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ERX4517448: NextSeq 500 sequencing; RNA-seq of Nematostella NvLsd1 mutants
1 ILLUMINA (NextSeq 500) run: 57.4M spots, 4.9G bases, 1.8Gb downloads

Design: RNA-seq of Nematostella NvLsd1 mutants
Submitted by: Sars Centre for Marine Molecular Biology
Study: RNA-seq of Nematostella NvLsd1 mutants
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RNAseq was performed on NvLsd1 mutants and controls (consisting of NvLsd1GFP/- and NvLsd1GFP/GFP animals) in quadruplicate at two different developmental stages: 4 day-old late planula and 13 day-old primary polyp
Sample: Polyp Control 4
SAMEA7302646 • ERS5061204 • All experiments • All runs
Name: Polyp Control 4_s
Instrument: NextSeq 500
Strategy: RNA-Seq
Selection: Oligo-dT
Layout: SINGLE
Construction protocol: We performed an NvLsd1GFP/- x NvLsd1GFP/- cross. 75% of the animals have at least one copy of the NvLsd1GFP allele, hereafter called control, and the homozygous mutant animals are GFP negative, hereafter NvLsd-/-. Anaimals were separated based on whether they were GFP negative or positive and 50 animals were used per sample. 50 animals per sample were lysed in 500 μl TRIzol reagent (Invitrogen, 15596026) by vortexing extensively and incubated at RT for 5 minutes. 100 μl of chloroform was added and mixed vigorously and the aqueous component was isolated using MaXtract High Density tubes (Qiagen, 129046) using the manufacturers protocol. One volume of 100% Ethanol was added to the aqueous phase. This was then processed using an RNeasy Micro Kit (Qiagen, 74004) using the manufacturers protocol including on column DNase digestion using the RNase-Free DNase Set (Qiagen, 79254). RNA quality was assessed using an RNA 6000 Pico Kit (Aligent, 5067-1513) and concentration determined using the Qubit™ RNA HS assay kit (Invitrogen, Q32852). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L), with following changes: 25ng RNA input, 1/100 adaptor dilution, 14 PCR cycles.
Experiment attributes:
Experimental Factor: genotype: Control (NvLsd1GFP/- and NvLsd1GFP/GFP )
Experimental Factor: developmental stage: primary polyp
Runs: 1 run, 57.4M spots, 4.9G bases, 1.8Gb
Run# of Spots# of BasesSizePublished


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