title: F.81 child Sty

description: Hybridized to 250K_Sty


title: F.63 mother NspI

status: Public on Mar 18 2012

type: genomic

city: Valencia

first: Joaquín

last: Dopazo

state: Valencia

address: c/ Eduardo Primo Yufera, 3

department: Computational Genomics

country: Spain

institute: Centro de Investigación Príncipe Felipe (CIPF)

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and images were obtained using an Affymetrix GeneChip® Scanner 3000.

data_processing:
CEL files were processed using Affymetrix Power Tools (APT v1.10.2) using BRLMM calling algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: phenotype

value: unaffected

tag: family

tag: family member

value: mother

tag: gender

value: female

tag: tissue

value: peripheral blood

tag: disease state


title: F.57 mother NspI

description: Hybridized to 250K_Nsp


title: F.89 father Sty

description: Hybridized to 250K_Sty

value: father

value: male


title: F.56 child NspI

description: Hybridized to 250K_Nsp

value: affected

value: child

value: Hirschsprung's disease


title: F.54 father NspI

description: Hybridized to 250K_Nsp


title: F.81 father Sty

description: Hybridized to 250K_Sty


title: F.81 mother Sty

description: Hybridized to 250K_Sty


title: F.52 mother NspI

description: Hybridized to 250K_Nsp


title: F.55 mother NspI

description: Hybridized to 250K_Nsp


title: F.54 mother NspI

description: Hybridized to 250K_Nsp


title: F.69 mother Sty

description: Hybridized to 250K_Sty


title: F.55 father NspI

description: Hybridized to 250K_Nsp


title: F.55 child NspI

description: Hybridized to 250K_Nsp


title: F.80 mother Sty

description: Hybridized to 250K_Sty


title: F.80 child StyI

description: Hybridized to 250K_Sty


title: F.54 child NspI

description: Hybridized to 250K_Nsp


title: F.69 child Sty

description: Hybridized to 250K_Sty


title: F.68 mother Sty

description: Hybridized to 250K_Sty


title: F.56 father NspI

description: Hybridized to 250K_Nsp


title: F.69 father Sty

description: Hybridized to 250K_Sty


title: F.31 father StyI

description: Hybridized to 250K_Sty


title: F.52 child NspI

description: Hybridized to 250K_Nsp


title: F.58 child NspI

description: Hybridized to 250K_Nsp


title: F.50 mother NspI

description: Hybridized to 250K_Nsp


title: F.52 father NspI

description: Hybridized to 250K_Nsp


title: F.65 mother Sty

description: Hybridized to 250K_Sty


title: F.65 father Sty

description: Hybridized to 250K_Sty


title: F.68 child Sty

description: Hybridized to 250K_Sty


title: F.63 mother Sty

description: Hybridized to 250K_Sty


title: F.50 father NspI

description: Hybridized to 250K_Nsp


title: F.64 mother Sty

description: Hybridized to 250K_Sty


title: F.48 father NspI

description: Hybridized to 250K_Nsp


title: F.63 child Sty

description: Hybridized to 250K_Sty


title: F.64 father Sty

description: Hybridized to 250K_Sty


title: F.50 child NspI

description: Hybridized to 250K_Nsp


title: F.64 child Sty

description: Hybridized to 250K_Sty


title: F.48 mother NspI

description: Hybridized to 250K_Nsp


title: F.63 father Sty

description: Hybridized to 250K_Sty


title: F.61 mother Sty

description: Hybridized to 250K_Sty


title: F.44 mother NspI

description: Hybridized to 250K_Nsp


title: F.49 child NspI

description: Hybridized to 250K_Nsp


title: F.44 child NspI

description: Hybridized to 250K_Nsp


title: F.44 father NspI

description: Hybridized to 250K_Nsp


title: F.65 child Sty

description: Hybridized to 250K_Sty


title: F.30 father NspI

description: Hybridized to 250K_Nsp


title: F.48 child NspI

description: Hybridized to 250K_Nsp

tag: comment

value: Down syndrome


title: F.49 father NspI

description: Hybridized to 250K_Nsp


title: F.58 child Sty

description: Hybridized to 250K_Sty


title: F.68 father Sty

description: Hybridized to 250K_Sty


title: HF+/+R , Group 8 - 2

type: RNA

city: Palo Alto

first: Wen-Jun

last: Shen

state: CA

address: 3801 Miranda Avenue

department: Medicine

country: USA

institute: Stanford University

hyb_protocol: The oligo microarray was hybridized overnight at 60°C with continuous but slow agitation at 5 to 10 rpm.

scan_protocol: The hybridized membrane was subjected to chemiluminesence analysis for quantification of the conjugation signals with CDP-Star. The resulting signals were captured on a Kodak Image Station (Kodak IS440CF, USA),

data_processing:
Data captured were analyzed with GEArray Expression Analysis Suite (SABiosciences, Frederick, MD) and SAM programs to comprehensively evaluate the differential gene expression of the various samples.
We did the whole array normalization with each of the array by first substrating the minimum signal from each array (which was not done before) and then normalize against the average of the whole array. It does bring the average (perhaps the median as well) more close together.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: HF+/+R

label_protocol:
TrueLabeling-AMP 2.0 (SABiosciences, Frederick, MD) was used to rapidly amplify, label and purify antisense RNA (aRNA) for hybridization.
The aRNA was labeled with 10 mM Biotin-16-UTP (Roche Applied Science, Germany).

extract_protocol: Total RNA was isolated from  WAT using TRIzol reagent (Invitrogen, Carlsbad, CA) and cleaned further using ArrayGradeTM Total RNA Isolation Kit (SABiosciences, Frederick, MD).

treatment_protocol:
Twelve week-old female HSL+/+ and HSL-/- littermate mice were randomized to
HF, NC, HF+R, and NC+R diets ad libitum for 16 weeks.
High-fat and control normal chow diets were from Research Diets, Inc. (New Brunswick, NJ),
product numbers D12309 and D12310, respectively.
Rosiglitazone contains 200 mg/kg rosiglitazone in the HF and NC diets respectively.

tag: strain

tag: diet

value: high fat + rosiglitazone

tag: genotype/variation

value: wild type

tag: age

value: 12 weeks


title: F.61 father Sty

description: Hybridized to 250K_Sty


title: F.42 child NspI

description: Hybridized to 250K_Nsp


title: F.42 mother NspI

description: Hybridized to 250K_Nsp


title: F.58 father Sty

description: Hybridized to 250K_Sty


title: F.41 mother NspI

description: Hybridized to 250K_Nsp


title: HF+/+R , Group 8 - 4


title: F.61 child Sty

description: Hybridized to 250K_Sty


title: HF+/+R , Group 8 - 1


title: F.41 father NspI

description: Hybridized to 250K_Nsp


title: F.42 father NspI

description: Hybridized to 250K_Nsp


title: F.58 mother Sty

description: Hybridized to 250K_Sty


title: F.33 mother NspI

description: Hybridized to 250K_Nsp


title: HF-/-R, Group 7 - 3

source_name: HF-/-R

value: HSL-/-


title: HF-/-R, Group 7 - 4


title: F.41 child NspI

description: Hybridized to 250K_Nsp


title: HF+/+R , Group 8 - 3


title: HF-/-R, Group 7 - 2


title: F.56 child Sty

description: Hybridized to 250K_Sty


title: F.56 father Sty

description: Hybridized to 250K_Sty


title: HF-/-R, Group 7 - 1


title: F.55 mother Sty

description: Hybridized to 250K_Sty


title: F.57 father Sty

description: Hybridized to 250K_Sty


title: F.56 mother Sty

description: Hybridized to 250K_Sty


title: F.33 child NspI

description: Hybridized to 250K_Nsp


title: F.54 mother Sty

description: Hybridized to 250K_Sty


title: F.54 father Sty

description: Hybridized to 250K_Sty


title: F.57 mother Sty

description: Hybridized to 250K_Sty


title: F.55 father Sty

description: Hybridized to 250K_Sty


title: F.31 mother NspI

description: Hybridized to 250K_Nsp


title: F.31 child NspI

description: Hybridized to 250K_Nsp


title: HF+/+, Group 6 - 4

value: high fat


title: F.30 mother NspI

description: Hybridized to 250K_Nsp


title: F.33 father NspI

description: Hybridized to 250K_Nsp


title: HF+/+, Group 6 - 3


title: F.50 father Sty

description: Hybridized to 250K_Sty


title: HF+/+, Group 6 - 2


title: HF+/+, Group 6 - 1


title: F.57 child Sty

description: Hybridized to 250K_Sty


title: F.55 child Sty

description: Hybridized to 250K_Sty


title: HF-/-, Group 5 - 4


title: F.29 father NspI

description: Hybridized to 250K_Nsp


title: F.52 father Sty

description: Hybridized to 250K_Sty


title: F.49 father StyI

description: Hybridized to 250K_Sty


title: F.50 child Sty

description: Hybridized to 250K_Sty


title: F.30 child NspI

description: Hybridized to 250K_Nsp


title: F.50 mother Sty

description: Hybridized to 250K_Sty


title: F.48 mother StyI

description: Hybridized to 250K_Sty


title: F.29 mother NspI

description: Hybridized to 250K_Nsp


title: F.52 child Sty

description: Hybridized to 250K_Sty


title: HF-/-, Group 5 - 2


title: HF-/-, Group 5 - 3


title: F.48 father StyI

description: Hybridized to 250K_Sty


title: F.54 child Sty

description: Hybridized to 250K_Sty


title: HF-/-, Group 5 - 1


title: F.29 child NspI

description: Hybridized to 250K_Nsp


title: F.44 mother StyI

description: Hybridized to 250K_Sty


title: F.48 child StyI

description: Hybridized to 250K_Sty


title: NC-/-R, Group 4 -4

source_name: NC-/-R

value: normal chow + rosiglitazone


title: NC-/-R, Group 4 -3


title: F.52 mother Sty

description: Hybridized to 250K_Sty


title: F.23 child NspI

description: Hybridized to 250K_Nsp


title: F.44 child StyI

description: Hybridized to 250K_Sty


title: F.11 father NspI

description: Hybridized to 250K_Nsp


title: F.23 father NspI

description: Hybridized to 250K_Nsp


title: F.23 mother NspI

description: Hybridized to 250K_Nsp


title: F.30 father StyI

description: Hybridized to 250K_Sty


title: F.49 child StyI

description: Hybridized to 250K_Sty


title: F.44 father StyI

description: Hybridized to 250K_Sty


title: F.42 father StyI

description: Hybridized to 250K_Sty


title: F.41 mother StyI

description: Hybridized to 250K_Sty


title: NC+/+ R, Group 3 - 4

source_name: NC+/+ R


title: F.42 mother StyI

description: Hybridized to 250K_Sty


title: F.41 father StyI

description: Hybridized to 250K_Sty


title: NC+/+ R, Group 3 - 3


title: F.41 child StyI

description: Hybridized to 250K_Sty


title: F.17 mother NspI

description: Hybridized to 250K_Nsp


title: F.33 father StyI

description: Hybridized to 250K_Sty


title: F.42 child StyI

description: Hybridized to 250K_Sty


title: F.12 child NspI

description: Hybridized to 250K_Nsp

value: Consanguineous


title: F.33 mother StyI

description: Hybridized to 250K_Sty

value: unaffected


title: F.17 father NspI

description: Hybridized to 250K_Nsp


title: F.31 mother StyI

description: Hybridized to 250K_Sty

value: mother


title: NC-/-R, Group 4 -1

value: female


title: F.12 mother NspI

description: Hybridized to 250K_Nsp

value: peripheral blood


title: F.17 child NspI

description: Hybridized to 250K_Nsp


title: F.30 mother StyI

description: Hybridized to 250K_Sty


title: NC-/-, Group 2 - 4

value: normal chow


title: NC+/+ R, Group 3 - 1


title: NC+/+ R, Group 3 - 2


title: F.33 child StyI

description: Hybridized to 250K_Sty


title: F.31 child StyI

description: Hybridized to 250K_Sty

value: male


title: F.30 child StyI

description: Hybridized to 250K_Sty

value: affected


title: NC-/-, Group 2 - 3


title: F.23 father Sty

description: Hybridized to 250K_Sty

value: father


title: F.29 mother Sty

description: Hybridized to 250K_Sty


title: F.8 father NspI

description: Hybridized to 250K_Nsp


title: NC-/-R, Group 4 -2


title: NC-/-, Group 2 - 2


title: F.29 child Sty

description: Hybridized to 250K_Sty

value: child

value: Hirschsprung's disease


title: F.11 child NspI

description: Hybridized to 250K_Nsp


title: F.11 father Sty

description: Hybridized to 250K_Sty


title: F.29 father Sty

description: Hybridized to 250K_Sty


title: F.11 mother NspI

description: Hybridized to 250K_Nsp


title: F.17 father Sty

description: Hybridized to 250K_Sty


title: F.23 mother Sty

description: Hybridized to 250K_Sty


title: F.23 child Sty

description: Hybridized to 250K_Sty


title: NC+/+, Group 1 - 4


title: NC+/+, Group 1 - 3


title: NC-/-, Group 2 - 1


title: F.7 child NspI

description: Hybridized to 250K_Nsp

value: Down syndrome


title: NC+/+, Group 1 - 2

value: wild type


title: F.7 mother NspI

description: Hybridized to 250K_Nsp


title: F.17 mother Sty

description: Hybridized to 250K_Sty


title: F.17 child Sty

description: Hybridized to 250K_Sty


title: NC+/+, Group 1 - 1

value: 12 weeks


title: F.8 child NspI

description: Hybridized to 250K_Nsp


title: F.12 child Sty

description: Hybridized to 250K_Sty


title: F.8 mother NspI

description: Hybridized to 250K_Nsp


title: F.8 father Sty

description: Hybridized to 250K_Sty


title: F.7 father NspI

description: Hybridized to 250K_Nsp


title: F.11 child Sty

description: Hybridized to 250K_Sty


title: F.11 mother Sty

description: Hybridized to 250K_Sty


title: F.12 mother Sty

description: Hybridized to 250K_Sty


title: DicerLyszCre_IL-4_72h_InVitro rep3

status: Public on Mar 17 2012

city: Seattle

first: James

last: Sissons

state: WA

address: 307 Westlake Avenue N # 500

institute: Seattle BioMed

hyb_protocol: Labeled, fragmented cDNA was hybridized for 16 hours at 45 deg C and 60rpm to an Affymetrix GeneChip.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor and the version 14 of the MoEx10stv1 CustomCDF from MBNI BrainArray

label_protocol: Samples were labeled according to the Affymetrix Whole Transcript Sense Target Labeling Assay, including the RiboMinus rRNA depletion step

growth_protocol: bone-marrow cells were grown with complete RPMI (10% FBS, 2mM l-glutamine) supplemeted with M-CSF1, for 7 days prior to experiments.

extract_protocol: RNA was extracted using the Invitrogen Trizol LDS reagent.

treatment_protocol: mature bone-marrow derived macrophages were stimulated with 50ng/mL IL-4 for 72h.

tag: strain background

value: Dicer fl/+ LysM-Cre by Dicer fl/+ crossed mice

tag: progeny strain

value: Dicer fl/fl LyszCre+/- (Dicer-deficient)

tag: cell type

value: mature bone-marrow derived macrophages

tag: stimulus

value: Interleukin 4 (50ng/mL)

tag: time point

value: 72 hours


title: DicerPlusLyszCre_IL-4_72h_InVitro rep3

value: Dicer fl/+ LyszCre+/- (wild type)


title: F.6 father NspI

description: Hybridized to 250K_Nsp

value: unaffected


title: F.6 mother NspI

description: Hybridized to 250K_Nsp

value: mother

value: female

value: peripheral blood


title: F.7 father Sty

description: Hybridized to 250K_Sty

value: male


title: DicerLyszCre_IL-4_72h_InVitro rep2


title: DicerPlusLyszCre_IL-4_72h_InVitro rep2


title: F.8 child Sty

description: Hybridized to 250K_Sty

value: affected


title: DicerPlusLyszCre_IL-4_72h_InVitro rep1


title: F.6 father Sty

description: Hybridized to 250K_Sty

value: father


title: liver control 4 weeks rep3

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the GeneSpring GX 7.3.4 software

source_name: liver, control, 4 weeks

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Mice were inoculated subcutaneously with J558 myeloma cells at the dorsum of the neck and given standard rodent chow

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

value: liver

tag: treatment

value: distilled water 4 weeks after J558 myeloma cell innoculation

tag: time

value: 4 weeks

value: BALB/c

value: 10 weeks

tag: experimental group

value: control


title: F.6 child NspI

description: Hybridized to 250K_Nsp

tag: phenotype

tag: family

tag: family member

value: child

value: Hirschsprung's disease


title: F.7 child Sty

description: Hybridized to 250K_Sty

tag: gender

value: Down syndrome

tag: tissue

tag: disease state


title: F.4 father NspI

description: Hybridized to 250K_Nsp


title: F.7 mother Sty

description: Hybridized to 250K_Sty


title: liver control 4 weeks rep2

description: replicate 2

tag: strain


title: F.6 mother Sty

description: Hybridized to 250K_Sty


title: liver treatment 4 weeks rep2

description: replicate 2

source_name: liver, treatment, 4 weeks

value: oil palm phenolics 4 weeks after J558 myeloma cell innoculation

value: treatment


title: F.4 mother NspI

description: Hybridized to 250K_Nsp

value: unaffected

value: mother


title: F.4 father Sty

description: Hybridized to 250K_Sty

value: peripheral blood


title: liver treatment 18 hours rep3

description: replicate 3

source_name: liver, treatment, 18 hours

value: 18 hours

value: 6 weeks

value: male


title: liver treatment 1 week rep1

description: replicate 1

source_name: liver, treatment, 1 week

value: liver

value: 1 week

value: 7 weeks


title: liver control 1 week rep3

description: replicate 3

source_name: liver, control, 1 week

value: distilled water 4 weeks after J558 myeloma cell innoculation

value: BALB/c


title: F.4 child Sty

description: Hybridized to 250K_Sty

value: affected


title: liver treatment 1 week rep2

description: replicate 2


title: liver control 4 weeks rep1

description: replicate 1

value: 4 weeks

value: 10 weeks

value: control


title: liver treatment 1 week rep3

description: replicate 3

value: oil palm phenolics 4 weeks after J558 myeloma cell innoculation


title: liver control 1 week rep1

description: replicate 1


title: F.4 mother Sty

description: Hybridized to 250K_Sty

value: female


title: liver control 1 week rep2

description: replicate 2


title: liver treatment 18 hours rep2

description: replicate 2

value: treatment


title: F.8 mother Sty

description: Hybridized to 250K_Sty

value: unaffected

value: mother


title: liver control 18 hours rep3

description: replicate 3

source_name: liver, control, 18 hours

value: 18 hours


title: liver treatment 18 hours rep1

description: replicate 1

value: 6 weeks


title: liver control 18 hours rep2

description: replicate 2

value: male


title: spleen treatment 4 weeks rep3

description: replicate 3

source_name: spleen, treatment, 4 weeks

value: spleen


title: spleen treatment 4 weeks rep2

description: replicate 2


title: liver control 18 hours rep1

description: replicate 1

value: liver


title: liver treatment 4 weeks rep3

description: replicate 3


title: spleen treatment 4 weeks rep1

description: replicate 1


title: spleen control 4 weeks rep3

description: replicate 3

source_name: spleen, control, 4 weeks


title: F.6 child Sty

description: Hybridized to 250K_Sty

value: child

value: peripheral blood

value: Hirschsprung's disease


title: spleen control 4 weeks rep2

description: replicate 2

value: distilled water 4 weeks after J558 myeloma cell innoculation

value: BALB/c


title: DicerLyszCre_IL-4_72h_InVitro rep1

value: Dicer fl/+ LysM-Cre by Dicer fl/+ crossed mice

value: Dicer fl/fl LyszCre+/- (Dicer-deficient)

value: mature bone-marrow derived macrophages

value: Interleukin 4 (50ng/mL)

value: 72 hours


title: spleen treatment 1 week rep2

description: replicate 2

source_name: spleen, treatment, 1 week

value: oil palm phenolics 4 weeks after J558 myeloma cell innoculation

value: 1 week

value: 7 weeks

value: treatment


title: spleen control 4 weeks rep1

description: replicate 1

value: 4 weeks

value: 10 weeks

value: male

value: control


title: spleen treatment 1 week rep3

description: replicate 3

value: spleen


title: spleen control 1 week rep1

description: replicate 1

source_name: spleen, control, 1 week


title: F.4 child NspI

description: Hybridized to 250K_Nsp

value: affected

value: child

value: peripheral blood

value: Hirschsprung's disease


title: spleen treatment 1 week rep1

description: replicate 1

value: BALB/c


title: spleen treatment 18 hours rep2

description: replicate 2

source_name: spleen, treatment, 18 hours

value: 18 hours

value: 6 weeks


title: liver treatment 4 weeks rep1

description: replicate 1

value: liver


title: spleen control 18 hours rep1

description: replicate 1

source_name: spleen, control, 18 hours

value: distilled water 4 weeks after J558 myeloma cell innoculation


title: RS3

city: Callaghan

first: Skye

last: McIver

state: NSW

address: University Drive

department: Biology

country: Australia

institute: University of Newcastle

hyb_protocol: standard illumina hybridisation protocal

scan_protocol: Standard illumina scaning protocol

data_processing: Illumina BeadStudio (version 3.0) was used to generate the raw data. This data was then divided by the mean of snoRNA142 and 234-1 (extension missmatch and PCR contamination control) to eliminate differences in loading of the array platform. The data was then analysed using Significance Analysis of Microarrays (SAM http://www-stat.stanford.edu/_tibs/SAM/ to identify differentially expressed miRNAs)

source_name: adult round spermatids

label_protocol: cy3-labeled cDNAS were prepared with the Illumina microRNA Expression Profiling Assay

extract_protocol: 2-4% BSA gradient sedementation, total RNA was extracted using a standard solution D protocol

value: Swiss

value: Male

value: Pachytene Spermatocytes


title: PS1

source_name: adult pachytene spermatocytes

value: Round Spermatid


title: spleen treatment 18 hours rep1

description: replicate 1

value: oil palm phenolics 4 weeks after J558 myeloma cell innoculation

value: treatment


title: PS2


title: spleen control 1 week rep2

description: replicate 2

value: 1 week

value: 7 weeks

value: male

value: control


title: spleen control 1 week rep3

description: replicate 3

value: spleen


title: spleen treatment 18 hours rep3

description: replicate 3


title: PS3


title: RS2


title: spleen control 18 hours rep3

description: replicate 3


title: spleen control 18 hours rep2

description: replicate 2


title: Th1

city: Kisarazu

first: Soichi

last: Tofukuji

address: 2-6-7 Kazusa-kamatari

department: Human Genome Research

country: Japan

institute: Kazusa DNA Research Institute

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in Th1 conditions

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using GeneChip Operating Software (GCOS) v1.2 software.

source_name: primary CD4 T cell from spleen

label_protocol: Total RNA was extracted using the IVT Labeling kit from Affymetrix

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57−597; 3 mg/ml) and anti-CD28 mAb under CD103+ Th1- or Th1-culture conditions for 2 days in vitro. CD103+ Th1 conditions: IL-4 (3ng/ml), IFNgamma (10ng/ml), TGFbeta (3ng/ml). Th1 conditions: IL-12 (1ng/ml) and an anti-IL-4 mAb (11B11) (1μg/ml). After culturing for 3 more days, the cells were harvested.

