title: UC_0179_1_RAP_27k_h1

description:
UC_0179_1_RAP_27k_h1
This is one of two samples that were hybridized to both 27k and 35k platforms. They were only used for merging of the two expression datasets.

hyb_protocol: Samples were dissolved in 42 mul of Universal Hybridization Solution (Corning, Acton, MA, USA) and hybridizations were carried out in a CMT-Hybridization Chamber (Corning) for 18 h at 42°C. Pre-hybridization of slides and post-hybridization washes were performed as described in the Universal Hybridization Kit (Corning)

source_name: Urinary bladder tumor UC_0179_1

label_protocol: 1.5 microrgram of sample and reference aRNA, amplified using the MessageAmp aRNA Kit (Ambion), were labeled using the CyScribe Post-Labeling Kit (Amersham Biosciences) followed by purification using the Cyscribe GFX Purification Kit (Amersham)


title: UC_0111_1_BAC_32k_h1

status: Public on Jun 14 2010

type: genomic

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: Differentially labeled DNA was pooled, mixed with 100 microgram Human Cot-1 DNA (Invitrogen), and lyophilized prior to resuspension in 55 microliter hybridization solution (50% formamide, 10% dextran sulfate, 2x SSC, 2% SDS, 10 mg/ml yeast tRNA). Probes were heated at 70°C for 15 minutes and at 37°C for 30 minutes before hybridization to micro arrays for 48-72 hours at 37°C. Prior to hybridization, micro arrays were UV-cross linked at 500 mJ/cm2 and pretreated using the Universal Micro array Hybridization Kit (Corning, Acton, MA) according to the manufacturer's instructions. The slides were washed in 2 x SSC, 0.1% SDS for 15 min, followed by 2 x SSC, 50% formamide (pH 7.0) for 15 min at 45°C, 2 x SSC, 0.1% SDS for 30 min at 45°C, and 0.2 x SSC for 15 min at room temperature.

scan_protocol: Fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies). Image analysis on scanned arrays was performed with GenePix 4.0 (Axon Instruments)

data_processing: Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad/missing or saturated during image analysis were removed. Poorly measured features with Ch1 or Ch2 signal to noise ratio (SNR) <5 were removed. Data was normalized using the popLowess method (Staaf, et al, BMC Genomics, 2007, 8:382)

molecule: genomic DNA

organism: Homo sapiens

source_name: Urinary bladder tumor UC_0111_1

label_protocol: 1.5 microgram sample and reference genomic DNA was fluorescently labeled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences), respectively, using the Array CGH labeling kit (Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).

extract_protocol: Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen)

tag: sample histology

value: Urothelial carcinoma

tag: tumor stage

tag: tumor grade

tag: dead of disease

value: YES

tag: follow up time (months)

tag: tat1 progress^to minv/cystectomy/dead

tag: distant metastasis

value: M+

source_name: Reference male DNA

tag: reference

value: Reference male DNA


title: UC_0115_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0115_1

value: NO


title: UC_0112_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0112_1

value: Ta


title: N_005_Hv3_35k_h1

type: RNA

hyb_protocol: Samples were dissolved in 42 microliter Universal Hybridization Solution (Corning) and hybridizations were carried out in a CMT-Hybridization Chamber (Corning) for 18 h at 42°C. Pre-hybridization of slides and post-hybridization washes were performed using the Pronto Plus System (Promega)

data_processing: Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad, missing or saturated during image analysis were removed. Poorly measured features with ch1 or ch2 intensities <15 were removed. Data was normalized using pin-based LOWESS algorithm.

molecule: total RNA

source_name: Urinary bladder tumor N_005

label_protocol: Labeling of 5 micrograms of sample RNA was performed using the Pronto Plus System (Promega)

extract_protocol: Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by purification of total RNA using RNeasy kit (Qiagen).

value: Normal bladder

source_name: Stratagene Universal Human Reference

value: RNA pooled from ten human cell lines


title: UC_0194_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0194_1


title: UC_0192_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0192_1


title: UC_0114_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0114_1


title: UC_0168_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0168_1


title: UC_0109_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0109_1

tag: cystectomy


title: UC_0165_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0165_1


title: UC_0173_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0173_1


title: UC_0172_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0172_1


title: UC_0095_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0095_1


title: UC_0106_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0106_1

label_protocol: 1.5 microgram sample and reference genomic DNA was labeled with Cy5-dCTP or with Cy3-dCTP (Amersham Biosciences) using random primer labeling (Bioprime array CGH genomic Labeling module, Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).

extract_protocol: Genomic DNA was extracted using Trizol reagent (Invitrogen) and further purified using the Wizard kit (Promega)

