BioMicroCenter:DNA HTL - Revision history

Hilo1: /* Nextera Flex */

2026-04-30T18:49:13Z

Nextera Flex

← Older revision		Revision as of 18:49, 30 April 2026
Line 91:		Line 91:
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* Nextera Flex */

2026-04-30T18:48:52Z

Nextera Flex

← Older revision		Revision as of 18:48, 30 April 2026
Line 89:		Line 89:
	\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)		\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
	\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL\|1st quadrant]] of 384-well hard-shell plate (BioRad)		\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL\|1st quadrant]] of 384-well hard-shell plate (BioRad)
	\|-
	~~\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS~~
	~~\| colspan="2" style="text-align: center; height: 2em;" \| All platforms except 40SE HiSeq~~
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY

Hilo1: /* 16S / AMPLICON SEQUENCING */

2026-04-30T18:48:12Z

16S / AMPLICON SEQUENCING

← Older revision		Revision as of 18:48, 30 April 2026
Line 200:		Line 200:
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| style="text-align: center; height: 2em;" \| ~~16 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 96~~ [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* Nextera XT */

2026-04-30T18:47:41Z

Nextera XT

← Older revision		Revision as of 18:47, 30 April 2026
Line 145:		Line 145:
	\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)		\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
	\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL#Quadrant_Layout\|1st quadrant]] of a 384-well LVSD plate (Available at BMC)		\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL#Quadrant_Layout\|1st quadrant]] of a 384-well LVSD plate (Available at BMC)
	\|-
	~~\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS~~
	~~\| colspan="2" style="text-align: center; height: 2em;" \| 40SE HiSeq~~
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY

Hilo1: /* Nextera XT */

2026-04-30T18:47:21Z

Nextera XT

← Older revision		Revision as of 18:47, 30 April 2026
Line 150:		Line 150:
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| colspan="2" style="text-align: center; height: 2em;" \| 16 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* Nextera Flex */

2026-04-30T18:46:44Z

Nextera Flex

← Older revision		Revision as of 18:46, 30 April 2026
Line 94:		Line 94:
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]] ~~''not available''~~		\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* NEB Ultra II */

2026-04-30T18:46:25Z

NEB Ultra II

← Older revision		Revision as of 18:46, 30 April 2026
Line 38:		Line 38:
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| colspan="2" style="text-align: center; height: 2em;" \|~~112~~ [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> ~~192~~ [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \|384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:DNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* 16S / AMPLICON SEQUENCING */

2025-06-09T19:14:56Z

16S / AMPLICON SEQUENCING

← Older revision		Revision as of 19:14, 9 June 2025
Line 219:		Line 219:
	\|		\|
	<br>		<br>
	[[image:16S_layout.jpg\|thumb\|200px\|~~(Lopez-Aladid et al Sci. Rep. 2023)~~ 16S v4 region is amplified in standard BioMicro Center preps. Other regions can be substituted by submitting oligos with different variable regions]]		[[image:16S_layout.jpg\|thumb\|200px\|16S v4 region is amplified in standard BioMicro Center preps. Other regions can be substituted by submitting oligos with different variable regions. (Lopez-Aladid et al Sci. Rep. 2023)]]
	:The BioMicro Center offers 16S and amplicon sequencing for metagenomics projects. Derived from the [http://be.mit.edu/directory/eric-alm Alm Lab] with support from a pilot grant from [http://cehs.mit.edu/ MIT CEHS], our protocol uses a two step amplification to first expand the 16S population and add defined 3' and 5' sequences which are then used to add Illumina anchors and sequences. This two step method allows easy multiplexing and the ability change the amplicon insert sequence at minimal cost.		:The BioMicro Center offers 16S and amplicon sequencing for metagenomics projects. Derived from the [http://be.mit.edu/directory/eric-alm Alm Lab] with support from a pilot grant from [http://cehs.mit.edu/ MIT CEHS], our protocol uses a two step amplification to first expand the 16S population and add defined 3' and 5' sequences which are then used to add Illumina anchors and sequences. This two step method allows easy multiplexing and the ability change the amplicon insert sequence at minimal cost.
	[[image:16S_diagram.jpg\|thumb\|400px\|Standard NGS amplicon design]]		[[image:16S_diagram.jpg\|thumb\|400px\|Standard NGS amplicon design]]

