|
| Status |
Public on Nov 16, 2016 |
| Title |
WT_Sil_n1 |
| Sample type |
SRA |
| |
|
| Source name |
WT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: WT
tissues: Siliques 1-5DAP
|
| Growth protocol |
Arabidopsis thaliana plants grown on soil under long day light conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Quiagen RNAeasy mini kit
Libraries construction was contracted out to Functionnal Genomic Center Zurich , barcoded libraries were prepared such that four samples could be run per lane.
Libraries were prepared according to Illumina's instructions accompanying the stranded sequencing Kit TruSeq™ SBS v3 and RNA enrichment was performed with RNA-Ribosomal Depletion (Ribo Zero).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.8.
RNAseq reads were aligned to the TAIR10 genome assembly using Tophat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cufflink output
Supplementary_files_format_and_content: merged.gtf is linked as a supplementary file on the Series record (because extra transcripts annotated by Cufflinks as CUFF are not detailed in the cufflinks files.)
|
| |
|
| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Antonin Marchais |
| E-mail(s) |
mantonin@ethz.ch
|
| Phone |
+41 44 632 64 08
|
| Organization name |
ETHZ
|
| Department |
Department of Biology
|
| Lab |
Group Prof. Olivier Voinnet
|
| Street address |
Universitatstrasse 2
|
| City |
Zurich |
| ZIP/Postal code |
8092 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE89617 |
RNA-seq of Arabidopsis thaliana Col-0 siliques |
|
| Relations |
| BioSample |
SAMN04244169 |
| SRA |
SRX2337209 |
