|
| Status |
Public on Dec 31, 2016 |
| Title |
Col-2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: wild type
tissue: rosette leaves
biological replicate: 2
|
| Treatment protocol |
none
|
| Growth protocol |
wt and mutant plants were grown in parallel at SD conditions for 15 days. Samples were harvested 1h before dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from rosette leaves using TRIzol Reagent according to manufactures recommendations (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols, Truseq SBS Kit v3. RIbosomal RNA was removed using the Ribo-Zero Magnetic kit Plant leaf (cat# MRZPL116, EpiCentre) starting with 1.5μg total RNA. Sequencing libraries were generated from the rRNA depleted RNA using the ScriptSeq v2 RNAseq library prep kit (cat# SSV21124, EpiCentre).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
reads quality was checked with FastQC
adapters were eliminated cutting 10bp with trimmomatic v0.32
paired end reads were mapped to TAIR10 genome with tophat v2.010, default options
counts mapping in genes were counted in bam files using Htseq using the TAIR10.gff annotation
counts mapping in introns present in the first isoform of genes annotated in TAIR10 were counted in bam files using Htseq and a intron.gff file derived form TAIR10.gff
counts were further processed in R. Batch effect was corrected using the RUVseq package. Differential gene expression and differential intron abundance analyses were performed in RUVseq-corrected counts with the package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_count.tsv file generated with HTseq contains RNA counts in whole genes acording to TAIR10 annotation
Supplementary_files_format_and_content: intron_count.tsv file generated with HTseq contains RNA counts in introns from the first isoform acording to TAIR10 annotation
|
| |
|
| Submission date |
Jan 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Angel Barco |
| E-mail(s) |
[email protected]
|
| Organization name |
NeuroSciences Institute of Alicante CSIC
|
| Department |
Neuro Plasticity
|
| Street address |
Ramon y Cajal
|
| City |
Alicante |
| ZIP/Postal code |
03550 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17311 |
| Series (1) |
| GSE65287 |
Arabidopsis thaliana cao mutant alternative splicing exploration by RNAseq |
|
| Relations |
| BioSample |
SAMN03294516 |
| SRA |
SRX852571 |
