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Series GSE137337 Query DataSets for GSE137337
Status Public on Apr 07, 2020
Title Epigenetic regulator function through mouse gastrulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Development of a multicellular organism uses the same genetic code to generate a broad diversity of cell types, which is instructed by extracellular cues and orchestrated by transcriptional activators and repressors. While transcription factors establish cell identities according to the central dogma, a number of enzymes, which index and regulate chromatin, appear to perform essential functions as well. We optimized a versatile experimental and analytical approach that allows for rapid perturbation of genes and the recovery of high replicate powered phenotypic information. We applied this set-up to investigate a panel of epigenetic regulators that are essential for early gestation. Our comparative analysis approach enabled us to pinpoint affected genetic pathways and cell lineage-specific effects that distinguish even closely related regulators, such as polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Moreover, by incorporating additional epigenetic data, we were able to identify early aberrations that partially explain how certain developmental abnormalities emerge at the onset of gastrulation.
 
Overall design Single-cell RNAseq data was collected on whole early mouse embryos generated using B6/CAST F1 sperm and B6D2F1 oocytes. Each experiment consists of 4-12 embryo replicates from developmental stages E6.5, 7.0, 7.5, 8.0, 8.5 for wild-type, of E8.5 for all epigenetic regulator knockouts (KOs) and for Eed KO additionally from E6.5 and 7.5. All scRNA-seq data was generated using the 10X Genomics single cell RNA sequencing platform. Sample titles with "a" or "b" represent distinct sets of cells sequenced from the same experiment. Additional epigenetic data was generated for E6.5 embryos generated by natural mating B6D2F1 females with B6D2F1 males for each KO and WT. Macroscopically dissected embryonic (epiblast) and extraembryonic (extraembryonic ectoderm) fractions were collected in pools of ~10 embryos per KO and whole-genome bisulfite sequencing data was generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences).
 
Contributor(s) Grosswendt S, Kretzmer H, Smith ZD, Sampath Kumar A, Klages S, Mukherji S, Meissner A
Citation(s) 32728215, 34140676
https://doi.org/10.1038/s41594-021-00603-8
Submission date Sep 12, 2019
Last update date Jul 27, 2021
Contact name Helene Kretzmer
E-mail(s) kretzmer@molgen.mpg.de
Organization name Max Planck Institute for Molecular Genetics
Department Genome Regulation
Lab Meissner Lab
Street address Ihnestra├če 63
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (54)
GSM4075592 EED_E6.5_1
GSM4075593 EED_E6.5_2
GSM4075594 EED_E7.5_1
Relations
BioProject PRJNA565210
SRA SRP221485

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
GSE137337_CDKN2A_E8.5_1ab.tar.gz 432.0 Mb (ftp)(http) TAR
GSE137337_DNMT1_E8.5_1ab.barcodes.tsv.gz 39.9 Mb (ftp)(http) TSV
GSE137337_DNMT1_E8.5_1ab.features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE137337_DNMT1_E8.5_1ab.matrix.mtx.gz 535.2 Mb (ftp)(http) MTX
GSE137337_DNMT3A_E8.5_1ab.barcodes.tsv.gz 39.9 Mb (ftp)(http) TSV
GSE137337_DNMT3A_E8.5_1ab.features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE137337_DNMT3A_E8.5_1ab.matrix.mtx.gz 394.5 Mb (ftp)(http) MTX
GSE137337_DNMT3B_E8.5_1ab.tar.gz 581.5 Mb (ftp)(http) TAR
GSE137337_EED.CDKN2A_E8.5_1ab.tar.gz 390.7 Mb (ftp)(http) TAR
GSE137337_EED_E6.5_1.tar.gz 119.8 Mb (ftp)(http) TAR
GSE137337_EED_E6.5_2.tar.gz 81.5 Mb (ftp)(http) TAR
GSE137337_EED_E7.5_1.tar.gz 196.4 Mb (ftp)(http) TAR
GSE137337_EED_E8.5_1ab.tar.gz 361.5 Mb (ftp)(http) TAR
GSE137337_G9A_E8.5_1ab.tar.gz 577.6 Mb (ftp)(http) TAR
GSE137337_KDM2B_E8.5_1ab.tar.gz 593.3 Mb (ftp)(http) TAR
GSE137337_KMT2A_E8.5_1ab.tar.gz 587.0 Mb (ftp)(http) TAR
GSE137337_KMT2B_E8.5_1ab.tar.gz 534.1 Mb (ftp)(http) TAR
GSE137337_L3MBTL2_E8.5_1.tar.gz 296.4 Mb (ftp)(http) TAR
GSE137337_RAW.tar 6.0 Gb (http)(custom) TAR (of BW)
GSE137337_RNF2_E8.5_1ab.tar.gz 469.2 Mb (ftp)(http) TAR
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