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Sample GSM2643680 Query DataSets for GSM2643680
Status Public on Aug 15, 2017
Title smb 24 hSL replicate 2
Sample type SRA
 
Source name germinating seed_smb 24 hSL
Organism Arabidopsis thaliana
Characteristics genotype: smb
tissue: germinating seed
Treatment protocol Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 24h.
Seeds wer collected at 24 h in continuous light and snap frozen in liquid nitrogen
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 Sigma Spectrum RNA extraction kit, with on-column DNase treatment.
RNA-seq libraries were generated using the TruSeq Stranded mRNA kit according to manufacturer’s instructions (Illumina).
polyA selection, random fragmentation, stranded library
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description smb_rep2
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: tab-delimited text file including raw counts for genes, output of featureCounts
 
Submission date May 30, 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 GPL19580
Series (2)
GSE94459 methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination
GSE99413 RNAseq data for Arabidopsis TF mutants during germination
Relations
BioSample SAMN07176371
SRA SRX2867800

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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