Bulk RNA seq of macrophages isolated from Kmo morphant or control morphant zebrafish larvae infected with Salmonella Typhimurium
Data files
Sep 29, 2025 version files 106.98 GB
-
Counts.csv
5.81 MB
-
ctrl_inf_BR_1_R1.fastq.gz
1.38 GB
-
ctrl_inf_BR_1_R2.fastq.gz
1.42 GB
-
ctrl_inf_BR_10_R1.fastq.gz
763.66 MB
-
ctrl_inf_BR_10_R2.fastq.gz
789.75 MB
-
ctrl_inf_BR_11_R1.fastq.gz
1.05 GB
-
ctrl_inf_BR_11_R2.fastq.gz
1.08 GB
-
ctrl_inf_BR_12_R1.fastq.gz
888.99 MB
-
ctrl_inf_BR_12_R2.fastq.gz
913.39 MB
-
ctrl_inf_BR_13_R1.fastq.gz
832.06 MB
-
ctrl_inf_BR_13_R2.fastq.gz
850.17 MB
-
ctrl_inf_BR_2_R1.fastq.gz
896.55 MB
-
ctrl_inf_BR_2_R2.fastq.gz
928.51 MB
-
ctrl_inf_BR_3_R1.fastq.gz
923.61 MB
-
ctrl_inf_BR_3_R2.fastq.gz
938.23 MB
-
ctrl_inf_BR_4_R1.fastq.gz
1.57 GB
-
ctrl_inf_BR_4_R2.fastq.gz
1.62 GB
-
ctrl_inf_BR_5_R1.fastq.gz
1.30 GB
-
ctrl_inf_BR_5_R2.fastq.gz
1.36 GB
-
ctrl_inf_BR_6_R1.fastq.gz
1.42 GB
-
ctrl_inf_BR_6_R2.fastq.gz
1.48 GB
-
ctrl_inf_BR_7_R1.fastq.gz
983.81 MB
-
ctrl_inf_BR_7_R2.fastq.gz
1.03 GB
-
ctrl_inf_BR_8_R1.fastq.gz
597.16 MB
-
ctrl_inf_BR_8_R2.fastq.gz
622.74 MB
-
ctrl_inf_BR_9_R1.fastq.gz
892.25 MB
-
ctrl_inf_BR_9_R2.fastq.gz
931.86 MB
-
ctrl_uninf_BR_1_R1.fastq.gz
939.65 MB
-
ctrl_uninf_BR_1_R2.fastq.gz
905.40 MB
-
ctrl_uninf_BR_2_R1.fastq.gz
849.50 MB
-
ctrl_uninf_BR_2_R2.fastq.gz
856.07 MB
-
ctrl_uninf_BR_3_R1.fastq.gz
855.44 MB
-
ctrl_uninf_BR_3_R2.fastq.gz
876.64 MB
-
ctrl_uninf_BR_4_R1.fastq.gz
375.24 MB
-
ctrl_uninf_BR_4_R2.fastq.gz
394.80 MB
-
ctrl_uninf_BR_5_R1.fastq.gz
1.03 GB
-
ctrl_uninf_BR_5_R2.fastq.gz
1.09 GB
-
ctrl_uninf_BR_6_R1.fastq.gz
1.48 GB
-
ctrl_uninf_BR_6_R2.fastq.gz
1.52 GB
-
ctrl_uninf_BR_7_R1.fastq.gz
37 MB
-
ctrl_uninf_BR_7_R2.fastq.gz
37.35 MB
-
exposed_ctrl_kmo.zip
24.03 GB
-
kmo_inf_BR_1_R1.fastq.gz
1.53 GB
-
kmo_inf_BR_1_R2.fastq.gz
1.63 GB
-
kmo_inf_BR_10_R1.fastq.gz
548.04 MB
-
kmo_inf_BR_10_R2.fastq.gz
565.74 MB
-
kmo_inf_BR_11_R1.fastq.gz
1.07 GB
-
kmo_inf_BR_11_R2.fastq.gz
1.11 GB
-
kmo_inf_BR_12_R1.fastq.gz
1.19 GB
-
kmo_inf_BR_12_R2.fastq.gz
1.21 GB
-
kmo_inf_BR_13_R1.fastq.gz
1.65 GB
-
kmo_inf_BR_13_R2.fastq.gz
1.65 GB
-
kmo_inf_BR_2_R1.fastq.gz
1.13 GB
-
kmo_inf_BR_2_R2.fastq.gz
976.37 MB
-
kmo_inf_BR_3_R1.fastq.gz
1.18 GB
-
kmo_inf_BR_3_R2.fastq.gz
1.19 GB
-
kmo_inf_BR_4_R1.fastq.gz
1.29 GB
-
kmo_inf_BR_4_R2.fastq.gz
1.31 GB
-
kmo_inf_BR_5_R1.fastq.gz
1.48 GB
-
kmo_inf_BR_5_R2.fastq.gz
1.53 GB
-
kmo_inf_BR_6_R1.fastq.gz
1.45 GB
-
kmo_inf_BR_6_R2.fastq.gz
1.52 GB
-
kmo_inf_BR_7_R1.fastq.gz
983.97 MB
-
kmo_inf_BR_7_R2.fastq.gz
1.03 GB
-
kmo_inf_BR_8_R1.fastq.gz
883.11 MB
-
kmo_inf_BR_8_R2.fastq.gz
918.22 MB
-
kmo_inf_BR_9_R1.fastq.gz
417.50 MB
-
kmo_inf_BR_9_R2.fastq.gz
437.25 MB
-
kmo_uninf_BR_1_R1.fastq.gz
1.06 GB
-
kmo_uninf_BR_1_R2.fastq.gz
1.11 GB
-
kmo_uninf_BR_2_R1.fastq.gz
804.79 MB
-
kmo_uninf_BR_2_R2.fastq.gz
833.35 MB
-
kmo_uninf_BR_3_R1.fastq.gz
862.31 MB
-
kmo_uninf_BR_3_R2.fastq.gz
903.30 MB
-
kmo_uninf_BR_4_R1.fastq.gz
590.81 MB
-
kmo_uninf_BR_4_R2.fastq.gz
631.12 MB
-
kmo_uninf_BR_5_R1.fastq.gz
929.41 MB
-
kmo_uninf_BR_5_R2.fastq.gz
982.34 MB
-
kmo_uninf_BR_6_R1.fastq.gz
1.36 GB
-
kmo_uninf_BR_6_R2.fastq.gz
1.43 GB
-
kmo_uninf_BR_7_R1.fastq.gz
1.40 GB
-
kmo_uninf_BR_7_R2.fastq.gz
1.45 GB
-
Metadata.csv
2.96 KB
-
README.md
18.66 KB
Abstract
The kynurenine pathway of tryptophan degradation has been implicated in various diseases, including cancer, neurodegenerative disorders, and infectious diseases. A key branchpoint in this pathway is production of the metabolite 3-hydroxy-kynurenine (3-HK) by the enzyme kynurenine 3-monooxygenase (Kmo). We recently found that administration of exogenous 3-HK promotes survival to Salmonella Typhimurium infection in zebrafish larvae by restricting bacterial expansion in macrophages via a systemic mechanism that targets kainate sensitive glutamate receptor (KAR) ion channels. Here, we show that endogenous production of 3-HK by Kmo, likewise, is required for defense against systemic Salmonella Typhimurium infection in vivo and that loss of endogenous production of 3-HK impairs macrophage microbicial activity, resulting in increased bacterial expansion. Mechanistically, 3-HK acts by antagonizing KARs to promote lysosome acidification and subsequent control of bacterial burden. Finally, we establish a novel link between activity at KARs and lysosomal acidification in macrophages, revealing a novel regulatory role for KARs in promoting macrophage microbicidal activity and a novel mechanism though which 3-HK promotes control of bacterial infection.
Dataset DOI: 10.5061/dryad.tht76hf8w
Description of the data and file structure
For the article: Kmo restricts Salmonella in macrophages by promoting lysosomal acidification through kainate receptor antagonism in a whole organism infection model. Bulk RNA sequencing of macrophages isolated from either kmo morphant or control morphant zebrafish larvae at 3 days post-fertilization infected intravenously with Salmonella Typhimurium or uninfected. The data shows that infected kmo morphant macrophages have suppression of lysosomal genes compared to infected control morphant macrophages using GSEA KEGG. For each biological replicate, five zebrafish larvae were dissociated together and macrophages sorted using FACS, with macrophages labelled using the transgenic line Tg(mpeg1.1:mCherry) and Salmonella with GFP. cDNA libraries were prepared with Smart-Seq2 protocol in combination with Nextera XT Library preparation kit (Illumina Inc). Samples were multiplexed and pair end sequences were generated with NovaSeq SP sequencing system (Illumina). Gene set enrichment analysis was performed with ClusterProfiler (v.4.0) with a FDR <0.05 using the Kyoto Encyclopedia of Genes and Genomes terms.
Files and variables
File: ctrl_uninf_BR_1_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 1, read 1.
File: ctrl_uninf_BR_7_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 7, read 1.
File: ctrl_uninf_BR_7_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 7, read 2.
File: ctrl_inf_BR_1_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 1, read 1.
File: ctrl_uninf_BR_2_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 2, read 2.
File: ctrl_inf_BR_2_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 2, read 1.
File: ctrl_uninf_BR_1_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 1, read 2.
File: ctrl_inf_BR_1_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 1, read 2.
File: ctrl_uninf_BR_2_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 2, read 1.
File: ctrl_uninf_BR_3_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 3, read 1.
File: ctrl_uninf_BR_3_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 3, read 2.
File: ctrl_inf_BR_3_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 3, read 1.
File: ctrl_inf_BR_2_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 2, read 2.
File: ctrl_uninf_BR_4_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 4, read 1.
File: kmo_inf_BR_1_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 1, read 1.
File: ctrl_inf_BR_3_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 3, read 2.
File: ctrl_uninf_BR_5_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 5, read 1
File: ctrl_uninf_BR_5_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 5, read 2.
File: ctrl_inf_BR_5_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 5, read 1.
File: ctrl_inf_BR_4_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 4, read 2.
File: ctrl_uninf_BR_4_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 4, read 2.
File: ctrl_inf_BR_4_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 4, read 1.
File: ctrl_uninf_BR_6_R1.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 6, read 1.
File: ctrl_inf_BR_6_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 6, read 1.
File: ctrl_inf_BR_8_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 8, read 1.
File: ctrl_inf_BR_6_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 6, read 2.
File: kmo_inf_BR_1_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 1, read 2.
File: ctrl_inf_BR_9_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 9, read 1.
File: ctrl_inf_BR_5_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 5, read 2.
File: ctrl_inf_BR_7_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 7, read 1.
File: kmo_inf_BR_2_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 2, read 2.
File: ctrl_inf_BR_9_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 9, read 2.
File: ctrl_inf_BR_7_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 7, read 2.
File: ctrl_inf_BR_8_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 8, read 2.
File: kmo_inf_BR_2_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 2, read 1.
File: ctrl_uninf_BR_6_R2.fastq.gz
Description: Macrophages from uninfected, naive control morphant larvae. Biological replicate 6, read 2.
File: kmo_inf_BR_8_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 8, read 2.
File: kmo_inf_BR_9_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 9, read 2.
File: kmo_inf_BR_5_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 5, read 2.
File: ctrl_inf_BR_13_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 13, read 2.
File: ctrl_inf_BR_10_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 10, read 1.
File: ctrl_inf_BR_11_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 11, read 1.
File: kmo_inf_BR_10_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 10, read 1.
File: kmo_inf_BR_6_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 6, read 2.
File: kmo_inf_BR_3_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 3, read 1.
File: kmo_inf_BR_12_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 12, read 1.
File: ctrl_inf_BR_10_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 10, read 2.
File: kmo_inf_BR_4_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 4, read 2.
File: kmo_inf_BR_11_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 11, read 2.
File: kmo_inf_BR_12_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 12, read 2.
File: kmo_inf_BR_8_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 8, read 1.
File: kmo_inf_BR_7_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 7, read 1.
File: kmo_inf_BR_9_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 9, read 1.
File: kmo_inf_BR_10_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 10, read 2.
File: kmo_inf_BR_13_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 13, read 1.
File: kmo_inf_BR_13_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 13, read 2.
File: ctrl_inf_BR_13_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 13, read 1.
File: kmo_inf_BR_5_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 5, read 1.
File: ctrl_inf_BR_11_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 11, read 2.
File: kmo_inf_BR_6_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 6, read 1.
File: kmo_inf_BR_11_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 11, read 1.
File: kmo_inf_BR_3_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 3, read 2.
File: ctrl_inf_BR_12_R1.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 12, read 1.
File: kmo_uninf_BR_1_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 1, read 1.
File: kmo_uninf_BR_4_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 4, read 2.
File: kmo_uninf_BR_3_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 3, read 2.
