title: Ffujikuroi_WT_120h_rep2

description: Wild-type

source_name: Fusarium fujikuroi IMI58289 wild-type

value: wild-type

value: 120 hrs


title: Ffujikuroi_WT_120h_rep1

status: Public on Dec 31 2010

type: RNA

city: Peoria

first: Daren

middle: W.

last: Brown

state: IL

address: 1815 N. University St.

department: Bacterial Foodborn Pathogens and Mycology Research

country: USA

institute: USDA-ARS

description: Wild-type

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Fusarium fujikuroi

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fusarium fujikuroi wild type IMI58289 and Ffvel1 mutant strains were grown in liquid ICI (Imperial Chemical Industries Ltd., UK) media containing 6 mM glutamine (10 % ICI medium).

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany).

tag: genotype variation

tag: growth time


title: DMSO treat 3

city: Shizuoka

first: Akinori

last: Ishihara

country: Japan

institute: Shizuoka University

hyb_protocol: Samples were hybridized to Xenopus laevis chips (Agilent, Santa Clara, CA) according to manufacturer's protocol.

scan_protocol: Hybridized chips were scanned using GenePix 4000B scanning equipment.

data_processing: Agilent Feature Extraction Software (version 9.5.3.1) was used for data extraction from scanner generated TIFF files. Global normalization settings were used with Subio platform with basic plug-in. See http://www.subio.jp/ for details. Briefly, the data that exhibited low raw signal were cut off by 1.0. The values were log transformed and were processed to global normalization with 75 percentile value. Finally, centering was performed with mean value.

organism: Xenopus laevis

source_name: DMSO vehicle

label_protocol: Probes were labeled with Cy3 using Quick Amp Labeling Kit (Agilent, Santa Clara, CA). Input is 400 ng RNA.

growth_protocol: Tadpoles were reared in dechlorinated tap water and transferred to FETAX buffer during experiment.

extract_protocol: RNA was extracted using SV total RNA Isolation System (Promega, Madison, WI) per the procedure supplied by the manufacturer.

treatment_protocol: Tadpoles were treated with DMSO vehicle, 1 nM T3 alone, or 1nM T3 and 500 nM hydroxylated PCBs for 4 days.

tag: developmental stage

value: Premetamorphic tadpole

tag: tissue

value: brain

tag: agent

value: control


title: DMSO treat 2


title: DMSO treat 1


title: yAPSp3b - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Experimental and reference probes were combined and hybridized to custom Agilent 44K whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to normalize the Agilent array data using Agilent's default protocol (essentially LOWESS dye normalization on background subtracted signal values). Spots of poor quality or average intensity levels <300 were removed from further analysis.

organism: Mus musculus

source_name: MGS

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following Agilent suggested protocols.

extract_protocol: Reference RNA was purified using Trizol (Life Technologies, Rockville, MD) following the manufacturer’s protocol. The RNA was then further purified by RNeasy maxi kit (Qiagen Inc, Valencia, CA) and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

tag: strain

value: Swiss-Webster

tag: age

value: Adult

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

tag: amplification

value: one round aRNA

growth_protocol: Young (4 month-old) and old (20-24 monthold) C57BL/6 male mice were obtained from the National Institutes of Aging (NIA) Rodent Colony at Harlan Sprague Dawley (Chicago, IL) and maintained in a barrier facility and cared for in accordance with approved IACUC protocols. Following shipment, mice were acclimated to a common temperature, day-night cycle, and diet for at least 12 days to minimize environmental differences. Mice from each age group were randomized for the day and time of sacrifice. Following halothane anesthesia, mice were sacrificed by cervical dislocation. Prostates were rapidly excised, immersed in OCT embedding compound (Miles Diagnostics, Elkhart, Ind., USA) and snap-frozen in liquid nitrogen and stored at -80º C.

extract_protocol: Approximately 10,000 cells were laser-capture microdissected using the Veritas LCM system (Arcturus Mountain View, CA). Total RNA from LCM experimental samples were isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl UTP incorporation into the second round aRNA using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: 4 month-old

value: pool of anterior lobe prostate stroma laser capture microdissected from three mice

value: two round aRNA


title: E15 heart sample2

type: genomic

city: St. Catharines

first: Ping

last: Liang

state: Ontario

address: 500 Glenridge Ave

department: Department of Biological Sciences

country: Canada

institute: Brock University

hyb_protocol: Hybridization performed according to standard procedures by Nimblegen

scan_protocol: Scanning performed according to standard procedures by Nimblegen using NimbleScan.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.  VALUE is the P score. To calculate the P score, the ratio of the input signals for input DNA and the MeDIP DNA from the same sample that were co-hybridized to the array is first computed and scaled to center the ratio data around zero.  Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. A fixed-length window (750bp) is then placed around each consecutive probe and the one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log-ratios than those in the rest of the array. The resulting score for each probe, called P score, is the -log10 p-value from the windowed KS test around that probe. The identification of methylation peaks is done by searching for at least 2 consecutive probes above a P score of 2. Peaks within 500bp of each other are merged.

molecule: genomic DNA

source_name: Cy3, total input sonicated DNA

label_protocol: Labeling performed according to standard procedures by Nimblegen

extract_protocol: Total genomic DNA was extracted using Qiagen DNeasy kit (Qiagen) according to the manufacture's instruction.  DNA was  sonicated to give fragments between 200bp and 1000bp.

value: heart

source_name: Cy5, methylated DNA enriched by MeDIP

extract_protocol: Sonicated total genomic DNA was digested with MseI (TTAA) (New England Biolabs) to produce small fragments (200 - 1,000bp) while keeping CpG islands  intact. Fragmented DNA was heat denatured to produce single-stranded DNA, and a portion of the denatured DNA stored as control (input) DNA.  Monoclonal mouse anti 5-methyl cytidine (Eurogentec, Reference ID: BI-MECY-0500; batch#: 080128) was used to  immunoprecipitate methylated DNA fragments. The immune complexes were captured with Protein A agarose beads (Invitrogen). Complexes were washed to remove nonspecifically bound material. MeDIP DNA was obtained by elution of bound complexes and ethanol precipitation.


title: yAPSp1b - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: BALB/cByJ_3

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

data_processing: qspline normalised log ratios

source_name: BALB/cByJ, Male, liver

extract_protocol: Genomic DNA was prepared from liver using a chloroform-based extraction protocol.

value: BALB/cByJ

value: Male

value: liver

source_name: C57BL/6J, Male, liver


title: Ffujikuroi_vel1_72h_rep2

description: Ffvel1 mutant

source_name: Fusarium fujikuroi IMI58289 delta vel1

value: Ffvel1 mutant

value: 72 hrs


title: yAPSp2b - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: invasive lobular carcinoma -4

city: Toronto

first: Susan

last: Done

state: ON

address: 200 Elizabeth Street, 11E444

institute: University Health Network

description:
ilc4a.gpr
ilc4b.gpr

hyb_protocol: Labelled products were mixed in appropriate combinations in DIG Easy Hyb hybridization buffer and hybridized for 16-24 hours at 37°C to the human 19K arrays from the University Health Network Microarray Centre (Toronto, Canada) which contains 19008 characterized and unknown human genes and/or ESTs. Slides were rinsed in 0.1X SSC to remove the cover slips and then washed 3 times in 0.1X SSC/0.1% SDS for 10 minutes at room temperature. Slides were rinsed once in 1X SSC and twice in 0.1X SSC and centrifuged to dryness.

scan_protocol: Arrays were scanned using the GenePix 4000A scanner (Axon Instruments, USA). The PMT gain for each laser was adjusted to give an average ratio of Cy3 to Cy5 of 1.0 and to minimize the number of saturated pixels. Images were then analyzed using the GenePix Pro 3.0 software.

data_processing: The resulting data were normalized using the printTipLoess algorithm in Bioconductor genomic analysis software package available on line at: http://www.bioconductor.org/. The data was normalized within each subarray as well as for the entire array. The values for the foreground and background for the duplicate spots were first averaged. Then the gene amplification level was calculated as the log base 2 of the ratio of the test to normal of the differences between foreground and background. The gene amplification level for each ‘fluor-flip’ experiment was averaged and filtered to exclude cDNA clones without mapping info.

organism: Homo sapiens

source_name: FFPE tissue

label_protocol: 2-3 mg of pooled DOP-PCR products from each sample as well as an equal amount of reference DNA was labelled by random priming in 3 separate reactions with either Cy3 or Cy5.

extract_protocol: 5 mm sections were cut from the FFPE samples and prepared for microdissection. LCIS and invasive components were identified and microdissected using laser capture microdissection on the PixCell II. Captured cells were incubated in 50 mL of Proteinase K extraction buffer (50 mm Tris, 1 mM EDTA, 0.5% Tween-20) for 72 hours at 55°C. Proteinase K was inactivated by incubation at 95°C for 10 minutes prior to use for PCR. Degenerate oligonucleotide primed (DOP) PCR was performed according to the usual protocol. Briefly, 10-100ng of DNA was amplified by Thermo Sequenase DNA Polymerase in a low stringency pre-amplification step (5 cycles) followed by regular PCR amplification in less stringent conditions. Several DOP-PCR reactions were pooled from each sample (to reduce the effect of bias on each sample) and cleaned by phenol:chloroform extraction prior to quantification and labeling. The resulting DNA was quantified using a DynaQuant 200 Fluorometer).

value: invasive lobular carcinoma

tag: patient

source_name: FFPE lymph nodes, pooled

value: pooled lymph nodes


title: E15 brain sample1


title: oAPSp4b - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: 20-24 month-old


title: invasive lobular carcinoma -3

description:
ilc3a.gpr
ilc3b.gpr


title: oAPSp3b - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: male


title: E15 brain sample2

value: brain


title: Ffujikuroi_vel1_72h_rep1

description: Ffvel1 mutant


title: AKR/J_3

scan_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

source_name: AKR/J, Male, liver

value: AKR/J


title: AKR/J_2

label_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.


title: EREB2-5 cells transfected with Rta vector, minus estradiol

type: protein

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

description: EREB2-5 cells were transfected and grown in the presence or absence of β-estradiol, as described. Seven days post-transfection, protein extracts were prepared, and 200 ugs. of each were analyzed using the RayBio Human Apoptosis Antibody Array Kit (RayBiotech) as per manufacturers suggestions.  The membranes were exposed to autoradiography film for different times to detect the chemiluminescent signals.  Images with signals in linear range were quantitated using the program ImageJ [59].

