DOI: 10.6084/m9.figshare.30586706
title: Transcriptomic analysis of active proliferation arrest in <i>Lemna minor</i> under elevated CO₂ and low-nutrient stress

description: <b>Description / Abstract:</b><br>This dataset accompanies the study <i>Li et al., Growth arrest in Lemna minor under elevated CO₂ and low nutrients</i>, submitted to <i>New Phytologist</i>.<br>It includes gene-expression matrices and associated metadata for <i>Lemna minor</i> 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.<br>Raw FASTQ files are available via the NCBI Sequence Read Archive. Please see the attached table <b>NCBI_SRA_Table.xlsx</b> for details. =====================FILES:<b>counts_1vs2.txt</b> Raw integer counts (featureCounts output). Rows = genes, columns = samples. Raw processed data matrix used for DESeq2 input.<b>tpm_counts_1vs2.txt </b>TPM-normalized gene expression matrix for all samples. Final processed (normalized) data.<b>DEG_1v2.txt</b> 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.<b>NCBI_SRA_Table.xlsx: </b>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<br>=====================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 0.9787<br>NOTE: 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.