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

treatment_protocol: CD103+Th1 and Th1 cells were collected and resuspendet in the Trizol solution (GibcoBRL).

value: CD4 T cell

tag: culture condition


title: RS1


title: VCaP_LBDsiRNA_R1881

city: baltimore

first: Jun

last: Luo

state: MD

address: 600 N Wolfe st

institute: Johns Hopkins University

description: Transient transfection followed by 48 hours in specified culture conditions

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially using washing buffers recommened by Agilent.

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization

source_name: VCaP cells treated with siRNA trageting AR-LBD and cultured in 1nM R1881

label_protocol: 2 µg of total RNA were processed accoridng to instructions in the Agilent Quick AMP Labeling Kit

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: VCaP

tag: genotype/variation

value: transfected with siRNA trageting AR-LBD

tag: culture conditions/treatment

value: cultured in 1nM R1881

value: Prostate

source_name: Total RNA from LNCaP cells grown in normal culture conditions

value: LNCaP

tag: reference


title: VCaP_ControlsiRNA_R1881

source_name: VCaP cells treated with control siRNA and cultured in 1nM R1881

value: transfected with control vector

value: Total RNA from LNCaP cells grown in normal culture conditions


title: CD103+ Th1

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in CD103+ Th1 conditions

tag: cell type


title: Spg2

source_name: day 7-9 Spermatogonia

value: Swiss

value: Male

value: Spermatogonia


title: VCaP_MDV_R1881

description: Treatment with MDV3100 for 24 hours in specified conditions

source_name: VCaP cells treated with MDV for 24 hours in 1nM R1881


title: Th9

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in Th9 conditions

hyb_protocol: Hybridization and washing were done according to Agilent protocol

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.7 software (Agilent). The dataset was normalized using the 75 percentile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

label_protocol: 500ng of RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57−597; 3 mg/ml) and anti-CD28 mAb under Th9+IFNgamma or Th9-culture conditions for 2 days in vitro. Th9+IFNgamma conditions: IL-4 (3ng/ml), IFNgamma (10ng/ml), TGFbeta (3ng/ml). Th9 conditions: IL-4 (10ng/ml), TGFbeta (3ng/ml), and an anti-IFNgamma mAb (1μg/ml). After culturing for 3 more days, the cells were harvested.

treatment_protocol: CD4+Th9 and Th9+IFNgamma cells were collected and resuspendet in the Trizol solution (GibcoBRL).


title: Th9+IFNgamma

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in Th9+IFNgamma conditions


title: LFP_18

city: Freising-Weihenstephan

first: Michal

last: Wysocki

address: Liesel-Beckmann-Straße (Hochfeldweg) 1

department: Chair of Animal Breeding

country: Germany

institute: Technical University Munich

hyb_protocol: 1.65 μg of each single cRNA sample was hybridized at 65°C for 17 hours on separate Chicken Gene Expression Microarrays (Agilent Technologies).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

data_processing: The software Feature Extraction 10.5.1.1, GeneSpring GX 11.0.1 as well as the software Spotfire Decision Site 9.1.2 were used for quality control, statistical data analysis, Gene Ontology annotation and visualization.

organism: Gallus gallus

source_name: Brain_low feather pecking (LFP)

label_protocol: 500 ng of total RNA per sample were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies). The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in vitro transcription (Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.

extract_protocol: The samples were homogenized using FastPrep system (MP Biomedicals). RNA was extracted with the Qiagen RNeasy Lipid Tissue Midi Kit (Qiagen) and entrusted to IMGM Laboratories (Martinsried).

treatment_protocol: Whole brains from two investigated lines (HFP and LFP) were collected at the approximate age of 2 years.

tag: line

value: low feather pecking (LFP)

value: brain


title: Spg1


title: LFP_15


title: LFP_17


title: Spg3


title: LFP_14


title: LFP_12


title: LFP_13


title: Go3

source_name: day 1 gonocytes

value: Gonocytes


title: LFP_10


title: LNCaP95_DBDsiRNA_R1881

description: Treatment with siRNA for 24 hours followed by 48 hours in specified culture conditions

source_name: LNCaP95 cells transfected with siRNA trageting AR-DBD and cultured in 1nM R1881

value: transfected with siRNA trageting AR-DBD


title: LNCaP95_LBDsiRNA_R1881

source_name: LNCaP95 cells transfected with siRNA trageting AR-LBD and cultured in 1nM R1881


title: VCaP_DMSO_R1881

description: Treatment with DMSO for 24 hours in specified conditions

source_name: VCaP cells treated with DMSO for 24 hours in 1nM R1881


title: LFP_16


title: LNCaP95_DBDsiRNA_CSS

source_name: LNCaP95 cells transfected with siRNA trageting AR-DBD and cultured in androgen depleted conditions


title: Go2


title: LNCaP95_ControlsiRNA_R1881

source_name: LNCaP95 cells transfected with control siRNA and cultured in 1nM R1881

value: transfected with control siRNA


title: LFP_11


title: Go1


title: HFP_08

source_name: Brain_high feather pecking (HFP)

value: high feather pecking (HFP)


title: HFP_07


title: LNCaP95_LBDsiRNA_CSS

source_name: LNCaP95 cells transfected with siRNA trageting AR-LBD and cultured in androgen depleted conditions


title: LNCaP95_ControlsiRNA_CSS

source_name: LNCaP95 cells transfected with control siRNA and cultured in androgen depleted conditions


title: HFP_05


title: HFP_04


title: LNCaP_V7_R1881

source_name: LNCaP cells transfected with AR-V7 and cultured in 1nM R1881

value: transfected with AR-V7


title: HFP_06


title: HFP_01


title: HFP_02


title: HFP_09


title: LNCaP_V7_CSS

source_name: LNCaP cells transfected with AR-V7 and cultured in androgen depleted conditions


title: LNCaP_Vector_CSS

source_name: LNCaP cells transfected with control vector and cultured in androgen depleted conditions


title: HFP_03


title: P11-930choline-wk0

status: Public on Mar 16 2012

city: Ithaca

first: Xinyin

last: Jiang

state: NY

address: 241 Kinzelberg Hall, Cornell University

department: Nutritional Sciences

institute: Cornell University

description: Gene expression at study baseline (week 0) in human peripheral blood leukocyte

hyb_protocol: Cy3-labelled aRNA 825ng was fragmented at 60°C for 30 minutes in a reaction volume of 55μL containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. After fragmentation, the samples were cooled on ice for 1 minute. The 2XGEx Hybridization buffer HI-RPM of 55 μL was added to the fragmented sample mixtures.  The sample mixtures prepared above (100μL) was used to hybridized to Agilent Whole Human Gene Expression Microarray 4×44K with an Agilent Microarray Hybridization Chamber (G2534A). Microarray hybridization was performed at 65℃ for 17 hours in the hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent Scanner G2505C using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using protocol GE1_105_Dec08 and Grid: 014850_D_20070820 to obtain background subtracted and spatially detrended Processed Signal intensities. The gBGSubSignal values were log2 transformed and median normalized to get the final normalized data used for between group analyses

source_name: Peripheral Blood leukocyte, pregnant, week 0, 930 mg choline/d

label_protocol: Antisense RNA amplification and cyanine 3 labeling was performed with an Amino Allyl MessageAmp II aRNA amplification kit (Ambion Inc., Grand island, NY) using 1000ng input total RNA according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Not applicable

extract_protocol: Peripheral blood samples were centrifuged at 1055 x g for 15 minutes at 4°C and the buffy coat layer that contains leukocytes was retrieved. The leukocyte samples for RNA extraction was transferred into 1mL TRIzol® Reagent (Invitrogen, Grand Island, NY) for RNA extraction immediately. Total RNA was purified via a commercially available kit (RNeasy Mini kit, Qiagen, Valencia, CA) with on-column DNase digestion. The concentration and quality of the isolated RNA was assayed with a NanoDrop® ND-1000 instrument (Thermo,Wilmington, DE). For RNA quality, a value higher than 1.8 for the ratio of 260 to 280 was deemed acceptable. The integrity of the RNA samples was further determined using an Agilent 2100 Bioanalyzer (Agilent Technologies,Santa Clara, CA). Only samples of an RNA Integrity Number (RIN) >8.0 were included for microarray.

