|
Status |
Public on May 07, 2014 |
Title |
BC03 |
Sample type |
SRA |
|
|
Source name |
flowers stage 1-12
|
Organism |
Arabidopsis halleri |
Characteristics |
tissus: flowers slocus genotype: S13-S12
|
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 |
Ion Torrent PGM |
|
|
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 |
GPL18640 |
Series (1) |
GSE57267 |
Dominance hierarchy arising from the evolution of a complex small RNA regulatory network |
|
Relations |
BioSample |
SAMN02746161 |
SRA |
SRX533515 |