|
| Status |
Public on Nov 20, 2018 |
| Title |
Col-0_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole rosette
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession: Col-0
genotype: wildtype
age: 23 d
replicate: 3
|
| Growth protocol |
Trays of soil-grown plants were covered with a transparent plastic dome for 10 days after seed sowing. Plants were maintained under a 16-h light (100 μE m-2 s-1) and 8-h dark photoperiod at 20 ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each replicate sample, approximately 20 plants (whole rosette, excluding roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80 ºC until processing. Wild-type Col-0 and mutant plants were grown in the same tray to minimize tray-to-tray variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Qiagen RNeasy kit with Qiagen on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 7.0.
Barcoded sequencing libraries were prepared using the Illumina RNAseq kit according to the manufacturer's instructions. Normalized libraries were sequenced on the Ilumina HiSeq 2000 platform with multiplexing of nine libraries per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used to convert and demultiplex basecall files to FASTQ.
Reads assessed for quality and filtered with Illumina quality control tools filters and FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.25 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data (jazD_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary_files_format_and_content: count data (jazD_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM
|
| |
|
| Submission date |
Jul 05, 2018 |
| Last update date |
Nov 20, 2018 |
| Contact name |
Qiang Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
Michigan State University
|
| Department |
Plant Research Laboratories
|
| Lab |
Gregg Howe
|
| Street address |
612 Wilson Rd
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE116681 |
Gene expression profiling shows that a jaz decuple mutation (jazD) promotes expression of defense-related genes while inhibiting expression of growth-related genes |
|
| Relations |
| BioSample |
SAMN09606972 |
| SRA |
SRX4343732 |
