title: Keratinocyte_k1_20_plusTNF

description: K1_20 keratinocytes

source_name: Keratinocytes immortalized from NPF family 1, individual 20, TNF

value: I

value: TNFa


title: 02-024

status: Public on May 09 2012

type: protein

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

description:
Antibody in CSF.
We used a CAMAG Automatic TLC Sampler (ATS4) robot to spray 200nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides.

hyb_protocol: Lipid arrays were produced using a CAMAG automatic TLC sampler robot (ATS4) adapted to print lipids onto PVDF membranes (Invitrogen, CA) taped onto the surface of Gold Seal Microslides microscope slides (Redding, CA) using double-sided scotch tape (3M). The lipids are solubilized in chloroform-methanol-water mixture. 200 nl of each lipid, at a range of 10 to 100 pmol, is sprayed onto each slide under nitrogen gas to form individual features. Printed membranes are stored dry and can retain reactivity for several months. Slides are then blocked at 4°C overnight (1 X phosphate-buffered saline (PBS), 1% Fatty Acid Free Bovine Serum Albumin (FAF-BSA)) and incubated with individual human CSF diluted at 1:10 in PBS/1% FAF-BSA for 2h at 4°C on a 40 rpm shaker. After washing twice with PBS/1% FAF-BSA, 10 min each time on a 45 rpm shaker at RT, reactive antibodies were detected using HRP-conjugated goat-anti-human IgG/IgM secondary antibody (1:8,000 dilution in PBS/1% FAF-BSA, Jackson Immunoresearch). After incubating with the secondary antibody for 60 minutes at 4°C on a 40 rpm shaker, the slides were washed on a 45 rpm shaker at RT, twice with PBS/1% FAF-BSA, 30 min each time; then twice with 1 X PBS, 15 min each time; then rinsed quickly twice with distilled water.

scan_protocol: The slides were incubated for 3 min in chemiluminescence solution (ECL Plus, Amersham) at room temperature before autoradiograph development. Digital images were then produced by scanning array autoradiographs.

data_processing: GenePix Pro 5.0 software (Molecular Devices, Sunnyvale, CA) was used to extract the net median pixel intensities for individual lipid features from the digital images. The data were not normalized. The mean net digital chemiluminescence units were then generated as the mean of the F450 Median – B450 values from two identical lipid features on each array. A "secondary antibody only" slide was included to subtract out non-specific binding. Data analysis was performed using Significance Analysis for Microarrays (SAM) software, version 1.21, (http://www-stat-class. stanford.edu /SAM/servlet/ SAMServlet) to identify antigen features with statistically significant differences in reactivities between the patient groups. Cluster software was then used to hierarchically group the samples and antigen features on the basis of a pairwise similarity function, and TreeView software was used to display the data as a heat map (http://rana.lbl.gov/EisenSoftware.htm).

label: Not applicable.

molecule: protein

organism: Homo sapiens

source_name: CSF, relapsing-remitting MS

label_protocol: Not applicable.

extract_protocol: All human CSF samples were collected by lumbar puncture and used under protocols approved by the Institutional Review Boards of the Karolinska Institute and Stanford University.

tag: tissue

value: cerebrospinal fluid (CSF)

tag: diagnosis

value: relapsing-remitting MS

tag: age

tag: gender

value: female

tag: treatment

value: Betaseron


title: 02-022

source_name: CSF, other neurological disease

value: other neurological disease:benign intracranial hypertension


title: 02-019

value: other neurological disease:vestibular neuritis

value: male


title: PPT 4h nodules biological rep 1

type: RNA

city: Porto

first: Helena

last: Carvalho

address: Rua do Campo Alegre,823

department: MBNA

country: Portugal

institute: Instituto de Biologia Molecular e Celular

description:
PPT 4.1
Mt_MtGeneChip0277_A594_jbecker_IGC_PP.CEL
Gene expression data from 20 dpi nodules 4 hours after PPT treatment

hyb_protocol: 12.5 µg of fragmented aRNA was used in a 250-µl hybridization cocktail containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: CEL files of the 12 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method available in DNA-Chip Analyzer 2010 (http://www.dchip.org, Cheng Li Lab, Harvard). Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model. Subsequently log2 transformed expression data for the 50963 probe sets on the array representing Medicago truncatula transcripts were imported into Partek Genomics Suite 6.5.

label: biotin

molecule: total RNA

organism: Medicago truncatula

source_name: 20 dpi nodules harvested from Medicago truncatula plants treated with PPT during 4 hours

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Medicago Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 8.5 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer, using an RNA 6000 Nano Assay.

growth_protocol: Medicago truncatula Gaertn cv Jemalong genotype A17 seeds were surface-sterilized and scarified. Plants were grown aeroponically in a climate chamber (photosynthetic photon flux: 150 to 200 μmol m-2 s-1) at a 16 h light (22 °C) and 8 h dark (19 °C) regime. One month-old plants were inoculated with Sinorhizobium meliloti strain Rm1021 pXLGD4 RCR 2011(GMI51) under nitrogen limiting conditions.

extract_protocol: Root nodule samples were ground using a chilled mortal and pestle prior to RNA extractions. Total RNA extraction was performed via RNeasy kits (Qiagen) according to the manufacturer’s instructions. RNA preparations were quality-checked both via spectrophotometry (NanoDrop ND-1000) and via capillary electrophoresis in RNA Nano chips (Agilent Bioanalyzer), as recommended by the manufacturers.

