title: spo70D_SK1_t=9hr

description: Analysis used meiotic 9h WT SK1 RNA as control for comparison to the spo70D_SK1 RNA sample taken at 9h during the meiotic time course.

treatment_protocol: Aliquots are taken at 9h for RNA preparation, spun down at room temperature, flash frozen in liquid nitrogen and stored at -80°C.

value: spo70D mutant

source_name: WT_SK1 meiosis 9h

value: WT_SK1 meiosis 9h


title: spo22D_SK1_t=9hr

status: Public on Apr 05 2011

type: RNA

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

country: USA

institute: UCSC

description: Analysis used meiotic 9h WT SK1 RNA as control for comparison to the spo22D_SK1 RNA sample taken at 9h during the meiotic time course.

hyb_protocol: Two color hybridization mixes were applied to the microarray under a LifterSlip and incubated in aluminum hybridization chambers overnight in a 63 degree water bath.  Hybridized slides were washed in SSC/SDS containing buffers.

scan_protocol: Arrays were scanned using an Axon 4000B Data was quantitated using GenePix Pro 6.1 (Axon)

data_processing: Log2 ratios were calculated from background subtracted median intensities and were LOESS normalized and summarized using Bioconductor

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: Amino-allyl dUTP labeled first strand cDNA was reverse transcribed from 10ug of total RNA primed with oligo dT and random primers.  cDNA was then coupled to Cy3 or Cy5 esters (GE Healthcare).  Dye swapped hybridizations were performed for each sample pair.

growth_protocol: To prepare cells for synchronous meiosis, cells are streaked from frozen stocks to YP-glycerol (3%) plates, and then single colonies from glycerol are streaked to YPD plates. After two days on YPD, a single colony is inoculated into 5mL of YPD, and 30 hours later, 50mL of YPA (1% potassium acetate, 1% yeast extract, 2% peptone) is inoculated to OD600 = 0.25 and shaken for 14 hours. After growth in YPA, cells are washed with water and suspended in SPM (1% potassium acetate, 0.02% raffinose), defining time zero of meiosis.

extract_protocol: Meitoic RNA is exracted according to protocol described in Rio DC, Ares MJr, Hannon GJ, Nilsen TW. 2010. RNA: A laboratory manual. Cold Spring Harbor Laboratory Press.

tag: strain

tag: genotype/variation

value: spo22D mutant

tag: meiotic time point

tag: reference


title: [E-MTAB-366] Chicken developmental stage HH6 2

city: Kobe

first: Naoki

last: Irie

state: Hyogo

address: 2-2-3 Minatojima-minami Chuo-ku

country: Japan

institute: RIKEN Center for Developmental Biology

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5, default settings

label: biotin

organism: Gallus gallus

source_name: whole embryo except yolk and amnion, developmental stage HH6

label_protocol: 3' IVT Labeling

growth_protocol: Parent chickens grown by Post Harvest  Free Corn. Incubation at 37.5 degrees celsius.

extract_protocol: Total RNA extraction by RNeasy Lipid Tissue Mini Kit.

tag: biosource provider

value: local farmer (Shiroyama Keien)  in Japan

tag: developmental stage

tag: genotype

value: wild type

tag: organism part

value: whole embryo except yolk and amnion

tag: Sex

value: mixed sex

tag: strain or line

value: Nera


title: mer3D_SK1_t=9hr

description: Analysis used meiotic 9h WT SK1 RNA as control for comparison to the mer3D_SK1 RNA sample taken at 9h during the meiotic time course.

value: mer3D mutant


title: [E-MTAB-366] Chicken developmental stage HH6 1


title: [E-MTAB-366] Chicken developmental stage HH8 1

source_name: whole embryo except yolk and amnion, developmental stage HH8


title: Normal human mammary fibroblast cells genotype 240 (MeDIP)

type: genomic

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

description: Biological replicate 3 of 3. Human mammary fibroblast cells.

hyb_protocol: Combined Cy3 and Cy5 labeled samples were vaccum concentrated to volume of 91.5 µl.  12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 26 µl of Agilent blocking agent (10x) and 130 µl of Agilent hybridization buffer (2x) were added.  Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then used for microarray hybridization for 28h at 65 oC.  After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm)

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package.  Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy.  The RG object was transformed to an MA object and M values were again loess normalized between arrays.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human mammary fibroblast cells

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction.  Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes respectively. DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min.  10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C.  Labeled targets were purified using the QIAquick PCR purification kit (Qiagen).  The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).  The typical yield was 200 - 300 pmol of dye incorporated in 7 - 8 ug of DNA per sample.

growth_protocol: HMEC were maintained in M87A medium supplemented with oxytocin and cholera toxin at 0.5 ng/ml, HMF were grown in DMEM/F12 with 10% FBS.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
immunoprecipitation protocol: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 ul of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

tag: cell line

value: HMF 240L

tag: tissue

value: mammary gland

tag: sample type

value: Immunoprecipitated DNA

tag: antibody

value: anti-Methylcytosine

value: Input DNA


title: Normal human mammary epithelial cells genotype 48 (MeDIP)

description: Biological replicate 2 of 3. Human mammary epithelial cells.

source_name: Human mammary epithelial cells

value: HMEC 48RT


title: [E-MTAB-366] Chicken developmental stage HH4 1

source_name: whole embryo except yolk and amnion, developmental stage HH4


title: Cre replicate 3

city: Saint-Hyacinthe

first: Derek

last: Boerboom

state: QC

address: 3200 Sicotte

department: Département de biomédecine Vétérinaire

country: Canada

institute: Université de Montréal, Faculty of veterinary medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Microarray data were analyzed using FlexArray 1.3 software (Génome Québec, Montreal, Qc, Canada)

The raw data were processed the following way:
Background correction: Force positive (add constant)
Variance Stabilization: VST
Normalization: Robust spline normalization

This was followed by a t-test

label: Biotin

organism: Mus musculus

source_name: Sertoli cells

label_protocol: Performed by Génome Québec (Montreal, Qc, Canada)

growth_protocol: Sertoli cells were obtained from 3wks-old Ctnnb1(tm1Mmt/tm1Mmt) mice. Testes were decapsulated under the dissection microscope. The seminiferous tubules were pooled and washed with phosphate-buffered saline (PBS) three times. The tubules then were incubated with 2 mg/ml collagenase I (Sigma) and 0.5 mg/ml DNase I (sigma) in DMEM for 30 minutes at 37°C on a shaker. The tubules were then washed twice with DMEM and further digested with 2 mg/ml collagenase I, 0.5 mg/ml DNase I and 1 mg/ml hyaluronidase type III (Sigma) for 20-30 minutes at 37°C on a shaker. The tubules were allowed to settle and were washed twice with DMEM. The tubules were further digested with 2 mg/ml collagenase I, 0.5 mg/ml DNase I, 2 mg/ml hyaluronidase, 1 mg/ml trypsin for 40-60 minutes at 37°C on a shaker. The dispersed cells were then washed twice with DMEM and placed into culture dishes in DMEM containing 10% fetal calf serum and incubated at 37°C and 5% CO2.

extract_protocol: Rneasy mini kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instruction

treatment_protocol: Cells were infected with adenoviruses to express eGFP or Cre for 24h in serum-free media

tag: cell type

value: Sertoli cells

tag: adenovirus infection

value: Cre


title: Normal human mammary epithelial cells genotype 240 (MeDIP)

description: Biological replicate 3 of 3. Human mammary epithelial cells.

value: HMEC 240LB


title: mer2D_SK1_t=9hr

description: Analysis used meiotic 9h WT SK1 RNA as control for comparison to the mer2D_SK1 RNA sample taken at 9h during the meiotic time course.

value: mer2D mutant

value: WT_SK1 meiosis 9h


title: mer1D_SK1_t=9hr

description: Analysis used meiotic 9h WT SK1 RNA as control for comparison to the mer1D_SK1 RNA sample taken at 9h during the meiotic time course.

value: mer1D mutant


title: mer1D_SK1_t=11hr_B

description: Analysis used Reference Pool WT SK1 RNA as control for comparison to the mer1D_SK1 samples taken at 0h, 0.5h, 2h, 5h, 7h, 9h, 11h during the meiotic time course.

treatment_protocol: Aliquots are taken at 0h, 30min, 2h, 5h, 7h, 9h, and 11h for RNA preparation, spun down at room temperature, flash frozen in liquid nitrogen and stored at -80°C.

source_name: REFERENCE POOL

value: Reference pool WT RNA comprised of 50% time zero RNA plus 10% each of time 2 hours, 5, hours, 7 hours, 9 hours and 11 hours


title: mer1D_SK1_t=9hr_B


title: [E-MTAB-366] Chicken developmental stage HH2 1

source_name: whole embryo except yolk and amnion, developmental stage HH2

value: local farmer (Shiroyama Keien)  in Japan

value: wild type

value: whole embryo except yolk and amnion


title: Normal human mammary epithelial cells genotype 184 (MeDIP)

description: Biological replicate 1 of 3. Human mammary epithelial cells.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
immunopreciptiation protocol: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 ul of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: HMEC 184D


title: GFP replicate 3

value: GFP


title: [E-MTAB-366] Chicken developmental stage HH1 2

source_name: whole embryo except yolk and amnion, developmental stage HH1

value: mixed sex

value: Nera


title: GFP replicate 2


title: GFP replicate 1


title: [E-MTAB-366] Chicken developmental stage HH2 2


title: HdIV2_13676854

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

description:
Hemo-PBS2_Cy3 vs Hemo-HdIV2_Cy5
Date:2007/12/13

hyb_protocol: Corning Pronto : 500.0 ng at 42 degree_C during 12 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : none, Intraslide norm. : loess, Background norm. : subtract, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Spodoptera frugiperda

label_protocol: Promega Chipshot labeling

extract_protocol: Qiagen

tag: label

tag: extract

tag: sample

value: hemocyte


title: HdIV2_13676786

description:
Hemo-HdIV2_Cy3 vs Hemo-PBS2_Cy5
Date:2007/12/13

data_processing: Interslide norm. : none, Intraslide norm. : loess, Background norm. : subtract, Software used : rscript --> VALUE data obtained from log of processed Green signal/processed Red signal.


title: mer1D_SK1_t=5hr_B

tag: strain

tag: genotype/variation

tag: meiotic time point


title: mer1D_SK1_t=2hr_B

tag: reference


title: mer1D_SK1_t=7hr_B


title: mer1D_SK1_t=0.5hr_B


title: HdIV1_13676785

description:
Hemo-HdIV1_Cy3 vs Hemo-PBS1_Cy5
Date:2007/12/13


title: Melanoma culture M010119

city: Zürich

first: Daniel

middle: Simon

last: Widmer

address: Gloriastrasse 31

department: Dermatology

country: Switzerland

institute: University Hospital Zürich

hyb_protocol: Hybridisation was done with a GeneChip Hybridisation oven 640

scan_protocol: Washing and scanning was done on the GeneChip Fluidics Station 450, the scanner we used was the Affymetrix GeneChip scanner 7G

data_processing: The data was analyzed with GeneSpring GX7.3 (RMA)

source_name: Skin metastasis shoulder

label_protocol: The biotin-labelled RNA was hybridized to Affymetrix HG-U133 plus 2.0 oligonucleotide microarrays

growth_protocol: RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum, 5 mM glutamine, 1 mM sodium pyruvate, 5% CO2.

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

tag: tumor stage

tag: braf

tag: nras

value: wt

tag: cell culture phenotype

value: invasive

tag: cell origin

value: Skin metastasis shoulder


title: HdIV3_13676853

description:
Hemo-PBS3_Cy3 vs Hemo-HdIV3_Cy5
Date:2007/12/13


title: Melanoma culture M081008

source_name: Primary face

value: Primary face

tag: cell line


title: HdIV1_13676856

description:
Hemo-PBS1_Cy3 vs Hemo-HdIV1_Cy5
Date:2007/12/13


title: [E-MTAB-366] Chicken developmental stage HH1 1

tag: biosource provider

tag: developmental stage

tag: genotype

tag: organism part

tag: Sex

tag: strain or line


title: mer1D_SK1_t=0hr_B


title: Cre replicate 1

tag: cell type

value: Sertoli cells

tag: adenovirus infection

value: Cre


title: Melanoma culture M061103

source_name: Skin metastasis capillitium

tag: hras

value: Skin metastasis capillitium


title: HdIV3_13676855

description:
Hemo-HdIV3_Cy3 vs Hemo-PBS3_Cy5
Date:2007/12/13

tag: label

tag: extract

tag: sample


title: Melanoma culture M080307

source_name: Soft tissue metastasis axilla

tag: tumor stage

tag: braf

value: Soft tissue metastasis axilla


title: mer1D_SK1_t=11hr_A

tag: strain

tag: genotype/variation

value: mer1D mutant

tag: meiotic time point

tag: reference

value: Reference pool WT RNA comprised of 50% time zero RNA plus 10% each of time 2 hours, 5, hours, 7 hours, 9 hours and 11 hours


title: mer1D_SK1_t=9hr_A


title: Cre replicate 2


title: MdBV2_13676748

description:
Hemo-PBS2_Cy3 vs Hemo-MdBV2_Cy5
Date:2007/12/13


title: Melanoma culture M080326

source_name: Primary plantar

tag: nras

tag: cell culture phenotype

value: proliferative

tag: cell origin

value: Primary plantar

tag: cell line


title: Melanoma culture M060125

source_name: Skin metastasis scapula

value: Skin metastasis scapula


title: mer1D_SK1_t=7hr_A


title: Normal human mammary fibroblast cells genotype 48 (H3Acet)

description: Biological replicate 2 of 3. Human mammary fibroblast cells.

extract_protocol:
Wash ~2x107 cells in a tissue culture dishes with 10 ml of HBSS (Hanks Balanced Salt Solution) with 2.5mM EDTA. Add 15 ml of HBSS with 2.5mM EDTA, with 400 ul of 37% formaldehyde added (final conc 1%).  Incubate at 37 C for 10 minutes. Aspirate off formaldehyde solution and add 5 ml of ice cold HBSS, 2.5mM EDTA with protease inhibitors (PIs) at a final concentration of 1 mM PMSF, 1 ug/ml Pepstatin A, 1 ug/ml Aprotinin. Gently detach cells with a cell scraper and transfer the cells to a conical tube.  Wash remaining cells out of flask with 5 ml of HBSS with PIs. Spin cells down ~700 g for 5 min at 4 C. After spin, aspirate HBSS then add PIPES buffer (5 mM PIPES buffer pH 8.0, 85mM KCl, 0.5% NP40) with protease inhibitors 400 ul/sample, transfer sample to microfuge tube, then incubate on ice for 10 min. After incubation, pellet cells at 700 g for 5 min at 4 C. Remove PIPES buffer and add SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) with protease inhibitors. Again 10 min on ice. Store at -80 C. Thaw samples on ice. Sonicate samples 6 x for 10 seconds on setting 7-8 watts until the majority of chromatin is between 500-1000 bp in length when checked on 1% agarose gel. After sonication spin samples at max speed at 4 C for 10 min to remove any cellular debris.  Dilute supernatant fraction 10 fold with ChIPs dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) with PIs.  Set aside 10 % of sample into a fresh microfuge tube - Input sample.
immunoprecipitation protocol: Pre-clear the diluted sample by adding 120 ul of protein-A sepharose slurry (Pharmacia).  Rotate for 1hr at 4 C. Spin down samples at 400 g at 4 C for 2 min to pellet beads. Divide samples equally into microfuge tubes for each Ab sample and add Abs. Rotate tubes overnight at 4 C. Next day add 90 ul of Pro-A sepharose slurry to each Ab tube. Rotate at 4 C for 1hr.  Spin samples in picofuge for 10 s, discard all but 400 ul of supernatant, resuspend sepahrose beads in remaining volume and transfer to Handee spin cup columns (Pierce), spin in picofuge for 10 s, discard flow through. Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA with 250 ul of elution buffer (1% SDS, 0.1M NaHCO3).  Mix well and rotate for 15 min at room temp.  Spin down, save flow through to a new microfuge tube. Repeat elution and combine eluates.  Total volume ~ 500 ul. Bring the Input sample volume up to 500 ul using the elution buffer. To reverse the cross-links add 40 ul of 5M NaCl to eluate or diluted input and incubate at 65 C for 4 hr. After incubation add 100 ul of 0.1M EDTA, 40 ul of 1M Tris-Cl pH 7.5, and 2 ul of 20 mg/ml proteinase K to each sample and incubate at 45 C for 1 hr. Purify samples using QIAquick PCR purification kit (Qiagen, Valencia, CA): Transfer samples to 10 ml tubes. Add 5 volumes of PB buffer, mix well, apply to Qiagen columns under vacuum, wash 2x with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: HMF 48

tag: tissue

value: mammary gland

tag: sample type

value: Immunoprecipitated DNA

tag: antibody

value: anti-acetylated histone H3

tag: vendor

value: Millipor

tag: catalog#

value: Input DNA


title: mer1D_SK1_t=2hr_A


title: Melanoma culture M080423

source_name: Lymph node metastasis hepatoduodenal

value: wt

value: Lymph node metastasis hepatoduodenal


title: mer1D_SK1_t=0hr_A


title: mer1D_SK1_t=5hr_A


title: mer1D_SK1_t=0.5hr_A


title: MdBV1_13676787

description:
Hemo-MdBV1_Cy3 vs Hemo-PBS1_Cy5
Date:2007/12/13

tag: label

tag: extract

value: hemocyte


title: Melanoma culture M050829

source_name: Skin metastasis retrauricular right

tag: tumor stage

value: Skin metastasis retrauricular right


title: MdBV1_13676749

description:
Hemo-PBS1_Cy3 vs Hemo-MdBV1_Cy5
Date:2007/12/13

tag: sample


title: MdBV3_13676750

description:
Hemo-MdBV3_Cy3 vs Hemo-PBS3_Cy5
Date:2007/12/13


title: Melanoma culture M080306

source_name: Primary capillitium

tag: braf

value: invasive

value: Primary capillitium


title: LSK CONTROL REP1

city: Madrid

first: Antonio

middle: Herrera

last: Merchan

address: Melchor Fernández Almagro, 3

department: Regenerative Cardiology

country: Spain

institute: CNIC

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 600 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Normalized signal intensities were obtained by a) background subtraction, b) threshold raw signals to 1, c) log base 2 transformation, d) global intra-array normalization to the 75.0 percentile, and e) per-gene baseline transformation by subtracting the median for that same gene in all samples.

source_name: LSK CONTROL

label_protocol:
Amount of nucleic acid labeled: 30ng. Amplification: by RNA polymerases. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90040 Ver 6.5 May 201
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.
Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

extract_protocol:
Total RNA isolated with Trizol.
Total RNA fraction. RNA Integrity Numbers were in the range 8.6 to 9.4 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

tag: strain

tag: cell type

value: LSK

tag: genotype/variation

value: control


title: MdBV3_13676789

description:
Hemo-PBS3_Cy3 vs Hemo-MdBV3_Cy5
Date:2007/12/13


title: LSK CONTROL REP2


title: Melanoma culture M000921

source_name: Epigastric metastasis

tag: nras

value: proliferative

value: Epigastric metastasis


title: LSK EZH2 REP2

source_name: LSK EZH2

value: EZH2 overexpression


title: LSK CONTROL REP3


title: MdBV2_13676788

description:
Hemo-MdBV2_Cy3 vs Hemo-PBS2_Cy5
Date:2007/12/13


title: Melanoma culture M980513

source_name: Lymph node metastasis iliacal

tag: hras

tag: cell culture phenotype

value: Lymph node metastasis iliacal


title: LSK EZH2 REP3


title: Non-Endo_BCELLS-2B

status: Public on Apr 04 2011

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: B cells from normal human discarded leukocytes from platelet donations by healthy donors. Donor PBMC were stained with pan B-cell specific CD20-FITC antibodies. Fluorescently labeled cells were sorted using a high speed cell sorter. (FACS Aria. BD biosciences San Jose. California).

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Human Genome HT_U133A and HT_U133B arrays. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: HT Plate Scanner

data_processing: The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: B cells

label_protocol: For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Human Genome U133A microarrays.

extract_protocol: Total RNA was isolated using the RNAeasy kit (QIAGEN) following the manufacturer’s instructions.

value: B cells


title: Non-Endo_BCELLS-1B


title: Melanoma culture M010817

source_name: Skin metastasis left upper arm

tag: cell origin

value: Skin metastasis left upper arm

tag: cell line


title: Non-Endo_TCELLS-2B

description: T cells from normal human discarded leukocytes from platelet donations by healthy donors. Donor PBMC were stained with pan T-cell specific CD3-PE antibodies. Fluorescently labeled cells were sorted using a high speed cell sorter. (FACS Aria. BD biosciences San Jose. California).

source_name: T cells

value: T cells (Cd4+ and CD8+)


title: Non-Endo_HASMC-1B

description: aortic smooth muscle cells from normal human

source_name: aortic smooth muscle cells

growth_protocol: cells are grown on EBM-2 (EC Cell Basal Medium-2) supplemented with EGM SingleQuots

value: aortic smooth muscle cells


title: Non-Endo_TCELLS-1B


title: LSK EZH2 REP1


title: Non-Endo_HASMC-2B


title: Normal human mammary fibroblast cells genotype 184 (MeDIP)

description: Biological replicate 1 of 3. Human mammary fibroblast cells.

source_name: Human mammary fibroblast cells

value: HMF 184

tag: tissue

value: mammary gland

tag: sample type

value: Immunoprecipitated DNA

value: anti-Methylcytosine

value: Input DNA


title: [E-MTAB-366] Chicken developmental stage HH4 2

source_name: whole embryo except yolk and amnion, developmental stage HH4

tag: biosource provider

value: local farmer (Shiroyama Keien)  in Japan

tag: developmental stage

tag: genotype

value: wild type

tag: organism part

value: whole embryo except yolk and amnion

tag: Sex

value: mixed sex

tag: strain or line

value: Nera


title: Endo_HCAEC-1B

description: coronary artery endothelial cells from normal human

source_name: Coronary Artery Endothelial Cells

value: coronary artery Endothelial Cells


title: SR1_1000nM_24hr

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Standard Affymetrix protocols

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: RNA extraction was performed by using RNeasy kits(Qiagen). The integrity and concentration of RNA was determined by microfluidic analysis on an Experion instrument (BioRad)

treatment_protocol: mPB CD34+ cells treated with compounds at the indicated time points

value: hematopoietic stem cell (HSC)

tag: agent

tag: dose

tag: time


title: LGC006_30nM_24hr

tag: cell type


title: SR1_30nM_24hr


title: SR1_100nM_24hr


title: Endo_HPAEC-2B

description: human pulmonary artery endothelial cells from normal human

source_name: Pulmonary Artery Endothelial Cells

value: Pulmonary Artery Endothelial Cells


title: Endo_HPAEC-1B


title: LGC006_1000nM_24hr


title: LGC006_300nM_24hr


title: Endo_HCAEC-2B


title: Endo_HMVEC-1B

description: dermal microvascular cells from normal human

source_name: Microvascular Endothelial Cells

value: Microvascular Endothelial


title: SR1_300nM_24hr


title: Non-Endo_BCELLS-2A

value: B cells


title: Endo_HUVEC-1B

description: HUVEC cells from normal human

source_name: HUVEC CELL

value: Umbilical Vein Endothelial Cells


title: Endo_HAEC-1B

description: aortic endothelial cells from normal human

source_name: Aortic Endothelial Cells

value: Aortic Endothelial Cells


title: Endo_HMVEC-2B


title: Endo_HAEC-2B


title: Non-Endo_TCELLS-2A

value: T cells (Cd4+ and CD8+)


title: SR1_0nM_24hr


title: Impedance_change1

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University, Heidelberg, Germany

description: Gene expression data from cisplatin treatment

hyb_protocol: The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and   scanner). Primary data were obtained with the Affymetrix microarray suite.

scan_protocol: Affymetrix scaner and Microarray Suite Software Package.

data_processing: Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).

source_name: MCF-7 cells

label_protocol: Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT-   T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled   NTPs (Enzo).  For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).

growth_protocol: Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).

extract_protocol: Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.

treatment_protocol: Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.


title: Control2

description: Gene expression data from control sample


title: Control1


title: Glycolysis_change2


title: Impedance_change2


title: Endo_HUVEC-2B

description: HUVEC cells from normal human


title: Non-Endo_BCELLS-1A


title: Non-Endo_TCELLS-1A


title: Glycolysis_change1


title: Non-Endo_HASMC-1A

value: aortic smooth muscle cells


title: HSF_rho0_4 h_control_rep1

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

hyb_protocol: 1.5 ug of cRNA (>9 pmol Cy3 per ug cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent.

scan_protocol: Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent).

data_processing: Background-corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Non-uniform outliers or features not significantly above background intensity in 20% or more of the hybridizations were filtered out.

source_name: Skin fibroblast, depleted mitochondria, control, 4 hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions.

growth_protocol: Human skin fibroblasts (HSF) immortalized by SV40 T antigen were maintained in a 4.5 g/L glucose DMEM with 4 mM L-glutamine and 100 mg/L sodium pyruvate supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 microg/ml streptomycin. Mitochondrial (mt) DNA-depleted rho0 cells were established from the corresponding parent rho+cells using prolonged exposure to ethidium bromide (50 ng/ml) in growth medium supplemented with 50 microg/ml uridine.

extract_protocol: RNA was isolated using Ribopure (Ambion, Applied Biosytems) according to the manufacturer’s instructions.

treatment_protocol: Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator.

tag: cell line origin

value: human skin fibroblast immortalized with SV40 TAg

tag: mitochondrial status

value: depleted

tag: treatment

tag: treatment time

value: 4 hours


title: HSF_rho0_4 h_control_rep3


title: Non-Endo_HASMC-2A


title: HSF_rho0_4 h_alpha_rep1

source_name: Skin fibroblast, depleted mitochondria, irradiated, 4 hr

value: irradiation


title: HSF_rho0_4 h_control_rep2


title: Endo_HCAEC-2A


title: HSF_rho0_4 h_alpha_rep2


title: Endo_HCAEC-1A


title: HSF_rho+_4 h_control_rep2

source_name: Skin fibroblast, normal mitochondria, control, 4 hr

value: normal


title: HSF_rho+_4 h_control_rep1


title: Endo_HPAEC-1A


title: HSF_rho0_4 h_alpha_rep3


title: HSF_rho+_4 h_control_rep3


title: Endo_HPAEC-2A


title: BPN active (BPN7)

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

description: Gene expression from adult normotensive BPN/3J mouse collected during active phase

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Mouse Gene 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) in the R application (version 2.11.1). Differentially expressed genes for each age were identified using the moderated two-sample t-test in the Limma package.

