|
| Status |
Public on Apr 05, 2013 |
| Title |
M82.Sun.leaf |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
strain: LA3475
light: Artificial sun
tissue: leaf
|
| Treatment protocol |
Shade and Sun treatments applied with light intensity averaged 95 µE with a red to far-red ratio of 0.48 or 3.1
|
| Growth protocol |
22C in conviron growth chamber. Seedling samples were harvested from plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extractions were used for the mixed tissue experiments and Qiagen plant mRNA easy for seedling tissues
Illumina mRNA-seq sample prerparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
SRX251996 SRX251997
|
| Data processing |
Basecalls performed using CASAVA version 1.4 and trimmed for quality
Reads were mapped to pseudoITAG sequences generated from alignement of cDNAs from S. lycopersicum and S, pennellii
Alignments of the first paired end only used BWA version 0.5.7 7 with parameters -k 1 -l 25 -n 0.02 -e 15 -i 10
Read counts for each ITAG were then summed and RPKM were calculated
genome build: S. lycopersicum var. Heinz v2.4
supplementary files format and content: space-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Koenig |
| E-mail(s) |
dan.koenig@tuebingen.mpg.de
|
| Organization name |
Max Planck Institute for Developmental Biology
|
| Department |
Molecular Biology
|
| Lab |
Weigel
|
| Street address |
Spemmannstr 30
|
| City |
Tuebingen |
| ZIP/Postal code |
72070 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10518 |
| Series (1) |
| GSE45774 |
Transcriptome Sequencing in wild and domesticated tomato species |
|
| Relations |
| BioSample |
SAMN02051425 |
| SRA |
SRX251996 |
| SRA |
SRX251997 |