172.18.0.1: /* Nextera Flex */

2025-05-02T14:55:40Z

Nextera Flex

← Older revision		Revision as of 14:55, 2 May 2025
Line 111:		Line 111:
	\|		\|
	<br>		<br>
	:Unlike XT, Nextera Flex utilizes bead-linked transposomes (BLT) to tagment and generate libraries from intact DNA samples. These BLTs control sizing during the tagmentation reaction by sterics, producing a much more consistent libraries with larger size distribution which makes it ideal for larger paired-end runs on sequencers.		:Unlike XT, Nextera Flex, also known as Illumina DNA Prep, utilizes bead-linked transposomes (BLT) to tagment and generate libraries from intact DNA samples. These BLTs control sizing during the tagmentation reaction by sterics, producing a much more consistent libraries with larger size distribution which makes it ideal for larger paired-end runs on sequencers.
	:Nextera Flex is currently run at a 1/10th miniaturization scale on the Mosquito HV with a broader dynamic range of input (1ng - 50ng) compared to XT. Nextera Flex self-normalizes at a certain input (if sample concentration is 3ng/µL or greater) and submissions do not have to be normalized so long as that threshold is met. Up to 384 libraries can be multiplexed using Nextera unique dual-indexes (UDI) which helps to avoid issues with 'barcode hopping'.		:Nextera Flex is currently run at a 1/10th miniaturization scale on the Mosquito HV with a broader dynamic range of input (1ng - 50ng) compared to XT. Nextera Flex self-normalizes at a certain input (if sample concentration is 3ng/µL or greater) and submissions do not have to be normalized so long as that threshold is met. Up to 384 libraries can be multiplexed using Nextera unique dual-indexes (UDI) which helps to avoid issues with 'barcode hopping'.
	::::[[IMAGE:Flex_Diagram.jpg \| 500px]]		::::[[IMAGE:Flex_Diagram.jpg \| 500px]]

Hilo1: /* 16S / AMPLICON SEQUENCING */

2025-04-30T12:45:24Z

16S / AMPLICON SEQUENCING

← Older revision		Revision as of 12:45, 30 April 2025
Line 221:		Line 221:
	[[image:16S_layout.jpg\|thumb\|200px\|(Lopez-Aladid et al Sci. Rep. 2023) 16S v4 region is amplified in standard BioMicro Center preps. Other regions can be substituted by submitting oligos with different variable regions]]		[[image:16S_layout.jpg\|thumb\|200px\|(Lopez-Aladid et al Sci. Rep. 2023) 16S v4 region is amplified in standard BioMicro Center preps. Other regions can be substituted by submitting oligos with different variable regions]]
	:The BioMicro Center offers 16S and amplicon sequencing for metagenomics projects. Derived from the [http://be.mit.edu/directory/eric-alm Alm Lab] with support from a pilot grant from [http://cehs.mit.edu/ MIT CEHS], our protocol uses a two step amplification to first expand the 16S population and add defined 3' and 5' sequences which are then used to add Illumina anchors and sequences. This two step method allows easy multiplexing and the ability change the amplicon insert sequence at minimal cost.		:The BioMicro Center offers 16S and amplicon sequencing for metagenomics projects. Derived from the [http://be.mit.edu/directory/eric-alm Alm Lab] with support from a pilot grant from [http://cehs.mit.edu/ MIT CEHS], our protocol uses a two step amplification to first expand the 16S population and add defined 3' and 5' sequences which are then used to add Illumina anchors and sequences. This two step method allows easy multiplexing and the ability change the amplicon insert sequence at minimal cost.
	[[image:16S_diagram.jpg\|thumb\|400px]]		[[image:16S_diagram.jpg\|thumb\|400px\|Standard NGS amplicon design]]
	:The same method used for 16S is also applicable to other amplicons as well with minor adaption. Because we use a nested PCR, only the internal sequences need to be modified. The adapter sequences - Green:Blue - are the key element of this method. On the 5' end, they contain a "YRYR" sequence that introduces the complexity required for Illumina sequencing.		:The same method used for 16S is also applicable to other amplicons as well with minor adaption. Because we use a nested PCR, only the internal sequences need to be modified. The adapter sequences - Green:Blue - are the key element of this method. On the 5' end, they contain a "YRYR" sequence that introduces the complexity required for Illumina sequencing.
	<br>		<br>

← Older revision		Revision as of 18:48, 30 April 2026
Line 89:		Line 89:
	\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)		\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
	\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL\|1st quadrant]] of 384-well hard-shell plate (BioRad)		\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL\|1st quadrant]] of 384-well hard-shell plate (BioRad)
	\|-
	~~\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS~~
	~~\| colspan="2" style="text-align: center; height: 2em;" \| All platforms except 40SE HiSeq~~
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY

← Older revision		Revision as of 18:47, 30 April 2026
Line 145:		Line 145:
	\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)		\| style="text-align: center; height: 2em;" \| Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
	\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL#Quadrant_Layout\|1st quadrant]] of a 384-well LVSD plate (Available at BMC)		\| style="text-align: center; height: 2em;" \| Samples arrayed by column in [[BioMicroCenter:DNA_HTL#Quadrant_Layout\|1st quadrant]] of a 384-well LVSD plate (Available at BMC)
	\|-
	~~\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS~~
	~~\| colspan="2" style="text-align: center; height: 2em;" \| 40SE HiSeq~~
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY