RNA-seq of mus musculus: juvenile female hippocampus born to Heligmosomoides bakeri infected dam
Tissue samples: On postnatal day 23 hippocampi were rapidly removed bilaterally, immediately flash frozen in liquid nitrogen, then stored at -80C. Hippocampal samples were sent to Genome Quebec for total RNA extraction and sequencing and FASTQ files were obtained. No pooled samples were used. Homogenization: 900L of RNeasy Plus Universal Mini Kit provided lysis buffer reagent (i.e. QIAzol) was added to previously weighted tissue (10-15 mg). Homogenization was done using a  QIAGEN TissueLyser II with 5 mm stainless beads, for 2 cycles of 30Hz x 2 min plus 1 cycle of 30 Hz x 1 min.  Extraction: Total RNA extraction was performed using the RNeasy Plus Universal mini kit (QIAGEN, cat.73404) according to the manufacturer's instructions. RNA was eluted in 35l buffer provided with the extraction kit. RNA quality was determined by the RNA Integrity Number (RIN), measured by 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano kit, following the manufacturers protocol. Library preparation: Libraries were generated from 250 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation Kit (Illumina), as per the manufacturers recommendations. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument. Sequencing: Libraries were normalized and pooled and then denatured in 0.02N NaOH and neutralized using HT1 buffer. The pool was loaded at 175pM on an Illumina NovaSeq 6000 S4 lane using Xp protocol as per the manufacturers recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate FASTQ reads.