source_name: Male BPN/3J hypothalamus

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

growth_protocol: The whole hypothalamus was removed from BPH/2J and age-matched BPN/2J (n=3/group, 19 week old, ‘trough’ blood pressure) in the inactive period, when the blood pressure levels of the BPH/2J and BPN/3J models are similar. Hypothalamus of BPH/2J and age-matched BPN/2J (n=6/group, 26 week old, ‘peak’ blood pressure) were collected on the same way at the peak of the circadian variation, when there blood pressure difference between the strains was maximal. Tissues were frozen and then RNA was extracted.

extract_protocol: RNeasy kit (Qiagen) was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Standard animal house treatment.

tag: strain

tag: age

value: 26 week-old

value: hypothalamus

tag: blood pressure

value: Normotensive

tag: circadian period

value: active


title: Endo_HAEC-2A


title: HSF_rho+_4 h_alpha_rep3

source_name: Skin fibroblast, normal mitochondria, irradiated, 4 hr


title: HSF_rho+_4 h_alpha_rep2


title: BPN active (BPN10)

tag: tissue


title: BPN active (BPN11)


title: Endo_HAEC-1A


title: HSF_rho+_4 h_alpha_rep1


title: BPN active (BPN5)


title: BPN active (BPN6)


title: Endo_HMVEC-2A


title: BPN active (BPN8)


title: BPH active (BPH8)

description: Gene expression from adult hypertensive BPH/2J mouse collected during active phase (peak blood pressure)

source_name: Male BPH/2J hypothalamus

value: Hypertensive


title: BPH active (BPH7)


title: BPH active (BPH9)


title: Endo_HUVEC-2A

description: HUVEC cells from normal human


title: Endo_HMVEC-1A


title: BPN inactive (BPN4)

description: Gene expression from adult hypertensive BPN/3J mouse collected during inactive phase

value: 18 weeks old

value: inactive


title: BPH active (BPH6)


title: Endo_HUVEC-1A

description: HUVEC cells from normal human


title: BPH active (BPH4)


title: BPH inactive (BPH3)

description: Gene expression from adult hypertensive BPH/2J mouse collected during inactive phase


title: BPN inactive (BPN1)


title: BPH inactive (BPH2)


title: ES_Day5_3

status: Public on Apr 03 2011

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

description: Control

hyb_protocol: Hyb was performed with Agilent hybridization SureHyb chamber kit and gasket slide kit according to manufacture

scan_protocol: Scanning was done on a GenePix 4100A scanner using GenePix 6.0 pro software at 10 micro and PMT 750

data_processing: Averages were calculated for replicate probes and probles were excluded if they had average value below a cutoff value of 100 or less than a value for the negative control (median value of negative control plus 3SD).  Data was normalized by calculating the media value for the the probes with the lowest CV and then using it as normalization factor across samples.  Data was processed on GenePix 6.0 and analyzed in Microsoft Excel.

source_name: ES cells differentiated on OP9 stromal cells

label_protocol: Labeled according to the manufactures protocol

growth_protocol: Murine ES cells were grown on a confluent OP-9 cells and differentiate along the hematopoitc lineage.

extract_protocol: Total RNA was extracted on Day 5 and Day 8 using Qiagen microRNeasy kit

treatment_protocol: At Day 5 Notch OFF cells were cultured in media with TET and Notch ON cells were cultured in media without TET

value: Day5 control

tag: cell line

value: Murine ES cells E14tg2a


title: ES_Day8NotchON_2

description: TET OFF inducible activated Notch vector

value: Day8 NotchON


title: ES_Day5_2

description: Control


title: ES_Day8NotchOFF_2

value: Day8 NotchOFF


title: ES_Day8NotchOFF_3


title: ES_Day8NotchON_3


title: BPH inactive (BPH1)


title: ES_Day8NotchOFF_1


title: BPH active (BPH5)


title: BPN inactive (BPN3)


title: ES_Day8NotchON_1


title: ES_Day5_1

description: Control


title: PhrB.2 transcriptional profile

first: Jai

middle: Justin

last: Tree

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

description: The transcriptional profile of PhrB  was assessed by providing EHEC O157:H7 TUV93-0 with multicopy PhrB on pGEM. RNA was extracted from late-exponential (OD 0.8) cultures grown in T3S permissive conditions (MEM-HEPES) and hybridised to UBEC 3 E. coli arrays.

hyb_protocol: Prior to hybridization, the slides were treated with the background-reducing Pronto! Pre-Soak System (Corning Life Sciences). The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42 °C and washed twice in 0.1_SSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5_ SSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1_ SSC, 0.1% SDS for 1 min and twice in 0.1_ SSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800_g. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 _l of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5_ SSC (1_ SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 _g of poly(A), and 1_Denhardt’s solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C. After hybridization was complete, the slides were washed in 2_SSC, 0.1% SDS at 42 °C for 2 min in 0.1_SSC, 0.1% SDS for 2 min at room temperature, and finally twice in 0.1_ SSC for 2 min at room temperature. The microarray slides were dried by centrifugation for 5 min at 800g.

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: LOWESS was used to normalise data generated by GenePix using Genespring GX 7.3.1.

organism: Escherichia coli O157:H7

source_name: TUV93-0 pGEM

label_protocol:
20 ug total RNA was converted to Cy5-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy5 NHS-dye esters to the amino-allyl-labelled
cDNAs.

growth_protocol: Sample was grown shaking at 37oC in MEM-HEPES to OD600 = 0.8.

extract_protocol: An RNeasy minikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd).

treatment_protocol: 10 ml of culture was mixed with 10 ml of RNAprotect bacterial reagent (QIAGEN Ltd).

value: O157:H7 EHEC TUV93-0 pGEM

tag: od

tag: media

value: MEM-HEPES

source_name: TUV93-0 pGEM::PhrB

value: O157:H7 EHEC TUV93-0 pGEM::PhrB


title: PhrB.3 transcriptional profile


title: PhrA.3 transcriptional profile

description: The transcriptional profile of PhrA  was assessed by providing EHEC O157:H7 TUV93-0 with multicopy PhrA on pGEM. RNA was extracted from late-exponential (OD 0.8) cultures grown in T3S permissive conditions (MEM-HEPES) and hybridised to UBEC 3 E. coli arrays.

source_name: TUV93-0 pGEM::PhrA

value: O157:H7 EHEC TUV93-0 pGEM::PhrA


title: PhrA.2 transcriptional profile


title: PhrA.1 transcriptional profile


title: KSR1 and H-RASV12, Replicate 3

status: Public on Apr 02 2011

city: Omaha

first: Robert

last: Lewis

state: NE

address: 12706 Lied Transplant Center

institute: Univ. of Nebraska Medical Center

hyb_protocol: Resultant cRNA probes were hybridized to the Affymetrix (Santa Clara, CA) Mouse Genome MG_U74Av2 Array per manufacturer's suggestion.

scan_protocol: Following washing and staining, the chips were scanned using a GeneChip Scanner 3,000 6 G in the UNMC microarray core facility.

data_processing: Data were processed using MAS5.0.

source_name: KSR1-null MEFs with H-RasV12 and KSR1

label_protocol: 2.5 ug of total RNA was reverse-transcribed and cRNA generated per Affymetrix instructions using the Affymetrix 1-cycle Target Labeling Kit.

extract_protocol:
1) Place freshly isolated tissue directly in TriReagent (1ml/50-100mg of tissue).
2) Immediately homogenize tissue and transfer to a sterile 50 ml centrifuge tube.
3) Cap the tube securely, shake, vortex vigorously, and incubate at room temperature 5 min. to assure dissociation of nucleoproteins.
4) Add 0.1 ml BCP/ ml of TriReagent used. Cap the tube, shake, and vortex. Incubate at RT for 10 min. Centrifuge at 3200 rpm in Sorvall tabletop centrifuge or equivalent (1800 g) for 30 min. at 40 C.
5) Of the three phases seen, RNA remains in the topmost aqueous phase. Transfer the aqueous layer to a fresh tube being careful not to disturb the protein-rich interface.
6) Precipitate the RNA by adding isopropanol (molecular biology grade) at 0.5 ml / ml TriReagent used. Shake vigorously, vortex, and leave at room temperature 10-15 min.
7) Centrifuge at 3200 rpm for 45 min. to one hour at 40 C.
8) Decant the isopropanol and wash the pellet gently with 10ml ice cold 75% ethanol (made with 100% ethanol (molecular biology grade) and HPLC grade-H2O). Centrifuge at 3200rpm for 20 min. at 4ºC.
9) Carefully decant the ETOH. Draw off the last with a pipet and allow excess ethanol to evaporate 5-10 min. Do not permit the pellet to completely dry as this will decrease its solubility.
10) Bring the volume of the sample up to 250ul (or appropriate volume) with HPLC-H20. Transfer the RNA sample to a 1.5ml microfuge tube.
11) Add 625μl (2.5X original volume) 100% ice cold ethanol.
12) Add 25μl (0.1X original volume) 3M sodium acetate, pH 5.2.
13) Mix well and place in -200C freezer for 30-60 minutes.
14) Microcentrifuge at top speed for 20-30 min. at 4º C.
15) Decant the ethanol mixture and wash the RNA pellet with 100μl 75% ethanol. Spin at top speed of microfuge for 10 minutes at room temperature. Draw off the supernatant with pipet and repeat the wash step. After drawing off the second 75% wash, invert the tube 5-10 min. to partially dry the sample. Do not completely dry the RNA pellet as this will decrease its solubility.
16) Resuspend in an appropriate amount of HPLC-H2O, depending on the size of the pellet.

