1 1 dioctadecyl 3 3 3 3 tetramethylindocarbocyanine

Manufactured by Thermo Fisher Scientific

Sourced in United States

1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine is a fluorescent dye used in biological research. It has an absorption maximum at 549 nm and an emission maximum at 565 nm, making it suitable for labeling and tracking cellular components.

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Lab products found in correlation

5 bromo 2 deoxyuridine brdu, by Merck Group (3 mentions) Rabbit anti cleaved caspase 3, by Cell Signaling Technology (2 mentions) Mouse anti brdu, by BD (2 mentions) Rabbit anti cux1, by Santa Cruz Biotechnology (2 mentions) Rabbit anti phospho histone h3, by Merck Group (2 mentions) Rabbit anti tbr2, by Abcam (2 mentions) Rabbit anti gli3, by Santa Cruz Biotechnology (2 mentions) Rabbit anti pax6, by Fortrea (2 mentions) Mouse anti tuj1, by Fortrea (2 mentions) Mc rack software, by MultiSciences Biotech (2 mentions) Polyethylene glycol stearate, by Merck Group (1 mentions) Phosphatidylcholine, by Avanti Polar Lipids (1 mentions)

6 protocols using 1 1 dioctadecyl 3 3 3 3 tetramethylindocarbocyanine

Cortical Development Immunofluorescence Staining

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Perfusion, dissection, and immunofluorescence staining were conducted according to standard protocols as previously described [17 (link)]. The following are the antibodies used: mouse anti-BrdU (1:50 dilution; BD Pharmingen, Franklin Lakes, NJ, USA), rabbit anti-Cux1 (1:100 dilution; Santa Cruz Biotechnology, Dallas, TX, USA), rabbit anti-Phospho-Histone H3 (1:250 dilution; Millipore, Billerica, MA, USA), rabbit anti-Pax 6 (1:500 dilution; Covance, Princeton, NJ, USA), rabbit anti-Tbr2 (1:500 dilution; Abcam, Cambridge, UK), mouse anti-Tuj1 (1:500 dilution; Covance, Princeton, NJ, USA), rabbit anti-Gli3 (1:100 dilution; Santa Cruz Biotechnology, Dallas, TX, USA), and rabbit anti-Cleaved Caspase 3 (1:300 dilution; Cell Signaling, Madison, WI, USA).
For 5-bromo-2-deoxyuridine (BrdU, Sigma, St. Louis, MO, USA) labeling, pregnant dams were treated with 50 μg/g BrdU by intraperitoneal injection for 4 h prior to dissection at E16.5. DiI labeling was conducted by placing small crystals of the lipophilic tracer (1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine; Invitrogen, Waltham, MA, USA) in the neocortex to target the upper layer (2/3) and then remained in 4% paraformaldehyde (PFA). After 6 weeks, brains were sectioned at 100 μm, counterstained with bisbenzimide, mounted, and imaged.

Yabut O.R., Ng H.X., Fernandez G., Yoon K., Kuhn J, & Pleasure S.J. (2016). Loss of Suppressor of Fused in Mid-Corticogenesis Leads to the Expansion of Intermediate Progenitors. Journal of Developmental Biology, 4(4), 29.

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Multimodal Analysis of Brain Development

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Perfusion, dissection, immunofluorescence, and Nissl staining were conducted according to standard protocols as previously described (Siegenthaler et al., 2009 (link)). Information on primary antibodies are listed in the Supplemental Experimental Procedures. For 5-bromo-2-deoxyuridine (BrdU, Sigma) labeling, pregnant dams were treated with 50 μg/g BrdU by intraperitoneal injection at indicated timepoints. DiI labeling were conducted by placing small crystals of the lipophilic tracer (1,1′-dioctadecyl- 3,3,3′,3′-tetramethylindocarbocyanine; Invitrogen) in the neocortex to target upper layer 2/3 and remained in 4% PFA. After 5 weeks, brains were sectioned at 100 μm, counterstained with bisbenzimide, mounted, and imaged.

Yabut O.R., Fernandez G., Huynh T., Yoon K, & Pleasure S.J. (2015). Suppressor of Fused is Critical for Maintenance of Neuronal Progenitor Identity During Corticogenesis. Cell reports, 12(12), 2021-2034.

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Immunofluorescence Staining of Developing Cortex

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Perfusion, dissection, and immunofluorescence staining were conducted according to standard protocols as previously described [17 (link)]. The following are the antibodies used: mouse anti-BrdU (1:50 dilution; BD Pharmingen, Franklin Lakes, NJ, USA), rabbit anti-Cux1 (1:100 dilution; Santa Cruz Biotechnology, Dallas, TX, USA), rabbit anti-Phospho-Histone H3 (1:250 dilution; Millipore, Billerica, MA, USA), rabbit anti-Pax 6 (1:500 dilution; Covance, Princeton, NJ, USA), rabbit anti-Tbr2 (1:500 dilution; Abcam, Cambridge, UK), mouse anti-Tuj1 (1:500 dilution; Covance, Princeton, NJ, USA), rabbit anti-Gli3 (1:100 dilution; Santa Cruz Biotechnology, Dallas, TX, USA), and rabbit anti-Cleaved Caspase 3 (1:300 dilution; Cell Signaling, Madison, WI, USA).
For 5-bromo-2-deoxyuridine (BrdU, Sigma, St. Louis, MO, USA) labeling, pregnant dams were treated with 50 μg/g BrdU by intraperitoneal injection for 4 h prior to dissection at E16.5. DiI labeling was conducted by placing small crystals of the lipophilic tracer (1,1′-dioctadecyl-3,3,3′, 3′-tetramethylindocarbocyanine; Invitrogen, Waltham, MA, USA) in the neocortex to target the upper layer (2/3) and then remained in 4% paraformaldehyde (PFA). After 6 weeks, brains were sectioned at 100 μm, counterstained with bisbenzimide, mounted, and imaged.

