other:
Incubation:
Article Title: Drebrin Upregulation Regulates Astrocyte Polarization and Supports Tissue Recovery After Spinal Cord Injury in Mice
Article Snippet: .. The slides were washed with PHEM and permeabilized with 0.5% (v/v) Triton X‐100 in 1X PHEM for 30 min. Tissue was then blocked with ChemiBLOCKER (1:10; Millipore, 2170), 0.3 M glycine, 0.2% (v/v) Triton X‐100 in 1X PHEM for 2 h. The sections were then incubated with the following primary antibodies: mouse anti‐Arg1 (OriGene Technologies Inc., UM800178, 1:500), rabbit anti‐DBN (Boster Biological Technology, Pleasanton CA, USA, M05530, 1:200), guinea pig anti‐GFAP (Synaptic Systems, 173,004), chicken anti‐GFAP (Abcam, ab4674‐50 μL, 1:1000), mouse anti‐GFAP (Cy3 conjugate, Sigma‐Aldrich, C9205), chicken anti‐IBA1 (Synaptic Systems, 234,009, IHC 1:500), rabbit anti‐iNOS (Invitrogen, PA1‐036, 1:500), rabbit anti‐MAG (Cell Signaling, 9043S, 1:200), and rabbit anti‐Synaptophysin (Abcam ab32127, 1:500) for 48 h at 4°C, washed, and labeled with fluorescent‐conjugated secondary antibodies (1:400, 4 h, room temperature). .. Cross‐absorbed secondary antibodies conjugated to cyanine or Alexa dyes were purchased from Dianova or Invitrogen: donkey anti‐guinea Pig IgG (H + L)‐Cy3 (Dianova,706–165‐148), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 647 (Dianova, 711–605‐152), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Dianova, 711–545‐152), donkey anti‐chicken IgY (H + L)‐Alexa Fluor 647 (Dianova, 703–605‐155), goat anti‐chicken IgY (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11039), goat anti‐chicken IgY (H + L)‐Alexa Fluor 633 (Invitrogen, A‐21103), goat anti‐mouse IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11001), goat anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11012).
Mouse Assay:Article Title: Spinal muscular atrophy-like phenotype in a mouse model of acid ceramidase deficiency
Article Snippet: .. Mice were assigned IDs and measurements for the most part were taken by blinded investigators; note that it is difficult for studies involving live mice or intact tissues to have proper blinding, as mutant mice/samples are easy to spot. anti-Cathepsin D (ab75852, Abcam), anti-Caspase-3 (9664S), anti-STAT3 (4904), anti-p-STAT3 (9145), anti-NF-#B (8242), anti-p-NF-#B (3033), anti-MBP (78896S), anti-MOG (96457S) and anti-MAG (9043T, all from Cell Signaling Technologies), anti-"-Actin (a3854, Sigma-Aldrich), anti-Rabbit IgG (A6154, Sigma–Aldrich), anti-Mac-2 clone M3/38 (Cedarlane CL8942AP), anti-Lamp1 clone D2D11 (Cell Signaling 9091S), anti-Cathepsin D clone EPR3057Y (Abcam ab75852), Cathepsin D (clone EPR3057Y, Abcam ab75852), CNPase (clone CL2887, Novus Biological NBP2-46617), "III-Tubulin (clone TuJ-1, R&D Systems MAB1195SP), GFAP (clone GA5, Cell Signaling 3670T), anti-mouse neuronal nuclear antigen (NeuN) (1:200) (E4M5P; Cell Signaling Technology), rabbit polyclonal anti-mouse/rat 3 n atu re p o rtfo lio | rep o rtin g su m m ary M a rch 2021 Validation Eukaryotic cell lines Policy information about cell lines Cell line source(s) Authentication Mycoplasma contamination Commonly misidentified lines (See ICLAC register) Animals and other organisms Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research Laboratory animals Wild animals Field-collected samples Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript. .. Magnetic resonance imaging Experimental design Design type Design specifications Behavioral performance measures Acquisition Imaging type(s) Field strength Sequence & imaging parameters Area of acquisition Diffusion MRI Used Not used Preprocessing Preprocessing software Normalization Normalization template Noise and artifact removal Volume censoring CD68 (1:200) (AB125212; Abcam), rabbit anti-mouse/rat NeuN (1:200) (MABN140; Millipore), and mouse anti-mouse/rat GFAP (1:100) (8-1E7; DSHB) Unless otherwise indicated, all antibodies were used as recommended by the manufacturer and results compared to those previously found in the literature for validity, or tested on different tissue for which we know the expected result.
Mutagenesis:Article Title: Spinal muscular atrophy-like phenotype in a mouse model of acid ceramidase deficiency
Article Snippet: .. Mice were assigned IDs and measurements for the most part were taken by blinded investigators; note that it is difficult for studies involving live mice or intact tissues to have proper blinding, as mutant mice/samples are easy to spot. anti-Cathepsin D (ab75852, Abcam), anti-Caspase-3 (9664S), anti-STAT3 (4904), anti-p-STAT3 (9145), anti-NF-#B (8242), anti-p-NF-#B (3033), anti-MBP (78896S), anti-MOG (96457S) and anti-MAG (9043T, all from Cell Signaling Technologies), anti-"-Actin (a3854, Sigma-Aldrich), anti-Rabbit IgG (A6154, Sigma–Aldrich), anti-Mac-2 clone M3/38 (Cedarlane CL8942AP), anti-Lamp1 clone D2D11 (Cell Signaling 9091S), anti-Cathepsin D clone EPR3057Y (Abcam ab75852), Cathepsin D (clone EPR3057Y, Abcam ab75852), CNPase (clone CL2887, Novus Biological NBP2-46617), "III-Tubulin (clone TuJ-1, R&D Systems MAB1195SP), GFAP (clone GA5, Cell Signaling 3670T), anti-mouse neuronal nuclear antigen (NeuN) (1:200) (E4M5P; Cell Signaling Technology), rabbit polyclonal anti-mouse/rat 3 n atu re p o rtfo lio | rep o rtin g su m m ary M a rch 2021 Validation Eukaryotic cell lines Policy information about cell lines Cell line source(s) Authentication Mycoplasma contamination Commonly misidentified lines (See ICLAC register) Animals and other organisms Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research Laboratory animals Wild animals Field-collected samples Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript. .. Magnetic resonance imaging Experimental design Design type Design specifications Behavioral performance measures Acquisition Imaging type(s) Field strength Sequence & imaging parameters Area of acquisition Diffusion MRI Used Not used Preprocessing Preprocessing software Normalization Normalization template Noise and artifact removal Volume censoring CD68 (1:200) (AB125212; Abcam), rabbit anti-mouse/rat NeuN (1:200) (MABN140; Millipore), and mouse anti-mouse/rat GFAP (1:100) (8-1E7; DSHB) Unless otherwise indicated, all antibodies were used as recommended by the manufacturer and results compared to those previously found in the literature for validity, or tested on different tissue for which we know the expected result.
Biomarker Discovery:Article Title: Spinal muscular atrophy-like phenotype in a mouse model of acid ceramidase deficiency
Article Snippet: .. Mice were assigned IDs and measurements for the most part were taken by blinded investigators; note that it is difficult for studies involving live mice or intact tissues to have proper blinding, as mutant mice/samples are easy to spot. anti-Cathepsin D (ab75852, Abcam), anti-Caspase-3 (9664S), anti-STAT3 (4904), anti-p-STAT3 (9145), anti-NF-#B (8242), anti-p-NF-#B (3033), anti-MBP (78896S), anti-MOG (96457S) and anti-MAG (9043T, all from Cell Signaling Technologies), anti-"-Actin (a3854, Sigma-Aldrich), anti-Rabbit IgG (A6154, Sigma–Aldrich), anti-Mac-2 clone M3/38 (Cedarlane CL8942AP), anti-Lamp1 clone D2D11 (Cell Signaling 9091S), anti-Cathepsin D clone EPR3057Y (Abcam ab75852), Cathepsin D (clone EPR3057Y, Abcam ab75852), CNPase (clone CL2887, Novus Biological NBP2-46617), "III-Tubulin (clone TuJ-1, R&D Systems MAB1195SP), GFAP (clone GA5, Cell Signaling 3670T), anti-mouse neuronal nuclear antigen (NeuN) (1:200) (E4M5P; Cell Signaling Technology), rabbit polyclonal anti-mouse/rat 3 n atu re p o rtfo lio | rep o rtin g su m m ary M a rch 2021 Validation Eukaryotic cell lines Policy information about cell lines Cell line source(s) Authentication Mycoplasma contamination Commonly misidentified lines (See ICLAC register) Animals and other organisms Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research Laboratory animals Wild animals Field-collected samples Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript. .. Magnetic resonance imaging Experimental design Design type Design specifications Behavioral performance measures Acquisition Imaging type(s) Field strength Sequence & imaging parameters Area of acquisition Diffusion MRI Used Not used Preprocessing Preprocessing software Normalization Normalization template Noise and artifact removal Volume censoring CD68 (1:200) (AB125212; Abcam), rabbit anti-mouse/rat NeuN (1:200) (MABN140; Millipore), and mouse anti-mouse/rat GFAP (1:100) (8-1E7; DSHB) Unless otherwise indicated, all antibodies were used as recommended by the manufacturer and results compared to those previously found in the literature for validity, or tested on different tissue for which we know the expected result.
Immunohistochemistry:Article Title: Drebrin Upregulation Regulates Astrocyte Polarization and Supports Tissue Recovery After Spinal Cord Injury in Mice
Article Snippet: .. The slides were washed with PHEM and permeabilized with 0.5% (v/v) Triton X‐100 in 1X PHEM for 30 min. Tissue was then blocked with ChemiBLOCKER (1:10; Millipore, 2170), 0.3 M glycine, 0.2% (v/v) Triton X‐100 in 1X PHEM for 2 h. The sections were then incubated with the following primary antibodies: mouse anti‐Arg1 (OriGene Technologies Inc., UM800178, 1:500), rabbit anti‐DBN (Boster Biological Technology, Pleasanton CA, USA, M05530, 1:200), guinea pig anti‐GFAP (Synaptic Systems, 173,004), chicken anti‐GFAP (Abcam, ab4674‐50 μL, 1:1000), mouse anti‐GFAP (Cy3 conjugate, Sigma‐Aldrich, C9205), chicken anti‐IBA1 (Synaptic Systems, 234,009, IHC 1:500), rabbit anti‐iNOS (Invitrogen, PA1‐036, 1:500), rabbit anti‐MAG (Cell Signaling, 9043S, 1:200), and rabbit anti‐Synaptophysin (Abcam ab32127, 1:500) for 48 h at 4°C, washed, and labeled with fluorescent‐conjugated secondary antibodies (1:400, 4 h, room temperature). .. Cross‐absorbed secondary antibodies conjugated to cyanine or Alexa dyes were purchased from Dianova or Invitrogen: donkey anti‐guinea Pig IgG (H + L)‐Cy3 (Dianova,706–165‐148), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 647 (Dianova, 711–605‐152), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Dianova, 711–545‐152), donkey anti‐chicken IgY (H + L)‐Alexa Fluor 647 (Dianova, 703–605‐155), goat anti‐chicken IgY (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11039), goat anti‐chicken IgY (H + L)‐Alexa Fluor 633 (Invitrogen, A‐21103), goat anti‐mouse IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11001), goat anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11012).
Labeling:Article Title: Drebrin Upregulation Regulates Astrocyte Polarization and Supports Tissue Recovery After Spinal Cord Injury in Mice
Article Snippet: .. The slides were washed with PHEM and permeabilized with 0.5% (v/v) Triton X‐100 in 1X PHEM for 30 min. Tissue was then blocked with ChemiBLOCKER (1:10; Millipore, 2170), 0.3 M glycine, 0.2% (v/v) Triton X‐100 in 1X PHEM for 2 h. The sections were then incubated with the following primary antibodies: mouse anti‐Arg1 (OriGene Technologies Inc., UM800178, 1:500), rabbit anti‐DBN (Boster Biological Technology, Pleasanton CA, USA, M05530, 1:200), guinea pig anti‐GFAP (Synaptic Systems, 173,004), chicken anti‐GFAP (Abcam, ab4674‐50 μL, 1:1000), mouse anti‐GFAP (Cy3 conjugate, Sigma‐Aldrich, C9205), chicken anti‐IBA1 (Synaptic Systems, 234,009, IHC 1:500), rabbit anti‐iNOS (Invitrogen, PA1‐036, 1:500), rabbit anti‐MAG (Cell Signaling, 9043S, 1:200), and rabbit anti‐Synaptophysin (Abcam ab32127, 1:500) for 48 h at 4°C, washed, and labeled with fluorescent‐conjugated secondary antibodies (1:400, 4 h, room temperature). .. Cross‐absorbed secondary antibodies conjugated to cyanine or Alexa dyes were purchased from Dianova or Invitrogen: donkey anti‐guinea Pig IgG (H + L)‐Cy3 (Dianova,706–165‐148), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 647 (Dianova, 711–605‐152), donkey anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Dianova, 711–545‐152), donkey anti‐chicken IgY (H + L)‐Alexa Fluor 647 (Dianova, 703–605‐155), goat anti‐chicken IgY (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11039), goat anti‐chicken IgY (H + L)‐Alexa Fluor 633 (Invitrogen, A‐21103), goat anti‐mouse IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11001), goat anti‐rabbit IgG (H + L)‐Alexa Fluor 488 (Invitrogen, A‐11012).
Western Blot:Article Title: Micro-scale control of oligodendrocyte morphology and myelination by the intellectual disability-linked protein acyltransferase ZDHHC9
Article Snippet: Antibody , Anti-Olig2 (goat IgG) , R&D , #AF2418 RRID: AB_2157554 , . .. Antibody , Anti-MAG (rabbit IgG) , Cell Signaling Technology , #9043 RRID: AB_2665480 , 1:500 (western blot). .. Antibody , Anti-Myc (rabbit IgG) , Cell Signaling Technology , #2278 (71D10) RRID: AB_490778 , 1:500 (western blot).
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