title: P90 MD to Control Gene Expression rep2


title: Wild-type_Lung_11

status: Public on Oct 20 2010

type: RNA

city: New Haven

first: Paulette

middle: Lee

last: Wright

state: CT

address: 10 Amistad St.

department: Pharmacology

country: USA

institute: Yale University

description: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com).

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent,).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent).

molecule: total RNA

organism: Mus musculus

source_name: WT

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tissue

value: lung

tag: gender

value: male

tag: age

value: 8 wks


title: P90 MD to Control Gene Expression rep4

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice

hyb_protocol: Standard Agilent protocol

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

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios were calculated for each MD to control comparisons in each of the 4 arrays separately.

source_name: P90 Control

label_protocol: RNA (0.4ug) samples were processed and labelled with Cy3 and Cy5 (Quick Amp labelling kit, two color, Agilent technologies)

extract_protocol: Total RNA was extracted by Quiagen Rneasy mini kit (Cat.no.74106)

value: 90 postnatal days

value: colonic mucosa

tag: strain

tag: treatment

value: control

source_name: P90 MD

value: methyl donor diet


title: Nogo-A/B_KO_Lung_1

source_name: KO


title: Female Dexamethasone 6 hr_rep 2

status: Public on Oct 31 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Female Treated - replicate 2
Agilent TIFF High File: US23502387_251486824227_S01_H.tif
Agilent TIFF Low File: US23502387_251486824227_S01_L.tif

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5) and the resulting data were imported into Rosetta Resolver (v7.1).

source_name: liver

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Livers were homogenized and total RNA from liver was extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen). Samples were aliquoted and frozen at -800C.

treatment_protocol: Male and female (diestrous 1) adrenalectomized C57BL/6 mice were treated with vehicle (phosphate buffered saline) or dexamethasone (1 mg/kg i.p.) (Steraloids) on the same day. Six hours after dexamethasone treatment the liver was harvested and kept in RNAlater solution at 4oC overnight. All samples were frozen and stored at -800C

value: female (Diestrous 1)

value: 11 weeks, Adrenalectomized

value: liver

tag: treatment group

value: dexamethasone 1mg/Kg (i.p.) for 6 hours


title: Wild-type_Lung_13


title: Nogo-A/B_KO_Lung_12


title: DCs-C2

city: North Grafton

first: Hanping

last: Feng

address: 200 Westboro Rd.

institute: Tufts University

hyb_protocol: The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50C.

scan_protocol: The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).

data_processing:
Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.

label: Biotin

source_name: Dendritic cells

label_protocol: Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically.

extract_protocol: RNA extracted and purified with RNeasy mini kit (Qiagen).

value: Female

value: Bone marrow

tag: cell type

value: Dendritic cells

tag: infection


title: No20-12PB

status: Public on Oct 18 2010

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

country: Canada

institute: University of British Columbia

description: All treated biologically replicated samples were hybridized with the same Universal Human Reference RNA (reference), which is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.

hyb_protocol: 3DNA array detection 350 kit (Genisphere).

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA). Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA).

data_processing: After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA). Data were normalized using default global LOWESS normalization.

organism: Homo sapiens

source_name: Pigmented hair bulb

label_protocol: 1ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. Sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

growth_protocol: Sample was stored in an RNA stabilization reagent.

extract_protocol: Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols. The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Samples of human hair follicles were collected from scalp biopsies of normal individuals undergoing cosmetic procedures. Hair follicles were microdissected to remove the lower one third, including the hair bulb, leaving the root sheaths, including the bulge region.

value: pigmented hair bulb

source_name: Universal Human Reference RNA (Stratagene)

label_protocol: Total 10ug RNA Universal Human Reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

extract_protocol: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues.

tag: cell line

value: multiple cell lines representing different human tissues


title: P90 MD to Control Gene Expression rep1


title: No21-16PB


title: No18-17NB

source_name: Non-pigmented hair bulb

value: non-pigmented hair bulb


title: DCs-C3


title: DCs-C1


title: No17-15NB


title: No19-13PB


title: No22-11NB


title: No16-14NB


title: No12-11PU

source_name: Pigmented hair upper root sheaths

value: pigmented hair upper root sheaths


title: No15-15NB


title: No13-11NU

source_name: Non-pigmented hair upper root sheaths

value: non-pigmented hair upper root sheaths


title: CA1_15B (MDD) vs. 18D (Control)

status: Public on Oct 17 2010

first: Vanja

last: Duric

address: 34 Park Street

description:
VDUR_303021 (15B+18D).gpr
CA1_15B+18D

hyb_protocol: In a two-step process, array chips were initially hybridized to cDNA overnight, followed by a series of stringent washes to reduce nonspecific probe binding, and then post-stained with fluorescent Cy5 (MDD) and Cy3 (Control) dendrimers (Genisphere, Hatfield, PA)

scan_protocol: Scanned on GenePix scanner (Axon Instruments, Union City, CA)

data_processing:
Data from all 30 two-channel arrays were analyzed using R/Bioconductor.  First, probes with more than three missing values out of 30 (10%) were dropped.  Data were normalized using linear-Log normalization to stabilize the variance of low expressing genes, and then spatial plus intensity based LOWESS to remove spatial and intensity related biases, using the MAANOVA library.  P values were then adjusted to control false discovery rate (FDR) at 0.05 using the Q-value package.  P values were calculated using distributions generated using permutation methods and standard error estimates were therefore not used in the P value calculations.
We can not provide a list of normalized values for each individual hybridization (per chip), but rather have a list of average expression values for all hybridizations used in the experiment (n=15).  See supplementary files on Series record.

source_name: CA1_MDD 15B

label_protocol: Total RNA (RIN > 4.8, A260/280 > 1.9) from MDD and matched control human samples (n = 15) were reverse-transcribed into cDNA and indirectly labeled with highly sensitive fluorescent technology (Genisphere, Hatfield, PA)

extract_protocol: Total RNA from the dentate gyrus granule and CA1 pyramidal cell layer punches was extracted using RNAqueous kit (Ambion, Austin, TX), followed by cleanup with RNeasy MinElute kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.

tag: sample id

tag: disease state

value: MDD

value: CA1 subregions of the hippocampus

tag: gender (sex)

value: F

tag: race

value: C

tag: Cause of death

value: suicide, fall from height

tag: pmi

tag: ph

tag: toxicology

value: ND

tag: medications

tag: depressive features

value: MDD NOS, Single episode

tag: axix i comorbidity

value: pathological gambling, delusional disorder

source_name: CA1_Control 18D

value: CVD


title: CA1_17B (MDD) vs. 23D (Control)

description:
VDUR_303018 (17B+23D).gpr
CA1_17B+23D

source_name: CA1_MDD 17B

tag: tissue

tag: age

value: M

value: suicide, hanging

value: nortriptyline, L-DOPA

value: Recurrent, Moderate severity, Nonpsychotic, with Melancholia

value: Parkinson’s disease

source_name: CA1_Control 23D

value: control


title: CA1_16B (MDD) vs. 16D (Control)

description:
VDUR_303022 (16B+16D).gpr
CA1_16B+16D

source_name: CA1_MDD 16B

value: suicide, SIGSW

value: Single Episode, Mild severity.  Nonpsychotic,  without melancholia

source_name: CA1_Control 16D

value: pulmonary embolism

value: propoxyphene


title: No14-14PB

value: pigmented hair bulb

value: multiple cell lines representing different human tissues


title: CA1_23B (MDD) vs. 17D (Control)

description:
VDUR_303008 (23B+17D).gpr
CA1_23B+17D

source_name: CA1_MDD 23B

value: MDD

value: CA1 subregions of the hippocampus

value: C

value: suicide, CO

value: CO

value: Single Episode, Moderate severity, secondary  Nonpsychotic.

source_name: CA1_Control 17D


title: CA1_13B (MDD) vs. 6D (Control)

description:
VDUR_303020 (13B+6D).gpr
CA1_13B+6D

source_name: CA1_MDD 13B

value: F

value: CVD

value: ND

value: fluoxetine

value: Recurrent, Moderate, Nonpsychotic, without melancholia

source_name: CA1_Control 6D

value: homicide


title: CA1_22B (MDD) vs. 22D (Control)

description:
VDUR_303034 (22B+22D).gpr
CA1_22B+22D

source_name: CA1_MDD 22B

value: M

value: risperidone, sertraline

value: Recurrent, Moderate severity, Nonpsychotic, PE MDD with psychotic symptoms

value: benzodiazepine abuse

source_name: CA1_Control 22D

value: control

value: aneurysm


title: CA1_9B (MDD) vs. 9D (Control)

description:
VDUR_303009 (9B+9D).gpr
CA1_9B+9D

source_name: CA1_MDD 9B

value: MDD

value: CA1 subregions of the hippocampus

value: suicide, hanging

value: Recurrent, Moderate severity, Nonpsychotic, without melancholia

source_name: CA1_Control 9D

value: pulmonary thromboemboli

value: propoxyphene


title: CA1_19B (MDD) vs. 19D (Control)

description:
VDUR_212124 (19B+19D).gpr
CA1_19B+19D

source_name: CA1_MDD 19B

value: F

value: C

value: aortic aneurysm

value: flurazepam

source_name: CA1_Control 19D

value: CVD


title: CA1_11B (MDD) vs. 13D (Control)

description:
VDUR_303017 (11B+13D).gpr
CA1_11B+13D

source_name: CA1_MDD 11B

value: ND

value: doxepine

value: Recurrent, Moderate severity, Seasonal, Nonpsychotic, without melancholia

value: agoraphobia, Hx stroke

source_name: CA1_Control 13D

value: AAm


title: CA1_8B (MDD) vs. 8D (Control)

description:
VDUR_212125 (8B+8D).gpr
CA1_8B+8D

source_name: CA1_MDD 8B

value: M

value: homicide

value: Single episode, mild severity Nonpsychotic, without melancholia

source_name: CA1_Control 8D

value: control

value: hemorrhagic pancreatitis


title: CA1_6B (MDD) vs. 7D (Control)

description:
VDUR_303016 (6B+7D).gpr
CA1_6B+7D

source_name: CA1_MDD 6B

value: MDD

value: CA1 subregions of the hippocampus

value: suicide, CO

value: ETOH, CO, alprazolam

value: alprazolam, valproic acid

value: Recurrent, Severe, without psychosis

value: Panic disorder w/ Agoraphobia

source_name: CA1_Control 7D


title: No10-PU10

source_name: Pigmented hair upper root sheaths

value: pigmented hair upper root sheaths

source_name: Universal Human Reference RNA (Stratagene)

value: multiple cell lines representing different human tissues


title: CA1_4B (MDD) vs. 4D (Control)

description:
VDUR_303010 (4B+4D).gpr
CA1_4B+4D

source_name: CA1_MDD 4B

value: C

value: CO, phenobarbital, phenytoin

value: sertraline

value: Chronic, Moderate severity, Nonpsychotic, without melancholia

source_name: CA1_Control 4D

value: hypertrophic cardiomyopathy

value: ND


title: CA1_3B (MDD) vs. 3D (Control)

description:
VDUR_303012 (3B+3D).gpr
CA1_3B+3D

source_name: CA1_MDD 3B

value: M

value: suicide, SIGSW

value: flurazepam

value: flurazepam, lorazepam

value: Recurrent, Severe, Nonpsychotic, with melancholia

value: Hx alcohol abuse

source_name: CA1_Control 3D

value: control

value: AAm

value: CVD


title: No9-12PU

value: pigmented hair upper root sheaths


title: CA1_7B (MDD) vs. 1D (Control)

description:
VDUR_303013 (7B+1D).gpr
CA1_7B+1D

source_name: CA1_MDD 7B

value: MDD

value: CA1 subregions of the hippocampus

value: F

value: CVD, accidental OD

value: morphine, codeine, hydrocodone

value: fluoxetine, temazepam, hydrocodone

value: Recurrent, In full remission

value: sedative, hypnotic and anxiolytic disorder NOS

source_name: CA1_Control 1D


title: No6-13PU

value: multiple cell lines representing different human tissues


title: No8-13NB

source_name: Non-pigmented hair bulb

value: non-pigmented hair bulb


title: No5-9NU

source_name: Non-pigmented hair upper root sheaths

value: non-pigmented hair upper root sheaths


title: CA1_5B (MDD) vs. 5D (Control)

description:
VDUR_303011 (5B+5D).gpr
CA1_5B+5D

source_name: CA1_MDD 5B

value: M

value: C

value: suicide, SIGSW

value: ND

value: buspirone [3], lorazepam [3]

value: Single Episode, Severe, Nonpsychotic, with melancholia

source_name: CA1_Control 5D


title: DG_21B (MDD) vs. 21D (Control)

description:
VDUR_211420 (21B+21D).gpr
DG_21B+21D

source_name: DG_MDD 21B

value: MDD

value: Dentate Gyrus (DG)

value: suicide, hanging

value: sertraline

value: Single episode, Severe Nonpsychotic, without melancholia

source_name: DG_Control 21D

value: control

value: CVD


title: DG_22B (MDD) vs. 22D (Control)

description:
VDUR_211408 (22B+22D).gpr
DG_22B+22D

source_name: DG_MDD 22B

value: suicide, CO

value: CO

value: risperidone, sertraline

value: Recurrent, Moderate severity, Nonpsychotic, PE MDD with psychotic symptoms

value: benzodiazepine abuse

source_name: DG_Control 22D

value: aneurysm


title: DG_20B (MDD) vs. 20D (Control)

description:
VDUR_212122 (20B+20D).gpr
DG_20B+20D

source_name: DG_MDD 20B

value: M

value: C

value: suicide, SIGSW

value: diazepam, codeine

value: Single Episode, Severe Nonpsychotic, without melancholia

source_name: DG_Control 20D

value: aortic aneurysm


title: DG_23B (MDD) vs. 17D (Control)

description:
VDUR_211411 (23B+17D).gpr
DG_23B+17D

source_name: DG_MDD 23B

value: MDD

value: Dentate Gyrus (DG)

value: Single Episode, Moderate severity, secondary  Nonpsychotic.

value: Parkinson’s disease

source_name: DG_Control 17D

value: ND


title: No4-8PU

source_name: Pigmented hair upper root sheaths

value: pigmented hair upper root sheaths

source_name: Universal Human Reference RNA (Stratagene)

value: multiple cell lines representing different human tissues


title: No3-8PB

source_name: Pigmented hair bulb

value: pigmented hair bulb


title: No2-9NB

value: non-pigmented hair bulb


title: No7-11PB


title: No1-12PB


title: DG_19B (MDD) vs. 19D (Control)

description:
VDUR_211413 (19B+19D).gpr
DG_19B+19D

source_name: DG_MDD 19B

value: F

value: flurazepam

value: Recurrent, Moderate severity, Nonpsychotic, without melancholia

source_name: DG_Control 19D

value: control

value: CVD


title: DG_10B (MDD) vs. 10D (Control)

description:
VDUR_211418 (10B+10D).gpr
DG_10B+10D

source_name: DG_MDD 10B

value: C

value: suicide, OD

value: diazepam temazepam

value: sertraline temazepam

value: Recurrent, Severe, Nonpsychotic, without melancholia

source_name: DG_Control 10D

value: AAm


title: DG_14B (MDD) vs. 7D (Control)

description:
VDUR_211404 (14B+7D).gpr
DG_14B+7D

source_name: DG_MDD 14B

value: MDD

value: Dentate Gyrus (DG)

value: M

value: suicide, SIGSW

value: ETOH

value: Chronic, Moderate severity, Nonpsychotic, without melancholia

value: Hx alcohol abuse

source_name: DG_Control 7D


title: DG_11B (MDD) vs. 13D (Control)

description:
VDUR_211421 (11B+13D).gpr
DG_11B+13D

source_name: DG_MDD 11B

value: F

value: aneurysm

value: ND

value: doxepine

value: Recurrent, Moderate severity, Seasonal, Nonpsychotic, without melancholia

value: agoraphobia, Hx stroke

source_name: DG_Control 13D


title: DG_13B (MDD) vs. 6D (Control)

description:
VDUR_211410 (13B+6D).gpr
DG_13B+6D

source_name: DG_MDD 13B

value: C

value: CVD

value: fluoxetine

value: Recurrent, Moderate, Nonpsychotic, without melancholia

source_name: DG_Control 6D

value: control

value: homicide


title: DG_12B (MDD) vs. 9D (Control)

description:
VDUR_211412 (12B+9D).gpr
DG_12B+9D

source_name: DG_MDD 12B

value: MDD

value: Dentate Gyrus (DG)

value: M

value: Recurrent, moderate severity, Nonpsychotic, without melancholia

source_name: DG_Control 9D

value: pulmonary thromboemboli

value: propoxyphene


title: DG_5B (MDD) vs. 23D (Control)

