|
| Status |
Public on Nov 27, 2018 |
| Title |
Wildtype, beginning of day [1_WT_BOD_3] |
| Sample type |
SRA |
| |
|
| Source name |
Wildtype, end of day
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaf
genotype: Wildtype
time of sampling: end of day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava-1.9software used for basecalling.
The software kallisto (v 0.43.0) was used for quantification with the Arabidopsis thaliana genome as a reference (TAIR10 cDNA). The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses.
Kallisto was run with 30 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
Means and standard deviation of tpm of biological triplicates group were calculated.
Supplementary_files_format_and_content: Tab-separated table (.tsv) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each of the mutant lines against the wildtype at the respective time of sampling
|
| |
|
| Submission date |
Sep 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas PM Weber |
| E-mail(s) |
aweber@hhu.de
|
| Organization name |
Heinrich-Heine-University
|
| Department |
Institute for Plant Biochemistry
|
| Street address |
Universitätsstr. 1
|
| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21179 |
| Series (1) |
| GSE86380 |
The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana |
|
| Relations |
| Alternative to |
GSM3063011 |
| BioSample |
SAMN05726139 |
| SRA |
SRX2100626 |