hyb_protocol: A. Blocking and Incubation 1. Place each membrane into the provided 8-well tray (top left corner marked with “-”). Note: The printed side should be facing upward. 2. Add 1 ml Blocking Buffer and incubate at room temperature with gentle shaking for 30 minutes to block membranes. 3. Decant Blocking Buffer from each well. Add 1 ml diluted sample onto each array membrane, and cover with the lid. Incubate at 2 – 8 0C overnight on a rocker or shaker (low speed 1-2 cycles/sec). Dilute sample using Blocking Buffer. RayBio® Human Apoptosis Antibody Array Kit Note: 1). Dilute cell lysates at least 5 folds with Blocking Buffer to avoid high background. Note: 2). Optimal sample dilution factors should be determined empirically. More of the sample can be used if signals are too weak. If signals are too strong, the sample can be diluted further. Note: 3). Incubation may be done at room temperature for 4 hours, but at the cost of impaired sensitivity of the signals. Decant the samples from each well, and wash 3 times with 1.5 ml of 1X Wash Buffer I at room temperature with shaking, 5 min per wash. Wash 2 times with 1.5 ml of 1X Wash Buffer II at room temperature with shaking, 5 min per wash. Carefully remove wash buffer from each well containing array membranes. Add 1 ml of diluted Cocktail of Biotin-Conjugated Antibody Mix to each membrane. Incubate at 2 – 8 0C with gentle shaking overnight. Note: Incubation may be done at room temperature for 2 hours. Wash as directed in steps 5 and 6. Add 1.5 ml of 1X HRP-conjugated Streptavidin to each membrane. Note: Mix tube containing 1X HRP-Conjugated Streptavidin well before use since precipitation may form during storage. 10. Incubate at room temperature for 1.5 hours. RayBio® Human Apoptosis Antibody Array Kit Note: incubation may be done overnight at 40C. 12. Wash as directed in steps 5 and 6.

scan_protocol: B. Detection * Do not let the membrane dry out during detection. The detection process must be completed within 40 minutes without stopping. 1. Proceed with detection reaction. Add 250 ?l of Detection Buffer C and 250 ?l of Detection Buffer D for one membrane; mix both solutions; Drain off excess wash buffer by holding the membrane vertically with forceps. Place membrane protein side up (“-” mark is on the protein side top left corner) on a clean plastic sheet (provided in the kit). Pipette the mixed Detection Buffer on to the membrane and incubate at room temperature with gentle shaking for 2 minutes. Ensure that the detection mixture is completely and evenly covering the membrane without any air bubbles. 2. Drain off excess detection reagent by holding the membrane vertically with forceps and touching the edge against a tissue. Gently place the membrane, protein side up, on a piece of plastic sheet (“-” mark is on the protein side top left corner). Cover the array with another piece of plastic sheet. Gently smooth out any air bubbles. Avoid using pressure on the membrane. 3. Detect signal directly from membrane using chemiluminescence imaging system or expose to x-ray film (we recommend to use Kodak X-OmatTM AR film) detect signal using film developer. Expose the membranes for 40 Seconds. Then re-expose the film according to the intensity of signals. If the signals are too strong (background too high), reduce exposure time (e.g., 5–30 seconds). If the signals are too weak, increase exposure time RayBio® Human Apoptosis Antibody Array Kit (eg, 2–20 min or overnight). Or re-incubate membranes overnight with 1X HRP-conjugated Streptavidin, and repeat detection on the second day. 4. Save membranes at –20 °C to –80 °C for future reference.

data_processing: For each membrane, signals from the negative control spots were averaged, and then subtracted from each of the other spots.  A signal was considered valid if its value exceeded both its average local background, and the average of all valid negative control values.  Valid signals were normalized using the positive control spots (for cellular BID protein).  Fold change in signals for each spot were quantitated by dividing by the valid signals for each corresponding spot on the minus β-estradiol membrane.  Average fold change, and standard deviation, were calculated for each protein.

label: bioin-labeled anti-apoptosis markers

molecule: protein

source_name: EREB2-5 cells

label_protocol: bioin-labeled anti-apoptosis markers from RayBio Human Apoptosis Antibody Array Kit

extract_protocol: cell lysates prepared as suggested by the array manufacturer

tag: sample type

value: EREB2-5 cells grown in the absence of beta-estradiol

tag: cell line

tag: transfection

value: Rta vector


title: AKR/J_1


title: oAPSp2b - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: Swiss-Webster

value: Adult

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

value: one round aRNA


title: invasive lobular carcinoma -1

description:
ilc1a.gpr
ilc1b.gpr


title: Ffujikuroi_vel1_24h_rep2

description: Ffvel1 mutant

value: 24 hrs


title: oAPSp1b - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: pool of anterior lobe prostate stroma laser capture microdissected from three mice

value: two round aRNA


title: lobular carcinoma in situ -4

description:
lcis4a.gpr
lcis4b.gpr

value: lobular carcinoma in situ


title: Ffujikuroi_WT_72h_rep2

description: Wild-type

value: wild-type

value: 72 hrs


title: EREB2-5 cells transfected with empty vector, plus estradiol

value: EREB2-5 cells grown in presence of beta-estradiol

value: beta-estradiol

value: empty vector


title: Control-111

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

tag: cell type

value: lymphoblast cell line

tag: disease state

value: control

tag: id (rutgers)

tag: nimh identifier

tag: sex

value: M

source_name: blood

value: blood


title: EREB2-5 cells transfected with empty vector, minus estradiol

value: EREB2-5 cells grown in absence of beta-estradiol


title: lobular carcinoma in situ -3

description:
lcis3a.gpr
lcis3b.gpr

value: pooled lymph nodes


title: Ffujikuroi_vel1_24h_rep1

description: Ffvel1 mutant

tag: genotype variation

value: Ffvel1 mutant

tag: growth time


title: Ffujikuroi_WT_24h_rep2

description: Wild-type


title: EREB2-5 cells transfected with EBNA2 vector, minus estradiol

value: EBNA2 vector


title: A/J_3

source_name: A/J, Male, liver

value: A/J

value: Male

tag: tissue

value: liver


title: PHHC-2

status: Public on Dec 30 2010

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

hyb_protocol: see manufacturer's web site at http://www.agilent.com/

scan_protocol: Images were scanned with the Agilent microarray scanner and the results were obtained by Agilent feature extraction software, Scan resolution 5μm, PMT 100%，5%

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software, the raw intensity data were quantile normalized and further analyzed using GeneSpring10.0 software.

source_name: normal primary human hepatocytes

growth_protocol: The hepatoma cell lines SK-HEP-1 [American Type Culture Collection (ATCC) number HTB-52], HepG2( ATCC number HB-8065), Hep 3B( ATCC number HB-8064), Huh7, MHCC97-H and MHCC97-L, SMMC-7721 (China Center for Type Culture Collection, resource number 3115CNCB00263), and HEK293 and HeLa cell lines were cultured and maintained in Dulbecco’s modified Eagle medium (DMEM) or modified Eagle's minimal essential medium (MEM), supplemented with 100 ml/l fetal calf serum (FCS, Gibco, USA), 100 IU/ml penicillin, 100μg /ml streptomycin at 37 ℃ in a humidified incubator with 5% CO2 (see Supplementary Figure S1). Normal primary human hepatocytes (PHHC-1， PHHC-2， PHHC-3) were isolated from 3 normal liver tissues adjacent to hepatic hemangioma under sterile conditions using a modified four-step retrograde perfusion technique as reported elsewhere.

extract_protocol: The MirVanaTM miRNA Isolation Kit (Ambion, AM1560) was used to isolate total RNA (including miRNA) from all cell lines according to the manufacturer’s protocol.

value: normal primary human hepatocytes

value: primary hepatocytes


title: PHHC-3

label_protocol: see manufacturer's web site at http://www.agilent.com/


title: Ffujikuroi_WT_24h_rep1

description: Wild-type

value: wild-type

value: 24 hrs


title: Hela

source_name: cervical carcinoma cell line

value: cervical carcinoma cell line

value: Hela


title: 4C Fab7 F12 rep2

city: Montpellier

first: Giacomo

last: Cavalli

email: itys.comet@bric.ku.dk, benjamin.leblanc@igh.cnrs.fr, frederic.bantignies@igh.cnrs.fr, giacomo.cavalli@igh.cnrs.fr

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics

hyb_protocol: 4C and control samples are pooled and co-hybridized to a NimbleGen ChIP-chip array.

scan_protocol: Nimblegen scan protocol for ChIP-chip

data_processing:
For the analysis of the microarray signals, I4c and Ictr represent hybridization levels of 4C and Control samples respectively, and the average signal intensity (A) and log-ratio (M) values are classically defined as:
A = (log2(I4c) + log2(Ictr))/2

M = log2(I4c) – log2(Ictr)
Raw microarray signal qualities were improved using a low-distortion normalization and a probe filtering steps described below.
Step 1: Low distortion normalization. To reduce biases correlated with variations of the average raw signal intensities, we directly applied lowess normalization (Cleveland, 1979) which led to important distortions. A similar problem of normalization was previously addressed to optimize correction for the dye bias that may exist in dual channel hybridizations for ChIP-on-chip data (Peng et al., 2007). Their strategy consists in a rotation in the {A, M} plane which is applied prior to lowess normalization. We therefore tested different rotation angles and selected values leading to reduced distortions during array normalization. These low-distortion normalized M signals were closely correlated to I4c hybridization levels.
Step 2: Probe filtering. Since microarray probes were originally designed using the FlyBase release 4 genome sequence, we first realigned all probes on FlyBase release 5 genome, and removed probes matching multiple genomic locations. Otherwise, we noticed that hybridization of DpnII digested DNA on conventional tiling arrays led to strong differences in raw hybridization levels for probes next to DpnII sites compared to probes closer to the middle of DpnII fragments. We therefore initially selected signals from the 94657 probes overlapping or located very next to DpnII sites, removing all probes targeting DpnII fragments inferior to 50bp in length. However, sample hybridization efficiency and specificity may be lower for probes containing a DpnII site within their oligonucleotide sequence, which correspond to 1/3 of this initial selection. We therefore refined the selection using ranked based quality scores to filter out the worst quality signals from initially selected probes, and to additionally select good signals from their direct neighbors according to DpnII sites. The best (B2) and worst (W1) probes were calculated as follows for each experiment:
B2 = { second closest to DpnII site | 20 Q(I4c) < Q(Ictr); Q(M) < Q(A) }

W1 = { closest/overlapping DpnII site | Q(I4c) > 20 Q(Ictr); Q(M) > Q(A) }

with Q(x) = (rank(x)-0.5)/N
 where N is the number of microarray probes realigned on the Flybase 5 genome release
At the end of this filtering procedure, 99% of the selected probes were less than 260 base pairs distant from a DpnII site, 70% didn't overlap with a DpnII site, and only 2% of the probes including a DpnII site had less than 25 nucleotides specifically hybridized on the matching DpnII fragment (data not shown).

organism: Drosophila melanogaster

source_name: DpnII digested genomic DNA (Control)

label_protocol: 4C and control samples are labeled in separate reactions with Cy5 and Cy3, respectively.

