Similar protocols

Protocol publication

[…] Strand-specific libraries were prepared as previously described (). Briefly, brain and liver were collected from nicotine-exposed and control F1 males. Hepatocytes were isolated as described above. For the hippocampus, after sectioning of brain into 1 mm slices, areas of interest were identified according to the Mouse Brain Atlas by Paxinos and Franklin and dissected using 0.5 mm punches.RNA from brain and liver was isolated using standard TriZol protocols, followed by rRNA depletion (RiboZero kit, Illumina, Inc.). After first- and second-strand synthesis, adapters were ligated to fragments and amplified using multiplexed PCR primers. Libraries were sequenced on a NextSeq 500 platform from Illumina, Inc. Quality-controlled reads were aligned to the reference genome (Mus musculus/mm10) with Bowtie2 and differential expression was calculated using DESeq2. For multiple comparison adjustments, we used Holm-Bonferroni correction as a more conservative approach.RNA-Seq data are available at GEO, accession # GSE94059. […]

Pipeline specifications

Software tools Bowtie2, DESeq2
Application RNA-seq analysis
Organisms Mus musculus
Chemicals Cocaine, Nicotine