source_name: Reference female DNA

value: Reference female DNA


title: UC_0159_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0159_1


title: UC_0096_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0096_1


title: UC_0097_1_BAC_32k_h3

source_name: Urinary bladder tumor UC_0097_1


title: UC_0149_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0149_1


title: UC_0110_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0110_1


title: UC_0101_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0101_1


title: UC_0162_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0162_1

source_name: Stratagene Universal Human Reference


title: UC_0147_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0147_1


title: UC_0093_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0093_1

source_name: Reference male DNA


title: UC_0089_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0089_1


title: UC_0086_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0086_1


title: UC_0145_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0145_1


title: UC_0140_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0140_1


title: UC_0137_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0137_1


title: UC_0132_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0132_1

value: YES^cystect


title: UC_0076_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0076_1

source_name: Reference female DNA


title: UC_0075_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0075_1


title: UC_0073_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0073_1


title: UC_0131_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0131_1


title: UC_0077_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0077_1


title: UC_0115_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0115_1


title: UC_0114_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0114_1

source_name: Stratagene Universal Human Reference


title: UC_0078_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0078_1


title: UC_0070_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0070_1

source_name: Reference male DNA


title: UC_0069_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0069_1


title: UC_0120_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0120_1


title: UC_0112_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0112_1


title: UC_0067_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0067_1


title: UC_0122_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0122_1


title: UC_0130_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0130_1


title: UC_0129_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0129_1


title: UC_0059_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0059_1


title: UC_0066_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0066_1

source_name: Reference female DNA


title: UC_0061_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0061_1


title: UC_0060_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0060_1


title: UC_0111_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0111_1


title: UC_0053_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0053_1

value: YES^cystectomy+met


title: UC_0057_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0057_1


title: UC_0135_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0135_1

source_name: Stratagene Universal Human Reference


title: UC_0051_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0051_1


title: UC_0130_1_BAC_32k_h2


title: UC_0110_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0110_1


title: UC_0106_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0106_1


title: UC_0047_1_BAC_32k_h2

source_name: Urinary bladder tumor UC_0047_1


title: UC_0101_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0101_1


title: UC_0040_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0040_1

source_name: Reference male DNA


title: UC_0043_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0043_1


title: UC_0034_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0034_1


title: UC_0104_1_RAP_27k_h2

source_name: Urinary bladder tumor UC_0104_1


title: UC_0099_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0099_1


title: UC_0097_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0097_1


title: UC_0025_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0025_1


title: UC_0021_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0021_1

source_name: Reference female DNA


title: UC_0029_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0029_1


title: UC_0098_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0098_1

source_name: Stratagene Universal Human Reference


title: UC_0096_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0096_1


title: UC_0076_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0076_1


title: UC_0161_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0161_1


title: UC_0089_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0089_1


title: UC_0078_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0078_1


title: UC_0023_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0023_1

source_name: Reference male DNA


title: UC_0008_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0008_1


title: UC_0007_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0007_1


title: UC_0095_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0095_1


title: UC_0009_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0009_1


title: UC_0017_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0017_1


title: UC_0002_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0002_1


title: UC_0070_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0070_1


title: UC_0066_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0066_1


title: UC_0075_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0075_1


title: UC_0073_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0073_1

source_name: Stratagene Universal Human Reference


title: UC_0001_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0001_1


title: UC_0077_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0077_1


title: UC_0056_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0056_1


title: UC_0064_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0064_1


title: UC_0061_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0061_1


title: UC_0060_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0060_1


title: UC_0049_2_RAP_27k_h1

source_name: Urinary bladder tumor UC_0049_2


title: UC_0051_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0051_1


title: UC_0057_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0057_1


title: UC_0053_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0053_1


title: UC_0037_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0037_1


title: UC_0040_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0040_1


title: UC_0035_1_RAP_27k_h1

description:
UC_0035_1_RAP_27k_h1
This is one of two samples that were hybridized to both 27k and 35k platforms. They were only used for merging of the two expression datasets.

source_name: Urinary bladder tumor UC_0035_1

value: Tx

value: Gx


title: UC_0043_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0043_1


title: UC_0042_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0042_1


title: UC_0032_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0032_1


title: UC_0033_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0033_1

source_name: Stratagene Universal Human Reference


title: UC_0145_1_BAC_32k_h1

source_name: Urinary bladder tumor UC_0145_1

source_name: Reference male DNA


title: UC_0052_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0052_1


title: UC_0017_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0017_1


title: UC_0025_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0025_1


title: UC_0026_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0026_1


title: UC_0029_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0029_1


title: UC_0023_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0023_1


title: UC_0047_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0047_1


title: UC_0010_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0010_1


title: UC_0019_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0019_1


title: UC_0021_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0021_1


title: UC_0012_1_RAP_27k_h4

source_name: Urinary bladder tumor UC_0012_1


title: N_011_RAP_27k_h1

source_name: Normal urinary bladder sample N_011


title: UC_0006_2_RAP_27k_h1

source_name: Urinary bladder tumor UC_0006_2


title: UC_0003_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0003_1

value: YES^cystectomy


title: UC_0009_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0009_1

source_name: Stratagene Universal Human Reference


title: UC_0005_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0005_1


title: N_002_RAP_27k_h1

source_name: Normal urinary bladder sample N_002


title: N_003_RAP_27k_h1

source_name: Normal urinary bladder sample N_003


title: N_005_RAP_27k_h1

source_name: Normal urinary bladder sample N_005


title: N_010_RAP_27k_h1

source_name: Normal urinary bladder sample N_010


title: UC_0011_3_RAP_27k_h1

source_name: Urinary bladder tumor UC_0011_3


title: N_001_RAP_27k_h1

hyb_protocol: Samples were dissolved in 42 microliter Universal Hybridization Solution (Corning) and hybridizations were carried out in a CMT-Hybridization Chamber (Corning) for 18 h at 42°C. Pre-hybridization of slides and post-hybridization washes were performed as described in the Universal Hybridization Kit (Corning)

source_name: Normal urinary bladder sample N_001


title: N_009_RAP_27k_h1

source_name: Normal urinary bladder sample N_009


title: N_004_RAP_27k_h1

source_name: Normal urinary bladder sample N_004


title: WW14bis with array type poplar from Affymetrix

status: Public on Jun 03 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Populus tremula x Populus alba

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: stem - 10-L potted in a mixture of blond and brown peat, horse manure, heather and disinfected compost (pH 5.8). Cuttings were grown in a greenhouse under controlled temperature (18-20°C) and natural light.

treatment_protocol: Name:irrigation conditions non limited - environmental treatment - abiotic stress,water:.

tag: harvest date

tag: treatment protocol

value: irrigation conditions non limited


title: UC_0008_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0008_1


title: Dental papillae of ICR mouse: 18-day

status: Public on Jun 05 2010

city: Chiba

first: Takashi

last: Muramatsu

address: 1-2-2, Masago, Mihama-ku

department: Pathology

country: Japan

institute: Tokyo Dental College

description: All RNA samples were extracted from over 20 dental papillae.

hyb_protocol: All processes in this experiment were carried out according to the manufacturer’s protocol (Affymetrix, 701024 Rev.3).  After hybridization, array chips were washed and stained automatically by Affymetrix® Fluidic Station 450.

scan_protocol: Affymetrix® GeneChip® Scanner 3000

data_processing:
GeneChip® Operating Software version 1.1 (GCOS; Affymetrix)
Image analysis software: GeneChip® Operating Software version 1.1 (Affymetrix)
Software for normalization and statistical analysis: GeneSpring® software version 7.0
Per Chip Normalization: normalized to 50th percentile
Per Gene Normalization: normalized to median

label: biotin

organism: Mus musculus

source_name: Dental papillae of ICR mouse

extract_protocol:
Dental papillae were dissected from mandibular first molar tooth germs by enzyme treatment and total RNA extracted.  All experiments were carried out according to the Guidelines for the Treatment of Animals at Tokyo Dental College.
Total RNA samples were extracted by acid guanidine phenol chloroform (AGPC) method using TRIzol RNA extraction mixture (Invitrogen).  Double-stranded cDNA was first synthesized by a two-cycle target labeling method, and then synthesized into Biotin-labeled cRNA using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Diagnostics).

tag: age


title: JXCT10bis with array type poplar from Affymetrix

treatment_protocol: Name:Water deficit - environmental treatment - abiotic stress,water deficit:quantity -1.25 time 14hour . water deficit at -1.25 Mega Pascal

value: Water deficit (WD)


title: JXCT9bis with array type poplar from Affymetrix


title: SHX-treated Delta dksA Cells Replicate 3

status: Public on Jun 01 2010

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description: Biological replicate 3 of 3. MG1655 delta lac delta dksA cells treated with SHX

hyb_protocol: Hybridization was performed following Agilent Two-Color Microarray-Based Prokaryote Analysis Protocol.

scan_protocol: Scanned on a GenePix 4000B Scanner (Axon Instruments).

data_processing: GenePix Pro (v 6.1) was used for background subtraction and normalization.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: SHX-treated Delta dksA Cells

label_protocol: 15 µg of RNA were primed with 2.5 µg of random hexamer at 70°C for 10 min, and reversed transcribed at 50°C for 1 h in the presence of 300 U SuperScript III RTase (Invitrogen), 5xRT Buffer, 10mM DTT, 20U RNaseOut (Invitrogen) and 500 µM each dATP, dCTP, dGTP, with 200 µM dTTP, 600 µM aa-dUTP. cDNA samples were incubated with Cy3 (reference) or Cy5 (sample) for 2hrs.

growth_protocol: Cells were grown in M9 medium supplemented with 0.2% glucose and 0.4% casamino acid at 37℃

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: At OD600~0.3, serine hydroxamate was added to a final concentration of 0.5mg/ml, cells were collected 40 minutes later.