description:
VDUR_211419 (5B+23D).gpr
DG_5B+23D

source_name: DG_MDD 5B

value: suicide, SIGSW

value: buspirone [3], lorazepam [3]

value: Single Episode, Severe, Nonpsychotic, with melancholia

source_name: DG_Control 23D


title: DG_3B (MDD) vs. 3D (Control)

description:
VDUR_211401 (3B+3D).gpr
DG_3B+3D

source_name: DG_MDD 3B

value: flurazepam

value: flurazepam, lorazepam

value: Recurrent, Severe, Nonpsychotic, with melancholia

value: Hx alcohol abuse

source_name: DG_Control 3D

value: AAm

value: ND


title: DG_4B (MDD) vs. 4D (Control)

description:
VDUR_303642 (4B+4D).gpr
DG_4B+4D

source_name: DG_MDD 4B

value: C

value: suicide, CO

value: CO, phenobarbital, phenytoin

value: sertraline

value: Chronic, Moderate severity, Nonpsychotic, without melancholia

source_name: DG_Control 4D

value: control

value: hypertrophic cardiomyopathy


title: DG_18B (MDD) vs. 18D (Control)

description:
VDUR_211403 (18B+18D).gpr
DG_18B+18D

source_name: DG_MDD 18B

value: MDD

value: Dentate Gyrus (DG)

value: F

value: CVD

value: propoxyphene

value: trazodone, thioridizine, venlafaxine, clonazepam

value: Chronic,  Severe, Nonpsychotic, with melancholia

source_name: DG_Control 18D


title: DG_8B (MDD) vs. 8D (Control)

description:
VDUR_212120 (8B+8D).gpr
DG_8B+8D

source_name: DG_MDD 8B

value: M

value: homicide

value: Single episode, mild severity Nonpsychotic, without melancholia

source_name: DG_Control 8D

value: hemorrhagic pancreatitis


title: control

status: Public on Oct 15 2010

type: genomic

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

hyb_protocol: manufacturer's recommendation

scan_protocol: Affy recommendation

data_processing:
The data was analyzed using TAS v1.1.02, and normalized using built-in quantile normalization and probe-level analysis with both perfect match and mismatch (PM/MM) probes and run with a bandwidth of 30.  Text versions of the processed data (BAR) files are also provided on the Series record.
Three Abf1 ts against wild type, and three Rap1 against WT; 2-sided t-test for pvalues

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wild type BY4741 DNA

label_protocol: Labeled with biotinylated ddATP using terminal deoxynucleotidyl transferase

growth_protocol: Wild type and matched mutant yeast were grown at 25 C, shifted for to 37 C and grown at 37 C for one hour before harvesting.  Note third Rap1 samples (Tsui samples) were grown 2 hrs at 37 C.

extract_protocol: Phenol/chloroform after proteinase K and cross link reversal; DNA was fragmented with DNase prior to labeling

treatment_protocol: Standard chromatin/Mnase prep, digesting to mostly mononucleosomal DNA

tag: strain

value: BY4741 wild type yeast


title: Rap1 wild type

description:
nucleosomal DNA
Rap1 wild type against genomic DNA

source_name: Rap1 wild type mononucleosomal DNA

value: Rap1 wild type


title: Abf1 ts

description:
nucleosomal DNA
Abf1 ts mutant against genomic DNA

source_name: Abf1 ts mononucleosomal DNA

value: abf1-1 ts mutant


title: Abf1 wild type

description:
nucleosomal DNA
Abf1 wild type against genomic DNA

source_name: Abf1 wt mononucleosomal DNA

value: Abf1 wild type


title: CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP), rep1

city: paris

first: isabelle

middle: catherine

last: vigon

address: 22 rue Méchain

country: France

institute: Institut Cochin, inserm u1016, cnrs umr8104, Université Paris-Descarte

hyb_protocol: After 1H of Pre-hybridization with ethanolamine and NaBorate, an over night direct hybridization sample (Cy5 vs Cy3) in agilent hybridization buffer was realized at 60°C.

scan_protocol: Slides were scanned with DNA Microarray Scanner (Agilent), with 10 µm resolution.The TIFF images were imported into GenePix Pro 6.0.1.00 (Axon, http://www.moleculardevices.com/pages/software/gn_genepix_pro.html)(MDC/Axon Instruments, Sunnyvale, CA, USA). This program was used for image and grid alignment, spot detection and extraction of Cy5 (635 nm) and Cy3 (532 nm) intensities for all detected spots. Spots with little or no signal and obvious defects were flagged as non utilizable spots and labeled ‘not assigned’ (NA), to exclude them from further analysis.

data_processing: Data for each slide were analyzed using the functions of the BioConductor marray package (http://www.bioconductor.org/) to check for the absence of abnormal bias during hybridization. Data were then normalized, using the Loess approach (window of 40%) implemented in the BioConductor marray package (Cleveland WS: Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 1979, 74:829-836. ) comparative analysis were done  with the limma modified t-test package of Bioconductor (Smyth, G. K.2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3. http://www.bepress.com/sagmb/vol3/iss1/art3).

source_name: CD34+ cells from cord blood cocultured during during 24h with MS5 cells secreting HOXC4 homeoprotein

label_protocol: One µg of total RNA was used to generate the double strand cDNA completed with a T7 sequence, after purification (Qiagen QIAquick PCR Purification,), cDNAs were used for synthesis and amplification  of dye labelled aRNAs. Message RNA amplification was carried out according to the manufacturer's protocol of the Amino Allyl MessageAmpII aRNA Amplificaion kit (Ambion) with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies). Cy5 or Cy3 mono-reactive Dye Pack GE HEALTHCARE were conjugated via an amino allyl group. The Cy3 and Cy5 labels were switched, or dye-flipped, between SP and MP aRNA.Labeling were performed using 60 pm of fluorescence for each sample aRNA.

growth_protocol: 4.106 human CD34+ cells from normal cord blood were cultured for 24 hours in the presence of irridiated MS-5 cells engineered to secrete HOXB4 or HOXC4 or GFP proteins.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol. The quality of the extracted RNA was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

value: hematopoietic, cord blood

tag: cell type

source_name: CD34+ cells from cord blood cocultured during during 24h with MS5 cells secreting gfp protein


title: CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4), rep2


title: Rap1 ts

description:
nucleosomal DNA
Rap1 ts mutant against genomic DNA

source_name: Rap1 ts mononucleosomal DNA

value: rap1-2 ts mutant


title: CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP), rep2


title: CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP) , rep2

source_name: CD34+ cells from cord blood cocultured during during 24h with MS5 cells secreting HOXB4 homeoprotein


title: CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4), rep1


title: CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4), rep2


title: CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4), rep1


title: CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4), rep2


title: CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4), rep1


title: CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4), rep1


title: CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP), rep1


title: CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4), rep2


title: Ea.hy926 cells treated with TCF11 siRNA and epoxomicin

status: Public on Oct 08 2010

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

country: Germany

institute: Charité Universitaetsmedizin Berlin

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133  Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS_v5_450 protocol

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4.0.036 (MAS 5.0) using Affymetrix default analysis settings. Normalization was performed by GCRMA.

source_name: Ea.hy926 cells treated with TCF11 siRNA and 10nM epoxomicin

label_protocol: Total RNA was amplified and labelled using Message AmpII-Biotin enhanced Kit, Ambion

growth_protocol: human Ea.hy926 cells were grown under standard conditions in Basal Iscove´s medium containing 10% fetal calf serum (FCS), 2 mM L-glutamine 100 U/ml penicillin and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted from frozen cell pellets using the High Pure RNA Isolation kit according to the manufacturer’s (Roche) protocol.

treatment_protocol: 0.6×105 cells/ml were transfected with 50nM smartpool siRNA (Dharmacon) for 48h using HiPerfect (Qiagen) transfection reagent and protocols and treated with 0.1%DMSO or 10nM epoxomicin for 24h


title: Ea.hy926 cells treated with control siRNA and epoxomicin

source_name: Ea.hy926 cells treated with control siRNA and 10nM epoxomicin


title: Sox10 rep. 1

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: custom array design 081105

hyb_protocol: Hybridization was performed by Nimblegen

scan_protocol: Arrays were scanned by Nimblegen

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Rattus norvegicus

source_name: Sox10 ChIP DNA from P15 rat sciatic nerve

label_protocol: ChIP DNA was amplified by whole genome amplification (Sigma), and then sent to Nimblegen for labeling with Cy3 or Cy5 per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: ChIP assays were performed on freshly dissected sciatic nerves, which were pooled from 6-10 P15 rat pups and minced in 1% formaldehyde in PBS as described (Jang et al., J. Neurochemistry, 2006; Jang and Svaren, JBC 2009). The in vivo FAIRE assay on rat myelinating sciatic nerve was performed at P14 using pooled nerves from 4 rat pups.  Freshly dissected sciatic nerves were minced in phosphate-buffered saline (PBS) containing 1% formaldehyde for 5 minutes at room temperature (22oC).  The nerves were washed with cold PBS, pooled, and frozen at -80oC.  The nerves were thawed and homogenized in buffer (150 mM NaCl, 10% glycerol, 50 mM Tris pH 8.0) containing protease inhibitor cocktail (Sigma, St Louis, MO, USA; 5µl of cocktail per ml of buffer).  The cells were then lysed using incubation in three buffers, L1, L2 and L3 as previously described (Giresi and Lieb 2009).  After cell lysis, cells were sonicated using the Bioruptor (Diagenode), and extracted with phenol:chloroform as previously described (Giresi and Lieb 2009).  The protocol only differed in that the cells were sonicated in 2 ml of Lysis Buffer 3 on high with 30 seconds on followed by 30 seconds off, all on ice. 20% of the crosslinked chromatin was kept without the initial phenol extraction as an input control, and the samples were all reverse crosslinked at 65oC overnight.

value: Sprague-Dawley

value: :P15 sciatic nerve

tag: antibody

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

tag: fraction

value: WGA-amplified ChIP DNA

source_name: input DNA

value: P15 sciatic nerve

value: WGA-amplified input DNA


title: 6h post-LH_547 vs. 22h post-LH_647

city: Quebec

first: Isabelle

last: Gilbert

state: Quebec

address: Pavillon INAF

department: Sciences Animales

institute: Universite Laval

description: Merged data (Biological replicates 1, 2 and 3): in a loop design

hyb_protocol: Hybridizations were performed in Slidehyb buffer #1 (Ambion, Austin, TX) at 50 ºC for 18 h in the SlideBooster hybridization station (Advalytix, San Francisco, CA). Slides were then washed twice with 2X SSC-0.5% SDS at 50 ºC for 15 min and twice with 0.5X SSC-0.5% SDS at 50 ºC for 15 min. The slides were dipped 3 times in 1X SSC and 3 times in H2O. Finally, the slides were dried by centrifugation at room temperature at 1,200 g for 5 min.

scan_protocol: The slides were scanned using the VersArray ChipReader System (Bio-Rad, Mississauga, ON, Canada) and visualized with the ChipReader software (Media Cybernetics, San Diego, CA). After the acquisition, scanned images were analyzed using ArrayPro Analyzer software (Media Cybernetics).

data_processing: Signal intensity data files were normalized and analyzed using the WebArray DB software (http://www.webarraydb.org/webarray) which is implemented with functions from Bioconductor (Xia X et al. 2005; Xia XQ et al. 2009). In the pre-processing step, the background of the intensity files was removed using Minimum Background Subtraction. Data were transformed in log2 and normalized for dye bias using a within array loess. A between array quantile normalization was then performed in order to obtain a similar distribution across the entire array. Normalized data was assessed using e-Bayes moderated t-test (LIMMA) included in the Webarray software. First, a cut-off threshold on minimum log intensity was applied on the data and this threshold was determined using the average of log-intensities of the negative controls present on the slide.

organism: Bos taurus

source_name: 6h post-LH

label_protocol: 500 ng of total RNA from three pools of 2 h pre-LH, 6 h post-LH and 22 h post-LH CG were amplified using T7 RNA polymerase (RiboAmp RNA Amplification Kit, Molecular Devices) according to the manufacturer’s indications. A fixed amount of 2.5 µg aRNA were labelled indirectly using ULS aRNA Fluorescent Labeling (Kreatec Biotechnology, Amsterdam, The Netherlands) according to the manufacturer’s protocol.

extract_protocol: Total RNA extraction of each pool of GC were performed using the Absolutely RNA Miniprep Kit (Stratagene, LaJolla, CA) following manufacturer's instructions. The RNA extraction procedure included an on-column DNase I treatment to remove genomic DNA.

treatment_protocol: The oestruses of cows were synchronized and tissues were obtained by ovariectomy of FSH stimulated ovaries where the endogenous LH surge was induced by gonadotropin releasing hormone on day 14.5. Three different groups of GC were collected; the first consisted of GC 2 h before the administration of LH, the second group of GC 6 h after the LH treatment and finally the third group is composed of GC collected 22 h after the LH dose.

value: in vivo granulosa cells recolted 6h after LH surge

source_name: 22h post-LH

value: in vivo granulosa cells recolted 22h after LH surge


title: Ea.hy926 cells treated with TCF11 siRNA and DMSO


title: Egr2 Ab.1-2

description: custom array design 081105

source_name: Egr2 ChIP DNA from P15 rat sciatic nerve

value: Abcam


title: Sox10 rep. 2

description: custom array design 081105


title: DRG_CFA_rat12

status: Public on Oct 07 2010

city: St. Louis

first: Meiping

last: Chang

state: MO

address: 700 Chesterfield Parkway West

department: PGRD

institute: Pfizer Inc.

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #12

hyb_protocol: Sample hybridization and wash was performed according to the standard protocol, 'One-Color Microarray-Based Gene Expression Analysis v.5.7 (P/N G4140-90040)', by Agilent Technologies. One exception was that Triton was excluded from the wash buffer.

scan_protocol: Scanning and feature extraction was performed according to the standard protocol, 'One-Color Microarray-Based Gene Expression Analysis v.5.7 (P/N G4140-90040)', by Agilent Technologies. Protocol GE1-v5_95_Feb07 was used for feature extraction and Agilent Technologies Scanner G2505B US45102978 was used for scanning.

data_processing: The Agilent rat whole genome microarray signals were normalized with a program developed internally. Briefly, signal normalization against a common sample was performed using a smoothed piecewise linear curve, trained on the log intensities that differed by < 10% rank order between two samples.  Local background subtraction was performed on each array prior to normalization.  A computational naïve control pool was created from the averaged normalized signals of the individual naïve control arrays.  Within the naïve control arrays, a median array was selected as the one least distant from the other naïve control arrays.  All naïve control arrays were normalized against the median array prior to calculating the averaged normalized signals of the control pool. Finally each sample was normalized against the computational naïve control pool.

source_name: L4 and L5 DRG, 4 day CFA

label_protocol: Sample preparation and labeling was performed according to the standard protocol, 'One-Color Microarray-Based Gene Expression Analysis v.5.7 (P/N G4140-90040)', by Agilent Technologies.

growth_protocol: A naive (control) group of rats and a group of rats injected with CFA, were used for gene expression profiling experiments. On day 4, rats were euthanized and ipsilateral L4 and L5 dorsal root ganglia (DRG) were extracted, pooled for each rat, and immediately frozen in liquid nitrogen. DRG were stored at -80C until used.

extract_protocol: RNA isolation and processing for gene arrays was done according to standard protocols by Genelogic (Boston, MA).  Briefly, dorsal root ganglia tissues were homogenized in guanidium isothiocyanate with beta-mercaptoethanol (GITC+BME), using the Omni TH-115 homogenizer. Trizol was added and mixed by repeated inversions. RNA aqueous phase was separated using Heavy Phase Lock Gel tubes. Chloroform and sample homogenate were added to the tube and shaken vigorously to remove protein contaminants, incubated on ice for 9-12 min, then centrifuged. The aqueous phase was cleaned using the Qiagen RNEasy Mini Kit (Cat # 74106). A bead cleanup was performed using Agencourt RNAClean magnetic beads (Cat # A29168) to further purify the RNA. RNA quality was evaluated by an Agilent Bioanalyzer. Only the RNA samples that passed the quality control measures proceeded for microarray.

value: Sprague Dawley

tag: agent

value: Complete Freund's Adjuvant (CFA)

value: L4 and L5 dorsal root ganglia (DRG)

tag: gender

value: male


title: Egr2 Ab.2-1

description: custom array design 081105

value: Covance


title: Egr2 Ab.2-2

description: custom array design 081105


title: DRG_CFA_rat8

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #8


title: DRG_CFA_rat10

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #10


title: Egr2 Ab.1-1

description: custom array design 081105


title: DRG_naive_rat2

description: Gene expression of L4 and L5 DRG from naïve/untreated adult male rat #2

source_name: L4 and L5 DRG, naïve/untreated

value: control


title: Ea.hy926 cells treated with control siRNA and DMSO


title: 22h post-LH_547 vs.2h pre-LH_647

source_name: 2h pre-LH

value: in vivo granulosa cells recolted 2h before LH surge


title: DRG_naive_rat5

description: Gene expression of L4 and L5 DRG from naïve/untreated adult male rat #5


title: DRG_naive_rat3

description: Gene expression of L4 and L5 DRG from naïve/untreated adult male rat #3


title: DRG_CFA_rat7

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #7


title: DRG_CFA_rat11

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #11


title: DRG_naive_rat4

description: Gene expression of L4 and L5 DRG from naïve/untreated adult male rat #4


title: muscle_exercised_SS49

status: Public on Oct 04 2010

city: Amherst

first: Robert

last: Hyldahl

state: MA

address: Totman Building 30 Eastman Lane

department: Department of Kinesiology

institute: University of Massachusetts Amherst

description: gene expression in muscle 3h following eccentric exercise

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 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 Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C 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 37Â°C 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Probe set means from microarrays were generated from the PLIER algorithm (typically 6 iterations) in Expression Console (Affymetrix Inc., Santa Clara, CA) and imported into Partek Genomics Suite software for statistical analysis. PLIER stands for “Probe Logarithmic Intensity Error” and is a model-based signal estimator beneficial to multi-array estimations. Data was log2 transformed and then analyzed by analysis of variance (ANOVA) using age and body mass index as covariates. The data outputs were stringently filtered on the basis of p-value (p<0.005).

source_name: vastus lateralis, eccentrically exercised

label_protocol: Cy3 labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: Percutaneous needle biopsies of both the exercised and non-exercised vastus lateralis muscle were obtained 3 hours following exercise. Under local anesthesia (Lidocaine), a small incision was made into the skin and fascia and the biopsy needle was inserted into the muscle. A small core of tissue (~100mg) was withdrawn and was immediately frozen in liquid nitrogen. The tissue was then stored at -80°C until it was packed and shipped in dry ice to Gene Logic (Gaithersburg, MD) for RNA extraction and expression profiling.

value: vastus lateralis

tag: bmi

tag: treatment

value: eccentrically exercised


title: muscle_exercised_SS48


title: DRG_naive_rat1

description: Gene expression of L4 and L5 DRG from naïve/untreated adult male rat #1


title: Faire

description: custom array design 081105

source_name: Faire DNA from P14 rat sciatic nerve

value: Sprague-Dawley

value: :P14 sciatic nerve

value: P14 sciatic nerve


title: muscle_exercised_SS47


title: 2h pre-LH_547 vs. 6h post-LH_647


title: muscle_exercised_SS46


title: muscle_exercised_SS43


title: muscle_exercised_SS42


title: muscle_exercised_SS45


title: muscle_exercised_SS39


title: muscle_exercised_SS37


title: muscle_exercised_SS40


title: muscle_exercised_SS36


title: muscle_exercised_SS41


title: muscle_exercised_SS34


title: muscle_exercised_SS28


title: muscle_exercised_SS27


title: muscle_exercised_SS38


title: muscle_exercised_SS24


title: muscle_exercised_SS22


title: muscle_exercised_SS23


title: muscle_exercised_SS32


title: muscle_exercised_SS31


title: muscle_exercised_SS29


title: muscle_exercised_SS14


title: muscle_exercised_SS33


title: muscle_exercised_SS6


title: muscle_exercised_SS35


title: muscle_exercised_SS10


title: muscle_exercised_SS8


title: muscle_exercised_SS7


title: muscle_exercised_SS30


title: muscle_exercised_SS9


title: muscle_exercised_SS11


title: DRG_CFA_rat9

description: Gene expression of L4 and L5 DRG from adult male rat injected with CFA in the left paws for 4 days to induce hyperalgesia, rat #9


title: muscle_exercised_SS4


title: muscle_exercised_SS2


title: muscle_control_SS49

source_name: contralateral vastus lateralis, not exercised

value: not exercised


title: muscle_exercised_SS3


title: muscle_control_SS46


title: muscle_control_SS48


title: muscle_control_SS43


title: muscle_control_SS37


title: muscle_control_SS31


title: muscle_control_SS40


title: muscle_control_SS42


title: muscle_control_SS36


title: muscle_control_SS38


title: muscle_control_SS39


title: muscle_control_SS45


title: muscle_control_SS30


title: muscle_control_SS34


title: muscle_control_SS33


title: muscle_control_SS47


title: muscle_control_SS29


title: muscle_control_SS41


title: muscle_control_SS35


title: muscle_control_SS23


title: muscle_control_SS11


title: muscle_control_SS22


title: muscle_control_SS27


title: muscle_control_SS28


title: muscle_control_SS24


title: muscle_control_SS10


title: muscle_control_SS9


title: muscle_control_SS8


title: muscle_control_SS3


title: muscle_control_SS6


title: muscle_control_SS4


title: muscle_control_SS14


title: muscle_control_SS32


title: muscle_control_SS7


title: muscle_control_SS2


title: HIV-specific CD8 T cells_Progressor_792092_B02

status: Public on Oct 03 2010

city: Boston

first: W.

middle: Nicholas

last: Haining

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from tetramer-sorted Gag-specific CD8 T cells

hyb_protocol: Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).

source_name: HIV-specific CD8 T cells

label_protocol: cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.

extract_protocol: RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt).  Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen).  RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).  Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction.  CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences).  Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA).  Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).

value: CD8 T cells

tag: clinical status

value: Progressor


title: HIV-specific CD8 T cells_Progressor_403998


title: HIV-specific CD8 T cells_Progressor_792092_B09


title: HIV-specific CD8 T cells_Progressor_981444


title: HIV-specific CD8 T cells_Progressor_806270


title: HIV-specific CD8 T cells_Progressor_350103


title: HIV-specific CD8 T cells_Progressor_752022


title: HIV-specific CD8 T cells_Progressor_881658


title: HIV-specific CD8 T cells_Progressor_280153


title: HIV-specific CD8 T cells_Progressor_560306


title: HIV-specific CD8 T cells_Progressor_941359


title: HIV-specific CD8 T cells_Progressor_554271


title: HIV-specific CD8 T cells_Progressor_139603


title: HIV-specific CD8 T cells_Progressor_264783


title: HIV-specific CD8 T cells_Progressor_388555


title: HIV-specific CD8 T cells_Controller_831969

value: Controller


title: HIV-specific CD8 T cells_Progressor_583127


title: HIV-specific CD8 T cells_Controller_950005


title: HIV-specific CD8 T cells_Controller_927078


title: HIV-specific CD8 T cells_Progressor_308811


title: HIV-specific CD8 T cells_Progressor_177154


title: HIV-specific CD8 T cells_Controller_366065


title: HIV-specific CD8 T cells_Controller_941849


title: HIV-specific CD8 T cells_Controller_711816


title: HIV-specific CD8 T cells_Controller_270245


title: HIV-specific CD8 T cells_Controller_518955


title: HIV-specific CD8 T cells_Controller_285873


title: HIV-specific CD8 T cells_Controller_245487


title: HIV-specific CD8 T cells_Controller_254912


title: HIV-specific CD8 T cells_Controller_719104


title: HIV-specific CD8 T cells_Controller_632723


title: HIV-specific CD8 T cells_Controller_756587


title: HIV-specific CD8 T cells_Controller_321797


title: HIV-specific CD8 T cells_Controller_187891


title: HIV-specific CD8 T cells_Controller_366356


title: HIV-specific CD8 T cells_Controller_553064


title: HIV-specific CD8 T cells_Controller_109477


title: HIV-specific CD8 T cells_Controller_832764


title: HIV-specific CD8 T cells_Controller_319564


title: Jurkat-PD1_3-28_rep6

description: Gene expression data from Jurkat cells cultured with beads

source_name: PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads

growth_protocol: PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.

extract_protocol: RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt).  Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen).  RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).

treatment_protocol: PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.

value: Jurkat cells


title: Jurkat-PD1_3-28_rep4


title: Jurkat-PD1_3-28_rep5


title: HIV-specific CD8 T cells_Controller_535367


title: HIV-specific CD8 T cells_Controller_940546


title: Jurkat-PD1_3-28-PD1_rep6

source_name: PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads


title: Jurkat-PD1_3-28_rep1


title: Jurkat-PD1_3-28-PD1_rep3


title: Jurkat-PD1_3-28_rep3


title: Jurkat-PD1_3-28-PD1_rep5


title: Jurkat-PD1_3-28-PD1_rep4


title: Jurkat-PD1_3-28-PD1_rep1


title: Jurkat-PD1_3-28-PD1_rep2


title: Serotype2_irondepleted_rep3

status: Public on Oct 01 2010

city: Copenhagen

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

country: Denmark

institute: National Veterinary Institute, Technical University of Denmark

description: Serotype 2

hyb_protocol: Hybridization was performed following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at 5 µm resolution using the NimbleGens MS 200 scanner (NimbleGen Systems, Madison, WI, USA).

data_processing: The raw data (.xys file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249). For RMA normalization we have used RGui version 2.9.2 (2009-08-24) (http://cran.r-project.org/bin/windows/base/), using the package Oligo.

organism: Actinobacillus pleuropneumoniae serovar 2 str. 4226

source_name: Actinobacillus pleuropneumoniae 4226 iron depleted

label_protocol: Labeling was performed at the Center for Biological Sequence Analysis at the Technical University of Denmark, Lyngby, Denmark, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Actinobacillus pleuropneumoniae was grown to mid-log phase (OD660nm 0.6) in brain heart infusion media supplemented with 0.03% NAD at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and the RNAeasy reagent (Ambion, Cambridgeshire, UK) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen) and subsequently by TURBO DNase (Ambion). RNA contration was measured by NanoDrop (Thermo Scientific, Wilmington, DE, USA) and RNA quality was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: At mid-log phase, the culture was split into two 10 ml portions. Iron-depleted conditions were established in one of the flasks by addition of 300 µM of the iron chelator 2,2'-dipyridyl. After 30 min growth the cultures were harvested.

tag: serotype

value: serotype 2 (4226)

tag: growth condition

value: iron depleted


title: Serotype1_irondepleted_rep3

description: Serotype 1

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

source_name: Actinobacillus pleuropneumoniae 4074 iron depleted

value: serotype 1 (4074)


title: Serotype3_irondepleted_rep3

description: Serotype 3

organism: Actinobacillus pleuropneumoniae serovar 3

source_name: Actinobacillus pleuropneumoniae 1421 iron depleted

value: serotype 3 (1421)


title: Serotype2_irondepleted_rep4

description: Serotype 2


title: Serotype7_irondepleted_rep3

description: Serotype 7

organism: Actinobacillus pleuropneumoniae serovar 7

source_name: Actinobacillus pleuropneumoniae WF87 iron depleted

value: serotype 7 (WF87)


title: Serotype1_irondepleted_rep4

description: Serotype 1


title: Serotype1_control_rep4

description: Serotype 1

source_name: Actinobacillus pleuropneumoniae 4074 control

value: control


title: Serotype3_control_rep4

description: Serotype 3

source_name: Actinobacillus pleuropneumoniae 1421 control


title: Serotype5_irondepleted_rep4

description: Serotype 5

organism: Actinobacillus pleuropneumoniae serovar 5

source_name: Actinobacillus pleuropneumoniae L20 iron depleted

value: serotype 5b (L209)


title: Serotype7_control_rep4

description: Serotype 7

source_name: Actinobacillus pleuropneumoniae WF87 control


title: Serotype5_irondepleted_rep3

description: Serotype 5


title: Serotype6_irondepleted_rep3

description: Serotype 6

organism: Actinobacillus pleuropneumoniae serovar 6

source_name: Actinobacillus pleuropneumoniae 7712640 iron depleted


title: Serotype6_irondepleted_rep4

description: Serotype 6


title: Serotype3_irondepleted_rep4

description: Serotype 3


title: Serotype2_control_rep4

description: Serotype 2

source_name: Actinobacillus pleuropneumoniae 4226 control


title: Serotype3_control_rep3

description: Serotype 3


title: Serotype6_control_rep3

description: Serotype 6

source_name: Actinobacillus pleuropneumoniae 7712640 control


title: Serotype6_control_rep4

description: Serotype 6


title: Serotype7_irondepleted_rep4

description: Serotype 7


title: Serotype2_control_rep3

description: Serotype 2


title: Serotype5_control_rep3

description: Serotype 5

source_name: Actinobacillus pleuropneumoniae L20 control


title: Serotype7_irondepleted_rep2

description: Serotype 7


title: Serotype1_control_rep3

description: Serotype 1


title: Serotype7_control_rep3

description: Serotype 7


title: HIV-specific CD8 T cells_Controller_632343


title: Serotype5_irondepleted_rep2

description: Serotype 5


title: Serotype6_irondepleted_rep2

description: Serotype 6


title: Serotype3_irondepleted_rep2

description: Serotype 3


title: Serotype5_control_rep1

description: Serotype 5


title: Serotype2_control_rep1

description: Serotype 2


title: Serotype3_control_rep1

description: Serotype 3


title: Serotype3_control_rep2

description: Serotype 3


title: Serotype1_control_rep1

description: Serotype 1


title: mature adult

city: Beijing

first: Yunfei

last: Wang

address: Chaoyang District, Datun Road, No. 15

country: China

institute: Institute of Biophysics, Chinsese Academy of Sciences

description: mature adult

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
The data is processed by Affymetrix Tiling Analysis Software (TAS, version 1.1.02), and the produced bed files were combined with the signal files, and mapped to UCSC ce6
Affymetrix Tiling Analysis Software (TAS, version 1.1.02) processed with windowsize=100, maxgap=30 and minrun=70 and quantile normalized.

organism: Caenorhabditis elegans

source_name: mature adult

label_protocol: Standard Affymetrix protocol

growth_protocol: L1 stage, 13 hours after L1s; L2 stage, 22 hours after L1s; L3 stage, 32 hours after L1s; L4 stage, 44 hours after L1s; Heatshock stage, 60 hours after L1s.

extract_protocol: Total RNA was extracted at each of the 6 different developmental stages and environmental conditions according to the Trizol (Invitrogen) protocol. Small RNAs (70-500nt) were isolated using a QIAGEN tip (QIAGEN), and remaining rRNAs were removed by adapting the MicrobExpress kits (Ambion). The enriched ncRNAs were dephosphorylated with CIAP (Fermentas) and then ligated to the 3’-adaptor oligonucleotide by T4 RNA ligase (Fermentas). Each RNA sample was reverse transcribed using random hexamers and a primer complementary to the 3’-adaptor.

treatment_protocol: Dauer worms were induced by growing mixed-stage N2 worms grown in liquid medium for 7-9 days at 20ºC until dauers had become plentiful. The culture was then washed with 0.1M NaCl and floated on sucrose for several times, and dauers were purified by treating with 1% SDS for 15-30 min, followed by 3 times of sucrose floatation. Heatshock worms were obtained by subjecting 60h worms to 30ºC for 3h. All developmental stages were determined by time of culture since feeding of L1s worms at 20ºC.

value: whole worm

tag: developmental stage

value: mature adult


title: Serotype6_control_rep2

description: Serotype 6


title: male adult CB1489

description: male

source_name: male

value: young adult, 56 hours after L1s

value: male


title: Serotype5_control_rep2

description: Serotype 5


title: Serotype1_irondepleted_rep1

description: Serotype 1


title: Serotype2_irondepleted_rep1

description: Serotype 2


title: Serotype2_control_rep2

description: Serotype 2


title: Serotype7_control_rep2

description: Serotype 7


title: Serotype7_irondepleted_rep1

description: Serotype 7


title: Serotype1_control_rep2

description: Serotype 1


title: Serotype6_control_rep1

description: Serotype 6


title: Serotype5_irondepleted_rep1

description: Serotype 5


title: Serotype3_irondepleted_rep1

description: Serotype 3


title: Serotype1_irondepleted_rep2

description: Serotype 1


title: Serotype2_irondepleted_rep2

description: Serotype 2


title: larve 4-2

description: larve 4-2

source_name: larve 4-2

value: larva 4


title: Serotype5_control_rep4

description: Serotype 5


title: larve 1-2

description: larve 1-2

source_name: larve 1-2

value: larva 1


title: larve 4-1

description: larve 4-1

source_name: larve 4-1


title: larve 3-1

description: larve 3-1

source_name: larve 3-1

value: larva 3


title: larve 2-1

description: larve 2-1

source_name: larve 2-1

value: larva 2


title: heat shock-2

description: heat shock-2

source_name: heat shock-2

value: heat shock, 60 hours after larva 1 stage


title: larve 1-1

description: larve 1-1

source_name: larve 1-1


title: dauer-2

value: dauer


title: Serotype7_control_rep1

description: Serotype 7


title: heat shock-1

description: heat shock-1

source_name: heat shock-1


title: larve 2-2

description: larve 2-2

source_name: larve 2-2


title: Serotype6_irondepleted_rep1

description: Serotype 6


title: stem cell primary culture, rep2

first: Lingsheng

last: Dong

address: 75 Francis Street

department: Renal Division

institute: Brigham and Women's Hospital

hyb_protocol: 10 μg of labeled cRNA was fragmented, denatured at 90°C for 5 min, and then hybridized at 37°C for 20 hours using direct hybridization array kits (from AppliedMicroarrays CodeLink). The arrays were then washed in buffer at 47°C for 60 minutes. After washing, the arrays were incubated at room temperature for 30 minutes with a fluorophore (Streptavidin-Alexa Fluor 647, Invitrogen Eugene, OR), run through a series of 5 minute rinses, and spun dry.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. The gene expression measurements were further normalized to a median expression level of 1.0 across the arrays. 1000 genes with the highest expression levels “>1” in the experimental samples was used for comparisons.

