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Alamar blue stain

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Alamar Blue stain is a fluorescent dye used to assess cell viability and proliferation in cell-based assays. It is a resazurin-based compound that is reduced by metabolically active cells, resulting in a fluorescent signal that can be measured.

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Lab products found in correlation

Human fgf basic, by Thermo Fisher Scientific (3 mentions) Neurobasal media, by Thermo Fisher Scientific (3 mentions) Laminin, by Merck Group (3 mentions) Human egf, by Thermo Fisher Scientific (3 mentions) Sodium pyruvate, by Thermo Fisher Scientific (2 mentions) Mk 1775, by Selleck Chemicals (2 mentions) Azd4547, by Selleck Chemicals (2 mentions) Plentiguide puro, by Addgene (2 mentions) Bovine serum albumin (bsa), by Merck Group (1 mentions) Glutamine, by Thermo Fisher Scientific (1 mentions) Heparin, by Merck Group (1 mentions) Dznep, by Cayman Chemical (1 mentions)

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Alamar Blue (1332 citations)

5 protocols using alamar blue stain

1

Primary Ependymoma Cell Culture and Treatments

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Primary ependymoma cells were isolated from patients and cultured on Laminin (Sigma)-coated plates in Neurobasal media (Invitrogen) consisting of N2 (Invitrogen), B27 (Invitrogen), glutamine (Invitrogen), BSA (Sigma), heparin (Sigma), human EGF (Invitrogen) and human basic FGF (Invitrogen). Media was replenished every other day while leaving ~50% conditioned media to encourage continued cell proliferation. Cell viability assays were performed in 96 wells using an Alamar Blue stain (Invitrogen) or MTS Aqueous One (Promega) according to manufacturer’s instructions. DAC (Sigma) was dissolved to a stock concentration of 2 mM in PBS and stored in aliquots at −20 °C. DAC was prepared fresh and added to treatment media on a daily basis at the appropriate final concentration, for a total of 7 days. DZNep (Cayman Chemical) was dissolved to a stock concentration of 25 mM in DMSO and stored in aliquots at −20 °C. DZNep treatments were performed every other day along with replenishment of cell culture medium for a total of 7 days. GSK343 (active compound) and GSK669 (inactive compound) were dissolved in DMSO and used to treat cells at varying concentrations with media replenishment every other day for a total of 11 days.
Mack S.C., Witt H., Piro R.M., Gu L., Zuyderduyn S., Stütz A.M., Wang X., Gallo M., Garzia L., Zayne K., Zhang X., Ramaswamy V., Jäger N., Jones D.T., Sill M., Pugh T.J., Ryzhova M., Wani K.M., Shih D.J., Head R., Remke M., Bailey S.D., Zichner T., Faria C.C., Barszczyk M., Stark S., Seker-Cin H., Hutter S., Johann P., Bender S., Hovestadt V., Tzaridis T., Dubuc A.M., Northcott P.A., Peacock J., Bertrand K.C., Agnihotri S., Cavalli F.M., Clarke I., Nethery-Brokx K., Creasy C.L., Verma S.K., Koster J., Wu X., Yao Y., Milde T., Sin-Chan P., Zuccaro J., Lau L., Pereira S., Castelo-Branco P., Hirst M., Marra M.A., Roberts S.S., Fults D., Massimi L., Cho Y.J., Van Meter T., Grajkowska W., Lach B., Kulozik A.E., von Deimling A., Witt O., Scherer S.W., Fan X., Muraszko K.M., Kool M., Pomeroy S.L., Gupta N., Phillips J., Huang A., Tabori U., Hawkins C., Malkin D., Kongkham P.N., Weiss W.A., Jabado N., Rutka J.T., Bouffet E., Korbel J.O., Lupien M., Aldape K.D., Bader G.D., Eils R., Lichter P., Dirks P.B., Pfister S.M., Korshunov A, & Taylor M.D. (2014). Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature, 506(7489), 445-450.
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2

