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Series GSE183765 Query DataSets for GSE183765
Status Public on Aug 10, 2023
Title BlCa: MSL2 is an allelic dosage sensor in mammals
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Biallelic expression is important to ensure adequate mRNA levels as well as protect cells from deleterious heterozygous mutations. However, the factors determining biallelic expression at individual gene loci are unknown. Deletion of the MSL complex component MSL2 in hybrid mouse NPCs uncovers an unprecedented function for MSL2 in allelic regulation. While biallelically expressed in wildtype NPCs, a class of MSL2 targets switches from bi to monoallelic expression upon MSL2 loss. The silenced allele loses nascent transcription, accompanied by dramatic changes in local chromatin landscape such as monoallelic gain of H3K27me3 and DNA methylation. Meanwhile, active histone modifications, RNA POL II, BRD4 and KANSL3 are retained on the active allele. MSL2 targets include several sex-biased genes on autosomes as well as X-chromosomal genes that escape X inactivation. Together, the allele-specific resolution allowed us to unravel an MSL2 mediated safeguarding mechanism to promote biallelic gene expression of sexually dimorphic and dosage-sensitive genes in mammals.
 
Overall design Allele specific differential analysis of various sequencing data from ESCs and NPCs of female and male hybrid clones.
 
Contributor(s) Sun Y, Hmadi R, Wiese M, Akhtar A
Citation(s) 38030723
Submission date Sep 09, 2021
Last update date Dec 14, 2023
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (118)
GSM5570522 BlCa: ESCs_Control_RNAseq_rep1
GSM5570523 BlCa: ESCs_Control_RNAseq_rep2
GSM5570524 BlCa: ESCs_Control_RNAseq_rep3
This SubSeries is part of SuperSeries:
GSE183556 MSL2 is an allelic dosage sensor in mammals
Relations
BioProject PRJNA762171
SRA SRP339236

