title: reference sample, male, 4 (custom array)

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

institute: The University of Queensland

description:
RM4
Self hybridization control, male reference sample.

hyb_protocol: Labelled samples were hybridized to arrays, and arrays were washed following the protocol recommended by Agilent and using the manufacturer's commercial kits and equipment.

scan_protocol: All arrays were scanned on an Agilent Sure Scan Microarray High Resolution Scanner at 5μm double pass resolution.

data_processing:
Array scans were converted to intensity data with the Agilent Feature Extraction Software v10.7, applying the default setting for aCGH arrays and analyzed further with the Agilent DNA Analytics v4.0.76 software. Normalization of data was performed using the default settings on the Feature Extraction software. On the DNA Analytics software 'centralization' and the 'fuzzy zero global error model' algorithms were applied to the resulting data sets to take into account global and local noise. The ADM-2 algorithm inherent to the DNA Analytics software was utilized for the detection of genomic aberrations based on the relative signal intensity ratio, which reflects the relative copy number (rCN) between the test sample and the respective male or female reference sample. All aberrations supported in at least one sample by at least five probes, an average log(2) ratio (LR) signal of at least 0.3 or less than -0.3 and not present on self-hybridization arrays were selected. To obtain an estimate of CNV size and to differentiate between nested and unnested CNVs, immediately adjacent aberrations on the chromosome with a median change in LR signal in the same direction and less than 0.5 different from each other were joined. Some CNVs, particularly at sites of segmental duplications, may have a complex, repetitive sub-structure resulting in uneven signals detected on aCGH array. This together with noise generated from individual, suboptimal probes, may contribute to type 1 error. Therefore, from the selected aberrations, we selected for further inspection those that were either (a) present in more than 75% of the animals, or (b) were present on both arrays, or (c) contained a minimum number of ‘high confidence’ probes with a minimum height in LR. In regards to the latter, CNVs supported by no more than 10 probes contained more than 4 probes with an LR signal height of 0.5, which was also at least 0.4 above the respective self-hybridization signal. Aberrations supported by more probes were further considered if they contained at least 3 probes complying with these criteria for signal height.

The Sample data table includes the data derived after analysis via the Agilent software and prior to post-filtering steps. The "post-filtering.txt" file, which is linked to the Series record as a supplementary file, includes all results that passed the analysis, i.e., for each CNV that passed the filtering criteria, all values are given for each probe contained within the CNV. These filtering steps included an analysis via the Agilent analysis software followed by further filtering to exclude false positives.

source_name: reference sample, male

label_protocol: Samples were processed following the protocol recommended by Agilent and using the manufacturer's commercial labelling kit.

growth_protocol: 2 old (12-16 months of age) sires and 2 control (3 months of age) sires were mated to dams (3 months of age) to create 6 offspring of advanced paternal age (A) and 6 control offspring (C), respectively, with an even number of sexes within each group of offspring.

extract_protocol: Tail tip DNA was extracted from all animals using standard phenol/chloroform extraction. DNA was washed twice with 70% ethanol, precipitated with 3M sodium acetate, resuspended in 10mM Tris and stored at 4C until use.

treatment_protocol: None.

value: tail tip

tag: Sex

tag: sample type

value: pool of male samples


title: NDS (4281807792_B)

status: Public on Jul 12 2011

type: genomic

city: Houston

first: Hon-chiu

middle: Eastwood

last: Leung

state: TX

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

country: USA

institute: Baylor College of Medicine

description: Genomic DNA extracted from bone marrow was genotyped using the Infinium Human 3700Duo BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from bone marrow was genotyped using Infinium Human370-Duo Genotyping BeadChips (Illumina). GenomeStudio v2009.1, the Genotyping Module v1.0 by Illumina Inc was used with no normalization and the following processing steps: 1) Gen Call Threshold = 0.15, 2) Import cluster from the cluster file: HumanCNV370v1_C.egt

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: normal, non-Downs Syndrome

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with B-precursor acute lymphoblastic leukemia and control patients without leukemia.

extract_protocol: Extraction of genomic DNA from Ficoll-enriched cryopreserved bone marrow samples was performed using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA).

treatment_protocol: No additional treatments were performed prior to extract preparation.

tag: raw data

tag: raw file sample id

tag: tissue

value: bone marrow

tag: gender

value: Female

tag: disease status

value: normal, non-Downs Syndrome


title: reference sample, male, 3 (custom array)

country: Australia

description:
RM3
Self hybridization control, male reference sample.

organism: Mus musculus

tag: strain

value: male


title: NDS ALL (4281807626_A)

source_name: ALL, Non-Down Syndrome

value: ALL, Non-Down Syndrome


title: DS ALL (4281807141_A)

source_name: ALL, Down Syndrome

value: Male

value: ALL, Down Syndrome


title: DS ALL (4281807166_A)


title: reference sample, male, 2 (custom array)

description:
RM2
Self hybridization control, male reference sample.


title: reference sample, male, 1 (custom array)

description:
RM1
Self hybridization control, male reference sample.


title: DS ALL (4281807578_A)


title: reference sample, female, 3 (custom array)

description:
RF3
Self hybridization control, female reference sample.

source_name: reference sample, female

value: female

value: pool of female samples


title: DS (4281807578_B)

source_name: normal, Down Syndrome

value: normal, Down Syndrome


title: reference sample, female, 2 (custom array)

description:
RF2
Self hybridization control, female reference sample.


title: DS (4281807140_B)


title: reference sample, female, 1 (custom array)

description:
RF1
Self hybridization control, female reference sample.


title: NDS ALL (4281807103_A)


title: DS ALL (4281807117_A)


title: tail tip DNA, control family 2, offspring3 (custom array)

description:
C2_O3
Biological replicate family 2 of 2. Offspring 2 of 3. Control group.

source_name: tail tip, control family, offspring

tag: test group

value: control, family 2

tag: family member

value: offspring


title: DS (4281807117_B)


title: tail tip DNA, control family 2, offspring2 (custom array)

description:
C2_O2
Biological replicate family 2 of 2. Offspring 2 of 3. Control group.


title: NDS ALL (4281807167_B)


title: NDS ALL (4281807103_B)


title: DS ALL (4281807140_A)


title: tail tip DNA, control family 2, offspring1 (custom array)

description:
C2_O1
Biological replicate family 2 of 2. Offspring 1 of 3. Control group.


title: NDS ALL (4281807101_B)


title: tail tip DNA, control family 2, sire (custom array)

description:
C2_S
Biological replicate family 2 of 2. Sire. Control group.

source_name: tail tip, control family, sire

value: sire

tag: age

value: 3 months


title: DS (4281807102_B)


title: DS (4281807166_B)


title: NDS ALL (4281807101_A)


title: tail tip DNA, control family 1, offspring2 (custom array)

description:
C1_O2
Biological replicate family 1 of 2. Offspring 2 of 3. Control group.

value: control, family 1


title: DS ALL (4281807102_A)


title: tail tip DNA, control family 1, sire (custom array)

description:
C1_S
Biological replicate family 1 of 2. Sire. Control group.

value: tail tip


title: tail tip DNA, control family 1, dam (custom array)

description:
C1_D
Biological replicate family 1 of 2. Dam. Control group.

source_name: tail tip, control family, dam

value: dam


title: tail tip DNA, control family 1, offspring3 (custom array)

description:
C1_O3
Biological replicate family 1 of 2. Offspring 3 of 3. Control group.

value: pool of male samples


title: tail tip DNA, control family 2, dam (custom array)

description:
C2_D
Biological replicate family 2 of 2. Dam. Control group.


title: tail tip DNA, control family 1, offspring1 (custom array)

description:
C1_O1
Biological replicate family 1 of 2. Offspring 1 of 3. Control group.


title: tail tip DNA, advanced paternal age family 2, offspring3 (custom array)

description:
A2_O3
Biological replicate family 2 of 2. Offspring 2 of 3. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, offspring

value: advanced paternal age, family 2


title: tail tip DNA, advanced paternal age family 2, offspring1 (custom array)

description:
A2_O1
Biological replicate family 2 of 2. Offspring 1 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 2, offspring2 (custom array)

description:
A2_O2
Biological replicate family 2 of 2. Offspring 2 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 2, dam (custom array)

description:
A2_D
Biological replicate family 2 of 2. Dam. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, dam


title: NDS ALL (4281807099_A)

description: Genomic DNA extracted from bone marrow was genotyped using the Infinium Human 3700Duo BeadChips (Illumina).

value: bone marrow


title: NDS ALL (4281807051_B)

value: Female


title: DS ALL (4281807090_B)


title: NDS ALL (4281807089_B)

value: ALL, Non-Down Syndrome


title: tail tip DNA, advanced paternal age family 1, offspring3 (custom array)

description:
A1_O3
Biological replicate family 1 of 2. Offspring 3 of 3. Advanced paternal age group.

value: male

value: advanced paternal age, family 1


title: tail tip DNA, advanced paternal age family 2, sire (custom array)

description:
A2_S
Biological replicate family 2 of 2. Sire. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, sire

value: 12-16 months


title: tail tip DNA, advanced paternal age family 1, offspring2 (custom array)

description:
A1_O2
Biological replicate family 1 of 2. Offspring 2 of 3. Advanced paternal age group.


title: DS (4281807090_A)


title: NDS ALL (4281807035_B)

value: Male


title: DS ALL (4281807098_A)

value: ALL, Down Syndrome


title: tail tip DNA, advanced paternal age family 1, offspring1 (custom array)

description:
A1_O1
Biological replicate family 1 of 2. Offspring 1 of 3. Advanced paternal age group.

value: female

value: pool of female samples


title: tail tip DNA, advanced paternal age family 1, sire (custom array)

description:
A1_S
Biological replicate family 1 of 2. Sire. Advanced paternal age group.

value: sire


title: tail tip DNA, advanced paternal age family 1, dam (custom array)

description:
A1_D
Biological replicate family 1 of 2. Dam. Advanced paternal age group.

value: 3 months


title: DS ALL (4256134540_A)


title: DS ALL (4281807098_B)


title: NDS ALL (4281807089_A)


title: Patient 5 dye reversal replicate

type: RNA

city: Boston

first: Richelle

middle: C.

last: Charles

state: MA

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

description: Analysis used in vitro RNA as control samples for comparison to the in vivo samples

hyb_protocol: Labeled products were added to activated Salmonella ORF microarray glass slides (version STv7S; McClelland Laboratory, Vaccine Research Institute of San Diego, CA, http://www.sdibr.org/Faculty/mcclelland/mcclelland-lab), and developed as previously described Larocque RC et. al. (2005). Infect Immun 73: 4488-4493.

scan_protocol: Arrays scanned using an Perkin Elmer scanner and ScanArray Express software version 4 software.

data_processing: For analyses, we subtracted local background from spot signal intensities.  For each individual patient, we considered a gene to be detected in vivo if at least 2 of the 3 replicate gene spots on each of the four slides for that infected human was at least ten median absolute deviations greater than the median of spots on the microarray corresponding to genes absent from the S. Typhi CT18 or Ty2 genomes.  For those genes we detected in vivo, we evaluated whether there was a difference in expression when compared to detection levels for in vitro grown organisms.  For this latter statistical analysis, we included genes with a coefficient of variation in signal intensity less than 50% within an array, and employed repeated measures ANOVA (to within slide replicate spots) with type (in vivo versus in vitro) and dye effects to LOESS-normalized, log-transformed data.  Those genes with a False Discovery Rate of less than 0.05 computed using Benjamini-Hochberg multiple testing adjustment and a 2-fold variation in signal intensity were considered differentially expressed in vivo versus in vitro.   Since the samples were hybridized to two-channel arrays, the data from different slides were not normalized to have the same median intensities. Instead we used a simple (standard) method of analysis described by Kerr et. al (2001) Genetical Research, 77:123-128 which included a slide effect in the analysis of variance model. Thus, for each gene when comparing in vivo and in vitro levels, the slide effect was adjusted for in the model fit, and there was no need to normalize data to have same median intensities across the slides.

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: in vivo

label_protocol: We differently labelled in vivo and in vitro SCOTS-cDNAs for each of 5 patients with Typhi bacteremia Dziejman et. al. (2002) PNAS, 99: 1556-1561.

growth_protocol: To create cDNA of organisms in the blood of bacteremic patients (in vivo sample), we used TRIzol preserved blood samples of patients whose day 0 culture subsequently grew S. Typhi.  To generate corresponding in vitro cDNA samples, we grew each patient's bacterial isolate in Luria Bertani broth until mid-log growth phase (OD600 0.45-0.6), and then immediately placed these samples into TRIzol at a 1 (mid-log culture):2 (TRIzol) volume ratio

extract_protocol: We recovered total RNA from TRIzol preserved in vivo and in vitro samples per manufacturer's instructions (Invitrogen), and treated with DNase on RNeasy columns (Qiagen).  We converted 5 µg of total extracted RNA into cDNA using random priming (T-PCR) to obtain a representative cDNA population as described by Froussard (Froussard P.1992. Nucleic Acids Res 20: 2900), with modifications as previously described by Graham (Graham JE. 1999. PNAS. 96: 11554-11559).  We performed three rounds of SCOTS on in vivo and in vitro cDNA samples, as previously described (Graham JE. 1999. PNAS. 96: 11554-11559).

tag: source

value: in vivo  - blood of bactermic patient

source_name: in vitro

value: In vitro - LB media


title: Patient 5 dye reversal


title: DS (4281807035_A)

value: normal, Down Syndrome


title: DS ALL (4281807008_A)


title: NDS ALL (4281807099_B)


title: NDS ALL (4281807051_A)


title: DS (4256134540_B)


title: Patient 4 dye reversal replicate


title: DS (4281807008_B)


title: Patient 5


title: DS ALL (4256134507_A)


title: DS (4256134539_B)


title: DS (4256134520_B)


title: Patient 4 replicate


title: Patient 4 dye reversal


title: Patient 4


title: Patient 3 dye reversal replicate


title: Patient 3 dye reversal


title: Patient 3 replicate


title: DS ALL (4256134539_A)


title: DS ALL (4256134520_A)


title: NDS ALL (4256134489_A)


title: NDS (4256134489_B)

value: normal, non-Downs Syndrome


title: Patient 5 replicate


title: NDS ALL (4256134505_A)


title: Patient 2 replicate


title: NDS ALL (4256134474_B)


title: NDS ALL (4256134474_A)


title: NDS (4256134505_B)


title: Patient 3


title: Patient 2 dye reversal


title: NDS ALL (4256134464_B)


title: NDS ALL (4256134462_A)


title: Patient 1 dye reversal replicate


title: NDS ALL (4256134467_A)


title: Patient 2 dye reversal replicate


title: NDS (4256134464_A)


title: NDS ALL (4256134467_B)


title: NDS (4256134462_B)


title: Patient 1


title: Patient 2


title: DS ALL (4256134446_A)


title: Patient 1 replicate


title: Tsc1-deficient CD8 naïve cells KAI286

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: sorted T cells

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using the RMA algorithmn

label: Biotin

source_name: Tsc1-deficient CD8 naïve cells

label_protocol: Affymetrix standard methods were applied after RNA isolation and amplification

growth_protocol: Naïve CD4 and CD8 T cells were cultured with Click medium for aCD3-CD28 stimulation.

extract_protocol: RNA was extracted using RNeasy kit (Qiagen).

treatment_protocol: Naïve CD4 and CD8 T cells were sorted from wild-type and HIF1a-deficeint mice. For activation, wild-type and Tsc1-deficient naïve CD4 T cells were stimulated by plate-bound aCD3-CD28 for 4h.

tag: genotype

tag: cell type

value: CD8 naive cells

tag: genetic background


title: Patient 1 dye reversal


title: NDS (4256134444_B)

value: bone marrow


title: wild-type naïve CD8 T cells KAI284

description: sorted T cells

source_name: wild-type naïve CD8 T cells

value: wild-type

value: naive CD8 T cells


title: Tsc1-deficient CD8 naïve cells KAI288

description: sorted T cells


title: DS (4256134365_B)

value: Female


title: DS ALL (4256134405_A)


title: NDS ALL (4256134444_A)

value: ALL, Non-Down Syndrome


title: Tsc1-deficient CD4 naïve cells KAI279

description: sorted T cells

source_name: Tsc1-deficient CD4 naïve cells

value: CD4 naive cells


title: Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI277

description: sorted T cells

source_name: Tsc1-deficient CD4 naïve cells with aCD3-CD28 stimulation for 4h

tag: treatment

value: CD3-CD28 stimulation for 4h


title: Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI280

description: sorted T cells


title: wild-type naïve CD8 T cells KAI282

description: sorted T cells


title: Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI274

description: sorted T cells


title: DS (4256134507_B)

value: Male


title: DS ALL (4256134365_A)

value: ALL, Down Syndrome


title: Tsc1-deficient CD4 naïve cells KAI273

description: sorted T cells


title: Tsc1-deficient CD4 naïve cells KAI276

description: sorted T cells


title: NDS ALL (4256134305_A)


title: NDS ALL (4256134305_B)


title: wild-type naïve CD4 T cells KAI270

description: sorted T cells

source_name: wild-type naïve CD4 T cells

value: naive CD4 T cells


title: DS (4256134364_B)


title: wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI268

description: sorted T cells

source_name: wild-type naïve CD4 T cells with aCD3-CD28 stimulation for 4h


title: DS ALL (4256134446_B)

source_name: ALL, Down Syndrome


title: wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI271

description: sorted T cells


title: DS (4256134252_B)


title: wild-type naïve CD4 T cells KAI267

description: sorted T cells


title: DS ALL (4256134253_B)


title: wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI265

description: sorted T cells


title: DS (4256134405_B)


title: DS (4256134180_B)


title: DS ALL (4256134250_A)


title: DS ALL (4094577134_B)


title: DS ALL (4256134252_A)


title: DS ALL (4256134180_A)


title: DS ALL (4094577113_B)


title: DS (4256134253_A)


title: wild-type naïve CD4 T cells KAI264

description: sorted T cells


title: DS ALL (4094577134_A)


title: DS ALL (4094577113_A)


title: DS ALL (4094577059_A)


title: DS ALL (4094577062_B)


title: DS ALL (4064204102_B)


title: DS ALL (4094577059_B)


title: DS ALL (4094577062_A)


title: DS ALL (4064204102_A)


title: DS ALL (4064204092_A)


title: nl (4064204087_A)

source_name: normal, control

value: normal, control


title: DS ALL (4064204070_B)


title: nl (4064204070_A)


title: DS ALL (4256134364_A)


title: NDS (4064204091_B)

source_name: normal, non-Downs Syndrome


title: DS ALL (4064204053_B)


title: DS ALL (4064204058_B)


title: NDS ALL (4064204052_B)

source_name: ALL, Non-Down Syndrome


title: NDS ALL (4064204091_A)


title: nl (4064204058_A)


title: NDS ALL (4064204085_A)


title: DS ALL (4064204092_B)


title: NDS ALL (4064204052_A)


title: DS ALL (4064204035_B)


title: DS (4064204059_B)

source_name: normal, Down Syndrome


title: NDS (4064204085_B)


title: A13R4_K

city: Austin

first: R. Dayne

last: Mayfield

address: 2500 Speedway

institute: University of Texas at Austin

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed using variance stabilization (variance-stabilization transformation, VST) and quantile normalization using the Bioconductor package lumi. Outliers removed with Grubb's test. Each of the four brain regions were processed separately.

label: biotin

source_name: Medial Nucleus of Amygdala, Alcoholic Region4

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

extract_protocol: Total RNA was extracted with the  mirVana miRNA Isolation Kit kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.

value: male

value: Medial Nucleus of Amygdala


title: A14R4_G

description: replicate 1


title: C14R4_B

description: replicate 1

source_name: Medial Nucleus of Amygdala, Control Region4


title: A15R4_H

description: replicate 1


title: C15R4_C

description: replicate 1


title: DS ALL (4256134250_B)


title: A11R4_K

description: replicate 1


title: A7R4_G

description: replicate 1


title: C13R4_E

description: replicate 1


title: nl (4064204087_B)


title: nl (4064204023_A)


title: DS ALL (4064204022_A)


title: C11R4_E

description: replicate 1


title: C7R4_A

description: replicate 1


title: DS ALL (4064204035_A)


title: DS ALL (4064204053_A)


title: DS (4064204059_A)


title: A10R4_J

description: replicate 1


title: C9R4_C

description: replicate 1


title: A12R4_L

description: replicate 1


title: A9R4_I

description: replicate 1


title: A8R4_H

description: replicate 1


title: A5R4_K

description: replicate 1

value: female


title: C8R4_B

description: replicate 1


title: C12R4_F

description: replicate 1


title: DS ALL (4064204022_B)


title: A16R4_I

description: replicate 1


title: C1R4_A

description: replicate 1


title: C5R4_E

description: replicate 1


title: DS ALL (4064204015_B)


title: A17R4_L

description: replicate 1


title: nl (4064204036_B)


title: A4R4_J

description: replicate 1


title: C3R4_C

description: replicate 1


title: A3R4_I

description: replicate 1


title: A6R4_L

description: replicate 1


title: C2R4_B

description: replicate 1


title: C6R4_F

description: replicate 1


title: A17R3_J

description: replicate 1

source_name: Central Nucleus of Amygdala, Alcoholic Region3

value: Central Nucleus of Amygdala


title: C13R3_A

description: replicate 1

source_name: Central Nucleus of Amygdala, Control Region3


title: A2R4_H

description: replicate 1


title: DS ALL (4064204036_A)


title: A16R3_L

description: replicate 1


title: DS ALL (4064204001_B)


title: C15R3_C

description: replicate 1


title: A15R3_H

description: replicate 1


title: A13R3_K

description: replicate 1


title: C14R3_B

description: replicate 1


title: A1R4_G

description: replicate 1


title: NDS ALL (4064204014_A)


title: A12R3_L

description: replicate 1


title: DS ALL (4064204012_B)


title: A8R3_H

description: replicate 1


title: C12R3_F

description: replicate 1


title: DS (4064204013_A)

value: normal, Down Syndrome


title: C10R4_D

description: replicate 1


title: A7R3_G

description: replicate 1


title: A11R3_K

description: replicate 1


title: C7R3_A

description: replicate 1


title: A14R3_G

description: replicate 1


title: C11R3_E

description: replicate 1


title: DS ALL (4064204015_A)


title: DS ALL (4064204012_A)


title: nl (4064204003_A)


title: C8R3_B

description: replicate 1


title: DS ALL (4064204014_B)


title: DS (4064204013_B)


title: A10R3_J

description: replicate 1


title: A6R3_L

description: replicate 1


title: A2R3_H

description: replicate 1


title: C9R3_C

description: replicate 1


title: C2R3_B

description: replicate 1


title: C10R3_D

description: replicate 1


title: nl (4064204003_B)


title: DS ALL (4064204001_A)


title: C6R3_F

description: replicate 1


title: A9R3_I

description: replicate 1


title: A5R3_K

description: replicate 1


title: C5R3_E

description: replicate 1


title: A1R3_G

description: replicate 1


title: C4R4_D

description: replicate 1


title: A13R2_F

description: replicate 1

source_name: Basolateral Amygdala, Alcoholic Region2

value: Basolateral Amygdala


title: C3R3_C

description: replicate 1


title: C4R3_D

description: replicate 1


title: A4R3_J

description: replicate 1


title: C1R3_A

description: replicate 1


title: C13R2_A

description: replicate 1

source_name: Basolateral Amygdala, Control Region2


title: C15R2_E

description: replicate 1


title: A3R3_I

description: replicate 1


title: A17R2_J

description: replicate 1


title: A15R2_L

description: replicate 1


title: A16R2_I

description: replicate 1


title: C12R2_F

description: replicate 1


title: A8R2_H

description: replicate 1


title: A9R2_I

description: replicate 1


title: A12R2_L

description: replicate 1


title: A14R2_G

description: replicate 1


title: C9R2_C

description: replicate 1


title: C8R2_B

description: replicate 1


title: C11R2_E

description: replicate 1


title: A11R2_K

description: replicate 1


title: A7R2_G

description: replicate 1


title: A10R2_J

description: replicate 1


title: C7R2_A

description: replicate 1


title: C10R2_D

description: replicate 1


title: A3R2_I

description: replicate 1


title: C14R2_B

description: replicate 1


title: C3R2_C

description: replicate 1


title: A6R2_L

description: replicate 1


title: A1R2_G

description: replicate 1


title: C1R2_A

description: replicate 1


title: A15R1_H

description: replicate 1

source_name: Superior Frontal Cortex, Alcoholic Region1

value: Superior Frontal Cortex


title: A16R1_I

description: replicate 1


title: C14R1_E

description: replicate 1

source_name: Superior Frontal Cortex, Control Region1


title: C4R2_D

description: replicate 1


title: C5R2_E

description: replicate 1


title: A4R2_J

description: replicate 1


title: A13R1_F

description: replicate 1


title: C13R1_A

description: replicate 1


title: A10R1_J

description: replicate 1


title: A17R1_J

description: replicate 1


title: A9R1_I

description: replicate 1


title: C10R1_D

description: replicate 1


title: A5R2_K

description: replicate 1


title: C15R1_C

description: replicate 1


title: A14R1_K

description: replicate 1


title: C6R2_F

description: replicate 1


title: A2R2_H

description: replicate 1


title: C2R2_B

description: replicate 1


title: A12R1_L

description: replicate 1


title: C8R1_B

description: replicate 1


title: A8R1_H

description: replicate 1


title: C12R1_F

description: replicate 1


title: C9R1_C

description: replicate 1


title: A7R1_G

description: replicate 1


title: A11R1_K

description: replicate 1


title: nl (4064204023_B)

value: bone marrow


title: tail tip DNA, control family 2, offspring3 (commercial array)

description:
CON2_O3
Biological replicate family 2 of 2. Offspring 2 of 3. Control group.

source_name: tail tip, control family, offspring

value: tail tip

value: control, family 2

value: offspring

source_name: reference sample, male

value: pool of male samples


title: tail tip DNA, control family 1, offspring2 (commercial array)

description:
CON1_O2
Biological replicate family 1 of 2. Offspring 2 of 3. Control group.

value: control, family 1


title: tail tip DNA, control family 1, offspring1 (commercial array)

description:
CON1_O1
Biological replicate family 1 of 2. Offspring 1 of 3. Control group.

source_name: reference sample, female

value: pool of female samples


title: tail tip DNA, control family 2, offspring2 (commercial array)

description:
CON2_O2
Biological replicate family 2 of 2. Offspring 2 of 3. Control group.


title: tail tip DNA, control family 2, sire (commercial array)

description:
CON2_S
Biological replicate family 2 of 2. Sire. Control group.

source_name: tail tip, control family, sire

value: sire

value: 3 months


title: tail tip DNA, control family 2, dam (commercial array)

description:
CON2_D
Biological replicate family 2 of 2. Dam. Control group.

source_name: tail tip, control family, dam

value: dam


title: A4R1_J

description: replicate 1

value: male


title: tail tip DNA, control family 1, offspring3 (commercial array)

description:
CON1_O3
Biological replicate family 1 of 2. Offspring 3 of 3. Control group.


title: C11R1_E

description: replicate 1


title: tail tip DNA, control family 1, dam (commercial array)

description:
CON1_D
Biological replicate family 1 of 2. Dam. Control group.


title: C6R1_F

description: replicate 1


title: tail tip DNA, control family 1, sire (commercial array)

description:
CON1_S
Biological replicate family 1 of 2. Sire. Control group.


title: A3R1_I

description: replicate 1


title: reference sample, female (commercial array)

description:
SH
Self-hybridization control, female reference sample.


title: A6R1_L

description: replicate 1


title: C5R1_E

description: replicate 1


title: A2R1_H

description: replicate 1


title: C1R1_A

description: replicate 1


title: tail tip DNA, advanced paternal age family 2, offspring2 (commercial array)

description:
APA2_O2
Biological replicate family 2 of 2. Offspring 2 of 3. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, offspring

value: advanced paternal age, family 2


title: A5R1_K

description: replicate 1

value: female


title: C3R1_C

description: replicate 1


title: C4R1_D

description: replicate 1


title: C2R1_B

description: replicate 1


title: tail tip DNA, control family 2, offspring1 (commercial array)

description:
CON2_O1
Biological replicate family 2 of 2. Offspring 1 of 3. Control group.


title: A1R1_G

description: replicate 1


title: tail tip DNA, advanced paternal age family 2, offspring3 (commercial array)

description:
APA2_O3
Biological replicate family 2 of 2. Offspring 2 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 2, offspring1, technical replicate (commercial array)

description:
APA2_O1REP
Technical replicate family 2 of 2. Offspring 1 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 2, offspring1 (commercial array)

description:
APA2_O1
Biological replicate family 2 of 2. Offspring 1 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 1, offspring2 (commercial array)

description:
APA1_O2
Biological replicate family 1 of 2. Offspring 2 of 3. Advanced paternal age group.

value: advanced paternal age, family 1


title: human brain tumor, Schwannoma - T3

city: Suwon

first: Myung Ae

last: Lee

state: Gyeonggi-do

address: Woncheon-dong, Yeongtong-gu

country: South Korea

institute: ajou univ school of medicine 607

description: gene expression in human brain tumor

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affimatrix ologonucleotied Chip Human U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics station protocol EukGE_WS1

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with GenPlex software Gcos using Affymetrix default analysis settings and global scaling as normalization method

source_name: brain tumor in shwannoma patient

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

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

value: 63 yr

value: brain tumor

tag: disease state

value: shwannoma


title: tail tip DNA, advanced paternal age family 2, sire (commercial array)

description:
APA2_S
Biological replicate family 2 of 2. Sire. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, sire

tag: Sex

value: 12-16 months


title: tail tip DNA, advanced paternal age family 2, dam (commercial array)

description:
APA2_D
Biological replicate family 2 of 2. Dam. Advanced paternal age group.

source_name: tail tip, advanced paternal age family, dam

value: tail tip

tag: sample type


title: tail tip DNA, advanced paternal age family 1, offspring1 (commercial array)

description:
APA1_O1
Biological replicate family 1 of 2. Offspring 1 of 3. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 1, dam (commercial array)

description:
APA1_D
Biological replicate family 1 of 2. Dam. Advanced paternal age group.


title: tail tip DNA, advanced paternal age family 1, offspring3 (commercial array)

description:
APA1_O3
Biological replicate family 1 of 2. Offspring 3 of 3. Advanced paternal age group.


title: Human normal brain - 3

description: gene expression in human normal brain

source_name: normal brain in shwannoma patient

value: normal brain


title: human brain tumor, Ganglioglioma - T2

description: gene expression in human brain tumor

source_name: brain tumor in ganglioglioma patient

value: 50 yr

value: ganglioglioma


title: ALL_NDS, K60 011409

hyb_protocol: Biotinylated cRNA (20ng) was fragmented,10 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 150.

source_name: ALL, Non-Down syndrome

label_protocol: Total RNA (50 ng) was used as template in a single-amplification protocol (RiboAmp OA, Mountain View, CA) according to manufacturer's instructions.

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA) and quality was verified by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Leukemic bone marrow samples were used for RNA extraction without further treatment.

value: bone marrow

value: B-precursor acute lymphoblastic leukemia, Non-Down syndrome


title: ALL_NDS, K61 011509


title: human brain tumor, Glioblastoma - T1

description: gene expression in human brain tumor

source_name: brain tumor in glioblastoma patient

value: 32 yr

value: glioblastoma


title: tail tip DNA, advanced paternal age family 1, sire (commercial array)

description:
APA1_S
Biological replicate family 1 of 2. Sire. Advanced paternal age group.

value: sire

value: pool of male samples


title: ALL_DS, K57 011509

source_name: ALL, Down syndrome

value: B-precursor acute lymphoblastic leukemia, Down syndrome


title: ALL_DS, K6 011509


title: ALL_NDS, K55 012109


title: Human normal brain - 2

description: gene expression in human normal brain

source_name: normal brain in ganglioglioma patient

value: female


title: ALL_DS, K56 011409


title: ALL_NDS, K54 011509


title: ALL_NDS, K63 011409


title: ALL_NDS, K62 011409


title: Human normal brain - 1

description: gene expression in human normal brain

source_name: normal brain in glioblastoma patient

value: male


title: ALL_NDS, K58 011509


title: ALL_NDS, K59 011509


title: ALL_NDS, K52 011609


title: nestinGFP PN0 retinal cells positive FAC sorted biological repliacte 2

city: Dresden

first: Kai

last: Postel

address: Fiedlerstraße 42

country: Germany

institute: DFG-Center for Regenerative Therapies Dresden

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C 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 Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GeneSpring GX 11.0.1 software (Agilent) using normalization algorithm RMA.

source_name: retina of PN0 nestinGFP mice, FAC-sorted

label_protocol: Biotinylated cRNA were prepared according to Ambion protocol from 200ng total RNA (MessageAmpTM II-Biotin Enhanced Kit, 2009, Ambion).

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

value: nestinGFP

value: nestinGFP positive retinal cell

value: postnatal day 0


title: nestinGFP PN0 retinal cells positive FAC sorted biological repliacte 3


title: ALL_NDS, K51 011509


title: ALL_NDS, K50 011409


title: nestinGFP PN0 retinal cells positive FAC sorted biological repliacte 1


title: rhoGFP PN4 retinal cells negative FAC sorted biological repliacte 3

source_name: retina of PN4 rhoGFP mice, FAC-sorted

value: rhoGFP

value: rhoGFP negative retinal cell

value: postnatal day 4


title: ALL_DS, K5 012109


title: ALL_NDS, K43 012109


title: rhoGFP PN4 retinal cells negative FAC sorted biological repliacte 2


title: ALL_NDS, K49 011509


title: rhoGFP PN4 retinal cells positive FAC sorted biological repliacte 3

value: rhoGFP positive retinal cell


title: ALL_NDS, K42 011509


title: ALL_DS, K4 011509


title: rhoGFP PN4 retinal cells negative FAC sorted biological repliacte 1


title: rhoGFP PN4 retinal cells positive FAC sorted biological repliacte 1


title: ALL_NDS, K41 011509


title: ALL_NDS, K39 011509


title: ALL_NDS, K40 012109


title: MSC 251485043451_1_3

city: Leuven

first: Valerie

middle: Dina

last: Roobrouck

address: Herestraat 49 bus 804

department: Interdepartmental Stem Cell Institute Leuven

country: Belgium

institute: Catholic University Leuven

description: RNA extracted from MSC

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65µg Cy3-labeled cRNA was hybridized overnight (17hrs, 65˚C) to Agilent Whole Human Genome Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. After hybridization, microarrays were washed once with 6xSSPE buffer containing 0.005% N-lauroylsarcosine for 1min at room temperature followed by a second wash with preheated 0.06xSSPE buffer containing 0.005% N-lauroylsarcosine for 1min. The last washing step was performed with acetonitrile for 30sec

scan_protocol: Slides were scanned using Agilent Technologies Scanner G2505C US22502695 with one channel protocol, 5 um scan resolution

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using protocol GE1-v5_10_Apr08 and Grid: 014850_D_F_2007082 to obtain  Processed Signal intensities. The signal intensities (gProcessedSignal) for each array were normalized by dividing the probe intensities by the array median signal intensity (median calculated after excluding control probes). The resulting values were log2 transformed to yield median normalized signal intensities. Probes whose signal intensity was not positive and significant above the background as determined by FES (gIsPosAndSignif) in at least two of the samples being compared were filtered out from analysis. Probe summarization (exclusion of duplicated probes) was performed in R Bioconductor environment using the Agi4x44PreProcess package.

source_name: Bone

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug total RNA using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.  Dye incorporation rate and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human MAPC were generated by flushing the bone fragment and plating the total cell fraction at 0.5x106 cells/cm2 in medium consisting of 60% DMEM low-glucose (Gibco, Invitrogen, Carlsbad, CA, USA), 40% MCDB-201 (Sigma-Aldrich, St Louis, MO, USA), supplemented with 50nM dexamethasone, 10-4M L-Ascorbic Acid, 1xSelenium-Insulin-Transferrin (ITS), 0.5xlinoleic acid-bovine serum albumin (LA-BSA) (all from Sigma-Aldrich), 1% Penicillin/Streptomycin (Gibco, Invitrogen), along with 2% Serum Supreme (Lonza BioWhittaker, Basel, Switzerland) and human PDGF-BB (R&D Systems, Minneapolis, MN, USA) and human EGF (Sigma-Aldrich) (both 10ng/ml). Human MAPC cultures were maintained under hypoxic conditions (5%O2) in a 5.5% CO2 humidified incubator at a density of 400 cells/cm2 and were passaged every 2-3 days. Clonal populations were obtained by plating 5 cells/well in a 96-well or 48-well plate between passage 2-12.   Human MSC were generated by flushing the bone fragment and plating the mononuclear fraction, obtained after Ficoll density gradient centrifugation, at 0.5x106 cells/cm2 in MSC growth medium (Lonza). Human MSC cultures were maintained at 5,000 cells/cm2, at normal oxygen levels in a 5% CO2 humidified incubator and were passaged every 4-7 days.   To isolate hMab, the muscle fragment was rinsed in PBS (w/o Ca2+Mg2+), cut into very small pieces (1-2 mm diameter) and transferred to a Petri dish coated with type I collagen (Sigma-Aldrich). The medium consisted of MegaCell DMEM (Sigma-Aldrich) supplemented with 5% FBS (Lonza BioWhittaker), 5ng/ml bFGF (R&D Systems), 2mM L-glutamine, 0.1mM β–mercaptoethanol, 1% non-essential aminoacids (NEAA) and 1% Penicillin/Streptomycin (all from Gibco, Invitrogen). The tissue fragments were cultured for 7-10 days and after the initial outgrowth of fibroblast-like cells, small round and refractile cells could be observed. Human Mab cultures were maintained at 5,000 cells/cm2, under hypoxic conditions (5%O2) in a 5.5% CO2 humidified incubator and were split every 2-3 days. The human Embryonic Stem Cell (hESC) line H9 (purchased from WiCell, Madison, WI, USA) was obtained with approval from the Ethical Committee of the K.U.Leuven. Cells were cultured as described on mitomycin-inactivated mouse embryonic fibroblasts (MEFs) in hESC expansion medium in a 5% CO2 normoxic humidified incubator and passaged 1:3 using collagenase IV (Gibco, Invitrogen) every 3-7 days.46 To obtain samples for RNA extraction, cells were cultured feeder-free in mTeSR medium (Stem Cell Technologies, Vancouver, Canada) on Matrigel (hESC-qualified Matrix, BD Biosciences, San Jose, CA, USA). Human MSC were obtained from Lonza and cultured under the same conditions as the other MSC.

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol) and RNA quality was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Cells were harvested with 0.05% Trypsin+EDTA, washed with PBS and stored in RNAlater at -80˚C until RNA was extracted

value: Mesenchymal Stem Cells


title: rhoGFP PN4 retinal cells positive FAC sorted biological repliacte 2


title: Mab_to_MAPC 251485043450_1_4

description: RNA extracted from Mab cultured under MAPC conditions

source_name: Skeletal Muscle

value: Mesoangioblasts


title: MAPC 251485043451_1_1

description: RNA extracted from MAPC

value: Multipotent Adult Progenitor Cells


title: Mab_to_MAPC 251485043450_1_3


title: MSC_to_MAPC 251485043450_1_2

description: RNA extracted from MSC cultured under MAPC conditions


title: MSC_to_MAPC 251485043450_1_1


title: ALL_NDS, K48 011409

value: bone marrow

value: B-precursor acute lymphoblastic leukemia, Non-Down syndrome


title: ALL_NDS, K38 011409


title: ALL_NDS, K35 011409


title: ALL_NDS, K36 011609


title: ALL_NDS, K37 011609


title: ALL_NDS, K34 011409


title: MAPC_to_MSC 251485043449_1_2

description: RNA extracted from MAPC cultured under MSC conditions


title: C7R1_A

description: replicate 1

source_name: Superior Frontal Cortex, Control Region1

value: Superior Frontal Cortex


title: MAPC 251485039309_1_3

description: RNA extracted from MAPC


title: MAPC_to_Mab 251485043449_1_3

description: RNA extracted from MAPC cultured under Mab conditions


title: ALL_NDS, K33 011609


title: MAPC_to_MSC 251485043449_1_1


title: MAPC_to_MSC 251485039302_1_2


title: ALL_DS, K28 011409


title: ALL_DS, K3 012109


title: MAPC_to_MSC 251485038197_1_2


title: MAPC 251485038198_1_2

description: RNA extracted from MAPC


title: ALL_DS, K29 011509


title: ESC - H9 251485039300_1_4

description: RNA extracted from cells cultured under ESC conditions

source_name: ICM

tag: cell line

value: embryonic stem cells


title: ALL_NDS, K32 011609


title: ALL_DS, K30 012109

value: B-precursor acute lymphoblastic leukemia, Down syndrome


title: ALL_DS, K26 011609


title: ESC - H9 251485039299_1_2

value: female


title: U87MG pSuper Retro AEG-1 RNAi Rep_2

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

description: U87MG pSuper Retro AEG-1 RNAi Rep_2

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

source_name: U87MG_AEG-1 RNAi

growth_protocol: The glioma cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: Transfection was performed following standard protocol of Lipofectamine 2000 transfection.

