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Series GSE117309 Query DataSets for GSE117309
Status Public on Apr 12, 2019
Title High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The dynamic nature of chromatin and transcription plays a critical role in normal differentiation and is expected to contribute to tumor evolution. Studying chromatin heterogeneity with single-cell resolution is mandatory to understand the role of epigenetic plasticity in cancer. Here, we describe a droplet microfluidics system that enables the profiling of chromatin marks of individual cells with an average coverage of up to 10,000 loci per cell. In patient-derived xenograft (PDX) models of breast cancer with acquired drug resistance, single-cell chromatin immunoprecipitation followed by sequencing (scChIP-seq) identified rare populations of cells in untreated, drug-sensitive tumors with chromatin features that match those of resistant cells. Loci depleted for transcriptional repressive mark H3K27me3 included genes know to promote resistance to chemotherapy, highlighting the potential to discover new drug targets.
Overall design Single-cell ChIP-seq and single-cell RNA-seq in patient-derived xenograft models of breast cancer with acquired drug resistance
Contributor(s) Grosselin K, Gerard A, Griffiths AD, Vallot C
Citation(s) 31152164
Submission date Jul 18, 2018
Last update date Jun 04, 2019
Contact name Kevin Grosselin
Organization name ESPCI Paris
Department CBI
Lab Andrew Griffiths
Street address 10 rue Vauquelin
City Paris
ZIP/Postal code 75005
Country France
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (10)
GSM3290887 H3K4me3_scChIPseq_Jurkat-Ramos
GSM3290888 H3K27me3_scChIPseq_Jurkat-Ramos
GSM3290889 H3K27me3_scChIPseq_HBCx-95
BioProject PRJNA481734
SRA SRP154341

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
GSE117309_BarcodeLibrary_scChIPseq.fasta.gz 7.4 Mb (ftp)(http) FASTA
GSE117309_RAW.tar 114.7 Mb (http)(custom) TAR (of TAR, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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