|
| Status |
Public on Aug 08, 2019 |
| Title |
WT_HEAT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type_HEAT_seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/vaiation: wild-type
condition: HEAT
age: Twelve-day old
growth: grown for 12 days in the cold (12°C) and then moved for 4h at 27°C
light cycle: long day (16h light / 8h dark)
temperature: 12 days at 12°C + 4h at 27°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_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-37_S26
|
| 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 |
SAMN08805247 |
| SRA |
SRX3856975 |
