Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq of round spermatids comparing WT (FVBNJ) to H2A.B3 knock-out mice

ABSTRACT: The histone variant H2A.B3 (H2A.Bbd/H2A.Lap1) has a tissue-specific expression pattern and is found to be most highly expressed during spermatogenesis. In order to investigate the role of H2A.B3 in chromatin packaging and regulation of spermatogenesis we created a line of TALEN-edited FVBN mice in which a deletion was introduced into the single exon of the H2AFB3 gene. The deletion was confirmed by Sanger sequencing and off-target effects investigated using exome sequencing. The deletion is visible in the RNA-Seq data of KO mouse, and the deleterious effect on the H2A.B3 protein has been confirmed using immunohistochemistry.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Sebastian Kurscheid

PROVIDER: E-MTAB-7277 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA sequencing of mouse germ cells

Project description:Spermatogenesis is a recurring differentiation process that results in the production of male gametes within the testes. During this process, spermatogonial stem cells differentiate to form spermatocytes, which undergo two rounds of meiotic division to form haploid spermatids. Throughout spermiogenesis, round spermatids elongate to form mature sperm. To profile maturing germ cells during the first wave of spermatogenesis, we generated droplet-based single cell RNAseq from juvenile animals at post-natal day P5-P35 as well as adult animals. Cells were isolated from whole testes. Furthermore, to assay the robustness of the meiotic cell division process, we profiled germ cells of the trans-chromosomal mouse model (Tc1) that carries a copy of the human chromosome 21.

2019-01-25 | E-MTAB-6946 | biostudies-arrayexpress

Abnormal X chromosome inactivation and sex-specific gene dysregulation after ablation of FBXL10

Project description:The FBXL10 protein (also known as KDM2B, JHDM1B, CXXC2, and NDY1) is bound to essentially all CpG-rich promoters in the mammalian genome. FBXL10 is expressed as two isoforms: FBXL10-1, a longer form that contains an N-terminal JmjC domain with C- terminal F-box, CXXC, PHD, RING, and leucine rich repeat (LRR) domains, and FBXL10-2, a shorter form that initiates at an alternative internal exon and which lacks the JmjC domain but retains the other domains. Selective deletion of Fbxl10-1 had been reported to produce a minor and variable phenotype, and most mutant animals were essentially normal. We show here that deletion of Fbxl10-2 (in a manner that does not perturb expression of Fbxl10-1) resulted in a very different phenotype with craniofacial abnormalities, greatly increased lethality, and female sterility in surviving homozygous mutants. The phenotype of the Fbxl10-2 deletion was more severe in female mutants. We found that mutants that lacked both FBXL10-1 and -2 showed embryonic lethality and even more extreme sexual dimorphism, with more severe gene dysregulation in mutant female embryos. X-linked genes were most severely dysregulated, and there was marked overexpression of Xist in mutant females although genes that encode factors that bind to Xist RNA were globally down-regulated in mutant female as compared to male embryos. FBXL10 is the first factor shown to be required both for the normal expression and function of the Xist gene. Expression analysis using RNA-seq was performed on WT and Fbxl10T/T male and female embryos.

2016-05-31 | E-GEOD-76552 | biostudies-arrayexpress

RNA-Seq of Streptomyces venezuelae to compare global gene expression between the wild-type and BldB deletion strains after 10, 14 and 22 hours of growth.

Project description:BldB is a regulatory protein in Streptomyces and most species have a number of paralogs in their genomes. Deletion of BldB leads to a developmental deficiency and the colonies fail to produce aerial mycelium. In this experiment global gene expression was compared between the WT and BldB deletion strain of Streptomyces venezuelae NRRL B65442 after 10, 14 and 22 hours of growth in liquid cultures.

2023-04-14 | E-MTAB-12832 | biostudies-arrayexpress

Host-symbiont interactions in the chemosynthetic Riftia model symbiosis

Project description:The deep-sea tubeworm Riftia pachyptila is a model system for a mutualistic association: The adult worm has no digestive system, but completely relies on one phylotype of endosymbiotic chemosynthetic bacteria for nutrition. The bacteria, in turn, are provisioned by the host. Metabolism and physiology of this symbiosis, particularly of the uncultured symbiont, have been subject to various studies. Yet, how both partners interact on the molecular level remains largely unknown. To study these host-symbiont interactions in detail, we sequenced the R. pachyptila host transcriptome de novo, and conducted comprehensive metaproteomic comparisons of symbiont-containing and symbiont-free R. pachyptila tissues under energy-rich and energy-limiting conditions. Our results demonstrate that R. pachyptila invests a considerable part of its proteome to provision the symbionts with inorganic compounds. It acquires symbiont-derived biomass primarily by digesting parts of the symbiont population. The R. pachyptila immune system apparently not only protects the holobiont from pathogens, but is also involved in symbiont population control. The symbiont expresses a repertoire of proteins dedicated to communication with the host, including eukaryote-like proteins that may counteract phagocytosis. During energy limitation, i.e., when reduced sulfur compounds are lacking, the host apparently increases symbiont digestion. We show here an intricate network of interaction pathways that shapes the R. pachyptila holobiont. Together with the metabolic flexibility of the association under varying energy conditions, this probably forms the basis for the success of this tight association under the highly challenging deep-sea conditions.

