Shape-Dependent Interactions of Gold Nanoparticles with Microalgae: Distinct Cellular and Molecular Responses
Description
mRNA-sequencing raw data. Method: We collected algae after 72 h exposure to 10 mg/L AuNP and AuNS for RNA-seq to analyze mRNA expression. Chlamydomonas_reinhardtii (Version: CC-503 cw92 mt+). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 criteria with the R package edgeR(https://bioconductor.org/packages/edgeR). Results: RNA sequencing identified 9 upregulated and 38 downregulated differentially expressed genes (DEGs) in the 10 mg/L AuNP treated cells, impairing photosynthesis and energy storage via the photosystem II subunit S1 (PSBS1)/ early light-inducible protein (ELI3) pathway. In contrast, the AuNS group exhibits 246 upregulated and 145 downregulated DEGs, affecting membrane integrity and nitrogen metabolism through the nitrate reductase (NIT1)/ aminomethyl transferase (AMT1)/ protein kinase domain-containing protein (A0A2K3CRU5) pathway.
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I got the data from Novogene company, details method: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Each sample’s RNA amount and purity was quantified using NanoDrop ND-1000 (NanoDrop, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50 μg total RNA using Dynabeads Oligo (dT) 25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then, the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA) under 86℃ for 7 min. An A-base was added to the blunt ends of each strand in preparation for the ligation of the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After heat-labile UDG enzyme (NEB, cat. m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. Finally, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform (CA, USA) following the vendor's recommended protocol. The sequence quality of the mRNA samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/). We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome Chlamydomonas_reinhardtii (Version: CC-503 cw92 mt+). Peak calling and diff peak analysis were performed in the R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using the R package ANNOVAR (http://www.openbioinformatics.org/annovar/). StringTie (https://ccb.jhu.edu/software/stringtie) was used to assess the expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 criteria with the R package edgeR(https://bioconductor.org/packages/edgeR).