source_name: Total RNA from primary culture

label_protocol: 2-3 ng sample (total RNA) is primed with the T7 oligo (dT) primer to synthesize cDNA containing a T7 promoter sequence.  Second-strand cDNA synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. In vitro transcription to synthesize cRNA generates multiple copies of biotinylated cRNA from the double-stranded cDNA templates.

extract_protocol: 100 µL of RLT Buffer solution (QIAGEN, 1% mercaptoethanol) was used to lyse the ejected cells and to preserve the RNA.  Qiagen RNeasy Minikit (QIAGEN) was used to purify the total RNA.

treatment_protocol: Manual dilution method: To investigate nonprinted cells, 0.5 µl samples were drawn from the cell solution and pipetted into the three wells as controls. The controls had 1000 cells on average.

tag: cell line

value: mouse embryonic stem cells


title: dauer-1

tag: tissue


title: larve 3-2

description: larve 3-2

source_name: larve 3-2


title: stem cell primary culture, rep3


title: 3-cell, rep2

source_name: Total RNA from 3 cells

treatment_protocol: Drop-on-demand total RNA analysis steps: 1) Heterogeneous sample was collected, 2) cells were stained with antibody and patterned with cell-encapsulating droplets, 3) specific homogeneous samples containing target cells were produced by a cell droplet patterning platform; homogeneous samples were identified by an automated imaging system, 4) total RNA gene expression analysis with microarray.


title: Vehicle Repl. 5

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip scanner; Pixel size 1.56, Filter 570.

data_processing: Raw data were processed using JMP Genomics 4.1 (SAS). Background subtraction:  RMA; Normalization: quantile; Transformation: Log2; Summarization: median polish.

source_name: hMEC

label_protocol: Affymetrix 1-cycle IVT

growth_protocol: Human mammary epithelial cells were were maintained in MEBM (Lonza, Basel, Switzerland) supplemented with MEGM SingleQuots (Lonza) at 37 degrees C in 5% CO2 atmosphere

extract_protocol: Total RNA was isolated by using either RNeasy kit (Qiagen, Valencia, CA) or Aurum total RNA mini kit (Bio-Rad, Hercules, CA).

treatment_protocol: Adenoviruses overexpressing hPR-B or β-Gal were generated using the ViraPower Adenoviral Expression System (Invitrogen), and were amplified and purified by CsCl2 centrifugation. Cells were infected at a multiplicity of infection (MOI) of 150 for 17.5 hr. Following infection, cells were treated with 10nM R5020 or vehicle for 16 hours.

tag: ligand

value: Ethanol

value: mammary epithelial cell


title: Vehicle Repl. 10


title: Vehicle Repl. 7


title: Vehicle Repl. 8


title: Vehicle Repl. 9


title: Vehicle Repl. 6


title: Vehicle Repl. 2


title: Vehicle Repl. 1


title: Vehicle Repl. 4


title: stem cell primary culture, rep1


title: R5020 Repl. 5


title: Vehicle Repl. 3


title: mock_rep3

city: Baltimore

first: hester

last: liu

state: MD

address: 1550 Orleans st

department: Radiation Oncology

institute: Johns Hopkins University

description: Replicate 3 of 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 with G7 upgrade.

data_processing: The data were analyzed with GCOS 1.4.1  using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: MCF7 cells, mock treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: MCF7 cells were grown in MEM with 10% FBS, 37C, 95% air, 5% CO2.

extract_protocol: Qiagen RNeasy Mini Kits.

treatment_protocol: MCF7 cells were treated with compound BMH-7 (10uM), BMH-9 (10uM), BMH-15 (5uM),  BMH-21 (0.5uM),  BMH-22 (5uM), or BMH-23 (5uM) for 6 hours.

tag: Control


title: BMH-23_rep2

description: Replicate 2 of 4

source_name: MCF7 cells, treated with BMH-23

tag: Treated with lead compound


title: R5020 Repl. 6

tag: cell type


title: R5020 Repl. 10


title: R5020 Repl. 3


title: R5020 Repl. 9


title: mock_rep1

description: Replicate 1 of 4


title: R5020 Repl. 2


title: mock_rep4

description: Replicate 4 of 4


title: R5020 Repl. 8


title: BMH-23_rep3

description: Replicate 3 of 4


title: R5020 Repl. 1


title: 3-cell, rep3


title: BMH-22_rep2

description: Replicate 2 of 4

source_name: MCF7 cells, treated with BMH-22


title: 3-cell, rep1


title: BMH-23_rep4

description: Replicate 4 of 4


title: mock_rep2

description: Replicate 2 of 4


title: R5020 Repl. 7


title: R5020 Repl. 4


title: BMH-23_rep1

description: Replicate 1 of 4


title: BMH-22_rep4

description: Replicate 4 of 4


title: BMH-22_rep3

description: Replicate 3 of 4


title: BMH-22_rep1

description: Replicate 1 of 4


title: BMH-21_rep4

description: Replicate 4 of 4

source_name: MCF7 cells, treated with BMH-21


title: BMH-21_rep3

description: Replicate 3 of 4


title: BMH-21_rep2

description: Replicate 2 of 4


title: BMH-15_rep4

description: Replicate 4 of 4

source_name: MCF7 cells, treated with BMH-15


title: BMH-15_rep2

description: Replicate 2 of 4


title: BMH-15_rep1

description: Replicate 1 of 4


title: BMH-9_rep3

description: Replicate 3 of 4

source_name: MCF7 cells, treated with BMH-9


title: BMH-21_rep1

description: Replicate 1 of 4


title: BMH-15_rep3

description: Replicate 3 of 4


title: U373 cells syk-transefected and treated with Ethanol and PonA at day 1

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

department: Biology

institute: Gustavus Adolphus College

description: human glioblastoma

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on the HU95Av2 genechips, which were washed and stained in the Affymetrix Fluidics Station.

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

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 Tukey Biweight trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: U373 cells transefected and treated with Ethanol and PonA at day 1

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

growth_protocol: rpmi plus 5-10% fetal calf serum, standard growth conditions at 37oC and 5% CO2

extract_protocol: Total RNA Isolation from Tripure Reagent and RNEasy Clean-up of the Total RNA.

treatment_protocol: 10 µM Pon-A used for 6-48 hours as per standard induction protocols of InVitrogen

value: ethanol and PonA

tag: transfection

value: syk-transfected

tag: time

value: day 1


title: BMH-9_rep2

description: Replicate 2 of 4


title: U373 cells sky-transefected and treated with Ethanol and PonA at day 2

description: human glioblastoma

source_name: U373 cells transefected and treated with Ethanol and PonA at day 2

value: day 2


title: BMH-7_rep4

description: Replicate 4 of 4

source_name: MCF7 cells, treated with BMH-7


title: BMH-9_rep4

description: Replicate 4 of 4


title: BMH-7_rep2

description: Replicate 2 of 4


title: U373 cells syk-transfected and no treatment at day 2

description: human glioblastoma

source_name: U373 cells transfected and no treatment at day 2


title: U373 cells syk-transfected and no treatment at day 1

description: human glioblastoma

source_name: U373 cells transfected and no treatment at day 1


title: BMH-9_rep1

description: Replicate 1 of 4


title: U373 cells syk-transfected and ethanol treatment at day1

description: human glioblastoma

source_name: U373 cells transfected and ethanol treatment at day1

value: ethanol


title: BMH-7_rep3

description: Replicate 3 of 4


title: BMH-7_rep1

description: Replicate 1 of 4


title: Y79 cells without scaffold_replicate

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of Y79 cells without scaffold_replicate

