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IlThoDeci

ABSTRACT: Tholera decimalis (feathered gothic), genomic and transcriptomic data

PROVIDER: PRJEB52580 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9682493_1.fastq.gz	Fastqsanger.gz
	ERR9682493_2.fastq.gz	Fastqsanger.gz
	ERR9682494_1.fastq.gz	Fastqsanger.gz
	ERR9682494_2.fastq.gz	Fastqsanger.gz
	ERR9682495_1.fastq.gz	Fastqsanger.gz

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1 - 5 of 17

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ilThoDeci

Project description:Tholera decimalis (feathered gothic)

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ilThoDeci1

Project description:Tholera decimalis (feathered gothic) genome assembly, ilThoDeci1

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ilThoDeci1 alternate haplotype

Project description:Tholera decimalis (feathered gothic) genome assembly, ilThoDeci1, alternate haplotype

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ilColPena

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ilThoDeci1.Wolbachia_sp_1

Project description:Wolbachia endosymbiont (group B) of Tholera decimalis genome assembly, ilThoDeci1.Wolbachia_sp_1

| PRJEB74850 | ENA

Promoter capture mESC and fetal liver

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Please note additional files included. These files were created using the following protocol: Significantly interacting regions were called using the GOTHiC BioConductor package (http://www.bioconductor.org/packages/devel/bioc/html/GOTHiC.html) as described in (Mifsud et al.).<br>Update on December 2015: the original additional file E-MTAB-2414.additional.1.zip contained an earlier iteration of processed data and not the one that was used for the published paper. The file now contains the correct list of interactions.

2015-02-01 | E-MTAB-2414 | biostudies-arrayexpress

tfGorAlbo

Project description:Gordius_albopunctatus, genomic and transcriptomic data

| PRJEB78907 | ENA

Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

ChIP-seq for embryonic chicken feather and scale samples

Project description:Feather evolution enabled feathered dinosaurs and early Mesozoic birds to venture into new ecological niches. Studying how feathers and scales are specified provides insight into how a new organ evolves. We use genome-wide analyses to identify feather-associated genes and test their feather-forming ability by expressing them in chicken and alligator scales. Intermediate morphotypes revealed five cardinal morphogenetic events: localized growth zone, follicle invagination, branching, feather keratin differentiation and dermal papilla formation. In contrast to molecules known to induce feathers on scales (retinoic acid, beta-catenin), we identify novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce only one or several of the five regulatory modules. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, while others demonstrate some characteristics of modern feathers. We propose that at least five morpho-regulatory modules were used to diversify ancient reptile scales. The regulatory combination and hierarchical integration led to extant feather forms.

2017-12-31 | GSE87248 | GEO

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