value: mouse embryonic fibroblasts (MEFs)

tag: genotype

tag: expression

value: H-RasV12, KSR1, and GFP

tag: background strain

value: DBA


title: KSR1 and H-RASV12, Replicate 1


title: KSR1 and H-RASV12, Replicate 2


title: KSR1 Alone, Replicate 1

source_name: KSR1-null MEFs with KSR1

value: KSR1 and GFP


title: H-RASV12 Alone, Replicate 2

source_name: KSR1-null MEFs with H-RasV12

value: H-RasV12 and GFP


title: H-RASV12 Alone, Replicate 3


title: GFP Alone, Replicate 3

source_name: KSR1-null MEFs with GFP

value: GFP


title: H-RASV12 Alone, Replicate 1


title: PEG8000 treated

city: Seoul

first: Jinki

last: Yeom

address: Anam-Dong, Sungbuk-Gu

department: Life Science

country: South Korea

institute: Korea University

hyb_protocol: The Cy3 or Cy5-labeled cDNA probes were mixed together and hybridized to a microarray slide. After overnight at 42C, the slide was washed twice with washing solution 1 containing 2X SSC, 0.1% SDS for 5 min at 42C, and once with washing solution 2 containing 0.1X SSC, 0.1% SDS for 10 min at room temperature, and finally four times with 0.1X SSC for 1 min at room temperature. The slide was dried by centrifugation at 650 rpm for 5min.

scan_protocol: Hybridization image on the slide was scanned by Axon 4000B (Axon Instrument, Union City, CA).

data_processing: Hybridization image was analyzed by GenePix Pro 3.0 software (Axon Instrument, Union City, CA) to obtain gene expression ratios (reference vs test sample). Gene expression ratios were normalized by GenePix Pro 3.0 software (Axon Instrument, Union City, CA)

organism: Escherichia coli

source_name: Control

label_protocol: The integrity of bacterial total RNA was checked by capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and further purified with an RNeasy Mini Kit ( Qiagen, Valencia, CA). cDNA probes for cDNA microarray analysis were prepared by the reverse-transcription of total RNA (50ug) in the presence of aminoallyl-dUTP and 6ug of random primers (Invitrogen, Carlsbad, CA) for 3 hrs. The cDNA probes were cleaned up using Microcon YM-30 column (Millipore, Bedford, MA) and then followed by coupling of Cy3 dye (for reference) or Cy5 dye (for test sample) (Amersham Pharmacia, Uppsala, Sweden). The Cy3 or Cy5-labeled cDNA probes were purified with QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Dried Cy3 or Cy5-labeled cDNA probes were resuspended in hybridization buffer containing 30% formamide, 5X SSC, 0.1% SDS, 0.1mg/ml salmon sperm DNA.

growth_protocol: After growth at the early exponential (1.5 h) phase at 37 ˚C, the bacterial cells were transferred to fresh LB media supplemented with PEG and incubated for 1 h at 37 °C

extract_protocol: Total RNA extracted using Qiagen RNA miniprep kit following manufacturer's instructions

treatment_protocol: Cells are supplemented with PEG 8000 and incubated for 1 h at 37 °C

value: E.coli O157:H7

source_name: Total RNA from PEG 8000 treated E.coli O157 cells


title: GFP Alone, Replicate 2


title: GFP Alone, Replicate 1


title: Myeloma tumor, sample 12

city: Brooklyn

first: Olcay

last: Batuman

address: 450 Clarkson Ave, Box 20

institute: SUNY Downstate Medical Center

description:
MM_TUMOR_12
Newly diagnosed patient.

hyb_protocol: RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Chips were scanned on a GeneArray scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).

source_name: Bone marrow, tumor cells, MM

label_protocol: Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).

growth_protocol: For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.

extract_protocol: Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Samples were untreated.

value: bone marrow

value: CD138+ tumor plasma cells

tag: gender

value: male

tag: disease state

value: advanced multiple myeloma (MM)


title: Myeloma tumor, sample 10

description:
MM_TUMOR_10
Newly diagnosed patient.

tag: cell type

value: female


title: Myeloma tumor, sample 9

description:
MM_TUMOR_09
Newly diagnosed patient.


title: Myeloma tumor, sample 7

description:
MM_TUMOR_07
Newly diagnosed patient.


title: KSR1 Alone, Replicate 3


title: Myeloma tumor, sample 6

description:
MM_TUMOR_06
Newly diagnosed patient.


title: Myeloma tumor, sample 3

description:
MM_TUMOR_03
Newly diagnosed patient.


title: KSR1 Alone, Replicate 2


title: PhrB.1 transcriptional profile


title: Myeloma tumor, sample 8

description:
MM_TUMOR_08
Newly diagnosed patient.


title: Myeloma tumor, sample 11

description:
MM_TUMOR_11
Newly diagnosed patient.


title: Myeloma tumor, sample 5

description:
MM_TUMOR_05
Newly diagnosed patient.


title: Myeloma tumor, sample 4

description:
MM_TUMOR_04
Newly diagnosed patient.


title: Myeloma tumor, sample 2

description:
MM_TUMOR_02
Newly diagnosed patient.


title: Myeloma Tumor aCGH, 16

description:
MM_Tumor_acg_16
Newly diagnosed patient.
The same reference was used in all arrays.

hyb_protocol: An Agilent G2565BA scanner was used according to the manufacturer's protocol (Agilent).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 4.0.76).

data_processing: Feature extraction data was obtained using Agilent Feature Extraction Software (Agilent). DNA Analytics version 4.0.76 (Agilent) was used to assess copy number calls made using Agilent’s algorithm (ADM-1) in order to identify all aberrant intervals in a given sample with consistently high or low log ratios, with at least 2 probes present in the aberration region and a minimum absolute average log2 ratio of 0.3 for the region (1.23 fold-changes from control).

source_name: Peripheral blood mononuclear cell control DNA

label_protocol: Control and test sample genomic DNA were fragmented with HindIII and individually fluorescently labeled using the CGH Labeling Kit for Oligo Arrays, as described by the manufacturer (Enzo Life Sciences).

growth_protocol: For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies. EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.

extract_protocol: Total genomic DNA (5 μg) for arrays was extracted independently from 6 X 10^6 MM EPCs and tumor cells according to the manufacturer’s instructions using cell lysis and ethanol precipitation (Gentra System Inc., Minneapolis, MN). DNA from healthy male peripheral blood mononuclear cells (PBMCs; Promega, Madison, WI) was used as the normal control DNA.

value: peripheral blood

value: mononuclear cells

value: healthy

tag: sample type

value: reference

value: CD138+ tumor plasma cell


title: Myeloma tumor, sample 1

description:
MM_TUMOR_01
Newly diagnosed patient.


title: Myeloma EPC, sample 16

description:
MM_EPC_16
Newly diagnosed MM patient.

data_processing: Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM EPCs were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).

source_name: Bone marrow, EPC, MM

growth_protocol: EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.

extract_protocol: Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: endothelial progenitor cell (EPC)


title: Myeloma Tumor aCGH, 15

description:
MM_Tumor_acg_15
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 17

description:
MM_EPC_17
Newly diagnosed MM patient.


title: Myeloma EPC, sample 18

description:
MM_EPC_18
Newly diagnosed MM patient.


title: Myeloma Tumor aCGH, 7

description:
MM_Tumor_acg_7
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 14

description:
MM_EPC_14
Newly diagnosed MM patient.


title: Myeloma Tumor aCGH, 9

description:
MM_Tumor_acg_9
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 8

description:
MM_Tumor_acg_8
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 19

description:
MM_EPC_19
Newly diagnosed MM patient.


title: Myeloma EPC, sample 20

description:
MM_EPC_20
Newly diagnosed MM patient.


title: Myeloma Tumor aCGH, 14

description:
MM_Tumor_acg_14
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 15

description:
MM_EPC_15
Newly diagnosed MM patient.


title: Myeloma EPC, sample 13

description:
MM_EPC_13
Newly diagnosed MM patient.


title: Myeloma Tumor aCGH, 5

description:
MM_Tumor_acg_5
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 6

description:
MM_Tumor_acg_6
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 3

description:
MM_Tumor_acg_3
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 4

description:
MM_Tumor_acg_4
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 9

description:
MM_EPC_acgh_09
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 8

description:
MM_EPC_acgh_08
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 11

description:
MM_Tumor_acg_11
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 12

description:
MM_EPC_12
Newly diagnosed MM patient.


title: Myeloma EPC aCGH, 7

description:
MM_EPC_acgh_07
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 11

description:
MM_EPC_11
Newly diagnosed MM patient.


title: Myeloma EPC, sample 10

description:
MM_EPC_10
Newly diagnosed MM patient.


