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  Breast Cancer cell line (SKBR3)

Overall DesignFirst, hand-picked single cells are lysed and reverse transcribed using a poly-A primer including cell-specific barcodes, a 5' Illumina adapter and a T7 promoter overhang to convert mRNA to single stranded cDNA (ss cDNA). The gDNA and single stranded cDNA are then subjected to quasilinear whole genome amplification, as previously described, using an adapter with a defined 27 nucleotide sequence at the 5’ end followed by 8 random nucleotides. After 7 rounds of amplification, the gDNA and cDNA are copied to generate a variety of different short amplicon (0.5–2.5 kb) species, with a majority of amplicons containing adapter Ad-2 at both ends and a small fraction of cDNA derived amplicons containing Ad-2 at one end and Ad-1x at the other. Next, the sample is split into two tubes to further amplify gDNA and cDNA. The tube used to sequence gDNA is amplified using PCR. Following sonication, adapter Ad-2 removal, and cell-specific indexed Illumina library preparation, this half is used to sequence gDNA. The tube used to sequence cDNA is converted to double-stranded cDNA and amplified using in vitro transcription such that the amplified RNA (aRNA) is uniquely produced from cDNA but not gDNA. 3’ Illumina adapters are then ligated to the aRNA followed by reverse transcription and PCR, allowing quantification of mRNA.
SummarySingle-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells.
Dataset viewGSE62952
PMID25599178

Samples in Breast Cancer cell line (SKBR3)

Displaying 11-20 of 21 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE62952GSM1537130.19Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.20Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.22Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.23Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.24Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.25Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.26Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.27Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.28Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)
GSE62952GSM1537130.29Illumina HiSeq 2500Homo sapienssingle cell mRNA sequencing data from single SKBR3 cells obtained with the DR-seq protocolBreast Cancer cell line (SKBR3)

Gene rank in Breast Cancer cell line (SKBR3)

Displaying 12001-12010 of 12151 results.
Rank orderGene SymbolEnsembl ID
12001ALKBH8ENSG00000137760
12002ANKMY2ENSG00000106524
12003ANKRD20A12P
12004ANXA2RENSG00000177721
12005ARHGAP39ENSG00000147799
12006ATP6V1B1ENSG00000116039
12007B3GNT7ENSG00000156966
12008BSXENSG00000188909
12009C11orf53ENSG00000150750
12010C1QTNF9ENSG00000240654