other~~ reads ~~require 40 µL at 100 µM.~~		* 150 PE (300 nt total): ~38 hours, ~400M reads/lane
			* 300 PE (600 nt total): ~60 hours, ~200M reads (single lane only)

	~~=== SINGLE LANE ===~~		Each flowcell has two independently-addressable lanes. Both lanes must be loaded to run a flowcell, but each can carry a different library pool. 300PE kits are single-lane only.<BR><BR>
	Each ~~lane of the AVITI24 can be loaded~~ independently~~; both~~ lanes must be ~~filled~~ to run a flowcell. 300PE kits ~~support only a~~ single lane. ~~Custom primers must not interfere with other users' samples. All non-standard requests require a full flowcell.~~

	~~=== MINIMUM READ GUARANTEE ===~~		'''Anchors:''' The BMC runs P5/P7-anchored (Illumina Freestyle) libraries as standard. Element Adept (SP5/SP27) libraries are also supported but require a 5′-phosphate on the forward strand for circularization — contact [mailto:biomicro@mit.edu biomicro@mit.edu] before preparing Adept libraries.<BR><BR>
	Guaranteed if: (a) BMC performed QC, (b) library diversity is high (especially in the first 5 bases of Read 1), and (c) concentration ≥ 2 nM.
			'''Indexing:''' Index orientation differs from standard Illumina: indexes are read from antisense primers with the P7-side first (index 1). Provide index sequences '''as read''' on the instrument, not as ordered. For dual-indexed libraries this is typically antisense to the ordered oligo sequence.<BR><BR>

			'''Custom primers:''' 70 µL at 100 µM for Read 1; 40 µL at 100 µM for all other reads. Custom primers must not interfere with other users' samples in the same lane.<BR><BR>

			'''Minimum read guarantee:''' Guaranteed if (a) BMC performed QC, (b) library diversity is high especially in the first 5 bases of Read 1, and (c) concentration ≥ 2 nM.

	'''Thanks to:''' Element Biosciences; Scott Ritterbush		'''Thanks to:''' Element Biosciences; Scott Ritterbush
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	== Singular Genomics ==		== Singular Genomics ==
	<span id="SINGULAR"></span>		<span id="SINGULAR"></span>

			The BioMicro Center operates a [https://www.singulargenomics.com G4] from Singular Genomics. The G4 uses a 4-color SBS chemistry on a patterned flowcell and delivers index-hopping rates comparable to non-patterned Illumina instruments (HiSeq/GAIIx level) — substantially lower than X-Amp patterned flowcells. This makes it a practical choice for experiments that do not require UDIs. The G4 supports four independently-addressable lanes per flowcell and up to four flowcells per run, offering per-lane flexibility at competitive per-lane cost.

	=== G4 ===		=== G4 ===
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	\|}		\|}
	\|		\|
	~~=== LIBRARY SUBMISSION ===~~
	~~Submit standard Illumina (P5/P7) libraries. The BMC will convert the pool to S1/S2 anchors by PCR prior to sequencing — do '''not''' submit S1/S2-anchored libraries directly.<BR><BR>~~

	~~=== INDEXING ===~~		'''Kits and run times:'''
	~~Indexes are read from~~ the S1/S2 ~~anchor sequences after~~ conversion~~. Index 1 is~~ read from S1, index 2 ~~from S2. Index sequences are~~ the '''same orientation''' as ordered in classical Illumina library preps. Dual ~~indexes (~~8 nt) are required for all lane-by-lane sequencing. Custom index primers are not permitted.		* 50 PE (100 nt total): ~11 hours, ~100M reads/lane
			* 150 PE (300 nt total): ~24 hours, ~100M reads/lane

			'''Library submission:''' Submit standard Illumina (P5/P7) libraries. The BMC converts the pool to S1/S2 anchors by PCR prior to sequencing — do '''not''' submit S1/S2-anchored libraries directly.<BR><BR>

