title: Dengue virus 4-210


title: Prostate Tissue PC636 Tumor

status: Public on Apr 19 2011

type: genomic

city: Stanford

first: Yuya

last: Kobayashi

state: CA

address: 259 Campus Dr

department: Genetics

country: USA

institute: Stanford University

description: Prostate Tumor

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

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

data_processing: Each raw intensity values were background subtracted and beta scores were calculated manually. Values were normalized using ComBat.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate Tissue PC636

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA were isolated from prostate tissue samples using Qiagen Allprep kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: prostate tissue

tag: disease state

value: Tumor

tag: age

tag: pre-treatment psa

tag: path gr (gleason)

tag: months followed-up

tag: recurrence

value: Biochemical

tag: days to recurrence


title: 14986402 - H3K4me2_WT_I_INPUT vs H3K4me2_WT_I_IP

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_I_IP Cy5 / H3K4me2_WT_I_INPUT Cy3 : 80pmol.

scan_protocol: NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

treatment_protocol: no treatment

tag: ecotype

value: 10 day

tag: dev.stage (boyes et al. plant cell 2001)

value: seedling

tag: antibody

tag: vendor


title: 14640502 - H3K4me3_WT_I_IP vs H3K4me3_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_I_INPUT Cy5 / H3K4me3_WT_I_IP Cy3 : 80pmol.


title: 14636402 - H3K27me3_WT_I_INPUT vs H3K27me3_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_I_IP Cy5 / H3K27me3_WT_I_INPUT Cy3 : 80pmol.

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hours photoperiod.

value: Upstate 07-449


title: 6302702 - H3K4me3_WT_II_INPUT vs H3K4me3_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_II_IP Cy5 / H3K4me3_WT_II_INPUT Cy3 : 80pmol.


title: Prostate Tissue PC599 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC599


title: 11994602 - H3K4me2_WT_I_IP vs H3K4me2_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_I_INPUT Cy5 / H3K4me2_WT_I_IP Cy3 : 80pmol.


title: Junin virus-209

type: RNA

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

description: hybridization of infected culture for use in testing the performance of VIPR

hyb_protocol: 70 degree incubation for 12 hours

scan_protocol: scanned using GenePix 4000B scanner

data_processing: The data was produced with the intention of being analyzed by several different diagnostic algorithms, each of which employs its own normalization method. Because there is no standard normalization procedure between the different software diagnosis tools, we decided to submit raw intensities that can be used as input to any of the various available programs and independently processed by each.

molecule: total RNA

organism: Mammarenavirus juninense

source_name: infected culture

label_protocol: amino-allyl Cy3 dye coupled to cDNA

extract_protocol: RNA extracted using Trizol extraction protocol

tag: culture

value: Vero or C6/36

tag: causes hf

value: Yes


title: Control_6

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: Control

hyb_protocol: The purified labeled miRNA probes were hybridized for 20 h at 55 °C.

scan_protocol: The arrays were washed and scanned at 5-micron resolution with a PerkinElmer ScanArray Express array scanner.

data_processing: The resulting images were quantified by using Agilent’s Feature Extraction software. Further, expression data was consolidated to make representative expression profile for each probe and then normalized using quantile method (MATLAB R2009b).

source_name: Lung tissue sample from lung transplant patient

label_protocol: T4 ligase was used to join cyanine 3-cytidine bisphosphate to the termini of all single-stranded RNA (including miRNA) and the labeled RNA was purified from these reactions by gel filtration on MicroBioSpin 6 columns (Bio-Rad).

extract_protocol: 100 ng of total RNA was dephosphorylated with calf intestinal alkaline phosphatase, followed by denaturation in dimethyl sulfoxide.

tag: tissue

value: lung

tag: disease status

value: Control

tag: diagnosis

value: Normal

tag: fvc-group


title: ILD_1

description: ILD patient

source_name: Lung tissue sample from the patient with ILD

value: ILD patient

value: UIP/IPF


title: 14640602 - H3K27me3_WT_II_INPUT vs H3K27me3_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_II_IP Cy5 / H3K27me3_WT_II_INPUT Cy3 : 80pmol.


title: Sudan ebolavirus-216

organism: Sudan ebolavirus


title: Prostate Tissue PC594 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC594

tag: gender

tag: sample type

tag: disease state


title: Prostate Tissue PC84 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC84

tag: age

tag: pre-treatment psa

tag: path gr (gleason)


title: Rift Valley fever virus-208

organism: Rift Valley fever virus


title: Prostate Tissue PC19.2 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC19.2


title: Control_1

description: Control

source_name: Uninvolved lung tissue sample from lung cancer patient


title: Control_5

description: Control


title: Prostate Tissue PC370 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC370

tag: months followed-up

tag: recurrence

tag: days to recurrence


title: Prostate Tissue PC45 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC45


title: Yellow fever virus-211

organism: Yellow fever virus


title: Control_4

description: Control


title: Prostate Tissue PC21 Tumor (1)

description: Prostate Tumor

source_name: Prostate Tissue PC21


title: Prostate Tissue PC184 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC184


title: 14638902 - H3K27me3_WT_I_IP vs H3K27me3_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_I_INPUT Cy5 / H3K27me3_WT_I_IP Cy3 : 80pmol.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

tag: antibody


title: Control_3

description: Control


title: Control_2

description: Control


title: Reston ebolavirus-203

organism: Reston ebolavirus

tag: culture

tag: causes hf

value: No


title: Dengue virus 3-207

organism: dengue virus type 3


title: preferring double-housed 3

city: Aurora

first: Laura

last: Saba

state: CO

address: 12801 E. 17th Avenue

department: Pharmacology

institute: University of Colorado Denver

description: doubly housed

hyb_protocol: Hybridization is performed overnight in a temperature-controlled shaking incubator.  Post-hybridization processing includes a stringent wash to remove unbound and nonspecifically hybridized target molecules, a staining step with a Cy™5-Streptavidin conjugate, and several non-stringent washing steps to remove unbound conjugate. Following a final rinse, the bioarrays are dried by centrifugation.  http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Arrays are scanned using GenePix 4000B scanner and analyzed using Amersham CodeLink Expression Analysis v.4.0 software.  Codelink Bioarray QC (Rat) Bioarrays are examined by eye, and by a physical mapping of the flagged spots to qualitatively assess whether or not the image has any obvious flaws: high background, smears, scratches, etc. Codelink EXP v4.1 software is used to analyze acquired bioarray images during scanning. The analysis generates both raw and median normalized intensities. Also, the software is used as a primary point for quality control checks. The Bioarray QC report details several adjustable pass/fail criteria. Listed below are descriptions, and the threshold cutoffs we have selected for chip hybridization failures. Note that our settings are different than the default settings. If any chip statistic is found lower than the threshold setting, the chip is failed. The failed chip data is still made available, but with a notation on the specific failure. The failed chip data can be more closely scrutinized using a variety of measurement methods, and may still be effectively used in an analysis. % Total Spots Flagged Exceeds: 40 default(50) Spots that exhibit background contamination, irregular shape, low signal, or saturated signal. % Near Background Exceeds: 40 default(50) Spots where spot mean intensity/local background < 1. We have chosen 40% based on a large quantity of chips. % Contaminated Exceeds: 3 default(10) Spots that have background contamination. The background pixel dispersion has high contrast as seen in the expected mean and median statistics, or the local background is very high, compared to global background. We typically see less than 3% of spots flagged contaminated. % Irregular Exceeds: 3 default(5) Spots where percentage of the difference between maximum and minimum diameter of the spot measured in different directions exceeds a set value. We typically see less than 3% of spots flagged irregular. % Saturated Exceeds: 5 default(5) The percent of spots that have saturated signals. % Excluded MSR/User Exceeds: 2 default(2) Spots that did not pass manufacturing QC are masked by the MSR file, and spots can be manually flagged by user if desired. % Positive Controls Below Noise: 20 default(10) The percent of positive control probes that have signal below the local background noise level. This percentage tends to be higher when low concentration spikes fall below the threshold. A recommended setting is 30%, however, based on a large amount of arrays, we have made the setting at 20%. % of Negatives Above Noise: 5 default(0) The percent of negative control probes that have signals above local background. A recommended setting is 30%, however, based on a large amount of arrays, we have chosen 5% as our setting.

data_processing: In preparation for normalization, probes were removed from the data sets if they were one of the negative or positive controls placed on the array by the manufacturer. Next, individual values were eliminated based on the quality flags assigned by the CodeLink Expression Analysis Software.  Values were eliminated if they were flagged as M (spot was identified to be defective through image inspection at manufacturing), C (spot has a high level of background contamination), I (spot has an irregular shape), or S (spot has a high number of saturated pixels).  Values were retained if they were flagged G (spot is good) or L (spot is below local background noise).  In addition, to be able to take the log base 2 transformation of the background adjusted intensity values, all background adjusted intensity values below zero were replaced with the value 0.00001.  The data was then normalized using a cyclic LOESS procedure executed in R with a procedure that accounted for the missing intensity values.

label: biotin

organism: Rattus norvegicus

source_name: whole brain, alcohol preferring

label_protocol: The MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit made by Ambion was used. The procedure consists of reverse transcription with an oligo(dT) primer bearing a T7 promoter using ArrayScript™ a reverse transcriptase (RT).  The cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription (IVT) in a reaction containing biotin-modified UTP and T7 RNA polymerase. Once purified, the biotin-labeled aRNA is suitable for use on microarray gene expression systems designed for biotin-labeled antisense RNA samples. http://www.ambion.com/techlib/prot/fm_1791.pdf

extract_protocol: RNA Extractions using Rneasy Lipid Tissue kit RNA extraction using QIAzol: 1. A 4 ml of QIAzol reagent. Do not allow tissue to thaw before addition of QIAzol reagent. 2. Homogenize with Polytron for 60 seconds at setting 4. 3. Let samples sit at RT for 5 minutes. 4. Add 1.0 ml chloroform per sample. 5. Cap tubes securely and shake vigorously by hand for 15 seconds. 6. Let sit at RT 3 minutes. 7. Centrifuge @ 5,000 x g for 15 minutes at 4oC. 8. Transfer the aqueous phase to an eppendorf tube (1 ml/tube). 9. Add 1 volume of 70% ethnol (about 3 ml) mix thoroughly by vortexing. Continue without delay with Rneasy Midi columns. B. RNeasy Midi Kit 1. Add 4 ml of the sample onto midi Spin column. Close the tube and centrifuge at 5000 x g for 5 min at room temp. Discard the flowthrough. 2. Repeat the step 1 with remainder of the sample. Discard the flowthrough. 3. Add 4.0 ml of Buffer RW1 onto the spin column and centrifuge at 5000 x g for 5 min to wash the column. Discard the flowthrough. 4. Add 2.5 ml of RPE Buffer to the spin column. Close the tube and centrifuge at 5000 x g for 2 min. Discard the flowthrough. 5. Add another 2.5 ml of RPE Buffer to the spin column. Close the tube and centrifuge at 5000 x g for 5 min. Discard the flowthrough. 6. Place column in fresh tube. Add 150 ìl of Rnase free water to elute total RNA. Let the column and the tubes stand for 10 min at room temp and then centrifuge at 5000 x g for 5 min. 7. Repeat the elution with the flow through (150 ìl). 8. Take Ods at 260 and 280 nm on the scanning spectrophotometer in AFFY core lab.

value: male

tag: developmental stage

value: adult

tag: genetic modification

value: selective breeding

tag: individual genotype

value: Alcohol Preferring (P)

tag: strain

value: Wistar


title: Toscana virus-206

organism: Toscana virus


title: non-preferring double-housed 3

description: doubly housed

source_name: whole brain, alcohol non-preferring

tag: gender

value: Alcohol Non-Preferring (NP)


title: Rocio virus-205

organism: Rocio virus


title: preferring double-housed 4

description: doubly housed


title: Prostate Tissue PC188 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC188

value: Male

tag: sample type

value: prostate tissue

tag: disease state


title: Prostate Tissue PC405 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC405

tag: age

tag: pre-treatment psa

value: Biochemical


title: US_MN_38_7 (methcathinone user)

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the protocol

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with GCRMA and further analyzed using Bioconductir software based on R language

source_name: blood

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

growth_protocol: Patients with chronic methcathinone administration

extract_protocol: Whole blood collected with Tempus RNA tubes. Blood extracted RNA (Tempus RNA Blood kit)

tag: tissue

value: peripheral blood

tag: patient

value: methcathinone user


title: US_MN_39_K6 (control)

value: control


title: Puumala virus-204

organism: Orthohantavirus puumalaense

value: Vero or C6/36

value: Yes


title: preferring double-housed 1

description: doubly housed


title: preferring double-housed 2

description: doubly housed


title: Prostate Tissue PC593 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC593

value: Normal

tag: path gr (gleason)

tag: months followed-up

tag: recurrence

tag: days to recurrence


title: US_MN_40_K20 (control)


title: US_MN_37_14 (methcathinone user)


title: non-preferring double-housed 2

description: doubly housed


title: US_MN_36_K14 (control)


title: non-preferring double-housed 4

description: doubly housed


title: 34677202 - H2Bub_WT_II_INPUT vs H2Bub_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H2Bub_WT_II_IP Cy5 / H2Bub_WT_II_INPUT Cy3 : 80pmol.

tag: ecotype

value: 10 day

tag: antibody

tag: vendor

value: Medimabs MM-0029


title: Ngari virus-202

organism: Ngari virus

source_name: infected culture

tag: culture

tag: causes hf


title: US_MN_35_K12 (control)


title: Prostate Tissue PC21.2 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC21.2


title: Prostate Tissue PC582 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC582


title: US_MN_34_2 (methcathinone user)


title: California encephalitis virus-201

organism: California encephalitis virus

value: No


title: US_MN_33_K18 (control)


title: 34672902 - H2Bub_WT_II_IP vs H2Bub_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H2Bub_WT_II_INPUT Cy5 / H2Bub_WT_II_IP Cy3 : 80pmol.


title: Prostate Tissue PC185 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC185


title: Prostate Tissue PC375 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC375


title: US_MN_29_11 (methcathinone user)


title: US_MN_32_6 (methcathinone user)


title: US_MN_30_17 (methcathinone user)


title: US_MN_31_19 (methcathinone user)


title: Prostate Tissue PC367 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC367

value: Tumor


title: Prostate Tissue PC629 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC629


title: Prostate Tissue PC19.2 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC19.2


title: US_MN_28_K17 (control)


title: Prostate Tissue PC166 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC166


title: 28985002 - H2Bub_WT_I_IP vs H2Bub_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H2Bub_WT_I_INPUT Cy5 / H2Bub_WT_I_IP Cy3 : 80pmol.

tag: dev.stage (boyes et al. plant cell 2001)

value: seedling


title: W2_Cy5_B4_Cy3_c

city: Incheon

first: Jaehyuk

last: Choi

address: 119 Academy-ro

country: South Korea

institute: Inceon National Univ

hyb_protocol: Labelled cDNA hybridised using Agilent Cryptococcus neoformans, custom anti-sense 8x15K (AMADID 019465) by Mogene, LC

scan_protocol: Arrays scanned using Agilent Microarray Scanner by Mogene, LC

data_processing: Each channel was background corrected by subtracting the lowest 10% of foreground signal intensities within each subgrid of the array.  The two channels of each array were normalized to each other by Huber's variance stabilization algorithm (Huber et al., 2002).  A linear mixed effects model was applied to the normalized data in each channel.  A fixed effect was included for each array, for the dye by gene interaction and for each treatment/strain combination.  Random effects were included for within-array variability (each gene appeared twice on each array), technical variability (replicate culture was hybridized twice) and biological variability (48 replicate cultures were employed).  The pairwise changes between treatments within strain and the pairwise changes between strains with treatment were estimated with standard errors and p-values based Student t statistics; q-values were computed to adjust for the false discovery rate.

organism: Cryptococcus neoformans

source_name: YPD o/n at 30 and then DOPA media for 6 h

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA by MOgene, LC

growth_protocol: Three independent biological replicates for each strain were grown in 25 ml of YPD overnight at 30oC. Cells were washed twice with water, re-suspended in L-DOPA medium and then incubated at 30oC for 6 h prior to RNA extraction.

extract_protocol: RNA was purified with the RNeasy kit (Qiagen) and treated with DNase (Qiagen) following the manufacturer’s recommendations.

treatment_protocol: DOPA medium (0.5 mM 3,4-hydroxyl-L-phenylalanine [L-DOPA], 1 mM MgSO4 • 7H2O, 22 mM • KH2PO4, 3 µM thiamine-HCl, 0.1% glucose, 0.1% L-asparagine, pH 5.6)

tag: strain


title: W2BA1_Cy3_B4_Cy5_a


title: W2BA1_Cy3_B4_Cy5_b


title: Prostate Tissue PC14 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC14

tag: gender

tag: sample type


title: 28985502 - H2Bub_WT_I_INPUT vs H2Bub_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H2Bub_WT_I_IP Cy5 / H2Bub_WT_I_INPUT Cy3 : 80pmol.

tag: age


title: Prostate Tissue PC563 Tumor

description: Prostate Tumor

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

source_name: Prostate Tissue PC563

tag: disease state

tag: pre-treatment psa


title: US_MN_26_5 (methcathinone user)

tag: tissue

tag: patient


title: US_MN_27_K10 (control)


title: W2_Cy5_B4_Cy3_b


title: W2_Cy5_B4_Cy3_a


title: Prostate Tissue PC366 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC366

tag: path gr (gleason)

tag: months followed-up


title: US_MN_25_K15 (control)


title: US_MN_24_9 (methcathinone user)


title: Prostate Tissue PC626 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC626

tag: recurrence

tag: days to recurrence


title: Prostate Tissue PC15 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC15


title: US_MN_23_1 (methcathinone user)

source_name: blood


title: US_MN_22_K19 (control)


title: W2_Cy3_B4_Cy5_a


title: W2_Cy3_B4_Cy5_b


title: ExVivoHybridomacell_4hr_0.2ug/ml_rep1

city: Nanjing

first: Pu

middle: Yan

last: Chen

address: No. 1, Weigang

country: China

institute: Nanjing Agriculture University

description: Gene expression after 4hr in 0.2ug/ml BPP-II-treated hybridoma cell

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome microarrays (G2505B) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization)

organism: Mus musculus

source_name: Hybridoma cell, 4hr, 0.2ug/ml, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA usingQuick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hybridoma cells were cultured with RPMI 1640 supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen) at 37℃ with 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hybridoma cell was treated by BPP-II with RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum. The cultures were incubated for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: Hybridoma cell

tag: condition

value: 4hr in 0.2ug/ml BPP-II


title: US_MN_21_16 (methcathinone user)


title: Prostate Tissue PC551 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC551


title: 6303402 - H3K4me2_WT_II_IP vs H3K4me2_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_II_INPUT Cy5 / H3K4me2_WT_II_IP Cy3 : 80pmol.

tag: ecotype

tag: antibody

tag: vendor


title: 14992002 - H3K4me2_WT_II_INPUT vs H3K4me2_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_II_IP Cy5 / H3K4me2_WT_II_INPUT Cy3 : 80pmol.

tag: dev.stage (boyes et al. plant cell 2001)


title: 34779602 - H2Bub_WT_II_IP vs H2Bub_WT_II_INPUT

description: Epigenomic mapping


title: 5759

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Cardiac progenitor cells: derived from aorta, atrium and ventricle biopsies of wild-type (WT) mice and dystrophic mice (beta-sarcoglycan null). WT cardiac progenitors differentiate into beating cardiomyocytes, Beta sarcoglycan O progenitor cells differentiate into skeletal muscle fibers.

hyb_protocol: For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 9.5 (Agilent Technologies).

