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Sample GSM4550593 Query DataSets for GSM4550593
Status Public on Feb 10, 2021
Title ddm1_2ndgen Rep2
Sample type SRA
 
Source name Leaves
Organism Arabidopsis thaliana
Characteristics genotype: ddm1(-/-) 2nd generation
age: 4-5 weeks
tissue: Leaves
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0, F1 DDM1/ddm1 (Col-0Xddm1) and ddm1 2nd generation. Contaminating DNA was removed with a DNA-free DNA removal kit (Thermo Fisher Scientific).
For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 4-5 week old Leaves
ribo Zero depletion
Data processing For alignment and visualization, reads were mapped to the TAIR10 Arabidopsis genome using the STAR aligner and bigwig files were generated using the bamCoverage function in DeepTools.
Kallisto v0.46.0 was used to estimate transcript abundance and read counts for all transcripts in TAIR10.
The resulting values per transcript were mapped to gene level using R v3.6.1 (https://www.R-project.org/) and packages tximport v1.12.3 and TxDb.Athaliana.BioMart.plantsmart28 v3.2.2 (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Athaliana.BioMart.plantsmart28.html). Statistical analysis was performed with R v3.5.1 (https://www.R-project.org/) using the DESeq2 v1.22.2 package.
The pairwise comparison between WT Col-0 and ddm1 was performed with default DESeq2 settings. In addition, the shrunken log2 fold changes were calculated using default settings. Genes with False Discovery Rate (FDR) adjusted p-value < 0.05 and an absolute shrunken log2 fold change > 2 were classified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Kallisto tsv files show the counts and TPMs for each sample.
 
Submission date May 12, 2020
Last update date Feb 11, 2021
Contact name Bhagyshree Babasaheb Jamge
E-mail(s) bhagyshree.jamge@gmi.oeaw.ac.at
Organization name Gregor Mendel Institute
Street address Dr. Bohr Gasse -3
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL17639
Series (2)
GSE150435 RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1
GSE150436 The chromatin remodeler DDM1 silences transposons through deposition of the histone variant H2A.W
Relations
BioSample SAMN14907156
SRA SRX8333477

Supplementary file Size Download File type/resource
GSM4550593_kallisto_105377_CATAATAATTAGCGCA_CE0EGANXX_4_20191210B_20191210.tsv.gz 382.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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