treatment_protocol: Healthy third trimester (gestational week 26-29) pregnant women and non-pregnant women were randomized to a 12-week choline controlled feeding study. The participants  consumed  either 480 (n=6 pregnant and n=5 non-pregnant) or 930 (n=6 pregnant and n=5 non-pregnant) mg choline/d for 12 weeks. Fasting (10-h) peripheral blood samples were drawn with 10 ml EDTA tubes (BD, Franklin Lakes, NJ) at week 0 and week 12

value: peripheral blood leukocyte

value: female

tag: pregnancy status

value: third trimester pregnant

tag: choline intake


title: P12-480choline-wk12

description: Gene expression after consuming 480 mg choline/d for 12 weeks in human peripheral blood leukocyte

source_name: Peripheral Blood leukocyte, pregnant, week 12, 480 mg choline/d


title: P10-480choline-wk12


title: NP10-480choline-wk12

source_name: Peripheral Blood leukocyte, non-pregnant, week 12, 480 mg choline/d

value: Non-pregnant


title: NP9-930choline-wk12

description: Gene expression after consuming 930 mg choline/d for 12 weeks in human peripheral blood leukocyte

source_name: Peripheral Blood leukocyte, non-pregnant, week 12, 930 mg choline/d


title: P11-930choline-wk12

source_name: Peripheral Blood leukocyte, pregnant, week 12, 930 mg choline/d


title: NP7-930choline-wk12


title: NP10-480choline-wk0

source_name: Peripheral Blood leukocyte, non-pregnant, week 0, 480 mg choline/d


title: LNCaP_Vector_R1881

source_name: LNCaP cells transfected with control vector and cultured in 1nM R1881

value: LNCaP

value: cultured in 1nM R1881

value: Prostate

source_name: Total RNA from LNCaP cells grown in normal culture conditions


title: P12-480choline-wk0

source_name: Peripheral Blood leukocyte, pregnant, week 0, 480 mg choline/d


title: P9-930choline-wk12


title: P10-480choline-wk0


title: NP6-930choline-wk0

source_name: Peripheral Blood leukocyte, non-pregnant, week 0, 930 mg choline/d


title: NP9-930choline-wk0


title: smc_moxLDL_3h

city: Toronto

first: Jochen

last: Weile

state: ON

address: 160 College Street

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

description: Human vSMCs 3h after treatment with moxLDL

hyb_protocol: Biotinylated cRNA samples were hybridized to HG-U133A oligonucleotide array Gene Chip (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

scan_protocol: The arrays were stained with streptavidin-phycoerythrin and scanned using the GeneChip Scanner 3000. The data files were analyzed using Affymetrix GeneChipH Software (GCOS) version 1.0 to identify differentially expressed genes.

data_processing: We processed the original Affymetrix HG-U133A CEL image data files using the Bioconductor Affy library for R. Background correction and normalization was performed on the datasets using the RMA method

label_protocol: cRNA samples were biotinylated for hybridization according to protocols supplied by Affymetrix

growth_protocol: Human coronary artery SMCs were purchased from Clonetics (Walkersville, MD) and cultured according to the manufacturer‟s instructions and used between passages 4-7. Confluent SMC cultures were synchronized to quiescence by incubation for 48h in basal medium (SmBM) containing 0.5% FBS.

extract_protocol: DNA-free mRNA was extracted from the cells and mRNA samples from corresponding cell cultures were pooled to reduce inter-sample variation.

treatment_protocol: The cells were then washed and incubated in SmBM+0.5% FBS in the absence or presence of unoxidized LDL or moxLDL (2 μg/ml) for 3h and 21h. These two time points were used for the analysis of the regulation of early and late atherogenesis response genes, respectively. Each reaction was performed in quadruplicate.

value: vascular smooth muscle

tag: treatment

value: with moxLDL (2 ug/ml)


title: smc_untreated LDL_21h

description: Human vSMCs 21h after treatment with unoxidized LDL

value: with unoxidized LDL


title: P9-930choline-wk0


title: NP7-930choline-wk0


title: NP8-480choline-wk0


title: NP5-480choline-wk12


title: NP8-480choline-wk12


title: NP5-480choline-wk0


title: NP6-930choline-wk12


title: P8-480choline-wk0


title: P8-480choline-wk12


title: smc_moxLDL_21h

description: Human vSMCs 21h after treatment with moxLDL


title: P7-930choline-wk12


title: P5-930choline-wk0


title: P5-930choline-wk12


title: P7-930choline-wk0


title: P4-480choline-wk0


title: NP3-930choline-wk12


title: NP2-480choline-wk12


title: NP1-930choline-wk12


title: NP1-930choline-wk0


title: NP4-480choline-wk12


title: NP3-930choline-wk0


title: P4-480choline-wk12


title: NP4-480choline-wk0


title: P3-480choline-wk0


title: P6-480choline-wk12


title: P6-480choline-wk0


title: P3-480choline-wk12


title: NP2-480choline-wk0


title: P2-930choline-wk0


title: Autoantibody profiling of normal sample 34

type: other

city: Stanford

first: Hogune

last: Im

address: 300 Pasteur Dr. Alway M308

department: Genetics

institute: Stanford

data_processing: The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15).  The arrays were then quantile normalized and a comparison of intensities of probes was carried out between the subject and the healthy control group using a two-tailed Mann-Whitney non-parametric test, P<0.01, in Mathematica 8.0 and using Benjamini-Hochberg to correct for multiple hypothesis tests, adjusted P<0.01.

label: Alexa Fluor 647

molecule: other

source_name: Human Blood

treatment_protocol: Precleared Plasma/serum samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner  the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

tag: individual

value: healthy control

value: Plasma/Serum


title: P1-930choline-wk12


title: Autoantibody profileing of test person at a disease contrated timepoint (1)

hyb_protocol: All probing conditions and procedure was followed as described in invitrogen website.  (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

scan_protocol: The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner  the Genepix Pro 6.1 software.

extract_protocol: Precleared Plasma/serum samples were diluted in Washing Buffer and applied to the protein array

value: test person


title: P2-930choline-wk12


title: Autoantibody profileing of test person at a disease contrated timepoint (2)

label_protocol: All probing conditions and procedure was followed as described in invitrogen website.  (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)


title: Autoantibody profiling of normal sample 30


title: Autoantibody profiling of normal sample 33


title: Autoantibody profiling of normal sample 31


title: P1-930choline-wk0


title: Autoantibody profiling of normal sample 28


title: Autoantibody profiling of normal sample 29


title: Autoantibody profiling of normal sample 23


title: Replicate 10

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Mesenchymal progenitor cells_replicate 10

hyb_protocol: hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed;no fractionation;probes were denatured for 3 min at 98 degree celcius;hybridization at 65 degree celcius;SSPE washes as recommended;slides were dipped in acetonitril (10 s) then dried

scan_protocol: scanned with a G2505B Microarray Scanner (Agilent Technologies) quantification software: Feature Extraction (Agilent Technologies)

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOESS normalization.

label_protocol: Low RNA input Fluor linear Amp Kit 5184-3523(Agilent Technologies)following manufacturer's instructions

growth_protocol: Mesenchymal progenitor cells (human MSCs) were obtained as previously described {Siggelkow, 2004 #69; Siggelkow, 1999 #90}. Spongiosa material was obtained during corrective surgery from an otherwise healthy patient (f, 59 y, tibia) and bone fragments were prepared as described previously {Siggelkow, 1998 #86; {Siggelkow, 1999 #90}; Siggelkow, 2003 #94}. When stimulated, cells differentiated to adipocytes, chondrocytes and osteoblasts. Using surface markers for FACS analysis, cells showed a profile consistent with cells of mesenchymal origin.

treatment_protocol: Five days after the cells reached confluence, 10 mM beta-glycerophosphate and 10 µM ascorbic acid 2-phosphate were used for basic osteogenic stimulation (day 13 in culture). In addition, cells were supplemented with 1% human CD-OPO+ serum, with 1% human -OPO-serum or 1% control serum (healthy blood donor) for 14 days.

value: bone spongiosa

tag: disease status

value: Metastatic Crohn's disease without osteoporosis

value: Metastatic Crohn's disease with osteoporosis


title: Replicate 6

description: Mesenchymal progenitor cells_replicate 6

value: Mesenchymal progenitor cells (human MSCs)


title: Autoantibody profiling of normal sample 32


title: Autoantibody profiling of normal sample 24


title: Autoantibody profileing of test person at a disease contrated timepoint (3)


title: Replicate 8

description: Mesenchymal progenitor cells_replicate 8


title: Replicate 12

description: Mesenchymal progenitor cells_replicate 12


title: Autoantibody profiling of normal sample 25


title: Replicate 9

description: Mesenchymal progenitor cells_replicate 9


title: Replicate 4

description: Mesenchymal progenitor cells_replicate 4


title: Replicate 11

description: Mesenchymal progenitor cells_replicate 11


title: Autoantibody profiling of normal sample 26


title: Autoantibody profiling of normal sample 22


title: genomic DNA from DKO1

first: Daniel

last: De Carvalho

address: 101 College Street, room 9-302

institute: Ontario Cancer Institute

description: HCT116 DKO subclone 1 (DKO1)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2.  Non_normalized data matrix contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: HCT116 DKO subclone 1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the cell lines using Qiagen DNeasy Kit according to standard instructions.

tag: cell line background

value: disruption of DNMT3B and DNMT1 (DKO)

value: colon adenocarcinoma cell


title: Replicate 7

description: Mesenchymal progenitor cells_replicate 7


title: Replicate 2

description: Mesenchymal progenitor cells_replicate 2


title: genomic DNA from DKO8

description: HCT116 DKO subclone 8 (DKO8)

source_name: HCT116 DKO subclone 8


title: Autoantibody profiling of normal sample 20


title: Autoantibody profiling of normal sample 21


title: Replicate 1

description: Mesenchymal progenitor cells_replicate 1


title: genomic DNA from HCT116

description: HCT116 wild type

source_name: HCT116 wild type

value: wild type


title: Autoantibody profiling of normal sample 19


title: Effects of LPS on seabream red muscle, 72h, Cy5-labeled reference

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

hyb_protocol: The slides were pretreated with 1% BSA (fraction V), 5 × SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) at room temperature and hybridized overnight at 60ºC in a cocktail containing 1.3 × Denhardt's, 3 × SSC, 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA. All chemicals were from Sigma. After hybridization, slides were washed at room temperature in 0.5 x SSC and 0.1% SDS for 15 min, 0.5 x SSC and 0.01% SDS for 15 min, and twice in 0.06 x SSC for 2 and 1 min, respectively.

scan_protocol: Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon).

data_processing: The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. Low quality spots were excluded from analysis and genes presented with less than three high quality spots on a slide were discarded. After subtraction of median background from median signal intensities, the expression ratios (ER) were calculated. Locally weighted non-linear regression (Lowess) normalization was performed, first for the whole slide and next for twelve rows and four columns per slide. To assess differential expression of genes, the normalized log intensity ratios, or difference of the mean Log2 ER from zero, were analyzed for every pair of slides with reverse labeling (6 spot replicates per gene on each slide, n = 12) with Student´s t-test (p < 0.01).

organism: Sparus aurata

label_protocol: Total RNA from pooled control (n = 5) and LPS-treated (n = 5) sea bream white and red muscle tissues was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain) using SuperScript III Transcriptase. The cDNA synthesis reaction was performed at 50ºC for 2 hours in a 20 µl reaction volume, followed with RNA degradation with 0.2 M NaOH at 37ºC for 15 min and alkaline neutralization with 0.6 M Hepes. Labeled cDNA was purified with Microcon YM30 (Millipore, Madrid, Spain).

growth_protocol: Fish were kept in two tanks of 500 L each with a closed seawater circulation system supplied with a continuous flow-through of oxygenated seawater at 18 oC and under controlled photoperiod (12 hours light – 12 hours dark). Fish were maintained and manipulated in accordance with national legislation for the welfare of animals. After two weeks of acclimatization period, fish were randomly divided into two experimental groups. One tank contained twenty untreated fish (control) and the other tank contained twenty lipopolysaccharide (LPS) treated fish. Before injection and sampling, fish were anesthetized using MS222 (0.1 g L-1; Sigma, Alcobendas, Spain) and were fasted 24 hours before the experiment and the sampling period.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. The quantity of the isolated RNA was tested spectrophotometrically, while its quality was tested by electrophoresis in agarose gel (1% W/V). Afterwards, cDNA was synthesized from 5 μg DNase-treated (RQ1 DNase, Promega, Barcelona, Spain) total RNA in a 20 μl reaction, using SuperScript III Transcriptase (Invitrogen) and a mix of oligo(dT) (Promega) and random primers (Promega) according to the manufacturer’s protocols. The RNA was stored at -80ºC until use.

