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  colon carcinoma HCT116

Overall Design109 single-cell human transcriptomes were analyzed in total; 96 using nanoliter volume sample processing on a microfluidic platform, Nextera library prep (biological replicates); 3 using the SMARTer cDNA synthesis kit, Nextera library prep (biological replicates); 3 using the Transplex cDNA synthesis kit, Nextera library prep (biological replicates); 7 using the Ovation Nugen cDNA synthesis kit (biological replicates) where 3 used Nextera library prep and 4 used NEBNext library prep. In addition, 4 bulk RNA samples were sequenced: bulk RNA generated using ~1 million pooled cells was used to make bulk libraries, 2 of which were made using SMARTer cDNA synthesis kit (technical replicates) and 2 made using Superscript RT kit with no amplification (technical replicates). All 4 bulk samples were made into libraries using Nextera.
SummaryWe generated single-cell transcriptomes from a large number of single cells using several commercially available platforms, in both microliter and nanoliter volumes, and compared performance between them. We benchmarked each method to conventional RNA-seq of the same sample using bulk total RNA, as well as to multiplexed qPCR, which is the current gold standard for quantitative single-cell gene expression analysis. In doing so, we were able to systematically evaluate the sensitivity, precision, and accuracy of various approaches to single-cell RNA-seq. Our results show that it is possible to use single-cell RNA-seq to perform quantitative transcriptome measurements of individual cells, that it is possible to obtain quantitative and accurate gene expression measurements with a relatively small number of sequencing reads, and that when such measurements are performed on large numbers of cells, one can recapitulate the bulk transcriptome complexity, and the distributions of gene expression levels found by single-cell qPCR.
Dataset viewGSE51254
PMID24141493

Samples in colon carcinoma HCT116

Displaying 1-10 of 109 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE51254GSM1241184Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 31colon carcinoma HCT116
GSE51254GSM1241185Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 32colon carcinoma HCT116
GSE51254GSM1241186Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 33colon carcinoma HCT116
GSE51254GSM1241187Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 34colon carcinoma HCT116
GSE51254GSM1241188Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 35colon carcinoma HCT116
GSE51254GSM1241189Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 36colon carcinoma HCT116
GSE51254GSM1241190Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 37colon carcinoma HCT116
GSE51254GSM1241191Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 38colon carcinoma HCT116
GSE51254GSM1241192Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 39colon carcinoma HCT116
GSE51254GSM1241193Illumina HiSeq 2000Homo sapiensSingle Cell C1 Microfluidics 40colon carcinoma HCT116

Gene rank in colon carcinoma HCT116