|
| Status |
Public on Jan 01, 2018 |
| Title |
WT_R3_apex |
| Sample type |
SRA |
| |
|
| Source name |
apices
|
| Organism |
Arabis alpina |
| Characteristics |
cultivar: Pajares
age: 2 weeks-old under long-day photoperiod
genotype/variation: wild type
tissue: apices
|
| Treatment protocol |
Apices or leaves from wild type or pep1-1 mutant were collected after two weeks at ZT8.
|
| Growth protocol |
Seeds were sown on soil and grown at 22°C for 2 weeks in a long day photoperiod
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Rneasy Plant Moni Kit (Qiagen) following manufacture´s protocol. To estimate the quality of the RNA, samples were measured with the Agilent 2100 Bioanalyzer using Agilent RNA high sensitivity CHIP
Libraries were prepared following the TruSeq RNA Sample preparation guideline (Illumina)
4µg of total RNA were polyA-purified, fragmented and first-strand cDNA synthesized by reverse transcriptase (SuperScript II-Invitrogen) and random hexamers. This was followed by RNA degradation and second strand cDNA synthesis. End repair process and adittion of a single ‘A’ nucleotide to the 3’ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included quality control and quantification. All libraries were pooled before sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Low-quality reads in the raw data (FASTQ files) were filtered out and reads kept were then mapped to the Arabis alpina reference assembly V3 (Willing et al, 2015) using TopHat with the GTF file used in (6) (--min-anchor-length 10; --max-multihits 5; library-type fr-unstranded)
Count tables for raw counts were obtained from bam files using coverageBed.
Differential gene expression was estimated using DESeq2 package 1.10.0 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
Genome_build: Arabis alpina (version from Willing et al 2015, Nature Plants, 1), see http://arabis-alpina.org/refseq.html (Version 3)
Supplementary_files_format_and_content: raw counts
|
| |
|
| Submission date |
Nov 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julieta L Mateos |
| E-mail(s) |
jmateos@leloir.org.ar
|
| Organization name |
Fundacion Instituto Leloir
|
| Street address |
Av. Patricias Argentinas 435
|
| City |
Buenos Aires |
| ZIP/Postal code |
C1405BWE |
| Country |
Argentina |
| |
|
| Platform ID |
GPL22647 |
| Series (1) |
| GSE89638 |
Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species |
|
| Relations |
| BioSample |
SAMN05991958 |
| SRA |
SRX2335979 |