treatment_protocol: Fish were injected intraperitoneally with either LPS from Escherichia coli (6 mg/kg body weight; Sigma) or with the same volume of PBS (control group). At the end of the experiment, fish were removed from tanks, anesthetized and the white and red muscles were collected from control and from LPS-injected fish after 24 and 72 hours (n = 5 for each sampling point and treatment), snap frozen in liquid nitrogen and stored at -80 °C.

value: red muscle

tag: sampling time point

value: 72hr after injection

source_name: LPS-injected


title: Effects of LPS on seabream red muscle, 72h, Cy3-labeled reference

tag: tissue


title: Replicate 5

description: Mesenchymal progenitor cells_replicate 5


title: Autoantibody profiling of normal sample 27


title: Autoantibody profiling of normal sample 18


title: Effects of LPS on seabream red muscle, 24h, Cy3-labeled reference

value: 24hr after injection


title: Effects of LPS on seabream red muscle, 24h, Cy5-labeled reference


title: Effects of LPS on seabream white muscle, 72h, Cy3-labeled reference

value: white muscle


title: Effects of LPS on seabream white muscle, 72h, Cy5-labeled reference


title: Effects of LPS on seabream white muscle, 24h, Cy5-labeled reference


title: Autoantibody profiling of normal sample 16


title: Autoantibody profiling of normal sample 14


title: Autoantibody profiling of normal sample 17


title: Autoantibody profiling of normal sample 15


title: Autoantibody profiling of normal sample 10


title: Autoantibody profiling of normal sample 9


title: Autoantibody profiling of normal sample 11


title: Autoantibody profiling of normal sample 13


title: Autoantibody profiling of normal sample 8


title: HUES9 Replicate 2

city: San Diego

first: Dave

last: Robbins

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

hyb_protocol: Hybridization to the Human Genome U133 Plus 2.0 GeneChips and staining were performed following Affymetrix protocols in a GeneChip Hybridization Oven 645. Staining was performed following Affymetrix protocols in a GeneChip Fluidics Station 450.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 using Affymetrix default RMA analysis settings.

source_name: Human Blastocyst

label_protocol: Biotinylated aRNA were prepared according to the standard Ambion MessageAmp II Biotin enhanced protocol from 100ng total RNA using the two round manufacturer's protocol.

growth_protocol: Cells were routinely passaged twice a week in respective medium

extract_protocol: PicoPure extraction of total RNA was performed according to Ambion's manufacturer protocol

treatment_protocol: SMC4 was added to appropriate culture conditions during the culture process

value: Blastocyst


title: H1 Replicate 2


title: hiPSC SMC4 from FTC1 - FTi91

source_name: FTC1 SMC4 iPSC - FTi91

value: Foreskin Fibroblast


title: Effects of LPS on seabream white muscle, 24h, Cy3-labeled reference

label_protocol: Total RNA from pooled control (n = 5) and LPS-treated (n = 5) sea bream white and red muscle tissues was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain) using SuperScript III Transcriptase. The cDNA synthesis reaction was performed at 50ºC for 2 hours in a 20 µl reaction volume, followed with RNA degradation with 0.2 M NaOH at 37ºC for 15 min and alkaline neutralization with 0.6 M Hepes. Labeled cDNA was purified with Microcon YM30 (Millipore, Madrid, Spain). We used a dye swap experimental design and each cDNA from a pooled RNA sample was hybridized to two microarrays. For the first slide, test and control cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. A total of eight slides were used in this study. The slides were pretreated with 1% BSA (fraction V), 5 × SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) at room temperature and hybridized overnight at 60ºC in a cocktail containing 1.3 × Denhardt's, 3 × SSC, 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA. All chemicals were from Sigma. After hybridization, slides were washed at room temperature in 0.5 x SSC and 0.1% SDS for 15 min, 0.5 x SSC and 0.01% SDS for 15 min, and twice in 0.06 x SSC for 2 and 1 min, respectively. Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon).


title: Autoantibody profiling of normal sample 7


title: Replicate 3

description: Mesenchymal progenitor cells_replicate 3


title: Autoantibody profiling of normal sample 12


title: Autoantibody profiling of normal sample 5


title: hiPSC Conventional from FTC1 - FTi99

source_name: FTC1 Conventional iPSC - FTi99


title: HUES9 Replicate 1


title: H1 Replicate 1


title: hiPSC SMC4 from FTC1 - FTi93

source_name: FTC1 SMC4 iPSC - FTi93


title: Autoantibody profiling of normal sample 4


title: Autoantibody profiling of normal sample 2


title: Autoantibody profiling of normal sample 3


title: FTC1 Foreskin Fibroblast

source_name: Foreskin Fibroblast


title: Autoantibody profiling of normal sample 6


title: Autoantibody profiling of normal sample 1


title: hiPSC Conventional from IMR-90 Replicate 2

source_name: IMR-90 Conventional iPSC

value: Lung Fibroblast


title: hiPSC SMC4 from IMR-90 Replicate 1

source_name: IMR-90 SMC4 iPSC


title: hiPSC SMC4 from IMR-90 Replicate 2


title: IMR-90 Replicate 2


title: hiPSC Conventional from IMR-90 Replicate 1


title: kidney ko1-vs-wt1

city: Bern

first: Beat

last: Trueb

address: Murtenstrasse 35

department: Dept. of Clinical Research

country: Switzerland

institute: University of Bern

hyb_protocol: Hybridization was performed at 65°C for 17h according to the manufacturer's instructions using reagents of the Gene Expression Hybridization Kit (Agilent 5188-5242).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software Version 10 was used for background subtraction and normalization.

source_name: kidney

label_protocol: RNA samples (600 ng each) were reverse-transcribed into double stranded cDNA in the presence of RNA poly-A controls (Agilent RNA Spike-In Kit 5188-5279). The cDNAs were transcribed into cRNA with T7 polymerase using Cy3-CTP for ko and C5-CTP for wt samples (Agilent Quick Amp labelling kit 5190-0444).

extract_protocol: Total RNA was extracted from 6-9 pooled kidney rudiments with the GeneElute miniprep from Sigma-Aldrich Co.

value: C57BL/6 Fgfrl1-/-

tag: age

value: C57BL/6 wt


title: Normozoospermic individual: Sample N4

status: Public on Mar 15 2012

first: Rafael

last: Oliva

address: C/Casanova 143

department: Ciències Fisiològiques I

institute: University of Barcelona

hyb_protocol: GeneChip Hybridization wash and stain kit

scan_protocol: GeneChip 3000 Scanner 3000 7G system; software: GeneChip  Command Console (AGCC 1.1)

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project.

source_name: Human sperm from a normozoospermic fertile control

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Labeling kit from  2ug total RNA.

growth_protocol: Human donor  Healthy human donor  Healthy human donor  Healthy human donor

extract_protocol: Semen was collected and to rule out the possibility of any somatic cells contamination, we performed a 50% Percoll Gradient followed by PBS washes. After this initial purification, the samples are treated with Somatic Cell Lysis Buffer (0.1% SDS, 0.5% TX-100). Microscopic examination was then used to verify the elimination of the somatic cells. The RNA was then extracted from 15- 30 x106 sperm cells and purified using the Qiagen miRNeasy kit according to the manufacture’s recommendations. The RNA samples were subjected to different quality controls.

tag: fertility status

value: Fertile


title: Normozoospermic individual: Sample N3


title: kidney ko3-vs-wt3

tag: strain


title: IMR-90 Replicate 1

extract_protocol: PicoPure extraction of total RNA was performed according to Ambion's manufacturer’s protocol

tag: cell line


title: Normozoospermic individual: Sample N1


title: Normozoospermic individual: Sample N2


title: kidney ko2-vs-wt2


title: Asthenozoospermic individual: Sample A1 .

source_name: Human sperm from a severe astenozoospermic infertile patient

value: Infetile


title: Asthenozoospermic individual: Sample A4 .

value: Infertile


title: Donor 5 sample9

city: Los Angeles

first: Mirjam

last: Schenk

address: 615 Charles E young Dr S

institute: UCLA

hyb_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility

data_processing: UCLA DNA microarray core facility, normalized with dCHIP using invariant set normalization method. Data were normalized and present calls used to calculate fold change vs media control.

label: pCp-Biotin

source_name: NOD2L+ TLR2/1L t24h

growth_protocol: Human monocytes were purified from healthy donors and subsequently cultured in RPMI/ 10% human serum (Vitamin D3 sufficient)

extract_protocol: RNA was extracted using trizol method and further purified using RNAeasy mini kit (Qiagen)

treatment_protocol: Monocytes were activated using the NOD2L (MDP) and/or the TLR2/1L (19kD)

value: healthy human blood

value: monocytes


title: Asthenozoospermic individual: Sample A2 .


title: Donor 5 sample8

scan_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility

source_name: TLR2/1L t24h


title: Donor 5 sample6

source_name: media t24h

label_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: Asthenozoospermic individual: Sample A3 .


title: Donor 5 sample7

source_name: NOD2L t24h


title: Donor 5 sample5

source_name: NOD2L+ TLR2/1L t6h


title: Donor 4 sample5


title: Donor 5 sample2

source_name: media t6h


title: Donor 4 sample6


title: Donor 5 sample3

source_name: NOD2L t6h


title: Donor 4 sample9


title: Donor 5 sample4

source_name: TLR2/1L t6h


title: Donor 4 sample4


title: Donor 4 sample1

source_name: media t0h


title: Donor 3 sample7


title: Donor 5 sample1


title: Donor 4 sample3


title: Donor 4 sample8


title: Donor 3 sample9


title: Donor 2 sample6


title: Donor 3 sample3


title: Donor 2 sample9


title: Donor 2 sample7


title: Donor 3 sample1


title: Donor 4 sample2


title: Donor 3 sample6


title: Donor 3 sample4


title: Donor 3 sample5


title: Donor 2 sample8


title: Donor 3 sample2


title: Donor 2 sample4


title: Donor 3 sample8


title: Donor 2 sample1


title: Donor 2 sample5


title: Donor 1 sample8


title: Donor 1 sample9


title: Donor 1 sample3


title: Donor 1 sample7


title: Donor 1 sample4


title: Donor 2 sample2


title: Donor 1 sample6


title: Donor 2 sample3


title: Donor 1 sample1


title: Donor 4 sample7


title: Donor 1 sample2


title: Donor 1 sample5


title: xenograft_treated_4hr_replicate_4_on_human_U133plus2

city: Auckland

first: Li

last: Wang

address: 85 Park Rd

department: Molecular Medicine & Pathology

country: New Zealand

institute: University of Auckland

description: human array results of xenograft 4h-DMXAA-treated 4

hyb_protocol: 7.5 ug of fragmented cRNA were hybridized to the indicated GeneChips

scan_protocol: GCOS v2 and G2500A scanner

data_processing: GSM646063, GSM646057, GSM646064 AND GSM646058 UNDERWENT SPIKE-BASED NORMALISATION using the hybridisation control spikes, all other arrays in this study underwent RMA normalisation using the Affy package in the R environment.