File: kmo_uninf_BR_2_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 2, read 1.
File: kmo_uninf_BR_3_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 3, read 1.
File: kmo_uninf_BR_1_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 1, read 2.
File: kmo_uninf_BR_4_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 4, read 1.
File: kmo_uninf_BR_7_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 7, read 1.
File: kmo_uninf_BR_2_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 2, read 2.
File: kmo_uninf_BR_5_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 5, read 1.
File: kmo_inf_BR_7_R2.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 7, read 2.
File: ctrl_inf_BR_12_R2.fastq.gz
Description: Infected macrophages from infected control morphant larvae. Biological replicate 12, read 2.
File: kmo_inf_BR_4_R1.fastq.gz
Description: Infected macrophages from infected Kmo morphant larvae. Biological replicate 4, read 1.
File: kmo_uninf_BR_5_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 5, read 2.
File: kmo_uninf_BR_6_R1.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 6, read 1.
File: kmo_uninf_BR_7_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 7, read 2.
File: kmo_uninf_BR_6_R2.fastq.gz
Description: Macrophages from uninfected, naive Kmo morphant larvae. Biological replicate 6, read 2.
File: exposed_ctrl_kmo.zip
Description: Macrophages from infected control or Kmo morphant larvae that are exposed but not actively infected. FASTQ files from biological replicates 1-7 with reads 1 and 2 from control morphant and Kmo morphant replicates.
File: Metadata.csv
Description: Table with metadata used for sample analysis.
Variables
- sample_name: Complete sample name, including condition, infection status, and biological replicate.
- infection: Infection status of the macrophage. Uninf: uninfected, naive. Inf: actively infected. Exp: exposed, not actively infected from infected larvae.
- condition: Morpholino treatment. Ctrl: control morphant larvae. Kmo: Kmo morphant larvae.
- combined_condition: Infection status combined with morpholino treatment. Ctrl uninf: uninfected macrophage from control morphant larvae. Kmo uninf: uninfected macrophage from Kmo morphant larvae. Kmo inf: actively infected macrophage from Kmo morphant larvae. Kmo exp: exposed macrophage from Kmo morphant larvae. Ctrl inf: actively infected macrophage from control morphant larvae. Ctrl exp: exposed macrophage from control morphant larvae.
- date: Date that macrophages were sorted using FACS. 11.19: sorted on 11.19.21. 11.12: sorted on 11.12.21
- br: Complete sample name. Same as Sample Name.
- replicate: Biological replicate number.
File: Counts.csv
Description: Raw count data table. ENSEMBL gene names in rows and sample names in columns.
Variables
- gene_name: ENSEMBL gene labels.
- ctrl_uninf_BR1: Control morphant, uninfected, biological replicate 1.
- ctrl_uninf_BR2: Control morphant, uninfected, biological replicate 2.
- ctrl_uninf_BR3: Control morphant, uninfected, biological replicate 3.
- ctrl_uninf_BR4: Control morphant, uninfected, biological replicate 4.
- ctrl_uninf_BR5: Control morphant, uninfected, biological replicate 5.
- ctrl_uninf_BR6: Control morphant, uninfected, biological replicate 6.
- ctrl_uninf_BR7: Control morphant, uninfected, biological replicate 7.
- kmo_uninf_BR1: Kmo morphant, uninfected, biological replicate 1.
- kmo_uninf_BR2: Kmo morphant, uninfected, biological replicate 2.
- kmo_uninf_BR3: Kmo morphant, uninfected, biological replicate 3.
- kmo_uninf_BR4: Kmo morphant, uninfected, biological replicate 4.
- kmo_uninf_BR5: Kmo morphant, uninfected, biological replicate 5.
- kmo_uninf_BR6: Kmo morphant, uninfected, biological replicate 6.
- kmo_uninf_BR7: Kmo morphant, uninfected, biological replicate 7.
- kmo_inf_BR10: Kmo morphant, infected, biological replicate 10.
- kmo_inf_BR11: Kmo morphant, infected, biological replicate 11.
- kmo_inf_BR12: Kmo morphant, infected, biological replicate 12.
- kmo_inf_BR13: Kmo morphant, infected, biological replicate 13.
- kmo_inf_BR1: Kmo morphant, infected, biological replicate 1.
- kmo_inf_BR2: Kmo morphant, infected, biological replicate 2.
- kmo_inf_BR3: Kmo morphant, infected, biological replicate 3.
