SingleCell - Revision history

Sgupta at 13:00, 18 December 2025

2025-12-18T13:00:30Z

Sgupta at 19:39, 21 January 2023

2023-01-21T19:39:29Z

Sgupta at 19:39, 21 January 2023

2023-01-21T19:39:11Z

Sgupta at 19:38, 21 January 2023

2023-01-21T19:38:43Z

Sgupta at 16:20, 5 February 2020

2020-02-05T16:20:30Z

Sgupta at 16:18, 5 February 2020

2020-02-05T16:18:05Z

Sgupta at 16:16, 5 February 2020

2020-02-05T16:16:42Z

Sgupta at 16:14, 5 February 2020

2020-02-05T16:14:01Z

Sgupta at 15:53, 5 February 2020

2020-02-05T15:53:16Z

Sgupta at 15:52, 5 February 2020

2020-02-05T15:52:25Z

← Older revision		Revision as of 13:00, 18 December 2025
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	Please refer to our FAQ section for commonly asked questions: http://genomecore.wi.mit.edu/index.php/Faq#10X_Single_Cell_RNA		Please refer to our FAQ section for commonly asked questions: http://genomecore.wi.mit.edu/index.php/Faq#10X_Single_Cell_RNA

−	Please review the 10X ~~FAQ on Single Cell Seq~~: https://kb.10xgenomics.com/~~hc/en-us/categories/201931746-General-Single-Cell-RNA-seq~~	+	Please review the 10X Support Hub: https://www.10xgenomics.com/support

← Older revision		Revision as of 19:39, 21 January 2023
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−	We offer two types of single-cell sequencing: ~~SMART-Seq2~~, and 10X Genomics.	+	We offer two types of single-cell sequencing: plexWell Rapid, and 10X Genomics.

	= 10X Genomics =		= 10X Genomics =

← Older revision		Revision as of 19:39, 21 January 2023
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−	= ~~SMART-Seq2~~ =	+	= plexWell Rapid =
	''Scale – up to 96 cells per plate/library''		''Scale – up to 96 cells per plate/library''

@@ Line 26: / Line 26: @@
 ''Output – Counts - Multiple reads across full length of the molecule''
-SMART-Seq2 is based on a paper published in Nature Protocols (Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, 9, no 1, (2014)). The protocol is derived from the Takara Bio “SMARTer” method, which uses a template switching oligo during RT to generate long, double stranded cDNA fragments from plates containing sorted cells, with one cell per well. This cDNA is then modified using Illumina Nextera XT technology, which uses a transposase to fragment the cDNA and ligate adapters for barcoding and amplification. The resulting single-cell libraries are typically pooled (96 to a pool) for Illumina sequencing, resulting in one final library sample per plate of cells.
+PlexWell Rapid Single Cell RNA Library Prep Kits enable the construction of 96 or 384 transcriptome libraries from single cells, or from 2-10 ng of purified, total RNA. PlexWell generates 96 individually barcoded cDNAs via transposase reactions, and then collapses them into a single, multiplexed library using universal primers. The 384 sample kit comes in versions A, B, & C to allow users to multi-plex up to 1152 samples, if required. The resulting single-cell libraries are typically pooled (96 to a pool) for Illumina sequencing, resulting in one final library sample per plate of cells.
 The user should submit sorted cells in Eppendorf Twin-Tec plates, resuspended in a specific lysis buffer and frozen at -80ºC. Detailed instructions are available from the Genome Core. These plates are fairly stable, so the sorting does not need to be coordinated with the Genome Core prior to submission.

@@ Line 24: / Line 24: @@
 ''Input – sorted cells in lysis buffer, frozen after lysis''
-''Output – Counts - Reads across full length of the molecule''
+''Output – Counts - Multiple reads across full length of the molecule''
 SMART-Seq2 is based on a paper published in Nature Protocols (Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, 9, no 1, (2014)). The protocol is derived from the Takara Bio “SMARTer” method, which uses a template switching oligo during RT to generate long, double stranded cDNA fragments from plates containing sorted cells, with one cell per well. This cDNA is then modified using Illumina Nextera XT technology, which uses a transposase to fragment the cDNA and ligate adapters for barcoding and amplification. The resulting single-cell libraries are typically pooled (96 to a pool) for Illumina sequencing, resulting in one final library sample per plate of cells.
 The user should submit sorted cells in Eppendorf Twin-Tec plates, resuspended in a specific lysis buffer and frozen at -80ºC. Detailed instructions are available from the Genome Core. These plates are fairly stable, so the sorting does not need to be coordinated with the Genome Core prior to submission.

@@ Line 6: / Line 6: @@
 ''Input – fresh cultures < ~30 minutes old''
-''Output – Counts - one read per RNA molecule''
+''Output – Counts - one read (close to the polyA tail) per RNA molecule''
 https://www.10xgenomics.com/single-cell/
@@ Line 24: / Line 24: @@
 ''Input – sorted cells in lysis buffer, frozen after lysis''
-''Output – Counts - one read per RNA molecule''
+''Output – Counts - Reads across full length of the molecule''
 SMART-Seq2 is based on a paper published in Nature Protocols (Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, 9, no 1, (2014)). The protocol is derived from the Takara Bio “SMARTer” method, which uses a template switching oligo during RT to generate long, double stranded cDNA fragments from plates containing sorted cells, with one cell per well. This cDNA is then modified using Illumina Nextera XT technology, which uses a transposase to fragment the cDNA and ligate adapters for barcoding and amplification. The resulting single-cell libraries are typically pooled (96 to a pool) for Illumina sequencing, resulting in one final library sample per plate of cells.
 The user should submit sorted cells in Eppendorf Twin-Tec plates, resuspended in a specific lysis buffer and frozen at -80ºC. Detailed instructions are available from the Genome Core. These plates are fairly stable, so the sorting does not need to be coordinated with the Genome Core prior to submission.

@@ Line 1: / Line 1: @@
 We offer two types of single-cell sequencing: SMART-Seq2, and 10X Genomics.
 = 10X Genomics =
@@ Line 24: / Line 14: @@
 The user provides a freshly collected cell suspension on the day of processing. '''[[You must coordinate an appointment time with the Genome Core to allow for immediate processing after cell collection and counting. The user is responsible for obtaining cell counts and percent viability prior to arrival for the appointment]]'''. Detailed protocols are available from the Genome Core.
-Detailed protocols are available from the Genome Core or on the 10x web site:
+Please refer to our FAQ section for commonly asked questions: http://genomecore.wi.mit.edu/index.php/Faq#10X_Single_Cell_RNA
-https://support.10xgenomics.com/single-cell-gene-expression/sample-prep
+Please review the 10X FAQ on Single Cell Seq: https://kb.10xgenomics.com/hc/en-us/categories/201931746-General-Single-Cell-RNA-seq
-Please review the 10X FAQ on Single Cell Seq:
-https://kb.10xgenomics.com/hc/en-us/categories/201931746-General-Single-Cell-RNA-seq
+= SMART-Seq2 =

← Older revision		Revision as of 15:53, 5 February 2020
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	https://support.10xgenomics.com/single-cell-gene-expression/sample-prep		https://support.10xgenomics.com/single-cell-gene-expression/sample-prep
		+
		+	Please review the 10X FAQ on Single Cell Seq:
		+	https://kb.10xgenomics.com/hc/en-us/categories/201931746-General-Single-Cell-RNA-seq