Table 1.

Reagent or resource

Reagent or resourceSourceIdentifier
Antibodies 
CD16/CD32 Fc block eBioScience; Thermo Fisher Scientific RRID:AB_467133 
CD45 PE Texas Red/AF700/PerCP Cy5.5 Biolegend RRID:AB_2564002/AB_493714/AB_893340 
CD3 FITC/PE Texas Red Biolegend RRID:AB_312661/AB_2565882 
CD19 FITC/BV605 Biolegend RRID:AB_313640/AB_2564000 
F4/80 FITC/PB Biolegend RRID:AB_893500/AB_893475 
CD11b AF700/PECy7 Biolegend RRID:AB_493705/AB_312798 
Ly-6G PECy-7/FITC Biolegend RRID:AB_1877261/AB_1236488 
CD8 BV510 Biolegend RRID:AB_2563057 
CD4 PerCP Cy5.5 Biolegend RRID:AB_893324 
NK1.1 APC Biolegend RRID:AB_313396 
Ly-6C BV510 Biolegend RRID:AB_2562351 
CD11c PE Texas Red Thermo Fisher Scientific RRID:AB_10373971 
BST2 PE Biolegend RRID:AB_1953283 
B220 AF700 Biolegend RRID:AB_493716 
CD103 APC Biolegend RRID:AB_2563906 
CD31 Pacific blue Biolegend RRID:AB_10613457 
EpCam PE Biolegend RRID:AB_1134172 
Ly6G 1A8 Biolegend RRID:AB_1089180 
CitH4 (citrulline 3) Merck/MilliporeSigma Cat#07–596 
Cy3-conjugated donkey anti-rat IgG Dianova Cat#712-165–153 
AF 647–labeled donkey anti-rabbit IgG Thermo Fisher Scientific RRID:AB_2536183 
Anti-mouse CD8α, clone YTS169 In-house NA 
Biological samples 
Human sample 1 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 2 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 3 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 4 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 5 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 6 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 7 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 8 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 9 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 10 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 11 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 12 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 13 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 14 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 15 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 16 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 17 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 18 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 19 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 20 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 21 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Chemicals, peptides, and recombinant proteins 
Dextran sulfate sodium salt, colitis grade (36,000–50,000) MP Biomedicals Cat#0216011080 
Peqlab peqGOLD TriFast, DNA/RNA/protein purification reagent Avantor, VWR Chemicals Cat#30–2010 
LunaScript Reverse Transcriptase (LunaScript RT Mastermix) New England Biolabs GmbH Cat#E3025 
Fluorescein isothiocyanate–dextran, average mol weight 3,000–5,000 Merck/MilliporeSigma Cat#FD4 
Ampicillin sodium salt ≥97%, BioScience Grade Carl Roth GmbH + Co Cat#K029.1 
Vancomycin hydrochloride Carl Roth GmbH + C. KG Cat#0242.3 
Streptomycin sulfate Carl Roth GmbH + Co Cat#0236.1 
Neomycin sulfate Carl Roth GmbH + Co Cat#8668.1 
DreamTaq DNA Polymerase (5 U/μl) Thermo Fisher Scientific Cat#EP0705 
SYTO 9 green fluorescent nucleic acid stain Thermo Fisher Scientific Cat#S34854 
eBioscience fixable viability dye eFluor 780 Thermo Fisher Scientific Cat#65–0865-14 
CountBright absolute counting beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 
DNAse I Merck/MilliporeSigma Cat#11284932001 
Collagenase A Gibco; Thermo Fisher Scientific Cat#17018029 
Dispase II Gibco; Thermo Fisher Scientific Cat#17105041 
Liberase TL TL Research Grade Fisher Scientific; Thermo Fisher Scientific Cat#NC1328423 
Hoechst 33342 Thermo Fisher Scientific Cat#62249 
Citrate, 0.5 M buffer soln., pH 3.5 Thermo Fisher Scientific Cat#15454239 
SYTOX green Thermo Fisher Scientific Cat#S7020 
a23187 Merck/MilliporeSigma Cat#C7522 
PMA Merck/MilliporeSigma Cat#19–144 
N-Formyl-Met-Leu-Phe (fMLP) Merck/MilliporeSigma Cat#F3506 
CellTrace CFSE cell proliferation kit Thermo Fisher Scientific Cat#C34570 
Red-fluorescent tetramethylrhodamine (TAMRA) azide Thermo Fisher Scientific Cat#T10182 
Q5 High-Fidelity DNA Polymerase NEB Cat#M0491 
qScript cDNA synthesis-set Avantor, VWR Chemicals Cat#733–1175 
Ultra-Plex 1-step ToughMix ROX (4X) Avantor, VWR Chemicals Cat#733–2466 
PerfeCTa SYBR Green SuperMixes and FastMixes Avantor, VWR Chemicals Cat#733–1387 
NucleoSpin 96 RNA Core Kit, 96-well Kit for RNA Isolation Macherey-Nagel Cat#740466.4 
Lyophilized carrier RNA Macherey-Nagel Cat#740514 
LunaScript RT SuperMix Kit NEB Cat#E3010 
Monarch DNA Gel Extraction Kit NEB Cat#T1120 
Critical commercial assays 
QIAamp Fast DNA Stool Kit Qiagen Cat#51604 
SequalPrep normalization plate kit, 96-well Thermo Fisher Scientific Cat#A1051001 
Illumina TruSeq Nano Kit Illumina Inc. Cat#A20015964 
Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling 10X Genomics,.Inc. Cat#1000414 
Chromium Fixed RNA Kit, Mouse Transcriptome, 4 rxns x 16 BC 10X Genomics, Inc. Cat#PN-1000497 
NEBNext Poly(A) mRNA Isolation Module NEB Cat#E7490 
NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat#E7765 
LEGENDplex Mouse Anti-Virus Response Panel Biolegend Cat#740622 
Neutrophil Isolation Kit, Mouse Miltenyi Biotec Cat#130-097-658 
Deposited data 
Microbiome sequencing data National Institutes of Health: BioProject - effect of filamin A editing on the gut microbiome BioProject ID: PRJNA1051489 
Bulk sequencing data of distal colon National Institutes of Health: GEO dataset GSE296059 
scRNA-seq of colon cells National Institutes of Health: GEO dataset GSE296058 
Flna amplicon sequencing (ampSeq) National Institutes of Health: GEO dataset GSE295910 
Experimental models: Organisms/strains 
WT mice C57BL/6J RRID:IMSR_JAX:000664 
FLNAQ mice Mouse breeding facility at Medical University of Vienna Refs 8 + 9 