- kmo_inf_BR4: Kmo morphant, infected, biological replicate 4.
- kmo_inf_BR5: Kmo morphant, infected, biological replicate 5.
- kmo_inf_BR6: Kmo morphant, infected, biological replicate 6.
- kmo_inf_BR7: Kmo morphant, infected, biological replicate 7.
- kmo_inf_BR8: Kmo morphant, infected, biological replicate 8.
- kmo_inf_BR9: Kmo morphant, infected, biological replicate 9.
- kmo_exp_BR1: Kmo morphant, exposed, biological replicate 1.
- kmo_exp_BR2: Kmo morphant, exposed, biological replicate 2.
- kmo_exp_BR3: Kmo morphant, exposed, biological replicate 3.
- kmo_exp_BR4: Kmo morphant, exposed, biological replicate 4.
- kmo_exp_BR5: Kmo morphant, exposed, biological replicate 5.
- kmo_exp_BR6: Kmo morphant, exposed, biological replicate 6.
- kmo_exp_BR7: Kmo morphant, exposed, biological replicate 7.
- ctrl_inf_BR10: Control morphant, infected, biological replicate 10.
- ctrl_inf_BR11: Control morphant, infected, biological replicate 11.
- ctrl_inf_BR12: Control morphant, infected, biological replicate 12.
- ctrl_inf_BR13: Control morphant, infected, biological replicate 13.
- ctrl_inf_BR1: Control morphant, infected, biological replicate 1.
- ctrl_inf_BR2: Control morphant, infected, biological replicate 2.
- ctrl_inf_BR3: Control morphant, infected, biological replicate 3.
- ctrl_inf_BR4: Control morphant, infected, biological replicate 4.
- ctrl_inf_BR5: Control morphant, infected, biological replicate 5.
- ctrl_inf_BR6: Control morphant, infected, biological replicate 6.
- ctrl_inf_BR7: Control morphant, infected, biological replicate 7.
- ctrl_inf_BR8: Control morphant, infected, biological replicate 8.
- ctrl_inf_BR9: Control morphant, infected, biological replicate 9.
- ctrl_exp_BR1: Control morphant, exposed, biological replicate 1.
- ctrl_exp_BR2: Control morphant, exposed, biological replicate 2.
- ctrl_exp_BR3: Control morphant, exposed, biological replicate 3.
- ctrl_exp_BR4: Control morphant, exposed, biological replicate 4.
- ctrl_exp_BR5: Control morphant, exposed, biological replicate 5.
- ctrl_exp_BR6: Control morphant, exposed, biological replicate 6.
- ctrl_exp_BR7: Control morphant, exposed, biological replicate 7.
Code/software
No specific software required.
Access information
Other publicly accessible locations of the data:
- None
Data was derived from the following sources:
- Data derived directly from Illumina NovaSeq SP sequencer and is not processed.
Bulk RNA sequencing transcriptomes of macrophages isolated from 3 days post-fertilization zebrafish larvae. Fluorescently labeled cells were isolated in bulk from a single cell suspension obtained by enzymatic digestion of groups consisting of 5 homozygous Tg(mpeg1:mCherry) transgenic animals (7-13 biological replicates/condition) injected with either the translation-blocking kmo morpholino (Kmo MO) or standard control morpholino (Ctrl MO). cDNA libraries were constructed from a range of 50-800 collected cells with an in-house adaptation of the Smart-seq2 protocol in combination with the Nextera XT Library preparation kit (Illumina, Inc., San Diego, CA). Library size and concentration were evaluated using the TapeStation 2200 system (Agilent) and a Qubit fluorometer (Invitrogen) before sequencing. Samples were multiplexed and pair end sequences were generated with NovaSeq SP sequencing system (Illumina) generating 5.5e10^7 reads per sample. Samples were demultiplexed and FASTQ files representing each sample were generated. Any remaining adapter sequences were removed using skewer (0.2.2) and FASTQ files were assessed for quality control using FASTQC (0.11.5). Reads were aligned to the Ensembl zebrafish reference genome GRCz11 using Hisat2 (2.1.0) and counts were quantified using HTSeq-Count (0.12.4). Differential gene expression analysis was performed using DESeq2 (1.38.3). Gene ontology analyses were performed using gene set enrichment analysis (GSEA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses with an FDR below 0.05 using gseKEGG from ClusterProfiler (v4.6.2).