Small RNA analysis of wildtype Mouse embryo and Adar1 null mouse embryo at E11.0 and E11.5 together with mRNA-seq results of E11.5
ABSTRACT: Adar1 is an essential gene for mouse embryonic development. Adar1 null mouse embryos dies around E11.5 because of massive apoptosis. Small RNA: 4 samples examined: wild type E11.0, ADAR1 null E11.0, wild type E11.5, ADAR1 null E11.5, mRNA-seq: wild type E11.5, ADAR1 null E11.5.
Project description:Total mRNA seq was perfomed on widtype and Ret null mouse embryonic gut at 2 stages of devlopment- E11.5 and E12.5 Overall design: Total RNA from 3 replicates each of wildtype and Ret null emryonic gut was converted to cDNA and run on HiSeq 2000 (75 bp paired end)
Project description:Heterozygous and homozygous Pax2 E11.5 embryos were collected and the intermediate mesoderm was dissected and dispersed into single cells. The Pax2 positive cells also expressed EGFP, which was knocked into the Pax2 locus. EGFP positive cells were sorted by FACS and RNA isolated. We compared RNA expression levels in EGFP positive cells from Pax2 null and Pax2 heterozygote embryos.
Project description:We used transgenic mouse embryos that are deficient in the two enzymatically active RNA editing enzymes ADAR1 and ADAR2 to compare relative frequencies but also sequence composition of mature miRNAs in these genetically modified backgrounds to wild-type mice by Illumina next gen sequencing. Deficiency of ADAR2 leads to a reproducible change in abundance of specific miRNAs and their predicted targets. Changes in miRNA abundance seem unrelated to editing events. Additional deletion of ADAR1 has surprisingly little impact on the mature miRNA repertoire, indicating that miRNA expression is primarily dependent on ADAR2. A to G transitions reflecting A to I editing events can be detected at few sites and at low frequency during the early embryonic stage investigated. Again, most editing events are ADAR2 dependent with only few editing sites being specifically edited by ADAR1. Besides known editing events in miRNAs a few novel, previously unknown editing events were identified. Some editing events are located to the seed region of miRNAs opening the possibility that editing leads to their retargeting. GSM852140-8: sequencing of mature miRNAs of wt, ADAR2-/- and ADAR1-/-/ADAR2-/- female mouse embryos at E11.5 GSM863778-81: Gene expression was measured in wiltype, ADAR2-/- and ADAR1-/-/ADAR2-/- E11.5 whole female mouse embryos using Agilent Whole Mouse Genome Oligo Microarrays 8x60K.
Project description:Targeted deletion of skNAC in mice resulted in early embryonic lethality with cardiac defects. In order to investigate the molecular mechanism of the cardiac defect, we designed the microarray comparing gene expression of the mutant E11.5 heart to wild type E11.5 heart. Keywords: genetic modification in mouse 3 for each genotypes, comparing Littermates of E11.5, total RNA (500ng) from ventricles, Affymetrix GeneChip Mouse Genome 430 2.0 Array
Project description:The cell identities of CD49f+GSCs were further identified by comparing them with the E11.5 PGCs and P2 GSCs. The transcriptomic analysis revealed that the CD49f+GSCs had 1/3 similar genes profile to the E11.5 PGCs and P2 GSCs. Further gene ontology (GO) analysis demonstrated that the E11.5 PGCs, P2 GSCs, and CD49f+GSCs shared the partial similar gene expression profile of pluripotency regulation signaling pathway, PI3K-AKT signaling, chemokine signaling, and HIF-1 signaling. Overall design: Isolation of the gonadal cells from 67 E11.5 ICR embryos, and testicular cells from 80 newborn to P2 ICR mice (0- to 2-day-old postpartum), followed by stem cell colony formation under 5% O2 hypoxia for 7 days, and subjected to transcriptome analysis. Meanwhile, CD49f+GSCs from 100 newborn to P2 ICR mice were purified and subjected to transcriptome analysis.
Project description:We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis. Transcriptome analysis of E11.5 mouse embryos: 16 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents; and 154 N2 embryos from reciprocal backcross of F1s to the C57BL/6J parent.
Project description:The aim of this experiment was to profile the DNase-I accessibility landscape of E11.5 whole mouse embryos. Separate fractions were taken for DNA cleavages of length 50-100bp and 175-400bp.
Project description:We preformed RNA sequencing on control and Prmt5cKO embryos at E11.5 to determine differentially expressed genes resulting from a loss of Prmt5. Overall design: We generated three control and two Prmt5cKO biological replicates for RNA sequencing
Project description:To gain insight into the role of Runx3 in TrkC neurons we performed RNA-seq on E11.5 TrkC neurons isolated from cervical ganglia of Runx3-P2+/- and Runx3-P2-/- mice Overall design: Runx3-P2 mice express GFP in TrkC neurons enabling the FACS isolation of TrkC neurons from E11.5 embryos, Heterozygote Runx3-P2+/-(n=pool of 4) and homozygote Runx3-P2-/- (n=pool of 4) TrkC/GFP neurons were isolated,