Transcriptomic analysis of active proliferation arrest in Lemna minor under elevated CO₂ and low-nutrient stress

Description / Abstract:This dataset accompanies the study Li et al., Growth arrest in Lemna minor under elevated CO₂ and low nutrients, submitted to New Phytologist.It includes gene-expression matrices and associated metadata for Lemna minor plants exposed for three days to either ambient (430 ppm) or elevated (860 ppm) CO₂ under nutrient-limited conditions. RNA-Seq was performed on six biological replicates on the Illumina NovaSeq 6000 platform (151 bp paired-end). The dataset supports the identification of transcriptomic signatures associated with active proliferation arrest under combined mild environmental stress.Raw FASTQ files are available via the NCBI Sequence Read Archive. Please see the attached table NCBI_SRA_Table.xlsx for details. =====================FILES:counts_1vs2.txt Raw integer counts (featureCounts output). Rows = genes, columns = samples. Raw processed data matrix used for DESeq2 input.tpm_counts_1vs2.txt TPM-normalized gene expression matrix for all samples. Final processed (normalized) data.DEG_1v2.txt Differential expression results for Condition 1 vs Condition 2 (the main comparison: eCO₂ vs aCO₂ under low nutrients). Columns include log₂ fold change, p-value, adjusted p-value, and gene annotation.NCBI_SRA_Table.xlsx: SRA accession numbers =====================SAMPLE SUMMARY=====================1=libraryName 2=SampleId 3=rawReads 4=filteredReads 5=sampleName 6=conditionNumber 7=groupName 8=sequencerType 9=runType 10=fileUsedNBBPO 274776 110508488 107812062 SaniHighCO2-1 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.CTCCTAGA-CTCCTAGA.filter-RNA.fastq.gzNBBPP 274777 95183854 93226546 SaniHighCO2-2 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.TCTGAGAG-TCTGAGAG.filter-RNA.fastq.gzNBBPS 274778 119946420 117517110 SaniHighCO2-3 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.GGACAATC-GGACAATC.filter-RNA.fastq.gzNBBPT 274779 96421438 94265388 SaniHighCO2-4 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.AAGTGTCG-AAGTGTCG.filter-RNA.fastq.gzNBBPU 274780 144270930 141264996 SaniHighCO2-5 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.CACAAGTC-CACAAGTC.filter-RNA.fastq.gzNBBPW 274781 133472466 130889178 SaniHighCO2-6 1 SaniHighCO2 NovaSeq S4 2x151 52704.3.422276.GTGTTCCT-GTGTTCCT.filter-RNA.fastq.gzNBBPX 274782 57978500 56667544 SaniAmbCO2-1 2 SaniAmbCO2 NovaSeq S4 2x151 52704.3.422276.CATAACGG-CATAACGG.filter-RNA.fastq.gzNBBPY 274783 88056716 86539114 SaniAmbCO2-2 2 SaniAmbCO2 NovaSeq S4 2x151 52704.3.422276.TGATGTCC-TGATGTCC.filter-RNA.fastq.gzNBBPZ 274784 84540154 83013788 SaniAmbCO2-3 2 SaniAmbCO2 NovaSeq S4 2x151 52702.2.421814.GTACTCTC-GTACTCTC.filter-RNA.fastq.gzNBBSA 274785 140711236 135337324 SaniAmbCO2-4 2 SaniAmbCO2 NovaSeq S4 2x151 52702.2.421814.CAGGAGAT-CAGGAGAT.filter-RNA.fastq.gzNBBSB 274786 79675562 77668868 SaniAmbCO2-5 2 SaniAmbCO2 NovaSeq S4 2x151 52702.2.421814.TGGTACAG-TGGTACAG.filter-RNA.fastq.gzNBBSC 274787 147891374 143769438 SaniAmbCO2-6 2 SaniAmbCO2 NovaSeq S4 2x151 52702.2.421814.AACCGTTC-AACCGTTC.filter-RNA.fastq.gz=====================MAPPING STATISTICS=====================1=libraryName 2=totalFragments 3=mappedFragments 4=assignedFragments 5=unassignedAmbiguous 6=unassignedNoFeatures 7=unassignedSecondaryHits 8=ratioStrandednessNBBPO 53906031 45425886 40255546 746962 4423378 0 0.9793NBBPP 46613273 39383494 34926967 680766 3775761 0 0.9790NBBPS 58758555 49619728 43809112 919838 4890778 0 0.9779NBBPT 47132694 39644894 35165470 711401 3768023 0 0.9786NBBPU 70632498 59489634 52639939 1178999 5670696 0 0.9779NBBPW 65444589 55089123 48745377 1070289 5273457 0 0.9780NBBPX 28333772 23979116 21206682 459524 2312910 0 0.9789NBBPY 43269557 36458240 32273045 601165 3584030 0 0.9777NBBPZ 41506894 35361361 31271032 821156 3269173 0 0.9779NBBSA 67668662 57653552 50987437 1485075 5181040 0 0.9777NBBSB 38834434 33038209 29287434 716976 3033799 0 0.9789NBBSC 71884719 61044942 53996567 1451567 5596808 0 0.9787NOTE: mappedFragments - fragments aligned to the reference genome.assignedFragments - aligned fragments assigned to the gene features.unassignedAmbiguous - aligned fragments overlapping two or more features.unassignedNoFeatures - aligned fragments not overlapping with any features included in the annotation.unassignedSecondaryHits - fragments marked as second alignment in the FLAG field in SAM/BAM input.