2 protocols
Basecalling performed using RTA version 1.13.48 Demultiplexing performed using CASAVA version 1.8.2 Alignments to reference assembly mm9 performed using ELAND v2e and bowtie version 0.12.8 Filtering and selection performed using in-house tools Expression analysis performed using CASAVA version 1.8.2 Differential analysis performed using CyberT: http://cybert.ics.uci.edu Genome_build: mm9 Supplementary_files_format_and_content: RPKM values for each replicate have been combined in a single text file (RPKM_Values.txt), the differential analysis results from CyberT have been summarized and annotated in a single excel file (Differential_Analysis.xls)
nucleic acid library construction protocol
RNA was isolated from bilateral, dorsal hippocampus using the using RNeasy minikit (Qiagen, 74104). cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (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 sequenced on an IlluminaHiSeq 2000 instrument during a single-end 50 cycles sequencing run by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine.