Table 3

An example of an IDF.

Investigation Title

University of Heidelberg H sapiens TK6

Experimental Designs

genetic_modification_design

time_series_design

Experimental Factors

GeneticModification

Time

Person Last Name

Maier

Fleckenstein

Li

Person First Name

Patrick

Katharina

Li

Person Email

patrick.maier@radonk.ma.uni-heidelberg.de

Person Phone

+496213833773

Person Address

Theodor-Kutzer-Ufer 1–3

Person Affiliation

Department of Radiation Oncology, University of Heidelberg

Person Roles

submitter; investigator

investigator

investigator

Quality Control Types

biological_replicate

Replicate Types

biological_replicate

Date of Experiment

2005-02-28

Public Release Date

2006-01-03

PubMed ID

12345678

Publication Author List

Patrick Maier; Katharina Fleckenstein; Li Li; Stephanie Laufs; Jens Zeller; Stefan Fruehauf; Carsten Herskind; Frederik Wenz

Publication Status

submitted

Experiment Description

Gene expression of TK6 cells transduced with an oncoretrovirus expressing MDR1 (TK6MDR1) was compared to untransduced TK6 cells and to TK6 cell transduced with an oncoretrovirus expressing the Neomycin resistance gene (TK6neo). Two biological replicates of each were generated and the expression profiles were determined using Affymetrix Human Genome U133 Plus2.0 GeneChip microarrays. Comparisons between the sample groups allow the identification of genes with expression dependent on the MDR1 overexpression.

Protocol Name

GROWTHPRTCL10653

EXTPRTCL10654

TRANPRTCL10656

Protocol Type

grow

nucleic_acid_extraction

bioassay_data_transformation

Protocol Description

TK6 cells were grown in suspension cultures in RPMI 1640 medium supplemented with 10% horse serum (Invitrogen, Karlsruhe, Germany). The cells were routinely maintained at 37 C and 5% CO2.

Approximately 10 cells were lysed in RLT buffer (Qiagen).Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

Mixed Model Normalization with SAS Micro Array Solutions (version 1.3).

Protocol Parameters

media

Extracted Product; Amplification

SDRF Files

e-mexp-428_tab.txt

Database

CTO

MO

nci_meta

Database URI

http://obo.sourceforge.net/cgi-bin/detail.cgi?cell webcite

http://mged.sourceforge.net/ontologies/MGEDontology.php webcite

http://ncimeta.nci.nih.gov/indexMetaphrase.html webcite

Database Version

1.3.0.1


The first column represents the qualifier name, while their values are given starting from column 2 (if the qualifier has two or more values, each is given in a separate column).

Rayner et al. BMC Bioinformatics 2006 7:489   doi:10.1186/1471-2105-7-489

Open Data