			'''Indexing:''' After conversion, indexes are read from S1 (index 1) then S2 (index 2), in the '''same orientation''' as ordered in classical Illumina library preps. Dual 8-nt indexes are required for all lane-by-lane sequencing. Custom index primers are not permitted.<BR><BR>

	~~=== LANE BY LANE ===~~		'''Lane by lane:'''
	* Must be 50 PE or 150 PE dual-indexed.		* Must be 50 PE or 150 PE dual-indexed.
	* Pool must be compatible with TruSeq, Nextera, smRNA, or Solexa sequencing primers.		* Pool must be compatible with TruSeq, Nextera, smRNA, or Solexa sequencing primers.
	* 4 lanes per flowcell; up to 4 flowcells per run.		* 4 lanes per flowcell; up to 4 flowcells per run.

	~~=== MINIMUM READ GUARANTEE ===~~		'''Minimum read guarantee:''' Guaranteed if (a) BMC performed QC, (b) no custom primers, and (c) concentration ≥ 4 nM.
	Guaranteed if: (a) BMC performed QC, (b) no custom primers, and (c) concentration ≥ 4 nM.

	'''Thanks to:''' Singular Genomics		'''Thanks to:''' Singular Genomics

Slevine: /* PLATFORM COMPARISON */

2026-04-20T23:54:21Z

PLATFORM COMPARISON

← Older revision		Revision as of 23:54, 20 April 2026
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	\| Patterned		\| Patterned
	\| Patterned (CMOS nanowell)		\| Patterned (CMOS nanowell)
	\| ~~Non-patterned (random cluster)~~		\| Random
	\|-		\|-
	\| '''Chemistry'''		\| '''Chemistry'''

Slevine: /* SUBMISSION */

2026-04-20T23:40:57Z

SUBMISSION

← Older revision		Revision as of 23:40, 20 April 2026
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	All sequencing is submitted through [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]. External users should contact [mailto:biomicro@mit.edu biomicro@mit.edu] directly. Samples must meet the minimum volume and concentration requirements listed above; coordinate with BMC staff before sending non-standard submissions.		All sequencing is submitted through [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]. External users should contact [mailto:biomicro@mit.edu biomicro@mit.edu] directly. Samples must meet the minimum volume and concentration requirements listed above; coordinate with BMC staff before sending non-standard submissions.

	~~Additional services:~~
	* [[BioMicroCenter:Illumina_Library_Preparation\|Short read library preparation]]
	* [[BioMicroCenter:BioInformaticsStaff\|Bioinformatics support]]
	* [[BioMicroCenter:Servers\|Data storage and computation]]
	* [[BioMicroCenter:Sequencing_Quality_Control\|Sequencing quality control]]

Slevine: /* FAQ */

2026-04-20T23:40:45Z

FAQ

@@ Line 344: / Line 344: @@
 == FAQ ==
 <span id="FAQ"></span>
 === My library has low complexity. Which platform should I use? ===
@@ Line 372: / Line 354: @@
 * '''Singular G4''' – Not required; patterned but does not use X-Amp chemistry; hopping is on par with HiSeq/GAIIx.
 * '''MiSeq classic''' – Not required; non-patterned flowcell has low hopping.
 === How long is my data stored? ===

Slevine: /* MiSeq classic */

2026-04-20T23:38:36Z

MiSeq classic

← Older revision		Revision as of 23:38, 20 April 2026
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	=== MiSeq classic ===		=== MiSeq classic ===

	The MiSeq classic uses 4-color SBS chemistry on a non-patterned (random cluster) flowcell. It is available for users with established protocols on v2/v3 chemistry~~, but is off contract and will be retired upon instrument failure~~.		The MiSeq classic uses 4-color SBS chemistry on a non-patterned (random cluster) flowcell. It is available for users with established protocols on v2/v3 chemistry. We maintain minimal reagent stocks so turn around times may vary.