tag: growth stage

value: log phase

tag: strain

value: MG1655 delta lac delta dksA

tag: treatment

value: 0.5mg/ml SHX for 40min

source_name: pooled reference RNA

value: MG1655 delta lac + MG1655 delta lac delta dksA

value: Pooled RNA from mixture of the same amount of wt, wt+SHX, dksA, dksA+SHX RNA samples


title: Dental papillae of ICR mouse: post-natal 3

label_protocol: Biotin-labeled cRNA using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Diagnostics).

value: post-natal 3 (P3)


title: SHR13bis with array type poplar from Affymetrix

treatment_protocol: Name:irrigation recovery after water deficit - environmental treatment - abiotic stress,water deficit:quantity 0 time 14hour . irrigation recovery after water deficit (water deficit 0 Mega Pascal)

value: irrigation recovery after water deficit (WDR)


title: Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. MG1655 delta lac cells untreated

source_name: Wild-type Cells

value: MG1655 delta lac

value: No treatment


title: SHX-treated Delta dksA Cells Replicate 2

description: Biological replicate 2 of 3. MG1655 delta lac delta dksA cells treated with SHX


title: Dental papillae of ICR mouse: 16-day


title: SHR8bis with array type poplar from Affymetrix


title: SHX-treated Delta dksA Cells Replicate 1

description: Biological replicate 1 of 3. MG1655 delta lac delta dksA cells treated with SHX


title: Delta dksA Cells Replicate 2

description: Biological replicate 2 of 3. MG1655 delta lac delta dksA cells untreated

source_name: Delta dksA Cells


title: Delta dksA Cells Replicate 3

description: Biological replicate 3 of 3. MG1655 delta lac delta dksA cells untreated


title: Delta dksA Cells Replicate 1

description: Biological replicate 1 of 3. MG1655 delta lac delta dksA cells untreated


title: SHX-treated Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. MG1655 delta lac cells treated with SHX

source_name: SHX-treated Wild-type Cells


title: SHX-treated Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. MG1655 delta lac cells treated with SHX


title: Wild-type Cells Replicate 2

description: Biological replicate 2 of 3. MG1655 delta lac cells untreated


title: SHX-treated Wild-type Cells Replicate 1

description: Biological replicate 1 of 3. MG1655 delta lac cells treated with SHX


title: Wild-type Cells Replicate 3

description: Biological replicate 3 of 3. MG1655 delta lac cells untreated


title: WW11bis with array type poplar from Affymetrix


title: LD_muscle_150d_rep1

city: Brisbane

first: Ross

middle: L

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

country: Australia

institute: CSIRO Animal, Food and Health Sciences

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep foetuses at 150 days development from muscle type (LD)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genomer Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, GCOSvs1.4

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Ovis aries

source_name: longissimus dorsi, new born lambs, 150 day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Animals were reared and euthanased in accordance with the animal ethics guidelines of Utah State University (Utah, USA)

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

treatment_protocol: LD muscle was dissected from each animal at a pre-determined site within 15 minutes of euthanasia, snap frozen under liquid nitrogen and stored at -80oC.

tag: developmental stage


title: LD_muscle_230d_rep1

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep foetuses at 230 days development from muscle type (LD)

source_name: longissimus dorsi, lambs, 230 day


title: LD_muscle_150d_rep3


title: LD_muscle_230d_rep3


title: LD_muscle_120d_rep3

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep foetuses at 120 days development from muscle type (LD)

source_name: longissimus dorsi, feotal, 120 day


title: UC_0015_1_RAP_27k_h1

source_name: Urinary bladder tumor UC_0015_1

value: Urothelial carcinoma

value: Ta

value: NO

source_name: Stratagene Universal Human Reference

value: RNA pooled from ten human cell lines


title: wt(iso)_ko(iso)_rep4

status: Public on May 31 2010

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

description: color swap

hyb_protocol: Hybridization was done in a humidity chamber at 42°C for 16 h. Hybridization buffer contains 50% FA, 5xSSC, 0.1%SDS.

scan_protocol: The GenePix 4000B laser scanner (Axon Inc., USA) was used for visualising fluorescence  signals and the GenePix Pro software (V 6.0) was used to calculate fluorescence intensities.

data_processing: Raw data were intensity dependent normalized using the lowess function in GenePix Acuity4.0

source_name: heart WT isoproterenol

label_protocol: Labelled cDNA probes were synthesized from 20 µg of total RNA. Reverse transcription was carried out in a 30 µl reaction volume with 0.5 µg oligo-dT18-primer, 10 mM DTT, 20 U RNaseOut, 200 µM of each (dATP, dCTP, dGTP), 80 µM dTTP, 40 µM Cy3-/Cy5-dUTP (Amersham Pharmacia Biosciences, Freiburg, Germany), 200 U of Superscript III (Invitrogen, Karlsruhe, Germany). The labelled cDNA was purified using QIAquick PCR purification columns (Qiagen GmbH, Hilden, Germany) according to manufacturers protocol.

growth_protocol: Mice were kept under conventional conditions and had access to tap water and rodent chow diet ad libitum.

extract_protocol: Total RNA was isolated form heart tissue using the TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacture’s instruction. Additionally, a cleanup step with the RNeasy Kit (Qiagen GmbH, Hilden, Germany) was performed. The integrity of total RNA was checked by capillary electrophoresis (2100 Bioanalyzer, Agilent Technologies, Inc. Palo Alto, CA,  U.S.A.).

treatment_protocol: The isoproterenol application (4 mg *kg -1 *d -1 ) was done via osmotic minipump over two weeks

value: NMRI

tag: tissue

value: heart

source_name: heart myo-/- isoproterenol


title: LD_muscle_120d_rep1


title: LD_muscle_100d_rep3

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep foetuses at 100 days development from muscle type (LD)

source_name: longissimus dorsi, feotal, 100 day


title: LD_muscle_120d_rep2


title: LD_muscle_80d_rep1

description: Gene expression data from Dorset/Suffolk/Rambouillet cross-bred sheep foetuses at 80 days development from muscle type (LD)

source_name: longissimus dorsi, feotal, 80 day


title: LD_muscle_80d_rep2


title: LD_muscle_80d_rep3


title: LD_muscle_100d_rep2


title: LD_muscle_100d_rep1


title: ko_ko(iso)_rep4

description: color swap

source_name: heart myo-/- vehicle


title: wt_wt(iso)_rep4

description: color swap

source_name: heart WT vehicle


title: ko_ko(iso)_rep2


title: ko_ko(iso)_rep1


title: wt_ko_rep2


title: ko_ko(iso)_rep3


title: wt_wt(iso)_rep3


title: wt(iso)_ko(iso)_rep1


title: wt(iso)_ko(iso)_rep4

description: color swap


title: wt(iso)_ko(iso)_rep3


title: wt_ko_rep3


title: wt_ko_rep1


title: wt(iso)_ko(iso)_rep2


title: wt_ko_rep4

description: color swap


title: wt_wt(iso)_rep1


title: LD_muscle_230d_rep2


title: wt_wt(iso)_rep2


title: ko_ko(iso)_rep4

description: color swap


title: HEK293_Mock_IP_4

status: Public on May 04 2010

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

description: Biological Replicate 3 of 5. Mock IP.

hyb_protocol: Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems).

scan_protocol: Arrays were scanned on a GenePix 4000B microarray scanner (Axon Instruments).

data_processing:
All arrays were subject to loess normalization within each array and scale normalization across all arrays using the Array Magic package in R. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates. In order to be considered for subsequent analysis, a probe had to be twofold above local background in all three biological replicates for any of the RIPs or the totals at any time point. Only ~35% of messages were deemed to be detected above background in this data set.
The Sample data table reports the final normalized/processed/filtered dataset that forms the basis of the conclusions in the accompanying manuscript.

source_name: HEK293 Cell Lysate

label_protocol: RNA from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, test RNA samples were labeled with Cy3 and reference samples were labeled with Cy5.

extract_protocol: RIPs utilized 100 μL pre-swollen and packed Protein-A Sepharose beads (Sigma) loaded with 20µg of DRBP76 antibody or mouse IgG1 as isotype negative control.  Antibody loaded beads were incubated with 3 mg (total protein) cell lysate for four hours at 4ºC, washed 4 times with ice-cold NT2 buffer (50mM Tris pH 7.4/150mM NaCl/1 mM MgCl2/0.05% Nonidet P-40) followed by 3 washes with ice-cold NT2 supplemented with 1M Urea. Extraction of associated RNA was performed as described, and total RNA was isolated using the Trizol reagent (Invitrogen).

tag: antibody

value: mouse anti-IgG1

tag: protocol

value: immunoprecipitation of mRNA (control)

source_name: Reference mRNA

tag: common reference


title: HEK293_Mock_IP_2

description: Biological Replicate 2 of 5. Mock IP.

value: Universal Human Reference RNA, Stratagene


title: HEK293_Mock_IP_5

description: Biological Replicate 4 of 5. Mock IP.


title: HEK293_Mock_IP_1

description: Biological Replicate 1 of 5. Mock IP.


title: HEK293_Total_6

description: Biological Replicate 5 of 5. Total mRNA.

value: control


title: HEK293_Total_4

description: Biological Replicate 3 of 5. Total mRNA.


title: HEK293_DRBP76_IP_6

description: Biological Replicate 5 of 5. DRBP76 IP.


title: HEK293_DRBP76_IP_5

description: Biological Replicate 4 of 5. DRBP76 IP.

value: immunoprecipitation of mRNA


title: HEK293_DRBP76_IP_4

description: Biological Replicate 3 of 5. DRBP76 IP.


title: HEK293_Total_1

description: Biological Replicate 1 of 5. Total mRNA.


title: HEK293_Total_2

description: Biological Replicate 2 of 5. Total mRNA.


title: HEK293_DRBP76_IP_2

description: Biological Replicate 2 of 5. DRBP76 IP.


title: HEK293_Mock_IP_6

description: Biological Replicate 5 of 5. Mock IP.


title: 13969149 - det1 dark-1 vs col0 dark-1

status: Public on May 01 2010

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

description: - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light

hyb_protocol: col0 dark-1 Cy5 / det1 dark-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: col0 dark-1

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

growth_protocol: plantlet - MS 1X without sucrose light: 100 micromol/m2/s

extract_protocol: col0 dark-1:10.7ug.

treatment_protocol: Name:dark - growth conditions - light,light:time 5day . after 1 hour exposed to light, seedlinds are grown in dark during 5 days

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

source_name: det1 dark-1

extract_protocol: det1 dark-1:7.35ug.

value: col-0 mutant (det1-1)


title: HEK293_DRBP76_IP_1

description: Biological Replicate 1 of 5. DRBP76 IP.


title: HEK293_Total_5

description: Biological Replicate 4 of 5. Total mRNA.


title: 13969144 - col0 dark-2 vs det1 dark-2

hyb_protocol: det1 dark-2 Cy5 / col0 dark-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: det1 dark-2

source_name: col0 dark-2

extract_protocol: col0 dark-2:13.9ug.


title: 13969147 - det1 light-2 vs col0 light-2

hyb_protocol: col0 light-2 Cy5 / det1 light-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 light-2

extract_protocol: col0 light-2:11ug.

treatment_protocol: no treatment

source_name: det1 light-2

extract_protocol: det1 light-2:11.4ug.


title: 13969145 - det1 dark-2 vs col0 dark-2

hyb_protocol: col0 dark-2 Cy5 / det1 dark-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969142 - col0 dark-2 vs col deet-2

hyb_protocol: col deet-2 Cy5 / col0 dark-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col deet-2

extract_protocol: col deet-2:7ug.

treatment_protocol: Name:deetiolation - growth conditions - light,light:. seedlings are exposed to dark treatment then, are exposed 3 hours to light


title: 13969143 - col deet-2 vs col0 dark-2

hyb_protocol: col0 dark-2 Cy5 / col deet-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969137 - col deet-1 vs col0 dark-1

hyb_protocol: col0 dark-1 Cy5 / col deet-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col deet-1

extract_protocol: col deet-1:6.05ug.


title: 13969141 - det1 light-1 vs col0 light-1

hyb_protocol: col0 light-1 Cy5 / det1 light-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 light-1

extract_protocol: col0 light-1:22ug.

source_name: det1 light-1

extract_protocol: det1 light-1:34.4ug.


title: 13969140 - col0 light-1 vs det1 light-1

hyb_protocol: det1 light-1 Cy5 / col0 light-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: LD_muscle_150d_rep2

source_name: longissimus dorsi, new born lambs, 150 day


title: 13969148 - col0 dark-1 vs det1 dark-1

hyb_protocol: det1 dark-1 Cy5 / col0 dark-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Spi-7, bio rep 5

city: stockholm

first: Jesper

last: Ryge

address: retziusvag 8

department: neuroscience

institute: karolinska institutet

description: Gene expression data from motor neurons of the sacral rat spinal cord 7 days post transection

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45 °C on Affymetrix Rat Genome 230 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated using R and Bioconductor. RMA expression summaries were calculated based on PM intensity values that were normalised (linear quantile plus quantile projection) and background subtracted (global minimization) (Ryge et al, Plos One, 2008). The genes were filtered prior to analysis such that only probe sets annotated in the Ensembl database was included (using biomaRt bioconductor package), so the probe set was reduced from 31099 to 12919.

organism: Rattus norvegicus

source_name: 100-200 motor neurons, sacral spinal cord, 7 days post injury

label_protocol: Motor neurons retrogradely labelled with flourogold injected into the muscle and intra peritoneally 5-7 days prior to cell extraction.

extract_protocol: Spinal cords were snap frozen in liquid nitrogen, cryosectioned into 10 micro meter slices, which were mounted onto POL-membrane metal frame slides (Leica) and fluorescently identied motor neurons were laser microdissected into a collector tube. Total RNA was extrated using the Picopure RNA isolation kit (Arcturus), which were then subject to a two round amplification using the RiboAmp HS RNA amplification kit (Arcturus) according to manufactors instructions. A DNAse treatment was included in the isolation protocol.

treatment_protocol: Injury: Laminectomy of lumbar vertebra L2-L3, spinal cord transect at S2 and 1-2mm of spinal cord tissue removed. Wound closed suturing muscles, muscle fascia and skin separately.  Pain relieved with buprenorfin the first 48 hours.  Spi-0 (Control): Sacral spinal cord removed and immediately frozen.

tag: injury stage

value: Spinal 7 days

tag: gender

value: male

value: Wistar

tag: cell type

value: motor neuron


title: Spi-7, bio rep 2


title: Spi-7, bio rep 3


title: Spi-60, bio rep 8

description: Gene expression data from motor neurons of the sacral rat spinal cord 60 days post transection

source_name: 100-200 motor neurons, sacral spinal cord, 60 days post injury

value: Spinal 60 days


title: 13969136 - col0 dark-1 vs col deet-1

hyb_protocol: col deet-1 Cy5 / col0 dark-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Spi-60, bio rep 4


title: Spi-60, bio rep 2


title: Spi-60, bio rep 3


title: Spi-60, bio rep 5


title: Spi-60, bio rep 7


title: Spi-60, bio rep 6


title: wt_ko_rep3

source_name: heart myo-/- vehicle


title: Spi-7, bio rep 4


title: Spi-60, bio rep 1


title: Spi-21, bio rep 7

description: Gene expression data from motor neurons of the sacral rat spinal cord 21 days post transection

source_name: 100-200 motor neurons, sacral spinal cord, 21 days post injury

value: Spinal 21 days


title: Spi-7, bio rep 1


title: Spi-2, bio rep 1

description: Gene expression data from motor neurons of the sacral rat spinal cord 2 days post transection

source_name: 100-200 motor neurons, sacral spinal cord, 2 days post injury

value: Spinal 2 days


title: Spi-21, bio rep 4


title: Spi-2, bio rep 5


title: Spi-2, bio rep 4


title: Spi-2, bio rep 3


title: Spi-21, bio rep 8


title: Spi-2, bio rep 2

source_name: 101-200 motor neurons, sacral spinal cord, 2 days post injury


title: Spi-21, bio rep 2


title: Spi-21, bio rep 3


title: Spi-21, bio rep 6


title: Spi-21, bio rep 5


title: Spi-0, bio rep 1

description: Gene expression data from motor neurons of the sacral rat spinal cord 0 days post transection (Control)

source_name: 100-200 motor neurons, sacral spinal cord, 0 days post injury (Control)

value: Spinal 0 days (Control)


title: Spi-0, bio rep 3


title: Spi-21, bio rep 1


title: b/b + Fe 6 days Top 3_Sample44

city: Shreveport

first: Kwo-yih

last: Yeh

state: LA

address: 1501 Kings Highway

department: Department of Medicine

institute: LSU Health Science Center

description: b/b + Fe 6 days Top 3_Sample44

hyb_protocol: Biotinylated cRNA was transcribed, purified, fragmented and hybridized to the Rat Genome 230 2.0 Array (Affymetrix).  Hybed according to standard Affymetrix protocol.

scan_protocol: After washing and staining, the arrays were scanned using a GeneChip Scanner 3000.

data_processing: Pixel intensities were measured, expression signals were analyzed.  Data mining and statistical analyses were performed with Data Mining Tool ver 3.0 (Affymetrix) algorithms.

source_name: a 1-cm duodenal segment 1 cm distal from the pylorus was cryostat sectioned at the right angle to the crypt-villus axis and the sections representing the top one-third of villus (top) and the bottom one-third of the villus were pooled for RNA isolation

label_protocol: The RNA was used to synthesize double-stranded cDNA using a T7-(dT)24 primer and the Superscript cDNA Synthesis Kit (Invitrogen, Carlsbad, CA).  Labeled according to standard Affymetrix protocol.

extract_protocol: RNA isolated with Tri Reagent (Molecular Research Center, Inc).

treatment_protocol:
Twelve one-month old ++ rats were separated into 3 groups of four rats each. Group 1 rats (samples 1-8) were fed a normal diet and served as control animals.  Group 2 (samples 9-16) and Group 3 rats (samples 17-22) were fed a low iron diet and bled 2-3 ml every three days for 4 weeks and served as iron deficient rats (low-iron). Group 3 rats, of which one rat died during anesthesia while undergoing phlebotomy, were fed iron supplementation in drinking water (50 µM Ferric ammonium citrate) for the three days before sacrifice (iron-fed).
For the study of Belgrade rats, eleven bb rats were divided into 3 groups with the 4 rats in Group 1 (samples 23-30) maintained on a normal diet, the 4 rats in Group 2 (samples 31-38) fed iron for 3 days prior to sacrifice, and the 3 rats in Group 3 (samples 39-44) fed iron for 6 days prior to sacrifice.  All procedures for the bb rats were the same as described above for the ++ rats.  An additional ++ rat (samples 45-46) was similarly analyzed in a separate experiment.

