Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

ABSTRACT: The RNA-seq experiment was designed to determine the effects of blastocyst transfer on the transcriptome of whole placentas at embryonic day (E) 10.5. C57Bl/6 blastocysts that were from natural matings without superovulation were transferred into the uteri of pseudopregnant B6D2F1 females (at gestational day 2.5 equivalent). RNA libraries were prepared from whole male placentas at E10.5 (N = 4 placentas) from the transfer group alongside RNA libraries from control placentas from C57Bl/6 conceptuses derived from natural matings and did not undergo the transfer process (N = 4 placentas). Libraries were muliplexed and pooled for sequencing on the Illumina NextSeq500 platform with 75-base-pair single-end reads. Sequencing was performed in duplicate to provide at least 18 million reads per sample, and 1% PhiX Control (Illumina) spike-in was used. Quality control of Fastq files was performed using FastQC and fastq_screen. Sequences were trimmed with Trim Galore!, and alinged to GRCm38 mouse genome using STAR aligner.Alignments were processed using custom ClusterFlow (v0.5dev) pipelines and assessed using MultiQC (0.9.dev0). Gene quantification was determined with HTSeq-Counts (v0.6.1p1). Additional quality control was performed with rRNA and mtRNA counts script, feature counts (v 1.5.0-p2) and qualimap (v2.2). Differential gene expression was performed with DESeq2 package (v1.16.1, R v3.4.0). Read counts were normalised on the estimated size factors.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Malwina Prater

PROVIDER: E-MTAB-8036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction. In vivo genome-wide examination of binding sites of the transcription factor GRHL2 by ChIP-seq using wild-type murine E17.5 placenta tissue. Two samples in total: one GRHL2 ChIP sample and one IgG ChIP sample using wild-type placentas tissue as antibody control.

Dataset Information

RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

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