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Series GSE100628 Query DataSets for GSE100628
Status Public on Jan 08, 2018
Title Cell-Type-Specific Survey of Epigenetic Modification by Tandem Chromatin Immunoprecipitation Sequencing
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary [Background]: Nervous system of higher eukaryotes is composed of numerous types of neurons and glia, which together orchestrate complex neuronal responses. However, the complex pool of cells usually poses analytic challenges to investigate gene expression profile and its epigenetic basis in specific cell type. Here we developed a novel method that enables cell-type-specific analyses of epigenetic modification using tandem chromatin immunoprecipitation sequencing (tChIP-Seq).

[Results]: FLAG-tagged histone H2B, a constitutive chromatin component, was firstly expressed in Camk2a-positive pyramidal cortical neurons and was used to purify the chromatin in a cell-type-specific manner. The subsequent chromatin immunoprecipitation using antibodies against H3K4me3—an active promoter mark—allowed us to survey neuron specific coding and noncoding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions as well as genes with unknown function expressed in cortical neurons.

[Conclusions]: tChIP-Seq thus provides a versatile approach to investigate epigenetic modifications of particular cell types in vivo.
Overall design ChIP-Seq
Contributor(s) Mito M, Kadota M, Tanaka K, Furuta Y, Abe K, Iwasaki S, Nakagawa S
Citation(s) 29348483
Submission date Jun 28, 2017
Last update date Jul 25, 2021
Contact name Shintaro Iwasaki
Organization name RIKEN
Department Cluster for Pioneering Research
Street address S205 Bioscience Bldg. 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (24)
GSM2689709 01-aH_No1_input
GSM2689710 02-aH_No1_H3K4me3
GSM2689711 03-aH_No1_M2
BioProject PRJNA392320
SRA SRP110708

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

Supplementary file Size Download File type/resource
GSE100628_RAW.tar 2.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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