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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 11-20 of 12151 results.
Rank orderGene SymbolEnsembl ID
11RPS3ENSG00000149273
12MINOS1ENSG00000173436
13H3F3AENSG00000163041
14RPL22ENSG00000116251
15RPL41ENSG00000229117
16H3F3AP4ENSG00000235655
17RPS24ENSG00000138326
18RAB3BENSG00000169213
19GAPDHENSG00000111640
20NEAT1ENSG00000245532