Ependymoma Cell Culture and Drug Screening

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Ependymoma cell cultures were isolated from patients and cultured on Laminin (Sigma) and in Neurobasal media (Invitrogen) consisting of: sodium pyruvate (Invitrogen), B27 (Invitrogen), Glutamine (Cleveland Clinic Media Core), human EGF (Invitrogen), human basic FGF (Invitrogen), and penicillin/streptomycin (Cleveland Clinic Media Core). Media was replenished every other day while leaving ~50% conditioned media to encourage continued cell proliferation. Cell viability assays were performed in 96 wells using an Alamar Blue stain (Invitrogen) according to manufacturer’s instructions. Drug response assays were performed by seeding cells overnight, treating the following day with increasing drug concentrations, and reading by Alamar Blue Absorption following 72 hours of treatment. AZD4547 and MK1775 were obtained from Selleck Chemicals. JQ1 was provided by the laboratory of James E. Bradner (Harvard). All cell lines were confirmed to be mycoplasma free using a PCR-based detection strategy with positive and negative controls.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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3

Ependymoma Cell Culture and Drug Screening

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Ependymoma cell cultures were isolated from patients and cultured on Laminin (Sigma) and in Neurobasal media (Invitrogen) consisting of: sodium pyruvate (Invitrogen), B27 (Invitrogen), Glutamine (Cleveland Clinic Media Core), human EGF (Invitrogen), human basic FGF (Invitrogen), and penicillin/streptomycin (Cleveland Clinic Media Core). Media was replenished every other day while leaving ~50% conditioned media to encourage continued cell proliferation. Cell viability assays were performed in 96 wells using an Alamar Blue stain (Invitrogen) according to manufacturer’s instructions. Drug response assays were performed by seeding cells overnight, treating the following day with increasing drug concentrations, and reading by Alamar Blue Absorption following 72 hours of treatment. AZD4547 and MK1775 were obtained from Selleck Chemicals. JQ1 was provided by the laboratory of James E. Bradner (Harvard). All cell lines were confirmed to be mycoplasma free using a PCR-based detection strategy with positive and negative controls.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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CRISPR/Cas9 Screening of Cell Viability

Cited 1 time
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CRISPR/Cas9 sgRNAs were identified and designed using the MIT CRISPR Design tool, and control (plenti-Guide-Puro D103), non-targeting sgRNAs were selected from the GeCKOv2 library. All sgRNA sequences may be found in (Supplementary Table 23). sgRNAs were cloned into plenti-Guide-Puro (Addgene, 52963). Lentivirus expressing dCAS9-KRAB (Gift from Matthew Meyerson Lab)28 (link) were used to infect EP1-NS, following which cells were selected 48h with 10 μg/ml blasticidin. These cells were then infected with selected lentiGuide-Puro sgRNA constructs and selected 48h with 1 μg/ml puromycin. These cells were plated 48h following selection in 96 - well plates and cell viability was assessed using an Alamar Blue Stain (Life Technologies).
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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5

CRISPR/Cas9 Screening of Cell Viability

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
CRISPR/Cas9 sgRNAs were identified and designed using the MIT CRISPR Design tool, and control (plenti-Guide-Puro D103), non-targeting sgRNAs were selected from the GeCKOv2 library. All sgRNA sequences may be found in (Supplementary Table 23). sgRNAs were cloned into plenti-Guide-Puro (Addgene, 52963). Lentivirus expressing dCAS9-KRAB (Gift from Matthew Meyerson Lab)28 (link) were used to infect EP1-NS, following which cells were selected 48h with 10 μg/ml blasticidin. These cells were then infected with selected lentiGuide-Puro sgRNA constructs and selected 48h with 1 μg/ml puromycin. These cells were plated 48h following selection in 96 - well plates and cell viability was assessed using an Alamar Blue Stain (Life Technologies).
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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