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Series GSE223590 Query DataSets for GSE223590
Status Public on Jun 07, 2023
Title Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence [ncRNA-Seq]
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNAs (hetsiRNAs) whose transcriptional activity were significantly changed in the absence of NDX. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further studies and analyses on NDX function.
Overall design sRNA expression analysis of RNA-seq data for A. thaliana Col-0 wild type and ndx1-4 mutant (5-week-old plant, flower, 3 replicas).
Contributor(s) Feró O, Karányi Z, Nagy É, Mosolygó-L Á, Szaker HM, Csorba T, Székvölgyi L
Citation(s) 37286661
Submission date Jan 24, 2023
Last update date Sep 06, 2023
Contact name Lorant Szekvolgyi
Organization name University of Debrecen
Department Department of Pharmacy
Lab Genome Architecture and Recombination Research Group
Street address Egyetem ter 1.
City Debrecen
ZIP/Postal code 4032
Country Hungary
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (6)
GSM6965102 sRNA, Col-0, rep1
GSM6965103 sRNA, Col-0, rep2
GSM6965104 sRNA, Col-0, rep3
This SubSeries is part of SuperSeries:
GSE223591 Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence
BioProject PRJNA926933

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Supplementary file Size Download File type/resource
GSE223590_RAW.tar 49.1 Mb (http)(custom) TAR (of BW)
GSE223590_diff_srna_flower_ndx1-4_vs_col0.tsv.gz 73.6 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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