Core-shell organization in the mouse claustrum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA628885 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Excitatory neurons form the long-range outputs of the claustrum. Here, we examined diversity in this cell type using single-cell RNA-seq.
2021-08-11 | GSE149495 | GEO
Project description:The appearance of hard mineralized exoskeletons is a critical leap for animal evolution and partially lead to the explosion of diverse animals during the Cambrian, for example, molluscs. A majority of molluscs have mineralized shells to protect themselves. Despite numerous studies that have studied the remarkable mechanical properties of shells, the origin of shell formation is still elusive. Hence, this study investigated the overlooked shell proteome of chitons, which belong to polyplacophoran, Aculifera of Mollusca. By comparing the shell proteome to well-studied Conchifera groups, we inferred possible ancestral biomineralization toolkits of stem-group Mollusca. Taking advantage of the recently sequenced chiton mantle transcriptome and genome, eight core biomineralization proteins were identified by proteomics. Surprisingly, in contrast to previous thought that shell formation is convergently evolved, two important shell matrix proteins, Nacrein-like and Pif-like proteins were found to be conserved among Aculifera and Conchifera groups. Our findings identify a missed link of mineralized shell evolution in Mollusca and pose a hypothesis that stem-group molluscs have already evolved core biomineralization toolkits, which likely facilitate the formation of mineralized shells for protection that partially leads to their explosion.
2023-01-03 | PXD033490 | Pride
Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. To determine whether the occlusions are consistent in mammalian pluripotent cells, we performed the same analyses in mouse embryonic stem cells and found similar relationships. MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)
2013-10-29 | E-GEOD-51766 | biostudies-arrayexpress
Project description:Strain N16961 was incubated with crab shell in artificial seawater media for 24 hours. cDNA from 1 ug RNA was labeled with Cy3 (planktonic bacteria) and Cy5 (crab attached bacteria). A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. Keywords: growth_condition_design
2005-08-11 | GSE3102 | GEO
Project description:Molluscan larval ontogeny is a highly conserved process typical of 3 principal developmental stages. A characteristic unique to each of these stages is shell design, termed prodissoconch I, prodissoconch II and dissoconch. These shells vary in morphology, mineralogy and microstructure. The discrete temporal transitions in shell biomineralization between these larval stages are utilized in this study to investigate transcriptional involvement in several distinct biomineralization events. Scanning electron microscopy and X-ray diffraction analysis of P. maxima larvae and juveniles collected throughout post-embryonic ontogenesis, document the mineralogy and microstructure of each shelled stage as well as establishing a timeline for transitions in biomineralization. P. maxima larval samples most representative of these biomineralization distinctions and transitions were analyzed for differential gene expression on the microarray platform PmaxArray 1.0. A number of transcripts are reported as differentially expressed in correlation to the mineralization events of P. maxima larval ontogeny. Some of those isolated are known shell matrix genes while others are novel, these are discussed in relation to potential shell formation roles. This interdisciplinary investigation has married the shell developments of P. maxima larval ontogeny with corresponding gene expression profiles, furthering the elucidation of shell biomineralization. Keywords: Temporal expression profiling by array
2010-02-05 | GSE14305 | GEO
Project description:Herein, bis(zinc(II)-dipicolylamine) functionalized sub-2 μm core-shell silica microspheres (SiO2@DpaZn) were tailored for N-phosphopeptide enrichment at pH 7.7. Contributed by the coordination bonding between Zn(II) and phosphate groups with the KD value of 13.14 μM, N-phosphopeptides could be captured efficiently under neutral conditions. Moreover, contributed by the core-shell structure of SiO2@DpaZn, the fast on-tip enrichment ensured the recovery of N-phosphopeptides up to 44.1%, 3-fold higher than that obtained by in-solution capture. Moreover, 40 determined N-pho sites on 32 substrates were identified in E. coli lysates, among which five had kinase activity. All these results demonstrate that our method is beneficial to promote the discovery of N-phosphoproteins with significant biological functions.
2020-08-22 | PXD021067 | iProX
Project description:Herein, bis(zinc(II)-dipicolylamine) functionalized sub-2 μm core-shell silica microspheres (SiO2@DpaZn) were tailored for N-phosphopeptide enrichment at pH 7.7. Contributed by the coordination bonding between Zn(II) and phosphate groups with the KD value of 13.14 μM, N-phosphopeptides could be captured efficiently under neutral conditions. Moreover, contributed by the core-shell structure of SiO2@DpaZn, the fast on-tip enrichment ensured the recovery of N-phosphopeptides up to 44.1%, 3-fold higher than that obtained by in-solution capture. Moreover, 40 determined N-pho sites on 32 substrates were identified in E. coli lysates, among which five had kinase activity. All these results demonstrate that our method is beneficial to promote the discovery of N-phosphoproteins with significant biological functions.
2020-06-12 | PXD019734 | iProX
Project description:Herein, bis(zinc(II)-dipicolylamine) functionalized sub-2 μm core-shell silica microspheres (SiO2@DpaZn) were tailored for N-phosphopeptide enrichment at pH 7.7. Contributed by the coordination bonding between Zn(II) and phosphate groups with the KD value of 13.14 μM, N-phosphopeptides could be captured efficiently under neutral conditions. Moreover, contributed by the core-shell structure of SiO2@DpaZn, the fast on-tip enrichment ensured the recovery of N-phosphopeptides up to 44.1%, 3-fold higher than that obtained by in-solution capture. Moreover, 40 determined N-pho sites on 32 substrates were identified in E. coli lysates, among which five had kinase activity. All these results demonstrate that our method is beneficial to promote the discovery of N-phosphoproteins with significant biological functions.
2020-02-07 | PXD017423 | iProX
Project description:Strain N16961 was incubated with crab shell in artificial seawater media for 24 hours. cDNA from 1 ug RNA was labeled with Cy3 (planktonic bacteria) and Cy5 (crab attached bacteria). A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. Using regression correlation
2005-08-11 | E-GEOD-3102 | biostudies-arrayexpress