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4 protocols using agilent bioanalyzer rna pico chip

1

RNA-seq Library Preparation Protocol

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RNA isolation was performed using the RNAeasy Plus Mirco Kit according to the manufacturer’s instructions. RNA quality and quantity was assessed by Agilent Bioanalyzer RNA Pico chip. Only samples with RIN > 6 were further processed. 50ng to 500ng of total RNA was used for cDNA generation utilizing the SMART-seq v4 Ultra low input RNA kit from Clontech. From these cDNAs, libraries were generated with the Illumina Nextera XT kit. cDNA and library samples were always analyzed by Agilent Bioanalyzer HS DNA chip for quality control and quantification. Up to 24 libraries were pooled and sequenced paired-ended using an Illumina HiSeq4000.
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2

RNA Sequencing Library Preparation

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RNA was prepared immediately using RNeasy purification kits (Qiagen) and quantified using Qubit 3.0 (ThermoFisher). RNA integrity was assessed using Agilent BioAnalyzer RNA Pico chip. Samples were submitted for Ribo-zero rRNA depletion (Illumina) and reassessed for RNA integrity. Samples were processed into libraries by the Ovation RNA-Seq System v2 (NuGEN) protocol. Quality control was performed on libraries using the KAPA qPCR QC assay (KAPA Biosystems). Libraries (36 total) were sequenced on an illumina HiSeq 1500 at the Marshall University Genomics Core facility, 2 × 50 bp resulting in ~16 M reads per sample. Sequencing data was deposited to the Sequence Read Archive (reference number SRP130256, BioProject number PRJNA430726).
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3

Isolation and Analysis of Cardiac RNA

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The cardiac samples stored at −80 °C for whole-transcriptome and miRNA analysis were processed with a Precellys 24 homogenizer with ceramic beads (Bertin Technologies, Montigny-le-Bretonneux, France). RNA was isolated with TRIzol reagent and treated with DNase I. An Agilent Bioanalyzer RNA pico chip (Agilent Technologies Inc., Santa Clara, CA, USA) was used to evaluate the integrity of RNA, and a Qubit RNA kit (Thermo Fisher Scientific Inc., Waltham, MA, USA) was used to quantitate RNA.
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4

Mosquito Pooling and RNA Extraction

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Collected mosquitoes were pooled per species, season, and collection location (indoor/outdoor) to a total of 10 mosquitoes maximum per minipool, and homogenized with 500 µL of PBS using a MagnaLyser version 1.1 (Roche, Mannheim, Germany) at 6000 rpm for 1 min. Crushing material was centrifuged for 2 min at 12,000× g and 4 °C, then 167 µL of supernatant was transferred individually to 835 µL of RNA later solution (Invitrogen). The mixture was incubated overnight at 4 °C and stored at −80 °C until shipment to Institut Pasteur in Paris. According to the mosquito species season and collection location (indoor/outdoor), minipools were combined to form large pools that contained a maximum of 100 mosquitoes per pool (Table S1). A total of 6646 mosquitoes were selected and subsequently distributed across 103 large pools. Overall, total RNA was extracted from the 103 large pools of mosquitoes in a Biosafety Level 3 (BSL-3) laboratory using the Maxwell RSC simply RNA tissue kit (Promega, Madison, WI, USA), according to the manufacturer’s instructions. RNA extracts were quantified with the Qubit RNA High sensitivity assay (Invitrogen, Waltham, MA, USA) and analyzed using an Agilent BioAnalyzer RNA pico chip (Agilent, Waldbronn, Germany).
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