organism:
Homo sapiens
Mus musculus

source_name: human melanoma tumour cells xenografted into immunodeficient mice

label_protocol: Biotinylated cRNA generated using the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: A375 cells were inoculated to CD-1 nude mice to form xenograft

extract_protocol: Trizol extraction of total RNA from tissues or cells from xenografts

treatment_protocol: The xenograft tumors on mice were treated or untreated by DMXAA for 4 hours.

tag: agent

value: 5,6-Dimethylxanthenone-4-acetic acid


title: xenograft_treated_4hr_replicate_5_on_human_U133plus2

description: human array results of xenograft 4h-DMXAA-treated 5

value: human melanoma tumour cells xenografted into immunodeficient mice


title: xenograft_untreated_4hr_replicate_5_on_human_U133plus2

description: human array results of xenograft untreated 5

value: untreated


title: xenograft_treated_4hr_replicate_3_on_human_U133plus2

description: human array results of xenograft 4h-DMXAA-treated 3


title: CRL-BT474_1

city: Brussels

first: Sandeep

middle: K.

last: Singhal

state: Brussels

address: Boulevard de Waterloo, 125

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA Bioconductor (default parameters) and log2 transformation.

source_name: Fibroblast

label_protocol: standard Affymetrix protocol

extract_protocol: Agilent Absolutely RNA microprep kit

tag: cell/tissue type

value: Fibroblast

tag: co-cultured with


title: CRL-MDA361_2


title: CRL-CTR_1


title: CRL-CTR_2


title: CRL-SKBR3_1


title: CRL-BT474_2


title: CRL-MDA231_1


title: CRL-CTR_3


title: CRL-SKBR3_2


title: xenograft_untreated_4hr_replicate_4_on_human_U133plus2

description: human array results of xenograft untreated 4

tag: cell type


title: CRL-LY2_2


title: xenograft_untreated_4hr_replicate_3_on_human_U133plus2

description: human array results of xenograft untreated 3


title: CRL-LY2_1


title: CRL-T47D_2


title: MSC-CTR_3

source_name: Mesenchymal Stem Cells (MSC)

value: MSC


title: CRL-MCF7_1


title: CRL-T47D_1


title: MSC-CTR_1


title: MSC-BT474_1


title: MSC-SKBR3_2


title: MSC-CTR_2


title: MSC-SKBR3_1


title: MSC-MDA231_2


title: MSC-MDA231_1


title: CRL-MDA231_2


title: MSC-LY2_2


title: MSC-MCF7_1


title: CRL-MDA361_1


title: MSC-MDA361_1


title: MSC-MCF7_2


title: HS578ST-CTR_1

source_name: Myoepithelial

value: Myoepithelial


title: MSC-LY2_1


title: MSC-T47D_1


title: HS578ST-CTR_2


title: HS578ST-BT474_2


title: HS578ST-MDA361_2


title: HS578ST-MDA231_2


title: HS578ST-BT474_1


title: HS578ST-MDA361_1


title: HS578ST-LY2_2


title: HS578ST-CTR_3


title: HS578ST-T47D_1


title: HS578ST-MCF7_1


title: HS578ST-MCF7_2


title: HS578ST-LY2_1


title: HS578ST-MDA231_1


title: IJB_Nor_3

source_name: Normal

label_protocol: TargetAMP 2-Round Aminoallyl-aRNA Amplification kit 1.0 kit from Epicentre Biotechnologies

extract_protocol: Rneasy Micro kit (Qiagen)

value: Normal


title: HS578ST-SKBR3_2


title: IJB_CD10_12

source_name: Tumor

value: Tumor

tag: her2_status (1= positive, 0= negative)

tag: er_status (1= positive, 0= negative)

tag: pgr_status (1= positive, 0= negative)

tag: grade

tag: size_tumor (cm)

tag: age (year)


title: IJB_CD10_15


title: IJB_Nor_1


title: IJB_Nor_2


title: HS578ST-T47D_2


title: IJB_CD10_11


title: IJB_CD10_16


title: IJB_CD10_13


title: IJB_CD10_14


title: IJB_CD10_10


title: IJB_CD10_5


title: IJB_CD10_9


title: IJB_CD10_8


title: IJB_CD10_7


title: IJB_CD10_2


title: IJB_CD10_1


title: IJB_CD10_6


title: IJB_CD10_27


title: IJB_CD10_25


title: CRL-MCF7_2


title: IJB_CD10_26


title: IJB_CD10_3


title: IJB_CD10_24


title: IJB_CD10_23


title: IJB_CD10_21


title: IJB_CD10_22


title: IJB_CD10_4


title: IJB_CD10_19


title: IJB_CD10_17


title: IJB_CD10_18


title: IJB_CD10_28


title: IJB_CD10_20


title: MCF7_siRNA_WT1_48h

description: Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 48 h after the corresponding gene was knocked down using siRNA

hyb_protocol: Following fragmentation, 15 ug of labelled cRNA was hybridized for 16 h at 45°C @ 60 RPM on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Data was analyzed with R using Affymetrix default analysis settings and RMA as normalization method.

source_name: MCF7 cells that were transfected by siRNA targeting the corresponding gene

label_protocol: Biotinylated cRNA was prepared from 4 ug total RNA according to the standard Affymetrix protocols  (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF7 cells were grown in DMEM medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, 0.01 mg/ml bovine insulin, 2 mM L-Glutamine, 1 U/ml penicillin G and 1 ug/ml streptomycin sulfate, at 37 ˚C in a fully humidified atmosphere containing 5% CO2

extract_protocol: Total RNA was extracted using Trizol reagent and the RNA was purified using RNA affinity columns according to the manufacturer's instructions.

treatment_protocol: MCF7 cells were seeded in antibiotic-free DMEM, 5% FBS, 1 mM sodium pyruvate, 0.01 mg/ml bovine insulin, 2 mM L-Glutamine, in a total volume of 2 ml/well in 6-well plates. After 24 h at a cell confluency of 30%, cells were transfected with 30 μl Oligofectamine and 100 nM siRNA using OptiMEM transfection media according to the manufacturer's instructions. The cells were incubated for 48 h and harvested in TRIzol reagent

tag: knocked out gene


title: MCF7_UNTREATED_2_48h


title: MCF7_UNTREATED_1_48h


title: MCF7_siRNA_TP53_48h


title: MCF7_siRNA_TOP2A_48h


title: MCF7_siRNA_TEL2_2_48h


title: MCF7_siRNA_TEL2_1_48h


title: MCF7_siRNA_TCEA1_48h


title: MCF7_siRNA_SMAD7_48h


title: MCF7_siRNA_SP100_48h


title: MCF7_siRNA_SICONTROL_3_48h


title: MCF7_siRNA_STAT1_48h


title: MCF7_siRNA_SKP2_48h


title: MCF7_siRNA_STAT5B_48h


title: MCF7_siRNA_SLC2A3_48h


title: MCF7_siRNA_RELA_48h

value: RELA


title: MCF7_siRNA_PIAS_48h

value: PIAS


title: MCF7_siRNA_SICONTROL_2_48h


title: MCF7_siRNA_PCNA_48h

value: PCNA


title: MCF7_siRNA_RBL2_48h


title: MCF7_siRNA_PAX3_2_48h


title: MCF7_siRNA_SICONTROL_1_48h


title: MCF7_siRNA_POLR2A_1_48h


title: MCF7_siRNA_RB1_48h


title: MCF7_siRNA_NFKB1_3_48h


title: MCF7_siRNA_NCOR2_48h


title: MCF7_siRNA_NFKB1_1_48h


title: MCF7_siRNA_MYBL2_48h


title: MCF7_siRNA_MYC_48h

value: MYC


title: MCF7_siRNA_NMI_48h

value: NMI


title: MCF7_siRNA_MAX_48h

value: MAX


title: MCF7_siRNA_PAX3_1_48h


title: HS578ST-SKBR3_1


title: MCF7_siRNA_NFKB1_2_48h


title: MCF7_siRNA_MCM2_48h


title: MCF7_siRNA_MAPK14_48h


title: MCF7_siRNA_POLR2A_2_48h


title: MCF7_siRNA_HOXB7_48h


title: MCF7_siRNA_JUND_48h

value: JUND


title: MCF7_siRNA_JUN_48h

value: JUN


title: MCF7_siRNA_HDAC3_48h


title: MCF7_siRNA_HSF2_48h


title: MCF7_siRNA_HDAC5_48h


title: MCF7_siRNA_FOXP1_48h


title: MCF7_siRNA_FOXO3A_48h


title: MCF7_siRNA_FOXO1A_48h


title: MCF7_siRNA_HIF1A_48h


title: MCF7_siRNA_ID1_48h


title: MCF7_siRNA_FOXJ2_48h


title: MCF7_siRNA_FOS_48h

value: FOS


title: MCF7_siRNA_MAPK1_48h


title: MCF7_siRNA_ESRRA_48h

value: ESRRA


title: MCF7_siRNA_ESR1_2_48h


title: MCF7_siRNA_GATA3_48h


title: MCF7_siRNA_ESR1_1_48h


title: MCF7_siRNA_E2F5_48h


title: MCF7_siRNA_E2F1_48h


title: MCF7_siRNA_ERBB2_48h


title: MCF7_siRNA_FOXC1_48h


title: MCF7_siRNA_ERF_48h

value: ERF


title: MCF7_siRNA_CTNNB1_48h


title: MCF7_siRNA_CDK2_48h


title: MCF7_siRNA_CENPF_48h

value: CENPF


title: MCF7_siRNA_CEBPA_48h

value: CEBPA


title: MCF7_siRNA_CDKN2A_48h


title: MCF7_siRNA_CDC2_48h


title: MCF7_siRNA_CCND3_48h


title: MCF7_siRNA_CDC25A_48h


title: MCF7_siRNA_CREBBP_48h

value: CREBBP


title: MCF7_siRNA_CHEK1_48h


title: MCF7_siRNA_CEBPD_48h

value: CEBPD


title: MCF7_siRNA_CCNG2_48h


title: MCF7_siRNA_CDC20_48h


title: MCF7_siRNA_CDC34_48h


title: MCF7_siRNA_CENPE_48h

value: CENPE


title: MCF7_siRNA_CEBPB_48h

value: CEBPB


title: MCF7_siRNA_CDK4_48h


title: MCF7_siRNA_CDC25B_48h


title: MCF7_siRNA_CCNA2_48h


title: MCF7_siRNA_BCL6_48h


title: MCF7_siRNA_CCNB1_48h


title: MCF7_siRNA_CCL5_48h


title: MCF7_siRNA_CDC16_48h


title: MCF7_siRNA_BRCA1_48h


title: MCF7_siRNA_BRCA2_48h


title: MCF7_siRNA_AKT1_48h


title: MCF7_siRNA_BCL2_48h


title: MCF7_siRNA_ABL1_48h


title: A375 UNTREATED3 48h

description: Gene expression profile of A375 cells 48 h after the corresponding gene was knockdown by siRNA  was analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays

hyb_protocol: Following fragmentation, 15 ug of labelled cRNA was hybridized for 16 hr at 45°C @ 60 RPM on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with R using Affymetrix default analysis settings and RMA as normalization method.

