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15 protocols using m3 media

1

Reagents and Antibodies for Cell Culture

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Dulbecco's modified Eagle's medium (DMEM), trypsin, and fetal bovine serum (FBS) were obtained from Hyclone (Hyclone, Logan, Utah) and M3 media from Sigma (St. Louis, MO, USA). The anti-AEG-1 antibody was from Epitomics (San Diego, CA, USA). Anti-beta-actin was purchased from Millipore (Billerica, MA, USA). pAMPK (T172) and AMP-activated protein kinase (AMPK) antibody were from Cell Signaling Technology (Beverly, MA, USA), while pPFK2 (S466) and phosphofructokinase-2 (PFK2) were from Santa Cruz (Santa Cruz, California, USA). Myc antibody was from Thermo Scientific (MA, USA). The AMPK inhibitor Compound C was provided by MERCK (Billerica, MA, USA). Other reagents used were of reagent grade or higher.
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2

Drosophila Chromatin Immunoprecipitation and Sequencing

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Drosophila S2 and S2R+ cells were grown to log phase in Schneider’s media (Gibco) supplemented with 10% FBS (HyClone). Drosophila DmBG3-c2 (BG3) cells were grown in M3 media (Sigma) supplemented with BPYE, 10% FBS, and 10 µg/mL insulin. Nuclei were harvested and digested with MNase as previously described (Henikoff et al. 2009 (link)). MNase-digested chromatin was then extracted and solubilized in 80 mM NaCl buffer by pushing through a 26-gauge needle as described (Kasinathan et al. 2014 (link)). Antibodies against Polycomb (Schuettengruber et al. 2009 (link)), TRL (Melnikova et al. 2004 (link)), ADF1 (Lang and Juan 2010 (link)), PHO (Klymenko et al. 2006 (link)), and H3K27me3 (Abcam, ab6002) were used for immunoprecipitation. Illumina sequencing libraries, paired-end sequencing, and base calling were performed as described using TruSeq primers (Henikoff et al. 2011 (link)).
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3

Immunoprecipitation of Myc- or Flag-tagged Proteins from Drosophila S2 Cells

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Drosophila S2 cells were cultured in M3 media (Sigma) with 10% Insect medium supplement (Sigma). Transfection was carried out with Effectene reagent (Qiagen) according to manufacturer’s instructions. Total of 1–2 μg DNA was used for each transfection. For immunoprecipitation, cells were lysed in 0.1% CHAPS buffer, and the lysates were precleared by incubating with protein G-sepharose beads (Roche) for 1 h at 4 °C. The G-sepharose beads were immunoprecipitated with anti-Myc (Abcam) or anti-Flag (Sigma) at 4 °C for 1 h. The immunoprecipitates captured by protein G-sepharose were incubated with the clear lysates overnight at 4 °C. Immunoprecipitates were washed three times in cold IP buffer. The samples were boiled in protein loading buffer at 94 °C for 5 min and then subjected to SDS-PAGE. Western blot was performed with mouse Flag (Sigma) or mouse V5 at 1:5000 (Invitrogen).
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4

Assessing Wg Signaling in Drosophila S2R+ Cells

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Drosophila S2R + cells express all of the Wg signaling components necessary to respond to exogenously added Wg36 (link). For Arm, UAS-ArmAR2 and USA-HA control transfections, 1 µg DNA, 1 µg WISER (luciferase reporter plasmid) (gift from J.P Vincent) and 1 µg act-Gal4 (in the well of UAS-HA) in 98 µl EC buffer were combined with 16 µl Enhancer (Qiagen), 38 µl Effectene (Qiagen) in 3.5 × 106 cells/1.6 mL of growth media in a 6-well plate. To assess the effect of Arm and Arm AR2 on Wg signaling, 400 µl of media with or without Wg protein was added 2 days after transfection. 1 day later, the cells were lysed to assess luciferase levels using the Dual-Luciferase Reporter Assay System (Promega) containing Tcf reporter (firefly luciferase) and a constitutively active control reporter (renilla luciferase). Wg activity was calculated as the ratio of firefly to renilla luciferase activities with SEM (Standard error of the mean) of three independent experiments with the HA control. Statistical significance was based on a two-tailed t test. To obtain Wg-containing media, S2 tub-wg cells (DGRC) and S2 cells were grown in M3 media (Sigma) as described37 (link). Cells were pelleted by centrifugation. The presence of Wg protein was confirmed by Western blotting by mouse anti-Wg antibody (DSHB).
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5

Drosophila and HEK293 Cell Culture Protocols

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Drosophila S2 cells were cultured in M3 media (Sigma) with 10% insect medium supplement (Sigma). Transfection was carried out with Effectene reagent (Qiagen, Hilden, Germany) according to manufacturer’s instructions.
HEK293 cells were cultured in Dulbecco’s modified Eagles medium (DMEM) with 10% fetal bovine serum (FBS). For siRNA-mediated gene silencing, siRNA was transfected into HEK293 cells by reverse transfection using Lipofectamin 2000 to a final concentration of 10 μM. siRNAs were generated from Bioneer (Korea). siRNA sequences are shown in Table S1. Total RNA of siRNA-transfected cells was extracted 48 hours after transfection by Qiazol (Qiagen, UAS) according to the manufacturer’s instruction. For plasmid transfection, pCEP4 SMAD2 (Addgene, #16484) and tetO-GATA4 (Addgene, #46030) were used. cDNA was synthesized using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Realtime PCR Master Mix (Toyobo, Japan) was used to perform qRT-PCR assays. qRT-PCR primer sequences are shown in Table S2.
ACE vector (Sino Biological, HG11598-UT) was used for overexpression experiment and western blot analysis, and Angiotensin II (Sigma-Aldrich, A9525) was treated for western blot analysis and cell viability assay. For western blot analysis, rabbit anti-ERK (Cell Signaling, 4595 T) and rabbit anti-phospho ERK (Cell Signaling, 3101 S) were used.
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6

Establishment of Stable S2 Cell Line Expressing sona-HA

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Drosophila S2 cells were grown in M3 media (Sigma-Aldrich) supplemented with 10% IMS (Sigma-Aldrich) at 25 °C. Transfections were carried out with transfection reagents effectene (Qiagen) or cellfectin (Invitrogen) according to the manufacturers’ instructions. For each transfection, a total of 1–2 μg DNA was used.
To establish S2 sona-HA cell line that stably expresses sona-HA, hygromycin B selection system was used according to the manufacturers’ instructions (Invitrogen life technologies). Briefly, 4 × 106S2 cells were cotransfected with total 1 μg of two plasmids, pAC sona-HA and pCoHygro (19:1 ratio), for 3 days. Then, the culture medium was changed to selective medium containing 150 μg/ml of hygromycin B (Invitrogen). The selective medium was replaced every 5 days, and the sona-HA cell lines were established after 3 weeks. The established sona-HA cell line was maintained in selective medium containing hygromycin B.
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7

Optimized Expansion of Drosophila Cell Lines

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Cl.8, S2, and Kc167 (Kc) cells were expanded in optimized serum-containing media, Cl.8, S2, and Kc167 media, respectively. Cl.8 media contains M3 media (Sigma-Aldrich®) supplemented with FBS (2%), insulin (5 µg/m), and fly extract (2.5%). S2 media is based on Schneider’s media (Gibco® Life Technologies) supplemented with FBS (10%). Kc media containing M3 media supplemented with yeast extract (10 mg/mL), bactopeptone (25 mg/mL), and 5% FBS. All cell lines were obtained and cultured according to instructions from the Drosophila Genomics Resource Center (DGRC). Fly extract was prepared from adult yw flies as described by the DGRC. For culture in chemically defined media, cells were rinsed three times in PBS to remove residual serum and seeded at around 70% confluency in ZO Fortified or ZB Media (ZO Fortified with 1 µM spermidine added at time of passage). Upon reaching confluency, cells were passaged 1:2 retaining half the spent media, similar to routine maintenance in complete media, with cells passaged in ZB Media receiving fresh doses of 1 µM spermidine.
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8

Drosophila S2 Cell Transfection and Co-IP

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Drosophila S2 cells were cultured in M3 media (Sigma, Saint Louis, Missouri) with 10% Fetal Bovine Serum (Thermo, Waltham, MA). S2 cells were transfected using Effectene (Qiagen, Venlo, Netherlands) or X-tremeGENE HP DNA transfection reagent (Roche, Basel, Switzerland) according to the manufacturer’s manual. pAc5.1 empty vector was used to transfect with an equal amount of plasmids. A total of 1–3 μg DNA was used for each transfection. For co-IP, transfected S2 cells were incubated during 2~3 day for producing proteins from transfected DNA.
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9

FM4-64 Live Pupae Cuticle Staining

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Live pupae with partially ripped cuticle were incubated in 10μg/ml FM4-64 (Life Technologies) in M3 media (Sigma-Aldrich) for 15-30m at 25°C. After the incubation, wings were directly subjected to confocal microscopy.
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10

S2R+ Cell Culture and Transfection

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S2R + cells were grown in M3 media (Sigma) supplemented with 10% 10X insect medium supplement (Sigma) and 1% penicillin–streptomycin solution. Cultured cells were transfected with 1–3 µg DNA using Cellfectin II Reagent following a protocol from the manufacturer (Thermo Fisher Scientific).
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