Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 18
Access: Public
Diseases: Nervous System Diseases
Chemicals: Chloroform
Genes: MYRF
Taxon: Martes pennanti, Mus musculus
Dataset link Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells

Experimental Protocol


Cells were lysed directly in 1 ml of TRIzol (Thermo Fisher) and stored at -80°C. Once all samples were collected, samples were thawed on ice and RNA was separated with chloroform using Phase Lock Gel tubes (5prime). RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacture’s protocol. One microgram of each sample was then subject to ribosome depletion, fragmented, and library prepared using the TruSeq Stranded Total RNA Kit with Ribo Zero Gold (Illumina) according to the manufacturer’s protocol and indexed using TruSeq adapters. One hundred base pair paired-end reads were generated for each sample on the Illumina HiSeq 2500 (Case Western Reserve University Sequencing Core; Cleveland, OH). Samples include mESC derived oligodendrocyte progenitor cells (OPCs) from four different wildtype mouse strains at 0 hr, 24, hr, 48 hr, and 72 hr after treatment with thyroid hormone T3 (n = 4 biological replicates per time point). Two additional samples include mutant OPCs (shiverer and MYRF knockout 'delMYRF') at 72 hr time point.

Repositories


GEO

GSE97444

ENA

SRP103116

BioProject

PRJNA381794

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Contact


Paul Tesar