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Series GSE66357 Query DataSets for GSE66357
Status Public on May 21, 2015
Title Scalable Microfluidics for Single Cell RNA Printing and Sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Single cell transcriptomics has emerged as a powerful approach to dissecting phenotypic heterogeneity in complex, unsynchronized cellular populations. However, many important biological questions demand quantitative analysis of large numbers of individual cells. Hence, new tools are urgently needed for efficient, inexpensive, and parallel manipulation of RNA from individual cells. We report a simple microfluidic platform for trapping single cell lysates in sealed, picoliter microwells capable of “printing” RNA on glass or capturing RNA on polymer beads. To demonstrate the utility of our system for single cell transcriptomics, we developed a highly scalable technology for genome-wide, single cell RNA-Seq. The current implementation of our device is pipette-operated, profiles hundreds of individual cells in parallel with library preparation costs of ~$0.10-$0.20/cell, and includes five lanes for simultaneous experiments. We anticipate that this system will ultimately serve as a general platform for large-scale single cell transcriptomics, compatible with both imaging and sequencing readouts.!Series_type = Expression profiling by high throughput sequencing
Overall design A microfluidic device that pairs sequence-barcoded mRNA capture beads with individual cells was used to barcode cDNA from individual cells which was then pre-amplified by in vitro transcription in a pool and converted into an Illumina RNA-Seq library. Libraries were generated from ~600 individual cells in parallel and extensive analysis was done on 396 cells from the U87 and MCF10a cell lines and from ~500 individual cells with extensive analysis on 247 cells from the U87 and WI-38 cell lines. Sequencing was done on the 3'-end of the transcript molecules. The first read contains cell-identifying barcodes that were present on the capture bead and the second read contains a unique molecular identifier (UMI) barcode, a lane-identifying barcode, and then the sequence of the transcript.
Contributor(s) Sims PA
Citation(s) 26047807
Submission date Feb 27, 2015
Last update date May 15, 2019
Contact name Peter A Sims
Organization name Columbia University
Street address 3960 Broadway, Lasker 203AC
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (643)
GSM1620347 PS034_R2_0_102
GSM1620348 PS034_R2_0_140
GSM1620349 PS034_R2_0_142
BioProject PRJNA276634
SRA SRP055569

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE66357_PS034_R2_0.txt.gz 255.9 Kb (ftp)(http) TXT
GSE66357_PS034_R2_1.txt.gz 329.0 Kb (ftp)(http) TXT
GSE66357_PS034_R2_2.txt.gz 238.8 Kb (ftp)(http) TXT
GSE66357_PS034_R2_3.txt.gz 241.5 Kb (ftp)(http) TXT
GSE66357_PS034_R2_4.txt.gz 316.8 Kb (ftp)(http) TXT
GSE66357_PS041-2_R2_0.txt.gz 266.6 Kb (ftp)(http) TXT
GSE66357_PS041-2_R2_1.txt.gz 182.2 Kb (ftp)(http) TXT
GSE66357_PS041-2_R2_2.txt.gz 240.7 Kb (ftp)(http) TXT
GSE66357_PS041-2_R2_3.txt.gz 166.1 Kb (ftp)(http) TXT
GSE66357_PS041-2_R2_4.txt.gz 147.9 Kb (ftp)(http) TXT
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