|
| Status |
Public on Apr 10, 2019 |
| Title |
KOZ1_t1-treated_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
KOZ1_t1-treated_leaf
|
| Organism |
Brachypodium distachyon |
| Characteristics |
ecotype/genotype: KOZ1
drought tolerance phenotype: high susceptibility to drought
treatment: no watering
time point: 4 days after treatment start
tissue: Leaf tissue
|
| Treatment protocol |
After 32 days, a progressive drought treatment was applied. For each of the ecotypes, leaf tissue was harvested at three time points for RNA extraction; at the start (T0, control (C)), after 4 days (T1, both C and treatment (D)) and after 8 days (T2, both C and D).
|
| Growth protocol |
ABR4, ABR8 and KOZ1, were grown in John Innes No 1 potting compost with grit-sand at a 4:1 ratio; controlled environment conditions: 21 °C, 16 h photoperiod. Plants were well-watered and grown for 32 days after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy MinElute Cleanup Kit columns (Qiagen, Valencia, CA, USA). On-column DNase I digestion (DNase-Free DNase Set, Qiagen) was performed according to manufacturer protocols to eliminate genomic DNA contamination.
BGI performed the TruSeq library construction and sequencing with Illumina HiSeqTM 2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FCC3NEKACXX-BRAdvlEABLRAAPEI-201_L4
|
| Data processing |
Raw FASTQ data trimmed using Trim Galore (version 0.4.1 with parameters: -q 28 --phred64)
Reads mapped using Tophat2 (tophat2 version 2.1.1 and bowtie2 version 2.2.9 using parameters: --phred64-quals)
Cufflinks version 2.2.1 used for cuffmerge and cuffdiff
Genome_build: Bdistachyon_314_v3.0.fa with Bdistachyon_314_v3.1.gene.gff3 annotation
Supplementary_files_format_and_content: fpkm
|
| |
|
| Submission date |
Feb 25, 2019 |
| Last update date |
Apr 10, 2019 |
| Contact name |
Maurice Bosch |
| E-mail(s) |
[email protected]
|
| Organization name |
Aberystwyth University
|
| Department |
Institute of Biological, Environmental & Rural Sciences
|
| Street address |
Gogerddan
|
| City |
Aberystwyth |
| ZIP/Postal code |
SY23 3EB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17337 |
| Series (1) |
| GSE126992 |
Transcriptional and metabolomic analyses implicate cell wall changes are associated with drought tolerance in Brachypodium distachyon. |
|
| Relations |
| BioSample |
SAMN10996130 |
| SRA |
SRX5417148 |