extract_protocol: DpnII digested genomic DNA

tag: stage

value: 3rd instar larvae

tag: fly line

source_name: 4C DNA

extract_protocol:
Chromosome Conformation Capture on Chip (4C)
Wild-type 3rd instar larvae were grown at 25°C. Larval brain and anterior discs from 200 larvae were dissected in Schneider’s Drosophila Medium and used for the 3C.  The 3C was performed as previously described (Hagege et al., 2007; Miele and Dekker, 2009) with the main differences being the use of DpnII (New England Biolabs), a 4 bp cutter restriction enzyme, and a fixation in 3% para-formaldehyde for 30 min, maximizing sensitivity and resolution of contact detection. The 4C method includes an “anchor biotinylated primer extension” procedure that involves 8 steps: step 1, linear amplification of the 3C material by Biotinylated Primer extension from the anchor fragment, step2, immobilization on streptavidin beads and denaturation, step 3, poly-G tail synthesis on the 3’ end of the single strand immobilized fragments, step 4, specific elution of immobilized products by directed digestion, step5, Linker synthesis on the 3’ end of the poly-G tail using a Biotinylated Universal Linker Synthesis Template, step6, second immobilization on streptavidin beads, step7, elution by denaturation, step8, DNA Amplification with a Forward nested anchor primer and a Reverse Universal Primer for microarray hybridization.
Excepted when mentioned, all primer extension and PCR reactions were performed with the FastStart DNA MasterPLUS SYBR Green I Kit (Roche Applied Science) using the LightCycler 2.0 Real-Time PCR System (Roche Applied Science). All incubations were performed in a Thermomixer (Comfort, Eppendorf).
The DNA obtained after the 3C procedure was resuspended in 44µl of 10mM Tris-HCl, pH8.0 and used for the 4C. The copy number of the anchor fragment was determined by real-time PCR using the Forward and Reverse Nested Anchor Primers.
Step1: Biotinylated Primer extension from the anchor fragment. The reaction volume was 20µl and contains 10E8 anchor copies of the 3C sample (input) and 0.5µM of the Biotinylated Primer. 2 reactions were performed in parallel. The primer extension program was: 1 cycle of (95ºC, 10min); 30 cycle of (95ºC, 5s; 65ºC, 5s; 72ºC, 12s). The 2 reactions were pooled, the volume adjusted to 400µl with water and separated into two samples (2x200µl) for step2.

Step2: Immobilization on streptavidin beads and denaturation. 2 batches of 1mg of Magnetic Streptavidin beads (Dynabeads MyOne Streptavidin C1, Invitrogen) were washed twice with 2X Binding Buffer (10mM Tris-HCl pH8.0; 2M NaCl) and resuspended in 200µl of this buffer. The two samples were added to the two bead batches. Incubation was performed at 25ºC under agitation at 1400rpm for 1h. The supernatants were discarded. Beads were then resuspended in 500µl of Denaturing Buffer (0.1N NaOH), and incubated at 25ºC under 1400rpm for 10min. Beads were washed once with 900µl of Denaturing Buffer and 3 times with 900µl of 10mM Tris-HCl pH8.0.
Step3: Poly-G tail synthesis. Beads were resuspended in 47.5µl of Poly-G tail synthesis Buffer (1.05X TdT Buffer (New England Biolabs (NEB)), 1.05X CoCl2 Solution (NEB), 5.26µM dGTP). Suspensions were incubated at 95ºC under 1400rpm for 1min, and then incubated on ice for 1min. 2.5µl of 20units/µl TdT (NEB) were then added to each sample, and incubated at 37ºC under 1400rpm for 20min. The TdT was inactivated at 70ºC under 1400rpm for 10min. Beads were then washed 3 times with 900µl of 10mM Tris-HCl pH8.0.
Step4: Specific elution of immobilized products by directed digestion of the anchored fragment, purification and concentration. Beads were resuspended in 50µl of Hybridization Solution (10mM Tris-HCl pH8.0; 50mM NaCl; 0.5µM Specific Elution Probe) and transferred to a 0.5 ml PCR tube. Probe hybridization was performed in a Thermocycler using the following program: (95ºC, 1min); (80ºC to 50ºC with 0.01ºC/s); (4ºC, pause). Beads were then transferred to 1.5ml eppendorf tubes. 50µl of cold Specific Elution Solution (1X Buffer 2; 250 units of 50units/µl HinfI, NEB) were added to the beads, and incubated at 37ºC under 1400rpm for 2h. The supernatants of the two samples were then collected and pooled into a new tube. Beads were then washed twice with 90µl of 10mM Tris-HCl pH8.0, and all supernatants collected during these washes were pooled (total volume of 460µl). The sample was extracted with Phenol/Chloroform/IsoAmyl Alcool pH8.0 (PCI). The aqueous phase was EtOH precipitated in the presence of 300 mM NaAc, pH5.2 and 35 µg of glycogen, at -80ºC for 10min. After centrifugation at 4ºC and 20000rcf for 90min, the DNA pellet was washed with 70% EtOH, air dried, and resuspended in 11µl of 10mM Tris-HCl, pH8.0. At this step, the anchor copy number was determined, and the yield was approximately 50% of the input.
Step5: Linker synthesis using a Biotinylated Universal Linker Synthesis Template. The reaction volume was 20µl and contained 10µl of the specific elution product and 0.5µM of the Universal Linker Synthesis Template. The linker synthesis program was: 1 cycle of (95ºC, 10min); 50 cycle of (95ºC, 5s; 32ºC, 10s; 72ºC, 5s). Linker synthesis product volume was adjusted to 200µl with water for step7.
Step 6: Second immobilization on streptavidin beads. 1mg of Magnetic Streptavidin beads was prepared as described in step2. The Linker products were added to the beads, and incubated at 25ºC under 1400rpm for 1h. The supernatant was collected into a new tube.

Step 7: Elution by denaturation, purification and concentration. Beads were mixed with 260µl Denaturing Buffer and incubated at 25ºC under 1400rpm for 10min. Supernatant was collected and mixed with 66µl of 5X Equilibration Buffer (1:1 of 1M Tris-HCl pH8.0 and 1N HCl). Beads were washed with 260µl Denaturing Buffer and the supernatant mixed with 66µl of 5X Equilibration Buffer. The 3 supernatants (collected in steps 6 and 7) were pooled and split into 2 samples (2x520µl).
The samples were extracted with PCI, and the aqueous phase was EtOH precipitated as described in step4 (but without adding NaAc). The DNA pellets were resuspended in 21µl of 10mM Tris-HCl pH8.0, and pooled. At this step, the anchor copy number was determined, and the yield was approximately 20% of the input.
Step 8: DNA amplification, purification and concentration. 8 reactions were performed in parallel using the FastStart High Fidelity PCR System, dNTPack (Roche Applied Science). Each reaction of 20µl contained 5µl (10E6 anchor copies
) of the sample in 1X FastStart High Fidelity Reaction Buffer without MgCl2, 3.5mM MgCl2, 5%(v/v) DMSO, 2µM Nested Anchor Primer (Forward), 2µM Universal Primer, 0.25mM PCR Grade Nucleotide Mix, 3.5 units of the FastStart High Fidelity Enzyme Blend. The amplification program was: 1 cycle of (95ºC, 10min); 35 cycle of (95ºC, 10s; 68ºC, 20s; 72ºC, 60s); 1 cycle of (72ºC, 5min).
All sample volumes were adjusted to 100µl with 10mM Tris-HCl pH8.0 and purified using the NucleoSpin Extract II kit (Macherey-Nagel). Elution was performed with 50µl Buffer NT (Macherey-Nagel), and samples were pooled and supplemented with 70µl 10mM Tris-HCl pH8.0. The sample was extracted with PCI, and the aqueous phase was EtOH precipitated as described in step 4. The DNA pellet was resuspended in 22µl of 10mM Tris-HCl pH8.0. More than 4µg of DNA were usually obtained after this amplification step, and 500ng were used to check the fragment size by electrophoresis on a 4% agarose denaturing gel. The fragment size is expected to range from 100bp (anchor fragment alone) to 500bp.


title: SK-HEP-1

source_name: human liver cancer cell line

value: human liver cancer cell line


title: lobular carcinoma in situ -2

description:
lcis2a.gpr
lcis2b.gpr

value: lobular carcinoma in situ


title: MHCC97-L


title: 4C Fab7 F12 rep1


title: HepG2


title: PHHC-1


title: MHCC97-H


title: 129S2_4

source_name: 129S2, Male, liver

tag: strain

tag: gender


title: lobular carcinoma in situ -1

description:
lcis1a.gpr
lcis1b.gpr


title: 4C Fab7 WT rep1

value: wild type


title: A/J_1


title: Ffujikuroi_WT_72h_rep1

description: Wild-type

source_name: Fusarium fujikuroi IMI58289 wild-type

value: 72 hrs


title: 4C Fab7 WT rep2


title: Anchorage_Island_vegetated_soil_OTC_rep2

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

hyb_protocol: The microarray hybridizations were carried out for 4 h at 50 °C in the presence of 50% formamide, as previously described (Yergeau et al. 2007, ISMEJ)

scan_protocol: The slides were scanned in a ScanArray Lite (Perkin Elmer, Boston, MA) at a 10 µm resolution. The resulting image files were gridded and quantified using ScanArray Express.

data_processing:
The signal-to noise ratio (SNR) was calculated based on the formula: SNR = (signal intensity - background)/standard deviation of background. Spots with SNR greater or equal to two were considered positive. Data processing, such as outlier removal, normalization, and poor spot removal, was carried out as previously described(35). GeoChip normalized intensity was summed for each of the gene categories present on the array (138 categories).
Additional details: Raw data from ImaGene were submitted to Microarray Data Manager in our website (http://ieg.ou.edu/microarray/) and analyzed using the data analysis pipeline with the following major steps: (i) The spots flagged as 1 or 3 by Imagene and with a signal to noise ratio (SNR) less than 2.0 (He & Zhou 2008) were removed as poor-quality spots; (ii) After removing the bad spots, normalized intensity of each spot was calculated by dividing the signal intensity of each spot by the mean intensity of the microarray; (iii) If any of replicates had (signal-mean) more than two times the standard deviation, this replicate was moved as an outlier. This process continued until no such replicates were identified; (iv) At least 0.34 time of the final positive spots (probes), or a minimum of two spots was required for each gene.

organism: environmental samples

source_name: Soil, Anchorage Island, vegetated, warmed (OTC) plots

label_protocol: Fifty nanograms of extracted soil DNA was amplified using whole-genome amplification as described previously. The amplified DNA was fluorescently labeled with Cy5 dye (GE Healthcare, Piscataway, NJ, USA) by using random primers and the large (Klenow) fragment of DNA polymerase I (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Nucleic acids were extracted from 500 mg soil sub-samples following bead-beating disruption in a CTAB buffer and subsequent phenol-chloroform purification. After extraction and confirmation of low intra-plot variability of resulting bacterial PCR-DGGE profiles, nucleic acids from the same plot were pooled to provide a single representative DNA sample.

treatment_protocol: Warmed (OTC)

tag: geographical region

value: Anchorage Island, Antarctica

value: soil

tag: soil type

value: vegetated

tag: plot

value: warmed (OTC) plots


title: Anchorage_Island_vegetated_soil_OTC_rep6

tag: sample type


title: Anchorage_Island_fell-field_soil_OTC_rep4

source_name: Soil, Anchorage Island, fell-field, warmed (OTC) plots

value: fell-field


title: Anchorage_Island_fell-field_soil_OTC_rep6


title: Signy_Island_vegetated_soil_OTC_rep3

source_name: Soil, Signy Island, vegetated, warmed (OTC) plots

value: Signy Island, Antarctica


title: Signy_Island_vegetated_soil_OTC_rep5


title: 129S2_2

value: Male

value: liver

source_name: C57BL/6J, Male, liver


title: Anchorage_Island_fell-field_soil_OTC_rep2


title: Anchorage_Island_fell-field_soil_OTC_rep1


title: A/J_2

value: A/J


title: Hep3B

tag: cell line


title: Signy_Island_fell-field_soil_OTC_rep2

source_name: Soil, Signy Island, fell-field, warmed (OTC) plots


title: Falkland_Islands_fell-field_soil_OTC_rep1

source_name: Soil, Falkland Islands, fell-field, warmed (OTC) plots

value: Falkland Islands


title: Falkland_Islands_fell-field_soil_OTC_rep3


title: Signy_Island_fell-field_soil_OTC_rep3


title: Signy_Island_vegetated_soil_OTC_rep2


title: Signy_Island_vegetated_soil_OTC_rep1


title: Falkland_Islands_vegetated_soil_OTC_rep9

source_name: Soil, Falkland Islands, vegetated, warmed (OTC) plots


title: Falkland_Islands_vegetated_soil_OTC_rep7


title: Falkland_Islands_vegetated_soil_OTC_rep5


title: Falkland_Islands_vegetated_soil_OTC_rep6


title: Falkland_Islands_vegetated_soil_OTC_rep4


title: Falkland_Islands_vegetated_soil_OTC_rep3


title: 129S2_1


title: Anchorage_Island_fell-field_soil_control_rep4

source_name: Soil, Anchorage Island, fell-field, control plots

treatment_protocol: Control

value: control plots


title: Falkland_Islands_vegetated_soil_OTC_rep2


title: Falkland_Islands_vegetated_soil_OTC_rep1


title: 129S2_3


title: Signy_Island_vegetated_soil_control_rep5

source_name: Soil, Signy Island, vegetated, control plots


title: Anchorage_Island_fell-field_soil_control_rep2


title: invasive lobular carcinoma -2

description:
ilc2a.gpr
ilc2b.gpr

source_name: FFPE tissue

value: invasive lobular carcinoma

tag: patient

source_name: FFPE lymph nodes, pooled

value: pooled lymph nodes


title: Signy_Island_vegetated_soil_control_rep4


title: SMMC-7721

tag: cell type

value: human liver cancer cell line


title: Signy_Island_fell-field_soil_control_rep3

source_name: Soil, Signy Island, fell-field, control plots


title: Signy_Island_fell-field_soil_control_rep4


title: Signy_Island_vegetated_soil_control_rep6


title: Anchorage_Island_fell-field_soil_control_rep1


title: Signy_Island_fell-field_soil_control_rep5


title: Signy_Island_vegetated_soil_control_rep2


title: Falkland_Islands_vegetated_soil_control_rep7

source_name: Soil, Falkland Islands, vegetated, control plots


title: Falkland_Islands_vegetated_soil_control_rep9


title: Falkland_Islands_vegetated_soil_control_rep5


title: Signy_Island_vegetated_soil_control_rep1


title: Falkland_Islands_vegetated_soil_control_rep6


title: Falkland_Islands_vegetated_soil_control_rep4


title: Signy_Island_vegetated_soil_control_rep3


title: Falkland_Islands_vegetated_soil_control_rep2


title: Falkland_Islands_vegetated_soil_control_rep3


title: Falkland_Islands_fell-field_soil_control_rep1

source_name: Soil, Falkland Islands, fell-field, control plots


title: Falkland_Islands_fell-field_soil_control_rep3


title: Signy_Island_fell-field_soil_control_rep1


title: Falkland_Islands_fell-field_soil_control_rep2


title: Signy_Island_fell-field_soil_control_rep2


title: Falkland_Islands_vegetated_soil_control_rep1


title: Brugia malayi array -3

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

hyb_protocol: Oligo arrays were hybridized to the cDNA probes in formamide based-hybridization buffer (MWG’s “Coverslips Hybridization buffer”) at 42C overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each. Fluorescent Cy3- and Cy5- capture reagents were combined in MWG’s “Coverslips hybridization buffer” and added to each array. The arrays were incubated for 3 hours at 50C and washed as above. Each experiment consisted of a pair wise competitive hybridization of cDNA samples from female and male worms

scan_protocol: Using Axon's GenePix 4000B fluorescent scanner.

data_processing: Axon's GenePix Pro software was used for extracting the data from the scanned images of the microarrays

organism: Brugia malayi

source_name: Brugia malayi adult female parasite

label_protocol: 30ug of total RNA labeled with Cy3 or CY5 as per manufcaturer's instructions (Amersham Pharmacia)

growth_protocol: Adult males and females of Brugia malayi were harvested from the peritoneal cavity of infected jird (Meriones unguiculatus)

extract_protocol: RNA was extracted using the Trizol kit from Invitrogen and passed over the RNeasy column from Qiagen

tag: Female

source_name: Brugia malayi adult male parasite

tag: Male


title: Brugia malayi array -1


title: Huh7

source_name: human liver cancer cell line


title: Brugia malayi array -2


title: 251209757234

city: Durham

first: Rick

middle: David

last: Fannin

state: NC

address: 111 T.W. Alexander Drive

department: Office of the Director

institute: The National Institute of Environmental Health Sciences

hyb_protocol: For each two-color comparison, 750 ng of each Cy3- (universal control) and Cy5-labeled sample cRNA were mixed and fragmented using the Agilent in situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were scanned using an Agilent Scanner (Agilent Technologies, Wilmington, DE).

data_processing: Microarray data were obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters. The Feature Extraction Software performs error modeling. Raw expression intensities were background subtracted and loess normalized using Agilent Feature Extraction software (v7.5). Normalized log ratios (ratio for each probe was calculated by dividing sample intensity by the universal control intensity followed by log2 transformation) were used for Principal Component Analysis (PCA) to investigate the effect of known sample variables such as subject age, gender, race, disease status, disease activity, medications, and peripheral white blood cell counts and differentials, as well as technical variables such as sample hybridizations performed at different times. We observed no obvious differences across the first three principal components due to age, gender, ethnicity, disease status, or treatment. However, we noticed that samples were segregating in groups represented by their hybridization batch (data not shown). To correct for this difference, we centered the ratios for each probe using the median for their hybridization group. The PCA plots generated using the corrected data showed no obvious groupings; hence we used this data for further analyses.  before data are loaded into a database system. Images and GEML files, including error and p-values, were exported from the Agilent Feature Extraction software and deposited into Rosetta Resolver (version 5.0, build 5.0.0.2.48) (Rosetta Biosoftware, Kirkland, WA). The Rosetta Resolver system combines data hybridizations using an error-weighted average that adjusts for additive and multiplicative noise. Resulting log ratios were exported for further analysis.

source_name: Universal Human Control RNA

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit, according to manufacturer’s protocol.

extract_protocol: RNA was purified using the PAXgene RNA Isolation Kit (Qiagen, Inc., Valencia, CA) according to manufacturer's recommendations.

treatment_protocol: Samples were peripheral blood drawn from MZ twins and related controls into Qiagen PAXtubes to preserve RNA for later extraction.

tag: source

value: RNA from human cell lines

source_name: Total RNA from whole blood

tag: sample id

tag: disease status

value: Healthy Twin

tag: disease subtype

value: RA

tag: family

value: Healthy Twin Family 112


title: 251209757233

value: Twin Proband

value: Twin Proband Family 112


title: 251209757315

value: IIM

value: Twin Proband Family 103


title: 251209756113

value: Control 1

value: Control 1 Family 132


title: 251209756222

value: Twin Proband Family 127


title: 251209757307

value: Twin Proband Family 129


title: Chip03_UPO_070637

city: Novara

first: Ilaria

last: Gregnanin

address: V. Solaroli 17

country: Italy

institute: Università del Piemonte Orientale

hyb_protocol: Hybridized to the LC Sciences miRNA microarray (miRBase v9.1) overnight at 34°C. Performed by LC Sciences (http://www.lcsciences.com/).

scan_protocol: Scanned using the GenePix 4000B scanner. Fluorescent images were digitized using Array-Pro image analysis. Performed by LC Sciences (http://www.lcsciences.com/).

data_processing: All of the statistical analyses were performed by LC Sciences (http://www.lcsciences.com/) using MeV software (http://www.tm4.org/mev.html). Normalization of the samples was performed using a global normalization approach (LOWESS).

source_name: Eutopic endometrium tissue RNA

extract_protocol: MicroRNAs were extracted from tissues with the miRNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol and quantified by the QuantiT RNA Kit with Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: female

tag: tissue

value: eutopic endometrium

tag: disease state

value: ovarian endometriosis

tag: disease stage

value: III

source_name: Ectopic endometrium tissue RNA

value: ectopic endometrium


title: Chip02_UPO_070634

label_protocol: Performed by LC Sciences (http://www.lcsciences.com/).

tag: gender


title: 251209757324

value: RNA from human cell lines

value: Control 1 Family 78


title: Donor4, treated, rep2

city: Los Angeles

first: Juyong

middle: Brian

last: Kim

state: CA

address: 675 Charles Young Dr.

department: Department of Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol; Iscan hardware running iScan control software version 3.2.30

data_processing: Average normalization computed with GenomeStudio; batch correction was performed using ComBat using R

label: biotin

source_name: HAEC, treated

label_protocol: Biotinylated cRNA were prepared with Illumina Total prep amp kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: donor

value: primary human aortic endothelial cells (HAEC)

tag: agent


title: Donor4, treated, rep3


title: Signy_Island_vegetated_soil_OTC_rep6

source_name: Soil, Signy Island, vegetated, warmed (OTC) plots

tag: geographical region

value: Signy Island, Antarctica

tag: sample type

value: soil

tag: soil type

value: vegetated

tag: plot

value: warmed (OTC) plots


title: Chip04_UPO_070641

value: IV

tag: patient


title: 251209757334

value: Twin Proband

value: IIM

value: Twin Proband Family 78


title: Donor4, treated, rep1

tag: cell line


title: Donor4, control, rep3

source_name: HAEC, control

value: control


title: 251209757321

tag: source

value: Control 1

value: SLE

value: Control 1 Family 61


title: 251209757339

tag: sample id

value: Healthy Twin

value: Healthy Twin Family 132


title: Donor4, control, rep2


title: Anchorage_Island_fell-field_soil_OTC_rep3

source_name: Soil, Anchorage Island, fell-field, warmed (OTC) plots

value: Anchorage Island, Antarctica

value: fell-field


title: 251209757322

value: RNA from human cell lines

tag: disease status

value: Control 2

value: Control 2 Family 61


title: wild-type NEM treated, replication 4

city: Memphis

first: Thomas

middle: R

last: Sutter

state: TN

address: 3774 Walker Ave.

department: Biology

institute: University of Memphis

description: Gene expression data from chemical treated with NEM

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using the GC-RMA algorithm.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae treated with NEM in early exponential phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Enzo BioArray High Yield RNA Transcript Labeling Kit).

growth_protocol: The yeast strain BY4741 was grown in yeast extract peptone dextrose (YEPD) medium at 30C and shaken at 250 rpm.

extract_protocol: Total RNA was extracted using STAT-60 (Tel-Test, Friendswood, TX).

treatment_protocol: Samples were treated with 0.3 mM H2O2, 0.05 mM acrolein, or 0.016 mM NEM for 1 hr at 30C.

tag: strain

tag: genome/variation

value: wild type

tag: treatment group

value: NEM treated

tag: cell cycle phase

value: early exponential


title: 251209757338

tag: disease subtype

tag: family

value: Control 1 Family 129


title: Donor4, control, rep1

tag: donor

value: primary human aortic endothelial cells (HAEC)


title: Donor3, treated, rep3

tag: agent


title: 251209757308

value: IIM

value: Healthy Twin Family 129


title: wild-type NEM treated, replication 2


title: 251209757318

value: Control 1

value: RA

value: Control 1 Family 004


title: 251209757323

value: Healthy Twin

value: Healthy Twin Family 78


title: Donor3, treated, rep1


title: wild-type NEM treated, replication 1


title: 251209757317

value: Healthy Twin Family 004


title: Donor3, treated, rep2


title: 251209757320

value: Twin Proband

value: Twin Proband Family 33


title: wild-type NEM treated, replication 3


title: 251209757316

value: RNA from human cell lines

value: Twin Proband Family 004


title: Donor3, control, rep3

value: control


title: 251209757325

value: Control 2

value: Control 2 Family 78


title: wild-type H2O2 treated, replication 4

description: Gene expression data from chemical treated with H2O2

source_name: Saccharomyces cerevisiae treated with H2O2 in early exponential phase

value: wild type

value: H202 treated

value: early exponential


title: tumor_33, aCGH

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were hybridized to Mouse CGH 3x720K WGT arrays as per manufacturer’s protocol.

scan_protocol: Arrays were scanned using Nimblegen MS 200 scanner.

data_processing: Arrays were processed and qspline normalized using Nimblegen’s standard protocol for NimbleScan v2.4.

source_name: Bl/6 Taconic APL mouse spleen

label_protocol: Samples were labeled as per Nimblegen standard protocol.

extract_protocol: Genomic DNA was isolated from banked splenocytes after being lysed with a 1% Triton X-100 lysis buffer with 2mg/ml of Proteinase K added (Sigma-Aldrich, Saint Louis, MO), followed by standard phenol-chloroform extraction.

value: Bl/6 Taconic

tag: tissue

value: APL spleen

tag: disease state

value: acute promyelocytic leukemia (APL)

source_name: Bl/6 Taconic WT pool

tag: genotype

tag: age

value: 6 weeks

value: spleen

value: reference


title: 251209757310

value: IIM

value: Control 2 Family 129


title: 251209757306

value: Control 2 Family 127


title: Donor3, control, rep2

value: primary human aortic endothelial cells (HAEC)


title: wild-type H2O2 treated, replication 3


title: Donor3, control, rep1


title: tumor_9520, aCGH

tag: sample type


title: wild-type H2O2 treated, replication 2


title: tumor_26, aCGH


title: 251209756225

value: RNA from human cell lines

value: Control 1

value: Control 1 Family 127


title: 251209756221

value: Control 2

value: RA

value: Control 2 Family 112


title: 251209757337

value: Healthy Twin

value: Healthy Twin Family 127


title: 251209757335

value: Twin Proband

value: Twin Proband Family 132


title: tumor_9514, aCGH

value: Bl/6 Taconic

value: APL spleen

value: acute promyelocytic leukemia (APL)

value: wild type

value: 6 weeks


title: Donor2, treated, rep2

tag: cell line


title: wild-type H2O2 treated, replication 1

value: H202 treated

value: early exponential


title: WT_129_SVJ

source_name: 129/SvJ WT mouse spleen

value: spleen

value: reference


title: wild-type acrolein treated, replication 4

description: Gene expression data from chemical treated with acrolein

source_name: Saccharomyces cerevisiae treated with acrolein in early exponential phase

value: acrolein treated


title: 251209757231

tag: source

value: RNA from human cell lines

value: Control 1

value: IIM

value: Control 1 Family 103


title: 251209757232

tag: sample id

value: Control 2

value: Control 2 Family 103


title: 251209756220

tag: disease status

value: RA

value: Control 1 Family 112


title: Donor2, control, rep2

value: primary human aortic endothelial cells (HAEC)

value: control


title: wild-type acrolein treated, replication 3

tag: strain

value: wild type


title: Donor2, treated, rep1


title: 251209757313

value: SLE

value: Control 1 Family 93


title: 251209757230

value: Healthy Twin

value: Healthy Twin Family 103


title: 251209757314

value: Control 2 Family 93


title: 251209756114

value: Control 2 Family 132


title: tumor_9529, aCGH

value: Bl/6 Taconic

value: APL spleen

value: acute promyelocytic leukemia (APL)

value: 6 weeks

value: spleen

value: reference


title: tumor_9523, aCGH


title: tumor_9500, aCGH


title: 251209757311

value: RNA from human cell lines

value: Twin Proband

value: Twin Proband Family 93


title: wild-type acrolein treated, replication 1

tag: genome/variation

value: acrolein treated

value: early exponential


title: Donor2, control, rep1

value: primary human aortic endothelial cells (HAEC)

value: control


title: 251209757312

value: Healthy Twin

value: SLE

value: Healthy Twin Family 93


title: tumor_9509, aCGH

value: wild type


title: tumor_9508, aCGH

value: Bl/6 Taconic


title: 251209757330

value: IIM

value: Healthy Twin Family 33


title: tumor_9504, aCGH

value: APL spleen

value: acute promyelocytic leukemia (APL)

value: 6 weeks


title: tumor_31, aCGH

value: spleen

value: reference


title: tumor_9495, aCGH


title: 251209757336

value: RNA from human cell lines

value: Healthy Twin Family 61


title: 251209757319

value: Control 2

value: RA

value: Control 2 Family 004


title: wild-type acrolein treated, replication 2

tag: treatment group

value: acrolein treated

value: early exponential


title: wild-type control, replication 4

description: Gene expression data from chemical untreated

source_name: Saccharomyces cerevisiae in early exponential phase

value: control

tag: cell cycle phase


title: 251209757332

tag: disease subtype

value: Control 2 Family 33


title: Donor1, treated, rep1

value: primary human aortic endothelial cells (HAEC)


title: wild-type control, replication 3

value: wild type


title: tumor_9492, aCGH

value: Bl/6 Taconic


title: 251209749472

value: Control 1

value: IIM

tag: family

value: Control 1 Family 10


title: Donor1, treated, rep2

tag: donor


title: wild-type control, replication 2


title: wild-type control, replication 1


title: tumor_36, aCGH

value: APL spleen

value: acute promyelocytic leukemia (APL)

value: 6 weeks

value: spleen


title: 251209757333

value: RNA from human cell lines

value: Twin Proband

value: SLE

value: Twin Proband Family 61


title: 251209749457

value: RA

value: Twin Proband Family 80


title: Donor1, control, rep2

tag: agent

value: control


title: 251209749471

value: Healthy Twin

value: Healthy Twin Family 10


title: 251209749460

value: Control 2

value: Control 2 Family 80


title: 251209749699

value: Control 2 Family 30


title: Donor1, control, rep4

value: primary human aortic endothelial cells (HAEC)


title: tumor_29, aCGH

value: Bl/6 Taconic

tag: tissue

value: APL spleen

value: wild type

value: reference


title: 251209757331

value: RNA from human cell lines

value: Control 1

value: IIM

value: Control 1 Family 33


title: 251209749458

value: RA

value: Healthy Twin Family 80


title: MYD88-7 shRNA - 48 hr - mAdbID:99294 [MYD88 study]

first: Louis

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 99294

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: Untreated HBL-1 cells

label_protocol:
Cy3 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

value: blood

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: shMYD88-7 shRNA - 48 hr

label_protocol:
Cy5 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy5.

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cell line was transduced with retroviral vectors expressing shMYD88-7. shRNA expression was induced with doxycycline for 48 hours.


title: Donor1, control, rep1

value: control


title: 251209749459

source_name: Universal Human Control RNA


title: 251209749360

source_name: Total RNA from whole blood

value: Twin Proband

value: Twin Proband Family 10


title: MYD88-4 shRNA - 48 hr - mAdbID:99296 [MYD88 study]

description: mAdb experiment ID: 99296

source_name: shMYD88-4 shRNA - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: HBL-1 cell line was transduced with retroviral vectors expressing shMYD88-4. shRNA expression was induced with doxycycline for 48 hours.


title: Subject 7 Baseline rep 2 4336687057_K

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Baseline

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using robust spline normalization (RSN) algorithm available in Bioconductor's lumi package

source_name: Human colorectal mucosal biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and purified with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Female

value: 49 years

value: Colorectal mucosa

value: Baseline


title: 251209752360

value: Control 2

value: Control 2 Family 10


title: MYD88-4 shRNA - 24 hr - mAdbID:99295 [MYD88 study]

description: mAdb experiment ID: 99295

source_name: shMYD88-4 shRNA - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cell line was transduced with retroviral vectors expressing shMYD88-4. shRNA expression was induced with doxycycline for 24 hours.


title: 251209749696

value: RNA from human cell lines

value: SLE

value: Twin Proband Family 30


title: Subject 10 Baseline rep 2 4336687057_L

description: Baseline

tag: age

value: 47 years


title: Donor1, control, rep3

value: primary human aortic endothelial cells (HAEC)


title: Donor1, treated, rep3

source_name: HAEC, treated


title: 251209749698

value: Control 1

value: Control 1 Family 30


title: MYD88-7 shRNA - 24 hr - mAdbID:99293 [MYD88 study]

description: mAdb experiment ID: 99293

value: blood

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: shMYD88-7 shRNA - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: HBL-1 cell line was transduced with retroviral vectors expressing shMYD88-7. shRNA expression was induced with doxycycline for 24 hours.


title: 251209749700

value: RA

value: Control 1 Family 86


title: 251209749697

value: Healthy Twin

value: Healthy Twin Family 30


title: 251209749655

value: Twin Proband

value: Twin Proband Family 86


title: Subject 11 After Weight Loss  4336687057_J

description: After Weight Loss

value: Female

value: 43 years

value: Colorectal mucosa

tag: sample type

value: After Weight Loss


title: Subject 11 Baseline  4336687057_I

description: Baseline

value: Baseline


title: 251209752364

value: RNA from human cell lines

value: Control 2

value: Control 2 Family 86


title: 251209749864

value: Control 1

value: Control 1 Family 85


title: JAK inhibitor I Treated HBL-1 - 6 hrs - mAdbID:102030 [MYD88 study]

description: mAdb experiment ID: 102030

source_name: DMSO Treated HBL-1 cells

value: blood

tag: cell line

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: JAK inhibitor I - 6 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK inhibitor I
Treatment dose: 5 uM
Treatment time: 6 hours


title: 251209749862

tag: source

value: RA

value: Twin Proband Family 85


title: 251209752362

tag: sample id

value: Control 2 Family 85


title: 251209752555

tag: disease status

value: Healthy Twin

value: Healthy Twin Family 85


title: Subject 9 After Weight Loss  4336687057_F

description: After Weight Loss

value: Female

value: 37 years


title: Subject 10 Baseline rep 1 4336687057_G

description: Baseline

value: 47 years

value: Colorectal mucosa


title: 251209749476

value: SLE

value: Control 1 Family 79


title: Subject 10 After Weight Loss  4336687057_H

description: After Weight Loss

value: After Weight Loss


title: 251209752061

value: RNA from human cell lines

value: Healthy Twin Family 86


title: JAK inhibitor I Treated HBL-1 - 2 hrs - mAdbID:102028 [MYD88 study]

description: mAdb experiment ID: 102028

source_name: JAK inhibitor I - 2 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK inhibitor I
Treatment dose: 5 uM
Treatment time: 2 hours


title: 251209749473

value: Twin Proband

value: Twin Proband Family 82


title: 251209749868

value: Control 2

value: Control 2 Family 82


title: 251209749477

value: Control 2 Family 79


title: Subject 9 Baseline  4336687057_E

description: Baseline

value: Baseline


title: 251209749866

value: Healthy Twin

value: Healthy Twin Family 82


title: K562-r_48H_Am8

city: Shanghai

first: wentao

last: yang

address: chong qing nan lu #225

department: Institute of Health Science

institute: Shanghai Institute for Biological Sciences,China Academy of Science

hyb_protocol: cDNA array control targets and hybridization buffer were added, and samples were applied to microarrays enclosed.After hybridization, slides were washed sequential

scan_protocol: Scanned on an Axon Genepix 4000B Scanner. Images were quantified using Axon GenePix Pro Software (version 4.1.1.4).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: K562-r,AMN107 treated,48h

label_protocol: 30 µg of total RNA were primed with 1.5 µl of 0.5 ug/ul oligo dT primer at 70°C for 5 min, then reversed transcribed at 42°C for 1.5 h in the presence of 200 U SuperScript™ II Reverse Transcriptase (Invitrogen), and 2 nM each dATP, dTTP, dGTP, with 1 nM dCTP, 1 nM Cy3-labe or 1 nM Cy5-labe

growth_protocol: The CML-derived imatinb-resistant induced cell line K562-r were cultured in RPMI 1640 (GIBCO, Los Angeles, USA) supplemented with 10% v/v fetal bovine serum (PAA, Linz, Austria), 1mM L-glutamine and penicillin (50 U)/streptomycin (50 mg) at 37°C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: treated with 8uM AMN107, collected after 48h

tag: culure intensity

tag: cell type

value: imatinib resistance clone derived from human leukemia cell line K562

value: chronic myelogenous leukemia

source_name: Total RNA from K562-r,untreated,0h


title: Subject 7 After Weight Loss  4336687057_D

description: After Weight Loss

value: Female

value: 49 years


title: JAK inhibitor I Treated HBL-1 - 4 hrs - mAdbID:102029 [MYD88 study]

description: mAdb experiment ID: 102029

value: blood

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: JAK inhibitor I - 4 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK inhibitor I
Treatment dose: 5 uM
Treatment time: 4 hours


title: K562-r_48H_A1.5Am8

treatment_protocol: treated with 1.5uM ATO and 8uM AMN107, collected after 48h

tag: treatment group


title: 251209749475

value: SLE

value: Healthy Twin Family 79


title: 251209749654

value: RNA from human cell lines

value: IIM

value: Control 2 Family 65


title: Subject 7 Baseline rep 1 4336687057_C

description: Baseline

value: Colorectal mucosa


title: 251209751990

value: Healthy Twin Family 65


title: 251209749474

value: Twin Proband

value: Twin Proband Family 79


title: JAK inhibitor I Treated HBL-1 - 8 hrs - mAdbID:102031 [MYD88 study]

description: mAdb experiment ID: 102031

source_name: JAK inhibitor I - 8 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK inhibitor I
Treatment dose: 5 uM
Treatment time: 8 hours


title: 251209749653

value: Control 1

value: Control 1 Family 65


title: K562-r_48H_A1.5

source_name: K562-r,ATO treated,48h

treatment_protocol: treated with 1.5uM ATO, collected after 48h

value: imatinib resistance clone derived from human leukemia cell line K562


title: 251209749867

value: Control 1 Family 82


title: 251209749651

value: Twin Proband Family 65


title: K562-r_24H_Am8

source_name: K562-r,AMN107 treated,24h

treatment_protocol: treated with 8uM AMN107, collected after 24h

value: chronic myelogenous leukemia


title: Subject 6 Baseline  4336687057_A

description: Baseline

value: Female

value: 24 years

value: Baseline


title: K562-r_24H_A1.5Am8

treatment_protocol: treated with 1.5uM ATO and 8uM AMN107, collected after 24h


title: Subject 6 After Weight Loss  4336687057_B

description: After Weight Loss

value: After Weight Loss


title: 251209749861

value: RNA from human cell lines

value: Control 2

value: SLE

value: Control 2 Family 49


title: 251209749829

value: Healthy Twin

value: Healthy Twin Family 49


title: K562-r_24H_con

value: untreated, collected after 24h


title: K562-r_24H_A1.5

source_name: K562-r,ATO treated,24h

treatment_protocol: treated with 1.5uM ATO, collected after 24h


title: 251209752363

source_name: Universal Human Control RNA

value: Twin Proband

value: Twin Proband Family 49


title: Subject 4 Baseline rep 2 4336687055_L

description: Baseline

value: 49 years

value: Colorectal mucosa


title: 251209749830

source_name: Total RNA from whole blood

value: Control 1

value: Control 1 Family 49


title: 251209749456

value: RA

value: Control 2 Family 12


title: K562-r_48H_con

value: imatinib resistance clone derived from human leukemia cell line K562

value: chronic myelogenous leukemia

value: untreated, collected after 48h


title: Subject 2 Baseline rep 2 4336687055_K

description: Baseline

value: Female

value: 43 years

value: Baseline


title: K562-r_12H_A1.5Am8

treatment_protocol: treated with 1.5uM ATO and 8uM AMN107, collected after 12h


title: 251209749478

treatment_protocol: Samples were peripheral blood drawn from MZ twins and related controls into Qiagen PAXtubes to preserve RNA for later extraction.

value: RNA from human cell lines

value: Twin Proband Family 12


title: K562-r_12H_con

value: untreated, collected after 12h


title: 251209749480

value: Control 1 Family 12


title: Subject 5 After Weight Loss  4336687055_J

description: After Weight Loss

value: 52 years

value: After Weight Loss


title: K562-r_12H_A1.5

source_name: K562-r,ATO treated,12h

treatment_protocol: treated with 1.5uM ATO, collected after 12h


title: Subject 5 Baseline  4336687055_I

description: Baseline

source_name: Human colorectal mucosal biopsy

value: Colorectal mucosa


title: Subject 4 After Weight Loss  4336687055_H

description: After Weight Loss

value: 49 years


title: K562-r_3H_con

value: untreated, collected after 3h


title: Subject 3 After Weight Loss  4336687055_F

description: After Weight Loss

value: 39 years


title: Subject 4 Baseline rep 1 4336687055_G

description: Baseline


title: Subject 3 Baseline  4336687055_E

description: Baseline


title: K562-r_3H_A1.5

source_name: K562-r,ATO treated,3h

treatment_protocol: treated with 1.5uM ATO, collected after 3h


title: K562-r_0H_Con

value: untreated


title: K562-r_3H_Am8

source_name: K562-r,AMN107 treated,3h

treatment_protocol: treated with 8uM AMN107, collected after 3h

value: imatinib resistance clone derived from human leukemia cell line K562


title: Input ChIP-Chip Array F rep1

status: Public on Dec 29 2010

city: Lebanon

first: Mathieu

last: Lupien

state: NH

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar

data_processing:
Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718
BAR files derived from MAT analysis on Hg18 for ChIP-chip samples.

source_name: Input DNA

value: EGF treated MCF7 breast cancer cells

tag: fraction

value: control Input DNA


title: K562-r_3H_A1.5Am8

source_name: K562-r,ATO combinied AMN107untreated,3h

treatment_protocol: treated with 1.5uM ATO and 8uM AMN107, collected after 3h

value: chronic myelogenous leukemia


title: ERa-EGF ChIP-Chip Array F rep2

hyb_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718

source_name: ERa ChIP DNA

value: ChIP

tag: reference

value: Input DNA from same sample used for ChIP against ERa


title: ERa-EGF ChIP-Chip Array F rep3

scan_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: ERa-EGF ChIP-Chip Array F rep1

label_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: Input ChIP-Chip Array F rep2

growth_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: Subject 2 Baseline rep 1 4336687055_C

description: Baseline

value: Female

value: 43 years

value: Baseline


title: Subject 2 After Weight Loss  4336687055_D

description: After Weight Loss


title: Subject 1 After Weight Loss  4336687055_B

description: After Weight Loss


title: Subject 1 Baseline  4336687055_A

description: Baseline


title: 251209749479

value: RNA from human cell lines

value: Healthy Twin

tag: disease subtype

value: RA

tag: family

value: Healthy Twin Family 12


title: Sham.8.b

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: L4-L5 rat DRGs after sciatic nerve lesion

