BioMicroCenter:RNA HTL - Revision history

Hilo1: /* 3'Digital Gene Expression */

2026-05-01T18:49:23Z

3'Digital Gene Expression

← Older revision		Revision as of 18:49, 1 May 2026
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	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY
	\| colspan="2" style="text-align: center; height: 2em;" \|24 ~~COMBINATORIAL~~ [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|~~Unique Dual Indexes~~]]		\| colspan="2" style="text-align: center; height: 2em;" \|24 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|COMBINATORIAL]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* 3'Digital Gene Expression */

2026-05-01T18:48:55Z

3'Digital Gene Expression

← Older revision		Revision as of 18:48, 1 May 2026
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	\| 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:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique ~~Dual Indexes]] <br> 96 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial~~ Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \|24 COMBINATORIAL [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* 3'Digital Gene Expression */

2026-04-30T18:52:42Z

3'Digital Gene Expression

← Older revision		Revision as of 18:52, 30 April 2026
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	\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS		\| style="text-align: center; height: 2em;" \| SEQUENCING RECOMMENDATIONS
	\| colspan="2" style="text-align: center; height: 2em;" \| ~~NextSeq~~		\| colspan="2" style="text-align: center; height: 2em;" \| Element single lane per 96
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY		\| style="text-align: center; height: 2em;" \| INDEX AVAILABILITY

Hilo1: /* ZapR */

2026-04-30T18:52:16Z

ZapR

← Older revision		Revision as of 18:52, 30 April 2026
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	\| 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:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \| 384 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* ZapR */

2026-04-30T18:52:05Z

ZapR

← Older revision		Revision as of 18:52, 30 April 2026
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	\|-		\|-
	\| 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:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique ~~Dual Indexes]] <br> 96 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial~~ Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \| 384[[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* NEB Ultra II Directional RNA with rRNA Depletion */

2026-04-30T18:50:45Z

NEB Ultra II Directional RNA with rRNA Depletion

← Older revision		Revision as of 18:50, 30 April 2026
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	\| 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:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> ~~192~~ [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \|384 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:RNA_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 Directional RNA with Poly(A) Selection */

2026-04-30T18:50:15Z

NEB Ultra II Directional RNA with Poly(A) Selection

← Older revision		Revision as of 18:50, 30 April 2026
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	\|-		\|-
	\| 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:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> ~~192~~ [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]		\| colspan="2" style="text-align: center; height: 2em;" \|384 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Unique Dual Indexes]] <br> 384 [[BioMicroCenter:RNA_HTL#Unique_versus_Combinatorial_Dual_Indexing\|Combinatorial Dual Indexes]]
	\|-		\|-
	\| style="text-align: center; height: 2em;" \| INCLUDED		\| style="text-align: center; height: 2em;" \| INCLUDED

Hilo1: /* 3'Digital Gene Expression */

2025-06-09T19:26:10Z

3'Digital Gene Expression

← Older revision		Revision as of 19:26, 9 June 2025
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	:Analysis of HT3DGE is not a standard method supported by most open source platforms. We have built pipelines to work with this data, but working closely with the Bioinformatics team is highly recommended.		:Analysis of HT3DGE is not a standard method supported by most open source platforms. We have built pipelines to work with this data, but working closely with the Bioinformatics team is highly recommended.
	\|<br>[[image:DGE_workflow.jpg\|right\|Standard 3'DGE workflow.]]		\|<br>[[image:DGE_workflow.jpg\|right\|Standard 3'DGE workflow.]] <br><br>
	[[image:HT3DGE_gene_example.jpg\|right\|Example 3'DGE Data]]<BR><BR>		[[image:HT3DGE_gene_example.jpg\|right\|Example 3'DGE Data]]<BR><BR>
	\|		\|

Hilo1: /* 3'Digital Gene Expression */

2025-06-09T19:25:52Z

3'Digital Gene Expression

← Older revision		Revision as of 19:25, 9 June 2025
Line 283:		Line 283:

	:Analysis of HT3DGE is not a standard method supported by most open source platforms. We have built pipelines to work with this data, but working closely with the Bioinformatics team is highly recommended.		:Analysis of HT3DGE is not a standard method supported by most open source platforms. We have built pipelines to work with this data, but working closely with the Bioinformatics team is highly recommended.
	\|<br>[[image:DGE_workflow.jpg~~\|thumb~~\|right~~\|275px~~\|Standard 3'DGE workflow.]]		\|<br>[[image:DGE_workflow.jpg\|right\|Standard 3'DGE workflow.]]
	[[image:HT3DGE_gene_example.jpg~~\|thumb~~\|right~~\|400px~~\|Example 3'DGE Data]]<BR><BR>		[[image:HT3DGE_gene_example.jpg\|right\|Example 3'DGE Data]]<BR><BR>
	\|		\|
	\|}		\|}

