Summary of Study ST001029

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 PR000687. The data can be accessed directly via it's Project DOI: 10.21228/M8W109 This work is supported by NIH grant, U2C- DK119886.

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

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001029
Study TitleAn integrated, high-throughput strategy for multi-omic systems level analysis
Study SummaryThis report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, Sample Preparation for multi-Omics Technologies (SPOT), provides equivalent performance to typical individual omic preparation methods, but it greatly enhances throughput and minimizes the resources required for multi-omic experiments. SPOT was applied to a multi-omics time course experiment for zinc-treated HL60 cells.
Institute
Vanderbilt University
DepartmentChemistry
Last NameGant-Branum
First NameRandi
Address2201 West End Ave, Nashville, TN 37235
Emailrandi.l.gant-branum@vanderbilt.edu
Phone9312065092
Submit Date2018-05-08
Num Groups6
Analysis Type DetailLC-MS
Release Date2018-08-27
Release Version1
Randi Gant-Branum Randi Gant-Branum
https://dx.doi.org/10.21228/M8W109
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000687
Project DOI:doi: 10.21228/M8W109
Project Title:An integrated, high-throughput strategy for multi-omic systems level analysis
Project Summary:This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, Sample Preparation for multi-Omics Technologies (SPOT), provides equivalent performance to typical individual omic preparation methods, but it greatly enhances throughput and minimizes the resources required for multi-omic experiments. SPOT was applied to a multi-omics time course experiment for zinc-treated HL60 cells.
Institute:Vanderbilt University
Last Name:Gant-Branum
First Name:Randi
Address:2201 West End Ave, Nashville, TN 37235
Email:randi.l.gant-branum@vanderbilt.edu
Phone:9312065092

Subject:

Subject ID:SU001068
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Female
Cell Biosource Or Supplier:ATCC
Cell Primary Immortalized:Yes
Cell Passage Number:12
Cell Counts:1 million/mL
Species Group:human

Factors:

