Gm12878

Manufactured by Coriell Institute for Medical Research

Sourced in United States

GM12878 is a human B-lymphocyte cell line derived from a female Caucasian individual. It serves as a reference standard for genomic studies and is widely used in research applications.

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GM12878 cells (13 citations) GM12878 cell line (3 citations) GM12878 human cell line (2 citations) GM12878 lymphoblast (2 citations) GM12878 gDNA (2 citations)

41 protocols using gm12878

Cell Culture Protocols for ENCODE

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K562 cells (ATCC CCL-243) were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10% FBS and antibiotics. T47D cells (ATCC HTB-133), NCI-H460 cells (ATCC HTB-177), A549 cells (ATCC CCL-185), LNCaP (ATCC CRL-1740), and GM12878 cells (Coriell) were cultured in RPMI-1640 supplemented with 10% FBS and antibiotics, or 15% FBS and antibiotics (GM12878). Caki2 cells (ATCC HTB-47), G-401 cells (ATCC CRL-1441) were cultured in McCoy’s 5a Medium Modified supplemented with 10% FBS and antibiotics. PANC-1 cells (ATCC CRL-1469) were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FBS and antibiotics. SK-N-MC (ATCC HTB-10), RPMI-7951 (ATCC HTB-66) cells were cultured in Eagle’s Minimum Essential Medium supplemented with 10% FBS and antibiotics. SK-N-AS cells (ATCC CRL-2137) were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FBS, 0.1mM Non-Essential Amino Acids (Gibco) and antibiotics All cell lines cultured as part of ENCODE data generation (A549, Caki2, G401, LNCaP, NCI-H460, Panc1, RPMI-7951, SJCRH30, SK-MEL-5, SK-N-DZ, SK-N-MC,T47D) were cultured using standardized protocols, the details of which can be found through the ENCODE consortium website (https://www.encodeproject.org/).

Dixon J.R., Xu J., Dileep V., Zhan Y., Song F., Le V.T., Gürkan Yardımcı G., Chakraborty A., Bann D.V., Wang Y., Clark R., Zhang L., Yang H., Liu T., Iyyanki S., An L., Pool C., Sasaki T., Rivera-Mulia J.C., Ozadam H., Lajoie B.R., Kaul R., Buckley M., Lee K., Diegel M., Pezic D., Ernst C., Hadjur S., Odom D.T., Stamatoyannopoulos J.A., Broach J.R., Hardison R.C., Ay F., Stafford Noble W., Dekker J., Gilbert D.M, & Yue F. (2018). Integrative Detection and Analysis of Structural Variation in Cancer Genomes. Nature genetics, 50(10), 1388-1398.

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Culturing Burkitt Lymphoma Cell Lines

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We maintained Burkitt lymphoma cell lines at 37 °C with 5% CO₂ (v/v) in RPMI-1640 media containing 25 mM HEPES and 10% (v/v) fetal bovine serum. We maintained LCLs similarly except with 15% (v/v) fetal bovine serum. MutuI [13 (link)] cells grew under standard conditions [14 ]. Raji [15 (link)] (CCL-86) and Daudi [16 (link)] (CCL-213) cell lines were obtained from ATCC (Manassas, VA). The GM12878 [17 (link)] (GM12878) cell line was obtained from the Coriell Institute for Medical Research (Camden, NJ). Jeffery T. Sample (Pennsylvania State University) provided the KemI and KemIII [18 (link)] cell lines, Andrew I. Bell (University of Birmingham) provided the RaeI [19 (link)] cell line, and Bill Sugden (University of Wisconsin, Madison) provided the 721 LCL [20 (link)]. We generated MutuIII by prolonged passaging of MutuI in cell culture [13 (link)].

Phan A.T., Fernandez S.G., Somberg J.J., Keck K.M, & Miranda J. (2016). Epstein-Barr virus latency type and spontaneous reactivation predict lytic induction levels. Biochemical and biophysical research communications, 474(1), 71-75.

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Sampling Tissues and Cell Lines for Genomic Analysis

Cited 2 times

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We sampled tissues (liver and blood cells) from a female purchased from a local farmer in Japan because the previous whole-genome sequencing used the whole blood of a female [26 (link)]. All experiments were conducted in accordance with the Guideline of the Institutional Animal Care and Use Committee of RIKEN Kobe Branch (Approval ID: A2017–12).
The human lymphoblastoid cell line GM12878 (Coriell Cat# GM12878, RRID:CVCL_7526) was purchased from the Coriell Cell Repositories and cultured in RPMI-1640 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 15% fetal bovine serum, 2 mM L-glutamine, and a 1× antibiotic-antimycotic solution (Thermo Fisher Scientific), at 37 °C, 5% CO₂, as described previously [37 (link)].

Kadota M., Nishimura O., Miura H., Tanaka K., Hiratani I, & Kuraku S. (2020). Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?. GigaScience, 9(1), giz158.

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Crosslinking and Fixation Protocols for HiChIP

Cited 1 time

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The University of Massachusetts Medical School Animal Care and Use Committees approved all animal work.
mESCs (v.6.5, Novus Biologicals: NBP1-41162) were cultured in knockout DMEM (Gibco) + 15% fetal bovine serum and leukemia inhibitory factor (Millipore) to 80% confluence. GM12878 (Coriell) cells were grown in RPMI 1640 (Gibco) with 15% fetal bovine serum to a concentration of 500,000 to 1 million cells per ml. lincRNA-EPS-knockout mice were obtained from a previous study^{22 (link)}. BMDMs were differentiated from bone marrow cells with 20% L929 supernatant for 7 d.
Detached cell lines were pelleted and resuspended in fresh 1% formaldehyde (Thermo Fisher) or 1% glutaraldehyde (Sigma) at a volume of 1 ml cross-linker for million cells. Cells were incubated at room temperature for 10 min with rotation. Glycine was added at a final concentration of 125 mM to quench the cross-linker, and cells were incubated at room temperature for 5 min with rotation. Finally, cells were pelleted and washed with PBS, pelleted again and stored at −80 °C or immediately taken into the HiChIP or HiChIRP protocols^{9 (link)}.

Mumbach M.R., Granja J.M., Flynn R.A., Roake C.M., Satpathy A.T., Rubin A.J., Qi Y., Jiang Z., Shams S., Louie B.H., Guo J.K., Gennert D.G., Corces M.R., Khavari P.A., Atianand M.K., Artandi S.E., Fitzgerald K.A., Greenleaf W.J, & Chang H.Y. (2019). HiChIRP reveals RNA-associated chromosome conformation. Nature methods, 16(6), 489-492.

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Culturing S. cerevisiae and Mammalian Cells

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S. cerevisiae strain FY3 was struck out on YPD plates and grown at 30 °C. Mammalian cells (lymphoblastoid cell line GM12878; Coriell) were cultured at 37 °C, 5% CO₂ in RPMI-1640 supplemented with 1X Anti-Anti (Gibco), 1X Plasmocin (Invivogen), and 15% FBS (Gibco).

Ramani V., Qiu R, & Shendure J. (2015). High-throughput determination of RNA structure by proximity ligation. Nature biotechnology, 33(9), 980-984.

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Genomic DNA Extraction and Size Selection

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The Institutional Review Board (IRB) at Stanford University School of Medicine approved the study. Informed consent was obtained and the samples were made available from the Stanford Cancer Center Tissue Bank. This study used a primary colorectal adenocarcinoma and matched normal tissue that were collected at time of surgical resection and flash frozen. Both samples had genomic DNA extracted with the E.Z.N.A. SQ DNA/RNA Protein Kit (Omega Bio-Tek). The genomic DNA did not require further size selection or processing. We quantified the DNA with Life Technologies Qubit.
For the commercially acquired genomic DNA, we size selected DNA molecules 20 kb or higher using the BluePippin (Sage Science) (NA12877 and NA12882 from Coriell, and NCI-H2228 from ATCC). In addition, we harvested immortalized human lymphocyte cells (GM12878 and GM20847 from Coriell) and genomic DNA was extracted using the Gentra Puregene Cell kit (Qiagen).

Zheng G.X., Lau B.T., Schnall-Levin M., Jarosz M., Bell J.M., Hindson C.M., Kyriazopoulou-Panagiotopoulou S., Masquelier D.A., Merrill L., Terry J.M., Mudivarti P.A., Wyatt P.W., Bharadwaj R., Makarewicz A.J., Li Y., Belgrader P., Price A.D., Lowe A.J., Marks P., Vurens G.M., Hardenbol P., Montesclaros L., Luo M., Greenfield L., Wong A., Birch D.E., Short S.W., Bjornson K.P., Patel P., Hopmans E.S., Wood C., Kaur S., Lockwood G.K., Stafford D., Delaney J.P., Wu I., Ordonez H.S., Grimes S.M., Greer S., Lee J.Y., Belhocine K., Giorda K.M., Heaton W.H., McDermott G.P., Bent Z.W., Meschi F., Kondov N.O., Wilson R., Bernate J.A., Gauby S., Kindwall A., Bermejo C., Fehr A.N., Chan A., Saxonov S., Ness K.D., Hindson B.J, & Ji H.P. (2016). Haplotyping germline and cancer genomes using high-throughput linked-read sequencing. Nature biotechnology, 34(3), 303-311.

