|
| Status |
Public on Feb 11, 2011 |
| Title |
aly_floral-16-mRNA2 |
| Sample type |
SRA |
| |
|
| Source name |
floral tissue
|
| Organism |
Arabidopsis lyrata |
| Characteristics |
strain: MN47
tissue: floral
developmental stage: stages 1-14
|
| Growth protocol |
16°C, 16 hour light period
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from floral tissue (stages 1-14) using the Trizol(Invitrogen) RNA extraction protocol. rRNAs were depleted from 10 μg of RNA using the Ribominus kit (Invitrogen). Tobacco acid pyrophosphatase (Epicentre Biotechnologies) was used to remove the 5’ CAP, followed by metal ion fragmentation for 10 minutes at 70oC (RNA fragmentation kit, Ambion). The RNA was dephosphorylated using CIP, then size selected for fragments of 100-150 nt by PAGE. RNA was extracted from the gel by semi-dry electrotransfer to DE81 chromatography paper (Whatman), followed by salt elution. The Illumina 3’ and 5’ sRNA adapters were sequentially ligated with size selection and re-phosphorylation by PNK between ligations. Following a further cycle of PAGE size selection, the RNA was reverse transcribed with Fermentas Revertaid and PCR amplified for 15 cycles with Phusion DNA polymerase (Finnzymes) before sequencing (Illumina sequencing-by-synthesis).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
bed: We mapped mRNA-seq data to the A. lyrata genome using SHORE (http://shore.sourceforge.net)
|
| |
|
| Submission date |
Oct 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Ott |
| Organization name |
Max Planck Institute for Developmental Biology
|
| Street address |
Spemannstr. 35-39
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11022 |
| Series (2) |
| GSE24571 |
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq] |
| GSE38113 |
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata |
|
| Relations |
| SRA |
SRX031052 |
| BioSample |
SAMN00120234 |