	{\| class="wikitable" border=1		{\| class="wikitable" border=1
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	! Notes		! Notes
	\|-		\|-
	\| 70 nt (V2) \|\| ~5M \|\| 30 or 70 SE		\| 70 nt (V2) \|\| ~15M \|\| 30 or 70 SE
	\|-		\|-
	\| 150 nt (V3) \|\| ~5M \|\| 75 PE		\| 150 nt (V3) \|\| ~25M \|\| 75 PE
	\|-		\|-
	\| 300 nt (V2) \|\| ~5M \|\| 150 PE		\| 300 nt (V2) \|\| ~15M \|\| 150 PE
	\|-		\|-
	\| 500 nt (V2) \|\| ~~~10M~~ \|\| 250 PE		\| 500 nt (V2) \|\| ~15M \|\| 250 PE
	\|-		\|-
	\| 600 nt (V3) \|\| ~~~15M~~ \|\| 300 PE		\| 600 nt (V3) \|\| ~25M \|\| 300 PE
	\|-		\|-
	\| 500 nt NANO \|\| ~1M \|\| Reduced output run		\| 500 nt NANO \|\| ~1M \|\| Reduced output run

Slevine: /* NovaSeqX Plus */

2026-04-20T23:37:10Z

NovaSeqX Plus

← Older revision		Revision as of 23:37, 20 April 2026
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	=== NovaSeqX Plus ===		=== NovaSeqX Plus ===

	NovaSeqX Plus sequencing is available through BMC's collaboration with local academic core facilities, and is well suited to projects requiring the deepest coverage or largest sample counts.		NovaSeqX Plus sequencing is available through BMC's collaboration with local academic core facilities, and is well suited to projects requiring the deepest coverage or largest sample counts. It is only available for MIT users. These collaborations provide advantaged pricing to MIT users.

	* Contact [mailto:biomicro@mit.edu biomicro@mit.edu] to request access and discuss flowcell sharing.		* See [[MIT:Pricing\|Pricing]] for rates.
	* See [[MIT:Pricing~~]] or [[BioMicroCenter:~~Pricing]] for ~~current lane and flowcell pricing~~.
	* Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.		* Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.
	* Minimum 2 nM concentration; 110 µL per lane. BMC QC required for read guarantees.

	=== MiSeq i100 ===		=== MiSeq i100 ===

Slevine: /* OUTPUT TIERS */

2026-04-20T23:34:53Z

OUTPUT TIERS

← Older revision		Revision as of 23:34, 20 April 2026
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	\|-		\|-
	\| <!-- no image yet: replace with [[Image:filename.ext\|center\|120px]] --> <br> '''MiSeq classic'''		\| <!-- no image yet: replace with [[Image:filename.ext\|center\|120px]] --> <br> '''MiSeq classic'''
	\| 5M – 25M reads/flowcell		\| 1M – 25M reads/flowcell
	\| 40 µL at 2 nM		\| 40 µL at 2 nM
	\|-		\|-

Asoberan: Create consolidated short read sequencing page (Illumina, Element, Singular)

2026-04-20T23:28:44Z

Create consolidated short read sequencing page (Illumina, Element, Singular)

New page

{{BioMicroCenter}}

The MIT BioMicro Center offers short-read sequencing on five platforms from three manufacturers, spanning low to high output. All sequencing includes library quality control (RT-PCR and Fragment Analyzer), demultiplexing, and FASTQ delivery. Pricing is available to MIT users at [[MIT:Pricing]] and to all users at [[BioMicroCenter:Pricing]].

<div style="background:#f8f9fa; border:1px solid #ccc; padding:12px 16px; margin:12px 0;">
'''Choosing a platform?''' Jump to [[#PLATFORM_COMPARISON|platform comparison]] and [[#FAQ|FAQ]] below, or contact [mailto:biomicro@mit.edu biomicro@mit.edu].
</div>

