|
| Status |
Public on Feb 04, 2013 |
| Title |
Col-0 6-week-old leaf tissues |
| Sample type |
SRA |
| |
|
| Source name |
Adult leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
age: 6 weeks
tissue: leaves
|
| Growth protocol |
The plants used in this study were grown at 21-23 °C with a 8h photoperiod. The plants were first grown on plates containing Murashige and Skoog medium (Duchefa), 0.5% sucrose and 0.8% agar and then transferred to soil at 10 day-post-germination (dpg).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The small RNA libraries have been prepared with the Small RNA v1.5 kit according to the manufacturer ("illumina") instructions, with the following exceptions: the size selection was done on 15-45nt fragments, the 3' adapter have been replaced by the Universal miRNA cloning linker (NEB) and the PCR primer have been replaced by Fasteris primers in order to add index during the amplification step.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
map to Arabidopsis genome TAIR9
keep fully matched sequences
count the number of times a sRNA mapped to the genome
create a fasta file with unique sRNA sequences
Vmatch for aligning sRNA sequences and Python for counting
Genome_build: TAIR9
Supplementary_files_format_and_content: fasta sRNA sequences
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Emmanuelle Lastrucci |
| E-mail(s) |
lastrucc@ens.fr
|
| Phone |
0144323569
|
| Organization name |
Institut de Biologie de l’Ecole Normale Supérieure
|
| Lab |
Lionel navarro
|
| Street address |
46 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE40044 |
Small RNA sequencing from Arabidopsis adult leaves and profiling of Arabidopsis transcripts in response to flg22 peptide |
|
| Relations |
| SRA |
SRX175998 |
| BioSample |
SAMN01112490 |
