GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE168455 Query DataSets for GSE168455
Status Public on Mar 15, 2024
Title Parallel tracking dosage compensation in the early mouse embryo
Organisms Mus musculus; Mus musculus castaneus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary We develop So-Smart-seq to interrogate a comprehensive transcriptome inclusive of coding, noncoding, and repetitive element transcription. We reveal that, surprisingly, de novo silencing pertains only to a subset of paternal X (Xp) genes. In contrast, a set of evolutionarily older genes and LINEs demonstrate constitutive Xp silencing, adopt epigenetically distinct signatures, and do not require Xist to initiate silencing. On maternal X (Xm), however, these elements are hyperactivated. Thus, a significant subset of Xp elements appears to be inherited in a “pre-inactive” state. We also find that Xm-hyperactivation is timed to Xp silencing on an individual gene basis, giving rise to heterogeneity in the parallel track of dosage compensation as well. These conclusions have significant implications for the mechanism and evolution of imprinting in early mammals.
Overall design Examining the full transcriptome of single preimplantation embryos at various stages from WT and Xist mutant mouse.
Contributor(s) Wei C, Kesner B, Lee JT
Citation(s) 38458200
Submission date Mar 08, 2021
Last update date Mar 16, 2024
Contact name Chunyao Wei
Organization name Massachusetts General Hospital
Department Molecular Biology
Street address 185 Cambridge St.
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (3)
GPL33196 Illumina HiSeq 2500 (Mus musculus; Mus musculus castaneus)
GPL33197 Illumina NovaSeq 6000 (Mus musculus; Mus musculus castaneus)
GPL33198 Illumina HiSeq 4000 (Mus musculus; Mus musculus castaneus)
Samples (235)
GSM7980593 RNAseq_zygote_MC_ rep1
GSM7980594 RNAseq_zygote_MC_ rep2
GSM7980595 RNAseq_zygote_MC_ rep3
BioProject PRJNA707448
SRA SRP309722

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
GSE168455_16C_CM.All_rep.allelic.geneCount.txt.gz 349.7 Kb (ftp)(http) TXT 327.4 Kb (ftp)(http) TXT
GSE168455_16C_MC.All_rep.allelic.geneCount.txt.gz 248.3 Kb (ftp)(http) TXT 242.5 Kb (ftp)(http) TXT 75.6 Mb (ftp)(http) TAR
GSE168455_4C_CM.All_rep.allelic.geneCount.txt.gz 275.5 Kb (ftp)(http) TXT 259.9 Kb (ftp)(http) TXT
GSE168455_4C_KO.All_rep.allelic.geneCount.txt.gz 336.9 Kb (ftp)(http) TXT 324.2 Kb (ftp)(http) TXT
GSE168455_4C_MC.All_rep.allelic.geneCount.txt.gz 392.8 Kb (ftp)(http) TXT 390.5 Kb (ftp)(http) TXT 4.7 Mb (ftp)(http) TAR
GSE168455_4sU-KO.Category1_4.gene_allelic_mismatch_count.txt.gz 875 b (ftp)(http) TXT 461.7 Kb (ftp)(http) TXT
GSE168455_4sU.rep1.comp.mismatch_gene.count.txt.gz 12.9 Kb (ftp)(http) TXT
GSE168455_4sU.rep10.comp.mismatch_gene.count.txt.gz 13.6 Kb (ftp)(http) TXT
GSE168455_4sU.rep11.comp.mismatch_gene.count.txt.gz 11.6 Kb (ftp)(http) TXT
GSE168455_4sU.rep12.comp.mismatch_gene.count.txt.gz 13.9 Kb (ftp)(http) TXT
GSE168455_4sU.rep2.comp.mismatch_gene.count.txt.gz 13.2 Kb (ftp)(http) TXT
GSE168455_4sU.rep3.comp.mismatch_gene.count.txt.gz 12.0 Kb (ftp)(http) TXT
GSE168455_4sU.rep4.comp.mismatch_gene.count.txt.gz 10.5 Kb (ftp)(http) TXT
GSE168455_4sU.rep5.comp.mismatch_gene.count.txt.gz 11.1 Kb (ftp)(http) TXT
GSE168455_4sU.rep6.comp.mismatch_gene.count.txt.gz 13.1 Kb (ftp)(http) TXT
GSE168455_4sU.rep7.comp.mismatch_gene.count.txt.gz 10.7 Kb (ftp)(http) TXT
GSE168455_4sU.rep8.comp.mismatch_gene.count.txt.gz 11.4 Kb (ftp)(http) TXT
GSE168455_4sU.rep9.comp.mismatch_gene.count.txt.gz 11.7 Kb (ftp)(http) TXT
GSE168455_8C_CM.All_rep.allelic.geneCount.txt.gz 309.2 Kb (ftp)(http) TXT 295.4 Kb (ftp)(http) TXT
GSE168455_8C_KO.All_rep.allelic.geneCount.txt.gz 330.8 Kb (ftp)(http) TXT 316.6 Kb (ftp)(http) TXT
GSE168455_8C_MC.All_rep.allelic.geneCount.txt.gz 357.6 Kb (ftp)(http) TXT 350.2 Kb (ftp)(http) TXT 55.8 Mb (ftp)(http) TAR
GSE168455_RAW.tar 16.2 Gb (http)(custom) TAR (of TAR)
GSE168455_early2C_MC.All_rep.allelic.geneCount.txt.gz 232.6 Kb (ftp)(http) TXT 234.0 Kb (ftp)(http) TXT
GSE168455_earlyB_CM.All_rep.allelic.geneCount.txt.gz 346.0 Kb (ftp)(http) TXT 321.6 Kb (ftp)(http) TXT
GSE168455_earlyB_KO.All_rep.allelic.geneCount.txt.gz 313.1 Kb (ftp)(http) TXT 299.2 Kb (ftp)(http) TXT
GSE168455_earlyB_MC.All_rep.allelic.geneCount.txt.gz 318.2 Kb (ftp)(http) TXT 299.0 Kb (ftp)(http) TXT
GSE168455_late2C_CM.All_rep.allelic.geneCount.txt.gz 305.3 Kb (ftp)(http) TXT 295.1 Kb (ftp)(http) TXT
GSE168455_late2C_KO.All_rep.allelic.geneCount.txt.gz 531.1 Kb (ftp)(http) TXT 504.2 Kb (ftp)(http) TXT
GSE168455_late2C_MC.All_rep.allelic.geneCount.txt.gz 302.1 Kb (ftp)(http) TXT 297.6 Kb (ftp)(http) TXT 9.0 Mb (ftp)(http) TAR 179.6 Kb (ftp)(http) TXT
GSE168455_zygote_MC.All_rep.allelic.geneCount.txt.gz 196.9 Kb (ftp)(http) TXT 197.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap