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| Status |
Public on Jul 04, 2024 |
| Title |
RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis, as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up- or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA-seq was conducted using a low dose infection (approximately 30 CFU) at 4 weeks post infection, from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria.
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| Overall design |
Identification of the up- and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed, from three to nine biological replicates in each group. Wild type (WT) sibling fish were used as a control. The groups were WT PBS injected, mutant PBS injected, WT M. marinum infected, mutant M. marinum infected.
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| Contributor(s) |
Uusi-Mäkelä M, Harjula S, Sillanpää A, Nätkin R, Niskanen M, Nykter M, Rämet M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 26, 2021 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Reetta Nätkin |
| E-mail(s) |
reetta.natkin@tuni.fi
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| Organization name |
Tampere University and Tays Cancer Center
|
| Department |
Faculty of Medicine and Health Technology, Prostate Cancer Research Center
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| Street address |
Arvo Ylpön katu 34
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| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
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| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (24)
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| GSM5704977 |
Mut_PBS_1 [210019_4_Mut_PBS_11_s4_S237] |
| GSM5704978 |
Mut_PBS_2 [210019_5_Mut_PBS_12_s5_S238] |
| GSM5704979 |
Mut_PBS_3 [210019_6_Mut_PBS_13_s6_S239] |
| GSM5704980 |
Mut_PBS_4 [210019_7_Mut_PBS_15_s7_S240] |
| GSM5704981 |
Mut_PBS_5 [210019_8_Mut_PBS_18_s8_S241] |
| GSM5704982 |
WT_Inf_1 [210019_9_WT_Inf_21_s9_S242] |
| GSM5704983 |
WT_Inf_2 [210019_10_WT_Inf_25_s10_S220] |
| GSM5704984 |
WT_Inf_3 [210019_11_WT_Inf_27_s11_S221] |
| GSM5704985 |
WT_Inf_4 [210019_12_WT_Inf_28_s12_S222] |
| GSM5704986 |
WT_Inf_5 [210019_13_WT_Inf_29_s13_S223] |
| GSM5704987 |
WT_Inf_6 [210019_14_WT_Inf_30_s14_S224] |
| GSM5704988 |
WT_Inf_7 [210019_15_WT_Inf_31_s15_S225] |
| GSM5704989 |
WT_Inf_8 [210019_16_WT_Inf_32_s16_S226] |
| GSM5704990 |
WT_Inf_9 [210019_17_WT_Inf_33_s17_S227] |
| GSM5704991 |
Mut_Inf_1 [210019_18_Mut_Inf_34_s18_S228] |
| GSM5704992 |
Mut_Inf_2 [210019_19_Mut_Inf_35_s19_S229] |
| GSM5704993 |
Mut_Inf_3 [210019_20_Mut_Inf_36_s20_S231] |
| GSM5704994 |
Mut_Inf_4 [210019_21_Mut_Inf_38_s21_S232] |
| GSM5704995 |
Mut_Inf_5 [210019_22_Mut_Inf_39_s22_S233] |
| GSM5704996 |
Mut_Inf_6 [210019_23_Mut_Inf_40_s23_S234] |
| GSM5704997 |
Mut_Inf_7 [210019_24_Mut_Inf_42_s24_S235] |
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| Relations |
| BioProject |
PRJNA783915 |
| SRA |
SRP348087 |
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