Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | Mouse/Slc9a6fl | This study |
|
Refer to Materials and methods section for detailed description of mouse model production |
| Strain, strain background (Mus musculus) | Mouse/Slc9a6- | This study |
|
Refer to Materials and methods section for detailed description of mouse model production |
| Strain, strain background (Mus musculus) | Mouse/ApoeAPOE3 | Sullivan et al., 1997 | IMSR_TAC:2,542 | Apoe APOE3 |
| Strain, strain background (Mus musculus) | Mouse/ApoeAPOE4 | Knouff et al., 1999 | IMSR_TAC:3,518 | Apoe APOE4 |
| Strain, strain background (Mus musculus) | Mouse/B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J | The Jackson Laboratory Madisen et al., 2010 | JAX #007909 | ROSA floxedStop-tdTomato |
| Strain, strain background (Mus musculus) | Mouse/CAG-cre/Esr15Amc/J | The Jackson Laboratory Hayashi and McMahon, 2002 | JAX #004682 | CAG-Cre ERT2 |
| Strain, strain background (Mus musculus) | Mouse/B6.129S4-Meox2tm1(cre)Sor/J | The Jackson Laboratory Tallquist and Soriano, 2000 | JAX 003755 | Meox-Cre |
| Strain, strain background (Mus musculus) | App NL-F | Saito et al., 2014 |
|
App NL-F |
| Strain, strain background (Mus musculus) | Tg2576 | Charles River Hsiao et al., 1996 | Charles River Tg2576 | Tg2576, APPSwe |
| Strain, strain background (Rattus norvegicus) | SD rat | Charles River | SC:400 |
|
| Cell line (Homo sapiens) | HEK293 | Thermo Fisher | R70507, RRID:CVCL_0045 |
|
| Cell line (Homo sapiens) | HEK293-T | ATCC | CRL-3216 |
|
| Cell line (Mus musculus) | Neuro-2a | ATCC | CCL-131 |
|
| Cell line (Mus musculus) | NHE6-KO (Slc9a6-) mouse embryonic fibroblasts (MEFs) | This study |
|
Refer to Materials and methods section for detailed description of MEF production |
| Cell line (Mus musculus) | Slc9a6+ MEFs (Slc9a6- littermate) | This study |
|
Refer to Materials and methods section for detailed description of MEF production |
| Antibody | Anti-Aβ (clone 6E10) (mouse monoclonal) | Covance | SIG-39320 RRID:AB_662798 | WB and IHC (1:1000) |
| Antibody | Anti-Aβ (clone 4 G8) (mouse monoclonal) | Covance | SIG-39220 RRID:AB_10175152 | IHC (1:1000) |
| Antibody | Anti-phospho tyrosine (clone 4 G10) (mouse monoclonal) | EMD Millipore | Millipore Cat# 05–321, RRID:AB_309678 | WB (1:1000) |
| Antibody | Anti-Apoer2 (rabbit polyclonal) | Herz Lab, #2561, Trommsdorff et al., 1999 |
|
WB (1:1000) |
| Antibody | Anti-β-Actin (rabbit polyclonal) | Abcam | Ab8227, RRID:AB_23051 86 | WB (1:3000) |
| Antibody | Anti-Calbindin D-28k (mouse monoclonal) | Swant | Swant Cat# 300, RRID:AB_10000347 | IHC (1:1000) |
| Antibody | Anti-GFAP (rabbit polyclonal) | Abcam | Abcam Cat# ab7260, RRID:AB_305808 | IHC (1:2000) |
| Antibody | Anti-GluA1 (rabbit polyclonal) | Abcam | ab31232, RRID:AB_2113447 | WB (1:1000) |
| Antibody | Anti-GluA2/3 (rabbit polyclonal) | EMD Millipore | 07–598, RRID:AB_31074 1 | WB (1:1000) |
| Antibody | Anti-GluN2B (rabbit polyclonal) | Cell Signaling Technology | 4,207 S, RRID:AB_12642 23 | WB (1:1000) |
| Antibody | Anti-Iba1 (rabbit polyclonal) | Wako | 019–19741, RRID:AB_839504 | IHC (1:1000) |
| Antibody | Anti-NHE6 (C-terminus) (rabbit polyclonal) | Herz Lab, Xian et al., 2018 |
|
WB (1:1000) |
| Antibody | Anti-mouse-IgG AF594 (goat polyclonal) | Thermo Fisher | A-11032, RRID:AB_2534091 | IHC (1:500) |
| Antibody | Anti-rabbit-IgG AF488 (goat polyclonal) | Thermo Fisher | A-11034, RRID:AB_2576217 | IHC (1:500) |
| Commercial assay or kit | Anti-mouse-IgG staining kit | Vector | MP-7602, RRID:AB_2336532 |
|
| Commercial assay or kit | Anti-rabbit-IgG staining kit | Vector | MP-7601, RRID:AB_2336533 |
|
| Chemical compound, drug | Antigen retrieval citrate buffer | BioGenex, Cat | HK086-9K |
|
| Chemical compound, drug | B-27 Supplement (50×), serum free | Thermo Fisher | 17504044 |
|
| Chemical compound, drug | Cytoseal 60 | Thermo Fisher | 8310 |
|
| Chemical compound, drug | DMEM | Sigma-Aldrich | D6046 |
|
| Chemical compound, drug | FuGENE | Promega | E2311 |
|
| Chemical compound, drug | HBSS (1×) | Gibco | 14175 |
|
| Chemical compound, drug | L-Glutamic acid (glutamate) | Sigma-Aldrich | G1251 |
|
| Chemical compound, drug | γ-Secretase inhibitor L-685458 | Tocris Bioscience | 2627 |
|
| Chemical compound, drug | Penicillin-streptomycin solution, 100× | Corning | 30–002 CI |
|
| Chemical compound, drug | Neurobasal Medium (1×) liquid without Phenol Red | Thermo Fisher | 12348017 |
|
| Chemical compound, drug | NeutrAvidin Agarose | Thermo Fisher | 29201 |
|
| Chemical compound, drug | Nonidet P-40 Alternative | EMD Millipore | 492016 |
|
| Chemical compound, drug | 32% Paraformaldehyde AQ solution | Fisher Scientific | 15714 S |
|
| Chemical compound, drug | PBS (1×) | Sigma-Aldrich | D8537 |
|
| Chemical compound, drug | Penisillin-streptomycin | Corning | 30–002 CI |
|
| Chemical compound, drug | Phosphatase inhibitor cocktail | Thermo Fisher | 78420 |
|
| Chemical compound, drug | Poly-D-lysine | Sigma-Aldrich | A-003-M |
|
| Chemical compound, drug | Protein A-Sepharose 4B | Thermo Fisher | 101042 |
|
| Chemical compound, drug | Proteinase Inhibitor Cocktail | Sigma-Aldrich | P8340 |
|
| Chemical compound, drug | Sulfo-NHS-SS-biotin | Pierce | 21331 |
|
| Chemical compound, drug | Triton X-100 | Sigma-Aldrich | CAS9002-93-1 |
|
| Chemical compound, drug | Tween 20 | Sigma | P1379 |
|
| Other | Vectashield with DAPI | Vector Labs | H-1200 | (DAPI 1.5 µg/ml) |
| Transfected construct (Mus musculus) | pCrl, Reelin expression vector | D’Arcangelo et al., 1997 | N/A |
|
| Transfected construct (Homo sapiens) | pcDNA3.1-ApoE3 | Chen et al., 2010 | N/A | Progenitor pcDNA3.1-Zeo |
| Transfected construct (Homo sapiens) | pcDNA3.1-ApoE4 | Chen et al., 2010 | N/A | Progenitor pcDNA3.1-Zeo |
| Transfected construct (Mus musculus) | pLKO.1 scramble shRNA | Xian et al., 2018 | N/A |
|
| Transfected construct (Mus musculus) | pLKO.1 shNHE6 | Open Biosystem Xian et al., 2018 |
TRCN0000068828 | Refer to shNHE6-a |
| Transfected construct (Mus musculus) | psPAX2 | Addgene | 12260 | Plasmid was a gift from Didier Trono |
| Transfected construct (Mus musculus) | pMD2.G | Addgene | 12259 | Plasmid was a gift from Didier Trono |
| Transfected construct (Mus musculus) | pJB-NHE6 targeting vector |
This study | N/A | Refer to Materials and methods section for detailed description |
| Recombinant DNA reagent | pJB1 (plasmid) | Braybrooke et al., 2000 | N/A |
|
| Recombinant DNA reagent | pCR4-TOPO (plasmid) | Thermo Fisher | K457502 |
|
| Recombinant DNA reagent | pLVCMVfull (plasmid) | Xian et al., 2018 | N/A |
|
| Recombinant DNA reagent | pME (plasmid) | Stawicki et al., 2014 | Addgene #73794 | Plasmid was a gift from David Raible |
