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Sample GSM2476073 Query DataSets for GSM2476073
Status Public on Aug 15, 2017
Title seed following 48 h of stratification (S) Replicate 1 [RNA-seq]
Sample type SRA
 
Source name seed following 48 h of stratification (S)
Organism Arabidopsis thaliana
Characteristics ecotype: Col0
genotype/variation: wild type
tissue: germinating seed
time point: seed during stratification 48 h S
Treatment protocol Samples were collected 48 h into dark stratification started at 4 °C.
Growth protocol Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to continious light at 22C.
Extracted molecule total RNA
Extraction protocol RNA isolation was carried out using the Ambion Plant RNA isolation aid and RNAqeous RNA isolation kit.
RNA-seq libraries were generated using the TruSeq Total RNA kit v2 according to manufacturer’s instructions (Illumina).
polyA selection, random fragmentation, unstranded library
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description 48hS_1
Data processing Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2
filered and trimmed reads were mapped onto A. thaliana TAIR10 genome with the Araport11 transcriptome annotation with HISAT2 v2.0.5. Gene counts were extracted with featureCounts v1.5.1 and analysed with DESeq2 v1.10.1
Araport11 transcripts were quantified with salmon v0.7.2, with a quasi-index built with k=31, 30 bootstraps and the VB optimizer. Transcript quantifications were then analysed for differential accumulation using Sleuth v0.28.1
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_counts.txt.gz: tab-delimited text file including raw counts for genes
Supplementary_files_format_and_content: DE_gene_expr.txt.gz: tab-delimited text file with estimates of gene expression from DESeq2
Supplementary_files_format_and_content: isoform_expression.txt.gz: tab-delimited text file with estimated abundances of isoforms
Supplementary_files_format_and_content: isoform_test_results.txt.gz: tab-delimited text file with results of testing for differential exression of the isoforns (sleuth, LRT)
 
Submission date Feb 03, 2017
Last update date May 15, 2019
Contact name Quentin Gouil
Organization name Walter and Eliza Hall
Department Epigenetics and Development
Lab Ritchie lab
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL17311
Series (2)
GSE94457 RNA-seq data over Arabidopsis thaliana germination
GSE94459 methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination
Relations
BioSample SAMN06293591
SRA SRX2536515

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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