GSM8066875: IZE explants, ET 5d c; Arabidopsis thaliana; RNA-Seq - SRA

SRX23556452: GSM8066875: IZE explants, ET 5d c; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 65.8M spots, 9.9G bases, 3Gb downloads

External Id: GSM8066875_r1

Submitted by: Faculty of Natural Sciences; Institute of Biology, Biotechnology and Environmental Protection, University of Silesia

Study: Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana

PRJNA1074004 • SRP488569 • All experiments • All runs

show Abstracthide Abstract

Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors TF) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants. Overall design: The immature zygotic embryos of Arabidopsis at the cotyledonary stage of development were cultured on two alternative SE-induction media, ET and EA, supplemented with TSA (1 µM) and auxin (5 µM 2,4-D), respectively. The explants that were cultured on a non-embryogenic medium (E0) developed into seedlings. The EA-, ET- and E0-cultured explant tissues were sampled for RNA-seq analysis at two culture points representing the early (5th day) and the advanced (10th day) stage of SE induction. In total, six experimental combinations in three replicates were used in RNA-seq analysis.

Sample: IZE explants, ET 5d c

SAMN39849207 • SRS20402751 • All experiments • All runs

Organism: Arabidopsis thaliana

Library:

Name: GSM8066875

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: An RNAqueous® Total RNA Isolation Kit (ThermoScientific) was used to isolate total RNA from the IZE explants induced on different media (E0, EA, ET) for 5 and 10 days. The freshly isolated tissues were wiped in frozen mortars. Depending on the age of the culture, from 250 (5th day) to 100 (10th day) explants were used for RNA isolation per repetition. RNA isolation, library preparation, and sequencing were produced in three biological replicates. The concentration and purity of RNA samples were evaluated with an ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was determined using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano chips (Agilent Technologies, Santa Clara, USA). RNA samples were treated with RNase-Free DNase and then purified using the Acid-Phenol: Chloroform with ammonium acetate method (ThermoScientific). The sequencing libraries were prepared using Illumina ScriptSeq™ Complete Kit (Plant; Illumina, San Diego, USA) following the manufacturer's protocol. Two micrograms of total RNA per sample were used as an input. Briefly, library prep involved the subsequent steps: ribosomal RNA removal with Ribo-Zero rRNA Removal Reagents (Plant Leaf; Illumina, San Diego, USA) followed by ethanol precipitation of the rRNA-depleted sample, RNA fragmentation, cDNA synthesis, RNA removal, terminal tagging of cDNA followed by bead cleanup, PCR amplification using Illumina indexes and final bead purification. The quality of the prepared Illumina libraries was analyzed using Agilent Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, USA), and the quantities were estimated using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, USA). For cluster generation, the libraries were pooled with equimolar concentration and sequenced using the Illumina HiSeq 4000 system (Illumina, San Diego, USA) in 2x 76 cycles paired-end (PE) mode with 6 barcoded samples per lane.

Runs: 1 run, 65.8M spots, 9.9G bases, 3Gb

Run	# of Spots	# of Bases	Size	Published
SRR27896197	65,847,909	9.9G	3Gb	2024-08-21

ID:: 31818938

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity