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6 protocols using 25g needle

1

Quantitative Analysis of CO in Tissue Samples

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The amount of CO in the tissue samples was measured by GC according to the reported method18 (link) with slight modifications. Tissues (100 mg) were homogenized (Power MasherII, nippi) in PBS (0.3 ml) and then disrupted by sonication (time: 10 s × 2, on ice, amplitude: 15; QSONICA). The solution and a 5 mmφ glass ball were placed in a 5 mL 25 G syringe (TERUMO) sealed with a septum cap (natural rubber, for a 7 mm tube). The atmosphere in the syringe (1 mL) was carefully replaced with He gas through inserting a 25 G needle (TERUMO) into the septum cap. Three drops of 30% sulfosalicylic acid (SSA) (Wako) were injected through the septum into the syringe. The mixture was then mixed well using a 5 mmφ glass ball. Methane gas (50 μl) was added to the head-space atmosphere through the septum in the syringe as an internal standard. CO liberated from the tissues into the gas phase (0.5 ml) was analyzed by GC (Shimadzu GC-2014, Shimadzu). The GC conditions were as follows: detector = TCD; column = SHINCARBON: carrier gas = He; column temperature = 40 °C; temperature at vaporizing chamber and detector = 120 °C; flow rate = 50 ml/min.
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2

CO Incubation of Tissue Samples

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Tissue samples were placed in a 5 ml 25G syringe (TERUMO) sealed with a septum cap (natural rubber, for a 7 mm tube). The atmosphere in the syringe was replaced with pure CO gas (4 ml) (Sumitomo Seika) through inserting a 25G needle (TERUMO) into the septum cap. Tissue samples were then incubated at 4 °C under a CO atmosphere. After 1 h, the syringe was opened under air atmosphere, samples were taken out from the syringe, and the amount of CO was measured by the hemoCD1 assay.
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3

Keratin 10 Expression Analysis in NIKS Cells

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A modified protocol was used based on previous studies 23. In brief, NIKS cells were first collected by trypsinization and after centrifugation and washing, cells were resuspended to ∼1 × 106 cells/ml in F medium and fixed in 1.5% PFA (J61899; Alfa Aesar, Lancaster, UK) for 10 min at room temperature. Cells were then recovered by centrifugation (3000 rpm) and permeabilized in ice‐cold methanol (1 × 106 cells/500 µl) (Sigma, Haverhill, UK) at 4 °C for 10 min. Cells were subsequently washed in PBS–1% bovine serum albumin (BSA) and passed gently through a 25G needle (Terumo, Leuven, Belgium) for to five times to avoid the formation of cell clumps. Cells were then incubated (1 × 106 cells/100 µl) with a mouse primary antibody to keratin 10 (Krt10) (PA5‐32459; Thermo Scientific, East Grinstead, UK) for 1 h on ice with occasional agitation. The optimal concentration of Krt10 antibody for use in these assays was determined experimentally to be 1 µg/µl. Cells were subsequently washed in PBS–1% BSA and incubated with Alexa Fluor 488 donkey anti‐mouse secondary antibody (A21202; Life Technologies, Paisley, UK) diluted to 1 µg/ml for 30 min at room temperature. After extensive washing (at least three times in PBS), cells were subjected to FACS sorting using either a DxP8 (Cytek, Ely, UK) or a MoFlo MLS cell sorter (DakoCytomation, London, UK).
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4

Brain Region Micro-dissection in Tilapia

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The brain micro-dissection was performed as previously described with modifications (Maruska et al., 2013 (link)). Fresh frozen whole brains were sectioned in coronal plane (60 μm) using a cryostat (Leica CM1860) and briefly thaw-mounted onto uncoated glass microscope slides (Sail Boat Lab Co., Zhejiang, China) and stored at −80°C until microdissection. Brain tissues were collected with a modified 200-μL pipette tip (ExtraGene, Taichung, Taiwan) and 25G needle (Terumo, Tokyo, Japan), and transferred into 200 μL TRIzol reagent (Thermo Fisher Scientific). To prevent cross-contamination and RNA degradation, the needle was cleaned with RNAse-Away (Thermo Scientific), ethanol, and diethyl pyrocarbonate (DEPC)-treated water in successive order between each sample. Tilapia brain atlases (Parhar, 1990 ; Soga et al., 2005 (link); Ogawa et al., 2016 (link)) were used to identify the following brain regions: the telencephalon, preoptic area (including minimal portions of ventral telencephalon), optic tectum, midbrain (including minimal portions of the medullary nuclei of the hindbrain), hypothalamus (including portions of the glomerular, preglomerular, subglomerular, and posterior thalamic nuclei), cerebellum, and hindbrain (Figure 7A).
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5

Phage Purification via PEG Precipitation

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According to a previously described method (44 (link)), 500 mL of phage lysate was precipitated with 10% (wt/vol) PEG 6000 (Sigma-Aldrich) and 0.5 M NaCl and incubated overnight at 4°C with agitation. Bacterial cells were removed by centrifugation at 4,400 × g (Beckman Coulter, Aventi JE Centrifuge) for 30 min at 4°C. The pellet was resuspended in TM buffer. PEG was removed twice by adding an equal volume of chloroform, mixed by gentle inversion for 30 s, and centrifuged at 3,800 × g (Beckman, GS-15R Centrifuge) for 10 min. Then, 0.75 g of cesium chloride (CsCl) was added per mL of the aqueous phase containing phage particles (45 (link)). The solution was centrifuged at 31,000 rpm (Beckman Coulter, Optima L80 XP Ultracentrifuge) for 48 h at 10°C in a SW 41 Ti rotor. The phage band was recovered by piercing through the ultracentrifuge tube with a sterile 25-G needle (Terumo Corporation). To remove CsCl, the sample was transferred in a dialysis cassette G2 (Thermo Fisher Scientific) and dialyzed against 1.5 L of TM buffer at 4°C overnight.
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6

Colon Extraction and Sample Collection

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Immediately following completion of in vivo bioluminescent imaging, animals were re-anesthetized under 5% v/v isoflurane before euthanised via cervical dislocation. Urine was collected either by neck scuffing before initiating deep anesthesia or taken directly from the bladder (using a 1 ml syringe fitted with a 25 G needle, Terumo, Australia) during the surgical resection of organs from each mouse. To avoid external contamination, fecal samples were collected directly from the resected colons by gently squeezing out the fecal material into the collection tube. Samples were snap frozen in liquid nitrogen and transferred to −80°C for storage until analyzed for the presence of hemoglobin.
Upon sacrifice, colons were immediately excised between the anus to the ascending colon. Isolated colon specimens were flushed twice with cold 10 mM phosphate buffered saline (PBS) using a syringe and then evenly divided into two longitudinal pieces with a surgical blade and prepared separately for histological and biochemical analysis.
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