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Intensities were base 2 log-transformed and in case of multiple probes for the same Agilent ID, log-intensities were averaged.  Control probes were removed  prior to analysis.

source_name: Cardiac progenitor cells

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).

extract_protocol: RNA, RNeasy Mini Ki, Qiagen

value: myogenic cells (C2C12)


title: W2_Cy3_B4_Cy5_c

tag: strain


title: msp3_b

city: Cambridge

first: Christina

last: Scheel

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

hyb_protocol: GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).

data_processing: Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.

label_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

growth_protocol: HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions

extract_protocol: Qiagen total RNA extraction kit was used according to manufacturer's protocols.

tag: cell line

value: HMLE

value: mesenchymal subpopulations


title: US_MN_19_K8 (control)


title: Prostate Tissue PC159 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC159

tag: gender

value: Male

tag: sample type

value: prostate tissue

tag: age


title: 5758

tag: genotype/variation

value: Knockout (beta-sarcoglycan null)

value: Cardiac progenitor cells

tag: tissue

value: aorta


title: 5757

value: ventricle


title: 12000602 - H3K4me3_WT_I_INPUT vs H3K4me3_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_I_IP Cy5 / H3K4me3_WT_I_INPUT Cy3 : 80pmol.


title: 6304602 - H3K4me3_WT_II_INPUT vs H3K4me3_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_II_IP Cy5 / H3K4me3_WT_II_INPUT Cy3 : 80pmol.


title: 14644302 - H3K4me3_WT_I_IP vs H3K4me3_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_I_INPUT Cy5 / H3K4me3_WT_I_IP Cy3 : 80pmol.


title: 28910502 - H2Bub_WT_I_INPUT vs H2Bub_WT_I_IP

description: Epigenomic mapping


title: msp1_b


title: msp2_b


title: 34782702 - H2Bub_WT_II_INPUT vs H2Bub_WT_II_IP

description: Epigenomic mapping


title: US_MN_17_K3 (control)

value: peripheral blood

tag: patient

value: control


title: US_MN_20_K2 (control)


title: 14640402 - H3K27me3_WT_I_IP vs H3K27me3_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_I_INPUT Cy5 / H3K27me3_WT_I_IP Cy3 : 80pmol.

value: 10 day

value: Upstate 07-449


title: US_MN_16_3 (methcathinone user)

value: methcathinone user


title: 14639302 - H3K27me3_WT_I_INPUT vs H3K27me3_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_I_IP Cy5 / H3K27me3_WT_I_INPUT Cy3 : 80pmol.

value: seedling


title: 5756

value: atrium


title: US_MN_15_K13 (control)

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the protocol


title: US_MN_18_K5 (control)


title: msp3_a


title: 12005002 - H3K27me3_WT_II_IP vs H3K27me3_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_II_INPUT Cy5 / H3K27me3_WT_II_IP Cy3 : 80pmol.


title: 5622

value: Wild type


title: 5623

value: myogenic cells (C2C12)


title: 24hi_b

description: gene expression of immortalized human mammary epithelial cells positively sorted for CD24 expression

value: HMLE

value: epithelial subpopulations


title: 11992402 - H3K4me2_WT_I_IP vs H3K4me2_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_I_INPUT Cy5 / H3K4me2_WT_I_IP Cy3 : 80pmol.


title: US_MN_14_K4 (control)


title: 18031402 - H3K4me3_WT_II_IP vs H3K4me3_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_II_INPUT Cy5 / H3K4me3_WT_II_IP Cy3 : 80pmol.


title: US_MN_13_K9 (control)


title: 5620


title: US_MN_12_10 (methcathinone user)


title: msp1_a

value: mesenchymal subpopulations


title: 5618


title: PCB153 treated PBMC cells at T48, biological replicate 3

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from PBMC Cells before PCB153 treatment.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray 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 arbitrarily set to 150.

source_name: Human PBMC cells from healthy donor.

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

growth_protocol: Grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.

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

treatment_protocol: Treated with 1.42ng/ml of PCB153 for 48hours

value: female

value: 18 years

value: PBMC

tag: treatment


title: 14644102 - H3K27me3_WT_II_INPUT vs H3K27me3_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_II_IP Cy5 / H3K27me3_WT_II_INPUT Cy3 : 80pmol.


title: 24hi_a


title: 5619


title: msp2_a


title: 28910302 - H2Bub_WT_I_IP vs H2Bub_WT_I_INPUT

description: Epigenomic mapping

hyb_protocol: H2Bub_WT_I_INPUT Cy5 / H2Bub_WT_I_IP Cy3 : 80pmol.

value: Medimabs MM-0029


title: PCB153 treated PBMC cells at T48, biological replicate 2


title: 359161A02 - H3K4me3_I_IP vs H3K4me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_I_INPUT Cy5 / H3K4me3_I_IP Cy3 : 80pmol.

growth_protocol: roots - 10 days on MS 0.5X agar plates at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.


title: NIH 3T3 cells expressing both SV40 and wt Nras (SV5 NN4, stable clone) rep2

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: Gene expression data from NIH 3T3 expressing both SV40 large T antigen and wt Nras

hyb_protocol: 10 ug of biotin-labeled cRNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430A 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Total RNA, SV5-NN4 cells

label_protocol: 5 ug total RNA was converted into cDNA and biotin labeled cRNA using the Affymetrix One-cycle protocol according to manufaturer's recommendations

growth_protocol: NIH 3T3, SV5 and SV5 NN4 cells were grown in DMDM supplemented with 10% calf serum in standard conditions of humidity (95%), CO2 atmosphere (5%) and temperature (37° C).

extract_protocol: Trizol (Invitrogen) was used to extract total cellular RNA according to the manufacturer's protocol

value: NIH 3T3

tag: genotype

value: SV40 large T antigen and wt Nras


title: 14992802 - H3K4me2_WT_I_INPUT vs H3K4me2_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_I_IP Cy5 / H3K4me2_WT_I_INPUT Cy3 : 80pmol.


title: 5617

hyb_protocol: For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

value: Knockout (beta-sarcoglycan null)

value: Cardiac progenitor cells

value: ventricle


title: 5621


title: US_MN_10_K16 (control)

value: peripheral blood

value: control


title: Control PBMC cells for PCB153, biological replicate 3

treatment_protocol: Untreated with PCB153


title: US_MN_11_13 (methcathinone user)

value: methcathinone user


title: PCB153 treated PBMC cells at T48, biological replicate 1


title: 359195A02 - H3K4me3_II_IP vs H3K4me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_II_INPUT Cy5 / H3K4me3_II_IP Cy3 : 80pmol.

value: 10 day

value: seedling


title: 359118A02 - H3K4me3_I_INPUT vs H3K4me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_I_IP Cy5 / H3K4me3_I_INPUT Cy3 : 80pmol.


title: NIH 3T3 cells expressing both SV40 and wt Nras (SV5 NN4, stable clone) rep3


title: 359118A01 - H3K27me3_I_INPUT vs H3K27me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_I_IP Cy5 / H3K27me3_I_INPUT Cy3 : 80pmol.

value: Upstate 07-449


title: 359195A01 - H3K27me3_II_IP vs H3K27me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_II_INPUT Cy5 / H3K27me3_II_IP Cy3 : 80pmol.


title: 358127A01 - H3K27me3_II_INPUT vs H3K27me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_II_IP Cy5 / H3K27me3_II_INPUT Cy3 : 80pmol.


title: NIH 3T3 cells transformed by SV40 (SV5, stable clone) rep3

description: Gene expression data from NIH 3T3 cells transforming by SV40 large T antigen

source_name: Total RNA, SV5 transformed cells

value: SV40 large T antigen


title: NIH 3T3 cells expressing both SV40 and wt Nras (SV5 NN4, stable clone) rep1


title: US_MN_09_18 (methcathinone user)


title: US_MN_05_K7 (control)


title: US_MN_08_12 (methcathinone user)


title: Control PBMC cells for PCB153, biological replicate 2


title: 358127A02 - H3K4me3_II_INPUT vs H3K4me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_II_IP Cy5 / H3K4me3_II_INPUT Cy3 : 80pmol.


title: 448316A02 - H3_Col_II_IP vs H3_Col_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3_Col_II_INPUT Cy5 / H3_Col_II_IP Cy3 : 80pmol.


title: US_MN_03_K11 (control)

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the protocol


title: NIH 3T3 cells rep2

description: Gene expression data from NIH 3T3 cells

source_name: Total RNA, control cells

value: wild type


title: NIH 3T3 cells rep3

description: Gene expression data from NIH 3T3 cells


title: US_MN_02_15 (methcathinone user)


title: Control PBMC cells for PCB153, biological replicate 1

value: female


title: PCB 138 treated PBMC cells at T48, biological replicate 3

description: Gene expression data from PBMC Cells after PCB138 treatment.

