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

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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GEND000287
Basic Information Samples Gene Expression Patterns Transcriptomic Profiles Visualization

GEND000287: Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice

BioProject ID:    PRJNA262032     Original Project ID:    SRP047482    

Strategy:
Species:
Oryza sativa
Tissue:
Development Stage:
Biological Context:
Baseline:
Yes
Genetic:
-
Phenotypic:
-
Environmental:
-
Spatial:
Tissue
Temporal:
-
Quality and Quantity:
RNA Type:
rRNA- RNA
Median Mapping Quality:
0.9542
Median Coverage:
23.95
Max Sequencing Length:
195
#Max Replicate:
1

Gene Expression Patterns

OR
Heatmap Boxplot

Transcriptomic Profiles

Note:
GENDX:
Gene Expression Profiles
GENDE:
RNA Editing Profiles
GENDS:
Alternative Splicing Profiles
GENDC:
CircRNA Expression Profiles
ID: GENDX000287 Download
Reference Genome: IRGSP-1.0.47
Genome Annotation: IRGSP-1.0.47
Data Processing:
  1. Read filtering: Fastp v0.20.0
  2. Strandness of RNA-seq library: RseQC v2.6.4
  3. Read mapping: STAR v2.7.1a
ID: GENDE000287 Download
Reference Genome: IRGSP-1.0.47
Genome Annotation: IRGSP-1.0.47
Data Processing:
  1. 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 -p -u -T 6-0 -v 3 -n 0.0 -s $value
  2. REDItools 1.2.1

Samples

Display Columns
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis: