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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GEND000434
Basic Information Samples Gene Expression Patterns Transcriptomic Profiles Visualization

GEND000434: AI-guided Discovery of a Paradoxical Immune Response in Fatal COVID-19 (Hamster)

BioProject ID:    PRJNA659996     Original Project ID:    GSE157058    

Strategy:
Species:
Mesocricetus auratus
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Biological Context:
Baseline:
No
Genetic:
-
Phenotypic:
Disease; Infection
Environmental:
-
Spatial:
Tissue
Temporal:
-
Quality and Quantity:
RNA Type:
Total RNA
Median Mapping Quality:
0.71085
Median Coverage:
2.69
Max Sequencing Length:
99
#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: GENDX000434 Download
Reference Genome: GCF_017639785.1_BCM_Maur_2.0
Genome Annotation: GCF_017639785.1_BCM_Maur_2.0
Data Processing:
  1. Fastp v0.20.0; fastp -q 20 -u 40 -l 50 -g -x -r -W 4 -M 20
  2. RseQC v2.6.4; python infer_experiment.py -r $index -I $Projectid/$SRXid/${SRXid}_Alignment-unsorted.bam > $Projectid/$SRXid/${SRXid}_RseQC.txt
  3. STAR v2.7.1a, RSEM v1.3.1; rsem-calculate-expression --keep-intermediate-files --temporary-folder $Projectid/$SRXid/${SRXid}_STAR_rsem --paired-end --forward-prob=$value -p $thread --time --star --star-path /software/biosoft/software/STAR-2.7/STAR/bin/Linux_x86_64/ --append-names --output-genome-bam --sort-bam-by-coordinate --star-gzipped-read-file $Projectid/$SRXid/${SRXid}_clean_1.fastq.gz $Projectid/$SRXid/${SRXid}_clean_2.fastq.gz $index $Projectid/$SRXid/${SRXid}_star_RSEM

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