Genomic profiling of collaborative cross founder mouse strains infected with respiratory viruses to discover novel transcripts and infection-related strain-specific gene and isoform expression

RNA-Seq mRNA differential
Organism: Mus musculus
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Sample Characteristics
Experimental Variables
Comparison
Reference/Test
Run
age
developmental stage
genotype
organism
organism part
sex
strain
infect
strain
time
•
'SARS coronavirus MA15; 2 day' vs 'mock' in '129S1/SvImJ' (9)
Test, Reference
9 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
129S1/SvImJ
SARS coronavirus MA15, mock
129S1/SvImJ
2 day,
•
'SARS coronavirus MA15; 4 day' vs 'mock' in '129S1/SvImJ' (8)
Test, Reference
8 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
129S1/SvImJ
SARS coronavirus MA15, mock
129S1/SvImJ
4 day,
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in '129S1/SvImJ' (8)
Reference, Test
8 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
129S1/SvImJ
2 infects
129S1/SvImJ
, 2 day
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 4 day' vs 'mock' in '129S1/SvImJ' (8)
Reference, Test
8 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
129S1/SvImJ
2 infects
129S1/SvImJ
, 4 day
•
none (18)
18 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
4 strains
2 infects
4 strains
2 day, 4 day
•
'SARS coronavirus MA15; 4 day' vs 'mock' in 'A/J' (11)
Test, Reference
11 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
A/J
SARS coronavirus MA15, mock
A/J
4 day,
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in 'A/J' (13)
Reference, Test
13 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
A/J
2 infects
A/J
, 2 day
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 4 day' vs 'mock' in 'A/J' (11)
Reference, Test
11 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
A/J
2 infects
A/J
, 4 day
•
'SARS coronavirus MA15; 2 day' vs 'mock' in 'C57BL/6J' (11)
Test, Reference
11 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
C57BL/6J
SARS coronavirus MA15, mock
C57BL/6J
2 day,
•
'SARS coronavirus MA15; 4 day' vs 'mock' in 'C57BL/6J' (12)
Test, Reference
12 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
C57BL/6J
SARS coronavirus MA15, mock
C57BL/6J
4 day,
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in 'C57BL/6J' (12)
Reference, Test
12 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
C57BL/6J
2 infects
C57BL/6J
, 2 day
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 4 day' vs 'mock' in 'C57BL/6J' (11)
Reference, Test
11 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
C57BL/6J
2 infects
C57BL/6J
, 4 day
•
'SARS coronavirus MA15; 2 day' vs 'mock' in 'CAST/EiJ' (11)
Test, Reference
11 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
CAST/EiJ
SARS coronavirus MA15, mock
CAST/EiJ
2 day,
•
'SARS coronavirus MA15; 4 day' vs 'mock' in 'CAST/EiJ' (12)
Test, Reference
12 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
CAST/EiJ
SARS coronavirus MA15, mock
CAST/EiJ
4 day,
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in 'CAST/EiJ' (9)
Reference, Test
9 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
CAST/EiJ
2 infects
CAST/EiJ
, 2 day
•
'SARS coronavirus MA15; 2 day' vs 'mock' in 'NOD/ShiLtJ' (7)
Test, Reference
7 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
NOD/ShiLtJ
SARS coronavirus MA15, mock
NOD/ShiLtJ
2 day,
•
'SARS coronavirus MA15; 4 day' vs 'mock' in 'NOD/ShiLtJ' (7)
Test, Reference
7 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
NOD/ShiLtJ
SARS coronavirus MA15, mock
NOD/ShiLtJ
4 day,
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in 'NOD/ShiLtJ' (8)
Reference, Test
8 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
NOD/ShiLtJ
2 infects
NOD/ShiLtJ
, 2 day
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 4 day' vs 'mock' in 'NOD/ShiLtJ' (7)
Reference, Test
7 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
NOD/ShiLtJ
2 infects
NOD/ShiLtJ
, 4 day
•
'Influenza A virus (A/Puerto Rico/8/1934(H1N1)); 2 day' vs 'mock' in 'NZO/HILtJ' (10)
Reference, Test
10 runs
8 to 16 week
adult
wild type genotype
Mus musculus
lung
female
NZO/HILtJ
2 infects
NZO/HILtJ
, 2 day
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