description: Gene expression data from a volunteer V54 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V54, challenged without vaccine


status: Public on Sep 30 2009

type: RNA

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

country: USA

institute: Walter Reed Army Institute of Research

description: Gene expression data from a volunteer V53 ;it belongs to InfectivityControl group

hyb_protocol: Follow Affymetrix's protocol

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: CEL files were normalized using RMA method. This dataset was further normalized with a dataset from Plus2.0 Genechip using quantiles normalization method available in the affy package of bioconductor. Probesets that are absent in all samples are eliminated in the later stage of analysis

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: A PBMC sample from volunteer V53, challenged without vaccine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PBMC samples are collected at various time points during a malaria vaccine trial

tag: group

value: InfectivityControl

tag: cell type

value: PBMC


description: Gene expression data from a volunteer V55 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V55, challenged without vaccine


description: Gene expression data from a volunteer V51 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V51, challenged without vaccine


title: volunteer V45 at time point T1

description: Gene expression data from a volunteer V45 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V45 at time point T1

value: Delay


title: volunteer V46 at time point T1

description: Gene expression data from a volunteer V46 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V46 at time point T1


description: Gene expression data from a volunteer V58 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V58, challenged without vaccine


title: volunteer V46 at time point T0

description: Gene expression data from a volunteer V46 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V46 at time point T0


title: wildtype_1 versus common reference

status: Public on Oct 01 2009

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: Material is derived from a population of neuroblast and GMC cells

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/).

data_processing: Spot finding and quantitation via the Dapple package. Normalization was done using variance stabilising normalization (VSN).

organism: Drosophila melanogaster

label_protocol: Klenow Labelling: Random primers are annealed to denatured DNA templates and extended by Klenow fragment using the Bioprime DNA Labeling System (Invitrogen) while fluorescent dyes Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated. (http://www.flychip.org.uk/protocols/gene_expression/)

growth_protocol: Embryos developed at 25oC

extract_protocol: 50-100 cells were lysed, RNA was reverse transcribed, cDNA tailed using terminal transferase and amplified using PCR

tag: strain

tag: tissue

value: ventral nerve cord

tag: developmental stage

value: embryo stage 11

source_name: TDSCR

extract_protocol: RNA from ~30 embryos was extracted using Trizol, RNA was reverse transcribed, cDNA tailed using terminal transferase and amplified using PCR

value: whole embryo

value: embryo stage 10-12

tag: sample type

value: reference


description: Gene expression data from a volunteer V50 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V50, challenged without vaccine


title: volunteer V45 at time point T0

description: Gene expression data from a volunteer V45 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V45 at time point T0


description: Gene expression data from a volunteer V57 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V57, challenged without vaccine


title: volunteer V45 at time point T3

description: Gene expression data from a volunteer V45 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V45 at time point T3


description: Gene expression data from a volunteer V52 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V52, challenged without vaccine


description: Gene expression data from a volunteer V47 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V47, challenged without vaccine


description: Gene expression data from a volunteer V49 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V49, challenged without vaccine


description: Gene expression data from a volunteer V48 ;it belongs to InfectivityControl group

source_name: A PBMC sample from volunteer V48, challenged without vaccine


title: wildtype_3 versus common reference


title: volunteer V46 at time point T4

description: Gene expression data from a volunteer V46 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V46 at time point T4


title: volunteer V45 at time point T4

description: Gene expression data from a volunteer V45 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V45 at time point T4


title: HaloCHIP CREB (no Forskolin) biological rep 1

type: genomic

city: Madison

first: Danette

last: Hartzell

state: WI

address: 2800 Woods Hollow Road

institute: Promega

description: no additional information

hyb_protocol: Standard Nimblegen protocol

scan_protocol: Standard Nimblegen protocol

data_processing: The raw data from the arrays were analyzed as follows: the log2 ratio (enriched-cy5/total input-cy3) was calculated for each probe and data were then smoothed by averaging across a sliding window of 3 neighbouring probes shifting 1 probe at a time, minimizing noise from single probes. The median and standard deviation were calculated from the smoothed ratios for each sample. The median was subtracted from each ratio and divided by the standard deviation to center and normalize the data from each array.  To summarize the enrichment for an entire promoter, the top 4 probe values were averaged for a given promoter region to approximate the 75th  percentile value.  The raw data, normalized data, and collapsed data for each array are available as supplemental at the following site: www.switchgeargenomics.com/creb_supp_data/.

molecule: genomic DNA

source_name: Hela Cells transfected with the HaloTag-CREB fusion constructs

label_protocol: Standard Nimblegen protocol

growth_protocol: HeLa cells (2-4 x 105) were plated in a single well of a standard 6-well plate. After reaching 70-80% confluency, typically 18-24 hours later, cells were transfected with the HaloTag-CREB fusion constructs.

extract_protocol: ChIP assays were performed as described in http://www.usbweb.com/proto/78460a.pdf. HaloCHIP experiments were performed as described in  http://www.promega.com/tbs/tm075/tm075.pdf.

treatment_protocol: Cells were crosslinked with 0.75% formaldehyde for 10min at 22C.

tag: cell line

value: HeLa cells

tag: genome/variation

value: HaloTag-CREB fusion construct

source_name: Hela Cells


title: volunteer V45 at time point T2

description: Gene expression data from a volunteer V45 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V45 at time point T2


title: volunteer V44 at time point T4

description: Gene expression data from a volunteer V44 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V44 at time point T4


title: volunteer V44 at time point T1

description: Gene expression data from a volunteer V44 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V44 at time point T1


title: volunteer V44 at time point T3

description: Gene expression data from a volunteer V44 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V44 at time point T3


title: volunteer V44 at time point T0

description: Gene expression data from a volunteer V44 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V44 at time point T0


title: volunteer V43 at time point T1

description: Gene expression data from a volunteer V43 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V43 at time point T1

value: NonProtected


title: volunteer V43 at time point T0

description: Gene expression data from a volunteer V43 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V43 at time point T0


title: volunteer V43 at time point T3

description: Gene expression data from a volunteer V43 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V43 at time point T3


title: volunteer V42 at time point T1

description: Gene expression data from a volunteer V42 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V42 at time point T1


title: volunteer V42 at time point T4

description: Gene expression data from a volunteer V42 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V42 at time point T4


title: volunteer V43 at time point T2

description: Gene expression data from a volunteer V43 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V43 at time point T2


title: volunteer V42 at time point T2

description: Gene expression data from a volunteer V42 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V42 at time point T2


title: volunteer V40 at time point T1

description: Gene expression data from a volunteer V40 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V40 at time point T1

value: Unknown


title: volunteer V41 at time point T2

description: Gene expression data from a volunteer V41 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V41 at time point T2

value: Protected


title: volunteer V41 at time point T3

description: Gene expression data from a volunteer V41 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V41 at time point T3


title: volunteer V44 at time point T2

description: Gene expression data from a volunteer V44 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V44 at time point T2


title: volunteer V41 at time point T1

description: Gene expression data from a volunteer V41 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V41 at time point T1


title: volunteer V40 at time point T2

description: Gene expression data from a volunteer V40 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V40 at time point T2


title: volunteer V43 at time point T4

description: Gene expression data from a volunteer V43 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V43 at time point T4


title: volunteer V41 at time point T4

description: Gene expression data from a volunteer V41 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V41 at time point T4


title: volunteer V40 at time point T3

description: Gene expression data from a volunteer V40 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V40 at time point T3


title: volunteer V42 at time point T0

description: Gene expression data from a volunteer V42 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V42 at time point T0


title: volunteer V41 at time point T0

description: Gene expression data from a volunteer V41 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V41 at time point T0


title: volunteer V39 at time point T1

description: Gene expression data from a volunteer V39 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V39 at time point T1


title: volunteer V39 at time point T2

description: Gene expression data from a volunteer V39 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V39 at time point T2


title: volunteer V42 at time point T3

description: Gene expression data from a volunteer V42 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V42 at time point T3


title: volunteer V39 at time point T0

description: Gene expression data from a volunteer V39 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V39 at time point T0


title: volunteer V39 at time point T3

description: Gene expression data from a volunteer V39 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V39 at time point T3


title: volunteer V39 at time point T4

description: Gene expression data from a volunteer V39 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V39 at time point T4


title: volunteer V38 at time point T0

description: Gene expression data from a volunteer V38 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V38 at time point T0


title: volunteer V38 at time point T1

description: Gene expression data from a volunteer V38 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V38 at time point T1


title: volunteer V38 at time point T4

description: Gene expression data from a volunteer V38 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V38 at time point T4


title: volunteer V37 at time point T3

description: Gene expression data from a volunteer V37 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V37 at time point T3


title: volunteer V37 at time point T2

description: Gene expression data from a volunteer V37 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V37 at time point T2


title: volunteer V36 at time point T3

description: Gene expression data from a volunteer V36 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V36 at time point T3


title: volunteer V35 at time point T3

description: Gene expression data from a volunteer V35 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V35 at time point T3


title: volunteer V35 at time point T1

description: Gene expression data from a volunteer V35 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V35 at time point T1


title: volunteer V36 at time point T1

description: Gene expression data from a volunteer V36 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V36 at time point T1


title: volunteer V36 at time point T2

description: Gene expression data from a volunteer V36 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V36 at time point T2


title: volunteer V36 at time point T0

description: Gene expression data from a volunteer V36 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V36 at time point T0


title: volunteer V34 at time point T3

description: Gene expression data from a volunteer V34 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V34 at time point T3


title: volunteer V34 at time point T2

description: Gene expression data from a volunteer V34 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V34 at time point T2


title: volunteer V37 at time point T1

description: Gene expression data from a volunteer V37 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V37 at time point T1


title: volunteer V35 at time point T2

description: Gene expression data from a volunteer V35 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V35 at time point T2


title: volunteer V36 at time point T4

description: Gene expression data from a volunteer V36 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V36 at time point T4


title: volunteer V34 at time point T0

description: Gene expression data from a volunteer V34 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V34 at time point T0


title: volunteer V34 at time point T1

description: Gene expression data from a volunteer V34 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V34 at time point T1


title: volunteer V34 at time point T4

description: Gene expression data from a volunteer V34 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V34 at time point T4


title: volunteer V38 at time point T2

description: Gene expression data from a volunteer V38 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V38 at time point T2


title: volunteer V33 at time point T2

description: Gene expression data from a volunteer V33 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V33 at time point T2


title: volunteer V33 at time point T4

description: Gene expression data from a volunteer V33 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V33 at time point T4


title: volunteer V32 at time point T3

description: Gene expression data from a volunteer V32 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V32 at time point T3


title: volunteer V33 at time point T1

description: Gene expression data from a volunteer V33 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V33 at time point T1


title: volunteer V33 at time point T3

description: Gene expression data from a volunteer V33 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V33 at time point T3


title: volunteer V32 at time point T1

description: Gene expression data from a volunteer V32 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V32 at time point T1


title: volunteer V31 at time point T3

description: Gene expression data from a volunteer V31 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V31 at time point T3


title: volunteer V32 at time point T2

description: Gene expression data from a volunteer V32 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V32 at time point T2


title: volunteer V31 at time point T0

description: Gene expression data from a volunteer V31 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V31 at time point T0


title: volunteer V38 at time point T3

description: Gene expression data from a volunteer V38 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V38 at time point T3


title: volunteer V31 at time point T4

description: Gene expression data from a volunteer V31 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V31 at time point T4


title: volunteer V31 at time point T2

description: Gene expression data from a volunteer V31 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V31 at time point T2


title: volunteer V31 at time point T1

description: Gene expression data from a volunteer V31 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V31 at time point T1


title: volunteer V30 at time point T4

description: Gene expression data from a volunteer V30 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V30 at time point T4


title: volunteer V28 at time point T3

description: Gene expression data from a volunteer V28 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V28 at time point T3


title: volunteer V30 at time point T2

description: Gene expression data from a volunteer V30 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V30 at time point T2


title: volunteer V29 at time point T0

description: Gene expression data from a volunteer V29 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V29 at time point T0


title: volunteer V30 at time point T3

description: Gene expression data from a volunteer V30 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V30 at time point T3


title: volunteer V29 at time point T1

description: Gene expression data from a volunteer V29 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V29 at time point T1


title: volunteer V29 at time point T4

description: Gene expression data from a volunteer V29 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V29 at time point T4


title: volunteer V30 at time point T1

description: Gene expression data from a volunteer V30 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V30 at time point T1


title: volunteer V27 at time point T0

description: Gene expression data from a volunteer V27 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V27 at time point T0


title: volunteer V28 at time point T1

description: Gene expression data from a volunteer V28 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V28 at time point T1


title: volunteer V27 at time point T2

description: Gene expression data from a volunteer V27 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V27 at time point T2


title: volunteer V28 at time point T0

description: Gene expression data from a volunteer V28 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V28 at time point T0


title: volunteer V27 at time point T3

description: Gene expression data from a volunteer V27 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V27 at time point T3


title: volunteer V27 at time point T1

description: Gene expression data from a volunteer V27 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V27 at time point T1


title: volunteer V29 at time point T2

description: Gene expression data from a volunteer V29 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V29 at time point T2


title: volunteer V30 at time point T0

description: Gene expression data from a volunteer V30 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V30 at time point T0


title: volunteer V28 at time point T2

description: Gene expression data from a volunteer V28 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V28 at time point T2


title: volunteer V28 at time point T4

description: Gene expression data from a volunteer V28 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V28 at time point T4


title: volunteer V26 at time point T0

description: Gene expression data from a volunteer V26 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V26 at time point T0


title: volunteer V29 at time point T3

description: Gene expression data from a volunteer V29 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V29 at time point T3


title: volunteer V27 at time point T4

description: Gene expression data from a volunteer V27 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V27 at time point T4


title: volunteer V26 at time point T1

description: Gene expression data from a volunteer V26 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V26 at time point T1


title: volunteer V26 at time point T4

description: Gene expression data from a volunteer V26 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V26 at time point T4


title: volunteer V26 at time point T3

description: Gene expression data from a volunteer V26 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V26 at time point T3


title: volunteer V26 at time point T2

description: Gene expression data from a volunteer V26 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V26 at time point T2


title: volunteer V25 at time point T2

description: Gene expression data from a volunteer V25 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V25 at time point T2


title: volunteer V24 at time point T4

description: Gene expression data from a volunteer V24 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V24 at time point T4


title: volunteer V24 at time point T0

description: Gene expression data from a volunteer V24 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V24 at time point T0


title: volunteer V25 at time point T1

description: Gene expression data from a volunteer V25 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V25 at time point T1


title: volunteer V25 at time point T4

description: Gene expression data from a volunteer V25 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V25 at time point T4


title: volunteer V24 at time point T3

description: Gene expression data from a volunteer V24 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V24 at time point T3


title: volunteer V25 at time point T3

description: Gene expression data from a volunteer V25 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V25 at time point T3


title: volunteer V20 at time point T3

description: Gene expression data from a volunteer V20 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V20 at time point T3


title: volunteer V23 at time point T4

description: Gene expression data from a volunteer V23 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V23 at time point T4


title: volunteer V20 at time point T1

description: Gene expression data from a volunteer V20 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V20 at time point T1


title: volunteer V22 at time point T2

description: Gene expression data from a volunteer V22 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V22 at time point T2


title: volunteer V23 at time point T3

description: Gene expression data from a volunteer V23 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V23 at time point T3


title: volunteer V22 at time point T4

description: Gene expression data from a volunteer V22 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V22 at time point T4


title: volunteer V24 at time point T1

description: Gene expression data from a volunteer V24 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V24 at time point T1


title: volunteer V23 at time point T1

description: Gene expression data from a volunteer V23 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V23 at time point T1


title: volunteer V20 at time point T2

description: Gene expression data from a volunteer V20 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V20 at time point T2


title: volunteer V22 at time point T0

description: Gene expression data from a volunteer V22 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V22 at time point T0


title: volunteer V24 at time point T2

description: Gene expression data from a volunteer V24 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V24 at time point T2


title: volunteer V23 at time point T0

description: Gene expression data from a volunteer V23 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V23 at time point T0


title: volunteer V22 at time point T1

description: Gene expression data from a volunteer V22 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V22 at time point T1


title: volunteer V19 at time point T1

description: Gene expression data from a volunteer V19 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V19 at time point T1


title: volunteer V25 at time point T0

description: Gene expression data from a volunteer V25 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V25 at time point T0


title: volunteer V19 at time point T2

description: Gene expression data from a volunteer V19 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V19 at time point T2


title: volunteer V19 at time point T3

description: Gene expression data from a volunteer V19 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V19 at time point T3


title: volunteer V19 at time point T0

description: Gene expression data from a volunteer V19 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V19 at time point T0


title: volunteer V17 at time point T3

description: Gene expression data from a volunteer V17 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V17 at time point T3


title: volunteer V17 at time point T1

description: Gene expression data from a volunteer V17 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V17 at time point T1


title: volunteer V18 at time point T0

description: Gene expression data from a volunteer V18 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V18 at time point T0


title: volunteer V18 at time point T4

description: Gene expression data from a volunteer V18 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V18 at time point T4


title: volunteer V19 at time point T4

description: Gene expression data from a volunteer V19 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V19 at time point T4


title: volunteer V16 at time point T4

description: Gene expression data from a volunteer V16 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V16 at time point T4


title: volunteer V18 at time point T2

description: Gene expression data from a volunteer V18 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V18 at time point T2


title: volunteer V16 at time point T3

description: Gene expression data from a volunteer V16 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V16 at time point T3


title: volunteer V17 at time point T0

description: Gene expression data from a volunteer V17 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V17 at time point T0


title: volunteer V17 at time point T4

description: Gene expression data from a volunteer V17 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V17 at time point T4


title: volunteer V18 at time point T3

description: Gene expression data from a volunteer V18 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V18 at time point T3


title: volunteer V16 at time point T1

description: Gene expression data from a volunteer V16 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V16 at time point T1


title: volunteer V16 at time point T2

description: Gene expression data from a volunteer V16 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V16 at time point T2


title: volunteer V18 at time point T1

description: Gene expression data from a volunteer V18 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V18 at time point T1


title: volunteer V15 at time point T1

description: Gene expression data from a volunteer V15 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V15 at time point T1


title: volunteer V15 at time point T0

description: Gene expression data from a volunteer V15 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V15 at time point T0


title: volunteer V15 at time point T4

description: Gene expression data from a volunteer V15 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V15 at time point T4


title: volunteer V22 at time point T3

description: Gene expression data from a volunteer V22 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V22 at time point T3


title: volunteer V15 at time point T3

description: Gene expression data from a volunteer V15 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V15 at time point T3


title: volunteer V14 at time point T1

description: Gene expression data from a volunteer V14 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V14 at time point T1


title: volunteer V16 at time point T0

description: Gene expression data from a volunteer V16 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V16 at time point T0


title: volunteer V15 at time point T2

description: Gene expression data from a volunteer V15 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V15 at time point T2


title: volunteer V14 at time point T4

description: Gene expression data from a volunteer V14 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V14 at time point T4


title: volunteer V14 at time point T0

description: Gene expression data from a volunteer V14 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V14 at time point T0


title: volunteer V14 at time point T2

description: Gene expression data from a volunteer V14 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V14 at time point T2


title: volunteer V13 at time point T1

description: Gene expression data from a volunteer V13 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V13 at time point T1


title: volunteer V12 at time point T4

description: Gene expression data from a volunteer V12 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V12 at time point T4


title: volunteer V13 at time point T4

description: Gene expression data from a volunteer V13 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V13 at time point T4


title: volunteer V11 at time point T3

description: Gene expression data from a volunteer V11 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V11 at time point T3


title: volunteer V12 at time point T0

description: Gene expression data from a volunteer V12 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V12 at time point T0


title: volunteer V12 at time point T2

description: Gene expression data from a volunteer V12 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V12 at time point T2


title: volunteer V12 at time point T3

description: Gene expression data from a volunteer V12 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V12 at time point T3


title: volunteer V10 at time point T4

description: Gene expression data from a volunteer V10 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V10 at time point T4


title: volunteer V13 at time point T2

description: Gene expression data from a volunteer V13 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V13 at time point T2


title: volunteer V09 at time point T2

description: Gene expression data from a volunteer V09 at time point: 24 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V09 at time point T2


title: volunteer V09 at time point T1

description: Gene expression data from a volunteer V09 at time point: the day of the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V09 at time point T1


title: volunteer V11 at time point T1

description: Gene expression data from a volunteer V11 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V11 at time point T1


title: volunteer V12 at time point T1

description: Gene expression data from a volunteer V12 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V12 at time point T1


title: volunteer V09 at time point T4

description: Gene expression data from a volunteer V09 at time point: two weeks post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V09 at time point T4


title: volunteer V10 at time point T2

description: Gene expression data from a volunteer V10 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V10 at time point T2


title: volunteer V09 at time point T0

description: Gene expression data from a volunteer V09 at time point: Baseline;it belongs to Delay group

source_name: A PBMC sample from volunteer V09 at time point T0


title: volunteer V09 at time point T3

description: Gene expression data from a volunteer V09 at time point: 72 hours post the third vaccination;it belongs to Delay group

source_name: A PBMC sample from volunteer V09 at time point T3


title: volunteer V11 at time point T2

description: Gene expression data from a volunteer V11 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V11 at time point T2


title: volunteer V10 at time point T0

description: Gene expression data from a volunteer V10 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V10 at time point T0


title: volunteer V08 at time point T1

description: Gene expression data from a volunteer V08 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V08 at time point T1


title: volunteer V08 at time point T2

description: Gene expression data from a volunteer V08 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V08 at time point T2


title: volunteer V07 at time point T3

description: Gene expression data from a volunteer V07 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V07 at time point T3


title: volunteer V07 at time point T4

description: Gene expression data from a volunteer V07 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V07 at time point T4


title: volunteer V07 at time point T1

description: Gene expression data from a volunteer V07 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V07 at time point T1


title: volunteer V13 at time point T3

description: Gene expression data from a volunteer V13 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V13 at time point T3


title: volunteer V23 at time point T2

description: Gene expression data from a volunteer V23 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V23 at time point T2


title: volunteer V06 at time point T3

description: Gene expression data from a volunteer V06 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V06 at time point T3


title: volunteer V07 at time point T0

description: Gene expression data from a volunteer V07 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V07 at time point T0


title: volunteer V06 at time point T1

description: Gene expression data from a volunteer V06 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V06 at time point T1


title: volunteer V05 at time point T4

description: Gene expression data from a volunteer V05 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V05 at time point T4


title: volunteer V07 at time point T2

description: Gene expression data from a volunteer V07 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V07 at time point T2


title: volunteer V04 at time point T2

description: Gene expression data from a volunteer V04 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V04 at time point T2


title: volunteer V06 at time point T4

description: Gene expression data from a volunteer V06 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V06 at time point T4


title: volunteer V04 at time point T4

description: Gene expression data from a volunteer V04 at time point: two weeks post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V04 at time point T4


title: volunteer V06 at time point T2

description: Gene expression data from a volunteer V06 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V06 at time point T2


title: volunteer V06 at time point T0

description: Gene expression data from a volunteer V06 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V06 at time point T0


title: volunteer V04 at time point T3

description: Gene expression data from a volunteer V04 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V04 at time point T3


title: volunteer V05 at time point T2

description: Gene expression data from a volunteer V05 at time point: 24 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V05 at time point T2


title: volunteer V05 at time point T1

description: Gene expression data from a volunteer V05 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V05 at time point T1


title: volunteer V04 at time point T0

description: Gene expression data from a volunteer V04 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V04 at time point T0


title: volunteer V05 at time point T3

description: Gene expression data from a volunteer V05 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V05 at time point T3


title: volunteer V08 at time point T3

description: Gene expression data from a volunteer V08 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V08 at time point T3


title: volunteer V03 at time point T3

description: Gene expression data from a volunteer V03 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V03 at time point T3


title: volunteer V04 at time point T1

description: Gene expression data from a volunteer V04 at time point: the day of the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V04 at time point T1


title: volunteer V03 at time point T1

description: Gene expression data from a volunteer V03 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V03 at time point T1


title: volunteer V03 at time point T4

description: Gene expression data from a volunteer V03 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V03 at time point T4


title: volunteer V14 at time point T3

description: Gene expression data from a volunteer V14 at time point: 72 hours post the third vaccination;it belongs to Protected group

source_name: A PBMC sample from volunteer V14 at time point T3


title: volunteer V13 at time point T0

description: Gene expression data from a volunteer V13 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V13 at time point T0


title: volunteer V03 at time point T0

description: Gene expression data from a volunteer V03 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V03 at time point T0


title: volunteer V02 at time point T2

description: Gene expression data from a volunteer V02 at time point: 24 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V02 at time point T2


title: volunteer V01 at time point T0

description: Gene expression data from a volunteer V01 at time point: Baseline;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V01 at time point T0


title: volunteer V02 at time point T1

description: Gene expression data from a volunteer V02 at time point: the day of the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V02 at time point T1


title: volunteer V01 at time point T4

description: Gene expression data from a volunteer V01 at time point: two weeks post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V01 at time point T4


title: volunteer V01 at time point T2

description: Gene expression data from a volunteer V01 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V01 at time point T2


title: volunteer V01 at time point T1

description: Gene expression data from a volunteer V01 at time point: the day of the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V01 at time point T1


title: volunteer V01 at time point T3

description: Gene expression data from a volunteer V01 at time point: 72 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V01 at time point T3


title: volunteer V02 at time point T3

description: Gene expression data from a volunteer V02 at time point: 72 hours post the third vaccination;it belongs to Unknown group

source_name: A PBMC sample from volunteer V02 at time point T3


title: Bc14579 pH5.5 Hl t30_t0

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

country: Netherlands

institute: Wageningen University

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated lactic acid (Hl) for 30 min

value: Bc ATCC 14579

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated lactic acid (Hl) for 0 min


title: Bc14579 pH5.5 Hl t0_t60

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated lactic acid (Hl) for 60 min


title: Bc14579 pH5.5 Hl t0_t30

description: No extra description.


title: Bc14579 pH5.5 Hl t10_t0

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated lactic acid (Hl) for 10 min


title: Bc14579 pH5.5 Hl t60_t0

description: No extra description.


title: Bc14579 pH5.5 Hl t0_t10

description: No extra description.


title: Bc14579 pH5.5 HCl t10_t0

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 (HCl) for 10 min

treatment_protocol: OD600 0.5 exposed to pH5.5 (HCl) for 0 min


title: Bc14579 pH5.5 HCl t60_t0

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 (HCl) for 60 min


title: Bc14579 pH5.5 HCl t30_t0

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 (HCl) for 30 min


title: Bc14579 pH5.5 HCl t0_t10

description: No extra description.


title: Bc14579 pH5.5 HAc/HCl t0_t60

description: No extra description.

source_name: Bc14579 pH5.5 HAc/HCl t0

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated acetic acid (HAc/HCl) for 0 min

source_name: Bc14579 pH5.5 HAc/HCl t60

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated acetic acid (HAc/HCl) for 60 min


title: Bc14579 pH5.5 HCl t0_t60

description: No extra description.


title: Bc14579 pH5.5 HAc/HCl t60_t0

description: No extra description.


title: Bc14579 pH5.5 HAc/HCl t30_t0

description: No extra description.

source_name: Bc14579 pH5.5 HAc/HCl t30

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated acetic acid (HAc/HCl) for 30 min


title: Bc14579 pH5.5 HAc/HCl t0_t30

description: No extra description.


title: Bc14579 pH5.5 HAc t0_t60

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 15 mM undissociated acetic acid (HAc) for 0 min

treatment_protocol: OD600 0.5 exposed to pH5.5 15 mM undissociated acetic acid (HAc) for 60 min


title: Bc14579 pH5.5 HAc t0_t30

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 15 mM undissociated acetic acid (HAc) for 30 min


title: Bc14579 pH5.5 HAc/HCl t0_t10

description: No extra description.

source_name: Bc14579 pH5.5 HAc/HCl t10

treatment_protocol: OD600 0.5 exposed to pH5.5 2 mM undissociated acetic acid (HAc/HCl) for 10 min


title: 1m-30(2)

city: bunkyo-ku

first: Kenji

last: Saito

department: Department of Applied Biological Chemistry

country: Japan

institute: The Univeristy of Tokyo

description: rats fed reduced amount of diet

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Expression Array 230A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: rat liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Wistar

tag: gender

value: male

value: 9 weeks

tag: dietary restriction

value: 30% reduction


title: Bc14579 pH5.5 HAc t60_t0

description: No extra description.


title: 1m-30(1)

description: rats fed reduced amount of diet


title: Bc14579 pH5.5 HAc t10_t0

description: No extra description.

treatment_protocol: OD600 0.5 exposed to pH5.5 15 mM undissociated acetic acid (HAc) for 10 min


title: Bc14579 pH5.5 HAc/HCl t10_t0

description: No extra description.


title: Bc14579 pH5.5 HAc t30_t0

description: No extra description.


title: 1m-20(2)

description: rats fed reduced amount of diet

value: 20% reduction


title: volunteer V05 at time point T0

description: Gene expression data from a volunteer V05 at time point: Baseline;it belongs to Protected group

source_name: A PBMC sample from volunteer V05 at time point T0

treatment_protocol: PBMC samples are collected at various time points during a malaria vaccine trial

value: PBMC


title: 1m-20(1)

description: rats fed reduced amount of diet


title: Bc14579 pH5.5 HAc t0_t10

description: No extra description.


title: 1m-10(1)

description: rats fed reduced amount of diet

value: 10% reduction


title: German Shorthaired Pointer

city: Vancouver

first: Bradley

middle: P

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

description: CNV Profile of Pedigree German Shorthaired Pointer

hyb_protocol: Hybridization was performed by NimbleGen using standard protocols

scan_protocol: Scanning was performed by NimbleGen using standard protocols

data_processing: Data processing was performed by NimbleGen using standard protocols

organism: Canis lupus familiaris

source_name: Pedigree German Shorthaired Pointer

label_protocol: Labeling was performed by NimbleGen using standard protocols

extract_protocol: DNA was extracted from Blood samples using standard molecular biology protocols

tag: pedigree

value: German Shorthaired Pointer

value: blood

source_name: Pedigree Boxer Reference

value: Boxer


title: 1m-10(2)

description: rats fed reduced amount of diet


title: 1m-5(2)

description: rats fed reduced amount of diet

value: 5% reduction


title: 1m-C(2)

description: rats fed reduced amount of diet


title: 1w-20(1)

description: rats fed reduced amount of diet

value: 6 weeks


title: 1w-5(2)

description: rats fed reduced amount of diet


title: 1m-5(1)

description: rats fed reduced amount of diet


title: 1w-10(1)

description: rats fed reduced amount of diet


title: Basset Hound

description: CNV Profile of Pedigree Basset Hound

source_name: Pedigree Basset Hound

value: Basset Hound


title: 1w-20(2)

description: rats fed reduced amount of diet


title: Akita 1

description: CNV Profile of Pedigree Akita 1

source_name: Pedigree Akita 1

value: Akita 1


title: Rottweiler

description: CNV Profile of Pedigree Rottweiller

source_name: Pedigree Rottweiller

value: Rottweiller


title: OSW Dog T-Cell Lymphoma Cell Line from an Airedale Terrier

description: CGH Profile of Airedale Terrier OSW Dog Lymphoma Cell Line

source_name: OSW Dog T Cell Lymphoma Cell Line

value: Airedale Terrier

value: OSW T cell lymphoma


title: Bulldog

description: CNV Profile of Pedigree Bulldog

source_name: Pedigree Bulldog

value: Bulldog


title: Collie

description: CNV Profile of Pedigree Collie

source_name: Pedigree Collie

value: Collie


title: Boxer

description: CNV Profile of Pedigree Boxer

source_name: Pedigree Boxer


title: 1m-C(1)

description: rats fed reduced amount of diet

value: Wistar

value: male

value: 9 weeks


title: 1w-5(1)

description: rats fed reduced amount of diet


title: 1w-C(2)

description: rats fed reduced amount of diet


title: 1w-10(2)

description: rats fed reduced amount of diet


title: 1w-30(1)

description: rats fed reduced amount of diet

value: 30% reduction


title: Stressed seed_Rep2

city: Cedar Falls

first: Tilahun

last: Abebe

state: IA

address: 191 McCollum Hall

department: Biology

institute: University of Northern Iowa

description: Gene expression data from drought-stressed seed

hyb_protocol: The labeled cRNA was purified and fragmented. Then, hybridization controls were added to the resulting cRNA and hybridized to the Barley1 GeneChips for 16 h at 45°C. Arrays were washed using the GeneChip® Fluidics Station 450.

scan_protocol: GenChips were scanned using the GeneChip® 3000 Scanner.

data_processing: Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction, normalization and summarization using the Microarray Analysis Suite v 5.0 (MAS5) algorithm. Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. Summarised values were normalized using global scaling. The mean signal of each array was scaled to 500

label: Biotin

organism: Hordeum vulgare

source_name: Drought-stressed barley plants

label_protocol: Biotinylated cRNA was prepared from total RNA according to the the Affymetrix One-Cycle Target Labeling protocol.

growth_protocol: Barley plants (Hordeum vulgare L. cv. Morex) were grown in a controlled environment chamber at 22°C/18°C day/night temperatures, 60% RH and a 16 h photoperiod. Plants were grown in 20 cm x 25 cm pots and fertilized using Osmocote® slow release fertilizer.

extract_protocol: RNA from the lemma, palea and awn was extracted with guanidinium thiocyanate (Chirgwin et al. 1979). Total RNA from the seed was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH), followed by precipitation of starch with 0.8 M sodium citrate and 1.2 M NaCl according to the manufacturer’s recommendation.

treatment_protocol: Drought stress was initiated at Zadok stage 71 (kernel watery-ripe; Zadoks et al., 1974) by withholding water for 4 days. Non-stressed (control) plants received 500 ml water every day.

tag: organ

value: Seed

tag: treatment

value: Stressed


title: Stressed awn_Rep2

description: Gene expression data from drought-stressed awn

value: Awn


title: volunteer V03 at time point T2

description: Gene expression data from a volunteer V03 at time point: 24 hours post the third vaccination;it belongs to NonProtected group

source_name: A PBMC sample from volunteer V03 at time point T2

value: NonProtected

value: PBMC


title: Stressed seed_Rep3


title: Stressed awn_Rep1


title: Stressed seed_Rep1


title: Control seed_Rep1

description: Gene expression data from well-watered seed

source_name: Well-watered barley plants

value: Control


title: 1w-C(1)

description: rats fed reduced amount of diet

value: 6 weeks


title: Stressed awn_Rep3


title: 1w-30(2)

description: rats fed reduced amount of diet


title: Control seed_Rep3


title: Control awn_Rep1

description: Gene expression data from well-watered awn


title: Control awn_Rep3


title: Stressed palea_Rep2

description: Gene expression data from drought-stressed palea

value: Palea


title: Control awn_Rep2


title: Stressed palea_Rep3


title: Bc14579 pH5.5 HCl t0_t30

description: No extra description.

value: Bc ATCC 14579


title: Stressed palea_Rep1


title: Control palea_Rep3

description: Gene expression data from well-watered palea


title: Control palea_Rep2


title: Control palea_Rep1


title: A-stat gene expression changes 0.47/0.3 h-1 repl.2.2

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

description: Biological replicate 2, second technical replicate

hyb_protocol: Microarray was incubated for 30 minutes at 42ºC in prehybridization solution containing (per slide): 0.5 g BSA, 12.5 ml 20 × SSC, 0.5 ml 10% SDS. Slide was rinsed 10 times in MilliQ water, twice in 2-propanol and dried with centrifugation. After purification of the labeled cDNA the following hybridization master mix was used (per slide): 20 × SSC 16.3 ul, 100% formamide 32.5 ul, 10% SDS 0.65 ul, E. coli tRNA 1 ul (5 ug). Hybridization lasted for 35 h at 42ºC.

scan_protocol: Microarray slide was scanned using a Genepix 4000B Scanner (Axon Instruments).

data_processing: Spot intensities and corresponding background signals were quantified with Genepix Pro (version 6; Axon Instruments [http://www.moleculardevices.com/pages/software/gn_genepix_pro.html]). Spots which had signal-to-noise ratio less than three were filtered. Further analysis was carried out in R environment (version 2.6.1; [http://www.r-project.org/]) using KTH package (KTH Microarray Center; [http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html]). Flagged spots and background were extracted before “printTipLoess” normalization.

organism: Escherichia coli

source_name: Specific growth rate 0.3 h-1

label_protocol: cDNA was synthesized overnight at 46ºC using 25 ug of total RNA per reaction as following: 1 ug random primers (Random decamers; Invitrogen, Carlsbad, CA), 6 ul 5 × first strand buffer (Invitrogen), 3 ul 0.1 M DTT (Invitrogen), 0.9 ul dNTPs (final concentrations: dATP 0.5 mM, dCTP 0.5 mM, dGTP 0.5 mM, dTTP 0.3 mM, Aminoallyl-dUTP 0.2 mM), 1 ul RNase Inhibitor (Bioron, Ludwigshafen, Germany), 2 ul Superscript III (Invitrogen). After cDNA synthesis, RNA strand was hydrolyzed by adding 4.5ul 1 M NaOH, incubating for 10 min at 70ºC and neutralized with 4.5 ul 1 M HCl. The cDNA was purified with MinElute PCR Purification Kit (QIAGEN) and labeled with Cy3 (Cy3 Mono Reactive Dye Pack; Amersham Biosciences, Buckinghamshire, UK). The staining of one sample was done by incubation at room temperature in the dark in 10 ul of NaHCO3 (pH 9) for an hour and purified again with MinElute PCR Purification Kit.

growth_protocol: Escherichia coli K12 MG1655 were grown in M9 minimal medium with 10 g/L glucose. The bacteria were cultivated in a chemostat at specific growth rate 0.3 h-1 and the samples were acquired after culture reached steady state.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA) and the genomic DNA was removed using RNase-Free DNase Set (QIAGEN).

value: Escherichia coli K12 MG1655

tag: specific growth rate

source_name: Specific growth rate 0.47 h-1

label_protocol: cDNA was synthesized overnight at 46ºC using 25 ug of total RNA per reaction as following: 1 ug random primers (Random decamers; Invitrogen, Carlsbad, CA), 6 ul 5 × first strand buffer (Invitrogen), 3 ul 0.1 M DTT (Invitrogen), 0.9 ul dNTPs (final concentrations: dATP 0.5 mM, dCTP 0.5 mM, dGTP 0.5 mM, dTTP 0.3 mM, Aminoallyl-dUTP 0.2 mM), 1 ul RNase Inhibitor (Bioron, Ludwigshafen, Germany), 2 ul Superscript III (Invitrogen). After cDNA synthesis, RNA strand was hydrolyzed by adding 4.5 ul 1 M NaOH, incubating for 10 min at 70ºC and neutralized with 4.5 ul 1 M HCl. The cDNA was purified with MinElute PCR Purification Kit (QIAGEN) and labeled with Cy5 (Cy5 Mono Reactive Dye Pack; Amersham Biosciences). The staining of one sample was done by incubation at room temperature in the dark in 10 ul of NaHCO3 (pH 9) for an hour and purified again with MinElute PCR Purification Kit.

growth_protocol: Escherichia coli K12 MG1655 were grown in M9 minimal medium with 10 g/L glucose. The bacteria were cultivated in a chemostat at specific growth rate 0.3 h-1. After reaching steady state, dilution rate was increased with constant rate (0.01 h-2) and the samples were acquired when specific growth rate reached 0.47 h-1.


title: A-stat gene expression changes 0.3/0.47 h-1 dye-flip repl.3

description: Biological replicate 3, dye-flip


title: Control lemma_Rep1

description: Gene expression data from well-watered lemma

value: Lemma


title: Control lemma_Rep3


title: Control lemma_Rep2


title: A-stat gene expression changes 0.47/0.3 h-1 repl.1

description: Biological replicate 1


title: 62706 DS

status: Public on Sep 29 2009

city: Chicago

first: Tao

last: Pan

state: IL

address: 929 East 57th street

department: Biochemistry & Molecular Biology

institute: University of Chicago

description: Dye swap, sample 20

hyb_protocol: Hybridization was performed in a GeneMachines Hyb4 at 60°C overnight (16 hours) with 1 to 2.5µg each of Cy3- or Cy5-labeled total RNA as previously described. Slides were washed with 2X SSC / 0.1% SDS, 0.1X SSC / 0.1% SDS, and 0.1X SSC prior to drying and scanning.

scan_protocol: Arrays were scanned using a GenePix 4000b scanner and GenePix Pro 6.0 (Axon Instruments). For both Cy3 and Cy5 wavelengths, PMT gain was set at 600 and power at 100%.

data_processing: Image and data analysis were carried out using GenePix Pro 6.0 and Microsoft Excel. Median Cy5/Cy3 ratios were obtained from all spot replicates. To account for differences in labeling and hybridization efficiencies, the following normalization procedure was used. First, the median Cy5/Cy3 ratio for each probe was divided by the corresponding MCF10A Cy5/Cy3 reference ratio. Second, the obtained value was divided by the averaged Cy5/Cy3 ratio value for the three tRNA standards added as controls (E. coli tRNALys, E. coli tRNATyr, and yeast tRNAPhe).

label_protocol: Cy3/Cy5 labeling: after deacylation, tRNA in the total RNA mixture was selectively labeled with either Cy3 or Cy5 fluorophore using an enzymatic ligation method. The ligation reaction relies on an 8-base pair RNA:DNA hybrid helix containing a Cy3 or Cy5 fluorophore pre-attached to the loop and an overhang complementary to the universally conserved 3'CCA nucleotides present in all tRNAs. The ligation reaction was carried out overnight (~16 hours) at 16°C with 1U/µL T4 DNA ligase (USB Corporation, 70042X) and 9µM labeling oligonucleotide.

growth_protocol: All cell lines were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained according to ATCC recommendations. MCF7 cells were cultured in DMEM medium (Invitrogen, 11965-092) supplemented with 10% FBS and 1% penicillin/streptomycin (P/S). MCF10A cells were cultured in 1:1 (+I factor, Vectro)-DMEM/F12 (Invitrogen, 11330-032) supplemented with 10% FBS, 1% P/S, 5μg/mL insulin, 10ng/mL EGF, and 0.5μg/mL hydrocortisone. All other cell lines were cultured in RPMI 1640 1X medium (Mediatech, 10-040-CV) supplemented with 10% FBS and 1% P/S.

extract_protocol: Cell lines: total RNA for each cell line was obtained at 80-90% confluency using the mirVanaTM miRNA Isolation Kit (Ambion, AM1560). This procedure isolates RNA species as short as 15 nucleotides and is therefore not biased against tRNA. Normal breast: two samples of human breast total RNA were purchased from Ambion (FirstChoice® Human Breast Total RNA, AM6952, lot numbers 0808001 and 0812006). An additional sample of human breast total RNA was purchased from Stratagene (MVP Total RNA Human Breast, 540045, lot number 0380023). Both providers certify small RNA content in total RNA samples and provide relevant donor information. Breast tumors: Breast tumor samples were obtained from the Human Tissue Resource Center (HTRC) at the University of Chicago. Pathology reports were provided for all samples. All breast tumor samples were obtained frozen and embedded in OCT (optimal cutting temperature compound). Following removal of the surrounding OCT and tissue pulverization, total RNA was isolated using TRIzol reagent (Invitrogen, 15596-018). In all cases, total RNA quality was checked on agarose gels.

treatment_protocol: Deacylation: 0.25µg/µl total RNA premixed with three tRNA standards (E. coli tRNALys, E. coli tRNATyr, and yeast tRNAPhe) at 0.2µM each was incubated in 100mM Tris-HCl (pH 9.0) at 37°C for 30 minutes. The solution was neutralized by the addition of an equal volume of 100mM Na-acetate/acetic acid (pH 4.8) plus 100mM NaCl, followed by ethanol precipitation. Deacylated total RNA was dissolved in water, and its integrity verified by agarose gel electrophoresis.

tag: total rna source

value: 80-90% confluent cell culture

tag: source type

value: Cell line

tag: tumor type

value: Fibrocystic disease

tag: receptor status

value: ER-, PR-, HER2-

value: OCT-embedded tumor sample

value: Tissue sample

value: Invasive ductal carcinoma


title: 41299 DS

description: Dye swap, sample 24

value: Unknown

value: ER+, PR+, HER2-


title: 58955 DS

description: Dye swap, sample 23

value: Ductal breast carcinoma

value: ER-, PR-, HER2+


title: 57731 DS

description: Dye swap, sample 25

value: Ductal carcinoma in situ


title: Stressed lemma_Rep3

description: Gene expression data from drought-stressed lemma

value: Stressed


title: 60046 DS

description: Dye swap, sample 19


title: Shetland Sheepdog

description: CNV Profile of Pedigree Shetland Sheepdog

source_name: Pedigree Shetland Sheepdog

value: Shetland Sheepdog

value: blood

value: Boxer


title: Stressed lemma_Rep1

value: Lemma


title: Stressed lemma_Rep2


title: 62944 DS

description: Dye swap, sample 21

value: 80-90% confluent cell culture


title: Colonic mucosal 90e/30e

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out  according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios within one SmaI interval were averaged and the mean of the P value log ratios of the probes within one interval was calculated.

organism: Mus musculus

source_name: P30 animal

label_protocol: 4ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

extract_protocol:
tissue isolation: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice
Total DNA was extracted by standard phenol-chloroform isolation

tag: age

value: 30 postnatal days

value: colonic mucosa

source_name: P90 animal

value: 90 postnatal days


title: 45163 DS

description: Dye swap, sample 26

value: Cell line

value: Fibrocystic disease

value: ER-, PR-, HER2-

value: OCT-embedded tumor sample

value: ER+, PR-, HER2+


title: Control seed_Rep2

value: Seed

value: Control


title: 13% CO2 microarray #2

city: Evanston

first: Taneli

last: Helenius

address: 2205 Tech Drive

department: BMBCB

institute: Northwestern University

hyb_protocol: About 30 µg of total RNA from each sample was labeled by incorporation of Cy3- or Cy5-dUTP into newly synthesized cDNA by a 2h reverse transcription reaction. After RNase H treatment, a Cy3-dUTP-labeled cDNA population was mixed with a Cy5-dUTP-labeled population, purified, resuspended, boiled, cooled and spun. Then the labeled cDNA mixture was loaded onto a microarray slide, put into a hybridization chamber and hybridized in a 65°C water bath for 16h.

scan_protocol: GenePix 4000B scanner, GenePix Pro 3.0.6.90 software

data_processing: GenePix median of ratios ("Value" column in samples) processed using "normalized deviation", per Liu, Roy & Johnson, Physiol Genomics. 2006 Mar 13;25(1):134-41.

source_name: RNA from flies in 13% CO2 for 24h

label_protocol: Incorporation of Cy5-dUTP into newly synthesized cDNA by a 2h reverse transcription reaction.

extract_protocol: Trizol

tag: specimen

value: 5-day old Oregon R male and female flies

source_name: RNA from flies in air for 24h

label_protocol: Incorporation of Cy3-dUTP into newly synthesized cDNA by a 2h reverse transcription reaction.


title: 13% CO2 microarray #3


title: S-23 DS

description: Dye swap, sample 17

value: Stratagene MVP total RNA, human breast

value: Tissue sample

value: ND


title: 184 B5 DS

description: Dye swap, sample 14

value: Normal


title: A-01 DS

description: Dye swap, sample 15

value: Ambion FirstChoice human breast total RNA


title: 46258 DS

description: Dye swap, sample 22

value: 80-90% confluent cell culture

value: Ductal breast carcinoma

value: ER-, PR-, HER2+


title: MDA-MB-231 (1) DS

description: Dye swap, sample 8

value: Invasive ductal carcinoma (ascites)

value: ER+, PR+, HER2-

value: Adenocarcinoma (pleural effusion)


title: 184 A1 DS

description: Dye swap, sample 13

value: Cell line

value: Fibrocystic disease

value: ER-, PR-, HER2-


title: MCF7 DS

description: Dye swap, sample 10

value: Invasive ductal carcinoma (pleural effusion)


title: MDA-MB-436 DS

description: Dye swap, sample 11


title: 57731

description: Sample 25

value: OCT-embedded tumor sample

value: Ductal carcinoma in situ


title: BT-474 DS

description: Dye swap, sample 12

value: Invasive ductal carcinoma (primary)

value: ER+, PR+, HER2+


title: MDA-MB-231 (2) DS

description: Dye swap, sample 9


title: Colonic mucosal 90b/30b

value: 30 postnatal days

tag: tissue

value: colonic mucosa

tag: strain

value: 90 postnatal days


title: HCC70 (1) DS

description: Dye swap, sample 6

value: 80-90% confluent cell culture

value: Ductal carcinoma (primary)

value: ER+, PR-, HER2-


title: 41299

description: Sample 24

value: Tissue sample

value: Unknown


title: 58955

description: Sample 23

value: Ductal breast carcinoma

value: ER-, PR-, HER2+


title: 46258

description: Sample 22

value: Cell line

value: Fibrocystic disease


title: 62944

description: Sample 21

value: Invasive ductal carcinoma

value: ER-, PR-, HER2-


title: 62706

description: Sample 20

value: OCT-embedded tumor sample


title: 60046

description: Sample 19

value: Ductal carcinoma in situ


title: 45163

description: Sample 26

value: ER+, PR-, HER2+


title: RNA_FT30-3-36mM_rep3

city: Zurich

first: Dominik

last: Heer

address: Wolfgang-Pauli-Str. 16

department: IMSB

country: Switzerland

institute: ETH Zurich

hyb_protocol: Biotin labeled cRNA samples were fragmented randomly to 35-200 bp at 94 _C in  fragmentation buffer (Affymetrix Inc., P/N 900371) and were suspended in 100 μl of hybridization  mix (Affymetrix Inc., P/N 900720) containing a hybridization control and control oligonucleotide  B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Yeast Genome 2.0 arrays  for 16 h at 45 _C. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450 0003  protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to determine the  fluorescent intensity emitted by the labeled target.

data_processing: The values in the matrix table are expression values normalised on quantiles, background and pm/mm corrected using the mas5 algorithm and summarised according to Li and Wong (the following command from the bioconductor package was used to obtain these intensities from the CEL files: raw_data <- ReadAffy(); eset <- expresso(raw_data, normalize.method=quantiles, bgcorrect.method=mas, pmcorrect.method=mas, summary.method=liwong); R version 2.7.2, bioconductor package (release 2.2).

organism: Saccharomyces cerevisiae

label_protocol: Total RNA samples were reverse-transcribed with One-Cycle cDNA Synthesis Kit (Affymetrix  Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample  Cleanup Module (Affymetrix Inc., P/N 900371). The purified double-stranded cDNA were in vitro  transcribed in presence of biotin labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc.,  P/N 900449). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix  15Inc., P/N 900371) and its quality and quantity was determined using NanoDrop ND 1000 and  Bioanalyzer 2100.

growth_protocol: glucose limited, micro-aerobic chemostat cultures

extract_protocol: RNA was extracted with a Qiagen RNAeasy Mini kit (cat Nr. 74104)

treatment_protocol: Furfural concentrations of either 15, 25 or 36mM were used in the feed medium; 36 mM could only be supported by the evolved strain TMB3400-FT30-3, the parent strain TMB3400 washed out at this concentration

tag: furfural concentration


title: RNA_TMB3400-25mM_rep3


title: RNA_FT30-3-36mM_rep2


title: A-06

description: Sample 16

value: Ambion FirstChoice human breast total RNA

value: Normal

value: ND


title: A-06 DS

description: Dye swap, sample 16

value: 80-90% confluent cell culture


title: A-01

description: Sample 15


title: RNA_TMB3400-15mM_rep2


title: 59826

description: Sample 18


title: RNA_FT30-3-15mM_rep3


title: RNA_TMB3400-15mM_rep1


title: S-23

description: Sample 17

value: Stratagene MVP total RNA, human breast


title: RNA_FT30-3-15mM_rep2


title: BT-474

description: Sample 12

value: Invasive ductal carcinoma (primary)

value: ER+, PR+, HER2+


title: 184 A1

description: Sample 13


title: 184 B5

description: Sample 14


title: RNA_FT30-3-25mM_rep1


title: RNA_FT30-3-25mM_rep2


title: MDA-MB-231 (2)

description: Sample 9

value: Adenocarcinoma (pleural effusion)


title: RNA_TMB3400-25mM_rep2


title: RNA_TMB3400-25mM_rep1


title: MDA-MB-231 (1)

description: Sample 8

value: Invasive ductal carcinoma (ascites)

value: ER+, PR+, HER2-


title: RNA_FT30-3-36mM_rep1


title: RNA_FT30-3-15mM_rep1


title: A-stat gene expression changes 0.47/0.3 h-1 repl.2.1

description: Biological replicate 2, first technical replicate

value: Escherichia coli K12 MG1655


title: MDA-MB-436

description: Sample 11

value: Cell line

value: Fibrocystic disease


title: ZR-75-1

description:
Sample 4
Self-self reference array


title: HCC70

description: Sample 6

value: Ductal carcinoma (primary)

value: ER+, PR-, HER2-


title: MCF7

description: Sample 10

value: Invasive ductal carcinoma (pleural effusion)

value: ER-, PR-, HER2-


title: MCF10A (3)

description:
Sample 3
Self-self reference array


title: MCF10A (2)

description:
Sample 2
Self-self reference array


title: MCF10A (1)

description:
Sample 1
Self-self reference array


title: 13_Peritoneum

city: Seattle

first: Barbara

middle: J.

last: Trask

state: WA

address: 1100 Fairview Avenue N., C3-168, P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
LCM collected tumor from patient 13, peritoneum metastasis
Alternate patient ID 99-069

hyb_protocol: Labeled test and reference samples were each mixed with 125 micrograms of Cot-1 DNA (Invitrogen) and 30 micrograms of yeast tRNA, concentrated, and hybridized to arrays under conditions described previously (L.W. Loo et al., Cancer Res., 2004).

scan_protocol: See L.W. Loo et al., Cancer Res., 2004.

data_processing: A custom R script was used to log2-transform raw intensity values, calculate the ratio of red to green fluorescence intensities, and apply a block-based loess normalization procedure based on intensity. The log2 ratios for the two spots for each remaining clone were averaged.

source_name: HuPr3655_99-069 G1_Peritoneum

label_protocol: 1 microgram of amplified material was labelled with Cy5-dUTP (GE Healthcare) using the Bioprime Array CGH kit (Invitrogen). Labeled material was cleaned using the columns included with the labeling kit.

extract_protocol: LCM-collected samples were incubated overnight in proteinase K buffer (1% Tween 20, 1 mg/ml Proteinase K, and 1 x TE) and DNA was isolated using the Qiagen QIAamp DNA Micro Kit (Qiagen Inc, Valencia, CA). Genomic material was amplified  by ligation-mediated PCR (LMP).

value: Peritoneum Metastasis

source_name: Female peripheral blood

label_protocol: 1 microgram of amplified material was labelled with Cy3-dUTP (GE Healthcare) using the Bioprime Array CGH kit (Invitrogen). Labeled material was cleaned using the columns included with the labeling kit.

extract_protocol: Reference DNA was obtained from the peripheral blood of a single female individual, isolated using the QIAamp DNA Blood Mini Kit (Qiagen Inc, Valencia, CA), and quantified using the Quant-iT PicoGreen dsDNA Assay (Invitrogen, Carlsbad, CA). The amplification method (i.e., LMP or WGA) and the amount of input DNA for all reference samples matched the test sample.

value: Female peripheral blood


title: 14_Liver

description:
LCM collected tumor from patient 14, liver metastasis
Alternate patient ID 99-090

extract_protocol: LCM-collected samples were incubated overnight in proteinase K buffer (1% Tween 20, 1 mg/ml Proteinase K, and 1 x TE) and DNA was isolated using the Qiagen QIAamp DNA Micro Kit (Qiagen Inc, Valencia, CA). Genomic material was amplified  using a whole genome amplification (WGA) kit, WGA2 (Sigma-Aldrich, St. Louis, MO).

value: Liver Metastasis


title: 14_LN

description:
LCM collected tumor from patient 14, periaortic Lymph Node metastasis
Alternate patient ID 99-090

value: Periaortic Lymph Node Metastasis


title: 10_LN4

description:
LCM collected tumor from patient 10, pleural Lymph Node metastasis
Alternate patient ID 05-144

value: Pleural Lymph Node Metastasis


title: 13_Prostate

description:
LCM collected tumor from patient 13, prostate primary
Alternate patient ID 99-069

source_name: HuPr3665_99-069 I_CaP_Bladder

value: Prostate Primary


title: 350 µM Si (Sample 19N) vs Si-free (Sample 22N)

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

country: France

institute: École Normale Supérieure

description: Technical replicate 2 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65¡C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37¡C. The array slides are then air dryed and ready for scaning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

organism: Phaeodactylum tricornutum

source_name: Si-free medium (Sample 22N)

label_protocol: 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cells acclimated for several weeks (light:dark regime (16h:8h) at 19°C), in an artificial sea water medium containing 350 µM Si, were collected during the exponential growth phase (at about 5.10e6 cells.ml-1).

extract_protocol: Extraction suing Trizol reagent (Invitrogen) followed by DNase I treatment, and RNEasy Mini Kit purification step (Quiagen)

tag: Si-free

source_name: silicic acid medium (Sample 19N)

label_protocol: 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cells already acclimated for several weeks (light:dark regime (16h:8h) at 19°C), in an Si-Free artificial sea water medium, were collected during the exponential growth phase (at about 5.10e6 cells.ml-1).

tag: 350 µM Si


title: 12_LN2

description:
LCM collected tumor from patient 12, pericaval Lymph Node metastasis
Alternate patient ID 97-201

value: Pericaval Lymph Node Metastasis


title: 11_Prostate2

description:
LCM collected tumor from patient 11, prostate metastasis
Alternate patient ID 05-187

value: Prostate Metastasis


title: 10_Spleen

description:
LCM collected tumor from patient 10, spleen metastasis
Alternate patient ID 05-144

value: Spleen Metastasis


title: 12_LN1


title: 11_Liver1

description:
LCM collected tumor from patient 11, liver metastasis
Alternate patient ID 05-187


title: 11_Liver2


title: 11_Prostate1


title: 12_Prostate2

description:
LCM collected tumor from patient 12, prostate primary
Alternate patient ID 97-201


title: Si-free (Sample 23N) vs 350 µM Si (Sample 20N)

description: Technical replicate 2 of 2.

source_name: silicic acid medium (Sample 20N)

source_name: Si-free medium (Sample 23N)


title: 12_Prostate1


title: 350 µM Si (Sample 18N) vs Si-free (Sample 11)

description: Technical replicate 1 of 2.

source_name: Si-free medium (Sample 18N)

source_name: silicic acid medium (Sample 11)


title: 11_LN

description:
LCM collected tumor from patient 11, periaortic Lymph Node metastasis
Alternate patient ID 05-187


title: 350 µM Si (Sample 20N) vs Si-free (Sample 23N)

description: Technical replicate 1 of 2.


title: 10_Adrenal

description:
LCM collected tumor from patient 10, adrenal metastasis
Alternate patient ID 05-144

value: Adrenal Metastasis


title: 12_LN3

description:
LCM collected tumor from patient 12, periaortic Lymph Node metastasis
Alternate patient ID 97-201


title: Si-free (Sample 22N) vs 350 µM Si (Sample 19N)

description: Technical replicate 1 of 2.


title: 10_LN3

description:
LCM collected tumor from patient 10, pelvic Lymph Node metastasis
Alternate patient ID 05-144

value: Pelvic Lymph Node Metastasis


title: 8_LN

description:
LCM collected tumor from patient 8, mediastinal Lymph Node metastasis
Alternate patient ID 05-092

source_name: HuPr3716_05-092 H1_Mediastinal_LN

value: Mediastinal Lymph Node Metastasis


title: 9_LN

description:
LCM collected tumor from patient 9, iliac Lymph Node metastasis
Alternate patient ID 05-123

value: Iliac Lymph Node Metastasis


title: 10_Liver

description:
LCM collected tumor from patient 10, liver metastasis
Alternate patient ID 05-144


title: 8_Prostate

description:
LCM collected tumor from patient 8, prostate primary
Alternate patient ID 05-092

source_name: HuPr3714_05-092 D1_CaP_Bladder


title: 10_LN1

description:
LCM collected tumor from patient 10, retroperitoneal Lymph Node metastasis
Alternate patient ID 05-144

value: Retroperitoneal Lymph Node Metastasis


title: 9_Prostate

description:
LCM collected tumor from patient 9, prostate primary
Alternate patient ID 05-123


title: 7_RM

description:
LCM collected tumor from patient 7, retromediastinal  metastasis
Alternate patient ID 04-101

value: Retromediastinal  Metastasis


title: Si-free (Sample 11) vs 350 µM Si (Sample 18N)

description: Technical replicate 2 of 2.

source_name: silicic acid medium (Sample 18N)

source_name: Si-free medium (Sample 11)


title: 7_LN2

description:
LCM collected tumor from patient 7, retroperitoneal Lymph Node metastasis
Alternate patient ID 04-101


title: 13% CO2 microarray #1

value: 5-day old Oregon R male and female flies


title: 59826 DS

description: Dye swap, sample 18

value: 80-90% confluent cell culture

value: Cell line

value: Fibrocystic disease

value: ER-, PR-, HER2-

value: OCT-embedded tumor sample

value: Tissue sample

value: Invasive ductal carcinoma


title: 7_Prostate

description:
LCM collected tumor from patient 7, prostate primary
Alternate patient ID 04-101

value: Prostate Primary

value: Female peripheral blood


title: 7_LN1

description:
LCM collected tumor from patient 7, periaortic Lymph Node metastasis
Alternate patient ID 04-101

value: Periaortic Lymph Node Metastasis


title: 13_Iliac

description:
LCM collected tumor from patient 13, iliac metastasis
Alternate patient ID 99-069

value: Iliac Metastasis


title: 7_Peritoneal

description:
LCM collected tumor from patient 7, peritoneal metastasis
Alternate patient ID 04-101

value: Peritoneal Metastasis


title: 6_LN1

description:
LCM collected tumor from patient 6, periaortic Lymph Node metastasis
Alternate patient ID 04-050


title: 6_Prostate1

description:
LCM collected tumor from patient 6, prostate primary
Alternate patient ID 04-050


title: 6_Prostate2


title: 8_Liver

description:
LCM collected tumor from patient 8, liver metastasis
Alternate patient ID 05-092

value: Liver Metastasis


title: 5_Prostate

description:
LCM collected tumor from patient 5, prostate primary
Alternate patient ID 03-192


title: 5_Spleen

description:
LCM collected tumor from patient 5, spleen metastasis
Alternate patient ID 03-192

value: Spleen Metastasis


title: 5_Lung

description:
LCM collected tumor from patient 5, lung metastasis
Alternate patient ID 03-192

value: Lung Metastasis


title: 4_Lung

description:
LCM collected tumor from patient 4, lung metastasis
Alternate patient ID 03-163


title: 5_Liver

description:
LCM collected tumor from patient 5, liver metastasis
Alternate patient ID 03-192


title: 4_Liver

description:
LCM collected tumor from patient 4, liver metastasis
Alternate patient ID 03-163


title: 430A plus GDNF sample 2

city: New YOrk

first: Benson

middle: Che-i

last: Lu

state: NY

department: Genetics and Development

institute: Columbia University Medical Center

description: No additional information

hyb_protocol: GeneChip® Hybridization Oven 640 according to Affymetrix protocol

scan_protocol: GeneChip® Scanner 3000

data_processing: Sample comparisons and statistical analysis were performed using dChip 1.3 (built April 2009), using the Comparison Analysis feature to identify genes differentially expressed between the two groups. The following filtering criteria were used: the lower limit for fold-change between the means of the +GDNF and -GDNF samples must exceed 1.2 with a 90% confidence limit, and the absolute difference between the two group means must exceed 100.

source_name: mouse isolated ureteric bud, with GDNF, 16 hours

label_protocol: IVT and labeling were performed with BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, P/N 900182).

extract_protocol: Cultured ureteric buds were removed from the Matrigel with a Wiretrol and added directly to 800 µL of TRIzol reagent (Invitrogen, Cat # 15596-018) and homogenized with a 26 gauge needle prior to chloroform addition.  After homogenization and before addition of chloroform, samples were quick frozen and stored at -80C.  To increase RNA precipitation, 25 ng/µL of RNase-free glycogen was added as a carrier to the aqueous phase.  RNA was isolated from batches of 30-40 pooled UBs, and the RNA samples were quantified and checked for integrity using the Agilent 2100 Bioanalyzer. RNA from approximately 5-6 different batches of cultured UBs was then pooled to obtain sufficient RNA (>8 ug) to prepare the probe for hybridization a single chip.

treatment_protocol: Cultured uteric buds grown in matrigel were treated with 100ng/mL GDNF for 16 hrs prior to extraction.

value: Swiss Webster

tag: developmental stage

value: ureteric buds

tag: treatment group

value: plus GDNF


title: 430A plus GDNF sample 3

description: No additional information


title: 430A minus GDNF sample 2

description: No additional information

source_name: mouse isolated ureteric bud, without GDNF, 16 hours

value: minus GDNF


title: 4_Prostate

description:
LCM collected tumor from patient 4, prostate primary
Alternate patient ID 03-163


title: 430A minus GDNF sample 1

description: No additional information


title: 6_LN2

description:
LCM collected tumor from patient 6, preaortic Lymph Node metastasis
Alternate patient ID 04-050

value: Preaortic Lymph Node Metastasis