| Recombinant DNA reagent | pLVCMV Vamp3pHluorin2 (plasmid) | This study | N/A | Refer to Materials and methods section for detailed description |
| Recombinant DNA reagent | BAC containing murine NHE6 sequence (bacterial artificial chromosome) |
BACPAC Resources Center |
RP23 364 F14 |
|
| Software, algorithm | Adobe Creative Cloud | Adobe | RRID:SCR_010279 |
|
| Software, algorithm | GraphPad Prism 7.0 | GraphPad Software | RRID:SCR_002798 |
|
| Software, algorithm | Fiji/ImageJ | NIH | RRID:SCR_002285 |
|
| Software, algorithm | LabView7.0 | National Instruments | RRID:SCR_014325 |
|
| Software, algorithm | NDP.view2 | Hamamatsu Photonics |
|
|
| Software, algorithm | Odyssey Imaging System |
LI-COR | RRID:SCR_014579 |
|
| Software, algorithm | Clustal Omega | EMBL-EBI | RRID:SCR_001591 |
|
| Software, algorithm | Leica TCS SPE | Leica | RRID:SCR_002140 |
|
| Sequence-based reagent | SA forward | IDT |
|
GGATCCGTGT GTGTGTTGGG GGAGGGA |
| Sequence-based reagent | SA reverse | Integrated DNA Technology |
|
CTCGAGCTCAC AATCAGCCCTTT AAATATGCC |
| Sequence-based reagent | GAP repair US forward | Integrated DNA Technology |
|
AAGCTTGCGGCC GCTTCAATTTCTG TCCTTGCTACTG |
| Sequence-based reagent | GAP repair US reverse |
Integrated DNA Technology |
|
AGATCTCAAGAA AGTTAGCTAGA AGTGTGTC |
| Sequence-based reagent | GAP repair DS forward |
Integrated DNA Technology |
|
AGATCTGTAGA GGATGTGGGA AAGAGAG |
| Sequence-based reagent | GAP repair DS reverse |
Integrated DNA Technology |
|
GTCGACGCGG CCGACACACA CAGATAAATAA CCTCAAAAG |
| Sequence-based reagent | 5’ flanking 1st LoxP fragment forward | Integrated DNA Technology |
|
GCTTCTCTCG AGCAAGAGTCAAC |
| Sequence-based reagent | 5’ flanking 1st LoxP fragment reverse | Integrated DNA Technology |
|
GATATCAGCA GGTACCACCAA GATCTCAACCT TATTGTCCTATA TGCACAAAC |
| Sequence-based reagent | 3’ flanking 1st LoxP fragment forward | Integrated DNA Technology |
|
GTCTTGTTGGTA CCTGATGAAATG GACTACCTCCACTTG |
| Sequence-based reagent | 3’ flanking 1st LoxP fragment reverse | Integrated DNA Technology |
|
ATCGATCTTCA TAACCCATCTGGATA |
| Sequence-based reagent | LoxP Oligo forward | Integrated DNA Technology |
|
GATCTGCTCAGC ATAACTTCGTATAG CATACATTATACG AAGTTATGGTAC |
| Sequence-based reagent | LoxP Oligo reverse | Integrated DNA Technology |
|
CATAACTTCGTA TAATGTATGCTAT ACGAAGTTATGC TGAGCAGATC |
| Sequence-based reagent | Genotyping NHE6-floxed and wt forward | Integrated DNA Technology |
|
GAGGAAGC AAAGTGTCA GCTCC |
| Sequence-based reagent | Genotyping NHE6-floxed and wt reverse | Integrated DNA Technology |
|
CTAATCCCCTC GGATGCTGCTC |
| Sequence-based reagent | Genotyping NHE6-KO forward | Integrated DNA Technology |
|
GAGGAAGC AAAGTGTCA GCTCC |
| Sequence-based reagent | Genotyping NHE6-KO reverse | Integrated DNA Technology |
|
CCTCACAAGACT AGAGAAATGGTTC |
| Sequence-based reagent | Vamp3 forward | Integrated DNA Technology |
|
TTCAAGCTTCAC CATGTCTACAGG TGTGCCTTCGGGGTC |
| Sequence-based reagent | Vamp3 reverse | Integrated DNA Technology |
|
CATTGTCATCAT CATCATCGTGTG GTGTGTCTCTAA GCTGAGCAACAG CGCCGTGGACGGC ACCGCCGGCCCCG GCAGCATCGCCAC CAAGCTTAAC |
| Sequence-based reagent | pHluorin2 forward | Integrated DNA Technology |
|
CCGGTCCCAAGCTT ATGGTGAGCAAGG GCGAGGAGCTGTTC |
| Sequence-based reagent | pHluorin2 reverse | Integrated DNA Technology |
|
GCCCTCTTCTAGAG AATTCACTTGTACAG CTCGTCCATGCCGTG |