|
| Status |
Public on Apr 28, 2022 |
| Title |
Setaria viridis (A10) seed head at anthesis replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
A10 seed head at anthesis
|
| Organism |
Setaria viridis |
| Characteristics |
tissue: Seed head
ecotype: A10
developmental stage: Anthesis
|
| Growth protocol |
Plants were grown in 1.7 L pots, soil mixture was Debco Green Wizard Premium Potting Mix in a Conviron PGC Flex growth Chamber with approx. 600 uE light intensity, 16 hr photoperiod, and day/night mean temperatures of 28°C / 20 °C, and 55% relative humidity.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit.
PolyA RNA-sequencing libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A10_Ant_rep2
|
| Data processing |
Raw read quality was first diagnosed using FastQC (v0.11.2).
Trim Galore! was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Paired-end alignments were performed using trimmed reads using Subread (v1.6.2) with flags -t 0 and -u to report uniquely mapping reads, prior to sorting, indexing and compressing using Samtools (v1.2).
Transcript quantification was performed at the gene-level with the Setaria viridis gene annotation (v2.1) using featureCounts (with flag -s 0 for non-stranded quantification). This output was utilized for differential gene expression testing with edgeR (quasi-likelihood pipeline).
Genome_build: Setaria viridis v2.1, DOE-JGI, http://phytozome.jgi.doe.gov/
Supplementary_files_format_and_content: .counts: raw counts per gene-level feature for each sample.
Supplementary_files_format_and_content: .csv: matrix of normalized log2 FPKM per gene-level feature across all samples per ecotype
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
Apr 28, 2022 |
| Contact name |
Diep R Ganguly |
| E-mail(s) |
dganguly@sas.upenn.edu
|
| Phone |
+1 215-898-0808
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 S University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL23621 |
| Series (1) |
| GSE131540 |
The role of SWEET4 proteins in the post-phloem sugar transport pathway of Setaria viridis sink tissues |
|
| Relations |
| BioSample |
SAMN11793521 |
| SRA |
SRX5874029 |
