|
| Status |
Public on Aug 15, 2017 |
| Title |
seed following 48 h of stratification (S) Replicate 2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
seed following 48 h of stratification (S)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
genotype/variation: wild type
tissue: germinating seed
time point: seed during stratification 48 h S
|
| Treatment protocol |
Samples were collected 48 h into dark stratification started at 4 °C.
|
| 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.
RNA-seq libraries were generated using the TruSeq Total RNA kit v2 according to manufacturer’s instructions (Illumina).
polyA selection, random fragmentation, unstranded library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
48hS_2
|
| 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: gene_counts.txt.gz: tab-delimited text file including raw counts for genes
Supplementary_files_format_and_content: DE_gene_expr.txt.gz: tab-delimited text file with estimates of gene expression from DESeq2
Supplementary_files_format_and_content: isoform_expression.txt.gz: tab-delimited text file with estimated abundances of isoforms
Supplementary_files_format_and_content: isoform_test_results.txt.gz: tab-delimited text file with results of testing for differential exression of the isoforns (sleuth, LRT)
|
| |
|
| 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) |
| GSE94457 |
RNA-seq data over Arabidopsis thaliana germination |
| GSE94459 |
methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination |
|
| Relations |
| BioSample |
SAMN06293590 |
| SRA |
SRX2536516 |