title: Myeloma EPC aCGH, 16

description:
MM_EPC_acgh_16
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 11

description:
MM_EPC_acgh_11
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 10

description:
MM_EPC_acgh_10
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 15

description:
MM_EPC_acgh_15
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 12

description:
MM_EPC_acgh_12
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 12

description:
MM_Tumor_acg_12
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 13

description:
MM_Tumor_acg_13
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 10

description:
MM_Tumor_acg_10
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 14

description:
MM_EPC_acgh_14
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 1

description:
MM_Tumor_acg_1
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 13

description:
MM_EPC_acgh_13
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 4

description:
MM_EPC_acgh_04
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma Tumor aCGH, 2

description:
MM_Tumor_acg_2
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC aCGH, 6

description:
MM_EPC_acgh_06
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 8

description:
MM_EPC_08
Newly diagnosed MM patient.


title: Myeloma EPC aCGH, 2

description:
MM_EPC_acgh_02
Newly diagnosed patient.
The same reference was used in all arrays.


title: EBS_3

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

description: Gene expression data from allergic asthmatic subject, without any stimulation. BAL was done at the same time of the day for each subject and only if he (she) did not experience inflammatory or allergen response.

hyb_protocol: Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and EBS samples.

scan_protocol: Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallel for control and EBS samples

data_processing: The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. Affy and Limma packages in Bioconductor (www.bioconductor.org) using R2.12.0 were used to perform quality tests, RMA normalization and Smyth's moderated t-test.

source_name: EBS

label_protocol: Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallel for control and EBS samples.

growth_protocol: The Biopsies were mechanically homogenized (Rotor/Stator homogeniser, PowerGen).

extract_protocol: RNA was extracted using the RNEasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment before extraction

value: allergic asthmatic

value: Keratinocytes

tag: tissue origin

value: skin biopsies with no stimulation


title: Control_5

description: Gene expression data from non EBS patients subject, without any stimulation.

value: healthy (non EBS)


title: Control_6


title: Myeloma EPC, sample 4

description:
MM_EPC_04
Newly diagnosed MM patient.


title: Myeloma EPC, sample 5

description:
MM_EPC_05
Newly diagnosed MM patient.


title: Myeloma EPC aCGH, 5

description:
MM_EPC_acgh_05
Newly diagnosed patient.
The same reference was used in all arrays.


title: Myeloma EPC, sample 6

description:
MM_EPC_06
Newly diagnosed MM patient.


title: Myeloma EPC, sample 7

description:
MM_EPC_07
Newly diagnosed MM patient.


title: EBS_4


title: Myeloma EPC aCGH, 3

description:
MM_EPC_acgh_03
Newly diagnosed patient.
The same reference was used in all arrays.


title: Pooled rpfF2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Gene expression after 28 hours of growth in Peptone sucrose media.

hyb_protocol: The labeled cRNA samples were hybridized onto a Genotypic designed Custom Gene Expression Xanthomonas oryzae 8x15k (AMADID: 25096). 600 ng of Cy3-labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent Technologies G2505C scanner. Images were quantified using Agilent Feature Extraction Software 10.5.1.1.

data_processing: The normalization was done using GeneSpring GX 11 Software.

organism: Xanthomonas oryzae pv. oryzae

source_name: RNA isolated from three independent cultures of rpfF mutant

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using the A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies). The samples  were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double-stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double-stranded cDNA were used as template for aRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Xanthomonas oryzae pv. oryzae wild type and DSF-deficient rpfF mutant cells were grown in Peptone sucrose medium, 200 rpm, 28o C and inoculated in the secondary culture at a cell density of 10^5 cells/ml (inoculum density) and grown for 28 hours under similar conditions.

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

tag: isolate

value: Indian

value: rpfF1 mutant

tag: growth time

value: 28 hours


title: Myeloma EPC, sample 3

description:
MM_EPC_03
Newly diagnosed MM patient.

value: bone marrow


title: Myeloma EPC aCGH, 1

description:
MM_EPC_acgh_01
Newly diagnosed patient.
The same reference was used in all arrays.

value: male


title: Pooled XOM2

source_name: RNA isolated from three independent cultures of wild type strain

value: wild type


title: Control_1


title: Myeloma EPC, sample 9

description:
MM_EPC_09
Newly diagnosed MM patient.

value: female

value: advanced multiple myeloma (MM)


title: EBS_2


title: EBS_6


title: Pooled XOM1


title: Myeloma EPC, sample 1

description:
MM_EPC_01
Newly diagnosed MM patient.


title: EBS_5


title: A_Cy5-vs-C_Cy3

status: Public on Apr 01 2011

city: Hagerman

first: Ken

last: Overturf

state: Idaho

address: 3059-F National Fish Hatchery Road

institute: USDA-ARS

description:
Comparison between the two trout families used in the study M45/F85 and M67/F143 when reared on the fishmeal diet
Analyzed data from arrays C1Cy3-A1Cy5, C2Cy3-A2Cy5, C3Cy3-A3Cy5, and C4Cy3-A4Cy5
Comparison between the two trout family groups on fishmeal
Comparing expression in liver between fish from a large sized family on a fishmeal diet to a fish from a medium sized family reared on a fishmeal diet
Study's genotypes: family groups M67/F143 and M45/F85
fam2.fam1.fm

hyb_protocol: Hybridization was carried out using a Tecan HS400 hybridization machine.  GRASP 16k microarray slides [16] were prepared by washing for 30 seconds at 23°C with 0.2x SSC, 0.05% SDS, soaking in the same buffer for 2 minutes at 23°C, and washing for 1 minute at 45°C with 4x SSC, 0.05% SDS.  Probes were injected onto slides and hybridization was carried out for 18 hours at 45°C with low agitation frequency.  Slides were washed for 30 seconds and soaked for 1 minute at 43°C with 2x SSC, 0.1% SDS; this step was repeated two more times.  Slides were then washed for 30 seconds and soaked for 1 minute at 25°C with 2x SSC; this step was repeated two more times.  Slides were then washed for 30 seconds and soaked for 30 seconds at 25°C with 0.2x SSC, 0.05% SDS. Cy3 and Cy5 capture reagents (Genisphere) were prepared according to Genisphere’s protocol, and mixed with 50 μl Ambion SlideHyb 3 buffer and 50 μl nuclease-free H2O.  The mixture was incubated at 80°C for 10 minutes, and then injected onto the slides.  Hybridization was carried out for 3 hours, 30 minutes at 45°C with low agitation frequency.  Slides were washed as described following first hybridization, and then dried for 2 minutes at 30°C.

scan_protocol: Scanning was performed using a Perkin Elmer ScanArray 5000.

data_processing:
Microarray design and analysis- Genotyped samples linked to families that had 4 or more members sampled on each diet were identified and ranked according to average family weight on each diet. Size rankings corresponded to large (>750 g), medium (600-640 g), and small (<500 g). From these identified groups 2 families were chosen for microarray expression analysis that demonstrated individuals with growth differences between the two diets. Data for the two families used for analysis and slide arrangements are listed in table 3. The families compared for growth differences between diets used for this study only differed by one growth range, large fish on fish meal compared to medium fish on plant-based diet and medium sized fish on fishmeal diet compared to small fish on plant-based diet. This strategy to use size separation within family was an attempt to identify gene changes more specific to diet utilization than specific for growth differences.  Array data pre-processing- The raw data intensities collected from two-channel arrays were pre-processed with scripts written in R language. These scripts included functions from the statistical packages MARRAY, ARRAYQUALITY and LIMMA from the Bioconductor project [81].  The array data pre-processing included arrays diagnostics, data quality assessment, data filtering, data background correction, and data normalization as outlined elsewhere.  The scripts for data pre-processing are available on request (roger.vallejo@ars.usda.gov). Data filtering-  The raw data intensities generated by the ScanArray Express software (Perkin Elmer, MA) had a column flag with values of 1= spot not found, 3= good spot, and 4= bad spot.   Spots with flags of 1 and 4 were filtered out, in addition to those with columns Name and ID that had these remarks: Name = “Empty,” “Blank Well,” “EmptySpot” and ID = “NAC.”Background correction- For background correction to assess differential expression, we used the method “normexp” with offset = 50 implemented in the computer package LIMMA, which was often found to be more robust than a simple background subtraction when using outputs from most image analysis programs.  This method adjusts the foreground adaptively for the background intensities and results in strictly positive adjusted intensities. The use of this offset allows for the filtering out of gene expression data with signal intensities <50. The effect of using this background adjustment method is to stabilize the variability of the M values [i.e., M = log 2(Cy5) - log 2(Cy3)] as a function of signal intensity. Data normalization. A within-array or two-channel normalization method was used to perform direct comparisons of RNA samples hybridized in the same array. The “robust spline normalization” method of data normalization was used. Statistical analysis of microarray data-The statistical analysis of pre-processed microarray data was performed with scripts written in R language.  These scripts included functions from the statistical package LIMMA  from the Bioconductor project [81].  The scripts for statistical data analysis are available on request (roger.vallejo@ars.usda.gov). The study design included two treatment factors with two levels each: diet and family. The focus of this study was to identify differentially expressed genes (DEGs) due to diet effects within each family and across families. We were also interested in identifying DEGs due to family effects within each diet and across diets.  Therefore, linear models were fitted for each of these four contrasts (family 1 vs. family 2 / diet 1; family 1 vs. family 2 / diet 2; diet 1 vs. diet 2 / family 1; and diet 1 vs. diet 2 / family 2) to identify genes that had significant differential gene expression for “treatment” effects.  By study design restrictions, we could model the “dye” effect in the fitted linear models only when comparing families within each diet. The basic statistic used for significance analysis is the moderated t-statistic, which is computed for each probe and for each contrast. This has the same interpretation as an ordinary t-statistic except that the standard errors have been moderated across genes (i.e., shrunk toward a common value) with a simple Bayesian model.  The adjusted P values (aka q values) are an estimate of the false discovery rate (FDR). We calculated the FDR by the Benjamini and Hochberg method.  For all hybridizations, all features with a a FDR of <0.2 were considered to be significantly different.
A within-array or two-channel normalization method was used to perform direct comparisons of RNA samples hybridized in the same array. The “robust spline normalization” method of data normalization was used. Statistical analysis of microarray data-The statistical analysis of pre-processed microarray data was performed with scripts written in R language.  These scripts included functions from the statistical package LIMMA  from the Bioconductor project.

