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Gelcount software

Manufactured by Oxford Optronix
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GelCount software is a digital image analysis tool developed by Oxford Optronix for quantitative analysis of gel electrophoresis images. The software provides automated counting and analysis of bands or colonies within the gel.

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Lab products found in correlation

Dmi1 inverted microscope, by Leica (3 mentions) Growth factor reduced matrigel, by BD (2 mentions) Dmem f12, by Thermo Fisher Scientific (1 mentions) Thiazolyl blue tetrazolium bromide mtt, by Merck Group (1 mentions) Glutamax, by Thermo Fisher Scientific (1 mentions) Epidermal growth factor (egf), by Thermo Fisher Scientific (1 mentions) Basic fibroblast growth factor (bfgf), by Thermo Fisher Scientific (1 mentions) Defined keratinocyte sfm, by Thermo Fisher Scientific (1 mentions) Gelcount machine, by Oxford Optronix (1 mentions) Methocult, by STEMCELL (1 mentions) Rpmi 1640, by Lonza (1 mentions) Glutamax, by Lonza (1 mentions) Hoechst 33342, by Thermo Fisher Scientific (1 mentions) Black clear bottom 96 well plates, by Greiner (1 mentions)

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GelCount (205 citations) Oxford Optronix GelCount Software Version 1.1.2.0 (2 citations)

9 protocols using gelcount software

1

Colony Formation Assay for Holoclones

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Cells cultured for 48 h in 2D or for 14 d on TEMPO-CNF were detached as described above and seeded in 6-well plates at a density of 50 cells/cm2, cultured for 6–7 d to form colonies and stained with crystal violet. Holoclones were identified as colonies (≥32 cells) with small clustered as well as differentiated cells and quantified using Gelcount software (Oxford Optronix, Oxford, UK).
Rosendahl J., Svanström A., Berglin M., Petronis S., Bogestål Y., Stenlund P., Standoft S., Ståhlberg A., Landberg G., Chinga-Carrasco G, & Håkansson J. (2021). 3D Printed Nanocellulose Scaffolds as a Cancer Cell Culture Model System. Bioengineering, 8(7), 97.
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2

Organoid Growth Assays for Tumor Models

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Ex vivo organoid growth assays were developed using a modified protocol.36 (link) Primary tumours were harvested from athymic nude (xenograft models) or SCID/Beige (PDX models) mice when tumour reached a volume of 800 mm3. Metastatic tumours were harvested at necropsy. Tumours were minced and digested in Advanced DMEM/F12 media (Corning, Tewksbury, MA) with 5% FBS, 50 µg/mL gentamicin, 5 µg/mL insulin, 1 mg/mL collagenase A, and 300 µg/mL trypsin by shaking for 30 min. Organoids were collected by differential centrifugation and plated in 24-well plates at 50 organoids per well. Organoids were supplemented with Advanced DMEM/F12 media containing 10% FBS, 1X penicillin-streptomycin, 1X Insulin-Transferrin-Selenium (ITS), 4 µg/mL basic fibroblast growth factor (bFGF) and 50 µg/mL epidermal growth factor (EGF). Two days after plating, the media was changed, and inhibitors were added. 4-Hydroxytamoxifen (Tam), BMS-777607/ASLAN002 (RONi), and taselisib (PI3Ki) were purchased from Selleck Chemicals, Houston, TX. Media and inhibitors were changed twice a week for 2 weeks. Organoids were imaged and analysed using GelCount software (Oxford Optronix LTD., Abingdon, UK). Data is represented as the number of organoids greater than 100 µm. Each treatment had a minimum of three replicates for analysis.
Dustin D., Gu G., Beyer A.R., Herzog S.K., Edwards D.G., Lin H., Gonzalez T.L., Grimm S.L., Coarfa C., Chan D.W., Kim B.J., De La O J.P., Ellis M.J., Liu D., Li S., Welm A.L, & Fuqua S.A. (2020). RON signalling promotes therapeutic resistance in ESR1 mutant breast cancer. British Journal of Cancer, 124(1), 191-206.
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3

3D Anchorage-independent Growth Assay

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MCF10A cells were seeded in growth factor-reduced Matrigel (Corning #356230) in EGF-free media + 1% CSS in 48-well plates following published protocols(20 (link)). T47D cells were seeded in phenol red-free growth factor-reduced Matrigel (Corning #356237) in phenol red-free IMEM + 1% CSS in 48-well plates. Inhibitors were added to the medium at the time of cell seeding. Fresh media and inhibitors were replenished every three days. After 7-10 days, colonies were stained with 5 mg/ml MTT for 20 min. Plates were scanned and colonies measuring ≥ 100 μm were quantified using GelCount software (Oxford Optronix). Colonies were photographed using a Leica DMi1 inverted microscope.
Marín A., Al Mamun A., Patel H., Akamatsu H., Ye D., Sudhan D.R., Eli L., Marcelain K., Brown B.P., Meiler J., Arteaga C.L, & Hanker A.B. (2023). Acquired secondary HER2 mutations enhance HER2/MAPK signaling and promote resistance to HER2 kinase inhibition in breast cancer. Cancer research, 83(18), 3145-3158.
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4

3D Cell Culture Quantification Assay

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MCF10A cells were seeded in growth factor-reduced Matrigel (Corning #356230) in EGF-free media + 1% CSS in 48-well plates following published protocols (20) . T47D cells were seeded in phenol red-free growth factorreduced Matrigel (Corning #356237) in phenol red-free IMEM + 1% CSS in 48-well plates. Inhibitors were added to the medium at the time of cell seeding. Fresh media and inhibitors were replenished every three days. After 7-10 days, colonies were stained with 5 mg/ml MTT for 20 min. Plates were scanned and colonies measuring ≥ 100 μm were quantified using GelCount software (Oxford Optronix). Colonies were photographed using a Leica DMi1 inverted microscope.
Marín A., Mamun A.A., Patel H., Akamatsu H., Ye D., Sudhan D.R., Eli L., Marcelain K., Brown B.P., Meiler J., Arteaga C.L, & Hanker A.B. (2023). Acquired Secondary HER2 Mutations Enhance HER2/MAPK Signaling and Promote Resistance to HER2 Kinase Inhibition in Breast Cancer. Cancer research, 83(18).
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5

Colony Formation Assay for Stem and Progenitor Cells

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Cells sorted by flow cytometry or bulk population single cells were plated in methylcellulose (Methocult from Stem Cell Technology, France) mixed with one of the following media: Stem cell medium I: 20 ng/ml EGF (PeproTech, USA), 10 ng/ml bFGF (PeproTech, USA), 1× B27 (Gibco) and 1× PS (Lonza) in 1× Defined Keratinocyte-SFM (Gibco); Stem Cell medium II: 20 ng/ml EGF, 20 ng/ml bFGF, 1× B27, 1× PS and 1× Glutamax (Gibco) in DMEM-F12 (Gibco); Pancreatic medium: Pancreatic culture media with pancreatic cell culture supplement and PS and RPMI medium: 10% FCS, 1× PS and 1× Glutamax in RPMI 1640 (Lonza) according to manufacturers' protocol. In brief, single cell suspensions were added to media with Methocult, mixed and seeded at a density of 1000 cells/well in a non-adhesive 24 well plate (Grenier Bio-One, Germany). Two weeks post plating, the colonies were stained with 150 µl 0.4 mg/ml Thiazolyl Blue Tetrazolium Bromide (MTT) (Sigma-Aldrich) at 37°C for 4 hours or overnight. Uniform colonies of minimum 50 µm were scanned using the GelCount machine and the number and sizes were quantified using GelCount software (both from Oxford Optronix, UK).
Wennerström A.B., Lothe I.M., Sandhu V., Kure E.H., Myklebost O, & Munthe E. (2014). Generation and Characterisation of Novel Pancreatic Adenocarcinoma Xenograft Models and Corresponding Primary Cell Lines. PLoS ONE, 9(8), e103873.
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6