value: glioma cells


title: ALL_DS, K31 012109


title: MAPC 251485039309_1_4

description: RNA extracted from cells cultured under MAPC conditions

value: male


title: Mab 251485043451_1_2

description: RNA extracted from cells cultured under Mab conditions


title: ALL_DS, K25 011509


title: MAPC_to_Mab 251485043449_1_4


title: U87MG pSuper Retro Vector Rep_1

description: U87MG pSuper Retro Vector Rep_1

scan_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

source_name: U87MG_ Vector


title: MSC 251485039309_1_2

description: RNA extracted from cells cultured under MSC conditions


title: Persistent injury #3 [HT_MG-430A]

first: Samir

last: Parikh

address: 330 Brookline Avenue, RN280C

institute: Beth Israel Deaconess Medical Center

description: SAMPLE 12_A file

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HT_MG-430A 24 A and B Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip HT Array Plate Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: t=42, persistent injury

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: Standard light-dark cycle and standard ad libitum diet prior to and during experiment

treatment_protocol: injection of LPS 10 mg/kg intraperitoneally at t=0hr followed by 0.9% saline 10 ml/kg injected intraperitoneally at t=18hr

value: 8 week old

tag: agent

value: LPS

tag: timepoint (hrs)

value: whole kidney

tag: renal function

value: persistent renal injury


title: ALL_DS, K24 011609

tag: tissue

tag: disease status


title: U87MG pSuper Retro Vector Rep_2

description: U87MG pSuper Retro Vector Rep_2

label_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.


title: Persistent injury #1 [HT_MG-430A]

description: SAMPLE 10_A file

tag: strain

tag: gender


title: MAPC 251485038197_1_4


title: ALL_DS, K2 011609


title: ALL_DS, K23 011409


title: Persistent injury #2 [HT_MG-430A]

description: SAMPLE 11_A file

tag: age


title: ALL_DS, K21 011509


title: Renal recovery #3 [HT_MG-430A]

description: SAMPLE 9_A file

source_name: t=42, recovered

value: recovered renal function


title: MSC 251485038198_1_3


title: MSC 251485039303_1_3


title: MAPC 251485038197_1_1


title: Renal recovery #2 [HT_MG-430A]

description: SAMPLE 8_A file


title: ALL_DS, K18 011409


title: MAPC 251485038198_1_4


title: Renal recovery #1 [HT_MG-430A]

description: SAMPLE 7_A file


title: Mab 251485039303_1_1


title: MAPC 251485039302_1_1


title: ALL_DS, K17 011409


title: Early injury #3 [HT_MG-430A]

description: SAMPLE 6_A file

source_name: t=18, renal injury

value: early renal injury


title: Mab 251485039301_1_3


title: ALL_DS, K15 011509


title: Early injury #2 [HT_MG-430A]

description: SAMPLE 5_A file


title: MSC 251485039301_1_1

value: Mesenchymal Stem Cells


title: Early Injury #1 [HT_MG-430A]

description: SAMPLE 4_A file


title: MAPC 251485039300_1_3


title: Baseline #3 [HT_MG-430A]

description: SAMPLE 3_A file

source_name: t=0, nl function

value: normal baseline renal function


title: ALL_DS, K16 011409


title: ALL_DS, K12 012109


title: MSC 251485039299_1_3


title: ccr4 mutant vs. wild type 10 min at 37C

status: Public on Jul 11 2011

city: Buffalo

first: John

last: Panepinto

state: NY

address: 955 Main St., Suite 5229

department: Microbiology and Immunology

institute: University at Buffalo SUNY

description: 10 minute shift from 30oC to 37oC

hyb_protocol: Ambion Hybridization Buffer #3; 15min prehyb @ 37degC; Denature probe @ 95degC; O/N hybridization @ 37degC; 3xWash 1xSSC 0.1% SDS @ 50degC; Wash 1xSSC

scan_protocol: ScanArray Lite

data_processing: QuantArray; Spot intensities corrected by local background subtraction.  Global normalization applied after background correction.  Significant differential expression between mutant (‘C’) and Wild-Type control (‘H’) samples performed by two-tailed test where H0: log2(H/C) = 0 at a significance of p <= 0.0001.

organism: Cryptococcus neoformans

source_name: Pooled C. neoformans total RNA

label_protocol: QIAGEN, LabelStar Kit, Cy3, Cy5; 25-35 ug total RNA per hybridization

growth_protocol: Replicate cultures of wild type C. neoformans H99 and a ccr4-delta mutant were grown to mid log phase at 30oC,

extract_protocol: Total RNA was harvested using the Qiagen RNEasy Mini Kit using mechanical disruption for cell lysis

treatment_protocol: Cells were harvested by cetnrifugation and resuspended in pre-warmed 37oC medium for 10 minutes, harvedsted again by centrifugation.

value: ccr4 delta mutant

value: 10 minute shift from 30oC to 37oC

source_name: Pooled C.neoformans total RNA

value: wild type


title: MAPC 251485039299_1_4

value: Multipotent Adult Progenitor Cells


title: ALL_NDS, K13 011609

source_name: ALL, Non-Down syndrome

value: bone marrow

value: B-precursor acute lymphoblastic leukemia, Non-Down syndrome


title: ALL_DS, K1 011409

source_name: ALL, Down syndrome

value: B-precursor acute lymphoblastic leukemia, Down syndrome


title: iMet tumor cMet6

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

description: Gene expression data from melanoma cells isolated from iMet mouse (Tyr-rtTA;Tet-Met;Ink4a/Arf-/-)

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Cel files were processed with R/Bioconductor (http://bioconductor.org/)

label_protocol: 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

extract_protocol: RNA was isolated using Trizol (Invitrogen) and the RNeasy mini kit (Qiagen).

value: iMet tumor

value: melanoma


title: iRas tumor ras1

description: Gene expression data from melanoma cells isolated from iRas mouse (Tyr-rtTA;Tet-HRASV12G;Ink4a/Arf-/-)

value: iRas tumor


title: iRas tumor ras5

source_name: melanoma cells isolated from iRas mouse (Tyr-rtTA;Tet-HRASV12G;Ink4a/Arf-/-)


title: iRas tumor ras3


title: Baseline #2 [HT_MG-430A]

description: SAMPLE 2_A file

value: male

value: 8 week old


title: iMet tumor cMet4

source_name: melanoma cells isolated from iMet mouse (Tyr-rtTA;Tet-Met;Ink4a/Arf-/-)


title: iRas tumor ras4


title: Baseline #1 [HT_MG-430A]

description: SAMPLE 1_A file

value: whole kidney


city: Cambridge

first: Jesse

middle: Jerome

last: Smith

address: 325 Vassar Street, Suite 2B

department: Biological Sciences

institute: Epizyme

description: Gene expression data from Vehicle treated, DAY 6, biological rep.3, MOLM-13 cells

hyb_protocol: RNA hybridization to Affymetrix HG-U133 Plus 2 arrays was performed by Expression Analysis, Inc. (Durham, NC).   Standard Affymetrix protocols were used with the Affymetrix FS450 Fluidics Station and the Affymetrix Hybridization, Washing and Staining kits.

scan_protocol: Microarray scanning and data extraction was perfomed by Expression Analysis, Inc. (Durham, NC).  The Affymetrix GeneChip Scanner 3000 7G was used. GeneChip Command Console (Affymetrix) was used to drive the scanners.  Expression Console (Affymetrix) was used to extract data from the scanned images.

data_processing: Expression file matrix data was generated using Genepattern Software for the Broad Institute (http://genepattern.broadinstitute.org/gp) with the ExpressionFileCreator Module.  GCRMA method was used with quantile normalization.

source_name: MOLM-13 cells

label_protocol: RNA labeling was peformed by Expression Analysis, Inc. (Durham, NC).  Total RNA was converted cDNA and in vitro transcribed to biotin-labeled anti-sense RNA, using the Enzo Single Round RNA Amplification and Biotin Labeling System (Enzo # ENZ-42420-10) according to the manufacturer’s protocol.

extract_protocol: RNA isolation was peformed by Expression Analysis, Inc. (Durham, NC).  RNA was purified using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol, including the on-column DNase I digestion.  RNA integrity and quantity was measured using an Agilent Bioanalyzer 2100.

tag: cell line description

value: acute myeloid leukemia (MLL-AF9 rearrangement)

tag: growth conditions

value: RPMI with 10% FBS

value: Vehicle

tag: time

value: day 6

tag: biological rep


description: Gene expression data from Vehicle treated, DAY 6, biological rep.2, MOLM-13 cells


title: iMet tumor cMet5

tag: genotype

tag: cell type


title: iRas tumor ras2

tag: disease state


title: iRas tumor ras6


title: ALL_DS, K19 011409


description: Gene expression data from Vehicle treated, DAY 6, biological rep.1, MOLM-13 cells


title: Melanocytes Cnt3

description: Gene expression data from mouse melanocytes

source_name: melanocytes isolated from mouse

value: melanocytes


title: iMet tumor cMet2


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.3, MOLM-13 cells


title: iMet tumor cMet1


title: Melanocytes Cnt2


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.1, MOLM-13 cells


description: Gene expression data from Vehicle treated, DAY 6, biological rep.3, MV4-11 cells

source_name: MV4-11 cells

value: biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment)

value: IMDM with 10% FBS


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.2, MOLM-13 cells


description: Gene expression data from Vehicle treated, DAY 6, biological rep.2, MV4-11 cells


title: fcafpa double mutant, 17 days, replicate C

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip Scanner 3000 7G.

data_processing:
Intensity values were corrected for probe sequence biases followed by quantile normalization in R.
The processed data .txt file includes log2-transformed normalized signal intensities for TAIR9 identifiers (chromosome_start coordinate).

organism: Arabidopsis thaliana

source_name: fcafpa double mutant, 17 days

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated using the RNeasy Plant Mini Kit (Qiagen). For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

tag: ecotype

value: fca-9 fpa-7 double mutation

value: seedling

tag: developmental stage

value: 17 days after germination


title: fcafpa double mutant, 17 days, replicate B


title: fcafpa double mutant, 17 days, replicate A


title: iMet tumor cMet3


title: Melanocytes Cnt1


title: WT 17 days, replicate C

source_name: WT, 17 days

value: wild-type


title: WT 17 days, replicate B


title: fcafpa double mutant, 7 days, replicate B

data_processing:
Intensity values were corrected for probe sequence biases followed by quantile normalization in R.

