Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Method

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

Yohei Sasagawa17, Itoshi Nikaido17, Tetsutaro Hayashi2, Hiroki Danno3, Kenichiro D Uno1, Takeshi Imai45 and Hiroki R Ueda136*

Author Affiliations

1 Functional Genomics Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

2 Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

3 Laboratory for Systems biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

4 Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

5 JST, PRESTO, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

6 Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

7 Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

For all author emails, please log on.

Genome Biology 2013, 14:R31  doi:10.1186/gb-2013-14-4-r31

Published: 17 April 2013

Additional files

Additional file 1:

Figure S1: Schematic of the whole-transcript amplification methods based on the poly-A-tailing reaction. Figure S2: Improvement parameters of whole-transcript amplification for Quartz-Seq. Figure S3: Key steps for robust suppression of byproducts. Figure S4: Optimization of suppression PCR for Quartz-Seq. Figure S5: Optimal DNA polymerase for whole-transcript amplification. Figure S6: Quality check of the library preparation for single-cell Quartz-Seq. Figure S8: Percentage of sequence reads of the suppression PCR primer or rRNA. Figure S9: Relationship between the read number and the reproducibility. Figure S10: Optimization of cDNA length in technical development for single-cell Quartz-Seq. Figure S11: Trend of unamplified isoforms in each single-cell RNA-seq method. Figure S12: Amplified cDNA lengths resulting from single-cell RNA-seq methods. Figure S13: Success rate of whole-transcript amplification from single cells sorted by fluorescence-activated cell sorting (FACS). Figure S14: Amount of total RNA from a single cell at each cell-cycle phase. Figure S15: Principal component analysis (PCA) of single cells from different cell types at different cell-cycle phases. Figure S16: Over-representation analyses for principal component (PC) of single cells from same cell types in the same cell-cycle phase (G1). Figure S17: Scatter plots of conventional RNA-seq and Quartz-Seq using 50 ES cells in the G1 phase of the cell cycle and Quartz-Seq using 10 pg of total ES RNA. Figure S18: Effect of carried-over buffer for PCR efficiency.

Format: PDF Size: 17.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Supplementary note.

Format: DOCX Size: 33KB Download file

Open Data

Additional file 3:

Figure S7: All scatter plots

Format: PDF Size: 3.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Table S1. All results of linear regression and correlation analyses.

Format: XLS Size: 219KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Supplementary movie 1. Principal component analysis (PCA) with single-cell Quartz-Seq data of embryonic stem (ES) and primitive endoderm (PrE) single-cell preparations.

Format: GIF Size: 2.4MB Download file

Open Data

Additional file 6:

Supplementary movie 2. Principal component analysis (PCA) with single-cell Quartz-Seq data of embryonic stem (ES) cells in different cell-cycle phases.

Format: GIF Size: 2MB Download file

Open Data

Additional file 7:

Table S2. Sequencing information.

Format: XLS Size: 44KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Table S3. Primer information.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data