== OUTPUT TIERS ==

{| class="wikitable" style="width:100%; text-align:center;"
|-
! style="width:8%; background:#dce8f5;" | OUTPUT
! style="width:18%; background:#dce8f5;" | PLATFORM
! style="width:22%; background:#dce8f5;" | READS / UNIT
! style="width:20%; background:#dce8f5;" | MIN SUBMISSION
! style="width:32%; background:#dce8f5;" | TYPICAL USE
|-
| style="background:#e8f0fe; font-weight:bold; vertical-align:middle;" rowspan="2" | HIGH
| [[Image:BMC_NovaXplus.jpg|center|120px]] '''NovaSeqX Plus'''
| 1.2B reads/lane (10B FC) 3.0B reads/lane (25B FC)
| 110 µL at 2 nM per lane
| rowspan="2" style="text-align:left; font-size:92%;" | Largest experiments requiring billions of reads: cohort-scale WGS, ultra-deep sequencing, high-replicate RNA-seq studies
|-
| colspan="3" style="font-size:90%; color:#555; text-align:left; padding:4px 10px;" | ''Available through collaboration with nearby academic shared resources. Contact [mailto:biomicro@mit.edu BMC staff] to inquire.''
|-
| style="background:#e6f4ea; font-weight:bold; vertical-align:middle;" | MID
| [[Image:Element_AVITI.jpg|center|120px]] '''Element AVITI24'''
| ~400M reads/lane (~800M per 2-lane flowcell)
| 15 µL at 2 nM
| style="text-align:left; font-size:92%;" | Standard depth experiments: RNA-seq, ChIP-seq, ATAC-seq, WGS at moderate coverage; tolerates low-complexity libraries well
|-
| style="background:#fff3e0; font-weight:bold; vertical-align:middle;" rowspan="4" | LOW
| [[Image:2023_Singular_G4.jpg|center|120px]] '''Singular G4'''
| ~100M reads/lane (4 lanes/flowcell)
| 12 µL at 4 nM
| rowspan="4" style="text-align:left; font-size:92%;" | Smaller experiments, amplicons, validation, pilot studies, and applications where cost-per-lane is the primary driver
|-
| [[Image:BMC_i100.jpg|center|120px]] '''MiSeq i100'''
| 5M – 100M reads/flowcell
| 40 µL at 2 nM
|-
|  '''MiSeq classic'''
| 5M – 25M reads/flowcell
| 40 µL at 2 nM
|-
| colspan="3" style="font-size:90%; color:#555; text-align:left; padding:4px 10px;" | ''MiSeq classic is off contract and will be retired upon instrument failure. MiSeq i100 offers walkup service (MIT only, training required).''
|}

== SEQUENCING PLATFORMS ==



== Illumina ==


=== NovaSeqX Plus ===

NovaSeqX Plus sequencing is available through BMC's collaboration with local academic core facilities, and is well suited to projects requiring the deepest coverage or largest sample counts.

* Contact [mailto:biomicro@mit.edu biomicro@mit.edu] to request access and discuss flowcell sharing.
* See [[MIT:Pricing]] or [[BioMicroCenter:Pricing]] for current lane and flowcell pricing.
* Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.
* Minimum 2 nM concentration; 110 µL per lane. BMC QC required for read guarantees.

=== MiSeq i100 ===

{|
|- style="vertical-align:top;"
| style="width:370px;" |
{| class="wikitable" border=1
! Service
! MiSeq i100 Sequencing
|-
| INPUT || Illumina libraries
|-
| MIN VOLUME || 40 µL
|-
| MIN CONCENTRATION || 2 nM (~0.4 ng/µL for 300 bp library)
|-
| INCLUDED SERVICES
|
* Quality Control: Fragment Analyzer and qPCR
* Illumina Sequencing
* Demultiplexing
|-
| DATA FORMATS
|
* FASTQ
* BCL (stored 30 days)
|-
| PRICING || [[MIT:Pricing]] · [[BioMicroCenter:Pricing]]
|-
| SUBMISSION
|
* MIT (Assisted) – [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]
* MIT (Walkup) – [https://mit.ilabsolutions.com/schedules/555535#/schedule/ iLabs calendar] (training required)
|-
|}
|

The MiSeq i100 uses Illumina's XLEAP-SBS chemistry on a patterned (CMOS nanowell) flowcell. It is the BMC's walkup-capable instrument, suited to amplicon panels, 16S rRNA surveys, validation runs, and applications requiring long reads (up to 1000 nt).