source_name: untreated A375 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A375 cells were grown in DMEM medium containing 10% FBS at 37 ˚C in a fully humidified atmosphere containing 5% CO2

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

treatment_protocol: A375 cells were seeded in 6-well plates.  20h after seeding when the cells reached 30% confluence, they were transfected with 100nm of siRNA with 30μl Oligofectamine accroding to the manufacture's instruction.  After 48h, the cells were harvested and  RNAs were used for the microarray analysis.

tag: knockdown

value: untreated


title: A375 siRNA-STAT6 48h

source_name: A375 cells that were transfected by siRNA targeting the corresponding gene


title: MCF7_siRNA_ARHGEF1_48h


title: A375 siRNA-SKP2 48h


title: A375 siRNA-TCEA1 48h


title: A375 siRNA-TP53 48h


title: A375 UNTREATED2 48h


title: A375 siRNA-STAT1 48h


title: MCF7_siRNA_ATR_48h

value: ATR


title: A375 siRNA-SP1 48h


title: A375 siRNA-CONTROL1 48h

source_name: A375 cells that were transfected by siRNA control

value: siRNA-CONTROL


title: A375 siRNA-CONTROL2 48h


title: A375 siRNA-SP100 48h


title: A375 siRNA-RBL2 48h


title: A375 siRNA-CONTORL3 48h


title: A375 siRNA-STAT3 48h


title: A375 siRNA-PIK3CB 48h


title: A375 siRNA-PIAS1 48h


title: A375 siRNA-NMI 48h

value: siRNA-NMI


title: A375 siRNA-RELA 48h

value: siRNA-RELA


title: A375 siRNA-RB1 48h


title: A375 UNTREATED1 48h


title: A375 siRNA-PCNA 48h

value: siRNA-PCNA


title: A375 siRNA-MITF 48h

value: siRNA-MITF


title: A375 siRNA-NCOR2 48h


title: A375 siRNA-MAP2K1 48h


title: A375 siRNA-HSF2 48h


title: A375 siRNA-MCM2 48h


title: A375 siRNA-FOXO3A 48h


title: A375 siRNA-MAPK1 48h


title: A375 siRNA-HDAC3 48h


title: A375 siRNA-GABARAP 48h

value: siRNA-GABARAP


title: A375 siRNA-FOXM1 48h


title: A375 siRNA-HDAC2 48h


title: A375 siRNA-ETS1 48h


title: Old Female 030, Batch 2

city: Boston

first: William

middle: R

last: Swindell

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

description: tail skin from old female CB6F1 mouse (age 30 months)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: Old Female 030

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Laboratory animals were maintained under standard conditions in accordance with protocols approved by animal welfare committees at the University of Michigan

extract_protocol: RNA was extracted using QIAGEN RNEasy mini kits

treatment_protocol: CB6F1 hybrid mice were obtained from NIA (n = 5 males at 5 months of age; n = 5 females at 5 months of age; n = 5 males at 30 months of age; n = 5 females at 30 months of age). For these treatments, young mice correspond to those at 5 months of age, and old mice correspond to those at 30 months of age. Mice were fasted for 6-8 hours and then sacrificed by CO2 inhalation. Upon sacrifice, tail skin was collected and samples were stored in RNAlater (Qiagen cat. no. 76106) and placed at 4oC for 24 hours before transitioning to -20oC. All samples were disrupted using a rotor-stator homogenizer and RNA extractions were performed using the Qiagen RNeasy Fibrous Tissue kit (Qiagen cat. no. 74704), with on-column DNAase digestion (Qiagen cat. no. 79254). Extracted RNA was quantified using the NanoDrop spectrophotometer and RNA quality was evaluated using the Agilent Bioanalyzer.

value: 30 mo

tag: tissue

value: tail skin

tag: gender

value: female


title: A375 siRNA-CHEK1 48h


title: Zn50uM_M9_10min_14028s_rep1

city: Cambridge

first: Lucas

middle: Blas

last: Pontel

state: cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: LMB-MRC

description: cy3: sample without metal; cy5:sample treated with metal

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.xys file) from Nimblescan software was subjeted to webarrayDB (http://www.webarraydb.org/webarray/index.html) Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y.  Bioinformatics, 2009, doi:10.1093/bioinformatics/btp430. The webarrayDB was set to processes the data using the function Half for background correction, then data normalization was done using the median of M-values (log-ratios). Finally, quantile normalization is used to ensure that the intensities have the same empirical distribution across arrays and across channels.
The data is the mediam M (group2-group1)=log2 (Ia/Ib), where Ia is the average intensity group2 and Ib is the average intensity group 1.  Group2 stands values for samples treated with metal and group1 samples grown without metal

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: sample without metal

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown up to OD 0.6 without metal and then 10 minutes in presences of metal

extract_protocol: RNA isolation using SV plus from Promega

treatment_protocol: 10 minutes in presence of metal

tag: medium

tag: metal

source_name: sample treated with metal

value: Zinc

tag: metal concentration


title: A375 siRNA-CDK4 48h

tag: cell line


title: Old Female 029, Batch 1

source_name: Old Female 029

tag: age

tag: strain


title: A375 siRNA-CDK7 48h


title: Zn50uM_M9_10min_14028s_rep2

description: cy3: sample treated with metal; cy5:sample without metal


title: Old Female 028, Batch 1

source_name: Old Female 028


title: A375 siRNA-CDC37 48h


title: Old Female 027, Batch 2

source_name: Old Female 027


title: A375 siRNA-CDK2 48h


title: A375 siRNA-CEBPZ 48h

value: siRNA-CEBPZ


title: Cu10uM_M9_10min_14028s_rep2

value: Copper


title: A375 siRNA-CDC16 48h


title: A375 siRNA-CDC25B 48h


title: A375 siRNA-CDC2 48h


title: Young Female 019, Batch 1

description: tail skin from young female CB6F1 mouse (age 5 months)

source_name: Young Female 019

value: 5 mo


title: Old Female 026, Batch 1

source_name: Old Female 026


title: A375 siRNA-CCND3 48h


title: A375 siRNA-CDKN2C 48h


title: Young Female 018, Batch 1

source_name: Young Female 018


title: Zn0.25mM_SLB_10min_14028s_rep2

value: SLB


title: A375 siRNA-CCNB2 48h


title: Young Female 020, Batch 1

source_name: Young Female 020


title: Cu1mM_SLB_10min_14028s_rep1


title: Zn0.25mM_SLB_10min_14028s_rep1


title: Cu10uM_M9_10min_14028s_rep1


title: A375 siRNA-CEBPD 48h

value: siRNA-CEBPD


title: Cu1mM_SLB_10min_14028s_rep2

value: untreated


title: A375 siRNA-CTNNB1 48h


title: Old Male 015, Batch 2

description: tail skin from old male CB6F1 mouse (age 30 months)

source_name: Old Male 015

value: male


title: A375 siRNA-ABL1 48h


title: Old Male 014, Batch 2

source_name: Old Male 014


title: A375 siRNA-CCNB1 48h


title: Young Male 003, Batch 1

description: tail skin from young male CB6F1 mouse (age 5 months)

source_name: Young Male 003


title: Young Male 005, Batch 1

source_name: Young Male 005


title: A375 siRNA-CCNA2 48h


title: Human A375 cell RNA_on_human_U133plus2 chip

description: sample contains human cells only

hyb_protocol: 7.5 ug of fragmented cRNA were hybridized to the indicated GeneChips.

scan_protocol: GCOS v2 and G2500A scanner.

source_name: human melanoma cell line A375

extract_protocol: Trizol extraction of total RNA from tissues or cells.

tag: agent


title: xenograft_treated_4hr_replicate 5_on_mouse_430v2 chip

description: mouse array results of xenograft 4h-DMXAA-treated 5

source_name: human melanoma tumour cells xenografted into immunodeficient mice

tag: cell type

value: 5,6-Dimethylxanthenone-4-acetic acid


title: Young Female 016, Batch 2

source_name: Young Female 016


title: xenograft_treated_4hr_replicate 2_on_human_U133plus2 chip

description: sample contains human and mouse cells

value: human melanoma tumour cells xenografted into immunodeficient mice


title: Old Male 011, Batch 2

source_name: Old Male 011


title: Mouse tissue RNA_on_human_U133plus2 chip

description: sample contains mouse cells only

source_name: mixed mouse tissues

value: mixed mouse tissues


title: Young Female 017, Batch 2

source_name: Young Female 017


title: Old Male 013, Batch 2

source_name: Old Male 013


title: Young Male 004, Batch 1

source_name: Young Male 004


title: Old Male 012, Batch 2

source_name: Old Male 012


title: HeLa S3 HBO1 control experiment 2

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

description: HeLa S3 transduced with a control siRNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw bead studio data were processed using R and the BioConductor package lumi. Data were log2 transformed and quantile normalized using subsequently the lumiT and lumiN functions.

source_name: cervical adenocarcinoma

growth_protocol: HeLa S3 cells were grown on 150mm plastic dishes at 37C, 5% CO2 to an approximate confluence of 90%

extract_protocol: Total cellular RNA was extracted with Trizol (Invitrogen) and purified using Macherey-Nagel NucleoSpin RNA II kit.

treatment_protocol: For JADE1 over-expression, HeLa S3 were infected with a retrovirus encoding FLAG-JADE1, and stable clones expressing the FLAG protein were isolated. For HBO1 knock-down, HeLa S3 cells were transiently transfected with siRNA directed against HBO1 using Invitrogen Oligofectamine as per manufacturer's protocol.

value: HeLa

tag: treatment

value: HBO1 control


title: xenograft_treated_4hr_replicate 1_on_human_U133plus2 chip

description: sample contains human and mouse cells


title: HeLa S3 HBO1 control experiment 1

description: HeLa S3 transduced with a control siRNA

label_protocol: Standard Illumina hybridization protocol


title: Young Male 002, Batch 2

source_name: Young Male 002


title: xenograft_untreated_4hr_replicate 2_on_human_U133plus2 chip

description: sample contains human and mouse cells


title: HeLa S3 HBO1 siRNA rep 1

description: HeLa S3 transiently transfected with HBO1 siRNA

value: HBO1 siRNA


title: xenograft_treated_4hr_replicate 3_on_mouse_430v2 chip

description: mouse array results of xenograft 4h-DMXAA-treated 3


title: HeLa S3 HBO1 siRNA rep 2


title: xenograft_untreated_4hr_replicate 1_on_human_U133plus2 chip

description: sample contains human and mouse cells


title: Young Male 001, Batch 2

source_name: Young Male 001


title: A375 siRNA-AKT1 48h

source_name: A375 cells that were transfected by siRNA targeting the corresponding gene


title: Infant_Placebo_F_571

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

institute: Cambridge University

description: Sample excluded following quality control, From the same individual as cord blood 29

