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Sample GSM2476117 Query DataSets for GSM2476117
Status Public on Aug 15, 2017
Title seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 3 [sRNA-seq]
Sample type SRA
 
Source name seed collected 24 h into countinuous light (post-stratification), 24 h SL
Organism Arabidopsis thaliana
Characteristics ecotype: Col0
genotype/variation: wild type
tissue: germinating seed
time point: seed germinating in countinuous light 24 h SL
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.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.
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.
sRNA-seq libraries were generated using the TruSeq small RNA kit (Illumina)
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 1000
 
Description 24hSL_3
Data processing Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2. Sequences ranging between 18 to 24 bases in length were selected for mapping.
filered and trimmed reads were mapped and clustered onto A. thaliana TAIR10 genome with ShortStack v3.6
The reads counts on all 87,000 defined clusters were subjected to differential analysis with DESeq2 v1.10.1
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files including cluster information, counts on all clusters, and the estimated sRNA abundance on differential sRNA loci
 
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)
GSE94458 sRNA-seq data over Arabidopsis thaliana germination
GSE94459 methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination
Relations
BioSample SAMN06293593
SRA SRX2536559

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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