organism: Mus musculus
description: Total RNA was purified from undifferentiated D3, E14, PRMT1-/-, shSCR and shPRMT1 cells by using TRIzol reagent. RNA-seq experiments were carried out using biological replicates. Library preparation and sequencing was performed at the Centre National de Genotypage (CNG) Paris. Briefly, indexed cDNA libraries were prepared from 1 microgram of total RNA following the TruSeq(TM) RNA Sample Preparation Kit (Illumina, Inc.) protocol. mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94Celsius for 5 min. The reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA) . The average size of insert was 132+-17 bp. The paired-end 100bp reads sequencing of the cDNA libraries was performed on pools of 4 samples in equal ratio in a single lane of the Illumina Hiseq 2000 sequencer. Quality criteria were checked during the run (Q30, base distribution, error rate, etc.). Raw images were processed for base calling and fastq files went through a quality check pipeline (duplication rate, coverage, number of genes/transcripts, etc.).
attributes.tag: strain
attributes.value: 129Sv
attributes.tag: age
attributes.value: embryo, blastocyst
attributes.tag: biomaterial_provider
attributes.value: Istvan Szatmari, Tomo Saric
attributes.tag: sex
attributes.value: male
attributes.tag: tissue
attributes.value: embryo
attributes.tag: BioSampleModel
attributes.value: Model organism or animal