'''Kits available:''' 100 nt (25M, 100M), 300 nt (5M, 25M, 100M), 600 nt (5M, 25M, 50M), 1000 nt (25M). 

'''Walkup service''' is not available to external users. Runs must be scheduled in the [https://mit.ilabsolutions.com/schedules/555535#/schedule/ iLabs calendar].

'''Thanks to:''' MIT VPR, Drs. Gene Li, Michael Birnbaum, Dept. of Biology, Scott Ritterbush '89 SM '92
|}

=== MiSeq classic ===

The MiSeq classic uses 4-color SBS chemistry on a non-patterned (random cluster) flowcell. It is available for users with established protocols on v2/v3 chemistry, but is off contract and will be retired upon instrument failure.

{| class="wikitable" border=1
! Kit
! Approx. reads
! Notes
|-
| 70 nt (V2) || ~5M || 30 or 70 SE
|-
| 150 nt (V3) || ~5M || 75 PE
|-
| 300 nt (V2) || ~5M || 150 PE
|-
| 500 nt (V2) || ~10M || 250 PE
|-
| 600 nt (V3) || ~15M || 300 PE
|-
| 500 nt NANO || ~1M || Reduced output run
|}

See [[MIT:Pricing]] · [[BioMicroCenter:Pricing]] for kit pricing.





== Element Biosciences ==


=== AVITI24 ===

{|
|- style="vertical-align:top;"
| style="width:370px;" |
{| class="wikitable" border=1
! Service
! Element Sequencing
|-
| SUBMISSION || Illumina (P5/P7) libraries
|-
| MIN VOLUME || 15 µL
|-
| MIN CONCENTRATION || 2 nM
|-
| INCLUDED SERVICES
|
* Quality Control: Fragment Analyzer and qPCR
* Element Sequencing
* Demultiplexing
|-
| ADDITIONAL SERVICES ||
* Quality Control
* Element library preparation
|-
| DATA FORMATS
|
* FASTQ (stored 1 year)
|-
| QUALITY CONTROL
|
* [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FASTQC]
* Basic run metrics (alignment rate, complexity)
* Basic RNAseq metrics (where applicable)
* Basic paired end metrics (where applicable)
* Contamination checks
|-
| PRICING || [[MIT:Pricing]] · [[BioMicroCenter:Pricing]]
|-
| SUBMISSION
|
* MIT – [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]
|-
|}
|
=== ANCHORS ===
Element supports both Illumina anchors (P5/P7) using Freestyle chemistry and Element anchors (SP5/SP27) for Adept chemistry. For standard runs at the BMC, P5/P7-anchored (Illumina) libraries are preferred. Element Adept libraries (SP5/SP27) require a 5′-phosphate on the forward end to circularize. 

=== INDEXING ===
Compared to Illumina, AVITI24 read direction is similar to Illumina's Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers — P7 side first (index 1). Index sequences should be provided '''as read''', not as ordered. 
* Custom primer submission: 70 µL at 100 µM for Read 1; all other reads require 40 µL at 100 µM.

=== SINGLE LANE ===
Each lane of the AVITI24 can be loaded independently; both lanes must be filled to run a flowcell. 300PE kits support only a single lane. Custom primers must not interfere with other users' samples. All non-standard requests require a full flowcell.

=== MINIMUM READ GUARANTEE ===
Guaranteed if: (a) BMC performed QC, (b) library diversity is high (especially in the first 5 bases of Read 1), and (c) concentration ≥ 2 nM.

