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5 protocols using anti hamster cy3

1

Spleen Tissue Immunofluorescence Imaging

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Spleens were embedded in OCT compound (Electron Microscopy Sciences), frozen and sectioned at a thickness of 4 μm. Sections were then fixed in 75% methanol/25% acetone for 10 min at −20°C. After blocking, sections were incubated with appropriate dilutions of primary Abs (eBioscience) overnight at 4°C. Secondary anti-mouse AF488, anti-rabbit AF488, anti-rabbit Cy5, anti-rat DyLight649, or anti-hamster Cy3 (Jackson Immunoresearch) Abs were incubated on the slides for 2 h at 25°C the following day. Slides were mounted with Fluoroshield (Electron Microscopy Sciences) and subsequently imaged on an EVOS FL Auto 2 Imaging System (Life Technologies).
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2

Immunofluorescence Staining of Splenic Sections

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Spleens were embedded and frozen in OCT compound (Electron Microscopy Sciences) prior to sectioning. Four micron splenic sections were then fixed in 75% ethanol/25% methanol for 10 mins at −20°C. After blocking, primary Abs CD3e and IgD (eBioscience) were applied for 4 hours at 25°C or overnight at 4°C. PNA-Fluorescein (Vector Labs), anti-rat DyLight649, and anti-hamster Cy3 (Jackson ImmunoResearch) secondary Abs were then applied for 1 hour at 25°C. Slides were mounted with Fluoroshield (Electron Microscopy Sciences) and subsequently imaged on a Cannon Ti-U fluorescent microscope. Images were acquired with a D5-QilMc digital camera in conjunction with NIS Elements software. For GC counts, staining was performed as above and images were captured on an EVOS FL Auto microscope (Life Technologies).
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3

Histopathological Scoring of Lung Injury in Mice

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Lungs were fixed in 4% formaldehyde overnight, and 3-μm paraffin-embedded sections were stained with hematoxylin and eosin (H&E). All images were obtained on an Olympus BX-51 microscope. To assess lung injury, slides were scored in a blinded fashion on a 12 point scale which addressed various aspects of histopathology including alveolar congestion, hemorrhage, presence of neutrophils in the airspaces, and degree of interstitial thickening (0 – 3 points each, based on severity).
For fluorescence imaging of paraffin embedded lung sections, Sections (4 μm) were cut, deparaffinized, and hydrated. Slides were incubated in Target Retrieval Solution (Dako #S1699) for 30 m in a pressure cooker, cooled to RT, and blocked in 5% goat / 5% donkey serum in tris buffered saline with 0.05% Tween (TTBS). Sections were then incubated with anti-pro-SPC (Millipore #AB3786) at 1:500 and anti-T1α (University of Iowa Developmental Studies Hybridoma Bank #8.1.1) at 1:100 overnight at 4°C. After washing in TTBS, sections were incubated with anti-rabbit Cy5 (Jackson #711-605-152) and anti-hamster Cy3 (Jackson #107166–142) antibodies for 1 h at RT, followed by DAPI for 10 m. Images were captures on a Nikon A1 inverted confocal microscope at 10X, serial images were tiled together to form a composite image of the entire lung section.
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4

Comprehensive Antibody List for Autophagy Research

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The antibodies used in this work are as follows. Mouse antibodies: anti-WIPI2 (Polson et al., 2010 (link)), anti-GM130 (BD Biosciences; 610822), anti-PI4KΙΙα (Santa Cruz; sc-390026), anti-GFP (CRUK; 4E12), anti-HA (Covance; MMS-101R), anti-PI4P (Echelon Bioscience; Z-P004), GAPDH (Millipore; MAB374), and Syntaxin 12/13 (SYSY; 110131). Rabbit antibodies: anti-ATG9A (STO215 and STO219; Young et al., 2006 (link)), anti-LC3 (Abcam; ab48394), anti-GM130 (Abcam; ab52649), anti-ULK1 (for Western blotting, Santa Cruz; sc-33182; for immunofluorescence, Cell Signaling; 8054 D8H5), anti-GABARAP (Abgent; AP1821a), anti-Actin (Abcam; ab8227), anti-ARFIP2 (Invitrogen; 40-2400), anti-HA (Covance; PRB-101P), anti-PI4KIIIβ (Upstate; 06578), anti-pS294 PI4KIIIβ (Hausser et al., 2005 (link)), and anti-ATG13 (Chan et al., 2009 (link)). The following antibodies were used: hamster antibody: anti-ATG9A (Webber and Tooze, 2010 (link)); sheep antibody: anti-TGN46 (Serotec, AHP500G); goat antibody: anti-ARFIP1 (clone I-19; Santa Cruz; sc-19246).
Secondary antibodies for immunofluorescence (from Life Technologies unless otherwise specified) were anti-rabbit IgG Alexa Fluor 488, 555, and 647; anti-mouse IgG Alexa Fluor 488, 555, and 647; and anti-HAmster Cy3 (Jackson ImmunoResearch). HRP-conjugated secondary antibodies used for Western blotting were from GE Healthcare.
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5

Histopathological Scoring of Lung Injury in Mice

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Lungs were fixed in 4% formaldehyde overnight, and 3-μm paraffin-embedded sections were stained with hematoxylin and eosin (H&E). All images were obtained on an Olympus BX-51 microscope. To assess lung injury, slides were scored in a blinded fashion on a 12 point scale which addressed various aspects of histopathology including alveolar congestion, hemorrhage, presence of neutrophils in the airspaces, and degree of interstitial thickening (0 – 3 points each, based on severity).
For fluorescence imaging of paraffin embedded lung sections, Sections (4 μm) were cut, deparaffinized, and hydrated. Slides were incubated in Target Retrieval Solution (Dako #S1699) for 30 m in a pressure cooker, cooled to RT, and blocked in 5% goat / 5% donkey serum in tris buffered saline with 0.05% Tween (TTBS). Sections were then incubated with anti-pro-SPC (Millipore #AB3786) at 1:500 and anti-T1α (University of Iowa Developmental Studies Hybridoma Bank #8.1.1) at 1:100 overnight at 4°C. After washing in TTBS, sections were incubated with anti-rabbit Cy5 (Jackson #711-605-152) and anti-hamster Cy3 (Jackson #107166–142) antibodies for 1 h at RT, followed by DAPI for 10 m. Images were captures on a Nikon A1 inverted confocal microscope at 10X, serial images were tiled together to form a composite image of the entire lung section.
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