source_name: Human PBMC cells from healthy donor

treatment_protocol: Treated with 0.87ng/ml of PCB138 for 48 hours

value: Female

value: 18 years

value: PCB 138


title: US_MN_06_20 (methcathinone user)


title: US_MN_07_4 (methcathinone user)


title: PCB 138 treated PBMC cells at T48, biological replicate 1

value: PBMC


title: NIH 3T3 cells transformed by SV40 (SV5, stable clone) rep2

value: NIH 3T3


title: NIH 3T3 cells transformed by SV40 (SV5, stable clone) rep1


title: PCB 138 treated PBMC cells at T48, biological replicate 2


title: Control PBMC cells, biological replicate 1

description: Gene expression data from PBMC Cells before PCB138 treatment.

treatment_protocol: Untreated with PCB138


title: 388629A03 - H3_Col_I_INPUT vs H3_Col_I_IP

description: Epigenomic mapping

hyb_protocol: H3_Col_I_IP Cy5 / H3_Col_I_INPUT Cy3 : 80pmol.


title: US_MN_04_K1 (control)


title: 359161A01 - H3K27me3_I_IP vs H3K27me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_I_INPUT Cy5 / H3K27me3_I_IP Cy3 : 80pmol.

tag: vendr


title: Control PBMC cells, biological replicate 3

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

tag: cell type


title: NIH 3T3 cells rep1

description: Gene expression data from NIH 3T3 cells


title: US_MN_01_8 (methcathinone user)


title: pol30-8 dot1Δ strain, biological replicate 2

status: Public on Apr 18 2011

city: Cold Spring Harbor

first: Bruce

last: Stillman

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Gene expression data from pol30-8 dot1Δ double mutant cells

hyb_protocol: After Fragmenting, 10ug of aRNA was hybridized to Yeast Genome 2.0 GeneChips (Affymetrix, Santa Clara, CA) 16 hours at 45C, 60rpm, in an Affymetrix Hybridization Oven 640. GeneChips were washed using GeneChip Hybridization Wash and Stain Kit, and Wash Stain protocol FS450_0003 in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner, using GCOS v 1.4.

data_processing: All raw data were processed using the FARMS method (Hochreiter, S., Clevert, D.A., and Obermayer, K., Bioinformatics, 2006), followed by “generally applicable gene-set enrichment” test statistics (GAGE; Luo, W., Friedman, M.S., Shedden, K., Hankenson, K.D., and Woolf, P.J., BMC Bioinformatics, 2009) for gene set or pathway analysis.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Cells grown to mid-logarithmic phase

label_protocol: Biotinylated aRNA was generated using MessageAmp II aRNA Amplification Kit (Ambion) for 2 rounds of amplification.

growth_protocol: 3 independent colonies per genotype were grown to a cell density of ~ 1.7 x 107 cells/ml and 10 ml of each culture was harvested.

extract_protocol: Total RNA was extracted from 10 ml of harvested cells using the hot acidic phenol method as described with modifications (Collart, M.A., and Oliviero, S., Curr. Protoc. Mol. Biol., 2001). Briefly, cultures were harvested over crushed ice for 5 min at 2,750 x g, 4 ˚C. Cells were transferred to an Eppendorf tube, and after spinning for 10 s at 20,800 x g, 4 ˚C, the pellet was frozen in liquid nitrogen. Cell pellets were resuspended in 400 μl of TES solution (10 mM Tris-Cl, pH 7.5, 10 mM EDTA, 0.5 % SDS). 400 μl of phenol solution (saturated with 0.1 M citrate buffer, pH 4.3; Sigma-Aldrich, St. Louis, MO) was added and samples were incubated at 65 ˚C for 1 h with short vortexing every 10 min. After 5 min of incubation on ice total RNA was extracted twice with phenol-chloroform-isoamyl alcohol (PCI), followed by two chloroform extractions. After ethanol precipitation, pellets were briefly dried at RT and resuspended in 50 μl of nuclease-free water (Ambion, Austin, TX). RNA quality was assessed using Series II RNA 6000 Pico chips on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and samples with an RNA Integrity number (RIN) score of 7.5 or greater were passed. Quantity was assessed by NanoDrop 1000 (NanoDrop products, Wilmington, DE). Total RNA was amplified by a modified Eberwine Technique, using a MessageAmp II aRNA Amplification Kit (Ambion) for 2 rounds of amplification. aRNA smear analysis for 3' bias was performed on select samples using Series II RNA 6000 Pico chips on an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: No treatment done.

tag: genetic background

value: MATalpha pol30-8 dot1Δ::kanMX6 ade2Δ::natMX4 ura3Δ::hphMX4 hmr::ADE2 URA3-VIIL


title: 388615A03 - H3_Col_I_IP vs H3_Col_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3_Col_I_INPUT Cy5 / H3_Col_I_IP Cy3 : 80pmol.

tag: ecotype


title: pol30-8 dot1Δ strain, biological replicate 1


title: pol30-8 dot1Δ strain, biological replicate 3


title: dot1Δ strain, biological replicate 3

description: Gene expression data from dot1Δ mutant cells

value: MATalpha dot1Δ::kanMX6 ade2Δ::natMX4 ura3Δ::hphMX4 hmr::ADE2 URA3-VIIL


title: 358426A02 - H3K27me1_I_INPUT vs H3K27me1_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me1_I_IP Cy5 / H3K27me1_I_INPUT Cy3 : 80pmol.

scan_protocol: Cy3:pmt voltage 532nm, laser power, Cy5:635nm,pmt voltage, laser power

tag: antibody


title: TC71-C3

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: TC71 treated with solvent control.

hyb_protocol: Per manufacturer recommendation.

scan_protocol: Per manufacturer recommendation.

data_processing: RMA-normalized.

organism: Homo sapiens

source_name: TC71 cell line, control

label_protocol: Per manufacturer recommendation.

growth_protocol: TC32 and TC71 were maintained under standard growth conditions and plated to a density of about 1.5 million cells per 10 cm dish.  3 biological replicates, each one getting a separate array. Cells were allowed to recover overnight.

extract_protocol: RNA collected using TriZol method and the Qiagen kit as per manufacturer's instructions.

treatment_protocol: Treated with drug (100 nM mithramycin) or control solvent for 6 hours.


title: Candida_parapsilosis_control_vs_voriconazole_rep3

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

hyb_protocol: Purified cDNA was denatured at 95 degrees for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

organism: Candida parapsilosis

source_name: Total RNA from C. parapsilosis BC014S

label_protocol: Twenty-four micrograms of total RNA was used for cDNA labeling. Briefly, RNA samples were incubated with 100 pmol of anchor oligonucleotide deoxyriboslthymine (Invitrogen) at 70 degrees for 10 min, after which following reaction reagents were added including 1 X first strand buffer, 6.67 mM dATP, dTTP, and dGTP; 2mM dCTP; 100 mM dithiothreitol; 2 µl Superscript II reverse transcriptase (Invitrogen). 37.5 µM Cy3-dCTP were then added into the mixture in dark. The mixture were left at 42 degrees for two hours followed by adding additional 2 µl Superscript II reverse transcriptase, and reaction was continued for one more hour. 50 µg/ml RNase A and 0.05 unit/µl RNase H were added and the reaction was incubated for 30 min at 37 degrees.

growth_protocol: Overnight cultures of C. parapsilosis were diluted to a A600 of 0.2 in 50 ml of YPD medium and culture was incubated at 200 rpm at 35 degrees until A600 of 1.

extract_protocol: RNA was isolated using a RiboPure Yeast kit (Ambion). The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment protocol.

tag: isolate

tag: growth condition

value: 35 degree celsius and 21% oxygen

tag: medium

value: YPD medium

source_name: Total RNA from C. parapsilosis cells BC014VRC

value: Blood culture C. parapsilosis isolate obtained from a patient admitted at intensive care unit in Hospital S. João, Portugal.


title: Candida_parapsilosis_control_vs_voriconazole_rep4


title: TC71-M3

description: TC71 treated with mithramycin.

source_name: TC71 cell line, mithramycin

tag: cell line

value: mithramycin


title: 358426A03 - H3K27me1_II_INPUT vs H3K27me1_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me1_II_IP Cy5 / H3K27me1_II_INPUT Cy3 : 80pmol.

organism: Arabidopsis thaliana

value: 10 day

tag: dev.stage (boyes et al. plant cell 2001)

tag: vendor


title: Candida_parapsilosis_control_vs_voriconazole_rep2


title: TC71-M2

description: TC71 treated with mithramycin.


title: 358338A02 - H3K27me1_I_IP vs H3K27me1_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me1_I_INPUT Cy5 / H3K27me1_I_IP Cy3 : 80pmol.

tag: age

value: seedling


title: dot1Δ strain, biological replicate 2


title: Control PBMC cells, biological replicate 2

tag: gender

value: control


title: TC71-C1

description: TC71 treated with solvent control.


title: dot1Δ strain, biological replicate 1


title: TC71-M1

description: TC71 treated with mithramycin.


title: pol30-8 strain, biological replicate 3

description: Gene expression data from pol30-8 mutant cells

value: MATalpha pol30-8 ade2Δ::natMX4 ura3Δ::hphMX4 hmr::ADE2 URA3-VIIL


title: Candida_parapsilosis_control_vs_voriconazole_rep1


title: Candida_parapsilosis_control_vs_posaconazole_rep3

value: 35 degree celsius

source_name: Total RNA from C. parapsilosis BC014PSC


title: TC32-S3

description: TC32 treated with solvent control.

source_name: TC32 cell line, control


title: pol30-8 strain, biological replicate 2


title: pol30-8 strain, biological replicate 1


title: 448459A02 - H3_Col_II_INPUT vs H3_Col_II_IP

description: Epigenomic mapping

hyb_protocol: H3_Col_II_IP Cy5 / H3_Col_II_INPUT Cy3 : 80pmol.


title: 388458A01 - H3K36me3_I_INPUT vs H3K36me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K36me3_I_IP Cy5 / H3K36me3_I_INPUT Cy3 : 80pmol.


title: TC32-S2

description: TC32 treated with solvent control.


title: wild type strain, biological replicate 3

description: Gene expression data from wild-type cells

value: MATalpha ade2Δ::natMX4 ura3Δ::hphMX4 hmr::ADE2 URA3-VIIL


title: wild type strain, biological replicate 2


title: Candida_parapsilosis_control_vs_posaconazole_rep2


title: Candida_parapsilosis_control_vs_fluconazole_rep4

source_name: Total RNA from C. parapsilosis BC014FLC


title: Candida_parapsilosis_control_vs_posaconazole_rep1


title: Candida_parapsilosis_control_vs_fluconazole_rep3


title: TC32-S1

description: TC32 treated with solvent control.


title: Candida_parapsilosis_control_vs_fluconazole_rep2


title: wild type strain, biological replicate 1


title: TC32-M1

description: TC32 treated with mithramycin.

source_name: TC32 cell line, mithramycin


title: 388447A02 - H3K36me3_II_IP vs H3K36me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K36me3_II_INPUT Cy5 / H3K36me3_II_IP Cy3 : 80pmol.


title: GFP-neg_P8_A_rep3

status: Public on Apr 17 2011

city: Kobe

first: Sentaro

last: Kusuhara

state: Hyogo

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Department of Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

description: Gene expression data from GFP-negative cells from P8 retina in homozygous Tie2-GFP transgenic mice

hyb_protocol: Biotin-labeled cRNA was fragmented in a 40-μl reaction mixture containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30mM magnesium acetate, and incubated at 94°C for 35 min, and then hybridized onto the MGU74v2 series of arrays.

scan_protocol: GeneChips were scanned with a GeneArray Scanner (Hewlett-Packard, Santa Clara, CA), controlled by MicroSuite 5.1 software (Affymetrix).

data_processing: The dChip software (version 1.3) was used to normalize the CEL files at probe level and compute model-based expression values using the PM only model.

label_protocol: Biotin-labeled cRNA was synthesized from the obtained RNA sample using the BioArray RNA Transcript labeling Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated using RNeasy Micro-Kit (QIAGEN) and was amplified using MessageAmpII aRNA Kit (Ambion, Austin, TX) to obtain aRNA (>60μg).

treatment_protocol: Eyes from homozygous Tie2-GFP transgenic mice were enucleated, rinsed with PBS, and kept in staining solution (PBS containing 2mM EDTA, 0.01%, NaN3, 5% fetal calf serum, 50U/ml penicillin, and 0.05mg/ml streptomycin). The retinas were dissected under stereomicroscope, pooled in staining solution, and minced into small pieces. Collected retinal pieces were rinsed twice in PBS and digested in 10 ml of papain/DNase solution (papain (33U/ml; Sigma-Aldrich, St. Louis, MI) in Dulbecco’s PBS (Invitrogen) containing L-cysteine (0.4mg/ml; Nacalai tesque, Kyoto, Japan), EDTA (0.50mM; Sigma), and DNase I (125U/ml; Sigma)) for 60 min at 37°C with gentle agitation. Following digestion, cells were pelleted and treated two times with DNase/ovomucoid solution (a solution containing ovomucoid (2mg/ml; Sigma), DNase I (125 U/ml; Sigma), and BSA (1mg/ml; Wako, Osaka, Japan)) in Dulbecco’s PBS for 60 min at 37°C with gentle agitation. Digested retinal cells were filtered through nylon mesh, centrifuged at 300x g for 5 min to pellet cells, resuspended again with 10ml of DNase/ovomucoid solution incubated at 37°C for 60 min. Cells were rinsed twice in staining solution, pelleted, resuspended with staining solution containing 5µg/ml of propidium iodide, and filtered through nylon mesh. These cells were analyzed and sorted by FACS Aria (Becton Dickinson, San Jose, CA).

tag: strain

value: FVB/N

tag: genotype/variation

value: Tie2-GFP transgenic

value: postnatal day 8

tag: tissue

value: retina

value: control (GFP-negative)


title: GFP-neg_P8_A_rep2

source_name: GFP-negative cells from P8 retina in homozygous Tie2-GFP transgenic mice


title: TC32-M3

description: TC32 treated with mithramycin.

tag: treatment


title: TC32-M2

description: TC32 treated with mithramycin.


title: GFP-neg_P8_A_rep1


title: GFP-pos_P8_A_rep3

description: Gene expression data from GFP-positive cells from P8 retina in homozygous Tie2-GFP transgenic mice

value: endothelial cell (GFP-positive)


title: GFP-neg_P8_C_rep3


title: GFP-neg_P8_C_rep2


title: 388447A03 - H3K36me3_II_INPUT vs H3K36me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K36me3_II_IP Cy5 / H3K36me3_II_INPUT Cy3 : 80pmol.


title: GFP-pos_P8_A_rep1

source_name: GFP-positive cells from P8 retina in homozygous Tie2-GFP transgenic mice


title: H7-EB

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: Expression profile of H7-derived embroid body.

hyb_protocol: Hybridization was performed according to the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual.

scan_protocol: Arrays were scanned with GCS3000 using the standard procedures recommended by Affymetrix.

data_processing: The data were normalized using RMA in R 2.10.1 and a CDF file that maps the Affymetrix probes to RefSeq genes.

source_name: H7-derived embroid body

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay.

growth_protocol:
The hepatocytes were obtained from Lonza (reference #: CC-2703W6). The newborn foreskin (BJ) fibroblasts were obtained from ATCC (reference #: CRL-2522). The melanocytes were obtained from Promocell (reference #: C-12402).

Somatic cells were grown in 425 mls High-glucose DMEM, 50 mls Atlanta FBS (10%), 5 mls L-glutamine, 10 mls Penicillin/Streptomycin, 5 mls Non-essential amino acids, 5 mls Sodium pyruvate, and 2 μl Beta-mercaptoethanol. ES and iPS cells were grown in a hES-KSR Basal Medium of 382.5 mls DMEM/F12 containing Hepes, 100 mls Knockout Serum ment (KSR), 2.5 mls L-glutamine, 5 mls Non-essential amino acids, 10 mls Penicillin/Streptomycin, and 3.5 μl Beta-mercaptoethanol.

extract_protocol: RNeasy Mini RNA isolation kit (Qiagen).

value: embryonic stem cell line-derived embroid body


title: H9

description: Expression profile of H9 human stem cell line (passage number 60).

source_name: H9 human stem cell line

value: embryonic stem cell line

tag: passage


title: Candida_parapsilosis_control_vs_fluconazole_rep1

value: YPD medium


title: H9-EB

description: Expression profile of H9-derived embroid body.

source_name: H9-derived embroid body

tag: cell type


title: H1-EB

description: Expression profile of H1-derived embroid body.

source_name: H1-derived embroid body


title: 358338A03 - H3K27me1_II_IP vs H3K27me1_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me1_II_INPUT Cy5 / H3K27me1_II_IP Cy3 : 80pmol.


title: 358095A01 - H3K36me3_I_IP vs H3K36me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K36me3_I_INPUT Cy5 / H3K36me3_I_IP Cy3 : 80pmol.

scan_protocol: NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%


title: GFP-pos_P8_C_rep3


title: GFP-pos_P8_C_rep2


title: H7

description: Expression profile of H7 human stem cell line (passage number 50).

source_name: H7 human stem cell line


title: H1

description: Expression profile of H1 human stem cell line (passage number 50).

source_name: H1 human stem cell line


title: Melanocyte-iPS, Rep 2

description: Expression profile of human melanocyte-derived iPS cell (passage number 15).

source_name: Melanocyte-derived iPS cell

treatment_protocol: iPS cells were generated by overexpressing the human transcription factors OCT4, SOX2, C-MYC, KLF4, and NANOG using a doxycycline-inducible lentivirus transgene system that has been previously documented to faithfully reprogram both human fibroblasts and keratinocytes to an hESC-like state (Maherali et al, 2008; Hockemeyer et al., 2008).

value: melanocyte-derived iPS cell


title: Melanocyte, Rep 2

description: Expression profile of human melanocyte (passage number 4).

source_name: Melanocyte

value: melanocyte


title: GFP-pos_P8_C_rep1


title: TC71-C2

description: TC71 treated with solvent control.

source_name: TC71 cell line, control


title: HITC6, Day 8 biological replicate 3, Affy153B

city: London

first: J. Geoffrey

last: Pickering

state: ON

address: 100 Perth Drive

country: Canada

institute: Robarts Research Institute

description: gene expression information from HITC6 SMCs at Day 8 after serum withdrawal

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Expression Console version 1.1 using the MAS 5.0 algorithm and scaled all probe sets to a target value of 150.

source_name: HITC6 smooth muscle cells, 8 days after serum withdrawal

growth_protocol: cultures of SMCs were maintained in M199 supplemented with 10% fetal bovine serum

treatment_protocol: cultures were rinsed twice with phosphate buffered saline and the media was replaced with M199 without fetal bovine serum

tag: time point

value: 8 days after serum withdrawal

value: human SMC line derived from the distal internal thoracic artery


title: GFP-neg_P8_C_rep1


title: Melanocyte-iPS, Rep 1


title: Fibroblast-iPS, Rep 3

description: Expression profile of human foreskin fibroblast-derived iPS cell (passage number 5).

source_name: Foreskin fibroblast-derived iPS cell

value: foreskin fibroblast-derived iPS cell


title: Melanocyte-iPS, Rep 3

description: Expression profile of human melanocyte-derived iPS cell (passage number 11).


title: HITC6, Day 8 biological replicate 1, Affy107B


title: Melanocyte, Rep 1


title: Melanocyte, Rep 3


title: HITC6, Day 0 biological replicate 3, Affy149B

description: gene expression information from HITC6 SMCs at Day 0 after serum withdrawal

source_name: HITC6 smooth muscle cells, before serum withdrawal

value: before serum withdrawal


title: HITC6, Day 8 biological replicate 2, Affy122B


title: HITC6, Day 0 biological replicate 2, Affy118B


title: HITC6, Day 0 biological replicate 1, Affy103B


title: 430329A01 - 5mC_Col_II_IP vs 5mC_Col_II_INPUT

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

institute: Ecole Normale Supérieure de Lyon

description: Epigenomic mapping

hyb_protocol: 5mC_Col_II_INPUT Cy5 / 5mC_Col_II_IP Cy3 : 80pmol.

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

tag: ecotype

value: 10 day

value: seedling


title: GFP-neg_P8_B_rep3

value: FVB/N


title: 430117A01 - 5mC_Col_II_INPUT vs 5mC_Col_II_IP

description: Epigenomic mapping

hyb_protocol: 5mC_Col_II_IP Cy5 / 5mC_Col_II_INPUT Cy3 : 80pmol.

tag: antibody


title: 388630A01 - 5mC_Col_I_INPUT vs 5mC_Col_I_IP

description: Epigenomic mapping

hyb_protocol: 5mC_Col_I_IP Cy5 / 5mC_Col_I_INPUT Cy3 : 80pmol.


title: HITC6, Day 8 biological replicate 3, Affy153A


title: Fibroblast-iPS, Rep 1


title: HITC6, Day 8 biological replicate 2, Affy122A


title: Fibroblast, Rep 2

description: Expression profile of human foreskin fibroblast (passage number 14).

source_name: Foreskin fibroblast

value: foreskin fibroblast


title: Fibroblast, Rep 1


title: Fibroblast-iPS, Rep 2


title: Fibroblast, Rep 3


title: GFP-pos_P8_B_rep1

value: Tie2-GFP transgenic

value: postnatal day 8


title: GFP-pos_P8_B_rep2

value: retina


title: GFP-neg_P8_B_rep1

value: control (GFP-negative)


title: GFP-neg_P8_B_rep2


title: HITC6, Day 8 biological replicate 1, Affy107A


title: Hepatocyte-iPS, Rep 3

description: Expression profile of human hepatocyte-derived iPS cell (passage number 7).

source_name: Hepatocyte-derived iPS cell

value: hepatocyte-derived iPS cell


title: HITC6, Day 0 biological replicate 3, Affy149A


title: GFP-pos_P8_B_rep3

value: endothelial cell (GFP-positive)


title: GFP-pos_P8_A_rep2


title: Hepatocyte-iPS, Rep 1

description: Expression profile of human hepatocyte-derived iPS cell (passage number 5).


title: HITC6, Day 0 biological replicate 1, Affy103A


title: HITC6, Day 0 biological replicate 2, Affy118A


title: Hepatocyte, Rep 2

description: Expression profile of human hepatocyte (passage number ~0).

source_name: Hepatocyte

value: hepatocyte


title: Hepatocyte, Rep 3


title: Hepatocyte, Rep 1


title: Control-siRNA bEnd3 cells

city: Beijing

first: Xiao

last: Yang

address: 20 Dongdajie

institute: Beijing Institute of Biotechnology

description:
mouse brain microvessel endothelial cells
cerebral cortex
Gene expression data from Control-siRNA bEnd3 cells

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using 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 arbitrarily set to 500.

source_name: transfected bEnd3 cells

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: Cells were cultured at 37°C and 5% CO2 in DMEM containing 15% FCS.

treatment_protocol: Cells were harvested in the TRIZOL solution (Invitrogen).

value: BALB/c

value: endothelial, polyoma middle T antigen transformed


title: Smad4-siRNA bEnd3 cells

description:
mouse brain microvessel endothelial cells
cerebral cortex
Gene expression data from Smad4-siRNA bEnd3 cells


title: 388490A03 - 5mC_Col_I_IP vs 5mC_Col_I_INPUT

description: Epigenomic mapping

hyb_protocol: 5mC_Col_I_INPUT Cy5 / 5mC_Col_I_IP Cy3 : 80pmol.

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .


title: ApoD transgenic mouse+PQ rep_3 (PQTG3)

status: Public on Apr 16 2011

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

country: Spain

institute: University of Seville

description: Gene expression data from cerebellum of ApoD gain-of-function transgenic mouse

hyb_protocol: Ten micrograms of the biotinylated and fragmented probes were hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays at 45ºC for 16 h, following the manufacturer’s protocols.

scan_protocol: After washes, the arrays were incubated with anti-biotin streptavidinphycoeritrin antibody and scanned with an Affymetrix GeneChip Scanner 7G.

data_processing: Software=GEPAS suite. Background correction=RMA. Normalization:Quantiles.PM correction=PM-only.Summary=Medianpolish

source_name: Paraquat Human-ApoD transgenic gain of function mutant

label_protocol: The generation, labeling and purification of cRNA was performed using the IVT kit (Affymetrix, Santa Clara, CA).

growth_protocol: Mice were housed in positive pressure-ventilated racks at 25±1°C with a 12 h light/dark cycle, fed ad libitum with a standard rodent pellet diet and allowed free access to filtered and UV-irradiated water

extract_protocol: Tissue was homogenized in TRIzol (Invitrogen), and total RNA extracted. A second purification using the RNeasy miniKit (Quiagen) was employed to prepare the Array probes from high-quality RNA samples. Equimolar amounts of total RNA from three randomly selected mice for each genotype and experimental condition were pooled, rendering three biological replicates to hybridize with the arrays.

treatment_protocol: Nine mice of each genotype were either treated with a single intraperitoneal injection of PQ (30 mg/kg) in 200ul sterile saline (Experimental group), or a similar volume of sterile saline (Control group). Six hours after injection, each mouse was euthanized with CO2 and the cerebellum was immediately removed and frozen.

value: male

value: adult (80±5 days-old)

value: cerebellum

tag: genotype


title: ApoD KO+PQ rep_2 (PQKO2)

description: Gene expression data from cerebellum of ApoD loss-of-function mouse

source_name: Paraquat ApoD knock-out

value: ApoD knock-out


title: ApoD transgenic mouse+PQ rep_2 (PQTG2)

value: Human-ApoD transgenic gain of function mutant


title: ApoD transgenic mouse rep_2 (CTG2)

source_name: Human-ApoD transgenic gain of function mutant


title: ApoD transgenic mouse rep_1 (CTG1)


title: ApoD KO+PQ rep_1 (PQKO1)


title: ApoD transgenic mouse rep_3 (CTG3)


title: IL-17-Biol Rep 2

type: protein

city: Winnipeg

first: Neeloffer

last: Mookherjee

state: MB

address: 799-JBRC, 715 McDermot Ave

department: Internal Medicine

institute: University of Manitoba

scan_protocol: Arrays were read using a GenePix Professional 4200A microarray scanner at 532-560 nm with a 580 nm filter to detect dye fluorescence. Images were collected using the GenePix 6.0 software and the spot intensity signal collected as the mean of pixel intensity using local feature background intensity background calculation with the default scanner saturation level.

data_processing: Foreground signal mean of pixel intensity. Background intensity for each spot as the average of pixels from four regions in the immediate vicinity of each spot. Perform global normalization to the 50th percentile on the raw data, using GeneSpring software. Evaluate reproducibility of the signal by comparing peptide signals to a baseline value of 1 for the normalized data from the replicates, using a sample t test.

label: green fluorescence

molecule: protein

source_name: Macrophage-like THP-1 cells, IL-17

label_protocol: Slides were submerged in phospho-specific fluorescent ProQ Diamond Phosphoprotein Stain with agitation for 1 hour. Arrays were then washed three times in destain containing 20% acetonitrile and 50 mM sodium acetate at pH 4.0 for 10 minutes. A final wash was done with distilled deionized H2O.

growth_protocol: Human monocytic THP-1 (ATCC® TIB-202) cells were cultured in RPMI-1640 media containing 2 mM L-glutamine and 1 mM sodium pyruvate (complete RPMI media), supplemented with 10 % (v/v) FBS, and maintained in a humidified incubator at 37˚C and 5% CO2. The THP-1 cells were differentiated to plastic-adherent macrophage-like cells by treatment with phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich Canada, Oakville ON) for 24 hr. Tissue culture supernatant was removed, and the cells were rested in complete media for additional 24 hr, before stimulation.

extract_protocol: Subsequently, cellular lysates were prepared in lysis buffer containing 20mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1mM EGTA, 1 mM sodium fluoride, 1mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, protease inhibitor cocktail (Sigma-Aldrich) and 1 % (v/v) Triton X-100.

treatment_protocol: Recombinant human cytokines IL-32g and IL-17A/F was obtained from eBioscience, Inc (San Diego, CA, USA). Macrophage-like THP-1 cells  were stimulated with either IL-32 (20 ng/ml) or IL-17 (20 ng/ml) for 15 min.

value: Macrophage


title: wild-type+PQ rep_1 (PQWT1)

description: Gene expression data from mouse cerebellum

source_name: Paraquat wild-type

value: wild-type


title: ApoD KO rep_3 (CKO3)

source_name: ApoD knock-out


title: ApoD transgenic mouse+PQ rep_1 (PQTG1)


title: wild-type+PQ rep_2 (PQWT2)


title: wild-type+PQ rep_3 (PQWT3)


title: ApoD KO+PQ rep_3 (PQKO3)


title: Unstimulated-Biol Rep 2

source_name: Macrophage-like THP-1 cells, control


title: ApoD KO rep_1 (CKO1)


title: ApoD KO rep_2 (CKO2)


title: Unstimulated-Biol Rep 1


title: IL-32-Biol Rep 2

source_name: Macrophage-like THP-1 cells, IL-32


title: wild-type rep_2 (CWT2)

source_name: wild-type

value: Wild type


title: wild-type rep_1 (CWT1)


title: wild-type rep_3 (CWT3)


title: IL-32-Biol Rep 1


title: IL-17-Biol Rep 1


title: Wild type (N2)_on ifg-1 RNAi_Fraction2_group4

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: Hybridization was carried out using a Lucidea Slide Pro machine. All wash solutions were made using Ambion Pre-Made Solutions (Nuclease-free Water, 20% SDS and 20XSSC) and filtered sterilized with a 500ml, 0.22uM filter unit. All C. elegans arrays from the Washington University in St. Louis Genomic Sequencing Center arrive pretreated; no blocking step was necessary. To prepare the aRNA sample for hybridization, the labeled aRNA sample was brought up to a volume with Nuclease-free water and Dextran Sulfate/ Hybe Buffer mix was added to the aRNA sample. The mixture was warmed to 50oC. Using a Hamilton syringe the labeled sample was loaded into the Lucidea chamber. The hybridization program was run for 16hrs at 42oC with a cycling speed of 10µl/sec every 30 minutes. The array was then washed at a speed of 50ul/sec with the following wash buffers in succession: 2X SSC +0.1% SDS (warmed to 42oC for 1st wash solution), 2X SSC, 0.2XSSC, and a 95% ethanol drying step.

scan_protocol: The array slide was loaded into a Perkin Elmer Scan Array Express 2-Laser Scanner. A QuickScan was performed, which scans the first 3-4 rows of the array. A surface calibration was then performed using the Spot Report control spots on the array. After surface calibration, the PMT and POW settings were adjusted to have the control spots match in intensity. The array was then scanned. Images were quantitated using GenePix 5.0 software package which overlays the GAL file (provided by the Washington University in St. Louis Genomic Sequencing Center) on the two array TIFF images (Cy3 and Cy5).  Pixels per spot, per channel were counted by the software and a gpr file was generated.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003)

organism: Caenorhabditis elegans

source_name: Wild type (N2)_pooled mix

label_protocol: Each sample, including the reference pool, was subjected to two rounds of linear amplification using the MessageAmp kit from Ambion for the first round and the Amino Allyl Message Amplification II kit from Ambion for the second round. After amplification, each sample was assessed for yield and overall quality via Bioanlayzer (Agilent) and Nanodrop. Samples that did not pass QC were discarded, and not used in the final analysis. Post Labeling Reactive Dyes (Cy3 and Cy5) from Amersham were used in conjunction with the reagents and protocol from the Ambion Amino Allyl Message Amplification II Kit to label the aRNA.  5ug of aRNA plus aRNA spike were labeled (aRNA Spike: equal amounts of the 10 Stratagene Spot Repot Spikes were combined and then amplified 1 round, to make an aRNA Spot Report Spike mix). All controls were labeled with the Cy3 dye and all experimental samples were labeled with the Cy5 dye. The Cy3 and Cy5 sample pairs were combined and purified.

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

source_name: Wild type (N2) on ifg-1 RNAi

tag: fraction

value: Fraction 2

tag: group

value: Group 4


title: Wild type (N2)_on ifg-1 RNAi_Fraction3_group4

value: Fraction 3


title: Wild type (N2)_on ifg-1 RNAi_Fraction3_group1

value: Group 1


title: Wild type (N2)_on ifg-1 RNAi_Fraction1_group4

value: Fraction 1


title: Wild type (N2)_on ifg-1 RNAi_Fraction2_group2

value: Group 2


title: Non-phosphorylated FTY720 induces apoptosis of human microglia by activating SREBP2(#4)

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

institute: Meiji Pharmaceutical University

description: The HMO6 cell line was established by immortalizing cultured microglia isolated from human embryonic telencephalon tissues with a retroviral vector PASK1.2 encoding v-myc oncogene. HMO6 cells express the markers of the microglia/macrophage lineage cells, including CD11b, CD68, CD86, HLA-ABC, HLA-DR, and ricinus communis agglutinin lectin-1 (RCA), serving as a model of human microglia both in vitro and in vivo.

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software version 1.1 (Affymetrix).

source_name: HMO6 human microglia treated with FTY720 dissolved in ETOH for 2 hours

label_protocol: One hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix)

growth_protocol: The cells were maintained in Dulbecco's Modified Eagle's medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 microgram/ml streptomycin (feeding medium).

extract_protocol: Total RNA was isolated from the cells by using the TRIZOL Plus RNA Purification kit (Invitrogen). The quality of total RNA was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HMO6 cells were exposed for 2 hours to 10 microM non-phosphorylated FTY720 (Calbiochem) or an equal amount of vehicle (ETOH).

tag: cells

value: HMO6 microglia

value: Brain


title: Wild type (N2)_on ifg-1 RNAi_Fraction1_group2


title: Wild type (N2)_on ifg-1 RNAi_Fraction3_group3

value: Group 3


title: Human hair follicles donor 1 (HF10-043)

city: Jerusalem

first: Yuval

last: Ramot

address: Kiryat Hadassah, p.o.b 12000

country: Israel

institute: Hadassah - Hebrew University Medical Center

description: Biological replicate 1. of 2

hyb_protocol: Hybridization procedure was performed according to the Two-color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol using the Agilent Gene Expression Hybridization Kit to Agilent Whole Human Genome 4x44K Oligo Microarrays using Agilent’s recommended hybridization chamber and oven. Slides were washed with GE Wash Buffers and Stabilization and Drying Solution according to the recommended protocol.

scan_protocol: Scanned on an Agilent’s Microarray Scanner G2565B

data_processing: Agilent Feature Extraction Software 9.5

source_name: Organ cultured hair follicles, control

label_protocol: 150ng of total RNA were amplified and labeled using the Agilent Quick Amp Labeling Kit following the manufacturer’s protocol

growth_protocol: Microdissected anagen VI hair follicles from normal temporofrontal human scalp skin were placed under under serum-free conditions composed of Williams E medium supplemented with insulin, l-glutamine, hydrocortisone, streptomycin, and penicillin

extract_protocol: Total RNA extracted using Qiagen miRNeasy kit according to the manufacturer's protocol

treatment_protocol: Vehicle or 0.5 µM spermidine

value: organ cultured hair follicle

value: control

source_name: Organ cultured hair follicles, spermidine treated

value: spermidine


title: Non-phosphorylated FTY720 induces apoptosis of human microglia by activating SREBP2(#2)

source_name: HMO6 human microglia treated with FTY720 dissolved in DMSO for 2 hours

treatment_protocol: HMO6 cells were exposed for 2 hours to 10 microM non-phosphorylated FTY720 (Calbiochem) or an equal amount of vehicle (DMSO).


title: Wild type (N2)_on ifg-1 RNAi_Fraction2_group3


title: 14054279 - r1r2r3r4 RB2 vs Col0 RB2

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

institute: INRA

description: What is the role of the RRM protein family in plants ?

hyb_protocol: Col0 RB2 Cy5 / r1r2r3r4 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

source_name: Col0 wild-type

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media: Soil     Temperature: 20°C  Light: 16 hours

extract_protocol: Col0 RB2:10ug.

treatment_protocol: no treatment

tag: dev.stage (boyes et al. plant cell 2001)


title: Human hair follicles donor 2 (HF-10-135)

description: Biological replicate 2. of 2


title: 14054278 - Col0 RB2 vs r1r2r3r4 RB2

hyb_protocol: r1r2r3r4 RB2 Cy5 / Col0 RB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Wild type (N2)_on ifg-1 RNAi_Fraction1_group3


title: Wild type (N2)_on ifg-1 RNAi_Fraction3_group2


title: Wild type (N2)_on ifg-1 RNAi_Fraction1_group1


title: Untreated H2373 mesothelioma cells

city: detroit

first: naimei

last: tang

state: mi

address: 110 E warren ave

department: internal medicine

institute: wanye state university

hyb_protocol: HumanHT-12 Expression BeadChip.

scan_protocol: Illumina BeadScan Version 3.5.49.29917

data_processing: The data were analyzed using BeadStudio version 3.1.3.0 using the quantilechip normalization method.

source_name: Untreated H2373

label_protocol: Bioltinylated cRNA were generated following manufacturer protocols usingnthe Illumina TotalPrep Amplication Kit from Ambion.

