Summary of study ST001142

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000763. The data can be accessed directly via it's Project DOI: 10.21228/M82677 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001142
Study TitleCancer Cell Line Encyclopedia Metabolomics
Study Summary928 cancer cell lines from 20 major cancer types were cultured in vitro for metabolomic profiling of 124 polar and 101 lipid species. Extracted polar and lipid metabolites were analyzed using hydrophilic interaction
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Emailjravilap@broadinstitute.org
Phone6177148264
Submit Date2019-02-25
Num Groups927
Total Subjects946
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2019-02-27
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M82677
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000763
Project DOI:doi: 10.21228/M82677
Project Title:The Landscape of Cancer Cell Line Metabolism
Project Summary:Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated
Institute:Broad Institute of MIT and Harvard
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Email:jravilap@broadinstitute.org
Phone:6177148264
Contributors:Haoxin Li, Shaoyang Ning, Mahmoud Ghandi, Gregory V. Kryukov, Shuba Gopal, Amy Deik, Amanda Souza, Kerry Pierce, Paula Keskula, Desiree Hernandez, Julie Ann, Dojna Shkoza, Verena Apfel, Yilong Zou1, Francisca Vazquez, Jordi Barretina, Raymond A. Pagliarini, Giorgio G. Galli, David E. Root, William C. Hahn, Aviad Tsherniak, Marios Giannakis, Stuart L. Schreiber, Clary B. Clish, Levi A. Garraway, William R. Sellers

Subject:

Subject ID:SU001206
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Classifications Cell Culture Media
SA078352OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML AMEM + 20% FBS
SA078353MUTZ3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML AMEM + 20% FBS
SA078354OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML AMEM + 20% FBS
SA078355MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 10% FBS
SA078356HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 20% FBS
SA078357KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 20% FBS
SA078358OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 20% FBS
SA078359SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 20% FBS
SA078360AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML IMDM + 5% FBS
SA078361KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML MEM + 10% FBS
SA078362MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078363NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078364HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078365EOL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078366MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078367HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078368THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078369TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078370CMK115_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078371ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078372P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078373GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078374NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078375M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 10% FBS
SA078376OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 15% FBS
SA078377KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078378MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078379KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078380CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078381MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078382PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078383F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078384SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEAML RPMI 1640 + 20% FBS
SA078385SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL IMDM + 10% FBS
SA078386JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL IMDM + 10% FBS
SA078387SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL IMDM + 20% FBS
SA078388KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 10% FBS
SA078389BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 10% FBS
SA078390RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 10% FBS
SA078391NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 10% FBS
SA078392REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 10% FBS
SA078393MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 20% FBS
SA078394MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 20% FBS
SA078395MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 20% FBS
SA078396MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_ALL RPMI 1640 + 20% FBS
SA078397GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other DMEM + 10% FBS
SA078398CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other DMEM + 20% FBS
SA078399MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other IMDM + 10% FBS
SA078400JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078401JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078402EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078403RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078404HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078405REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 10% FBS
SA078406NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 15% FBS
SA078407MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 15% FBS
SA078408JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 20% FBS
SA078409RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 20% FBS
SA078410MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 20% FBS
SA078411BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEB-cell_lymphoma_other RPMI 1640 + 20% FBS
SA078459SNU869_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078460SNU1196_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078461HUCCT1_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078462SNU478_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078463SNU308_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078464HUH28_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078465SNU1079_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078466SNU245_BILIARY_TRACTbile_duct RPMI 1640 + 10% FBS
SA078467HDQP1_BREASTbreast DMEM + 10% FBS
SA078468CAL120_BREASTbreast DMEM + 10% FBS
SA078469KPL1_BREASTbreast DMEM + 10% FBS
SA078470HS606T_BREASTbreast DMEM + 10% FBS
SA078471JIMT1_BREASTbreast DMEM + 10% FBS
SA078472HS578T_BREASTbreast DMEM + 10% FBS
SA078473CAL851_BREASTbreast DMEM + 10% FBS
SA078474MDAMB468_BREASTbreast DMEM + 10% FBS
SA078475CAL51_BREASTbreast DMEM + 20% FBS
SA078476CAL148_BREASTbreast DMEM + 20% FBS
SA078477BT474_BREASTbreast DMEM + 20% FBS
SA078478MCF7_BREASTbreast EMEM + 10% FBS
SA078479CAMA1_BREASTbreast EMEM + 10% FBS
SA078480BT20_BREASTbreast EMEM + 10% FBS
SA078481UACC893_BREASTbreast Leibovitzs L-15 + 10% FBS
SA078482MDAMB134VI_BREASTbreast Leibovitzs L-15 + 20% FBS
SA078483SKBR3_BREASTbreast McCoys 5A + 10% FBS
SA078484HCC2218_BREASTbreast RPMI 1640 + 10% FBS
SA078485MDAMB453_BREASTbreast RPMI 1640 + 10% FBS
SA078486HCC1569_BREASTbreast RPMI 1640 + 10% FBS
SA078487HCC1187_BREASTbreast RPMI 1640 + 10% FBS
SA078488HMC18_BREASTbreast RPMI 1640 + 10% FBS
SA078489ZR751_BREASTbreast RPMI 1640 + 10% FBS
SA078490MDAMB175VII_BREASTbreast RPMI 1640 + 10% FBS
SA078491HCC1395_BREASTbreast RPMI 1640 + 10% FBS
SA078492HCC1806_BREASTbreast RPMI 1640 + 10% FBS
SA078493HCC1954_BREASTbreast RPMI 1640 + 10% FBS
SA078494MDAMB231_BREASTbreast RPMI 1640 + 10% FBS
SA078495T47D_BREASTbreast RPMI 1640 + 10% FBS
SA078496HCC1428_BREASTbreast RPMI 1640 + 10% FBS
SA078497HCC1937_BREASTbreast RPMI 1640 + 10% FBS
SA078498HCC1599_BREASTbreast RPMI 1640 + 10% FBS
Showing page 1 of 10     Results:    1  2  3  4  5  Next  Last     Showing results 1 to 100 of 928

