Dataset - GEND000255 - Gene Expression Nebulas

A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

A data portal of transcriptome profiles across multiple species

BioProject ID: PRJNA474721 Original Project ID: GSE115371

Strategy:	Bulk RNA-seq
Species:	Oryza sativa
Tissue:	Coleoptile Embryo
Development Stage:	dry seed 0 h seeds following 1 h of aerobic germination (1hA) seeds following 1 h of anaerobic germination (1hN) seeds following 12 h of aerobic germination (12hA) seeds following 12 h of anaerobic germination (12hN) seeds following 2 d of aerobic germination (2dA) seeds following 2 d of anaerobic germination (2dN) seeds following 24 h of aerobic germination (24hA) seeds following 24 h of anaerobic germination (24hN) seeds following 3 d of aerobic germination (3dA) seeds following 3 d of anaerobic germination (3dN) seeds following 3 d of anaerobic germination followed by 1 d under aerobic conditions (3dN1dA) seeds following 3 h of aerobic germination (3hA) seeds following 3 h of anaerobic germination (3hN) seeds following 4 d of aerobic germination (4dA) seeds following 4 d of anaerobic germination (4dN)
Biological Context:	Baseline: No Genetic: - Phenotypic: - Environmental: Abiotic stress Spatial: Tissue Temporal: Development; Time series
Quality and Quantity:	RNA Type: rRNA- RNA Median Mapping Quality: 0.9749 Median Coverage: 6.13 Max Sequencing Length: 95 #Max Replicate: 3

Note:

GENDX:

Gene Expression Profiles

GENDE:

RNA Editing Profiles

GENDS:

Alternative Splicing Profiles

GENDC:

CircRNA Expression Profiles

ID: GENDX000255 Download

Reference Genome: IRGSP-1.0.47

Genome Annotation: IRGSP-1.0.47

Data Processing:

ID: GENDE000255 Download

Reference Genome: IRGSP-1.0.47

Genome Annotation: IRGSP-1.0.47

Data Processing:

python2.7 REDItoolDenovo.py -i ./$project/$samlpe/${sample}_Alignment-sorted.bam -f ./rice_IRGSP.fa -o ./$project/$sample -t 20 -c 10 -q 25 -e -d -m 20 -u -T 6-0 -v 3 -n 0.0 -s $value
REDItools 1.2.1

GEN Sample ID	GEN Sample Name	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate