{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Angeles Aroca Aguilar"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15916"],"description":["Role of sulfide under non photorespiratory conditions in Arabidopsis plants. Plants were grown under non photorespiratory conditions and transfered to active photorespiration conditions and were treated or not exogenously with NaHS."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Before library construction, several analyses were performed to check RNA quantification, purification using poly-T-oligo-attached magnetic beads and integrity and purity using an Agilent 5400 analyzer. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Subsequent end repair, A-tailing, adapter ligation, size selection, amplification and purification were performed. Purified mRNA was used to construct sequencing library, which was checked using Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Clustering of the index-coded samples was performed, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.","Sample Collection - Leaves from 30 days old plants were harvested and grounded under liquid nitrogen, pestle and mortar.","Sequencing - Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  The obtained clean reads were compared with the Arabidopsis thaliana reference genome using HISAT2 v2.0.5 software (ncbi_arabidopsis_thaliana_gcf_000001735_4_tair10_1). Feature Counts v1.5.0-p3 was used to count the number of reads mapped to each gene. The fragments per kilobase of transcript sequence per million base pairs (FPKM) of each gene were calculated based on the length of the gene and the number of reads mapped to that gene. Differential expression analysis of two conditions (four biological replicates per condition) was performed using the DESeq2 R package (1.20.0). The resulting P values were adjusted using the Benjamini and Hochberg’s approach to control for the false discovery rate. Genes with an adjusted P value < 0.05 and log2 (fold change) >1 according to DESeq2 were considered differentially expressed.","Growth Protocol - Arabidopsis thaliana Col-0 wild-type plants were grown at constant humidity of 70% with 16 h of light (120 µEm-2 s-1) at 20 °C and 8 h of dark at 18 °C. Plants were grown for 30 days under nonphotorespiratory conditions by automatically injecting CO2 to a final concentration of 0.7% (v/v), and harvested at 30 days (high CO2 treatment-nonphotorespiratory conditions, NPC). and other batches of plants were transferred for 3 days from high CO2 (0.7% CO2 v/v) to normal CO2 conditions (0.04% CO2 v/v) and then harvested for further analysis (active-photorespiratory conditions, APC).  For the sulfide treatment, plants were irrigated and sprayed with 200 µM NaHS every 3 days at least 5 times before harvesting the NPC samples and transferring to APC conditions. Control plants were treated with water.","Nucleic Acid Extraction - The total RNA was extracted from Arabidopsis plants grown under different conditions described above, NPC and APC with or without NaHS treatment, using an RNA prep Pure Plant Kit (Qiagen according to the manufacturer’s instructions)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - After the gene expression is quantified, statistical analysis of the expression data is required to screen the genes whose expression levels are significantly different in different conditions. The differential analysis is mainly divided into three steps.  First, the raw readcount is normalized, mainly to correct the sequencing depth; Next, the statistical model is used to calculate the hypothesis test's probability (pvalue); Finally, multiple hypothesis test corrections are used to obtain FDR values (false discovery rate)(Anders et al., 2010)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Angeles Aroca Aguilar"],"additional_accession":[]},"is_claimable":false,"name":"Role of sulfide under non photorespiratory conditions in Arabidopsis plants","description":"Role of sulfide under non photorespiratory conditions in Arabidopsis plants. Plants were grown under non photorespiratory conditions and transfered to active photorespiration conditions and were treated or not exogenously with NaHS.","dates":{"release":"2026-06-30T00:00:00Z","modification":"2026-06-30T01:00:54.022Z","creation":"2025-10-30T16:13:56.116Z"},"accession":"E-MTAB-15916","cross_references":{"ENA":["ERP183409"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}