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Series GSE109262 Query DataSets for GSE109262
Status Public on Jan 17, 2018
Title Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells
Organisms Mus musculus; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
 
Overall design scNMT-seq (single-cell nucleosome, methylation and transcription sequencing)
 
Contributor(s) Clark S, Argelaguet R, Kapourani C, Stubbs T, Lee H, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni J, Stegle O, Reik W
Citation(s) 29472610
Submission date Jan 16, 2018
Last update date Mar 25, 2019
Contact name Felix Krueger
E-mail(s) felix.krueger@babraham.ac.uk
Organization name The Babraham Institute
Department Bioinformatics
Street address Babraham Hall
City Cambridge
ZIP/Postal code CB22 3AT
Country United Kingdom
 
Platforms (4)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL15228 Illumina HiSeq 2000 (synthetic construct)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (244)
GSM2936019 EBcontrol_P1D12_NOMe-seq
GSM2936020 EBcontrol_P1E12_NOMe-seq
GSM2936021 EBcontrol_P1F12_NOMe-seq
Relations
BioProject PRJNA430259
SRA SRP131024

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109262_EB_RNA_counts.txt.gz 603.3 Kb (ftp)(http) TXT
GSE109262_ESC_RNA_counts.txt.gz 1.1 Mb (ftp)(http) TXT
GSE109262_RAW.tar 4.6 Gb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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