organism: Oncorhynchus mykiss

source_name: liver from large sized rainbow trout  family fish on  fish meal based diet

label_protocol: Total RNA for each individual fish was isolated by the TRIzol method from liver and purified using Promega’s SV RNA Isolation Kit.  cDNA was prepared and either Cy3- or Cy5-labeled using Superscript II Reverse Transcriptase (Invitrogen) and Genisphere’s Array 50 Kit.  Each cDNA probe set was concentrated using Microcon YM-30 cut-off columns (Eppendorf), mixed with 100 μl SlideHyb 3 hybridization buffer (Ambion) and 1 μg human Cot-1 DNA (Invitrogen), incubated at 95°C for 10 minutes, then held at 45°C (hybridization temperature) until ready to use.

growth_protocol: One hundred and sixty females were mated to 80 males. After the eggs had eyed-up the family numbers were reduced to 95 full sib families and the same number of eggs from each family were pooled and mixed and then split into two separate lots of 4750 eggs. At first feeding the fry were separated into six 6000 l rearing tanks supplied with constant temperature (12 degree C) spring water. The fish were then transferred to 6 concrete rearing raceways when they averaged 25g and maintained in the raceways until they were harvested at an average weight of 600g.

extract_protocol: At an average harvest weight of approximately 600g, a random sample of 1032 fish from each diet group (344/raceway) was obtained. Each fish was weighed and measured for length and a fin clip was taken and stored in 100% ethanol for DNA extraction. Liver and muscle tissue collected for RNA isolation was placed in RNAlater (Ambion, Carlsbad, CA USA) and stored at 4°C for no longer than 3 weeks, according to the protocol recommended by Ambion.  RNA was isolated using the TRIzol (Invitrogen, Carlsbad, CA USA) method.  Briefly, tissue was first homogenized by placing a 5mm sterile, RNase-free, stainless steel bead into a round-bottom 2ml tube containing TRIzol and the tissue, then the tubes were placed in a Retsch MM300 Laboratory Vibration Mill for four min at 20 Hz.  The protocol recommended by Invitrogen was followed for the rest of the RNA isolation.

treatment_protocol: On raceway of the fish received a standard diet contaiing fishmeal and 10 percent fish oil, the experimental fish were fed a diet without fishmeal and protein source replaced with wheat gluten, corn gluten and soybean meal. The experimental diet also only used 5 percent fish oil and contained soybean oil in its place.

tag: family

value: mixed

tag: strain

value: Kamloop

tag: size

value: large

tag: diet

value: fishmeal-based diet

value: liver

source_name: liver from medium sized rainbow trout  family fish on  fishmeal  based diet

value: medium


title: Pooled rpfF1


title: Control_2

value: Keratinocytes


title: blood_GlobinReduced_DASL_DAP+_C00311_rep2

city: Grand Rapids

first: Mary

middle: E

last: Winn

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

description: C00311 (GC RNA) DAP+ rep2

hyb_protocol: Illumina IVT or DASL hybridization protocol.

scan_protocol: Illumina protocol for the HumanRefv3 BeadChip.

data_processing: No data processing was performed.

source_name: whole blood, GLOBINclear, DASL, DAP+

label_protocol: Illumina IVT or DASL labeling protocol.

extract_protocol: RNA isolation was performed using the PAXGene Blood RNA Isolation System (Qiagen, Valencia, CA, USA). Alpha and beta globin mRNA were reduced from a portion of the total RNA samples using the GLOBINclear™ Human kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions with the recommended start quantity of 2 μg of total RNA.

treatment_protocol: 2.5 ml whole blood was collected in a PAXgene Blood RNA collection tube (Qiagen, Valencia, CA, USA) and stored frozen at -80C prior to RNA isolation.

tag: tissue

value: peripheral whole blood

tag: globin treatment

value: GLOBINclear

tag: target preparation

value: whole-genome DASL (WG-DASL)

tag: dasl assay oligo pool

value: DAP+

tag: donor identifier


title: blood_GlobinReduced_DASL_DAP+_C00179_rep1

description: C00179 (GC RNA) DAP+ rep1


title: Control_4

value: healthy (non EBS)

value: skin biopsies with no stimulation


title: blood_GlobinReduced_DASL_DAP+_C00342_rep1

description: C00342 (GC RNA) DAP+ rep1


title: Control_3


title: Myeloma EPC, sample 2

description:
MM_EPC_02
Newly diagnosed MM patient.

value: bone marrow

value: endothelial progenitor cell (EPC)


title: A_Cy3-vs-B_Cy5

description:
Comparison between the fishmeal and plantmeal diets within family M67/F143
Analyzed data from arrays A1Cy3-B1Cy5, A2Cy3-B2Cy5, A3Cy3-B3Cy5, and A4Cy3-B4Cy5
Comparison between diets for family M67/F143
Comparing expression in liver between fish from a large sized family on fishmeal to a fish from a medium sized family reared on a plant based diet
Study's genotypes: family groups M67/F143 and M45/F85
fm.pm.fam1

source_name: liver from medium sized rainbow trout  family fish on plant-based diet

value: plant-based diet


title: blood_GlobinReduced_DASL_DAP+_C00275_rep2

description: C00275 (GC RNA) DAP+ rep2


title: blood_GlobinReduced_DASL_DAP+_C00304_rep1

description: C00304 (GC RNA) DAP+ rep1


title: blood_GlobinReduced_DASL_DAP+_C00311_rep1

description: C00311 (GC RNA) DAP+ rep1


title: blood_GlobinReduced_DASL_DAP+_C00275_rep1

description: C00275 (GC RNA) DAP+ rep1


title: B_Cy3-vs-D_Cy5

description:
Comparison between both rainbow trout families when reared on the plant based diet
Analyzed data for arrays B1Cy3-D1Cy5, B2Cy3-D2Cy5, B3Cy3-D3Cy5, B4Cy3-D4Cy5
Comparison between family M67/F143 and M45/F85 raised on the plant based diet
Comparing expression in liver between fish from a medium sized family on a plant based diet to a fish from a small sized family reared on a plant based diet
Study's genotypes: family groups M67/F143 and M45/F85
fam1.fam2.pm

source_name: liver from small sized rainbow trout  family fish on plant-based diet

value: small


title: D_Cy3-vs-C_Cy5

description:
Comparison between between fishmeal and plantmeal diet within family M45/F85
Analyzed array data for D1Cy3-C4Cy5, D2Cy3-C3Cy5, D3Cy3-C2Cy5, and D4Cy3-C1Cy5
Comparison between diets for family M45/F85
Comparing expression in liver between fish from a small sized family on a plant based diet to a fish from a medium sized family reared on a fishmeal diet
Study's genotypes: family groups M67/F143 and M45/F85
pm.fm.fam2

value: mixed


title: blood_GlobinReduced_DASL_DAP+_C00179_rep2

description: C00179 (GC RNA) DAP+ rep2


title: blood_GlobinReduced_DASL_DAP+_C00304_rep2

description: C00304 (GC RNA) DAP+ rep2


title: EBS_1

value: allergic asthmatic


title: blood_GlobinReduced_DASL_DAP+_C00342_rep2

description: C00342 (GC RNA) DAP+ rep2


title: blood_whole_DASL_DAP-_C00311_rep1

description: C00311 (tRNA) DAP- rep1

source_name: whole blood, untreated, DASL, DAP-

value: untreated

value: DAP-


title: blood_whole_DASL_DAP-_C00304_rep1

description: C00304 (tRNA) DAP- rep1


title: blood_GlobinReduced_DASL_DAP+_C00169_rep2

description: C00169 (GC RNA) DAP+ rep2


title: blood_whole_DASL_DAP-_C00304_rep2

description: C00304 (tRNA) DAP- rep2


title: blood_GlobinReduced_DASL_DAP+_C00027_rep1

description: C00027 (GC RNA) DAP+ rep1


title: blood_GlobinReduced_DASL_DAP+_C00169_rep1

description: C00169 (GC RNA) DAP+ rep1


title: blood_whole_DASL_DAP-_C00275_rep2

description: C00275 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP-_C00169_rep2