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Culturing HEK293T, GM12878, and HG002 Cells

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HEK293T cells (CRL-3216, ATCC, Manassas, VA; validated by microsatellite typing and mycoplasma tested) were maintained in DMEM (high glucose, with GlutaMAX, with phenol red, without sodium pyruvate; Gibco 10566016) supplemented with 10% Fetal Bovine Serum (VWR 89510-186) and 1% Pen Strep (Gibco 15070063) at 37°C in 5% CO₂. GM12878 cells (GM12878, Coriell Institute, Camden, NJ; mycoplasma tested) and HG002 cells (GM24385, Coriell Institute, Camden, NJ; mycoplasma tested) were maintained in RPMI-1640 with L-glutamine (Gibco 11875093) supplemented with 15% Fetal Bovine Serum (VWR 89510-186) and 1% Pen Strep (Gibco 15070063) at 37°C in 5% CO₂.

Altemose N., Maslan A., Smith O.K., Sundararajan K., Brown R.R., Mishra R., Detweiler A.M., Neff N., Miga K.H., Straight A.F, & Streets A. (2022). DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide. Nature methods, 19(6), 711-723.

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Fibroblast and Lymphoblastoid Cell Lines for Radiation Studies

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Fibroblast cell lines include: BJ-5ta (ATCC, CRL-4001), BJ1-hTERT (kind gift from Vilhelm A. Bohr, Laboratory of Molecular Genetics, Gerontology Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD), MRC-5 (kind gift from Tim Sparer, University of Tennessee, Knoxville, Knoxville, TN), AG04405 (ATM-hTERT) (kind gift from Peter Lansdorp, University of British Columbia, Vancouver, Canada), and GM02052 (Coriell). The lymphoblastoid cell line GM12878 (Coriell) was also used. Information about cell lines and media formulations is summarized in Supplementary Table 2. All growth media and fetal bovine serum was purchased from Corning, except for GM12878 growth media from Gibco. All fibroblast lines were passaged at a density of 80%. For irradiation experiments, fibroblast lines were grown to confluency prior to X-ray exposure. For the GM12878 suspension cell line, cells were passaged at a density around 500,000 cells per 1 mL of medium. For irradiation experiments, GM12878 cells were grown to a density of 1 million cells per 1 mL of medium prior to X-ray exposure.

Sanders J.T., Freeman T.F., Xu Y., Golloshi R., Stallard M.A., Hill A.M., San Martin R., Balajee A.S, & McCord R.P. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11, 6178.

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Lymphoblastoid Cell RNA Isolation and Tetrahymena Ribozyme Doping

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Human lymphoblastoid cell lines GM12878, GM12891 and GM12892 were obtained from Coriell. Total RNA was isolated from lymphoblastoid cells using Trizol reagent (Invitrogen). Poly(A)+ RNA was obtained by purifying twice using the MicroPoly(A)Purist kit (Life Technologies). The Tetrahymena ribozyme RNA was in vitro transcribed using T7 RiboMax Large scale RNA production system (Promega) and doped into 2µg of polyA+ RNA (1% by mole) for structure probing and library construction.

Wan Y., Qu K., Zhang Q.C., Flynn R.A., Manor O., Ouyang Z., Zhang J., Spitale R.C., Snyder M.P., Segal E, & Chang H.Y. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505(7485), 706-709.

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Cell Viability Assay Protocols

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T4 polynucleotide kinase was purchased from Epicenter (Lexington, KY) and [γ-³²P]ATP (6000 Ci/mmol) from PerkinElmer (Waltham, MA). DNA oligomers were purchased from IDT (Coralville, IA). The concentrations of the dNTPs (Promega, Madison WI) were each determined by UV absorbance.³⁵ HNK, BLM, and TMZ, purchased from Sigma-Aldrich (St. Louis, MO), were freshly prepared in DMSO, stored at −80 °C, and diluted in buffer or complete medium just before use. 3-(4,5-Dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) was purchased from Promega (Madison, WI, USA), and phenazine metho-sulfate (PMS) was purchased from Sigma-Aldrich (St. Louis, MO, USA). MTS/PMS solution was prepared at a concentration of 2 mg/mL of MTS and 0.92 mg/mL of PMS in phosphate-buffered saline (PBS) and stored in dark bottle at 4 °C. Fetal bovine serum was purchased from Atlanta Biologicals Inc. The human cancer cell lines, MCF7, A549, PANC-1, UACC903, were purchased from American Type Culture Collection (ATCC), and GM12878 cells were purchased from Coriell Institute for Medical Research.

Prakasha Gowda A.S., Suo Z, & Spratt T.E. (2017). Honokiol Inhibits DNA Polymerases β and λ and Increases Bleomycin Sensitivity of Human Cancer Cells. Chemical research in toxicology, 30(2), 715-725.

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