|
| Status |
Public on Aug 15, 2017 |
| Title |
lmi1 24 hSL replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
germinating seed_lmi1 24 hSL
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: lmi1
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 |
lmi1_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 |
SAMN07176374 |
| SRA |
SRX2867796 |
