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Chunk #50 — Online Methods — RNA-Sequencing

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The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.
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RNA was isolated from bilateral, dorsal hippocampus using the using RNeasy minikit (Qiagen, 74104). RNA quality was assessed by Bioanalyzer, and only samples with a RIN greater than 9 were included for analysis. cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina). Briefly, 3ug of total RNA from each animal was used as starting material. The mRNA was purified with poly-T oligo-attached magnetic beads and heat fragmented. The first and second strand cDNA were then synthesized and purified. The ends were blunted and the 3′ end was adenylated to prevent concatenation of the template during adapter ligation. For each group a unique adapter set was added to the ends of the cDNA and the libraries amplified by PCR. The quality of the library was assessed by Bioanalyzer and quantified using qRT-PCR with a standard curve prepared from a purchased sequencing library (Illumina). Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and