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Cortical Neural Activity Recordings

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On the day of the experiment, animals were anesthetized as described above. A cranial window of 1.5 × 1.5 mm was opened above the center of the mapped barrel columns with a dental drill (Ultimate XL-F, NSK, Trier, Germany) and covered with sterile injectable saline solution. Care was taken not to damage the dura. A silver wire was fixed over the cerebellum to serve as a ground electrode. Neural activity was recorded with a 2‐shank 64‐channel silicon probe (Cambridge NeuroTech, H-series Probe, 250 µm distance between shanks) inserted perpendicular into the barrel cortex targeting C1 or C2 columns identified with intrinsic optical imaging. Each of the two shanks (length 8 mm) contained 32 recording sites spaced 25 μm apart. Before insertion, the probe was labeled with DiI (1,1′‐dioctade‐cyl‐3,3,3′3′‐tetramethylindocarbocyanine; Molecular Probes, Eugene, OR) dissolved in 70% ethanol. The tracks of the shanks could be identified by DiI fluorescence in post-mortem histology. Data was continuously digitized at 20 kHz and stored offline on an extracellular recording system running MC_Rack software (Multi Channel Systems, Reutlingen, Germany).

Yeganeh F., Knauer B., Guimarães Backhaus R., Yang J.W., Stroh A., Luhmann H.J, & Stüttgen M.C. (2022). Effects of optogenetic inhibition of a small fraction of parvalbumin-positive interneurons on the representation of sensory stimuli in mouse barrel cortex. Scientific Reports, 12, 19419.

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Sirolimus-Loaded Microbubble Formulation

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Microbubbles (MBs) were formulated as described previously.^{42 (link)} Briefly, an aqueous micellar dispersion of phosphatidylcholine (2 mg/mL) (Avanti Lipids, Alabaster, AL, USA), polyethylene glycol stearate (2 mg/mL) (Sigma Chemical Co., St. Louis, MO, USA), and either sirolimus (0.4 mg/mL, Chemwerth Inc, Woodbridge, CT, USA) or 1,1′-dioctadecyl-3,3,3′3′-tetramethylindocarbocyanine (DiI, Molecular Probes, Eugene, OR, USA, ≈1% molar ratio DiI:DSPC, MW: 925.49 Da; Ex\Em: 549\565) was prepared in saline. This dispersion was sonicated in the presence of decafluorobutane (DFB, Flura, Newport, TN, USA). Prior to use, microbubbles were washed via centrifugation to remove excess lipids and DiI/sirolimus. A 200 µg dose, similar to the dose of a commercial DES, was selected to determine the total number of sirolimus-loaded microbubbles to infuse.^{1 ,9} The sirolimus concentration of the prepared microbubbles was previously determined through HPLC-mass spectrometry analysis to be 29 ng/10⁶ MBs.^{45 (link)} The microbubbles had an average diameter of 2.2 µm.

Kilroy J.P., Dhanaliwala A.H., Klibanov A.L., Bowles D.K., Wamhoff B.R, & Hossack J.A. (2015). Reducing Neointima Formation in a Swine Model with IVUS and Sirolimus Microbubbles. Annals of biomedical engineering, 43(11), 2642-2651.

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High-Density Electrophysiology of Barrel Cortex

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Neural activity was recorded with a 4-shank 80-channel silicon probe (NeuroNexus Technologies, Ann Arbor, MI) inserted perpendicular into the C1 and C2 columns of barrel cortex. Each of the four shanks (length 3 mm) contained 20 recording sites spaced 50 μm apart. The distance between shanks was 150 μm. Insertion of the probe was guided by intrinsic optical imaging. Before insertion, the probe was impregnated with the DiI (1,1′-dioctade-cyl-3,3,3′3′-tetramethylindocarbocyanine; Molecular Probes, Eugene, OR) which was dissolved in 70% ethanol. The tracks of the four shanks were identified by the DiI fluorescence. All data were continuously digitized at 20 kHz and stored offline on a 256channel extracellular recording system running MC_Rack software (Multi Channel Systems, Reutlingen, Germany).

van der Bourg A., Yang J.W., Stüttgen M.C., Reyes-Puerta V., Helmchen F, & Luhmann H.J. (2019). Temporal refinement of sensory-evoked activity across layers in developing mouse barrel cortex. The European journal of neuroscience, 50(6).

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