Collection:

Collection ID:CO001200
Collection Summary:Cancer Cell Line Encyclopedia: a collection of 928 cancer cell lines
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001221
Treatment Summary:No treatment applied to cells

Sample Preparation:

Sampleprep ID:SP001214
Sampleprep Summary:Polar metabolite extraction LC-MS grade solvents were used for all of the metabolite extraction in this study. For adherent cells, the media were aspirated off as much as possible and the cells were washed with 4 mL cold Phosphate Buffered Saline (PBS, no Mg2+/Ca2+). After vacuum aspiration of PBS, the metabolites were extracted by adding 4 mL 80% methanol (-80°C) immediately and the samples were transferred to a -80°C freezer. The flasks were kept on dry ice during the transfer and were incubated at -80°C for 15 min. Then the lysate was collected by a cell scraper and transferred to a 15 mL conical tube on dry ice. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL conical tube on dry ice and the tube with the pellet was kept for further extraction. Then, 500 μL 80% methanol (-80°C) was added to each pellet. The mixture was resuspended by vortexing or pipetting and transferred to a 1.5 ml centrifuge tube on dry ice. The cell debris was removed by centrifuging samples at 10,000 rpm for 5 min (4°C). The supernatant was transferred to the corresponding 15 mL conical tube on dry ice so that all extracts were combined. The pooled extracts were stored at - 80°C before LC-MS analysis. For cells growing in suspension, they were centrifuged to pellet at 300g for 5 min (4°C) and the supernatant was then aspirated off as much as possible. These cells were washed once with 4 mL cold PBS (no Mg2+/Ca2+) and they were pelleted at 300g for 5 min (4°C). After vacuum aspiration of PBS, the metabolites were extracted by adding 4 mL 80% methanol (-80°C) immediately and the samples were transferred to a -80°C freezer after brief vortexing. The samples were kept on dry ice during the transfer and were incubated at -80°C for 15 min. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The subsequent steps were the same as those used for adherent cell lines Lipid extraction For adherent cells, the medium was aspirated off as much as possible and the cells were washed with 4 mL cold PBS (no Mg2+/Ca2+). After vacuum aspiration of PBS, the lipid metabolites were extracted by adding 4 mL isopropanol (4°C) and the lysate was collected by a cell scraper and transferred to a 15 mL conical tube on ice. The samples were covered to avoid exposure to light and were allowed to sit for 1h at 4°C. Samples were then vortexed and the cell debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL centrifuge tube on ice and stored at -20°C before LC-MS analysis. For cells growing in suspension, they were centrifuged to pellet at 300g for 5 min (4°C) and the supernatant was then aspirated off as much as possible. These cells were washed once with 4 mL cold PBS (no Mg2+/Ca2+) and they were pelleted at 300g for 5 min (4°C). After vacuum aspiration of PBS, the lipid metabolites were extracted by adding 4 mL isopropanol (4°C) immediately. After brief vortexing, the samples were covered to avoid exposure to light and were allowed to sit for 1h at 4°C. The insoluble debris was removed by centrifuging at 3500 rpm for 10 min (4°C). The supernatant was transferred to a new 15 mL centrifuge tube on ice and stored at -20°C before LC-MS analysis.

Combined analysis:

Analysis ID AN001875 AN001876 AN001877
Analysis type MS MS MS
Chromatography type HILIC HILIC Reversed phase
Chromatography system Agilent 1100 Waters Acquity Agilent 1200
Column Unspecified Phenomenex Luna NH2 (150 x 2.1mm, 3um) Unspecified
MS Type ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 4000 QTrap ABI Sciex 5500 QTrap ABI Sciex 4000 QTrap
Ion Mode POSITIVE NEGATIVE POSITIVE
Units Abundances Abundances Abundances

Chromatography:

Chromatography ID:CH001356
Chromatography Summary:HILIC-pos
Instrument Name:Agilent 1100
Column Name:Unspecified
Chromatography Type:HILIC
  
Chromatography ID:CH001357
Chromatography Summary:HILIC-neg
Instrument Name:Waters Acquity
Column Name:Phenomenex Luna NH2 (150 x 2.1mm, 3um)
Chromatography Type:HILIC
  
Chromatography ID:CH001358
Chromatography Summary:C4-pos
Instrument Name:Agilent 1200
Column Name:Unspecified
Chromatography Type:Reversed phase

MS:

MS ID:MS001731
Analysis ID:AN001875
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:n/a
Ion Mode:POSITIVE
  
MS ID:MS001732
Analysis ID:AN001876
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:n/a
Ion Mode:NEGATIVE
  
MS ID:MS001733
Analysis ID:AN001877
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Full scan data were acquired using Q1 scanning
Ion Mode:POSITIVE
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