The processed data .txt file includes log2-transformed normalized signal intensities for TAIR9 identifiers (chromosome_start coordinate).

source_name: fcafpa double mutant, 7 days

value: 7 days after germination


title: fcafpa double mutant, 7 days, replicate A


description: Gene expression data from Vehicle treated, DAY 6, biological rep.1, MV4-11 cells

tag: cell line

tag: agent


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.2, MV4-11 cells


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.3, MV4-11 cells


title: WT 7 days, replicate C

source_name: WT, 7 days


title: fcafpa double mutant, 7 days, replicate C


title: TG fl/fl 3

city: Oxford

first: Hedia

last: Chagraoui

address: john radcliffe hospital headley way headington

department: Molecular Hematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

description: replicate 3

data_processing: Data were transformed to log (base 2) and normalised using quantile normalisation. Differentially expressed genes were identified using LIMMA for R.

source_name: sorted MK progenitors

label_protocol: Amplification and labeling of the RNA was performed using the Illumina TotalPrep RNA amplification kit (Ambion).

growth_protocol: Directly after the sort , MK progenitors were put in lysis buffer for RNA extraction

extract_protocol: RNA was extracted using RNAqueous-micro (Ambion) and assessed for integrity using the Agilent Bioanalyser 2100 (Agilent Technologies).

value: 3 to 4 months old

value: bone marrow


title: TG fl/fl 2

description: replicate 2


title: WT 17 days, replicate A


title: TG fl/fl 1

description: replicate 1


title: TG +/+ 2

description: replicate 2


title: TG +/+ 3

description: replicate 3


description: Gene expression data from Vehicle treated, DAY 4, biological rep.2, MV4-11 cells

value: day 4


title: U87MG pSuper Retro AEG-1 RNAi Rep_1

description: U87MG pSuper Retro AEG-1 RNAi Rep_1

source_name: U87MG_AEG-1 RNAi

value: glioma cells


description: Gene expression data from Vehicle treated, DAY 4, biological rep.3, MV4-11 cells


description: Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.3, MV4-11 cells


title: TG +/+ 1

description: replicate 1


description: Gene expression data from Vehicle treated, DAY 4, biological rep.1, MV4-11 cells


description: Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.1, MV4-11 cells


title: WT 7 days, replicate B


description: Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.2, MV4-11 cells


title: WT 7 days, replicate A


title: homozygous_TGFb_24hr_2

city: San Diego

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

data_processing: gcRMA, unlogged

label_protocol: 2 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Mouse embryonic fibroblasts (MEF) cells were harvested as described. Briefly, timed pregnancies were set up; E12.5 to E14.5 fetuses were harvested. After carefully removing the embryo’s head, liver and blood clots, the rest of the tissues were washed with PBS, minced and digested with Trypsin at 37?C for 10 min. After digestion, fetal tissues were vigorously pipetted until it is a single cell suspension. The cells were spun down and cultured in DMEM supplemented with Gentamicin, Glutamine, non-essential amino acids, 2-mercaptoethanol and 10% FBS at 37 ?C in a 5% CO2 incubator.  MEFs with 3 different genotypes were treated with or without 5 ng/mL TGF-b1 (R&D systems) for indicated times.


description: Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.1, MV4-11 cells


title: SIRT3KO, high-fat diet, rep3

city: Durham

first: Matthew

last: Hirschey

state: NC

address: 300 N. Duke Street

department: Department of Medicine

institute: Duke University Medical Center

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a high-fat diet
12-KO3

hyb_protocol: Affymetrix GeneChip Whole Transcript protocol

data_processing: RMA (Robust Multi-array Analysis) was used for normalizing and summarizing probe-level intensity measurements from Affymetrix Gene Chips (Affymetrix Expression Console). Starting with the probe-level data from a set of Gene Chips, the perfect-match (PM) values were background-corrected, normalized and finally summarized resulting in a set of expression measures.

source_name: Mouse liver tissue

growth_protocol: Mice were fed a standard diet, or weaned onto a high-fat Western diet (42% fat)

treatment_protocol: Mice were fasted 24 hours, sacrificed, and whole livers were removed.

value: liver

tag: genotype/variation

value: 12 weeks

tag: nutrient state

value: 24h fasted

tag: diet

value: High-fat diet


title: homozygous_TGFb_4hr_2


title: homozygous_TGFb_24hr_1


title: SIRT3KO, high-fat diet, rep1

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a high-fat diet
10-KO1

label_protocol: Affymetrix GeneChip Whole Transcript protocol

tag: strain

tag: tissue


title: homozygous_1


title: homozygous_2


title: Control, high-fat diet, rep2

description:
Gene expression data from 12 week old wt mouse liver tissue fed a high-fat diet
08-WT2

tag: age


title: HUVEC cells, CO, rep1

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

description: Gene expression data from Human umbilical vein endothelial cells (HUVEC) treated with Carbon monoxide

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of HG133A -type from Affymetrix. A Custom CDF Version 10 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: HUVEC cells treated with Carbon monoxide

growth_protocol: Cells were grown in basal endothelial medium (Promocell, Heidelberg, Germany) supplemented with 10% FBS (PAA laboratories GmbH, Pasching, Austria) and essential growth factors until they formed a confluent monolayer.

extract_protocol: Total RNA was isolated from these cultures using Trizol®-Reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: Cells were stimulated with 50ng/ml (1000u) of TNF-α in the presence or absence of 1 mM of CORM-3. This concentration was chosen on the basis of dose response studies and was not toxic to HUVEC. Unstimulated cells served as control.

value: HUVEC

tag: treatment

value: Carbon monoxide (CO)


title: Control, high-fat diet, rep3

description:
Gene expression data from 12 week old wt mouse liver tissue fed a high-fat diet
09-WT3


title: SIRT3KO, high-fat diet, rep2

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a high-fat diet
11-KO2


title: homozygous_TGFb_4hr_1


description: Gene expression data from Vehicle treated, DAY 2, biological rep.2, MV4-11 cells

tag: cell line description

value: biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment)

tag: growth conditions

value: Vehicle

value: day 2


title: HUVEC cells, TNF_CO, rep1

description: Gene expression data from Human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha with Carbon monoxide

source_name: HUVEC cells treated with TNF-alpha and Carbon monoxide

value: TNF-alpha and Carbon monoxide (CO)


description: Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.3, MV4-11 cells

value: IMDM with 10% FBS

tag: time

tag: biological rep


title: SIRT3KO, standard diet, rep2

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a standard diet
05-KO4

value: Standard diet


description: Gene expression data from Vehicle treated, DAY 2, biological rep.3, MV4-11 cells


title: HUVEC cells, M, rep1

description: Gene expression data from Human umbilical vein endothelial cells (HUVEC) untreated for control

source_name: untreated HUVEC cells


title: heterozygous_TGFb_24hr_1


title: Control, high-fat diet, rep1

description:
Gene expression data from 12 week old wt mouse liver tissue fed a high-fat diet
07-WT1


title: SIRT3KO, standard diet, rep1

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a standard diet
04-KO1


title: SIRT3KO, standard diet, rep3

description:
Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a standard diet
06-KO5


title: heterozygous_TGFb_24hr_2


title: HUVEC cells, TNF, rep1

description: Gene expression data from Human umbilical vein endothelial cells (HUVEC) treated with TNF-alpha

source_name: HUVEC cells treated with TNF-alpha

value: TNF-alpha


title: heterozygous_TGFb_4hr_2


description: Gene expression data from Vehicle treated, DAY 2, biological rep.1, MV4-11 cells


description: Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.2, MV4-11 cells


title: heterozygous_TGFb_4hr_1


title: HUVEC cells, M, rep2


title: HUVEC cells, CO, rep2


title: Control, standard diet, rep3

description:
Gene expression data from 12 week old wt mouse liver tissue fed a standard diet
03-WT5


title: HUVEC cells, TNF_CO, rep2


description: Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.1, MV4-11 cells


title: heterozygous_2


title: Control, standard diet, rep2

description:
Gene expression data from 12 week old wt mouse liver tissue fed a standard diet
02-WT4


title: HUVEC cells, TNF, rep2


title: DHT for 48h, biological rep1

first: Yiwen

last: Chen

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from 48h DHT treated MDA-MB-453 cells

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the Robust Multichip Average (RMA) algorithm and the MultiExperiment Viewer (MeV) software.

source_name: MDA-MB-453 cells treated with 10nM DHT for 48h

growth_protocol: The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37oC incubator.

treatment_protocol: The MDA-MB-453 cells were grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 3 days, followed by treatment of vehicle or 10 nM DHT for time course.

tag: time point

value: breast cancer


title: wt_TGFb_24hr_2


title: DHT for 48h, biological rep2

tag: disease state


title: Control, standard diet, rep1

description:
Gene expression data from 12 week old wt mouse liver tissue fed a standard diet
01-WT3


title: Y4143 vs. Y2946

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Technical replicate 2 of 2.

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

scan_protocol: Scanned on a GenePix 4000B scanner (Axon). Scanning software: GenePix Pro 6.1

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

organism: Saccharomyces cerevisiae

source_name: Total RNA extracted from Y4143 labeled with Cyanine5 (red)

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in the presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

growth_protocol: Cell growth 24 hours at 30°C in SD medium (Casaminoacid 0.2%, Adenin 300µM, Uracil 200µM, Tryptophan 200µM) to an OD = 0.5.

extract_protocol: Hot phenol extract procedure followed by RNeasy Mini Kit purification step (Qiagen).

tag: genotype

value: Mat alpha ade3::KanMx4 his3Delta1 leu2Delta0 ura3Delta0

source_name: Total RNA extracted from Y2946 labeled with Cyanine3 (green)

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in the presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

value: Mat alpha his3Delta1 leu2Delta0 ura3Delta0


title: Y2946 vs. Y4143

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Y2946 labeled with Cyanine5 (red)

source_name: Total RNA extracted from Y4143 labeled with Cyanine3 (green)


title: HUVEC cells, M, rep3


title: HUVEC cells, TNF_CO, rep3


title: wt_TGFb_24hr_1


title: heterozygous_1


title: DHT for 4h, biological rep2

description: Gene expression data from 4h DHT treated MDA-MB-453 cells

source_name: MDA-MB-453 cells treated with 10nM DHT for 4h


title: HUVEC cells, CO, rep3

description: Gene expression data from Human umbilical vein endothelial cells (HUVEC) treated with Carbon monoxide


title: wt_TGFb_4hr_2


title: DHT for 16h, biological rep2

description: Gene expression data from 16h DHT treated MDA-MB-453 cells

source_name: MDA-MB-453 cells treated with 10nM DHT for 16h


title: wt_TGFb_4hr_1


title: wt_2


title: DHT for 4h, biological rep1


title: HUVEC cells, TNF, rep3


title: Y3188 +AICAr vs. Y3188 -AICAr

description: Biological replicate 2 of 2.

scan_protocol: Scanned on a Agilent G2505C (Agilent). Scanning software: Feature Extraction v10.7.3.1 (Agilent)

data_processing:
Normalization using the Goulphar WebTool (http://transcriptome.ens.fr/goulphar/).
Flags are removed from the analysis. Background is not subtracted from the main signal. Global Lowess normalization method.

source_name: Total RNA extracted from Y3188 +AICAr labeled with Cyanine5 (red)

growth_protocol: Cells were grown for 24 hours at 30°C in SD medium (Casaminoacid 0.2%, Adenine 300 µM, Uracil 200 µM, Tryptophan 200 µM) supplemented (+AICAr) or not (-AICAr) with 5-amino-4-imidazolecarboxamide ribotide (AICAr) at 1 mM, diluted to  OD = 0.1, grown in the same media and harvested at OD = 1.

value: Mat alpha ade16::KanMx4 ade17::KanMX4 ade8::KanMX4 his1::KanMX4 ado1::LEU2 his3Delta1 leu2Delta0 ura3Delta0

tag: growth condition

value: +AICAr

source_name: Total RNA extracted from Y3188 -AICAr labeled with Cyanine3 (green)

value: -AICAr


title: Y3188 -AICAr vs. Y3188 +AICAr

description: Biological replicate 1 of 2.

scan_protocol: Scanned on an Agilent G2505C (Agilent). Scanning software: Feature Extraction v10.7.3.1 (Agilent)

source_name: Total RNA extracted from Y3188 -AICAr labeled with Cyanine5 (red)

source_name: Total RNA extracted from Y3188 +AICAr labeled with Cyanine3 (green)


title: Melanocytes Cnt4

description: Gene expression data from mouse melanocytes

source_name: melanocytes isolated from mouse

tag: cell type

value: melanocytes


title: Y2950 +AICAr vs. Y2950 -AICAr

description: Biological replicate 2 of 2.

source_name: Total RNA extracted from Y2950 +AICAr labeled with Cyanine5 (red)

value: Mat alpha ade16::KanMx4 ade17::KanMX4 ade8::KanMX4 his1::KanMX4 his3Delta1 leu2Delta0 ura3Delta0

source_name: Total RNA extracted from Y2950 -AICAr labeled with Cyanine3 (green)


title: Y2950 -AICAr vs. Y2950 +AICAr

description: Biological replicate 1 of 2.

source_name: Total RNA extracted from Y2950 -AICAr labeled with Cyanine5 (red)

source_name: Total RNA extracted from Y2950 +AICAr labeled with Cyanine3 (green)


title: Slide 188560

status: Public on Jul 10 2011

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 4

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of copY mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Wild type control

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to OD600 of 0.3 in CDM media without any added copper.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Four replicate cultures.

value: Wild type

source_name: copY mutant

value: copY mutant


title: Slide 188558

description: Sample 3


title: DHT for 16h, biological rep1

city: Houston

tag: agent

tag: cell line


title: Slide 188566

description: Sample 4

source_name: without copper

growth_protocol: Cells were grown to OD600 of 0.3 in CDM media without or with 0.05 mM copper.

tag: copper conc.

value: Without copper

source_name: with 0.05mM copper


title: Slide 188557

description: Sample 2

tag: genotype/variation


title: Slide 188564

description: Sample 2


title: Slide 188561

description: Sample 1


title: vehicle, biological rep1

description: Gene expression data from vehicle treated MDA-MB-453 cells

source_name: MDA-MB-453 cells treated with vehicle

value: vehicle


title: wt_1


title: Slide 188555

description: Sample 1


title: GT2

status: Public on Jul 09 2011

city: Kawasaki

first: Takashi

last: Osanai

state: Kanagawa

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

country: Japan

institute: Meiji University

description: Glucose-tolerant Synechocystis strain

hyb_protocol: Labeling cDNAs are spotted onto CyanoChip (slide glass), and covered by slide glass, followed by incubation at 60 degree for overnight

scan_protocol: Hybridization signals were measured with a 428 Array scanner (Affymetrix) and a software Affymetrix 428 array scanner version 1.1. Cy3 or Cy5 signals were scanned with 532 nm or 635 nm laser. Resolution were 2200 x 5760 pixels. Scanned pictures were saved as 16-bit TIFF files.

data_processing: Normalization was performed for adjusting total signal intensities between cy3 and cy5 by Excel (Microsoft).

organism: Cyanobacteriota

source_name: Synechocystis

label_protocol: cDNAs were synthetized from total RNA by RNA Fluorescence Labeling Core Kit （M-MLV Version） Ver.2.0 (Takara Bio).

growth_protocol: Cells grown in modified BG-11 liquid medium (5 mM NH4Cl as nitrogen sources) under 50-70 micromolphotons/m2s.

extract_protocol: Total RNAs were isolated by hot-phenol method.

value: Glucose-tolerant Synechocystis strain

tag: Stage

value: log-phase


title: SigEox3

description: SigE overexpression strain

value: SigE overexpression strain


title: Slide 188565

description: Sample 3


title: SigEox2

description: SigE overexpression strain


title: GT3

description: Glucose-tolerant Synechocystis strain


title: SigEox1

description: SigE overexpression strain


title: GT1

description: Glucose-tolerant Synechocystis strain


title: CDC1551 wild type vs aprABC null mutant rep 1

city: Ithaca

first: David

last: Russell

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

description: Image: http://smd.stanford.edu/MicroArray/gifs//88904.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis

source_name: CDC1551 aprABC null mutant

label_protocol: not provided

growth_protocol: Growth Temperature: 37oC; Static or Shaking: Static; Media: Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol

extract_protocol:
QIAgen RNeasy kit
Ambion MessageAmp-II T7 RNA polymerase amplification

tag: strain

value: CDC1551 aprABC null mutant

source_name: Wild type Mtb CDC1551

value: Wild type Mtb CDC1551


title: Sp +2 vs PvSp -1 251485710028

city: Barcelona

first: Hernando

middle: A

last: del Portillo

state: Barcelona

address: rosello, 132 (4a)

country: Spain

institute: Barcelona Centre for International Health Research

description: Agilent's recommended procedures

hyb_protocol: Agilent's recommended procedures

scan_protocol: Agilent's recommended procedures

data_processing: The VALUE field is the normalized log-ratio. The normalization is achieved by LOWESS in the M-A-plot space, where A = log2(Cy5)/2+log2(Cy3)/2 and M = log2(Cy5/Cy3). A filter eliminates spots that: log2(Cy3) < 5 or log2(Cy5) < 5 or neg/pos controls.

organism: Plasmodium vivax

source_name: Sp +2

label_protocol: Agilent's recommended procedures

treatment_protocol: monkey leukocytes removed by MidiMacs. Only mature stages used for RNA analysis

tag: tissue

value: P. vivax asexual blood stage parasites; only mature stages used for RNA analysis; leukocytes removed by MidiMacs

tag: host

value: infected monkey CJ42 Cali with intact spleen

source_name: PvSp -1

treatment_protocol: monkey leukocytes removed by CF11 columns

value: P. vivax asexual blood stage parasites

value: splenectomized infected monkeys CDC


title: vehicle, biological rep2

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

value: breast cancer


title: PPP 6h, biological rep 1

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

institute: Rudbeck Laboratory, Uppsala University

description: Gene Expression Data from RPMI 8266 6 hrs treated with PPP

hyb_protocol: Hybridization was done for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev2, Affymetrix Inc., Santa Clara, CA)

scan_protocol: Scanning was done using GeneChip® Scanner 3000 7G

data_processing: Data analysis and normalization done using GeneSpring v11. RMA and quantile normalization was used to normalized the data.

source_name: Multiple myeloma cell line RPMI 8266 (treated with PPP)

label_protocol: Biotinylated cRNA were prepared from 250 nanogram total RNA of each sample according to the GeneChip® 3’ IVT Express Kit Manual (PN 702646 Rev1, Affymetrix Inc., Santa Clara, CA).

growth_protocol: RMPI 8266 were grown in RPMI1640 and 10% FCS.

treatment_protocol: RPMI 8266 cells were treated with LBH589 (20nM), picropodophyllin (PPP)(0.375uM) , and the combination of these two drugs (same concentrations).

