|
| Status |
Public on May 07, 2014 |
| Title |
HF_70 |
| Sample type |
SRA |
| |
|
| Source name |
flowers stage 1-12
|
| Organism |
Arabidopsis halleri |
| Characteristics |
tissus: flowers
slocus genotype: S13-S28
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by TRI reagent (Sigma) from 10-20 floral buds at various stages of development
Small RNA libraries were prepared for sequencing using standard SOLiD and PROTON protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
small RNA (15-40bp)
|
| Data processing |
Adaptators from SOLiD small RNA sequences were trimmed using an homemade script (SOLID adaptor sequence : C33020103031311231230222031111222203122020 ).
Sequences were aligned against different S-locus haplotypes and the genome of Arabidopsis lyrata (araly1) using Bowtie (no mismatch authorized)
Reads aligned on the arabidopsis genome and on the S-locus haplotypes were removed
microRNA genes were detected on the S-locus haplotypes according to a set of criterias
Genome_build: araly1
Supplementary_files_format_and_content: abundance measurements
motif_miARN.fa: the fasta file of the 17 putative miRNA sequences.
|
| |
|
| Submission date |
May 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Vincent Castric |
| E-mail(s) |
Vincent.Castric@univ-lille1.fr
|
| Organization name |
CNRS
|
| Lab |
GEPV
|
| Street address |
Lille1 university
|
| City |
Villeneuve d'Ascq |
| ZIP/Postal code |
59655 |
| Country |
France |
| |
|
| Platform ID |
GPL18638 |
| Series (1) |
| GSE57267 |
Dominance hierarchy arising from the evolution of a complex small RNA regulatory network |
|
| Relations |
| BioSample |
SAMN02746152 |
| SRA |
SRX533504 |