tag: Belgrade strain


title: Spi-0, bio rep 4


title: Spi-0, bio rep 2


title: b/b + Fe 6 days Top 1_Sample40

description: b/b + Fe 6 days Top 1_Sample40


title: +/+ Lower crypt_Sample45

description: +/+ Lower crypt_Sample45

tag: Wistar strain


title: b/b + Fe 6 days Bottom 3_Sample43

description: b/b + Fe 6 days Bottom 3_Sample43


title: b/b + Fe 6 days Bottom 2_Sample41

description: b/b + Fe 6 days Bottom 2_Sample41


title: +/+ Upper crypt_Sample46

description: +/+ Upper crypt_Sample46


title: b/b + Fe 6 days Bottom 1_Sample39

description: b/b + Fe 6 days Bottom 1_Sample39


title: b/b + Fe 3 Days Top 2_Sample34

description: b/b + Fe 3 Days Top 2_Sample34


title: Spi-2, bio rep 6


title: b/b Top 4_Sample30

description: b/b Top 4_Sample30


title: b/b Top 1_Sample24

description: b/b Top 1_Sample24


title: b/b + Fe 6 days Top 2_Sample42

description: b/b + Fe 6 days Top 2_Sample42


title: b/b Top 3_Sample28

description: b/b Top 3_Sample28


title: b/b Bottom 3_Sample27

description: b/b Bottom 3_Sample27


title: b/b + Fe 3 Days Top 3_Sample36

description: b/b + Fe 3 Days Top 3_Sample36


title: b/b + Fe 3 Days Bottom 1_Sample31

description: b/b + Fe 3 Days Bottom 1_Sample31


title: b/b Top 2_Sample26

description: b/b Top 2_Sample26


title: b/b Bottom 4_Sample29

description: b/b Bottom 4_Sample29


title: b/b + Fe 3 Days Top 1_Sample32

description: b/b + Fe 3 Days Top 1_Sample32


title: b/b + Fe 3 Days Top 4_Sample38

description: b/b + Fe 3 Days Top 4_Sample38


title: b/b + Fe 3 Days Bottom 3_Sample35

description: b/b + Fe 3 Days Bottom 3_Sample35


title: b/b Bottom 1_Sample23

description: b/b Bottom 1_Sample23


title: b/b Bottom 2_Sample25

description: b/b Bottom 2_Sample25


title: Fe-repletion (3d) Top 3_Sample22

description: Fe-repletion (3d) Top 3_Sample22


title: b/b + Fe 3 Days Bottom 4_Sample37

description: b/b + Fe 3 Days Bottom 4_Sample37


title: b/b + Fe 3 Days Bottom 2_Sample33

description: b/b + Fe 3 Days Bottom 2_Sample33


title: Fe-repletion (3d) Top 2_Sample20

description: Fe-repletion (3d) Top 2_Sample20


title: Fe-repletion (3d) Bottom 1_Sample17

description: Fe-repletion (3d) Bottom 1_Sample17


title: Fe-repletion (3d) Top 1_Sample18

description: Fe-repletion (3d) Top 1_Sample18


title: Iron-def Top 4_Sample16

description: Iron-def Top 4_Sample16


title: Fe-repletion (3d) 3 Bottom_Sample21

description: Fe-repletion (3d) 3 Bottom_Sample21


title: Iron-def Top 3_Sample14

description: Iron-def Top 3_Sample14


title: Iron-def Top 2_Sample12

description: Iron-def Top 2_Sample12


title: Iron-def Top 1_Sample10

description: Iron-def Top 1_Sample10


title: Fe-repletion (3d) 2 Bottom_Sample19

description: Fe-repletion (3d) 2 Bottom_Sample19


title: Iron-def Bottom 4_Sample15

description: Iron-def Bottom 4_Sample15


title: Tumor-her2pos-3

status: Public on Apr 29 2010

city: Galway

first: Paul

last: Geeleher

address: University Road

department: Mathematics

country: Ireland

institute: National University of Ireland, Galway

hyb_protocol: Labelled RNA was hybridized to LNA™ miChip array platforms (Exiqon version 7, containing 453 miRNA sequences) over 16 hours at 54°C using a rotational hybridization chamber. Arrays were subsequently washed in varying stringency washes, rinsed, drained and scanned using a GenePix 4000AL laser scanner (Axon Instruments, Foster City, CA, USA).

scan_protocol: Images generated by the GenePix 4200AL scanner

data_processing: Background subtraction and quantiles normalization were performed in R and Bioconductor using the Limma package.

source_name: ductal

label_protocol: Briefly, 5.5 μg total RNA was 3' ligated to Cy3 dye-linked 2'-deoxyuridine-5'-triphosphate using T4 RNA ligase (catalogue number 2141; Ambion, Woodward, Austin, TX, USA), in the presence of RNase inhibitor (catalogue number 2682; Ambion, Woodward, Austin, TX, USA), ATP (Grade I, catalogue number A2383-1G; Sigma-Aldrich Corp. St. Louis, MO, USA), and polyethylene glycol 50% aqueous solution (PEG 6000, catalogue number 81304; Fluka, Sigma-Aldrich Corp, St. Louis, MO, USA). Following a 12-hour to 16-hour incubation, labelled RNA was washed in ethanol, and precipitated in sodium acetate (3 M) using linear acrylamide.

extract_protocol: Depending on whether samples were destined for microarray or RQ-PCR analysis, slightly modified RNA extraction methods were employed. For the microarray experiment, total RNA was required. Breast tumour tissue (50 to 100 mg) was homogenized using a bench-top homogenizer (Polytron® PT1600E; Kinematica AG, Littau-Luzem, Switzerland) in 1 ml QIAzol lysis reagent (Qiagen, Crawley, UK). Total RNA was isolated from homogenized breast tissue using the RNeasy® Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. For RQ-PCR, miRNA was selectively isolated from approximately 100 mg tissue. Large RNA fractions (> 200 nucleotides) and small RNA fractions (< 200 nucleotides) were isolated separately using the RNeasy Plus Mini Kit and RNeasy MinElute® Cleanup Kit (Qiagen) according to the supplementary protocol: purification of miRNA from animal cells. The concentration and purity of total RNA were assessed using a NanoDrop™ 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was assessed using the RNA 6000 Nano LabChip Series II Assay with the 2100 Bioanalyzer System (Agilent Technologies, Palo Alto, CA, USA). Electropherograms and gel-like images were evaluated using the Agilent 2100 Expert software (version B.02.03; Agilent Technologies, Palo Alto, CA, USA), which generated the RNA integrity number to ensure that only RNA of good integrity was used in these experiments (RNA integrity number range, 7.6 to 9.5). The miRNA concentration and purity were also assessed by NanoDrop™ 1000 spectrophotometry. Small miRNA-enriched fractions were analysed using the Small RNA Assay on the Agilent 2100 Bioanalyzer.

value: ductal breast cancer

tag: genome/variation


title: Tumor-her2pos-2


title: Tumor-her2pos-4


title: Tumor-her2neg-3


title: Iron-def Bottom 3_Sample13

description: Iron-def Bottom 3_Sample13


title: +/+ Bottom 4_Sample7

description: +/+ Bottom 4_Sample7


title: Iron-def Bottom 1_Sample9

description: Iron-def Bottom 1_Sample9


title: Tumor-her2neg-1


title: Tumor-her2neg-2


title: +/+ top 3_Sample6

description: +/+ top 3_Sample6


title: 13300758 - drn-like vs ler

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

description: DRN targets

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

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

source_name: ler

growth_protocol: seed - Media=soil	 Temperature=23° C	 Light=long day

tag: ecotype

value: landsberg erecta

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

value: ovules containing heart-stage/torpedo-stage embryos

source_name: drn-like

value: mutant (drn-like)


title: 13189601 - drn- vs col

description: DRN targets

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

source_name: col

value: columbia

source_name: drn-

value: mutant (drn-)


title: 13189600 - col vs drn-

description: DRN targets

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


title: +/+ Bottom 2_Sample3

description: +/+ Bottom 2_Sample3


title: +/+ Top 4_Sample8

description: +/+ Top 4_Sample8


title: +/+ Top 2_Sample4

description: +/+ Top 2_Sample4


title: Iron-def Bottom 2_Sample11

description: Iron-def Bottom 2_Sample11


title: +/+ Bottom 1_Sample1

description: +/+ Bottom 1_Sample1


title: +/+ Bottom 3_Sample5

description: +/+ Bottom 3_Sample5


title: 13300759 - ler vs drn-like

description: DRN targets

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


title: +/+ Top 1_Sample2

description: +/+ Top 1_Sample2


title: Tyk2-/-, mouse 2, 0 LPS

status: Public on Apr 01 2010

city: Vienna

first: Claus

last: Vogl

state: Vienna

address: Veterinaerplatz 1

department: Biomedical Sciences

country: Austria

institute: University of Veterinary Medicine, Vienna

hyb_protocol: CodeLink protocol: Streptavidin-Cy5 staining

scan_protocol: GenePix Array scanner 4000B; GenePix Pro 4.0 (Axon Instruments, Inc.)