FLNAR mice Mouse breeding facility at Medical University of Vienna Refs 8 + 9 
IL-10 KO mice 129(B6)-Il10tm1Cgn/J, the Jackson Laboratory RRID:IMSR_JAX:004368 
Vav1-Cre mice Tg(Vav1-cre)1Cgp MGI ID: 2450339 
FLNAQiR mice Mouse breeding facility at Medical University of Vienna This paper 
LysM-Cre mice B6.129P2-Lyz2tm1(cre)Ifo/J RRID:IMSR_JAX:004781 
Oligonucleotides (5′→3′) 
5′-GTC​AAG​TTC​AAC​GAG​GAG​CAC-3′ MicrosynthAG Human Flna editing locus fw primer 
5′-GTGCACCTTGG CATCAATTGC-3′ MicrosynthAG Human Flna editing locus rev primer 
5′-CCG​CCT​TAC​TGT​TTC​TAG​TCT-3′ MicrosynthAG Mouse Flna editing locus fw primer 
5′-GCT​GGT​TGA​CCT​TTA​ACC​CTG-3′ MicrosynthAG Mouse Flna editing locus rev primer 
5′-GTGYCAGCMGCCGCGGTAA-3′ MicrosynthAG 16S RNA barcoding 515F 
5′-GGACTACNVGGGTWTCTAAT-3′ MicrosynthAG 16S RNA barcoding 806R 
5′-ACA​CGA​CGC​TCT​TCC​GAT​CTG​AGC​ACA​TAC​CTG​ATA​GCC​CC-3′ MicrosynthAG Flna editing detection fw primer for ampSeq 
5′-CAG​ACG​TGT​GCT​CTT​CCG​ATC​TTC​TCT​CGT​GGG​ATG​AAA​CGC-3′ MicrosynthAG Flna editing detection rev primer for ampSeq 
5′-CAA​GCA​GAA​GAC​GGC​ATA​CGA​GAT​NNN​NNN​NNG​TGA​CTG​GAG​TTC​AGA​CGT​GTG​CTC​TTC​CGA​TCT-3′ MicrosynthAG ampSeq—barcoding primers fw 
5′-AAT​GAT​ACG​GCG​ACC​ACC​GAG​ATC​TAC​ACN​NNN​NNN​NAC​ACT​CTT​TCC​CTA​CAC​GAC​GCT​CTT​CCG​ATC​T-3′ MicrosynthAG ampSeq—barcoding primers rev 
5′-GAT​GAC​CAG​TCT​GGA​GGT​GC-3′ MicrosynthAG Mouse Adar fw 
5′-GCA​GCA​AAG​CCA​TGA​GAT​CG-3′ MicrosynthAG Mouse Adar rev 
5′-CAG​TTG​CAT​TTG​CCA​CAG​GTA​T-3′ MicrosynthAG Mouse Adarb1 fw 
5′-ACC​GTT​GAT​ACA​CTT​CGT​CCC-3′ MicrosynthAG Mouse Adarb1 rev 
5′-5′-GAA​CTG​GCA​GAA​GAG​GCA​CT-3′ MicrosynthAG Mouse Tnf fw 
5′-GGT​CTG​GGC​CAT​AGA​ACT​GA-3′ MicrosynthAG Mouse Tnf rev 
5′-CAA​AAT​ACC​TGT​GGC​CTT​GG-3′ MicrosynthAG Mouse Il1b fw 
5′-TAC​CAG​TTG​GGG​AAC​TCT​GC-3′ MicrosynthAG Mouse IL1b rev 
5′-CAG​CAA​CCA​TGG​GAG​AGA​ATG​CTG​A-3′ MicrosynthAG Mouse Ifit1 fw 
5′-GGC​ACA​GTT​GCC​CCA​GGT​CG-3′ MicrosynthAG Mouse Ifit1 rev 
5′-GAC​CAT​GGC​TGG​GAT​TCA​CC-3′ MicrosynthAG Mouse Cxcl1 fw 
5′-TCA​GAA​GCC​AGC​GTT​CAC​CA-3′ MicrosynthAG Mouse Cxcl1 rev 
5′-AAG​CTG​TAG​TTT​TTG​TCA​CCA​AG-3′ MicrosynthAG Mouse Ccl2 fw 
5′-CCA​TTT​GGT​TCC​GAT​CCA​GGT​TT-3′ MicrosynthAG Mouse Ccl2 rev 
5′-CCT​GGC​GGT​GCT​GAG​CTA​CT-3′ MicrosynthAG Mouse Ifna fw 
5′-TTC​TCC​TGC​GGG​AAT​CCA​AA-3′ MicrosynthAG Mouse Ifna rev 
5′-TGA​GGC​GCT​GTC​ATC​GAT​TT-3′ MicrosynthAG Mouse Il10 fw 
5′-CAT​GGC​CTT​GTA​GAC​ACC​TT-3′ MicrosynthAG Mouse Il10 rev 
5′-CCA​CGG​CCT​TCC​CTA​CTT​CA-3′ MicrosynthAG Mouse Il6 fw 
5′-TGC​AAG​TGC​ATC​GTT​GTT​C-3′ MicrosynthAG Mouse Il6 rev 
Software and algorithms 
BBDuk (BBTools) Bushnell, B., https://sourceforge.net/projects/bbmap NA 
Python package demultiplex Laros, J.F.J., https://github.com/jfjlaros/demultiplex NA 
DADA2 (v1.16.0) R package https://www.r-project.org/, R 4.0.2 NA 
Vegan (v2.4.3) R package https://www.r-project.org/, R 3.4.0 NA 
Phyloseq (v1.30.0) R package https://www.r-project.org/, R 3.4.1 NA 
DESeq2 (v1.26.0) R package https://www.r-project.org/, R 3.4.1 NA 
CellRanger (v7.1.0) 10X Genomics, Inc. NA 
Seurat (v.4.3.0) https://github.com/satijalab/seurat/releases NA 
Scanpy AnnData (v.1.9.1) https://scanpy.readthedocs.io/en/stable/installation.html NA 
SOLO (adaption of SCVI) https://github.com/calico/solo NA 
DoubletFinder https://github.com/chris-mcginnis-ucsf/DoubletFinder NA 
SCVI https://github.com/YosefLab/scVI NA 
SingleR https://github.com/dviraran/SingleR NA 
Scanpy https://github.com/theislab/Scanpy NA 
MAST https://www.bioconductor.org/packages/release/bioc/html/MAST.html NA 
FASTP https://github.com/OpenGene/fastp NA 
STAR (v.2.7.9a) https://github.com/alexdobin/STAR NA 
FeatureCounts https://subread.sourceforge.net/featureCounts.html NA 
Limma https://bioconductor.org/packages/release/bioc/html/limma.html NA 
R (v.4.1.0 or R 4.0.2) and python (v.3.8.12) https://www.r-project.org/and https://www.python.org/downloads/release/python-3812/ NA 
TissueFAXS scan software TissueGnostics GmbH NA 
Imaris 9.9.1 Oxford Instruments NA 
Cutadapt https://cutadapt.readthedocs.io/en/stable/installation.html NA 
Hisat2 https://daehwankimlab.github.io/hisat2/ NA 
Jacusa2 https://github.com/dieterich-lab/JACUSA2 NA 
Reagent or resourceSourceIdentifier
Antibodies 
CD16/CD32 Fc block eBioScience; Thermo Fisher Scientific RRID:AB_467133 
CD45 PE Texas Red/AF700/PerCP Cy5.5 Biolegend RRID:AB_2564002/AB_493714/AB_893340 
CD3 FITC/PE Texas Red Biolegend RRID:AB_312661/AB_2565882 
CD19 FITC/BV605 Biolegend RRID:AB_313640/AB_2564000 
F4/80 FITC/PB Biolegend RRID:AB_893500/AB_893475 
CD11b AF700/PECy7 Biolegend RRID:AB_493705/AB_312798 
Ly-6G PECy-7/FITC Biolegend RRID:AB_1877261/AB_1236488 
CD8 BV510 Biolegend RRID:AB_2563057 
CD4 PerCP Cy5.5 Biolegend RRID:AB_893324 
NK1.1 APC Biolegend RRID:AB_313396 
Ly-6C BV510 Biolegend RRID:AB_2562351 
CD11c PE Texas Red Thermo Fisher Scientific RRID:AB_10373971 
BST2 PE Biolegend RRID:AB_1953283 
B220 AF700 Biolegend RRID:AB_493716 
CD103 APC Biolegend RRID:AB_2563906 
CD31 Pacific blue Biolegend RRID:AB_10613457 
EpCam PE Biolegend RRID:AB_1134172 
Ly6G 1A8 Biolegend RRID:AB_1089180 
CitH4 (citrulline 3) Merck/MilliporeSigma Cat#07–596 
Cy3-conjugated donkey anti-rat IgG Dianova Cat#712-165–153 
AF 647–labeled donkey anti-rabbit IgG Thermo Fisher Scientific RRID:AB_2536183 
Anti-mouse CD8α, clone YTS169 In-house NA 
Biological samples 
Human sample 1 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 2 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 3 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 4 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 5 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 6 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 7 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 8 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 9 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 10 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 11 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 12 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 13 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 14 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 15 Proximal and distal colon biopsies of healthy patient Ethics Committee number: 1692/2020 
Human sample 16 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 17 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 18 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Human sample 19 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 20 Proximal and distal colon biopsies of patient in remission from UC Ethics Committee number: 1692/2020 
Human sample 21 Proximal and distal colon biopsies of patient with active UC Ethics Committee number: 1692/2020 
Chemicals, peptides, and recombinant proteins 
Dextran sulfate sodium salt, colitis grade (36,000–50,000) MP Biomedicals Cat#0216011080 
Peqlab peqGOLD TriFast, DNA/RNA/protein purification reagent Avantor, VWR Chemicals Cat#30–2010 
LunaScript Reverse Transcriptase (LunaScript RT Mastermix) New England Biolabs GmbH Cat#E3025 
Fluorescein isothiocyanate–dextran, average mol weight 3,000–5,000 Merck/MilliporeSigma Cat#FD4 
Ampicillin sodium salt ≥97%, BioScience Grade Carl Roth GmbH + Co Cat#K029.1 
Vancomycin hydrochloride Carl Roth GmbH + C. KG Cat#0242.3 
Streptomycin sulfate Carl Roth GmbH + Co Cat#0236.1 
Neomycin sulfate Carl Roth GmbH + Co Cat#8668.1 
DreamTaq DNA Polymerase (5 U/μl) Thermo Fisher Scientific Cat#EP0705 
SYTO 9 green fluorescent nucleic acid stain Thermo Fisher Scientific Cat#S34854 
eBioscience fixable viability dye eFluor 780 Thermo Fisher Scientific Cat#65–0865-14 
CountBright absolute counting beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 
DNAse I Merck/MilliporeSigma Cat#11284932001 
Collagenase A Gibco; Thermo Fisher Scientific Cat#17018029 
Dispase II Gibco; Thermo Fisher Scientific Cat#17105041 
Liberase TL TL Research Grade Fisher Scientific; Thermo Fisher Scientific Cat#NC1328423 
Hoechst 33342 Thermo Fisher Scientific Cat#62249 
Citrate, 0.5 M buffer soln., pH 3.5 Thermo Fisher Scientific Cat#15454239 
SYTOX green Thermo Fisher Scientific Cat#S7020 
a23187 Merck/MilliporeSigma Cat#C7522 
PMA Merck/MilliporeSigma Cat#19–144 
N-Formyl-Met-Leu-Phe (fMLP) Merck/MilliporeSigma Cat#F3506 
CellTrace CFSE cell proliferation kit Thermo Fisher Scientific Cat#C34570 
Red-fluorescent tetramethylrhodamine (TAMRA) azide Thermo Fisher Scientific Cat#T10182 
Q5 High-Fidelity DNA Polymerase NEB Cat#M0491 
qScript cDNA synthesis-set Avantor, VWR Chemicals Cat#733–1175 
Ultra-Plex 1-step ToughMix ROX (4X) Avantor, VWR Chemicals Cat#733–2466 
PerfeCTa SYBR Green SuperMixes and FastMixes Avantor, VWR Chemicals Cat#733–1387 
NucleoSpin 96 RNA Core Kit, 96-well Kit for RNA Isolation Macherey-Nagel Cat#740466.4 
Lyophilized carrier RNA Macherey-Nagel Cat#740514 
LunaScript RT SuperMix Kit NEB Cat#E3010 
Monarch DNA Gel Extraction Kit NEB Cat#T1120 
Critical commercial assays 
QIAamp Fast DNA Stool Kit Qiagen Cat#51604 
SequalPrep normalization plate kit, 96-well Thermo Fisher Scientific Cat#A1051001 
Illumina TruSeq Nano Kit Illumina Inc. Cat#A20015964 
Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling 10X Genomics,.Inc. Cat#1000414 
Chromium Fixed RNA Kit, Mouse Transcriptome, 4 rxns x 16 BC 10X Genomics, Inc. Cat#PN-1000497 
NEBNext Poly(A) mRNA Isolation Module NEB Cat#E7490 
NEBNext Ultra Directional RNA Library Prep Kit for Illumina NEB Cat#E7765 
LEGENDplex Mouse Anti-Virus Response Panel Biolegend Cat#740622 
Neutrophil Isolation Kit, Mouse Miltenyi Biotec Cat#130-097-658 
Deposited data 
Microbiome sequencing data National Institutes of Health: BioProject - effect of filamin A editing on the gut microbiome BioProject ID: PRJNA1051489 
Bulk sequencing data of distal colon National Institutes of Health: GEO dataset GSE296059 
scRNA-seq of colon cells National Institutes of Health: GEO dataset GSE296058 
Flna amplicon sequencing (ampSeq) National Institutes of Health: GEO dataset GSE295910 
Experimental models: Organisms/strains 
WT mice C57BL/6J RRID:IMSR_JAX:000664 
FLNAQ mice Mouse breeding facility at Medical University of Vienna Refs 8 + 9 
FLNAR mice Mouse breeding facility at Medical University of Vienna Refs 8 + 9 
IL-10 KO mice 129(B6)-Il10tm1Cgn/J, the Jackson Laboratory RRID:IMSR_JAX:004368 
Vav1-Cre mice Tg(Vav1-cre)1Cgp MGI ID: 2450339 
FLNAQiR mice Mouse breeding facility at Medical University of Vienna This paper 
LysM-Cre mice B6.129P2-Lyz2tm1(cre)Ifo/J RRID:IMSR_JAX:004781 
Oligonucleotides (5′→3′) 
5′-GTC​AAG​TTC​AAC​GAG​GAG​CAC-3′ MicrosynthAG Human Flna editing locus fw primer 
5′-GTGCACCTTGG CATCAATTGC-3′ MicrosynthAG Human Flna editing locus rev primer 
5′-CCG​CCT​TAC​TGT​TTC​TAG​TCT-3′ MicrosynthAG Mouse Flna editing locus fw primer 
5′-GCT​GGT​TGA​CCT​TTA​ACC​CTG-3′ MicrosynthAG Mouse Flna editing locus rev primer 
5′-GTGYCAGCMGCCGCGGTAA-3′ MicrosynthAG 16S RNA barcoding 515F 
5′-GGACTACNVGGGTWTCTAAT-3′ MicrosynthAG 16S RNA barcoding 806R 
5′-ACA​CGA​CGC​TCT​TCC​GAT​CTG​AGC​ACA​TAC​CTG​ATA​GCC​CC-3′ MicrosynthAG Flna editing detection fw primer for ampSeq 
5′-CAG​ACG​TGT​GCT​CTT​CCG​ATC​TTC​TCT​CGT​GGG​ATG​AAA​CGC-3′ MicrosynthAG Flna editing detection rev primer for ampSeq 
5′-CAA​GCA​GAA​GAC​GGC​ATA​CGA​GAT​NNN​NNN​NNG​TGA​CTG​GAG​TTC​AGA​CGT​GTG​CTC​TTC​CGA​TCT-3′ MicrosynthAG ampSeq—barcoding primers fw 
5′-AAT​GAT​ACG​GCG​ACC​ACC​GAG​ATC​TAC​ACN​NNN​NNN​NAC​ACT​CTT​TCC​CTA​CAC​GAC​GCT​CTT​CCG​ATC​T-3′ MicrosynthAG ampSeq—barcoding primers rev 
5′-GAT​GAC​CAG​TCT​GGA​GGT​GC-3′ MicrosynthAG Mouse Adar fw 
5′-GCA​GCA​AAG​CCA​TGA​GAT​CG-3′ MicrosynthAG Mouse Adar rev 
5′-CAG​TTG​CAT​TTG​CCA​CAG​GTA​T-3′ MicrosynthAG Mouse Adarb1 fw 
5′-ACC​GTT​GAT​ACA​CTT​CGT​CCC-3′ MicrosynthAG Mouse Adarb1 rev 
5′-5′-GAA​CTG​GCA​GAA​GAG​GCA​CT-3′ MicrosynthAG Mouse Tnf fw 
5′-GGT​CTG​GGC​CAT​AGA​ACT​GA-3′ MicrosynthAG Mouse Tnf rev 
5′-CAA​AAT​ACC​TGT​GGC​CTT​GG-3′ MicrosynthAG Mouse Il1b fw 
5′-TAC​CAG​TTG​GGG​AAC​TCT​GC-3′ MicrosynthAG Mouse IL1b rev 
5′-CAG​CAA​CCA​TGG​GAG​AGA​ATG​CTG​A-3′ MicrosynthAG Mouse Ifit1 fw 
5′-GGC​ACA​GTT​GCC​CCA​GGT​CG-3′ MicrosynthAG Mouse Ifit1 rev 
5′-GAC​CAT​GGC​TGG​GAT​TCA​CC-3′ MicrosynthAG Mouse Cxcl1 fw 
5′-TCA​GAA​GCC​AGC​GTT​CAC​CA-3′ MicrosynthAG Mouse Cxcl1 rev 
5′-AAG​CTG​TAG​TTT​TTG​TCA​CCA​AG-3′ MicrosynthAG Mouse Ccl2 fw 
5′-CCA​TTT​GGT​TCC​GAT​CCA​GGT​TT-3′ MicrosynthAG Mouse Ccl2 rev 
5′-CCT​GGC​GGT​GCT​GAG​CTA​CT-3′ MicrosynthAG Mouse Ifna fw 
5′-TTC​TCC​TGC​GGG​AAT​CCA​AA-3′ MicrosynthAG Mouse Ifna rev 
5′-TGA​GGC​GCT​GTC​ATC​GAT​TT-3′ MicrosynthAG Mouse Il10 fw 
5′-CAT​GGC​CTT​GTA​GAC​ACC​TT-3′ MicrosynthAG Mouse Il10 rev 
5′-CCA​CGG​CCT​TCC​CTA​CTT​CA-3′ MicrosynthAG Mouse Il6 fw 
5′-TGC​AAG​TGC​ATC​GTT​GTT​C-3′ MicrosynthAG Mouse Il6 rev 
Software and algorithms 
BBDuk (BBTools) Bushnell, B., https://sourceforge.net/projects/bbmap NA 
Python package demultiplex Laros, J.F.J., https://github.com/jfjlaros/demultiplex NA 
DADA2 (v1.16.0) R package https://www.r-project.org/, R 4.0.2 NA 
Vegan (v2.4.3) R package https://www.r-project.org/, R 3.4.0 NA 
Phyloseq (v1.30.0) R package https://www.r-project.org/, R 3.4.1 NA 
DESeq2 (v1.26.0) R package https://www.r-project.org/, R 3.4.1 NA 
CellRanger (v7.1.0) 10X Genomics, Inc. NA 
Seurat (v.4.3.0) https://github.com/satijalab/seurat/releases NA 
Scanpy AnnData (v.1.9.1) https://scanpy.readthedocs.io/en/stable/installation.html NA 
SOLO (adaption of SCVI) https://github.com/calico/solo NA 
DoubletFinder https://github.com/chris-mcginnis-ucsf/DoubletFinder NA 
SCVI https://github.com/YosefLab/scVI NA 
SingleR https://github.com/dviraran/SingleR NA 
Scanpy https://github.com/theislab/Scanpy NA 
MAST https://www.bioconductor.org/packages/release/bioc/html/MAST.html NA 
FASTP https://github.com/OpenGene/fastp NA 
STAR (v.2.7.9a) https://github.com/alexdobin/STAR NA 
FeatureCounts https://subread.sourceforge.net/featureCounts.html NA 
Limma https://bioconductor.org/packages/release/bioc/html/limma.html NA 
R (v.4.1.0 or R 4.0.2) and python (v.3.8.12) https://www.r-project.org/and https://www.python.org/downloads/release/python-3812/ NA 
TissueFAXS scan software TissueGnostics GmbH NA 
Imaris 9.9.1 Oxford Instruments NA 
Cutadapt https://cutadapt.readthedocs.io/en/stable/installation.html NA 
Hisat2 https://daehwankimlab.github.io/hisat2/ NA 
Jacusa2 https://github.com/dieterich-lab/JACUSA2 NA 
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