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

mb_sample_id local_sample_id time point sample type
SA064561sds_20160428s_18h_HILIC_Zn_HL60_challenge_Con118 hr Control
SA064562rgb_20160511_RTA_18Hr_Zn_HL60_challenge_CON0218 hr Control
SA064563rgb_20160511_RTA_18Hr_Zn_HL60_challenge_CON0118 hr Control
SA064564rgb_20160511_RTA_18Hr_Zn_HL60_challenge_CON0318 hr Control
SA064565sds_20160428s_18h_HILIC_Zn_HL60_challenge_Con218 hr Control
SA064566sds_20160428s_18h_HILIC_Zn_HL60_challenge_Con318 hr Control
SA064567sds_20160520s_18h_HILIC_Zn_HL60_challenge_rgb_QC_10uL_C1818 hr QC
SA064568sds_20160520s_18h_HILIC_Zn_HL60_challenge_rgb_10uL_QC18 hr QC
SA064569rgb_20160511_RTA_18Hr_Zn_HL60_challenge_QC18 hr QC
SA064570sds_20160520s_18h_Zn_HL60_challenge_rgb_QC18 hr QC
SA064571sds_20160428s_18h_HILIC_Zn_HL60_challenge_Treated318 hr Treated
SA064572rgb_20160511_RTA_18Hr_Zn_HL60_challenge_TREAT0218 hr Treated
SA064573sds_20160428s_18h_HILIC_Zn_HL60_challenge_Treated118 hr Treated
SA064574sds_20160428s_18h_HILIC_Zn_HL60_challenge_Treated218 hr Treated
SA064575rgb_20160511_RTA_18Hr_Zn_HL60_challenge_TREAT0318 hr Treated
SA064576rgb_20160511_RTA_18Hr_Zn_HL60_challenge_TREAT0118 hr Treated
SA064543sgc_050516r_HL60_Zn1h_C_011 hr Control
SA064544sgc_050516r_HL60_Zn1h_C_031 hr Control
SA064545sgc_050516r_HL60_Zn1h_C_041 hr Control
SA064546sgc_050516r_HL60_Zn1h_C_021 hr Control
SA064547sds_20160509s_HL60_Zn_practice_1hr_Control11 hr Control
SA064548sds_20160509s_HL60_Zn_practice_1hr_Control21 hr Control
SA064549sds_20160509s_HL60_Zn_practice_1hr_Control31 hr Control
SA064550sds_20160509s_HL60_Zn_practice_1hr_Control41 hr Control
SA064551sgc_050516r_HL60_Zn1h_QC1 hr QC
SA064552sds_20160509s_HL60_Zn_practice_1hr_QC1 hr QC
SA064553sgc_050516r_HL60_Zn1h_T_021 hr Treated
SA064554sgc_050516r_HL60_Zn1h_T_031 hr Treated
SA064555sgc_050516r_HL60_Zn1h_T_041 hr Treated
SA064556sgc_050516r_HL60_Zn1h_T_011 hr Treated
SA064557sds_20160509s_HL60_Zn_practice_1hr_Treated31 hr Treated
SA064558sds_20160509s_HL60_Zn_practice_1hr_Treated21 hr Treated
SA064559sds_20160509s_HL60_Zn_practice_1hr_Treated11 hr Treated
SA064560sds_20160509s_HL60_Zn_practice_1hr_Treated41 hr Treated
SA064577rgb_20160511_RTA_24Hr_Zn_HL60_challenge_CON0324 hr Control
SA064578rgb_20160511_RTA_24Hr_Zn_HL60_challenge_CON0224 hr Control
SA064579rgb_20160511_RTA_24Hr_Zn_HL60_challenge_CON0424 hr Control
SA064580rgb_20160511_RTA_24Hr_Zn_HL60_challenge_CON0124 hr Control
SA064581sds_20160428s_24h_HILIC_Zn_HL60_challenge_Con424 hr Control
SA064582sds_20160428s_24h_HILIC_Zn_HL60_challenge_Con324 hr Control
SA064583sds_20160428s_24h_HILIC_Zn_HL60_challenge_Con124 hr Control
SA064584sds_20160428s_24h_HILIC_Zn_HL60_challenge_Con224 hr Control
SA064585sds_20160520s_24h_HILIC_Zn_HL60_challenge_rgb_QC_10uL_C1824 hr QC
SA064586rgb_20160511_RTA_24Hr_Zn_HL60_challenge_QC24 hr QC
SA064587sds_20160521s_24h_Zn_HL60_challenge_rgb_QC24 hr QC
SA064588sds_20160521s_24h_HILIC_Zn_HL60_challenge_rgb_QC_10uL_0524 hr QC
SA064589rgb_20160511_RTA_24Hr_Zn_HL60_challenge_QCRM24 hr QC
SA064590sds_20160520s_24h_HILIC_Zn_HL60_challenge_rgb_10uL_QC24 hr QC
SA064591sds_20160428s_24h_HILIC_Zn_HL60_challenge_Treated224 hr Treated
SA064592sds_20160428s_24h_HILIC_Zn_HL60_challenge_Treated324 hr Treated
SA064593sds_20160428s_24h_HILIC_Zn_HL60_challenge_Treated424 hr Treated
SA064594sds_20160428s_24h_HILIC_Zn_HL60_challenge_Treated124 hr Treated
SA064595rgb_20160511_RTA_24Hr_Zn_HL60_challenge_TREAT0124 hr Treated
SA064596rgb_20160511_RTA_24Hr_Zn_HL60_challenge_TREAT0324 hr Treated
SA064597rgb_20160511_RTA_24Hr_Zn_HL60_challenge_TREAT0224 hr Treated
SA064598rgb_20160511_RTA_24Hr_Zn_HL60_challenge_TREAT0424 hr Treated
SA064599rgb_20160520_RTA_HL60_ZN_36HR_CON336 hr Control
SA064600rgb_20160520_RTA_HL60_ZN_36HR_CON436 hr Control
SA064601rgb_20160520_RTA_HL60_ZN_36HR_CON236 hr Control
SA064602sds_20160606s_36h_HILIC_Zn_HL60_challenge_Con536 hr Control
SA064603sds_20160606s_36h_HILIC_Zn_HL60_challenge_Con136 hr Control
SA064604sds_20160606s_36h_HILIC_Zn_HL60_challenge_Con236 hr Control
SA064605rgb_20160520_RTA_HL60_ZN_36HR_CON136 hr Control
SA064606sds_20160606s_36h_HILIC_Zn_HL60_challenge_Con336 hr Control
SA064607sds_20160606s_36h_HILIC_Zn_HL60_challenge_rgb_QC36 hr QC
SA064608rgb_20160520_RTA_HL60_ZN_36HR_QC36 hr QC
SA064609sds_20160606s_36h_HILIC_Zn_HL60_challenge_Treated136 hr Treated
SA064610sds_20160606s_36h_HILIC_Zn_HL60_challenge_Treated536 hr Treated
SA064611sds_20160606s_36h_HILIC_Zn_HL60_challenge_Treated336 hr Treated
SA064612sds_20160606s_36h_HILIC_Zn_HL60_challenge_Treated236 hr Treated
SA064613sds_20160607s_48h_HILIC_Zn_HL60_challenge_Con248 hr Control
SA064614sds_20160607s_48h_HILIC_Zn_HL60_challenge_Con448 hr Control
SA064615rgb_20160520r_b_RTA_HL60_ZN_48HR_CON448 hr Control
SA064616rgb_20160520r_b_RTA_HL60_ZN_48HR_CON348 hr Control
SA064617rgb_20160520r_b_RTA_HL60_ZN_48HR_CON148 hr Control
SA064618sds_20160607s_48h_HILIC_Zn_HL60_challenge_Con348 hr Control
SA064619sds_20160607s_48h_HILIC_Zn_HL60_challenge_Con148 hr Control
SA064620rgb_20160520r_b_RTA_HL60_ZN_48HR_QC48 hr QC
SA064621sds_20160607s_48h_HILIC_Zn_HL60_challenge_rgb_QC_C18_10uL48 hr QC
SA064622sds_20160607s_48h_HILIC_Zn_HL60_challenge_rgb_QC48 hr QC
SA064623sds_20160607s_48h_HILIC_Zn_HL60_challenge_Treated248 hr Treated
SA064624sds_20160607s_48h_HILIC_Zn_HL60_challenge_Treated448 hr Treated
SA064625sds_20160607s_48h_HILIC_Zn_HL60_challenge_Treated348 hr Treated
SA064626rgb_20160520r_b_RTA_HL60_ZN_48HR_TREAT148 hr Treated
SA064627rgb_20160520r_b_RTA_HL60_ZN_48HR_TREAT448 hr Treated
SA064628rgb_20160520r_b_RTA_HL60_ZN_48HR_TREAT348 hr Treated
SA064629rgb_20160520r_b_RTA_HL60_ZN_48HR_TREAT248 hr Treated
SA064630sds_20160607s_48h_HILIC_Zn_HL60_challenge_Treated148 hr Treated
SA064631RGB_20160509r_RTA_6hr_Zn_HL60_challenge_CON036 hr Control
SA064632RGB_20160509r_RTA_6hr_Zn_HL60_challenge_CON046 hr Control
SA064633sds_20160512s_HILIC_HL60_Zn_Practice_6hr_Con26 hr Control
SA064634sds_20160512s_HILIC_HL60_Zn_Practice_6hr_Con36 hr Control
SA064635RGB_20160509r_RTA_6hr_Zn_HL60_challenge_CON026 hr Control
SA064636sds_20160512s_HILIC_HL60_Zn_Practice_6hr_Con16 hr Control
SA064637sds_20160512s_HILIC_HL60_Zn_Practice_6hr_Con46 hr Control
SA064638RGB_20160509r_RTA_6hr_Zn_HL60_challenge_QC6 hr QC
SA064639sds_20160512s_HILIC_HL60_Zn_Practice_6hr_QC6 hr QC
SA064640RGB_20160509r_RTA_6hr_Zn_HL60_challenge_TREAT036 hr Treated
SA064641RGB_20160509r_RTA_6hr_Zn_HL60_challenge_TREAT046 hr Treated
SA064642sds_20160512s_HILIC_HL60_Zn_Practice_6hr_Treat26 hr Treated
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Collection:

Collection ID:CO001062
Collection Summary:no collection protocol
Sample Type:Leukemia cells

Treatment:

Treatment ID:TR001082
Treatment Summary:The HL60 cells were cultured in Isocove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with 10% v/v heat-inactivated fetal bovine serum (Atlanta Biologicals) at 37˚C with 5% CO2 atmosphere and treated with 225 µM Zn or deionized H2O.

Sample Preparation:

Sampleprep ID:SP001075
Sampleprep Summary:The remaining HL60 cells (approximately one million) were lysed in 100 µL of 1:1:2 MeCNCH3CN: CH3MeOH:NH4HCO3 (50 mM, pH 8.0) followed by one freeze-thaw cycle (three minutes each) and a ten-minute sonication in an ice bath. Protein concentration was obtained using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific). An aliquot of 100 or 150 µg of each sample in a total of 100 µL of lysis buffer was precipitated with 300 µL of ice cold 75:25 acetone:methanol for 2 h at -80°C. Samples were spun for 15 minutes at 6,800 x g and the supernatant was removed and utilized for metabolomics analysis. The pellets were rinsed with 300 µL of ice cold acetone and spun as above. Acetone was removed and the pellet was allowed to dry briefly. Metabolite supernatants were dried and reconstituted in 50 uL of appropriate reverse phase liquid chromatography (0.1% formic acid in 98:2 H2O: CH3CNMeCN) or hydrophilic interaction chromatography (80:20 CH3CNMeCN: H2O) compatible buffers prior to analyses.

Combined analysis:

Analysis ID AN001687 AN001688
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Waters NanoAcquity Waters Acquity
Column Waters Acquity HSS T3 (100 x 2.1mm,1.8um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE POSITIVE
Units absorbance Abundance

Chromatography:

Chromatography ID:CH001187
Chromatography Summary:see formatted metadata template
Instrument Name:Waters NanoAcquity
Column Name:Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001188
Chromatography Summary:see formatted metadata template
Instrument Name:Waters Acquity
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Chromatography Type:HILIC

MS:

MS ID:MS001562
Analysis ID:AN001687
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001563
Analysis ID:AN001688
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
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