Hilo1: /* High-throughput RNA Library Preparation */

2025-06-09T19:25:10Z

High-throughput RNA Library Preparation

← Older revision		Revision as of 19:25, 9 June 2025
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	{{BioMicroCenter}}		{{BioMicroCenter}}
	= High-throughput RNA Library Preparation =		= High-throughput RNA Library Preparation =
	The BioMicro Center offers high-throuhgput RNA library preparation [[BioMicroCenter:FAQ#STANDARD_versus_HIGH_THROUGHPUT_LIBRARY_PREPARATION\|(HTL-RNA)]] for both standard input and low input samples. Together, these high-throughput methodologies provide a comprehensive set of options to address a diverse range of experiments investigating RNA biology. High-throughput library generation focuses on reducing price and processing time on a per sample basis. To do this, there are several key differences from our standard library preparation service. First, HTL-RNA services have set batch sizes (24 and 96) with fixed price points (i.e. charge for 16 samples will be the as 24 samples; similarly for 80 samples as 96). If under these batch sizes, DO MORE REPLICATES to simultaneously enhance experimental power and reduce price per sample. Some samples may fail and the cost of re-prepping those samples is NOT included in the quoted cost. Re-prep is only deemed necessary by the core where we have found evidence of a reagent failure. User request re-preps of individuals samples can be done by hand, but at a higher rate. HTL focuses on reducing price and processing time per sample, so some routine services provided with standard library preparation - such as initial and final quality control for all samples, sample arraying, or automatic re-prep of failed samples - are not built in. These services are available as add ons to the original service request. <br><br>

	[[Image:DE_HTL_RNA.jpeg\|thumb\|right\|400px\|Increased biological replicates increases power of analysis. (Liu et al. 2014 Bioinformatics 30(3): 301-4)]]		[[Image:DE_HTL_RNA.jpeg\|thumb\|right\|400px\|Increased biological replicates increases the power of analysis. (Liu et al. 2014 Bioinformatics 30(3): 301-4)]]

			The BioMicro Center offers high-throughput RNA library preparation [[BioMicroCenter:FAQ#STANDARD_versus_HIGH_THROUGHPUT_LIBRARY_PREPARATION\|(HTL-RNA)]] for both standard input and low input samples. Together, these high-throughput methodologies provide a comprehensive set of options to address a diverse range of experiments investigating RNA biology. High-throughput library generation focuses on reducing price and processing time on a per sample basis. To do this, there are several key differences from our standard library preparation service. First, HTL-RNA services have set batch sizes (24 and 96) with fixed price points (i.e. charge for 16 samples will be the as 24 samples; similarly for 80 samples as 96). If under these batch sizes, DO MORE REPLICATES to simultaneously enhance experimental power and reduce price per sample. Some samples may fail and the cost of re-prepping those samples is NOT included in the quoted cost. Re-prep is only deemed necessary by the core where we have found evidence of a reagent failure. User request re-preps of individuals samples can be done by hand, but at a higher rate. HTL focuses on reducing price and processing time per sample, so some routine services provided with standard library preparation - such as initial and final quality control for all samples, sample arraying, or automatic re-prep of failed samples - are not built in. These services are available as add ons to the original service request. <br><br>

	<b>Reminder: </b> high throughput projects are treated with <b>one condition</b> (PCR cycles, fragmentation time, etc...). They are meant for allowing high replicates of the same samples. High throughput submissions for projects with multiple sub-projects from separate individuals combined on the same plate result in a low success rate due to the different conditions for each sub project. Therefore, htl submissions from multiple projects will tolerate and may expect, failure rates well over 10%.		<b>Reminder: </b> high throughput projects are treated with <b>one condition</b> (PCR cycles, fragmentation time, etc...). They are meant for allowing high replicates of the same samples. High throughput submissions for projects with multiple sub-projects from separate individuals combined on the same plate result in a low success rate due to the different conditions for each sub project. Therefore, htl submissions from multiple projects will tolerate and may expect, failure rates well over 10%.