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Series GSE62952 Query DataSets for GSE62952
Status Public on Dec 11, 2014
Title Integrated genome and transcriptome sequencing from the same cell
Organisms Homo sapiens; Mus musculus
Experiment type Genome variation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Single-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.
Overall design First, 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.
Contributor(s) Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A
Citation(s) 25599178
Submission date Nov 04, 2014
Last update date May 15, 2019
Contact name Lennart Kester
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (20)
GSM1537116 Bulk whole genome sequencing data from SKBR3 cells
GSM1537117 single cell whole genome sequencing data from SKBR3 cell 3 obtained with the DR-seq protocol
GSM1537118 single cell whole genome sequencing data from SKBR3 cell 10 obtained with the DR-seq protocol
BioProject PRJNA266282
SRA SRP049500

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Supplementary file Size Download File type/resource
GSE62952_96BC.csv.gz 304 b (ftp)(http) CSV
GSE62952_RAW.tar 5.0 Mb (http)(custom) TAR (of TXT)
GSE62952_processed_data_files_description.txt.gz 385 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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