VIMSS Data and Analysis Pipeline/Off-Pipeline Summary

Note: the information on this page is no longer being updated.
Please visit vimss.lbl.gov/EIDR/ for more current information

VIMSS Experimental Data and Analysis Pipeline/Off-Pipeline Summary

The table below summarizes information and QA/QC data about biomass produced at LBNL for the VIMSS project, and the results of transcriptomic, proteomic, and metabolomic experiments performed using the LBNL biomass. The table is organized by the quarter that the LBNL biomass was produced. The first column contains the LBNL Exp ID; the second column provides information about stressor or experiment design and the organism(s); the third column contains links to information about the biomass production experiment, including QA/QC data (AODC, FTIR, OD, photomicrographs, and protein); and the fourth column lists the type of downstream experiments performed using the biomass (transcriptomic, proteomic, or metabolomic).

Pipeline experiments are defined as those for which there is a control biomass and a stressed biomass. Off-pipeline experiments are defined as those in which unstressed biomass is produced and used for a specific investigation or to test an experimental technique. Pipeline experiments are color-coded light blue, and off-pipeline experiments are pale gold. Experiments that have been canceled or are on hold are colored pale orange.

N.B. Most of the links below are password protected. You must have a Biofiles account to access information stored in Biofiles. Contact Keith Keller at KKeller@lbl.gov to request a Biofiles account. Contact Katherine Huang at KHHuang@lbl.gov to request access to analyses by the LBNL Computational Core (CC). For access to all other password-protected links, contact Janet Jacobsen at JSJacobsen@lbl.gov.

The table is indexed in three ways:

by stressor or experiment design,
by quarter,
by LBNL Exp ID.

Index of VIMSS Experiments E28-E74 by Stressor or Experiment Design

Pipeline Experiments
(sorted by stressor)

E45 (C)	chromium stress, 0.3 mM
E47	chromium stress, 0.55 mM	T
E62 (C)	chromium stress, 0.45 mM
E63 (H)	chromium stress, 0.45 mM
E68 (C)	chromium stress, 0.45 mM
E71	chromium stress, 0.45 mM	T

E36	cold shock, 8° Celsius	T

E30	nitrate stress, 3,500 ppm	T
E33 (H)	nitrate stress, 6,500 ppm
E34	nitrate stress, 6,500 ppm	T
E37	nitrate stress, 6,500 ppm	P T
E48	nitrate stress, 6,500 ppm	P T

E40	pH stress, pH 10	T
E42	pH stress, pH 5.5	T

E29	oxygen stress, 500 ppm	T
E32 (H)	oxygen stress, 1,000 ppm
E35	oxygen stress, 1,000 ppm	T
E41	oxygen stress, 1,000 ppm	P T
E74	oxygen stress: air; 1,000 ppm	T

E39	salt (KCl) stress, 250 mM	T

E28	salt (NaCl) stress, 250 mM	T
E31	salt (NaCl) stress, 250 mM	P T
E52 (C)	salt (NaCl) stress, 250 mM
E53	salt (NaCl) stress, 250 mM

Off-Pipeline Experiments
(sorted by experiment number and design)

E38	pH stress (pH 4, pH 10)

E43	¹³C labeling study
E46	¹³C labeling study
E61	¹³C labeling study

E44	used for Cr MIC

E49 (C)	strep-tagged mutants: DVU0503, DVU1577, DVU2928, DVU2929
E51	strep-tagged mutants: DVU0503, DVU1577, DVU2928, DVU2929	P
E58	strep-tagged mutant: DVU1577 (run 2)	P
E64	strep-tagged mutant: DVU0503 (run 2)	P
E69	strep-tagged mutant: DVU0811	P
E73	strep-tagged mutants: DVU0503, DVU1397, DVU1568

E50	for metabolomics testing

E54	wt DvH for protein complex study
E59	wt DvH for protein complex study

E56	growth of wt DvH vs. JW707 (fur mutant); regular LS4D	T
E60 (C)	growth of wt DvH vs. JW707 (fur mutant); iron-limited media
E65 (C)	growth of wt DvH vs. JW707 (fur mutant); iron-limited media
E66	growth of wt DvH vs. JW707 (fur mutant); iron-limited media	T

E72	growth of mutant JW905

C - canceled, H - on hold
M - metabolomics, P - proteomics, T - transcriptomics

Index by Quarter 2004-3rd 2004-4th 2005-1st 2005-2nd 2005-3rd 2005-4th

Index by LBNL Exp ID

E28   E29
E30   E31   E32   E33   E34   E35   E36   E37   E38   E39
E40   E41   E42   E43   E44   E45   E46   E47   E48   E49
E50   E51   E52   E53   E54   E55   E56            E58   E59
E60   E61   E62   E63   E64   E65   E66            E68   E69
E71   E72   E73   E74

2004 - 3rd Quarter (approx.) [ top ]
LBNL Exp ID E28	Organism DVH Stressor salt (NaCl) stress 250 mM Culture Method batch	Biomass Production (9/04) Excel file uploaded to Biofiles design details FTIR QA/QC data (AODC,OD,P) *	Transcriptomics (10/04) ORNL microarray data LBNL CC analysis
LBNL Exp ID E29	Organism DVH Stressor oxygen stress 500 ppm Culture Method batch	Biomass Production (9/04) Excel file uploaded to Biofiles design details FTIR QA/QC data (AODC,OD) *	Transcriptomics (10/04) ORNL microarray data LBNL CC analysis
LBNL Exp ID E30	Organism DVH Stressor nitrate stress 3,500 ppm Culture Method batch	Biomass Production (9/04) Excel file uploaded to Biofiles design details QA/QC data (AODC,OD) *	Transcriptomics (10/04) ORNL microarray data LBNL CC analysis
2004 - 4th Quarter (approx.) [ top ]
LBNL Exp ID E31	Organism DVH Stressor salt (NaCl) stress 250 mM Culture Method batch	Biomass Production (10/04) Excel file uploaded to Biofiles design details QA/QC data (AODC,OD,P) *	Transcriptomics (11/04) ORNL microarray data LBNL CC analysis
LBNL Exp ID E31			Proteomics (01/05, 03/05, 05/05) Diversa analysis: summary (Biofiles) Diversa analysis: data package (Biofiles) Diversa analysis: changed proteins (Biofiles) SNL analysis: summary of DIGE/MALDI-MS analysis (Biofiles) UCB data/analysis: ICAT data (Biofiles)
LBNL Exp ID E32	ON HOLD Organism DVH Stressor oxygen stress 1,000 ppm Culture Method batch	Biomass Production (11/04) Excel file uploaded to Biofiles
LBNL Exp ID E33	ON HOLD Organism DVH Stressor nitrate stress 6,500 mg/l Culture Method batch	Biomass Production (11/04) Excel file uploaded to Biofiles
LBNL Exp ID E34	Organism DVH Stressor nitrate stress 6,500 ppm Culture Method batch	Biomass Production (11/04) Excel file uploaded to Biofiles design details FTIR photomicrographs T0C1, T0C3, T0V3, T1C2, T1V1, T2C2, T2V2, T3V1, T4C1, T4V2 QA/QC data (AODC,OD) *	Transcriptomics (01/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E35	Organism DVH Stressor oxygen stress 1,000 ppm Culture Method batch	Biomass Production (12/04) Excel file uploaded to Biofiles design details FTIR photomicrographs T0C1, T0V2, T1C2, T1V2, T2C3, T2V1, T2V3, T3C2, T3V2, T4C2, T4V2, T4V3 QA/QC data (AODC,OD,P) *	Transcriptomics (03/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E36	Organism DVH Stressor cold shock 8° Celsius Culture Method batch	Biomass Production (12/04) Excel file uploaded to Biofiles design details photomicrographs QA/QC data (AODC,OD,P) *	Transcriptomics (02/05) ORNL microarray data LBNL CC analysis
2005 - 1st Quarter (approx.) [ top ]
LBNL Exp ID E37	Organism DVH Stressor nitrate stress 6,500 ppm Culture Method batch	Biomass Production (02/05) Excel file uploaded to Biofiles design details QA/QC data (AODC,OD,P) * photomicrographs T0C1, T0V1, T1C2, T1V2	Transcriptomics (02/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E37			Proteomics (04/05, 09/05) Diversa analysis: summary (Biofiles) Diversa analysis: data package (Biofiles) Diversa analysis: changed proteins (Biofiles) SNL analysis: DIGE data (Biofiles)
LBNL Exp ID E38	Organism DVH Stressor pH stress pH 4, 10 Culture Method batch	Biomass Production (02/05) Excel file uploaded to Biofiles design details QA/QC data (AODC,OD) *	Samples for LBNL research only.
LBNL Exp ID E39	Organism DVH Stressor salt stress 250 mM KCl Culture Method batch	Biomass Production (02/05) Excel file uploaded to Biofiles design details photomicrographs T0C1, T0V2, T1C2, T1V2, T2C3, T2V3, T3C1, T3V1, T4C1, T4V2 QA/QC data (AODC,OD) *	Transcriptomics (05/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E40	Organism DVH Stressor pH stress pH 10 Culture Method batch	Biomass Production (02/05) Excel file uploaded to Biofiles design details FTIR photomicrographs T0C1, T0V1, T1C2, T1V1, T2C3, T2V3, T3C1, T3V2, T4C2, T4V1, T4V2, T4V3 QA/QC data (AODC,OD) *	Transcriptomics (05/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E41	Organism DVH Stressor oxygen stress 1000 ppm Culture Method batch	Biomass Production (03/05) Excel file uploaded to Biofiles design details FTIR QA/QC data (AODC,OD,P) * photomicrographs T0C1, T0C2, T0C3, T0V1, T0V2, T0V3, T1C1, T1C1B, T1C2, T1C3, T1V1, T1V2, T1V3, T1V3B	Transcriptomics (04/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E41			Proteomics (05/05, 06/05, 10/05, 12/05) Diversa analysis: summary (Biofiles) Diversa analysis: data package (Biofiles) Diversa analysis: changed proteins (Biofiles) SNL data: DIGE data (Biofiles) UCB data: zip file UCB analysis: ITRAQ ProGroup Report (Biofiles) UCB analysis: LongSCX ProGroup Report
LBNL Exp ID E42	Organism DVH Stressor pH stress pH 5.5 Culture Method batch	Biomass Production (03/05) Excel file uploaded to Biofiles design details FTIR photomicrographs T0C1, T0V1, T2C3, T2V2, T3C2, T3V1, T4C1 QA/QC data (AODC,OD,P) *	Transcriptomics (05/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E43	Organism DVH Design unstressed DVH; assess amount of lactate needed for ¹³C labeling study Culture Method batch	Biomass Production (03/05) Excel file uploaded to Biofiles
LBNL Exp ID E44	Organism DVH Design unstressed DVH; used for MIC Culture Method batch
LBNL Exp ID E45	CANCELED Organism DVH Stressor chromium stress 0.3 mM Culture Method batch	Biomass Production (03/05) Excel file uploaded to Biofiles
LBNL Exp ID E46	Organism DVH Design unstressed DVH; assess amount of lactate needed for ¹³C labeling study Culture Method batch	Biomass Production (03/05) Excel file uploaded to Biofiles
2005 - 2nd Quarter (approx.) [ top ]
LBNL Exp ID E47	Organism DVH Stressor chromium stress 0.55 mM Culture Method batch	Biomass Production (04/05) Excel file uploaded to Biofiles design details FTIR photomicrographs T0C1, T0V1, T1C1, T1V2, T2C3, T2V3, T3C1, T3V1, T4C2, T4V2 QA/QC data (AODC,OD,P) *	Transcriptomics (07/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E48	Organism DVH Stressor nitrate stress 6,500 ppm Culture Method batch	Biomass Production (05/05) Excel file uploaded to Biofiles design details photomicrographs T0C1, T0V1, T1C2, T1V2, T2C3, T2V3 QA/QC data (AODC,OD,P) *	Transcriptomics (07/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E48			Proteomics (10/05, 12/05) Diversa analysis: data package (Biofiles) Diversa analysis: summary file (Biofiles) Diversa analysis: updated data package (Biofiles) Diversa analysis: updated summary file (Biofiles) Diversa analysis: changed proteins: C0 v. C1 Diversa analysis: changed proteins: C0 v. V1 Diversa analysis: changed proteins: C1 v. V1 Diversa analysis: changed proteins: C1 v. C2 Diversa analysis: changed proteins: V1 v. V2 Diversa analysis: changed proteins: C2 v. V2
2005 - 3rd Quarter (approx.) [ top ]
LBNL Exp ID E49	CANCELED Organism JW907-0503, JW907-1577, JW907-2928, JW907-2929 Design biomass for strep- tagged mutants Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles design details
LBNL Exp ID E50	Organism DVH Design biomass for testing for metabolomics Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles design details
LBNL Exp ID E51	Organism JW907-0503, JW907-1577, JW907-2928, JW907-2929 Design biomass for strep- tagged mutants Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles	Proteomics (09/05) SNL: pull down data DVU0503 (Biofiles) SNL: pull down data DVU1577 (Biofiles) SNL: pull down data DVU2928 (Biofiles) SNL: pull down data DVU2929 (Biofiles) SNL: in-solution trypsin-digest (Biofiles)
LBNL Exp ID E52	CANCELED Organism DVH Stressor salt (NaCl) stress 250 mM Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles design details
LBNL Exp ID E53	Organism DVH Stressor salt (NaCl) stress 250 mM Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles design details	Metabolomics
LBNL Exp ID E54	Organisms DVH Design biomass for proteomics analysis and protein complex identification Culture Method batch	Biomass Production (11/05) Excel file uploaded to Biofiles	Proteomics
