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Series GSE99991 Query DataSets for GSE99991
Status Public on Jun 07, 2018
Title Investigating the role of SMCHD1 in de novo X chromosome inactivation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary To investigate the effect of Smchd1 ablation on de novo X chromosome inactivation (XCI), we derived clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem cells (ES cells; ESC). We generated allele-specific RNA-seq datasets from WT and Smchd1-/- NPCs to examine the effect of Smchd1 ablation on gene silencing. In addition, we produced allele-specific ChIP-seq profiles of H3K4me3, H3K27me3, CTCF, and RAD21 and Xist CHART-seq profiles in WT and Smchd1-/- NPCs to investigate the role of SMCHD1 on the distribution of euchromatin, facultative heterochromatin, architectural proteins, and Xist RNA on the inactive X chromosome (Xi). To determine the localization of SMCHD1 on the Xi, we employed allele-specific DamID-seq to map SMCHD1-binding regions in female mouse embryonic fibroblasts. Furthermore, we performed in situ Hi-C on WT NPCs, Smchd1-/- NPCs, and female ES cells undergoing XCI, in order to explore the role of SMCHD1 in regulating the higher-order structure of the Xi.
Overall design RNA-seq, ChIP-seq for H3K4me3, H3K27me3, CTCF, and RAD21, Xist CHART-seq, and in situ Hi-C in neural progenitor cell clones derived from WT and Smchd1-/- female mouse embryonic stem cells (ES cells). DamID-seq for SMCHD1 and CBX1 in female mouse embryonic fibroblasts. In situ Hi-C on WT female mouse ES cells at different stages of X chromosome inactivation.
Contributor(s) Wang C, Lee JT
Citation(s) 29887375
Submission date Jun 13, 2017
Last update date Jul 25, 2021
Contact name Chen-Yu Wang
Organization name Massachusetts General Hospital
Department Molecular Biology
Lab Jeannie T. Lee
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (53)
GSM2667220 RNA-seq WT clone 1 rep1
GSM2667221 RNA-seq WT clone 2 rep1
GSM2667222 RNA-seq Smchd1-/- clone 1 rep1
Reanalysis of GSM1412989
Reanalysis of GSM1868575
BioProject PRJNA390409
SRA SRP109128

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
GSE99991_CTCF.peaks.rep1.bed.gz 36.7 Kb (ftp)(http) BED
GSE99991_D0.HiC.Xa.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_D4.HiC.Xa.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_D4.HiC.Xi.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_D7.HiC.Xa.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_D7.HiC.Xi.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_Downsampled.KO1.HiC.Xa.PC1.bedGraph.gz 4.0 Kb (ftp)(http) BEDGRAPH
GSE99991_Downsampled.KO1.HiC.Xi.PC1.bedGraph.gz 3.9 Kb (ftp)(http) BEDGRAPH
GSE99991_Downsampled.WT1.HiC.Xa.PC1.bedGraph.gz 4.1 Kb (ftp)(http) BEDGRAPH
GSE99991_Downsampled.WT1.HiC.Xi.PC1.bedGraph.gz 4.0 Kb (ftp)(http) BEDGRAPH
GSE99991_Giorgetti.D0.HiC.Xa.comp.PC1.bedGraph.gz 3.8 Kb (ftp)(http) BEDGRAPH
GSE99991_KO1.HiC.Xa.PC1.bedGraph.gz 4.2 Kb (ftp)(http) BEDGRAPH
GSE99991_KO1.HiC.Xi.PC1.bedGraph.gz 4.2 Kb (ftp)(http) BEDGRAPH
GSE99991_RAD21.peaks.rep1.bed.gz 11.0 Kb (ftp)(http) BED
GSE99991_RAW.tar 82.0 Gb (http)(custom) TAR (of BW, TXT)
GSE99991_RNAseq_raw_read_count_table.txt.gz 2.7 Mb (ftp)(http) TXT
GSE99991_WT1.HiC.Xa.PC1.bedGraph.gz 4.2 Kb (ftp)(http) BEDGRAPH
GSE99991_WT1.HiC.Xi.PC1.bedGraph.gz 4.2 Kb (ftp)(http) BEDGRAPH
GSE99991_X-linked.gene.classes.bed.gz 17.1 Kb (ftp)(http) BED
GSE99991_X_chromosome.insulation_score.txt.gz 98.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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