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Array data were preprocessed with the robust multichip analysis algorithm (RMA), and data quality was assessed by principal components analysis.

organism: Rattus norvegicus

label_protocol: Affymetrix protocol

growth_protocol: Eight- to 12-week-old Wistar rats were subjected to crush lesion

extract_protocol: Qiagen Rneasy

treatment_protocol: L4/L5 DRG were dissected from crush-lesioned animals at the indicated time points

tag: strain

value: Wistar

tag: lesion

value: Sham

tag: time (hours)


title: Sham.24.c


title: Sham.3.a


title: Sham.28.b


title: Sham.8.c


title: Sham.3.b


title: Sham.8.a


title: Sham.18.b


title: Sham.28.a


title: Sham.24.b


title: Sham.16.a


title: Sham.3.c


title: Sham.1.c


title: Sham.18.c


title: Sham.28.c


title: Sham.1.b


title: Sham.1.a


title: Sham.18.a


title: Sham.12.a


title: Sham.24.a


title: Inj.3.c

value: Proximal


title: Inj.3.a


title: Inj.28.c


title: Sham.12.b


title: K562-r_12H_Am8

source_name: K562-r,AMN107 treated,12h

treatment_protocol: treated with 8uM AMN107, collected after 12h


title: Inj.8.a


title: Inj.1.b


title: Inj.28.b


title: Inj.16.b


title: Inj.18.b


title: Inj.1.c


title: Dis.8.eo

value: Distal


title: Dis.8.a


title: Inj.8.c


title: Dis.8.do


title: Inj.24.b


title: Dis.8.c


title: Inj.24.a


title: Inj.18.c


title: Inj.12.a


title: Dis.3.b


title: Inj.8.b


title: Dis.3.c


title: Inj.18.a


title: Inj.1.a


title: Inj.3.b


title: Inj.24.c


title: Inj.12.b


title: Dis.8.b


title: Dis.28.c


title: Inj.28.a


title: Inj.16.a


title: Dis.28.b


title: Dis.3.a


title: Gr1+CD11b+ sorted mononuclear cells from spleen of Neu+ tumor bearing mice Replicate 1

city: Chapel Hill

first: June

last: Brickey

address: 450 West Drive

institute: UNC

description: Biological replicate 1 of 2. Myeloid-derived suppressor cells (Gr1+ CD11b+) from spleen of neu+ tumor bearing FVB/neu-N mice

hyb_protocol: Cy-labeled experimental (Red, Cy5) and Universal reference (Cy3, Green) probes were combined in hybridization buffer (40% formamide in SSC, poly(dA) oligo, COT-1 DNA), heated, and samples were applied to microarrays enclosed by Maui Mixer (SC, BioMicroSystems). After 18 hour hybridization at 42C with constant mixing, slides were washed briefly in SSC-SDS buffers.

scan_protocol: Scanned on a GenePix 4000B scanner (Molecular Dynamics). Images were quantified using GenePix Pro Software (version 6.0).

data_processing: normalized to housekeeping Actinb and Ribosomal Rpl13a signals, background subtracted data, filtered for present or marginal flags only, log (base2) of processed Cy5 signal/processed Cy3 signal ratio using GeneSpring v7

source_name: FACS sorted splenic cells

label_protocol: 100 ng of total RNA were amplified and labeled using Oligo dT primer, SuperScriptIII reverse transcriptase, and aminoallyl-UTP using TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit 101 according to manufacturer's instructions (Epicentre). Amplified aa-RNA probes were coupled to Cy5 or Cy3 dyes (GE HealthCare) and RNeasy column purified (Qiagen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (Invitrogen) and cleaned over the RNEasy column (Qiagen).

treatment_protocol: Neu+ tumor-bearing (2cm^2)

value: FVB/neu-N

value: Gr1+ CD11b+ sorted cells from spleen

tag: treatment of mouse

value: Neu+ tumor bearing

source_name: Universal Mouse Reference RNA

treatment_protocol: Mice treated with Neu+ tumor cells; splenic cells isolated and sorted with cel surface binding antibodies by flow cytometry.

tag: reference source

value: Stratagene (#740100)

tag: tissue

value: Cell lines (11):embryo, fibroblast,kidney, hepatocyte, lung macrophage, B and T lymphocytes, mammary gland, myoblast, skin, testis


title: Gr1+CD11b+ sorted mononuclear cells from spleen of Neu+ tumor bearing mice Replicate 2

description: Biological replicate 2 of 2. Myeloid-derived suppressor cells (Gr1+ CD11b+) from spleen of neu+ tumor bearing FVB/neu-N mice


title: Gr1+CD11b+ sorted mononuclear cells from tumor site Replicate 1

description: Biological replicate 1 of 2. Tumor-infiltrating mononuclear cells (Gr1+ CD11b+) from neu+ tumor bearing FVB/neu-N mice

value: Gr1+ CD11b+ sorted cells from tumor


title: Gr1+CD11b+ sorted mononuclear cells from tumor site Replicate 2

description: Biological replicate 2 of 2. Tumor-infiltrating mononuclear cells (Gr1+ CD11b+) from neu+ tumor bearing FVB/neu-N mice


title: splenic cells from Neu+ tumor-bearing FVB-neuN mice Replicate 2

description: Biological replicate 2 of 3. Splenic cells from neu+ tumor bearing FVB/neu-N mice

source_name: total splenic cell homogenate

value: splenic cells


title: splenic cells from Neu+ tumor-bearing FVB-neuN mice Replicate 1

description: Biological replicate 1 of 3. Splenic cells from neu+ tumor bearing FVB/neu-N mice


title: splenic cells from Neu+ tumor-bearing FVB-neuN mice Replicate 3

description: Biological replicate 3 of 3. Splenic cells from neu+ tumor bearing FVB/neu-N mice


title: splenic cells from normal FVB-neuN mice Replicate 3

description: Biological replicate 3 of 3. Splenic cells from normal FVB/neu-N mice

treatment_protocol: untreated, normal

value: normal


title: splenic cells from normal FVB-neuN mice Replicate 2

description: Biological replicate 2 of 3. Splenic cells from normal FVB/neu-N mice


title: splenic cells from normal FVB-neuN mice Replicate 1

description: Biological replicate 1 of 3. Splenic cells from normal FVB/neu-N mice


title: Dis.28.a


title: Dis.24.a


title: Dis.24.c


title: Dis.24.b


title: Dis.18.c


title: Dis.18.eo


title: Dis.18.do


title: Input ChIP-Chip Array A rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P01R_v01-3_NCBIv36.NR.bpmap_matscore.bar

extract_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718

tag: agent

value: EGF treated MCF7 breast cancer cells

value: control Input DNA


title: Dis.18.fo


title: Input ChIP-Chip Array A rep1

treatment_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: Dis.18.a


title: Input ChIP-Chip Array E rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P05R_v01-3_NCBIv36.NR.bpmap_matscore.bar


title: Dis.16.b


title: Hybrid rep3

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

hyb_protocol: Samples were hybridized with GeneChip Medicago genome Arrays (Affymetrix) and scanned at the NASC Microarray Core Facility according to manufacturer's instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) using the Affymetrix 3000 7G scanner

data_processing: Data analysis and statistical analysis was performed using the Genespring GX programme from Agilent technologies. Raw data was pre-normalised using the RMA algorithm.

organism: Medicago truncatula

source_name: hybrid leaves, early flowering stage

label_protocol: RNA was labeled and fragmented using the Affymetrix IVT express kit according to manufacturer's instructions.

growth_protocol: Plants were grown in a growth chamber under 16 hours daylight at 22C and 8 hours darkness at 18C. Plants were grown in 12cm pots containing a mixture 9:1 vol/vol of a sandy loam soil and laterlite sand.

extract_protocol: Total RNA was extracted using the Qiagen RNeay mini kit according to the manufacturer's instructions.

tag: age

value: Early flowering stage

value: Leaves

tag: line


title: Dis.16.c


title: Input ChIP-Chip Array E rep1


title: ERa-EGF ChIP-Chip Array A rep2

value: ChIP

value: Input DNA from same sample used for ChIP against ERa


title: Hybrid rep2

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Dis.12.a

value: Wistar


title: ERa-EGF ChIP-Chip Array E rep3


title: Dis.12.c


title: ERa-EGF ChIP-Chip Array A rep3


title: Parent 2 rep3

source_name: parent 2 leaves, early flowering stage


title: Dis.1.do


title: Parent 5 rep3

source_name: parent 5 leaves, early flowering stage


title: Dis.18.b


title: Dis.1.c


title: ERa-EGF ChIP-Chip Array E rep2


title: Dis.12.b


title: Parent 5 rep2


title: Input ChIP-Chip Array B rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P02R_v01-3_NCBIv36.NR.bpmap_matscore.bar


title: Parent 2 rep2


title: Dis.1.b


title: ERa-EGF ChIP-Chip Array E rep1


title: ERa-EGF ChIP-Chip Array A rep1


title: Parent 5 rep1


title: C4-2_miR-99a

city: Charlottesville

first: Anindya

last: Dutta

state: VA

department: Biochemistry and Molecular Genetics

institute: University of Virginia

hyb_protocol: Total RNAs were hybridized to the Human HG-U133_Plus_2 array as described in the Affymetrix GeneChIP protocol (Affymetrix).

scan_protocol: Each microarray was scanned, visualized, and analyzed for the level of each individual transcript using a GeneChIP Scanner 3000 and GeneChIP Operating Software (GCOS; Affymetrix). Transcript signal was mapped against the chromosome coordinates (probe-by-probe basis) using the HG-U133_Plus_2 Annotations, CSV provided by the manufacturer (Affymetrix)

data_processing: Each microarray was scanned and analyzed for signal intensities by GeneChIP Scanner 3000 and GeneChIP operating software software (Affymetrix).

source_name: miR-99a transfection, 48hr

label_protocol: Labeling and hybridyzation was performed accoding to the affymetrix protocol.

extract_protocol: Total RNA extraction is according to the manufacturer's instructions (Invitrogen) using Trizol reagent.

treatment_protocol: siRNA transfection using RNAiMax for 48hr.

tag: cell line

value: prostate cancer


title: Dis.1.a

value: Distal


title: C4-2_si-GL2

source_name: si-GL2 transfection, 48hr


title: Hybrid rep1


title: Wild-type 3

hyb_protocol: Samples were hybridized with GeneChip Medicago Genome Arrays (Affymetrix) at the NASC Microarray Core Facility according to manufacturer's instructions.