data_processing: CodeLink Expression Analysis software (GE Healthcare); values below 25 and unannotated genes filtered out; log transformed values adjusted to mean of zero and standard deviation of one within each sample

source_name: peritoneal macrophage

label_protocol: CodeLink protocol: from ds cDNA in vitro transcription and biotin labelling of cRNA

growth_protocol: Peritoneal macrophages prepared from three threereplicates of three wild type and three Tyk2 deficient mice

extract_protocol: TRiZOL

treatment_protocol: 100 ng/ml LPS (E. coli serotype O55:B5, Sigma) for 6 hours, or untreated

tag: time point

value: 0 LPS

tag: genotype

value: peritoneal macrophage


title: WT, mouse 3, 0 LPS

value: Wt


title: Tyk2-/-, mouse 2, 6h LPS

value: 6h LPS


title: Tyk2-/-, mouse 3, 6h LPS


title: Tyk2-/-, mouse 3, 0 LPS


title: WT, mouse 2, 6h LPS


title: Tyk2-/-, mouse 1, 0 LPS


title: Tyk2-/-, mouse 1, 6h LPS


title: WT, mouse 3, 6h LPS


title: 13832882 - Flower Thellungiella vs Leaf Thellungiella

description: Suitability of CATMA for the analysis of the transcriptome of Thellungiella halophila

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

organism: Eutrema halophilum

source_name: Leaf Thellungiella

growth_protocol: leaf - Media=mold + perlite; Temperature=22°C; Light=16h light, 8h night

extract_protocol: Leaf Thellungiella:5.5ug.

value: Leaf

tag: strain

value: Thellungiella halophila

value: boyes (boyes et al. plant cell 2001):6.10

source_name: Flower Thellungiella

growth_protocol: pistil,stamen - Media=mold + perlite; Temperature=22°C; Light=16h light, 8h night

extract_protocol: Flower Thellungiella:6.41ug.

value: Flower


title: 13832879 - Leaf Thellungiella vs Flower Thellungiella

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

tag: developmental stage


title: 13852113 - Leaf Arabidopsis vs Flower Arabidopsis

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

source_name: Flower Arabidopsis

extract_protocol: Flower Arabidopsis:14.39ug.

tag: tissue

value: Arabidopsis thaliana

value: Columbia

source_name: Leaf Arabidopsis

extract_protocol: Leaf Arabidopsis:4.65ug.


title: WT, mouse 2, 0 LPS


title: 13832877 - Flower Arabidopsis vs Leaf Arabidopsis

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


title: 13852075 - WT 4 weeks 2 vs cb1-1 4 weeks 2

description: What is the physiological function of cytochromes b561 in arabidopsis thaliana

hyb_protocol: cb1-1 4 weeks 2 Cy5/WT 4 weeks 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: cb1-1 4 weeks 2

growth_protocol: leaf - Media=soil; hygrometry=70% humidity; Temperature=22°C

value: Cytb1 -/-

value: boyes (boyes et al. plant cell 2001):1.07

source_name: WT 4 weeks 2

extract_protocol: WT 4weeks 2:20.47ug.

value: wild type


title: 13852769 - cb1-1 6 weeks 2 vs WT 6 weeks 2

hyb_protocol: WT 6 weeks 2 Cy5/cb1-1 6 weeks 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT 6 weeks 2

extract_protocol: WT 6weeks 2:40.59ug.

source_name: cb1-1 6 weeks 2


title: WT, mouse 1, 0 LPS


title: WT, mouse 1, 6h LPS


title: 13852767 - cb1-1 6 weeks 1 vs WT 6 weeks 1

hyb_protocol: WT 6 weeks 1 Cy5/cb1-1 6 weeks 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT 6 weeks 1

extract_protocol: WT 6weeks 1:79.13ug.

source_name: cb1-1 6 weeks 1


title: 13852766 - WT 6 weeks 1 vs cb1-1 6 weeks 1

hyb_protocol: cb1-1 6 weeks 1 Cy5/WT 6 weeks 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852072 - WT 4 weeks 1 vs cb1-1 4 weeks 1

hyb_protocol: cb1-1 4 weeks 1 Cy5/WT 4 weeks 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: cb1-1 4 weeks 1

source_name: WT 4 weeks 1

extract_protocol: WT 4weeks 1:33.98ug.


title: 13852073 - cb1-1 4 weeks 1 vs WT 4 weeks 1

hyb_protocol: WT 4 weeks 1 Cy5/cb1-1 4 weeks 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852076 - cb1-1 4 weeks 2 vs WT 4 weeks 2

hyb_protocol: WT 4 weeks 2 Cy5/cb1-1 4 weeks 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852768 - WT 6 weeks 2 vs cb1-1 6 weeks 2

hyb_protocol: cb1-1 6 weeks 2 Cy5/WT 6 weeks 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer (20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 75% epiboly

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

country: Netherlands

institute: University of Amsterdam

scan_protocol: See Agilent Two-Color Microarray Based Gene Expression Analysis (v5.5) Agilent G2565BA scanner Scans performed at 5 um and XDR

data_processing:
Median signals (gMedianSignal and rMedianSignal) were log2 transformed. Ratios were obtained by subtraction;
log2(gMedianSignal)-log2(rMedianSignal).

organism: Danio rerio

source_name: 75% epiboly

label_protocol: Indirectly via Amino-Allyl-dUTP

extract_protocol:
Qiazol & RNeasy (Qiagen)
Amino-Allyl MessageAmp II (Ambion)

value: AB

source_name: Common reference pooled samples


title: 128-cell

description: See Agilent Two-Color Microarray Based Gene Expression Analysis (v5.5)


title: Dome

hyb_protocol: See Agilent Two-Color Microarray Based Gene Expression Analysis (v5.5)

source_name: Dome


title: Shield

source_name: Shield


title: 16-cell


title: Norm03

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

description: miRNA profiling in normal adrenal cortex

hyb_protocol: Hybridization was performed according to the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565A) at 100% and 5% sensitivity settings. Agilent Feature Extraction software version 8.1 was used for image analysis.

data_processing: No normalization was applied to signal intensity data.

source_name: Normal adrenal

label_protocol: RNA was labelled according to the manufacturer's instructions.

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen).

value: Adrenal cortex

tag: disease state

value: normal


title: ACT25

description: miRNA profiling in ACT samples

source_name: ACT

value: adrenocortical tumor


title: Norm02


title: Norm04


title: ACT23

description: miRNA profiling in ACT samples


title: Norm01


title: Norm05


title: ACT20

description: miRNA profiling in ACT samples


title: ACT21

description: miRNA profiling in ACT samples


title: ACT24

description: miRNA profiling in ACT samples


title: ACT22

description: miRNA profiling in ACT samples


title: Sphere

source_name: Sphere


title: Semi-single embryo 3 vs Common reference 20 embryos

source_name: Semi-single 3

tag: stage

value: germ ring

source_name: Common reference 20 embryos


title: Single embryo 3 vs Common reference 20 embryos

source_name: Single 3


title: ACT19

description: miRNA profiling in ACT samples


title: Single embryo 2 vs Common reference 20 embryos

scan_protocol: See Agilent Two-Color Microarray-Based Gene Expression Analysis (v5.5) Agilent G2565BA scanner Scans performed at 5 um and XDR

source_name: Single 2


title: Semi-single embryo 2 vs Common reference 20 embryos

source_name: Semi-single 2


title: Semi-single embryo 4 vs Common reference 20 embryos

source_name: Semi-single 4


title: Germ ring

source_name: Germ ring


title: Semi-single embryo 1 vs Common reference 20 embryos

description: See Agilent Two-Color Microarray-Based Gene Expression Analysis (v5.5)