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Normalization is done in Genespring GX 11.0 using 75th percentile normalization and Base line transformation with respect to control samples. Significant genes up and down regulated showing one fold and above among the groups was identified. Differentially regulated genes were clustered using hierarchical clustering to identify significant expression patterns.

source_name: human retinoblastoma cell line without scaffold_replicate

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Y79 retinoblastoma cell line was cultured in the complete RPMI 1640 medium supplemented with 10% fetal bovine serum, glutamine and antibiotics for 5 days

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden) following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Y79 cells were co-cultured with polymeric scaffold in the complete medium for 5 days for microarray analysis to compared the gene expression between cells grown with scaffold and cells without scaffold

value: retinoblastoma tumor


title: WW-ctrl for pDr, Rep1

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

description:
pDr_WW-ctrl_Rep1
Well-watered control for pDr.

hyb_protocol: 4 µg RNA samples were hybridized to the Affymetrix (ATH1 25K) GeneChip. The hybridization protocol was done using the GeneChip Hybridization, Wash, and Stain kit. The cocktail includes 12.5 ug aRNA, control oligo B2, 20x hyb controls of bioB, bioC, bioD, and cre, 2X hyb mix, and DMSO. The hybridization mix was heated at 99C for 5 min, 45C for 5 min, and then hybridized for 16h at 45C.

scan_protocol: Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).

data_processing:
For each of the drought experiments, mDr-Day1, mDr-Day10 and pDr, raw data were background corrected, normalized and summarized according to the custom CDF using RMA (Irizarry et al., 2003). RMA was implemented in the 'affy' Bioconductor package within the R statistical computing environment.

Each of the mDr-Day01, mDr-Day10 and pDr sample groups (along with their controls, for a total of 4 samples per group) were normalized separately.

The custom CDF was built by uniquely mapping 232,697 probe sequences to 21,389 Arabidopsis (TAIR8) gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>99% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).

organism: Arabidopsis thaliana

source_name: Young leaf samples from plants subjected to well-watered conditions after 35 DAS

label_protocol: RNA preparation/labeling was done using the Affymetrix 3' IVT Express kit, with biotin as label. The cRNA (or aRNA) is purified via beads and fragmented before hybridization.

growth_protocol: Arabidopsis (Columbia) seeds were sown in moistened peat pellets, stratified at 4°C for 2 days, and then transferred to a growth room kept at 10 hours light (100 µmole m-2 s-1) and 22°C.

extract_protocol: For RNA isolation, two biological replicate samples of 5 pooled plants were collected at early (day1) and late stage (day10) for mDr, and first day of wilting for pDr, along with controls for mDr and pDr. RNA was isolated using RNeasy Kit (Qiagen, USA).  After that, genomic DNA was eliminated using DNase kit (Qiagen, USA).

treatment_protocol: For drought treatment, pellets were weighed before sowing to determine the amount of water in pellets at the beginning of the experiment. Controlled moderate drought (mDr) was maintained by giving plants water to keep the soil moisture level at 30% of field capacity, which is 200% or 2 g H2O g-1 dry soil. Water was withheld at 30 days after sowing (DAS). For progressive drought (pDr) treatment, plants were grown in a growth room as described above, water was withheld at 35 DAS, and pellets were allowed to dry and monitored by weighing the pellets until the required pDr level was reached.

tag: ecotype

value: Columbia

value: young leaves

value: well-watered control


title: mDr Day10, Rep2

description:
mDr-Day10_Stress_Rep2
mDr Day10 drought stress treated.

source_name: Young leaf samples from plants subjected to 10 days of mDr treatment after 30 DAS

value: moderate drought

tag: treatment time

value: 10 days


title: Y79 cells with scaffold

description: Gene expression of Y79 cells grown with scaffold

source_name: human retinoblastoma cell line with scaffold


title: pDr, Rep1

description:
pDr_Stress_Rep1
pDr drought stress treated.

source_name: Young leaf samples from plants subjected to pDr treatment after 35 DAS

value: progressive drought


title: Y79 cells with scaffold_replicate

description: Gene expression of Y79 cells grown with scaffold_replicate

source_name: human retinoblastoma cell line with scaffold_replicate


title: WW-ctrl for mDr Day10, Rep1

description:
mDr-Day10_WW-ctrl_Rep1
Well-watered control for mDr Day10.

source_name: Young leaf samples from plants subjected to 10 days of well-watered conditions after 30 DAS


title: WW-ctrl for mDr Day10, Rep2

description:
mDr-Day10_WW-ctrl_Rep2
Well-watered control for mDr Day10.


title: mDr Day01, Rep2

description:
mDr-Day01_Stress_Rep2
mDr Day01 drought stress treated.

source_name: Young leaf samples from plants subjected to 1 day of mDr treatment after 30 DAS

value: 1 day


title: U373 cells with no transfection and no treatment at day 1

description: human glioblastoma


title: pDr, Rep2

description:
pDr_Stress_Rep2
pDr drought stress treated.


title: WW-ctrl for mDr Day01, Rep1

description:
mDr-Day01_WW-ctrl_Rep1
Well-watered control for mDr Day01.

source_name: Young leaf samples from plants subjected to 1 day of well-watered conditions after 30 DAS


title: mDr Day10, Rep1

description:
mDr-Day10_Stress_Rep1
mDr Day10 drought stress treated.


title: Y79 cells without scaffold

description: Gene expression of Y79 cells without scaffold

source_name: human retinoblastoma cell line without scaffold


title: mDr Day01, Rep1

description:
mDr-Day01_Stress_Rep1
mDr Day01 drought stress treated.


title: 13969362 - WOX14-10D Repeat1 vs N8514-10D Repeat1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Our scope is to establish a functional link to organ initiation and development in Arabidopsis by identifying genes that are deregulated in the wox14 mutant background.

hyb_protocol: N8514-10D Repeat1 Cy5 / WOX14-10D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: seedling - Media=1/2 MS 1% sucrose  Temperature=22  Light=long day

treatment_protocol: no treatment

tag: genotype/variation

tag: age

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

value: mutant (wox14 -/-)


title: 13969409 - WOX14-6D Repeat2 vs WOX14-10D Repeat2

hyb_protocol: WOX14-10D Repeat2 Cy5 / WOX14-6D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: WW-ctrl for mDr Day01, Rep2

description:
mDr-Day01_WW-ctrl_Rep2
Well-watered control for mDr Day01.

tag: treatment


title: 13969401 - WOX14-6D Repeat2 vs N8514-6D Repeat2

hyb_protocol: N8514-6D Repeat2 Cy5 / WOX14-6D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969408 - N8514-10D Repeat2 vs N8514-6D Repeat2

hyb_protocol: N8514-6D Repeat2 Cy5 / N8514-10D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969407 - N8514-6D Repeat2 vs N8514-10D Repeat2

hyb_protocol: N8514-10D Repeat2 Cy5 / N8514-6D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969399 - WOX14-10D Repeat1 vs WOX14-6D Repeat1

hyb_protocol: WOX14-6D Repeat1 Cy5 / WOX14-10D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969400 - N8514-6D Repeat2 vs WOX14-6D Repeat2

hyb_protocol: WOX14-6D Repeat2 Cy5 / N8514-6D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969398 - WOX14-6D Repeat1 vs WOX14-10D Repeat1

hyb_protocol: WOX14-10D Repeat1 Cy5 / WOX14-6D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969402 - N8514-10D Repeat2 vs WOX14-10D Repeat2

hyb_protocol: WOX14-10D Repeat2 Cy5 / N8514-10D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969410 - WOX14-10D Repeat2 vs WOX14-6D Repeat2

hyb_protocol: WOX14-6D Repeat2 Cy5 / WOX14-10D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969396 - N8514-6D Repeat1 vs N8514-10D Repeat1

hyb_protocol: N8514-10D Repeat1 Cy5 / N8514-6D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969397 - N8514-10D Repeat1 vs N8514-6D Repeat1

hyb_protocol: N8514-6D Repeat1 Cy5 / N8514-10D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969361 - N8514-10D Repeat1 vs WOX14-10D Repeat1

hyb_protocol: WOX14-10D Repeat1 Cy5 / N8514-10D Repeat1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969406 - WOX14-10D Repeat2 vs N8514-10D Repeat2

hyb_protocol: N8514-10D Repeat2 Cy5 / WOX14-10D Repeat2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.