2019-11-25 | PXD012439 | Pride

RNA sequencing of gamma-delta T cell subsets from young and old mice

Project description:Organismal ageing is associated with loss of immune function and higher incidence of cancer. Whether the γδ T cell pool changes upon organismal ageing is not known. In this study we have characterized γδ T cells in peripheral lymph nodes from old and young mice. We found that the γδ T cell pool is severely altered in old mice. The IL-17 producing γδ lineage becomes dominating while IFN-γ producing γδ1 T cells are declining. γδTCR sequencing revealed no collapse in diversity but oligoclonal expansions in Vγ4 γδ17 subsets. Pro-tumourigenic invariant Vγ6 cells are present only in aged lymph nodes, represent the majority of γδ T cells in the tumour, and are associated with faster tumour progression.

2019-05-22 | E-MTAB-7178 | biostudies-arrayexpress

Impact of Hells loss-of-function on DNA methylation in B cells during humoral immune responses: kinetic comparison of Mb1-Hells knockout and control mice by bulk RNA sequencing.

Project description:The transcriptomic impact of Hells loss-of-function was quantified by RNA sequencing of sample from conditional knockout (Mb1-Cre+/WT HellsF/F) and littermate control mice (Mb1-CreWT/WT HellsF/F). Three time points were chosen to follow the kinetic: day 0 for naïve B cells collection, day 7 and day 14 post NP-CGG intraperitoneal immunization for germinal center B cells collection. At each time point, 4 mice of each genotype were used. Live cells were FACS sorted (AriaIII) using surface markers as follows: B220+CD21+CD23+ for naïve B cells, and B220+CD95+GL7+ for germinal center B cells. Due to their low frequency, germinal center B cells were FACS-sorted twice using the same gating strategy. Collected samples were lysed and processed for RNA extraction.

2023-07-25 | E-MTAB-12638 | biostudies-arrayexpress

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RNA-Seq)

Project description:Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. Deletion of key components of Polycomb Repressive Complexes 1 and 2 did not lead to ectopic de novo methylation. These results indicate that FBXL10 defends Polycomb-occupied promoters against ectopic de novo methylation. FBXL10 is the first reported factor whose loss leads to a gain in genomic DNA methylation. DNA methylation analysis using RRBS and expression analysis using RNA-seq was performed on WT and Fbxl10T/T ES cells.

2015-04-06 | E-GEOD-65582 | biostudies-arrayexpress

Testis single-cell RNA-sequencing in the cynomolgus macaque reveals conserved transcriptional profiles during mammalian spermatogenesis

Project description:Spermatogenesis in mammals is a complex and highly orchestrated process, which involves the differentiation of diploid (2n-DNA content) spermatogonia into haploid (n) sperm. This process begins with spermatogonia, a niche of stem cells, which drive this process. Spermatogonial stem cells (SSCs) undergo mitotic self-renewal to maintain this niche, while sub-populations of spermatogonia progressively undergo differentiation and later gain competence to initiate meiosis and form sperm. SSCs undergo extensive chromatin remodelling and major morphological changes, while maintaining genome integrity and parental imprints. To study this in greater detail we performed single-cell RNA sequencing of spermatogenic cells derived from the testis of the non-human primate Macaca fascicularis.

2020-08-13 | E-MTAB-8979 | biostudies-arrayexpress

RNA-Seq of Streptomyces venezuelae NRRL B65442 to compare global gene expression between the wild-type and bldB deletion strain and, wild-type and bldB plus whiJ9 double mutant after 14 hours growth in liquid medium.

Project description:Expression of iosA is greatly activated in the bldB deletion strain. whiJ9 is divergently transcribed from iosA and the double mutant (whiJ9 + bldB) was made to determine if WhiJ mediates the activation of iosA in the absence of BldB.

2023-04-14 | E-MTAB-12836 | biostudies-arrayexpress

Transcriptional profile of XBP1-deficient ovarian cancer-associated dendritic cells (DCs)

Project description:ID8-based ovarian tumors were developed for 3 weeks in wild type (WT, N=3) or conditional knockout mice selectively deleting XBP1 in CD11c positive cells (KO, N=3). Tumor-associated DCs were independently sorted via FACS and used for transcriptional profiling. Total RNA from sorted tumor-associated DCs (N=3/genotype) was independently isolated using the miRVANA kit (Life Technologies) and further purified and concentrated using minElute columns (Qiagen). RNA integrity was confirmed using an Agilent Bioanalyzer 2100.

2015-06-11 | E-GEOD-68472 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data