|
| Status |
Public on Dec 16, 2024 |
| Title |
Shoot, drought, CR:gf14h-1, R3 |
| Sample type |
SRA |
| |
|
| Source name |
5 leaf stage shoot
|
| Organism |
Brachypodium distachyon |
| Characteristics |
cultivar: 21-3
tissue: 5 leaf stage shoot
genotype: Mutant gf14h-1
treatment: 15 day drought
|
| Treatment protocol |
After their intiial growth, plants were subjected to 16 h light and 8 h dark conditions with 15 days no water.
|
| Growth protocol |
Plants were grown for 18 days at 20°C with 14 h light and 18°C for 10 h dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriReagent (Ambion) according to the manufacturer's instructions. Contaminating DNA was removed with a TURBO DNase treatment and RNA was stabilized with addition of RNaseInhibitor.
Libraries were constructed using the protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HJ35
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt
|
| Data processing |
Partek® Flow® software v.10.0, build 10.0.22.0729, FastQC v0.11.9
Reads were demultiplexed and then assessed for quality using the FastQC v0.11.9 and Partek Flow® pre-alignment QAQC tools, followed by quality trimming and filtering according to quality score (Q30) at the 3' end and a fixed-length trimming (12) of bases at the 5' end using the Flow® trimbases tool (25 bp minimum length).
Curated reads were aligned to the B. distachyon v3.0 genome obtained from the NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/505/) with HISAT2 (Kim et al., 2019).
Aligned reads were quantified at the gene level based on the B. distachyon v3.0 annotation model in gff format from the same URL above using a modified full expectation-maximization (EM) algorithm (Xing et al., 2006), as implemented in Flow® with default values and strand specificity set to autodetect.
Differential expression analyses were conducted at the gene-level using unfiltered raw read counts in DESeq2 (Love et al., 2014), and genes with very low read counts were excluded from the false discovery rate (FDR) calculation using the default parameter independentFiltering=true.
Reads were median ratio normalized as part of the DESeq2 analysis.
Assembly: B. distachyon v3.0 genome from the NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/505/)
Supplementary files format and content: Tab-delimited text file includes raw gene counts for each sample
Supplementary files format and content: Tab-delimited text file includes median ratio normalized gene counts for each sample
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Dec 16, 2024 |
| Contact name |
Heather Elizabeth Driscoll |
| Organization name |
Norwich University
|
| Department |
Biology
|
| Street address |
158 Harmon Drive
|
| City |
Northfield |
| State/province |
VT |
| ZIP/Postal code |
05663 |
| Country |
USA |
| |
|
| Platform ID |
GPL17337 |
| Series (1) |
| GSE240619 |
Conserved functions of angiosperm ε-clade 14-3-3 proteins in growth, flowering, and abiotic stress resilience |
|
| Relations |
| BioSample |
SAMN36939473 |
| SRA |
SRX21331964 |
