Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 20
Release date: Mar 11 2017
Last update date: Jun 10 2017
Access: Public
Diseases: DNA Repair-Deficiency Disorders
Dataset link A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress [RNA-seq]

Experimental Protocol


Synchronized, starved L1 stage worms were grown on NGM plates under one of two conditions. Condition 1: growth was at 20°C (hpl-2, let-418, lin-61, met-2 set-25, and wild-type N2) until the L4 stage and then worms were shifted to 25°C for 15-18 hours until they reached young adult stage. Condition 2: growth was at 15°C (lin-13, prg-1, nrde-2, nrde-2; let-418, and wild-type N2) until the L4 stage, and then worms were shifted to 25°C for 15-18 hours until they reached young adult stage. Worms were then washed off plates, flash frozen in liquid nitrogen, and stored at -80°C until use. RNA was extracted from frozen worms using TriPure (Roche). RNA was purified with Zymo Research RNA Clean and Concentrator-5 (Cambridge Bioscience) following DNase I digestion. Ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Two biological replicates were prepared for each strain.

Repositories


GEO

GSE87523

ENA

SRP090696

BioProject

PRJNA345014

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Contact


Julie Ahringer

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