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Transcriptional analysis of anole lungs at E18

ABSTRACT: This project aims to establish the embryonic anole lung as a model for investigating lung development and more general epithelial morphogenesis by generating a set of single-cell RNA-seq (scRNA-seq) data from late-stage embryonic lungs taken from brown anoles (Anolis sagrei). The anole lung, with its simple architecture, provides a novel tool for investigating signaling in a less complex respiratory system than the murine lung, and this data set would be a large advance in making this system more widely known and accesible among developmental biologists.

ORGANISM(S): Anolis sagrei

PROVIDER: GSE182814 | GEO | 2021/08/30

REPOSITORIES: GEO

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Transcriptional analysis of anole lungs at E18

Project description:Transcriptional analysis of anole lungs at E18

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Project description:Anolis carolinensis embryos were collected 0-1 days post egg laying, and total RNA was extracted for RNA-Seq analysis (Illumina Hi-Seq2000). Transcriptome sequence from these stages in the green anole, equivalent to mouse 9.5-10.5 dpc embryos, will help to improve gene annotations in A. carolinensis and provide expression level information for key organogenesis and patterning processes. Anolis carolinensis embryos were collected 0-1 days post egg laying for RNA-Seq analysis. The two embryos collected were at 28 somite-pair (28S) and 38 somite-pair (38S), equivalent to mouse 9.5 dpc and 10.5 dpc embryos, respectively. Total RNA was extracted using the total RNA component of the mirVana (Ambion) kit, RNA-Seq library prep was carried out using the NuGEN Ovation RNA-Seq kit, and sequencing was carried out on an Illumina HiSeq 2000, following the manufacturer's protocol. The untrimmed data was then aligned to the Anolis carolinensis reference genome (Anocar2.0) using tophat. Published: Eckalbar WL, Lasku E, Infante CR, Elsey RM, Markov GJ, Allen AN, Corneveaux JJ, Losos JB, DeNardo DF, Huentelman MJ, Wilson-Rawls J, Rawls A, Kusumi K. Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock. Dev Biol. DOI: 10.1016/j.ydbio.2011.11.021

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Project description:In order to study the green anole dosage compensation mechanism we generated strand-specific RNA-seq libraries for a total of 186 samples from the green anole and other representative amniotes (human, mouse, opossum, platypus, chicken and xenopus). Moreover, in order to understand the dosage compensation mechanism of A. carolinensis, we generated ChIP-Seq data for the histone modification H4K16ac and compared levels of acetylation between males and females. Moreover, we reconstructed 7 Y-linked transcripts of Anolis carolinensis based on a male/female subtraction approach and validate these Y sequences using re-sequenced genomes.

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The transcriptome of embryos of the green anole, Anolis carolinensis, at 28 and 38 somite pair stages

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