source_name: Semi-single 1


title: Single embryo 1 vs Common reference 20 embryos

source_name: Single 1


title: 8-somite


title: ACT18

description: miRNA profiling in ACT samples


title: Single embryo 4 vs Common reference 20 embryos

source_name: Single 4


title: ACT15

description: miRNA profiling in ACT samples


title: ACT16

description: miRNA profiling in ACT samples


title: ACT14

description: miRNA profiling in ACT samples


title: ACT13

description: miRNA profiling in ACT samples


title: ACT11

description: miRNA profiling in ACT samples


title: ACT17

description: miRNA profiling in ACT samples


title: ACT12

description: miRNA profiling in ACT samples


title: ACT09

description: miRNA profiling in ACT samples


title: ACT08

description: miRNA profiling in ACT samples


title: ACT07

description: miRNA profiling in ACT samples


title: ACT10

description: miRNA profiling in ACT samples


title: ACT06

description: miRNA profiling in ACT samples


title: ACT04

description: miRNA profiling in ACT samples


title: ACT05

description: miRNA profiling in ACT samples


title: ACT03

description: miRNA profiling in ACT samples


title: ACT01

description: miRNA profiling in ACT samples


title: ACT02

description: miRNA profiling in ACT samples


title: Rugose ΔvpsT pBAD-vpsT-WT

city: Santa Cruz

first: Nicholas

middle: Jun

last: Shikuma

state: CA

address: 1156 High St.

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

description: ch2 organism is reference for comparison to ch1 organism (treatment sample)

hyb_protocol: Dye-coupled test samples were mixed with the corresponding reference sample and dried. Amine silane slides containing 70-mer oligonucleotides, representing most of the open reading frames present in the V. cholerae N16961 genome, were UV cross-linked at 250 mJ and prehybridized in a solution containing 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin for at least 45 min at 42°C. The hybridization mix was prepared by resuspending dried samples in a solution containing 15 µg salmon sperm DNA, 15 µg tRNA, 3x SSC, and 0.1% sodium dodecyl sulfate. Concentrated hybridization mix was applied to the slides and incubated at 65°C for 12 to 20 h.

scan_protocol: Slides were washed, dried, and scanned using an Axon scanner to determine the fluorescence in each open reading frame-specific spot. The raw data were obtained by using the software package GenePix 4.1 (Axon).

data_processing: Normalized signal ratios were obtained with LOWESS print-tip normalization using the Bioconductor packages (http://www.bioconductor.org) in R environment. Differentially regulated genes were determined (with three biological and two technical replicates for each data point) with the significance analysis of microarrays (SAM) package using twofold differences in gene expression and a 3% false discovery rate as a cutoff value.

label: Cy3, Cy5

organism: Vibrio cholerae

source_name: Rugose ΔvpsT pBAD-vpsT-WT

label_protocol: RNA samples from test and reference samples were used in a reverse transcription reaction as follows: 3 µg of RNA and 5 µg of random hexamers were denatured at 80°C for 8 min and then chilled on ice for 5 min. The reaction mixture, containing first-strand buffer, 0.01 M dithiothreitol, aminoallyl deoxynucleoside triphosphate labeling mix with amino acid-dUTP in a 3 (dTTP):2 (amino acid-dUTP) ratio, and 400 U SuperScript III (Invitrogen), was added to cooled samples and incubated at 42°C for 3 to 4 h. The cDNA-RNA mixture, samples were incubated at 65°C for 10 min in the presence of 100 mM NaOH and 10 mM EDTA. Reactions were neutralized by the addition of 1 M HEPES, pH 7.0, at a final concentration of 0.5 M HEPES. cDNA was purified from the reactions using a PCR purification kit with phosphate wash and phosphate elution buffers and dried. Cleaned and dried samples were resuspended in freshly prepared 50 mM Na-bicarbonate buffer, pH 9.0. One vial of Cy3/Cy5 fluor was mixed with each sample and incubated for 1 h in the dark at room temperature. Unincorporated dye molecules were removed using PCR purification kit. Dye incorporation and cDNA concentrations were determined by measuring optical densities at 260, 550, and 650 nm.

growth_protocol: V. cholerae cells were grown aerobically overnight in LB in the absence of arabinose.  Cultures were diluted 1:500 in fresh media with the inducer arabinose (0.1%) and grown aerobically at 30˚C with shaking at 200 rpm to an OD600 of 0.3 to 0.4.

extract_protocol: Total RNA was isolated from the cell pellets according to the manufacturer’s instructions (Invitrogen).  Contaminating DNA was removed by incubating RNA with RNase-free DNase I (Ambion), and an RNeasy Mini kit (QIAGEN) was used to clean up RNA after DNase digestion.

treatment_protocol: Two ml aliquots of cultures were collected by centrifugation for 2 min at room temperature.  Cell pellets were immediately resuspended in 1 ml Trizol reagent (Invitrogen) and stored at –80˚C.

value: Rugose V. cholerae cells with an in-frame deletion of vpsT (VCA0952)

source_name: Rugose ΔvpsT pBAD


title: Rugose ΔvpsT pBAD-vpsT-I141E

source_name: Rugose ΔvpsT pBAD-vpsT-I141E


title: Rugose ΔvpsT pBAD-vpsT-R134A

source_name: Rugose ΔvpsT pBAD-vpsT-R134A


title: Rugose ΔvpsT pBAD-vpsT-M17D

source_name: Rugose ΔvpsT pBAD-vpsT-M17D


title: Rugose ΔvpsT pBAD-vpsT-D60A

source_name: Rugose ΔvpsT pBAD-vpsT-D60A


title: Rugose ΔvpsT pBAD


title: JR1

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden

data_processing: Microarray Suite version 5.0 (MAS 5.0).

source_name: Vascular smooth muscle cells

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

growth_protocol: Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.

extract_protocol: Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.

tag: stress/flow condition

value: Static control

tag: sample pairing


title: Muscle.HFD.2

status: Public on Mar 31 2010

city: Bar Harbor

first: Rachael

middle: S

last: Hageman

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: HFD: biological replicate 2

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Probe set data, mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package

data_processing: log2 transformation quantile normalization

source_name: Muscle: HFD

label_protocol: Standard Illumina hybridization protocol

extract_protocol: Total RNA was isolated by TRIzolTM Plus after tissue homogenization (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocols. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Total RNA was then reverse transcribed followed by second strand cDNA synthesis. An in vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion, Austin TX). 1.5µg biotin-labeled cRNA was hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.

value: Muscle

tag: treatment

value: high fat diet


title: JR5

scan_protocol: Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden

value: Fluid shear stress


title: JR2


title: Liver.HFD.6

description: HFD: biological replicate 6

source_name: Liver: HFD

value: Liver


title: Muscle.SBD.4

description: SBD: biological replicate 4

source_name: Muscle: SBD

value: standard breeding diet


title: JR6


title: Muscle.SBD.5

description: SBD: biological replicate 5


title: JR3


title: Liver.HFD.3

description: HFD: biological replicate 3


title: Muscle.SBD.3

description: SBD: biological replicate 3


title: Muscle.HFD.5

description: HFD: biological replicate 5


title: Muscle.SBD.2

description: SBD: biological replicate 2