description: C00169 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP-_C00179_rep1

description: C00179 (tRNA) DAP- rep1


title: blood_GlobinReduced_DASL_DAP+_C00027_rep2

description: C00027 (GC RNA) DAP+ rep2


title: blood_GlobinReduced_DASL_DAP+_C00023_rep1

description: C00023 (GC RNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00311_rep1

description: C00311 (tRNA) DAP+ rep1

source_name: whole blood, untreated, DASL, DAP+


title: blood_whole_DASL_DAP-_C00342_rep1

description: C00342 (tRNA) DAP- rep1


title: blood_whole_DASL_DAP+_C00304_rep2

description: C00304 (tRNA) DAP+ rep2


title: blood_GlobinReduced_DASL_DAP+_C00023_rep2

description: C00023 (GC RNA) DAP+ rep2


title: blood_whole_DASL_DAP-_C00169_rep1

description: C00169 (tRNA) DAP- rep1


title: blood_whole_DASL_DAP-_C00342_rep2

description: C00342 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP-_C00311_rep2

description: C00311 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP+_C00342_rep2

description: C00342 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP+_C00311_rep2

description: C00311 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP-_C00179_rep2

description: C00179 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP-_C00023_rep1

description: C00023 (tRNA) DAP- rep1


title: blood_whole_DASL_DAP-_C00027_rep1

description: C00027 (tRNA) DAP- rep1


title: blood_whole_DASL_DAP-_C00023_rep2

description: C00023 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP+_C00342_rep1

description: C00342 (tRNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00304_rep1

description: C00304 (tRNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00275_rep2

description: C00275 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP-_C00027_rep2

description: C00027 (tRNA) DAP- rep2


title: blood_whole_DASL_DAP-_C00275_rep1

description: C00275 (tRNA) DAP- rep1


title: blood_whole_DASL_DAP+_C00275_rep1

description: C00275 (tRNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00179_rep1

description: C00179 (tRNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00179_rep2

description: C00179 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP+_C00023_rep2

description: C00023 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP+_C00027_rep2

description: C00027 (tRNA) DAP+ rep2


title: blood_whole_DASL_DAP+_C00169_rep1

description: C00169 (tRNA) DAP+ rep1


title: blood_whole_DASL_DAP+_C00027_rep1

description: C00027 (tRNA) DAP+ rep1


title: blood_day6_patient6

city: Lørenskog

first: Jan-Erik

last: Berdal

state: Akershus

address: Sykehusvn.

department: medical department

country: Norway

institute: AHUS

hyb_protocol: Fragmented and labeled DNA (2500ng) was used in 100 µl hybridization cocktail containing control oligonucleotide B2 (50pM) and hybridization controls (Affymetrix #900454), of which 80 µl was hybridised to each chip for 17h in the hybridization oven at 45ºC and rotating at 60rpm. Arrays were processed using Genechip Fluidics Station 450 according to recommended protocols (FS450_007) of double-staining and post-hybridization washes using GeneChip hybridization, wash and stain kit (Affymetrix #900720).

scan_protocol: Fluorescent images were captured using gene Array scanner 3000 7G and Affymetrix GeneChip Command Console, v 3.1 software (Affymetrix).

data_processing: Raw data were processed using Partek Genomics Suite v. 6.5 to generate RMA normalised intensities. Differential expression was assessed using One-way or Two-way ANOVA in the Partek software dependent of if the samples were paired or not.

source_name: Blood

label_protocol: Isolated total RNA was used with GeneChip WT cDNA synthesis and amplification kit (Affymetrix#900672) to produce fragmented single-stranded DNA, which was labeled using terminal labeling kit (Affymetrix#900670) to generate biotin-labeled sense targeted DNA probes.

growth_protocol: Peripheral blood cells

extract_protocol: RNA extraction was performed with PAXgene Blood RNA kit according to manufactors instructions, and RNA quality assesed with Bioanalyzer

treatment_protocol: Blood samples were collected with PAXgene Blood RNA tubes

value: blood

tag: patient

value: male

tag: age


title: blood_day0_patient4

tag: gender

value: female


title: blood_whole_DASL_DAP+_C00169_rep2

description: C00169 (tRNA) DAP+ rep2

value: peripheral whole blood


title: Blood_Control 4

tag: control


title: blood_day0_patient6


title: Blood_Control 3


title: Blood_Control 5


title: blood_day6_patient5


title: blood_day0_patient5


title: Blood_Control 2


title: blood_day0_patient7


title: Blood_Control 1


title: Blood_Control 7


title: blood_day6_patient3


title: blood_day6_patient1


title: blood_day6_patient4


title: blood_whole_DASL_DAP+_C00023_rep1

description: C00023 (tRNA) DAP+ rep1


title: MOLT-4_MABL_6h_2

city: Gotemba

first: Naoshi

last: Fukushima

state: Shizuoka

address: Komakado 1-135

department: Fuji Gotemba labs.

institute: Chugai pharmaceutical co., ltd.

description: Expression profiling of MOLT-4 cells treated with MABL

hyb_protocol: The cRNA products were fragmented, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was carried out using the GeneChip Scanner and image analysis was performed using GeneChip Operating Software.

data_processing: Signal intensities processed with GC-RMA algorithm.

source_name: MOLT-4 treated with MABL for 6 h-2

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (Affymetrix Expression Analysis Technical Manual, Rev. 4).

growth_protocol: MOLT-4 cell line was obtained from the American Type Culture Collection (ATCC) and grown in RPMI1640 medium (SIGMA) with 10% FBS(JBS). It was maintained at 37C and 5% CO2.

extract_protocol: Sepazol RNA I super (Nacalai Tesque) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were washed with PBS(-) followed by treatment with 10 ug/mL MABL (anti-CD47 antibody) for 0, 0.5, 1, 3 and 6 h.

tag: cell line

value: MOLT-4 (Leukemia)

tag: agents

value: 10 ug/mL MABL + 50 ug/mL GAM

tag: time

value: 6 h


title: blood_day6_patient7


title: SON siRNA rep2

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Drive, Mail Stop 0815

department: Cancer Center

institute: University of California San Diego

description: Gene expression data from HeLa cells trnasfected with SON siRNA

hyb_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps (see the attached EXP files).

scan_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps.

data_processing: The data were analyzed using the RMA algorithm with RMAExpress version 0.5. Affymetrix default analysis settings and global scaling were used as normalization method.

source_name: HeLa cells transiently transfected with SON siRNA

label_protocol: Biotinylated cRNA were prepared using MessageAmp II-Biotin Enhanced kit according to the manufacturer's instructions from 1.5 ug total RNA (MessageAmp II-Biotin Enhanced Kit Instruction Manual, 2006, Ambion).

extract_protocol: Qiagen RNeasy Mini column extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HeLa cells grown in 100 mm dishes were transiently transfected with negative control siRNA or SON siRNA (400 pmol siRNA / dish) using Lipofectamine 2000 reagent. RNAs were isolated after 66 hours.

value: cervical cancer cell line HeLa


title: MOLT-4_MABL_0h_2

source_name: MOLT-4 treated with MABL for 0 h-2

value: 0 h


title: Blood_Control 6


title: blood_day0_patient3


title: MOLT-4_MABL_6h_1

source_name: MOLT-4 treated with MABL for 6 h-1


title: control siRNA rep3

description: Gene expression data from HeLa cells trnasfected with control siRNA

source_name: HeLa cells transiently transfected with control siRNA


title: MOLT-4_MABL_3h_2

source_name: MOLT-4 treated with MABL for 3 h-2

value: 3 h


title: SON siRNA rep3


title: SON siRNA rep1


title: MOLT-4_MABL_3h_1

source_name: MOLT-4 treated with MABL for 3 h-1


title: MOLT-4_MABL_0h_1

source_name: MOLT-4 treated with MABL for 0 h-1


title: blood_day6_patient2


title: MOLT-4_MABL_1h_2

source_name: MOLT-4 treated with MABL for 1 h-2

value: 1 h


title: MOLT-4_MABL_1h_1

source_name: MOLT-4 treated with MABL for 1 h-1


title: ABI_Human Dermal Lymphatic Endothelial Cells Donor 3

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

hyb_protocol: Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Scan protocol Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescent Digoxigenin-UTP labeled cRNA

source_name: Neonatal human foreskin

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

tag: CD45-/CD34-/CD31+ Human Lymphatic Endothelial Cell (LEC).


title: control siRNA rep2


title: MOLT-4_MABL_0.5h_1

source_name: MOLT-4 treated with MABL for 0.5 h-1


title: ABI_Human Dermal Blood Vascular Endothelial Cells Donor 1

tag: CD45-/CD34+ Human Blood Vascular Endothelial Cell (BVEC)


title: ABI_Human Dermal Blood Vascular Endothelial Cells Donor 2

tag: CD45-/CD34+ Human Blood Vascular Endothelial Cell (BVEC).


title: control siRNA rep1


title: blood_day0_patient2


title: ABI_Human Dermal Blood Vascular Endothelial Cells Donor 3