'''Thanks to:''' Element Biosciences; Scott Ritterbush
|}



== Singular Genomics ==


=== G4 ===

{|
|- style="vertical-align:top;"
| style="width:370px;" |
{| class="wikitable" border=1
! Service
! Singular G4 Sequencing
|-
| INPUT || Illumina (P5/P7) libraries
|-
| MIN VOLUME || 12 µL
|-
| MIN CONCENTRATION || 4 nM
|-
| INCLUDED SERVICES
|
* Quality Control: Fragment Analyzer and qPCR
* Pool conversion: P5/P7 → S1/S2 by PCR
* Singular Sequencing
* Demultiplexing
|-
| ADDITIONAL SERVICES ||
* Quality Control
* Singular library preparation
|-
| DATA FORMATS
|
* FASTQ (stored 1 year)
|-
| QUALITY CONTROL
|
* [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FASTQC]
* Basic run metrics (alignment rate, complexity)
* Basic RNAseq metrics (where applicable)
* Contamination checks
|-
| PRICING || [[MIT:Pricing]] · [[BioMicroCenter:Pricing]]
|-
| SUBMISSION
|
* MIT – [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]
|-
|}
|
=== LIBRARY SUBMISSION ===
Submit standard Illumina (P5/P7) libraries. The BMC will convert the pool to S1/S2 anchors by PCR prior to sequencing — do '''not''' submit S1/S2-anchored libraries directly. 

=== INDEXING ===
Indexes are read from the S1/S2 anchor sequences after conversion. Index 1 is read from S1, index 2 from S2. Index sequences are the '''same orientation''' as ordered in classical Illumina library preps. Dual indexes (8 nt) are required for all lane-by-lane sequencing. Custom index primers are not permitted.

=== LANE BY LANE ===
* Must be 50 PE or 150 PE dual-indexed.
* Pool must be compatible with TruSeq, Nextera, smRNA, or Solexa sequencing primers.
* 4 lanes per flowcell; up to 4 flowcells per run.

=== MINIMUM READ GUARANTEE ===
Guaranteed if: (a) BMC performed QC, (b) no custom primers, and (c) concentration ≥ 4 nM.

'''Thanks to:''' Singular Genomics
|}

== PLATFORM COMPARISON ==


{| class="wikitable" style="width:100%; text-align:center;"
|-
! style="background:#dce8f5;" | SPEC
! style="background:#e8f0fe;" | NovaSeqX Plus
! style="background:#e6f4ea;" | Element AVITI24
! style="background:#fff3e0;" | Singular G4
! style="background:#fff3e0;" | MiSeq i100
! style="background:#fff3e0;" | MiSeq classic
|-
| '''Read lengths'''
| 100 nt, 300 nt
| 75 PE, 150 PE, 300 PE
| 50 PE, 150 PE
| 100–1000 nt
| 70–600 nt
|-
| '''Flowcell type'''
| Patterned (X-Amp)
| Random
| Patterned
| Patterned (CMOS nanowell)
| Non-patterned (random cluster)
|-
| '''Chemistry'''
| 2-color XLEAP-SBS (G=dark)
| 4-color avidity SBS
| 4-color SBS
| 2-color XLEAP-SBS (G=dark)
| 4-color SBS
|-
| '''Index hopping'''
| High — UDIs required
| Low — UDIs not needed
| Low (patterned, non-XLEAP)
| Present — UDIs recommended
| Low (non-patterned)
|-
| '''Low-complexity libraries'''
| Struggles
| Handles well
| Handles well
| Struggles
| Handles well
|-
| '''Lane flexibility'''
| Lane-by-lane (full FC priority)
| Lane-by-lane
| Lane-by-lane
| Full flowcell only
| Full flowcell only
|-
| '''Walkup'''
| No (collaboration)
| No
| No
| Yes (training required)
| No
|-
| '''Illumina lib compatible'''
| Yes (native)
| Yes (P5/P7 Freestyle)
| Yes — BMC converts pool by PCR
| Yes (native)
| Yes (native)
|-
| '''Donated / supported by'''
| Local core collaboration
| Element Biosciences; Scott Ritterbush
| Singular Genomics
| MIT VPR; Drs. Gene Li, Michael Birnbaum; Dept. of Biology; Scott Ritterbush '89 SM '92
| 
|}

== FAQ ==


=== How do I choose the right platform? ===
Start with your '''read count requirement''' and '''library type''':
* '''Millions of reads or fewer''' → MiSeq i100 (amplicons, long reads up to 1000 nt) or Singular G4 (most cost-effective for standard 50/150 PE).
* '''Hundreds of millions of reads''' → Element AVITI24 (lane-by-lane flexibility, low index hopping, tolerates low-complexity libraries).
* '''Billions of reads''' → NovaSeqX Plus (contact BMC to coordinate flowcell sharing).

