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

Study ID	ST001142
Study Title	Cancer Cell Line Encyclopedia Metabolomics
Study Summary	928 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 Name	Avila-Pacheco
First Name	Julian
Address	415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Email	jravilap@broadinstitute.org
Phone	6177148264
Submit Date	2019-02-25
Num Groups	927
Total Subjects	946
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2019-02-27
Release Version	1

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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
SA078352	OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	AMEM + 20% FBS
SA078353	MUTZ3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	AMEM + 20% FBS
SA078354	OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	AMEM + 20% FBS
SA078355	MV411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 10% FBS
SA078356	HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 20% FBS
SA078357	KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 20% FBS
SA078358	OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 20% FBS
SA078359	SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 20% FBS
SA078360	AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	IMDM + 5% FBS
SA078361	KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	MEM + 10% FBS
SA078362	MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078363	NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078364	HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078365	EOL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078366	MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078367	HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078368	THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078369	TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078370	CMK115_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078371	ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078372	P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078373	GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078374	NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078375	M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 10% FBS
SA078376	OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 15% FBS
SA078377	KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078378	MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078379	KASUMI6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078380	CMK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078381	MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078382	PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078383	F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078384	SKM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	AML	RPMI 1640 + 20% FBS
SA078385	SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	IMDM + 10% FBS
SA078386	JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	IMDM + 10% FBS
SA078387	SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	IMDM + 20% FBS
SA078388	KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 10% FBS
SA078389	BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 10% FBS
SA078390	RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 10% FBS
SA078391	NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 10% FBS
SA078392	REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 10% FBS
SA078393	MHHCALL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 20% FBS
SA078394	MHHCALL3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 20% FBS
SA078395	MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 20% FBS
SA078396	MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_ALL	RPMI 1640 + 20% FBS
SA078397	GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	DMEM + 10% FBS
SA078398	CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	DMEM + 20% FBS
SA078399	MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	IMDM + 10% FBS
SA078400	JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078401	JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078402	EHEB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078403	RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078404	HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078405	REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 10% FBS
SA078406	NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 15% FBS
SA078407	MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 15% FBS
SA078408	JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 20% FBS
SA078409	RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 20% FBS
SA078410	MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 20% FBS
SA078411	BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	B-cell_lymphoma_other	RPMI 1640 + 20% FBS
SA078459	SNU869_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078460	SNU1196_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078461	HUCCT1_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078462	SNU478_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078463	SNU308_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078464	HUH28_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078465	SNU1079_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078466	SNU245_BILIARY_TRACT	bile_duct	RPMI 1640 + 10% FBS
SA078467	HDQP1_BREAST	breast	DMEM + 10% FBS
SA078468	CAL120_BREAST	breast	DMEM + 10% FBS
SA078469	KPL1_BREAST	breast	DMEM + 10% FBS
SA078470	HS606T_BREAST	breast	DMEM + 10% FBS
SA078471	JIMT1_BREAST	breast	DMEM + 10% FBS
SA078472	HS578T_BREAST	breast	DMEM + 10% FBS
SA078473	CAL851_BREAST	breast	DMEM + 10% FBS
SA078474	MDAMB468_BREAST	breast	DMEM + 10% FBS
SA078475	CAL51_BREAST	breast	DMEM + 20% FBS
SA078476	CAL148_BREAST	breast	DMEM + 20% FBS
SA078477	BT474_BREAST	breast	DMEM + 20% FBS
SA078478	MCF7_BREAST	breast	EMEM + 10% FBS
SA078479	CAMA1_BREAST	breast	EMEM + 10% FBS
SA078480	BT20_BREAST	breast	EMEM + 10% FBS
SA078481	UACC893_BREAST	breast	Leibovitzs L-15 + 10% FBS
SA078482	MDAMB134VI_BREAST	breast	Leibovitzs L-15 + 20% FBS
SA078483	SKBR3_BREAST	breast	McCoys 5A + 10% FBS
SA078484	HCC2218_BREAST	breast	RPMI 1640 + 10% FBS
SA078485	MDAMB453_BREAST	breast	RPMI 1640 + 10% FBS
SA078486	HCC1569_BREAST	breast	RPMI 1640 + 10% FBS
SA078487	HCC1187_BREAST	breast	RPMI 1640 + 10% FBS
SA078488	HMC18_BREAST	breast	RPMI 1640 + 10% FBS
SA078489	ZR751_BREAST	breast	RPMI 1640 + 10% FBS
SA078490	MDAMB175VII_BREAST	breast	RPMI 1640 + 10% FBS
SA078491	HCC1395_BREAST	breast	RPMI 1640 + 10% FBS
SA078492	HCC1806_BREAST	breast	RPMI 1640 + 10% FBS
SA078493	HCC1954_BREAST	breast	RPMI 1640 + 10% FBS
SA078494	MDAMB231_BREAST	breast	RPMI 1640 + 10% FBS
SA078495	T47D_BREAST	breast	RPMI 1640 + 10% FBS
SA078496	HCC1428_BREAST	breast	RPMI 1640 + 10% FBS
SA078497	HCC1937_BREAST	breast	RPMI 1640 + 10% FBS
SA078498	HCC1599_BREAST	breast	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.

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