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Sample GSM3070185 Query DataSets for GSM3070185
Status Public on Aug 08, 2019
Title wt_LIGHT4h_rep2
Sample type SRA
 
Source name wild-type_LIGHT4h_seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/vaiation: wild-type
condition: LIGHT4h
age: Five-day old
growth: grown for 5 days in the dark and then exposed for 4h to white light
light cycle: 5 days dark + 4h white light
temperature: 21°C
tissue: seedlings
Treatment protocol For the photomorphogenesis experiment, at the end of the 5 days of growth in the dark, 3 plates were maintained in the dark, 3 plates were exposed to white light for 2h and 3 plates were exposed to white light for 4h. For the heat shock experiment, after the 12 days at 12°C, 3 plates were maintained at 12°C and 3 plates were exposed to 27°C for 4h.
Growth protocol Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. For the photomorphogenesis experiment, plates were grown in the dark for 5 days at 21°C. For th eheat shock experiment, plates were transfered to a growth chamber at 12°C under long day conditions (16h light/8h dark) for 12 days.
Extracted molecule total RNA
Extraction protocol The seedlings were ground into fine powder in liquid nitrogen. Total RNA was extracted by Spectrum Plant total RNA kit (Sigma) following the manufacturer's instructions
Libraries were prepared from 1.5µg of total RNA using Illumina TruSeq Stranded mRNA Library Prep kit. Libraries were sequenced on a NextSeq500 instrument at Indiana University Center for Genomics and Bioinformatics.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-11_S8
Data processing Alignment : STAR v2.5.2b (Dobin et al., Bioinformatics, 2013) with default parameters
Filtering : samtools v1.3.1 was used to keep only primary alignments of reads with mapping quality above 10 (MapQ>10)
Counting: featureCounts from the Rsubread package (v 1.24.2) of R (v. 3.3.2) / Bioconductor (v. 3.4) was used to count uniquely mapping read pairs on TAIR10 annotated genes.
DE analysis : Differential expression analysis was performed using the DESeq2 package (v1.14.1) on protein-coding genes (excluding genes with zero counts in all samples or overlapping with blacklisted regions)
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF1238_RawCounts_photomorphogenesis.txt contains the raw counts from featureCounts for the dark/light experiment
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_photomorphogenesis.txt contains the DESeq2-normalized counts for the dark/light experiment
Supplementary_files_format_and_content: GSF1238_RawCounts_heatshock.txt contains the raw counts from featureCounts for the cold vs heat shock experiment
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_heatshock.txt contains the DESeq2-normalized counts for the cold vs heat shock experiment
 
Submission date Mar 28, 2018
Last update date Aug 08, 2019
Contact name Pascal GP Martin
E-mail(s) pascal.martin@inrae.fr
Organization name INRAE
Department UMR1332 BFP
Lab FDFE
Street address 71 avenue Edouard Bourlaux
City Villenave d'Ornon
ZIP/Postal code 33140
Country France
 
Platform ID GPL19580
Series (2)
GSE112442 Gene expression profiling (RNA-seq) in wild-type and bdrs triple mutant Arabidopsis seedlings in response to light or to a heat shock
GSE112443 RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings
Relations
BioSample SAMN08805262
SRA SRX3856960

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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