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
GSE183765_ESCs_DEgenes_classification.txt.gz 33.3 Kb (ftp)(http) TXT
GSE183765_ESCs_DEseq_allelic_DEresults.tsv.gz 1.3 Mb (ftp)(http) TSV
GSE183765_ESCs_DEseq_basic_DEresults.tsv.gz 1.5 Mb (ftp)(http) TSV
GSE183765_NPCs_Control_BRD4.bw 507.9 Mb (ftp)(http) BW
GSE183765_NPCs_Control_BRD4.genome1.bw 252.1 Mb (ftp)(http) BW
GSE183765_NPCs_Control_BRD4.genome2.bw 230.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_BSseq.bw 1.3 Gb (ftp)(http) BW
GSE183765_NPCs_Control_BSseq.genome1.bw 1.0 Gb (ftp)(http) BW
GSE183765_NPCs_Control_BSseq.genome2.bw 995.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27ac.bw 206.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27ac.genome1.bw 84.9 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27ac.genome2.bw 78.2 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27me3.bw 249.9 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27me3.genome1.bw 105.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K27me3.genome2.bw 96.4 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K36me3.bw 265.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K36me3.genome1.bw 121.1 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K36me3.genome2.bw 111.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me1.bw 240.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me1.genome1.bw 103.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me1.genome2.bw 95.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me3.bw 201.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me3.genome1.bw 82.1 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K4me3.genome2.bw 75.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K9me3.bw 247.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K9me3.genome1.bw 103.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H3K9me3.genome2.bw 94.5 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K12ac.bw 217.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K12ac.genome1.bw 88.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K12ac.genome2.bw 80.8 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K5ac.bw 230.9 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K5ac.genome1.bw 96.5 Mb (ftp)(http) BW
GSE183765_NPCs_Control_H4K5ac.genome2.bw 87.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_KANSL3.bw 361.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_KANSL3.genome1.bw 181.5 Mb (ftp)(http) BW
GSE183765_NPCs_Control_KANSL3.genome2.bw 168.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_KANSL3_peaks.bed.gz 133.1 Kb (ftp)(http) BED
GSE183765_NPCs_Control_MOF.bw 512.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MOF.genome1.bw 258.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MOF.genome2.bw 240.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MSL2.bw 522.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MSL2.genome1.bw 271.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MSL2.genome2.bw 248.8 Mb (ftp)(http) BW
GSE183765_NPCs_Control_MSL2_peaks.bed.gz 51.1 Kb (ftp)(http) BED
GSE183765_NPCs_Control_NRF1.bw 509.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_NRF1.genome1.bw 255.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_NRF1.genome2.bw 235.3 Mb (ftp)(http) BW
GSE183765_NPCs_Control_POL2.bw 480.6 Mb (ftp)(http) BW
GSE183765_NPCs_Control_POL2.genome1.bw 237.7 Mb (ftp)(http) BW
GSE183765_NPCs_Control_POL2.genome2.bw 218.0 Mb (ftp)(http) BW
GSE183765_NPCs_Control_RNAseq.bw 45.8 Mb (ftp)(http) BW
GSE183765_NPCs_Control_RNAseq.genome1.bw 22.5 Mb (ftp)(http) BW
GSE183765_NPCs_Control_RNAseq.genome2.bw 21.4 Mb (ftp)(http) BW
GSE183765_NPCs_Control_SP1.bw 503.4 Mb (ftp)(http) BW
GSE183765_NPCs_Control_SP1.genome1.bw 253.4 Mb (ftp)(http) BW
GSE183765_NPCs_Control_SP1.genome2.bw 233.4 Mb (ftp)(http) BW
GSE183765_NPCs_DEgenes_classification.txt.gz 133.0 Kb (ftp)(http) TXT
GSE183765_NPCs_DEseq_allelic_DEresults.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE183765_NPCs_DEseq_basic_DEresults.tsv.gz 1.4 Mb (ftp)(http) TSV
GSE183765_NPCs_MSL2KO1_BRD4.bw 489.8 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_BRD4.genome1.bw 245.3 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_BRD4.genome2.bw 230.5 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_BSseq.bw 1.3 Gb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_BSseq.genome1.bw 1.0 Gb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_BSseq.genome2.bw 983.8 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27ac.bw 173.2 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27ac.genome1.bw 65.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27ac.genome2.bw 62.7 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27me3.bw 195.2 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27me3.genome1.bw 75.7 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K27me3.genome2.bw 71.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K36me3.bw 208.2 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K36me3.genome1.bw 85.4 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K36me3.genome2.bw 80.8 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me1.bw 193.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me1.genome1.bw 76.8 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me1.genome2.bw 73.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me3.bw 172.0 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me3.genome1.bw 65.4 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K4me3.genome2.bw 62.5 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K9me3.bw 140.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K9me3.genome1.bw 50.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H3K9me3.genome2.bw 47.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K12ac.bw 187.2 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K12ac.genome1.bw 71.5 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K12ac.genome2.bw 68.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K5ac.bw 184.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K5ac.genome1.bw 71.4 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_H4K5ac.genome2.bw 67.7 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_KANSL3.bw 363.0 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_KANSL3.genome1.bw 181.3 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_KANSL3.genome2.bw 171.7 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_KANSL3_peaks.bed.gz 123.5 Kb (ftp)(http) BED
GSE183765_NPCs_MSL2KO1_MOF.bw 489.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_MOF.genome1.bw 244.7 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_MOF.genome2.bw 230.5 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_NRF1.bw 473.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_NRF1.genome1.bw 229.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_NRF1.genome2.bw 217.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_POL2.bw 490.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_POL2.genome1.bw 243.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_POL2.genome2.bw 229.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_RNAseq.bw 43.1 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_RNAseq.genome1.bw 20.9 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_RNAseq.genome2.bw 20.3 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_SP1.bw 493.6 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_SP1.genome1.bw 245.3 Mb (ftp)(http) BW
GSE183765_NPCs_MSL2KO1_SP1.genome2.bw 232.5 Mb (ftp)(http) BW
GSE183765_NPCs_diff.peak.BS.RData.gz 49.2 Mb (ftp)(http) RDATA
GSE183765_RAW.tar 26.6 Mb (http)(custom) TAR (of TXT)
GSE183765_raw.counts.object.cluster.allelic.rds.gz 1.7 Gb (ftp)(http) RDS
GSE183765_raw.counts.object.cluster.total.rds.gz 6.6 Gb (ftp)(http) RDS
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