|
Status |
Public on Nov 17, 2018 |
Title |
A2: WT_PAC_GA_rep1 |
Sample type |
SRA |
|
|
Source name |
Seven-day-old seedlings
|
Organism |
Arabidopsis thaliana |
Characteristics |
accession: Nossen tissue: whole seedlings genotype/variation: wild-type (No-0) treatment: 10 μM PAC+100 μM GA3
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAwas extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instructions, treated with the DNase Kit (Ambion), and then frozen at −80°C until analyzed.RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Truseq Stranded mRNA Illumina protocols
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Illumina Casava1.8 software used for basecalling. Raw data preprocessing (clipping adapters, and filter sequences <20 nt, 3’ end quality-trimmed threshold Q28) :cutadapt v1.8.3. FASTQC (v0.11.5) was used to assess data quality All sequenced libraries were mapped to the Arabidopsis thaliana genome (Arabidopsis_thaliana.TAIR10.22) with GTF information (Arabidopsis_thaliana.TAIR10.22.gtf) using TopHat(v.2.1). Seqmonk v.1.35 was used to generate per gene raw count matrix from unique mapped reads with the same GTF file used for the alignment step (opposing strand specific, merge transcript isoforms). Differential expression analysis performed with DESeq2 v.1.16.1 and edgeR v.3.0.2 (P-adj.value cutoff 0.05) Genome_build: Arabidopsis_thaliana.TAIR10.22 Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.
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|
|
Submission date |
Nov 16, 2018 |
Last update date |
Nov 17, 2018 |
Contact name |
David Alabadi |
E-mail(s) |
dalabadi@ibmcp.upv.es
|
Phone |
34963877723
|
Organization name |
Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)
|
Department |
Biologia del Desarrollo
|
Lab |
2.08
|
Street address |
Av de los Naranjos s/n, Campus UPV, Edificio 8E
|
City |
Valencia |
State/province |
Valencia |
ZIP/Postal code |
46022 |
Country |
Spain |
|
|
Platform ID |
GPL19580 |
Series (1) |
GSE122617 |
Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction |
|
Relations |
BioSample |
SAMN10435183 |
SRA |
SRX5017291 |