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Series GSE112554 Query DataSets for GSE112554
Status Public on Apr 12, 2018
Title Highly scalable generation of DNA methylation profiles in single cells
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We present a novel method: single-cell combinatorial indexing for methylation analysis (sci-MET), which is the first highly scalable assay for whole genome methylation profiling of single cells. We use sci-MET to produce 3,282 total single-cell bisulfite sequencing libraries and achieve read alignment rates of 68± 8%, comparable to those of bulk cell methods. As a proof of concept, we applied sci-MET to deconvolve the cellular identity of a mixture of three human cell lines. Next, we applied sci-MET to mouse cortical tissue, which successfully identified excitatory and inhibitory neuronal populations as well as non-neuronal cell types.
Overall design Tissue culture cell lines (GM12878, Coriell; HEK293, ATCC CRL-1554; Primary Fibro., inguinal fibroblast, GM05756, Coriell, passage 7) were cultured and nuclei were isolated. The three cell lines were both pooled to serve as randomized controls, and processed independently, as described in the available Methods section. Sixty-day-old C57BL/6J mice had their entire cortex isolated. Three biological replicates were independently processed as described in the available Methods section. Additional files are available under BioProject ID: PRJNA397747 and Study Accession: SRP127273.
Contributor(s) Mulqueen RM, Pokholok D, Norberg S, Fields AJ, Sun D, Torkenczy KA, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC
Citation(s) 29644997
BioProject PRJNA397747
Submission date Mar 30, 2018
Last update date Mar 27, 2019
Contact name Ryan M Mulqueen
Organization name Oregon Health and Science
Department Molecular and Medical Genetics
Lab Andrew Adey, PhD
Street address 3181 SW Sam Jackson Park Rd
City Portland
State/province OR
ZIP/Postal code 97239
Country USA
Platforms (4)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM3072971 HumanCellLineSplit_Barcoded_CG_G00144
GSM3072972 HumanCellLineSplit_Barcoded_CG_NS500556
GSM3072973 HumanCellLineSplit_Barcoded_CG_ST-E00107
SRA SRP127273

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE112554_HumanCellLineSplit_Barcoded_CG.bed.gz 1.5 Gb (ftp)(http) BED
GSE112554_MouseCortex_Barcoded_CG.bed.gz 407.6 Mb (ftp)(http) BED
GSE112554_MouseCortex_Barcoded_CH.bed.gz 6.7 Gb (ftp)(http) BED
GSE112554_SupplementaryCode.tar.gz 3.7 Kb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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