=== Can I use my existing Illumina libraries? ===
* '''AVITI24''' – Yes. P5/P7 libraries run natively using Freestyle chemistry.
* '''MiSeq i100 / classic''' – Yes. Standard Illumina libraries run natively.
* '''Singular G4''' – Yes. Submit standard P5/P7 libraries; the BMC converts the pool to S1/S2 anchors by PCR. Do not submit S1/S2 libraries directly.
* '''NovaSeqX Plus''' – Yes. Standard Illumina libraries run natively.

=== What are the minimum submission requirements? ===
* AVITI24: 15 µL at 2 nM
* MiSeq i100 / classic: 40 µL at 2 nM
* Singular G4: 12 µL at 4 nM
* NovaSeqX Plus: 110 µL per lane at 2 nM (contact BMC)

=== My library has low complexity. Which platform should I use? ===
Avoid the NovaSeqX Plus and MiSeq i100 — both use 2-color XLEAP-SBS chemistry where G bases are inferred from signal absence, making low-diversity early cycles prone to run failure. The AVITI24, Singular G4, and MiSeq classic all use 4-color chemistry and handle low-complexity libraries well. Always contact [mailto:biomicro@mit.edu biomicro@mit.edu] before submitting unconventional libraries.

=== Do I need unique dual indexes (UDIs)? ===
* '''NovaSeqX Plus''' – Yes, required (patterned X-Amp flowcell).
* '''MiSeq i100''' – Recommended (patterned CMOS flowcell).
* '''AVITI24''' – Not required; index hopping is low on random flowcells.
* '''Singular G4''' – Not required; patterned but does not use X-Amp chemistry; hopping is on par with HiSeq/GAIIx.
* '''MiSeq classic''' – Not required; non-patterned flowcell has low hopping.

=== How long until my data is delivered? ===
Queue times are typically short — most samples run within a few days. Full flowcells have sequencing priority over individual lanes. Contact [mailto:biomicro@mit.edu biomicro@mit.edu] for current wait times.

=== How long is my data stored? ===
* FASTQ files: 1 year for AVITI24, Singular G4, MiSeq i100.
* BCL files (MiSeq): 30 days.
* Long-term storage is available; see [[BioMicroCenter:Pricing]] for active storage and tape archive options.

=== What quality control is included? ===
All runs include a final pool QC (RT-PCR and Fragment Analyzer) and post-sequencing QC (FastQC, run metrics, alignment rate, complexity, RNAseq metrics where applicable, contamination checks). Users who opt out of pre-sequencing QC by providing their own concentration forfeit read guarantees.

=== Can I pool samples from multiple labs? ===
Yes, but users are responsible for minimizing index cross-contamination and [https://www.illumina.com/science/education/minimizing-index-hopping.html index crosstalk]. The BMC does not combine projects within a lane.

== SUBMISSION ==

All sequencing is submitted through [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 iLabs]. External users should contact [mailto:biomicro@mit.edu biomicro@mit.edu] directly. Samples must meet the minimum volume and concentration requirements listed above; coordinate with BMC staff before sending non-standard submissions.

Additional services:
* [[BioMicroCenter:Illumina_Library_Preparation|Short read library preparation]]
* [[BioMicroCenter:BioInformaticsStaff|Bioinformatics support]]
* [[BioMicroCenter:Servers|Data storage and computation]]
* [[BioMicroCenter:Sequencing_Quality_Control|Sequencing quality control]]