scan_protocol: Arrays were scanned at the NASC Microarray Core Facility according to the manufacturer's instructions (Affymetrix).

data_processing: Data analysis and statistical analysis was performed using the GeneSpring GX 11 programm from Agilent Technologies. Raw data was pre-normalised using the RMA algorithm.

source_name: wild-type leaves, 2 months old

growth_protocol: CYP716A12 mutant and wild-type R108 plants were grown in a growth chamber under 16 hours daylight at 22C and 8 hours darkness at 18C. Plants were grown in 12cm pots containing a mixture 9:1 vol/vol of a sandy loam soil and laterlite sand.

tag: genotype

value: wild-type

value: 2 months

value: leaves


title: Parent 2 rep1


title: Input ChIP-Chip Array B rep1


title: Input ChIP-Chip Array G rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P07R_v01-3_NCBIv36.NR.bpmap_matscore.bar


title: ERa-EGF ChIP-Chip Array B rep3


title: ERa-EGF ChIP-Chip Array G rep3


title: Input ChIP-Chip Array G rep1


title: Input ChIP-Chip Array C rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P03R_v01-3_NCBIv36.NR.bpmap_matscore.bar


title: ERa-EGF ChIP-Chip Array B rep1


title: ERa-EGF ChIP-Chip Array G rep2


title: ERa-EGF ChIP-Chip Array G rep1


title: ERa-EGF ChIP-Chip Array B rep2


title: Lin28b-LoVo xenograft metastasis biological replicate 2

city: Philadelphia

first: Catrina

last: King

state: PA

address: 415 Curie Blvd

department: Gastroenterology

institute: University of Pennsylvania

description: Gene expression data from MSCV-PIG-LIN28B-LoVo xenograft metastasis

hyb_protocol: The resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated. cDNA yields were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm

data_processing: Significance Analysis of Microarrays (SAM v3.0, www-stat.stanford.edu/~tibs/SAM/) was used to generate lists of statistically significant differentially expressed genes in pairwise comparisons of replicate averages between conditions

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

growth_protocol: LoVo cells were transduced with MSCV-PIG or MSCV-PIG-LIN28B (cultured in DMEM + 10% FBS). Xenograft tumors were produced by injection 1x106 cells subcutaneously into the rear flanks of nude NCr mice.

extract_protocol: RNA isolated using a mirVana RNA isolation kit (Ambion, Austin, TX)

treatment_protocol: Extraneous tissues were stripped from dissected tumors. Tumors were homogenized mechanically in RIPA buffer (Tris 50mM, NaCl 150 mM, SDS 0.1%, Na.Deoxycholate 0.5%, Triton X 100 1%) + protease inhibitor cocktail (Roche Diagnostics, Manheim Germany).

value: xenograft metastasis from primary tumor developed from modified LoVo ATCC cell line (#CCL-229)

tag: expression


title: Input ChIP-Chip Array C rep1


title: ERa-EGF ChIP-Chip Array C rep3


title: ERa-EGF ChIP-Chip Array C rep2


title: Lin28b-LoVo xenograft metastasis biological replicate 1


title: ERa-EGF ChIP-Chip Array C rep1


title: Mutant 3

source_name: mutant leaves, 2 months old

value: CYP716A12 mutation


title: Input ChIP-Chip Array D rep2

description: result file: ERa_inpEGF_MCF7_n3_Hg18_F20.Hs35b_P04R_v01-3_NCBIv36.NR.bpmap_matscore.bar


title: Mutant 2


title: Input ChIP-Chip Array D rep1


title: Lin28b-LoVo xenograft metastasis biological replicate 3


title: ERa-EGF ChIP-Chip Array D rep3


title: vector-LoVo xenograft tumor biological replicate 2

description: Gene expression data from MSCV-PIG-LoVo xenograft primary tumor

source_name: MSCV-PIG-LoVo xenograft tumor

value: xenograft tumor developed from modified LoVo ATCC cell line (#CCL-229)

value: control


title: Lin28b-LoVo xenograft tumor biological replicate 2

description: Gene expression data from MSCV-PIG-LIN28B-LoVo xenograft primary tumor


title: vector-LoVo xenograft tumor biological replicate 1


title: Wild-type 1


title: Wild-type 2


title: Lin28b-LoVo xenograft tumor biological replicate 3

source_name: MSCV-PIG-LIN28B-LoVo xenograft primary tumor


title: Lin28b-LoVo xenograft tumor biological replicate 1


title: ERa-EGF ChIP-Chip Array D rep2


title: ERa-EGF ChIP-Chip Array D rep1


title: Manisopliae_RootExudate_0h-12h_R2

city: College Park

first: Monica

last: Pava-Ripoll

address: 4112 Plant Sciencies Bldg

department: Entomology

institute: University of Maryland

description: Hybridization using Loop design where every time point is compared to the next one (Time0h-Rep2/Time12h-Rep2).

hyb_protocol: Hybridization of 5 mg labeled cDNA to Metarhizium anisopliae arrays was conducted following the recommendations of the array manufacturer (http://www.umbi.umd.edu/carb/core-facilities/microarray-services/facility.php).

scan_protocol: Axon 4200 microarray scanner (Molecular Devices).

data_processing: Intensity of spots was extracted by Spotfinder program (http://www.pfgrc.tigr.org/tools.shtml, JCVI, Rockville, MD) as MEV files. Data of the MEV files were normalized using LOWESS (LOcally WEighted Scatterplot Smoothing) technique using the software MIDAS (http://www.pfgrc.tigr.org/tools.shtml, JCVI, Rockville, MD).  MIDAS output files project included standard deviation regularization, low intensity filter and in-slide replicate analysis. Normalized files were analized using Bayesian Analysis of Time Series microarray experiments (BATS) (http://www.na.iac.cnr.it/bats/).

organism: Metarhizium anisopliae

source_name: Fungal mycellium, root exudate, time 0 h

label_protocol: Direct labeling of mRNA/cDNA was performed with Cy3 (green) and Cy5 (red) cyanine dyes using the Ovation™ Aminoallyl system (Nugen, San Carlos, CA), according to manufacturer's instructions.

growth_protocol: Samples were incubated in a shaker/incubator at 27°C/220 rpm (New Brunswick Scientific, Edison, NJ).

extract_protocol: Total RNA was immediately extracted from the samples using the Qiagen RNeasy Mini kit, according to manufacturer's instructions.

treatment_protocol: 5 ml of Metarhizium anisopliae mycelium suspension (previously grown for 30 hours on Saboreaud dextrose broth (SDB) at 27C, collected through vacuum filtration and washed three times with sterile distilled water) were transferred for a final concentration of 5 mg/mL of bean RE. Samples were incubated in a shaker/incubator at 27°C/220 rpm (New Brunswick Scientific, Edison, NJ) and mycelium was collected from individual flasks before (time 0) and after 1, 4, 8 and 12 hours of incubation

value: ARSEF 2575

value: Fungal Mycellium grown for 30 h at 27C

tag: bean root exudate concentration (mg/ml)

source_name: Fungal mycellium, root exudate, time 12 h


title: Manisopliae_RootExudate_12h-0h_R1

description: Hybridization using Loop design where every time point is compared to the next one (Time12h-Rep1/Time0h-Rep1).


title: Manisopliae_RootExudate_12h-8h_R2

description: Hybridization using Loop design where every time point is compared to the next one (Time12h-Rep2/Time8h-Rep2).

source_name: Fungal mycellium, root exudate, time 8 h


title: LIN28B-LoVo

description: Gene expression data from LoVo cell line constitutively expressing LIN28B

source_name: LoVo colon cancer cell line transduced with MSCV-PIG-LIN28B

growth_protocol: Cells cultured in DMEM + 10% FBS

treatment_protocol: Cells were trypsinized to remove from plate, then lysed in RIPA buffer (Tris 50mM, NaCl 150 mM, SDS 0.1%, Na.Deoxycholate 0.5%, Triton X 100 1%) + protease inhibitor cocktail (Roche Diagnostics, Manheim Germany).

tag: sample type

value: modified ATCC cell line (#CCL-229)

value: LoVo

tag: transduction


title: vector-DLD1

description: Gene expression data from vector-DLD-1 cell line

source_name: DLD-1 colon cancer cell line transduced with MSCV-PIG

value: modified ATCC cell line (#CCL-221)

value: MSCV-PIG


title: vector-LoVo

description: Gene expression data from vector-LoVo cell line

source_name: LoVo colon cancer cell line transduced with MSCV-PIG


title: Manisopliae_RootExudate_8h-12h_R1

description: Hybridization using Loop design where every time point is compared to the next one (Time8h-Rep1/Time12h-Rep1).


title: vector-LoVo xenograft tumor biological replicate 3


title: LIN28B-DLD1

description: Gene expression data from DLD-1 cell line constitutively expressing LIN28B

source_name: DLD-1 colon cancer cell line transduced with MSCV-PIG-LIN28B


title: Manisopliae_RootExudate_8h-4h_R2

description: Hybridization using Loop design where every time point is compared to the next one (Time8h-Rep2/Time4h-Rep2).

source_name: Fungal mycellium, root exudate, time 4 h


title: Mutant 1


title: LIN28B-LoVo (2)

description: Gene expression data from additional LoVo cell line constitutively expressing LIN28B

source_name: LoVo colon cancer cell line transduced with MSCV-PIG-LIN28B (2)

value: MSCV-PIG-LIN28B (2)


title: Manisopliae_RootExudate_4h-8h_R1

description: Hybridization using Loop design where every time point is compared to the next one (Time4h-Rep1/Time8h-Rep1).


title: Control+TPO_rep2

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression of the rat heart tissue after exposure TPO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B US45102920) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid:014879_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.
GeneSpring data process settings:
Threshold: 1
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 75.0 percentile
Baseline Transformation: Median of all samples
FlagSettings:  Feature is not Uniform:A
Feature is a population outlier:A
Feature is Saturated:A
Feature is not positive and significant:A
Feature is not above background:A

source_name: TPO+Control heart_day 6_replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Doxorubicin-induced cardiomyopathy in rat acute model

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy Mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: Thrombopoietin treatment at day-1, day 1, 3 and 5 (10 ug/Kg TPO per dose).  A single dose of DOX was adminstrated at day 0 (17.5mg/ Kg body weight).

value: Whole Heart


title: Control+TPO_rep1

source_name: TPO+Control heart_day 6_replicate 1


title: Manisopliae_RootExudate_4h-1h_R2

description: Hybridization using Loop design where every time point is compared to the next one (Time4h-Rep2/Time1h-Rep2).

source_name: Fungal mycellium, root exudate, time 1 h


title: Manisopliae_RootExudate_1h-4h_R1

description: Hybridization using Loop design where every time point is compared to the next one (Time1h-Rep1/Time4h-Rep1).