|
| Status |
Public on Jun 01, 2021 |
| Title |
mCherry.24h.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background line: Col-0
construct: mCherry
developmental stage: 7-day old seedling
|
| Treatment protocol |
Transgene expression was induced by incubation in estradiol plates for 5h or 24h.
|
| Growth protocol |
Arabidopsis seedlings grown in ½ MS plates for 7 days. Then transferred to a new ½ MS plate supplemented with Estradiol (5uM)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extractions were performed with RNAeasy Plant kit (QIAGEN) and mRNA was isolated by Poly(A) RNA Selection kit (Lexogen) from 1µg of total RNA.
RNA libraries were prepared for sequencing using Lexogen SENSE mRNA-Seq Library Prep Kit V2 following manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
NextSeq Control Software 2.2.0.4 was used to control the sequencer
RTA v2.4.11 software was used for basecalling
raw RNA-seq reads were aligned to TAIR10 genome using STAR v2.5.1 (Dubin et al doi: 10.1093/bioinformatics/bts635) (non-default parameters: --alignIntronMax 6000 --alignMatesGapMax 6000 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1). Each sample has two fastq files (sequenced on 2 lanes) that were pooled for the alignment.
RNA-seq read counts for all TAIR10 protein-coding genes were calculated using featureCounts tool from Subread (version 1.4.6) package (Liao et al, Bioinformatics, 2014)
Genome_build: TAIR10
Supplementary_files_format_and_content: process data file is a tab separated text file which contains raw read counts for Arabidopsis thaliana TAIR10 protein-coding genes in all 24 sequenced samples
|
| |
|
| Submission date |
Dec 06, 2019 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Fernando Navarrete |
| E-mail(s) |
fernando.navarrete@gmi.oeaw.ac.at
|
| Organization name |
Gregor Mendel Institute
|
| Street address |
Dr. Bohr Gasse 3
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE141597 |
Naked1 targets Topless to up-regulate Auxin signaling and suppress immunity |
|
| Relations |
| BioSample |
SAMN13500005 |
| SRA |
SRX7283179 |
