run_metadata: 76470
This data as json
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| 76470 | SRR24976460 | SRX20733648 | SRS18024487 | SRP445049 | PRJNA985650 | Ancient vertebrate dermal armor evolved from trunk neural crest | GSE235280 | Other | Bone is an evolutionary novelty of vertebrates likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor we have performed in vivo lineage tracing in the sterlet sturgeon a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone dentin and hypermineralized covering tissues in various combinations that resemble those of the first armored vertebrates. Taken together our results support a primitive skeletogenic role for the neural crest along the entire body axis that was later progressively restricted to the cranial region during vertebrate evolution. Thus the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor we performed bulk RNA sequencing of sterlet sturgeon scutes scales of the Senegal bichir and zebrafish scales. | pubmed:37459514 | Zebrafish scale 30mm replicate 2 | GSM7498272 | source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing | Zebrafish scale 30mm replicate 2 | In brief every sterlet/bichir protein sequence was queried locally against the zebrafish proteome following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al. 2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample | cells of elasmoid scale | RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols. | tissue:cells of elasmoid scale|genotype:WT|measure:30 mm | GSM7498272 | GSM7498272: Zebrafish scale 30mm replicate 2; Danio rerio; RNA Seq | GSM7498272 r1 | GSM7498272 | 1 | RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP445049 | DR_scale_2.fastq.gz | fastq | 3233423900.0 | 64668478.0 | GSM7498272 r1 | 0:50 | A:867694073;C:728518022;G:750424718;T:885367521;N:1419566 | 50 | 867694073 | 728518022 | 750424718 | 885367521 | 1419566 | SRX20733648 | SRS18024487 | SRA1659604 | Bronner, California Institute of Technology | Bronner, California Institute of Technology | 1 | 0.89607 | 0.08896 | 0.72612 | 0.4695 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2023-06-20 | Undetermined | Undetermined | Scale | Surface Structure |