value: RPMI 8266

value: B lymphocyte

tag: gender

value: Male


title: Sp -3 vs PvSp -1 251485710027

description: Agilent's recommended procedures

source_name: Sp -3

value: infected monkey 814*058 Cali without spleen


title: LBH 24h, biological rep 1

description: Gene Expression Data from RPMI 8266 24 hrs treated with LBH589

source_name: Multiple myeloma cell line RPMI 8266 (treated with LBH589)


title: Combo 24h, biological rep 1

description: Gene Expression Data from RPMI 8266 24 hrs treated with Combo

source_name: Multiple myeloma cell line RPMI 8266 (treated with combo LBH589 & PPP)


title: PPP 24h, biological rep 1

description: Gene Expression Data from RPMI 8266 24 hrs treated with PPP


title: CDC1551 wild type vs aprBC null mutant rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs//88909.gif

source_name: CDC1551 aprBC null mutant

value: CDC1551 aprBC null mutant


title: CDC1551 wild type vs aprABC null mutant rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs//88906.gif


title: untreated 24h, biological rep 1

description: Gene Expression Data from RPMI 8266 24 hrs untreated

source_name: Multiple myeloma cell line RPMI 8266 (untreated)


title: 20060130_04_05-220_NP

city: Seattle

first: Alvin

middle: Y

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

institute: University of Washington

description: bulk tissue

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45 deg C to 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

source_name: Normal prostate tissue

label_protocol: GeneChip® One-Cycle Target Labeling Kit

growth_protocol: Cells were isolated after overnight tissue digestion with collagenase in serum-free RPMI1640 media.

extract_protocol: Sorted cell populations were lysed in RLT buffer for RNA isolation.

treatment_protocol: Cells were labeled with dye conjugated-antiCD monoclonal antibodies and sorted by MACS

tag: tissue/origin

value: normal prostate

value: Normal prostate tissue


title: CDC1551 wild type vs phoP Tn mutant rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs//88915.gif

source_name: CDC1551 phoP transposon mutant

value: CDC1551 phoP transposon mutant


title: CDC1551 wild type vs phoP Tn mutant rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs//88914.gif


title: Combo 6h, biological rep 1

description: Gene Expression Data from RPMI 8266 6 hrs treated with Combo

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


title: CDC1551 wild type vs aprBC null mutant rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs//88907.gif


title: CDC1551 wild type vs aprABC null mutant rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs//88905.gif


title: CDC1551 wild type vs aprC null mutant rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs//88911.gif

source_name: CDC1551 aprC null mutant

value: CDC1551 aprC null mutant


title: untreated 6h, biological rep 1

description: Gene Expression Data from RPMI 8266 6 hrs untreated


title: CDC1551 wild type vs aprC null mutant rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs//88910.gif


title: CDC1551 wild type vs phoP Tn mutant rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs//88913.gif


title: 20060130_03_05-220_CaP

description: bulk tissue

source_name: Prostate cancer tissue

value: prostate cancer

value: Prostate cancer tissue


title: 20060130_01_05-218_CaP

description: bulk tissue


title: CDC1551 wild type vs aprC null mutant rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs//88912.gif

value: Wild type Mtb CDC1551


title: 20060130_02_05-218_NP

description: bulk tissue


title: Sp -2 vs PvSp -1 251485710024

description: Agilent's recommended procedures

source_name: Sp -2

value: P. vivax asexual blood stage parasites; only mature stages used for RNA analysis; leukocytes removed by MidiMacs

value: infected monkey 318*879 Cali without spleen


title: CDC1551 wild type vs aprBC null mutant rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs//88908.gif


title: PvSp -1 vs PvSp -1 (self-self) 251485710025

description: Agilent's recommended procedures

treatment_protocol: monkey leukocytes were removed by CF11 columns

value: P. vivax asexual blood stage parasites; not known the percentages of different asexual blood stages though presumably mostly mature stages

value: infected monkeys with removed spleen


title: LBH 6h, biological rep 1

description: Gene Expression Data from RPMI 8266 6 hrs treated with LBH589


title: Sp -1 vs PvSp -1 251485710023

description: Agilent's recommended procedures

source_name: Sp -1

value: infected monkey 334*080 Cali without spleen

value: P. vivax asexual blood stage parasites

value: splenectomized infected monkeys CDC


title: 20051221_10_05-213_CaP

description: bulk tissue


title: lung tissues 0.5mg SWCNTs treated on day 7, biological rep1

city: Taipei

first: Huei-Wen

address: No.1, Sec.1, Re-Ai Rd

department: Medical College

country: Taiwan

institute: National Taiwan University

description: Gene expression data from mice lung tissues treated with 0.5 mg SWCNTs in sub-chronic response phase, day 7).

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430A plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The expression data were analyzed by the SAS JMP Genomics software (Version 4.0; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.

source_name: lung tissue (right side, lobe 1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: Adult male ICR mice (5~6 weeks old), were purchased from the laboratory animal center of National Taiwan University College of Medicine (Taipei, Taiwan). Mice were cared and used humanely according to the Guide for the Care and Use of Laboratory Animals as adopted and promulgated by the National Health Research Institutes (NHRI, Taiwan).

treatment_protocol: The intratracheal instillation procedure: anesthetized with pentobarbital (80 mg•kg-1, Sigma, St. Louis, MO, USA; intraperitoneally), individual mice were secured on an inclined plastic platform. The trachea was exposed by a 1 cm incision in the ventral neck skin for instillation of Pluronic F-68 (PF68, solvent control) or the SWCNTs [0.5 mg per mouse in a 50 µl 0.1% Pluronic F-68 aliquot]; SWCNTs (SE grade, purity > 95%) was purchased from CarboLex, Inc, (McCarty, Court, Lexington).

value: right lung, lobe 1

value: ICR

tag: age

value: 5 to 6 weeks old

tag: treatment group

value: 0.5mg SWCNTs treated on day 7


title: 20051222_07_05-215_NP

description: bulk tissue

value: normal prostate

value: Normal prostate tissue


title: 20051222_08_05-215_CaP

description: bulk tissue


title: 20051221_09_05-213_NP

description: bulk tissue


title: lung tissues 0.5mg SWCNTs treated on day 7, biological rep2


title: lung tissues PF68 treated on day 7, biological rep1

description: Gene expression data from mice lung tissues treated with PF 68 (as solvent control) in sub-chronic response phase, day 7).

value: PF68 treated on day 7


title: lung tissues PF68 treated on day 7, biological rep2


title: lung tissues 0.5mg SWCNTs treated on day 1, biological rep2

description: Gene expression data from mice lung tissues treated with 0.5 mg SWCNTs in acute response phase, day 1).

value: 0.5mg SWCNTs treated on day 1


title: 20071120_10_07-068_CB_CD9nega_CD13posi

description: CD13+ cancer-associated stromal cells

source_name: Bladder cancer-associated stromal cells

label_protocol: GeneChip® Two-Cycle Target Labeling Kit

value: bladder cancer stroma

value: Bladder cancer-associated stromal cells


title: control, biological rep1

city: Reno

first: Richard

middle: Leonard

last: Tillett

state: NV

address: University of Nevada Reno Mailstop 330

department: Department of Biochemistry & Molecular Biology

institute: University of Nevada Reno

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45C on Affymetrix GeneChip® 16K Vitis vinifera (Grape) Genome Arrays ver. 1.0. GeneChips were washed and stained in the Affymetrix® 3000 7G Scanner, Hybridization, and Fluidics System.

scan_protocol: GeneChips were scanned using the Affymetrix® 3000 7G Scanner, Hybridization, and Fluidics System.

data_processing: Raw hybridization intensity values were processed by Robust Multi-Array Average (RMA), using the R package affy. Specifically, expression values were extracted from raw CEL files by first applying the RMA model of probe-specific correction to PM (perfect match) probes. Corrected probe values were then normalized via quantile normalization, and a median value computed for the PM probeset. Resulting RMA expression values were log2-transformed.

organism: Vitis vinifera

source_name: Empty control line '8-6'

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Affymetrix GeneChip Expression Analysis Technical Manual, 2009).

growth_protocol: Vines were clonally propagated in sterile Magenta GA-7 boxes and transferred to soil. Specifically, green cuttings (2-3 internodes) were rooted in boxes containing 80 ml of 0.8% (w/v) Plant Tissue Culture Agar (#A111, Phytotechnology Laboratories, Shawnee Mission, KS) with Murashige and Skoog modified Basal Medium w/ Gamborg Vitamins (#M404, Phytotechnology Laboratories), 1.5% sucrose, pH 5.6-5.7 and 300 mM Indoleacetic Acid (IAA) for 14 days. Rooted cuttings were transferred to media lacking IAA for 10 further days. Lastly, the young vines were transferred to soil and grown for 14 days in a Percival Scientific growth chamber (model# AR75L).

extract_protocol: Total RNA was extracted using RNeasy Midi column (Qiagen, Inc., Valencia, CA) with 2% Polyethylene Glycol (PEG, mw = 20,000, Sigma Aldrich, Inc., St. Louis, MO) added to the RLT buffer, on-column DNase digestion, phenol:chloroform:isoamyl-alcohol (25:24:1) extraction and final clean-up on RNeasy Mini column (Qiagen) with 2% PEG (Tattersall et al., 2005).

treatment_protocol: Grapevines of the Vitis hybrid rootstock cv. ‘Freedom’ were transformed with a 35S::VvCBF4 construct or an empty vector control. Clones of the regenerated plantlets (grown as above) were collected under well-watered conditions.

tag: cultivar

value: Freedom

value: whole aerial tissues (stem + 5 leaves)

value: Empty control line '8-6'

value: young cuttings


title: VvCBF4 overexpressor, biological rep4

source_name: 35S::VvCBF4 overexpressor '9-12'

value: 35S::VvCBF4 overexpressor '9-12'


title: control, biological rep4


title: control, biological rep3


title: lung tissues 0.5mg SWCNTs treated on day 1, biological rep1


title: lung tissues PF68 treated on day 1, biological rep1

description: Gene expression data from mice lung tissues treated with PF 68 (as solvent control) in acute response phase, day 1).

value: PF68 treated on day 1


title: control, biological rep2


title: lung tissues PF68 treated on day 1, biological rep2


title: 20051221_08_05-206_CaP

description: bulk tissue

value: prostate cancer

value: Prostate cancer tissue


title: VvCBF4 overexpressor, biological rep3


title: 20070619_06_07-008_CB_epi_CD9posi

description: CD9+ bladder cancer cells

source_name: Bladder cancer cells

value: bladder cancer

value: Bladder cancer cells


title: 20061218_03_CD104t_11-06-06

description: CD104+ basal cells

source_name: Normal bladder basal cells

value: normal urinary bladder

value: Normal bladder basal cells


title: VvCBF4 overexpressor, biological rep2