LBNL Exp ID E56	Organisms DVH, JW707 Design growth of wt DVH vs. JW 707 (fur mutant); regular LS4D (60 μM) Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles	Transcriptomics (10/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E58	Organism JW907-1577 Design biomass for strep- tagged mutant Culture Method batch	Biomass Production (08/05) Excel file uploaded to Biofiles	Proteomics (10/05) SNL: pull down data DVU1577, run 2 (Biofiles)
LBNL Exp ID E59	Organisms DVH Design biomass for proteomics analysis and protein complex identification Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles	Proteomics
LBNL Exp ID E60	CANCELED Organisms DVH, JW707 Design growth of wt DVH vs. JW 707 (fur mutant); iron limited media Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles
LBNL Exp ID E61	Organism DVH Design unstressed DVH; assess amount of lactate needed for ¹³C labeling study Culture Method batch	Biomass Production (09/05)
LBNL Exp ID E62	CANCELED Organism DVH Stressor chromium stress 0.45 mM Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles
LBNL Exp ID E63	ON HOLD Organism DVH Stressor chromium stress 0.45 mM Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles photomicrographs T0C1, T0V1, T1C2, T1V2, T2C3, T2V3
LBNL Exp ID E64	Organism JW907-0503 Design biomass for strep- tagged mutant Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles	Proteomics (10/05) SNL: pull down data DVU0503, run 2 (Biofiles)
LBNL Exp ID E65	POSTPONED (new design) Organisms DVH, JW707 Design growth of wt DVH vs. JW 707 (fur mutant); iron limited media Culture Method batch	Biomass Production (09/05) Excel file uploaded to Biofiles
2005 - 4th Quarter (approx.) [ top ]
LBNL Exp ID E66	Organisms DVH, JW707 Design growth of wt DVH vs. JW 707 (fur mutant); iron limited media (5 μM) Culture Method batch	Biomass Production (10/05) Excel file uploaded to Biofiles	Transcriptomics (12/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E68	CANCELED Organism DVH Stressor chromium stress 0.45 mM Culture Method batch	Biomass Production (10/05) Excel file uploaded to Biofiles
LBNL Exp ID E69	Organism JW903-0811 Design biomass for strep- tagged mutant Culture Method batch	Biomass Production (??/05)	Proteomics (10/05) SNL: pull down data DVU0811 (Biofiles)
LBNL Exp ID E71	Organisms DVH Stressor chromium stress 0.45 mM Culture Method batch	Biomass Production (11/05) Excel file uploaded to Biofiles photomicrographs T0C1, T0V1, T1C1, T1V2, T2C3, T2V2, T3C1, T3V1, T4C2, T4V2	Transcriptomics (12/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E72	Organism JW905 Design biomass for proteomics analysis and protein complex identification Culture Method batch	Biomass Production (11/05) Excel file uploaded to Biofiles	Proteomics
LBNL Exp ID E73	Organism JW907-0503, JW907-1568, JW913-1397 Design proteomics analysis Culture Method batch	Biomass Production (11/05) Excel file uploaded to Biofiles	Proteomics
LBNL Exp ID E74	Organisms DVH Stressor oxygen stress air; 1,000 ppm oxygen Culture Method batch	Biomass Production (12/05) Excel file uploaded to Biofiles FTIR photomicrographs T0C1, T0VA1, T0VO1, T1C2, T1VA2, T1VO2, T2C1, T2VA1, T2VA1, T2VO1	Transcriptomics (12/05) ORNL microarray data LBNL CC analysis
LBNL Exp ID E74			Proteomics
[ top ]

*	AODC	Acridine orange direct counts
*	^OD	Optical density
*	^P	Protein data

If you have data or analyses to contribute or to be listed in the table, please email the URL to your Web site to Janet Jacobsen at the email address above.

© 2006 The Arkin Lab | For more information about the Arkin Lab, contact Adam Arkin.
Comments/Questions | This site was last revised on January 5, 2006.

Note: the information on this page is no longer being updated.Please visit vimss.lbl.gov/EIDR/ for more current information

VIMSS Experimental Data and Analysis Pipeline/Off-Pipeline Summary

Note: the information on this page is no longer being updated.
Please visit vimss.lbl.gov/EIDR/ for more current information