Synergistic anti-melanoma effects

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A375 and SK-MEL-28 cells were seeded in 6-well plates at a density of 500 cells per well. Both cell lines were maintained in culture by feeding with 2 ml fresh complete culture medium. Cells were treated for two weeks with AT13387 (18 nM) and vemurafenib (2 μM) as single agents or in combination; fresh compound was added every three days. Colonies were fixed and stained with 0.1% crystal violet solution. Plates were scanned and colonies quantified using the GelCount software (Oxford Optronix).
Smyth T., Paraiso K.H., Hearn K., Rodriguez-Lopez A.M., Munck J.M., Haarberg H.E., Sondak V.K., Thompson N.T., Azab M., Lyons J.F., Smalley K.S, & Wallis N.G. (2014). Inhibition of HSP90 by AT13387 Delays the Emergence of Resistance to BRAF Inhibitors and Overcomes Resistance to dual BRAF and MEK Inhibition in Melanoma Models. Molecular cancer therapeutics, 13(12), 2793-2804.
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7

Soft Agarose Assay for 5-FU Sensitivity

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Soft agarose assay was performed as previously described (Zhang et al, 2010 (link)). After 48 h growth, cells were treated with media containing 10 μM or 20 μM 5-FU. Media was replaced every other day. Picture of colonies was taken by phase-contrast microscope 10 days after cell plating and colonies were counted using the GELCOUNT software (Oxford Optronix Ltd., Abingdon, UK).
Zhang B., Zhang B., Chen X., Bae S., Singh K., Washington M.K, & Datta P.K. (2014). Loss of Smad4 in colorectal cancer induces resistance to 5-fluorouracil through activating Akt pathway. British Journal of Cancer, 110(4), 946-957.
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8

3D Cell Invasion Assay with MTT Staining

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Cells were seeded on growth factor–reduced Matrigel (BD Biosciences) in 48-well plates following published protocols (Debnath et al., 2003 (link)). Inhibitors were added to the medium at the time of cell seeding. Fresh media and inhibitors were replenished every 3 d. Following 7–10 d, colonies were stained with 5 mg/ml MTT for 20 min. Plates were scanned and colonies measuring ≥100 μm were counted using GelCount software (Oxford Optronix). Colonies were photographed using a Leica DMi1 inverted microscope.
Hanker A.B., Brown B.P., Meiler J., Mann A., Harikrishna S., Ye D., Lin C.C., Akamatsu H., Lee K.M., Chatterjee S., Sudhan D.R., Servetto A., Brewer M.R., Koch J.P., Sheehan J.H., He J., Lalani A.S, & Arteaga C.L. (2021). Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity. Cancer cell, 39(8), 1099-1114.e8.
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9

Evaluating Inhibitor Efficacy in 2D and 3D Cell Assays

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MCF10A cells were seeded in black clear-bottom 96-well plates (Greiner Bio-One) at a density of 1,000 cells per well in growth factor-depleted media. The next day, media was replaced with 100 μl media containing increasing amounts of inhibitor (0.17 nM–10 μM in 3-fold dilutions). After 5–6 days, nuclei were stained with 10 μg/ml Hoechst 33342 (Thermo Fisher Scientific) at 37°C for 20 min. Fluorescent nuclei were counted using the ImageXpress Micro XL automated microscope imager (Molecular Devices).
For three-dimensional (3D) growth assays, cells were seeded on growth factor–reduced Matrigel (BD Biosciences) in 48-well plates following published protocols (37 (link)). Inhibitors were added to the medium at the time of cell seeding. Fresh media and inhibitors were replenished every 3 days. Following 9–14 days, colonies were stained with 5 mg/ml MTT for 20 min. Plates were scanned and colonies measuring ≥100 μm were counted using GelCount software (Oxford Optronix). Colonies were photographed using an Olympus DP10 camera mounted in an inverted microscope.
Hanker A.B., Brewer M.R., Sheehan J.H., Koch J.P., Sliwoski G.R., Nagy R., Lanman R., Berger M.F., Hyman D.M., Solit D.B., He J., Miller V., Cutler RE J.r., Lalani A.S., Cross D., Lovly C.M., Meiler J, & Arteaga C.L. (2017). An acquired HER2 T798I gatekeeper mutation induces resistance to neratinib in a patient with HER2 mutant-driven breast cancer. Cancer discovery, 7(6), 575-585.
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