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v2011.1

extract_protocol: Gentra Puregene (Qiagen)

treatment_protocol: Consenting, non-pregnant women aged 17-45 resident in West Kiang, Gambia were randomised to receive daily supplementation with either UNIMMAP [daily dose; Vitamin A (800 RE), Vitamin D (200 IU), Vitamin E (10 mg), Vitamin C (70 mg),Vitamin B1(1.4 mg), Vitamin B2 (1.4 mg), Niacin (18 mg), Vitamin B6 (1.9 mg), Vitamin B12 (2.6 mg), Folic acid (400 μg), Iron (30 mg), Zinc (15 mg), Copper (2 mg), Selenium (65 μg) and Iodine (150 μg)] or placebo.  Once pregnancy was confirmed by positive pregnancy test at mean gestational age 9.5 weeks women ceased supplementation, and all women received a standard antenatal preparation of iron (60 mg) and folate (250 μg).  Women were excluded from this analysis if they were enrolled for less than 14 days before last menstrual period, or if they apparently consumed less than 70% of allocated tablets.  The trial was approved by the MRC / Gambian Government Ethics Committee, and the current study was also approved by the MRC Laboratories Fajara Scientific Co-ordinating Committee (L2007.77, 21/9/07) and the Gambian Government Ethics Committee (25/10/07).

value: Peripheral blood

value: Placebo

tag: month of conception (estimated)


title: xenograft_untreated_4hr_replicate 4_on_mouse_430v2 chip

description: mouse array results of xenograft untreated 4


title: Cord_UNIMMAP_M_21

description: Sample excluded following quality control

value: Umbilical cord blood

value: UNIMMAP (micronutrient supplemented)


title: Infant_Placebo_F_597

description: From the same individual as cord blood 422

value: female


title: xenograft_untreated_4hr_replicate 3_on_mouse_430v2 chip

description: mouse array results of xenograft untreated 3


title: Cord_UNIMMAP_M_15

description: Sample excluded following quality control, From the same individual as infant peripheral blood 548


title: xenograft_treated_4hr_replicate 4_on_mouse_430v2 chip

description: mouse array results of xenograft 4h-DMXAA-treated 4


title: xenograft_treated_4hr_replicate 1_on_mouse_430v2 chip

description: sample contains human and mouse cells


title: xenograft_untreated_4hr_replicate 2_on_mouse_430v2 chip

description: sample contains human and mouse cells


title: E15 iron deficient kidney pull 1

city: New York

first: Max

last: Werth

address: 630WEST 168th STREET P&S 10-501

institute: Columbia University

description: gene expression data from pull of 16 mouse kidneys at the developmental stage E15 under iron defecient diet

hyb_protocol: Following fragmentation, 15 ug of fragmented and labeled cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrics GeneChip Scanner 3000

data_processing: The data were analyzed with robust multichip analysis (RMA) using the Affymetrix microarray *.cel image file and GeneTraffic(R) (Silicon Genetics) software

source_name: pull of 16 mouse kidneys at the developmental stage E15 under iron deficient diet

label_protocol: biotinylated cRNA was prepared using Encore Biotin Module (Nugen) according to the manufacturer's instructions.

extract_protocol: total RNA was extracted using RNAqueous Micro Kit (Ambion) according to the manufacturer's instruction.

treatment_protocol: Female mice C57BL/6 (Charles River, USA) were used in the experiments. 8-weeks-old female mice were divided into two groups, control and iron deficient. The iron deficient group was maintained on an iron deficient synthetic diet containing approximately 2-6ppm iron (TD.80396, Harlan,USA). The control group was provided with an iron sufficient diet containing 220ppm iron. Water was served ad libitum in plastic bottles. At least 20 mice were included in each group. Both experimental and control groups were fed the diets for 3 weeks prior to gestation. After one month the females were mated with C57BL/6 males. The following morning, females were checked for the presence of vaginal plugs. If a plug was present, that morning was designated as E0.5. Females were fed their designated diets during the breeding period and throughout pregnancy

tag: diet

value: iron deficient diet

value: Kidney

tag: developmental stage


title: Infant_UNIMMAP_F_588

description: Sample excluded following quality control, From the same individual as cord blood 151


title: Mouse tissue RNA_on_mouse_430v2 chip

description: sample contains mouse cells only


title: Infant_Placebo_F_583

description: From the same individual as cord blood 10


title: Infant_Placebo_F_543

description: From the same individual as cord blood 290


title: Cord_Placebo_M_6


title: Infant_UNIMMAP_F_546

description: From the same individual as cord blood 334


title: E15 control kidney pull 2

description: gene expression data from pull of 16 mouse kidneys at the developmental stage E15 under normal diet

value: normal diet


title: Infant_Placebo_F_585

description: From the same individual as cord blood 328


title: Human A375 cell RNA_on_mouse_430v2 chip

description: sample contains human cells only


title: E15 iron deficient kidney pull 2


title: Infant_UNIMMAP_F_601

description: From the same individual as cord blood 291


title: Infant_Placebo_F_559

description: From the same individual as cord blood 144


title: Infant_Placebo_F_558

description: From the same individual as cord blood 437


title: Infant_UNIMMAP_F_522

description: From the same individual as cord blood 272


title: Infant_UNIMMAP_M_565

description: From the same individual as cord blood 162


title: Infant_Placebo_M_561


title: Infant_UNIMMAP_F_517

description: From the same individual as cord blood 412


title: xenograft_untreated_4hr_replicate 1_on_mouse_430v2 chip

description: sample contains human and mouse cells


title: E15 control kidney pull 1

source_name: pull of 16 mouse kidneys at the developmental stage E15 under normal diet


title: Infant_UNIMMAP_M_530

description: From the same individual as cord blood 316


title: Infant_Placebo_F_542


title: Infant_UNIMMAP_M_510

description: From the same individual as cord blood 325


title: xenograft_treated_4hr_replicate 2_on_mouse_430v2 chip

description: sample contains human and mouse cells


title: Infant_UNIMMAP_M_548


title: Infant_Placebo_M_509


title: Cord_UNIMMAP_M_438


title: Cord_UNIMMAP_M_287


title: Cord_UNIMMAP_M_285


title: Infant_UNIMMAP_F_589

description: From the same individual as cord blood 8


title: Infant_Placebo_M_498

description: From the same individual as cord blood 170


title: Cord_UNIMMAP_M_150


title: Infant_Placebo_M_519

description: From the same individual as cord blood 429


title: Infant_Placebo_M_507

description: From the same individual as cord blood 295


title: Infant_Placebo_M_541

description: From the same individual as cord blood 318


title: Cord_UNIMMAP_M_316

description: From the same individual as infant peripheral blood 530


title: Infant_Placebo_M_527


title: Cord_UNIMMAP_M_162

description: From the same individual as infant peripheral blood 565


title: Cord_UNIMMAP_M_325

description: From the same individual as infant peripheral blood 510


title: Cord_UNIMMAP_M_423


title: Cord_UNIMMAP_M_36


title: Cord_UNIMMAP_M_28


title: Cord_Placebo_M_439


title: Cord_Placebo_M_431


title: Cord_Placebo_M_175


title: Cord_Placebo_M_333


title: Cord_Placebo_M_429

description: From the same individual as infant peripheral blood 519


title: 132V

city: rochester

first: keyi

last: liu

address: 1425 portland ave

institute: Rochester General Research Institute

description:
3 technical replicates: V3_H013, V3_H014, V3_H015
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.

hyb_protocol: 10 μg Cy5-labeled aRNA was hybridized to Human OneArray glass slide containing 30,968 human genome probes and 1,082 experimental control probes according to the manufacturer's standard protocols (PhalanxBio, CA, USA). The Human OneArray slide was prehybridized for 2 h at 42C with OneArray Pre-hybridization buffer and then hybridized for 16 h at 42C with OneArray hybridization buffer. The slides were then washed according to the manufacturer’s instruction (PhalanxBio Inc, CA, USA).

scan_protocol: The arrays were scanned at 5 μm resolution using a Molecular Dynamics Axon 4100A scanner. Raw intensity signals for each microarray were captured and computed using the GenePixPro™ Software. Raw data formats were stored in TIFF images and GPR data files.

data_processing: The data from all microarrays in each experimental set was then analyzed using Omicsoft Array Studio software; control and missing features were removed, and the remaining signals were quantile normalized. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques.

source_name: PBMCs

label_protocol: 10 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA Amplification Kit (Cat. No. 1753) (Applied Biosystems) according to the instructions. The aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Lifesciences). RNA was purified and fragmented using Ambion’s RNA Fragmentation Reagents.

growth_protocol: Blood was collected from children with acute otitis media caused by Nontypeable Haemophilus influenzae and their pre-infection healthy stage.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll gradient and total RNA was extracted from PBMCs using the QIAamp RNA blood Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions.

value: blood

value: peripheral blood mononuclear cells (PBMCs)

tag: patient

tag: infection stage

value: pre-infection


title: Comparative experiment (#2-2) of wild type vs ntrBC mutant

city: Seattle

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

hyb_protocol: The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath for 14-16 h of hybridization.

scan_protocol: After hybridization, the slides were washed and scanned with a scanner from PerkinElmer or Agilent.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

organism: Rhodopseudomonas palustris

source_name: wild type (Cy3)

label_protocol: Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction.

extract_protocol: Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: genotype/variation

value: wild-type cells

tag: growth

value: NF with succinate and yeast extract

source_name: ntrBC mutant (Cy5)

value: ntrBC mutant cells


title: 136A

description:
3 technical replicates: A4_H022, A4_H023, A4_H024
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.

tag: tissue

value: infection


title: 128V

description:
3 technical replicates: V2_H007, V2_H008, V2_H009
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: Cord_Placebo_M_282

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

label_protocol: Standard Illumina Protocol

tag: gender

value: male


title: Cord_Placebo_M_314


title: 136V

description:
3 technical replicates: V4_H019, V4_H020, V4_H021
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: Cord_Placebo_M_295

description: From the same individual as infant peripheral blood 507


title: xenograft_untreated_4hr_replicate 5_on_mouse_430v2 chip

description: mouse array results of xenograft untreated 5

source_name: human melanoma tumour cells xenografted into immunodeficient mice

value: untreated


title: Adult male HVC replicate 4

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: no data processing (providing only raw data)

organism: Taeniopygia guttata

source_name: universal SoNG reference

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Brain regions HVC and Shelf were laser-capture microdissected from brain sections of adult male zebra finches.

tag: brain region

value: Telencephalon

value: Male and female

value: Adult

source_name: HVC

value: HVC

value: Male


title: Adult male HVC replicate 6


title: 116A

description:
3 technical replicates: A1_H004, A1_H005, A1_H006
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: 128A

description:
3 technical replicates: A2_H010, A2_H011, A2_H012
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: 132A

description:
3 technical replicates: A3_H016, A3_H017, A3_H018
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.