{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Christine Faulkner"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16996"],"description":["The fungal pathogen Colletotrichum higginsianum secretes effector proteins during infection of Arabidopsis. To explore the host processes perturbed by the effector candidate ChEC108 in host plants, transgenic Arabidopsis lines were generated to express AtUBQ10pro:ChEC108-eGFP or AtUBQ10pro:ChEC108^D164R-eGFP in the Col-0 background. D164R refers to a mutation that prevents binding of ChEC108 to the Arabidopsis protein, HIPP6. Three replicate samples (A, B, C) were collected per genotype (Col-0, AtUBQ10pro:ChEC108-eGFP or AtUBQ10pro:ChEC108^D164R-eGFP). Total RNA was extracted from 19-day-old whole seedlings grown on sterile media."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Total RNA samples were submitted to Genewiz for library preparation with polyA selection and standard RNA-sequencing.","Sequencing - Illumina sequencing by Genewiz generated 150 bp paired-end reads and was carried out at a depth of 20 million reads per sample.","Sample Collection - Seven 19-day-old whole seedlings (equating to 70-90 mg of fresh weight per sample) were removed from sterile plates and immediately frozen in liquid nitrogen.","Growth Protocol - Seedlings were grown vertically on GM agar plates [4.4 g/L Murashige Skoog Medium (Duchefa M0222), 0.50 g/L MES hydrate pH6 (Sigma M8250), 20 g/L agar (Difco 214030)] under long-day conditions (16 h light/8 h dark photoperiod) at 20 °C.","Nucleic Acid Extraction - Frozen seedlings were homogenised using a 2010 Geno/Grinder (SPEX SamplePrep) at 1200 rpm for 1 min. RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) using buffer RLT according to the manufacturer’s instructions with the following modification: after tissue homogenisation using the QIAshredder column, two or three centrifugation steps were performed to maximise removal of debris. RNA was eluted from RNeasy spin columns in 30 µl of H2O. RNA extracts were DNase-treated using the TURBO DNA-free^TM Kit (Invitrogen) according to the manufacturer’s rigorous procedure."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Adaptors and low quality reads (Phred score < 20) were trimmed using TrimGalore v0.5.0 (Krueger et al. 2018) and Cutadapt v3.4 (Martin 2011). Pre- and post-trimming, data quality was assessed using FastQC v0.11.8 (Andrews 2018). Reads were mapped to the Arabidopsis reference genome (TAIR10; NCBI Refseq GCA_000001735.1) using HISAT2 v2.1.0 (Kim et al. 2019). Mapping quality was assessed using and MultiQC v.1.7 (Ewels et al. 2016) before data were imported into Seqmonk v.1.49.0 (Babraham Bioinformatics) for quantification. Replicate sets were assigned, and the default RNA-seq quantitation pipeline in Seqmonk was used to generate a gene count matrix.","Data Transformation - Mapped reads were imported into Seqmonk v.1.49.0 (Babraham Bioinformatics) for quantification. Replicate sets were assigned, and the default RNA-seq quantitation pipeline in Seqmonk was used to generate a gene count matrix. Gene counts were used for differential expression analysis using the R package, DEseq2 v1.48.2 (Love et al. 2014)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_title":["Colletotrichum higginsianum effector ChEC108 binds a plasmodesmal HMA protein and elicits plant defence"],"pubmed_authors":["Emma Turley","Emma K. Turley, Daniel S. Yu, Andrew Breakspear, Joanna Jennings, Mark Jave Bautista, Sally Jones, Barkha Ravi, Rafał Zdrzałek, Weibin Ma, Adam Bentham, Lauren Ryder, Nicholas J. Talbot, Mark J. Banfield, Christine Faulkner","Christine Faulkner"],"additional_accession":[]},"is_claimable":false,"name":"RNA-sequencing of transgenic Arabidopsis seedlings constitutively expressing a Colletotrichum higginsianum effector","description":"The fungal pathogen Colletotrichum higginsianum secretes effector proteins during infection of Arabidopsis. To explore the host processes perturbed by the effector candidate ChEC108 in host plants, transgenic Arabidopsis lines were generated to express AtUBQ10pro:ChEC108-eGFP or AtUBQ10pro:ChEC108^D164R-eGFP in the Col-0 background. D164R refers to a mutation that prevents binding of ChEC108 to the Arabidopsis protein, HIPP6. Three replicate samples (A, B, C) were collected per genotype (Col-0, AtUBQ10pro:ChEC108-eGFP or AtUBQ10pro:ChEC108^D164R-eGFP). Total RNA was extracted from 19-day-old whole seedlings grown on sterile media.","dates":{"release":"2026-05-21T00:00:00Z","modification":"2026-05-21T01:00:38.646Z","creation":"2026-05-05T16:33:03.097Z"},"accession":"E-MTAB-16996","cross_references":{"ENA":["ERP193042"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}