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ABSTRACT: Pleurodeles Waltl Transcriptome assembly 2022

PROVIDER: PRJNA956320 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR24186616_1.fastq.gz	Fastqsanger.gz
	SRR24186616_2.fastq.gz	Fastqsanger.gz
	SRR24186617_1.fastq.gz	Fastqsanger.gz
	SRR24186617_2.fastq.gz	Fastqsanger.gz
	SRR24186618_1.fastq.gz	Fastqsanger.gz

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Project description:The goal of this study was to test if lipid-based cell hashing worked in salamander species and to test how lipid-based hashing compared to demultiplexing samples based on species origin and single nucleotide polymorphisms (SNP). Spleens were taken from four animals in total: one adult Pleurodeles waltl (female, 23.5grams and 16.1cm snout-to-tail, strain: tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon), one adult Pleurodeles waltl (male, 13.95g and 15.7cm, tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon), one adult Notophthalmus (female, 4.45g and 10.6cm, WT), and one adult Notophthalmus (male, 3.55g and 10.2cm, WT). Samples were stained with CM304 (Pleurodeles female), CMO305 (Pleurodeles male), and CMO306 (pool of both Notophthalmus samples) as per 10x Genomics 3’ Cellplex labeling protocol (Demonstrated Protocol, CG000391). These samples were processed through the 10x Controller and with Cellranger 7.0 using a dual species reference. The sample origin was determined by lipid-based hashing and then compared to mapping rates to each species transcriptome and using SNP-based demultiplexing.

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