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SRX16369899: GSM6364816: 2 hpf; Lytechinus variegatus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 406.2M spots, 121.9G bases, 56.5Gb downloads

External Id: GSM6364816_r1
Submitted by: Brown University
Study: Elements of divergence in germline determination in closely related sea urchin species
show Abstracthide Abstract
Evolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germline in which fitness is a direct readout of evolutionary change. Here, we focused on two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched scRNA seq datasets from these two sea urchins revealed, amongst others, a broader expression of Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). In Sp, Nanos2 mRNA expression is highly restricted to the PGCs by a lability element in its 3'UTR. This element is lacking in Lv Nanos2, explaining how this mRNA more broadly accumulates in the Lv embryos. We discovered that the Lv Nanos2 3'UTR instead leads to a germline specific translation of the protein. The results emphasize that regulatory mechanisms resulting in germline diversity rely less on transcriptional regulation and more on post-transcriptional and post-translational restrictions of key gene products, such as Nanos2. Overall design: Developmental time points in the sea urchin Lytechinus variegatus and integration with the sea urchin Strongylocentrotus purpuratus dataset
Sample: 2 hpf
SAMN29855639 • SRS14007078 • All experiments • All runs
Library:
Name: GSM6364816
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3' Reagent kit v3 Chemistry. Libraries were sequenced by Genewiz on the Illumina Hiseq (2x150 bp paired-end runs). Single cell unique molecular identifier (UMI) counting was performed using Cell Ranger Single Cell Software Suite 3.0.2 from 10X Genomics. Duplicate blastula and gastrula stage libraries were aggregated using the cellranger aggr function. Cellranger gene expression matrices were further analyzed using the R package Seurat v 3.1.4. A seurat object was created by simply combining the individual datasets and then normalized by scaling gene expression in each cell by total gene expression. The top 2000 highly variable genes were then used for downstream analysis. The batch effects between samples were corrected by Harmony with default setting. UMAP analysis was performed with the following parameters: dims = 1:20, resolution = 1.
Runs: 1 run, 406.2M spots, 121.9G bases, 56.5Gb
Run# of Spots# of BasesSizePublished
SRR20336826406,168,030121.9G56.5Gb2023-01-19

ID:
23090776

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