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  MCF10a human breast cancer cells

Overall DesignA 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.
SummarySingle 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.type = Expression profiling by high throughput sequencing
Dataset viewGSE66357
PMID26047807

Samples in MCF10a human breast cancer cells

Displaying 1-10 of 102 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE66357GSM1620620Illumina NextSeq 500Homo sapiensPS034_R2_4_115MCF10a human breast cancer cells
GSE66357GSM1620621Illumina NextSeq 500Homo sapiensPS034_R2_4_128MCF10a human breast cancer cells
GSE66357GSM1620622Illumina NextSeq 500Homo sapiensPS034_R2_4_143MCF10a human breast cancer cells
GSE66357GSM1620623Illumina NextSeq 500Homo sapiensPS034_R2_4_151MCF10a human breast cancer cells
GSE66357GSM1620624Illumina NextSeq 500Homo sapiensPS034_R2_4_161MCF10a human breast cancer cells
GSE66357GSM1620625Illumina NextSeq 500Homo sapiensPS034_R2_4_180MCF10a human breast cancer cells
GSE66357GSM1620626Illumina NextSeq 500Homo sapiensPS034_R2_4_190MCF10a human breast cancer cells
GSE66357GSM1620627Illumina NextSeq 500Homo sapiensPS034_R2_4_197MCF10a human breast cancer cells
GSE66357GSM1620628Illumina NextSeq 500Homo sapiensPS034_R2_4_198MCF10a human breast cancer cells
GSE66357GSM1620629Illumina NextSeq 500Homo sapiensPS034_R2_4_203MCF10a human breast cancer cells

Gene rank in MCF10a human breast cancer cells

Displaying 1-10 of 18975 results.
Rank orderGene SymbolEnsembl ID
1MT-CO1ENSG00000198804
2MIR4485
3NEAT1ENSG00000245532
4MT-ND4ENSG00000198886
5MT-CO3ENSG00000198938
6TPT1ENSG00000133112
7MALAT1ENSG00000251562
8GAPDHENSG00000111640
9EEF1A1ENSG00000156508
10MT-CYBENSG00000198727