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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GEND000322
Basic Information Samples Gene Expression Patterns Transcriptomic Profiles Visualization

GEND000322: Transcriptional regulation of cell division and cytokinin response in Arabidopsis shoot apical meristem

BioProject ID:    PRJNA602984     Original Project ID:    GSE144048    

Strategy:
Species:
Arabidopsis thaliana
Tissue:
Biological Context:
Baseline:
No
Genetic:
Mutation
Phenotypic:
-
Environmental:
-
Spatial:
Tissue
Temporal:
-
Quality and Quantity:
RNA Type:
poly(A)+ RNA
Median Mapping Quality:
0.9923
Median Coverage:
58.38
Max Sequencing Length:
296
#Max Replicate:
3

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: GENDX000322 Download
Reference Genome: TAIR10.48
Genome Annotation: TAIR10.48
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: GENDE000322 Download
Reference Genome: TAIR10
Genome Annotation: TAIR10
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:
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