growth_protocol: H2373 cell line derived from patients with malignant plural mesothelioma was cultured in RPMI 1640 (HyClone) supplemented with 100 units/ml of penicillin, 100 µg/ml streptomycin, and 10% fetal calf serum (HyClone).

extract_protocol: Total RNAs were isolated with Ambion RiboPure™ Kit in accordance with  the prescribed protocol provided with kit. Quality of RNA was analyzed with Agilent Bioanalyser.

treatment_protocol: H2373 cells were treated with 36 µM H342 or H258 for 3 h.

value: untreated

tag: cell line


title: Non-phosphorylated FTY720 induces apoptosis of human microglia by activating SREBP2(#3)

source_name: HMO6 human microglia treated with ethanol for 2 hours


title: Non-phosphorylated FTY720 induces apoptosis of human microglia by activating SREBP2(#1)

source_name: HMO6 human microglia treated with DMSO for 2 hours

label_protocol: One hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).


title: Hoechst 33342-treated H2373 cells

source_name: Hoechst 33342-treated H2373

value: Hoechst 33342


title: Hoechst 33258-treated H2373 cells

source_name: Hoechst 33258-treated H2373

value: Hoechst 33258


title: 14054271 - Col0 RB1 vs r1r2r3r4 RB1

hyb_protocol: r1r2r3r4 RB1 Cy5 / Col0 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0 RB1:10ug.

value: wild-type


title: Hepatocyte-iPS, Rep 2

description: Expression profile of human hepatocyte-derived iPS cell (passage number 6).

source_name: Hepatocyte-derived iPS cell

value: hepatocyte-derived iPS cell


title: Control siRNA

city: Shinjuku-ku

first: Masanao

last: Tabuse

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChipOperationSoftware (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: U87 glioma cells transfected with control siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: U87 cells were seeded in tissue culture dishes 48 h prior to RNAi transfection.

extract_protocol: U87 cells were used for total RNA extraction using Trizol(Invitrogen) and RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Control or HOXD9 siRNA-2 were transfected at a concentration of 50 nM using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions.

tag: knockdown


title: 14054274 - r1r2r3r4 RB1 vs Col0 RB1

hyb_protocol: Col0 RB1 Cy5 / r1r2r3r4 RB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Wild type (N2)_on ifg-1 RNAi_Fraction2_group1

value: Fraction 2


title: Setdb1 2lox/1lox/Cre plus tamoxifen 2

status: Public on Apr 15 2011

city: Cambridge

first: Felix

last: Lohmann

address: 250 Mass Ave

institute: Novartis Institutes for BioMedical Research

hyb_protocol: The Affymetrix GeneChip Hybridization, Wash, and Stain Kit was used according to manufacturer's instructions in combination with Molecular Probes Streptavidin R-phycoerythrin conjugate (SAPE)

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

data_processing: The R/Bioconductor Limma open-source software was used to analyze microarray data

source_name: embryonic stem cells

label_protocol: Biotinylated cRNA was prepared using the Affymetrix GeneChip 3’ IVT Express Kit according to manufacturer's instructions

growth_protocol: Mouse ES cells were maintained without feeders on gelatinized tissue culture plates in ‘‘knock-out’’ DMEM supplemented with 20% FBS, 2 mM L-glutamine, 100 U/ml Penicillin, 100 lg/ml Streptomycin, 0.14 mM b-mercapto-ethanol, 0.1 mM non-essential amino acids, LIF (1000 U/ml ‘‘ESGRO’’)

extract_protocol: ES cells were lysed in QIAGEN Buffer RLT, homogenized using QIAshredder and total RNA was purified using QIAGEN RNeasy Mini spin columns according to manufacturer's instructions

treatment_protocol: 500 nM tamoxifen ((Z)-4-hydroxytamoxifen) was added to induce recombination as noted

tag: genetic background

value: C57BL/6-129Sv hybrid background

value: Setdb1 2lox/1lox/Cre

value: tamoxifen

value: embryonic stem cell


title: Setdb1 2lox/1lox/Cre minus tamoxifen 2


title: Setdb1 2lox/1lox/Cre minus tamoxifen 1


title: Setdb1 2lox/1lox/Cre plus tamoxifen 1


title: Setdb1 2lox/1lox/Cre plus tamoxifen 3


title: Setdb1 2lox/1lox/Cre minus tamoxifen 3


title: HOXD9 siRNA

source_name: U87 glioma cells transfected with HOXD9 siRNA


title: Setdb1 2lox/1lox plus tamoxifen 1

value: Setdb1 2lox/1lox


title: Setdb1 2lox/1lox plus tamoxifen 3


title: D2-Gpnmb+ control rep1 (retina)

city: Mount Desert

first: Gareth

middle: Rhys

last: Howell

address: 600 Main Street

institute: The Jackson Laboratory

description: Retina R113413

hyb_protocol: Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChipTM  Scanner 3000 laser confocal slide scanner

data_processing: The images were quantified using GeneChipTM Operating Software (GCOS) v1.2.  Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

source_name: Retina no glaucoma

label_protocol: Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were housed in a 14 h light to 10 h dark cycle

extract_protocol: For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)

tag: phenotype

value: no glaucoma

tag: gender

value: female

tag: strain

value: retina

tag: age

value: 10.5 months


title: D2-Gpnmb+ control rep4 (retina)

description: Retina L113417

tag: tissue


title: Severe rep9 (retina)

description: Retina R119778

source_name: Retina severe glaucoma

value: severe glaucoma


title: Setdb1 2lox/1lox plus tamoxifen 2

tag: treatment

tag: cell type


title: Severe rep6 (retina)

description: Retina R115844


title: D2-Gpnmb+ control rep9 (retina)

description: Retina R113445


title: D2-Gpnmb+ control rep7 (retina)

description: Retina R113441


title: Severe rep5 (retina)

description: Retina R113695


title: D2-Gpnmb+ control rep6 (retina)

description: Retina L113441


title: D2-Gpnmb+ control rep3 (retina)

description: Retina R113415


title: Severe rep8 (retina)

description: Retina L115899


title: Severe rep7 (retina)

description: Retina R115846


title: D2-Gpnmb+ control rep5 (retina)

description: Retina R113417


title: Severe rep10 (retina)

description: Retina L120272


title: D2-Gpnmb+ control rep8 (retina)

description: Retina L113442


title: D2-Gpnmb+ control rep10 (retina)

description: Retina L113446


title: Severe rep4 (retina)

description: Retina L113695


title: D2-Gpnmb+ control rep2 (retina)

description: Retina L113415


title: Severe rep3 (retina)

description: Retina R113657


title: Severe rep2 (retina)

description: Retina L112897


title: Severe rep1 (retina)

description: Retina R112876


title: Moderate rep10 (retina)

description: Retina L120287

source_name: Retina moderate glaucoma

value: moderate glaucoma


title: Moderate rep7 (retina)

description: Retina R115866


title: Moderate rep8 (retina)

description: Retina R115873


title: Moderate rep9 (retina)

description: Retina R118072


title: Moderate rep4 (retina)

description: Retina L113658


title: Moderate rep3 (retina)

description: Retina L113657


title: No or early 2 rep8 (retina)

description: Retina R115871

source_name: Retina no or early glaucoma

value: no or early glaucoma


title: Moderate rep2 (retina)

description: Retina L112876


title: No or early 2 rep10 (retina)

description: Retina L120252


title: Moderate rep1 (retina)

description: Retina R112858


title: No or early 2 rep9 (retina)

description: Retina L120227


title: No or early 2 rep6 (retina)

description: Retina L115836


title: No or early 2 rep7 (retina)

description: Retina L115862


title: No or early 2 rep4 (retina)

description: Retina R113655


title: No or early 2 rep3 (retina)

description: Retina L113655


title: No or early 2 rep1 (retina)

description: Retina L112848


title: No or early 2 rep2 (retina)

description: Retina L113654


title: No or early 2 rep5 (retina)

description: Retina R115825


title: No or early 1 rep5 (retina)

description: Retina L115831


title: No or early 1 rep7 (retina)

description: Retina L120243


title: No or early 1 rep9 (retina)

description: Retina L120273


title: No or early 1 rep6 (retina)

description: Retina L120231


title: No or early 1 rep8 (retina)

description: Retina L120253


title: No or early 1 rep10 (retina)

description: Retina L120275


title: No or early 1 rep2 (retina)

description: Retina R112847


title: No or early 1 rep4 (retina)

description: Retina L115809


title: No or early 1 rep1 (retina)

description: Retina R112840


title: No or early 1 rep3 (retina)

description: Retina R113656


title: Severe rep8 (OHN)

description: ONH L115899

source_name: ONH severe glaucoma

value: optic nerve head


title: Severe rep9 (OHN)

description: ONH R119778


title: Severe rep1 (OHN)

description: ONH R112876


title: Moderate rep8 (OHN)

description: ONH R115873

source_name: ONH moderate glaucoma


title: Severe rep4 (OHN)

description: ONH L113695


title: Severe rep6 (OHN)

description: ONH R115844


title: Severe rep7 (OHN)

description: ONH R115846


title: Severe rep10 (OHN)

description: ONH L120272


title: Moderate rep1 (OHN)

description: ONH R112858


title: Severe rep5 (OHN)

description: ONH R113695


title: Moderate rep9 (OHN)

description: ONH R118072


title: Severe rep2 (OHN)

description: ONH L112897


title: Moderate rep4 (OHN)

description: ONH L113658


title: Moderate rep7 (OHN)

description: ONH R115866