treatment_protocol: Nodulated plants (20 days post inoculation) were treated with a volume of the herbicide BASTA® corresponding to 0.25 mM of PPT. The herbicide was added to the nutrient solution of the aeroponic container. Root nodules were harvested just before the PPT treatment (control; PPT 0h), and at 4, 8 and 24 hours after PPT application (PPT 4h, PPT 8h, and PPT 24h) The root nodule were separated from roots at 4 ºC, pooled and immediately frozen in liquid nitrogen and stored at -80ºC.

value: Root nodule

tag: genotype

value: Jemalong A17

value: 20 days

tag: agent

value: PPT

tag: time

value: 4 hrs


title: PPT 0h nodules biological rep 2

description:
PPT 0.2
Mt_MtGeneChip0161_A072_jbecker_IGC_PP.CEL
Gene expression data from 20 dpi nodules before PPT treatment

source_name: 20 dpi nodules harvested from Medicago truncatula plants

value: untreated

value: 0 hrs


title: PPT 4h nodules biological rep 2

description:
PPT 4.2
Mt_MtGeneChip0278_A595_jbecker_IGC_PP.CEL
Gene expression data from 20 dpi nodules 4 hours after PPT treatment


title: 02-017


title: PPT 0h nodules biological rep 1

description:
PPT 0.1
Mt_MtGeneChip0160_A071_jbecker_IGC_PP.CEL
Gene expression data from 20 dpi nodules before PPT treatment


title: Keratinocyte_K5_14

city: St. Louis

first: Elisha

last: Roberson

state: MO

address: 660 South Euclid Ave., CB 8045

department: Internal Medicine & Genetics

institute: Washington University in St. Louis

description: K5_15 keratinocytes

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were imported into R using the Beadarray package. Data were log2 transformed and quantile normalized to create the normalized data.

source_name: Keratinocytes immortalized from NPF family 5, member 14

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion, AMIL1791). Cleanup with DNA Clean-up and Concentrator 5 columns (zymo research).

extract_protocol: microRNeasy or Rneasy

tag: rna extraction

value: Qiagen microRNeasy

tag: sentrix id

tag: sentrix position

value: A

tag: cell line

value: Immortalized keratinocytes

tag: growth

value: 37C; 5% CO2; Keratinocyte-SFM.


title: Keratinocyte_K5_14_plusTNF

description: K5_15 keratinocytes

source_name: Keratinocytes immortalized from NPF family 5, member 14, treated with TNF

value: L

value: TNFa


title: PPT 0h nodules biological rep 3

description:
PPT 0.3
Mt_MtGeneChip0162_A073_jbecker_IGC_PP.CEL
Gene expression data from 20 dpi nodules before PPT treatment


title: CL superovulated -  biological rep3

city: Sao Paulo

first: Luciana

middle: Alves

last: Fatima

state: Sao paulo

address: Orlando marques de Paica, 87

department: Surgery - Animal Anatomy

country: Brazil

institute: University of Sao Paulo

description:
Nelore crossbred cows aged between 2 and 5 years
Gene expression data from corpus luteum on day 6 pos ovulation - eCG superovulated animals

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affimetrix, Santa Clara, CA).

data_processing: Treatment of the data was performed with the FlexArray Software V1.3 (Genome Quebec Innovation Center, Montreal, Canada, http://genomequebec.mcgill.ca/FlexArray/). Raw fluorescence data were processed and normalized with the affx Bioconductor package (http://bioconductor.org/) vesion 1.1.0.

organism: Bos indicus

source_name: Superovulated - Bovine CL- colected day 6 pos ovulation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (New Affymetrix Protocol, 2004

growth_protocol: Nelore crossbred cows aged between 2 and 5 years were used. The animals were maintained on pasture and supplemented with corn meal (17.03%), soybean meal (4.65%), urea (1.13%), ammonium sulfate (0.11%), minerals (1.69%), salt (0.53%) and corn silage (74.86%).

extract_protocol: Trizol Reagent (Life Technologies, Carlsbad, CA, USA) was used to extract total RNA, according to manufacturer’s recommendations. RNA was further purified using an RNAeasy kit with DNase treatment to eliminate genomic contamination (Qiagen, Valencia, CA, USA)

treatment_protocol: Animals (Bos indicus) were randomly distributed in three groups (Control, stimulated and superovulated). All animals were submitted to estrous cycle synchronization using progesterone devices  and  estradiol benzoate. The stimulated group received 400 IU of eCG on day 8 and the superovulated group received 2000 IU of eCG on day 4 after the beginning of the protocol. Animals were slaughtered on Day 6 after ovulation and the Cl were collected and committed  liquid nitrogen.

value: 2000 IU of eCG on day 4 after the beginning of synchronization

value: Corpus luteum

tag: genetic background

value: Nelore crossbred

value: 2 - 5 yrs


title: HEK001_Cardsh_transfected

description: HEK001 cells

source_name: HEK001 cells transfected with Wildtype CARD14

value: G


title: Keratinocyte_K1_1_plusTNF

description: K1_1 keratinocytes

source_name: Keratinocytes immortalized from NPF family 1, individual 1, treated with TNF

value: J


title: HEK001_E138A_transfected

description: HEK001 cells

source_name: HEK001 cells transfected with CARD14 E138A mutation

value: B


title: CL superovulated -  biological rep1


title: Keratinocyte_K1_1

description: K1_1 keratinocytes

source_name: Keratinocytes immortalized from NPF family 1, individual 1

value: D


title: HEK001_G117S_transfected

description: HEK001 cells

source_name: HEK001 cells transfected with CARD14 G117S mutation

value: K


title: 02-023

value: cerebrospinal fluid (CSF)

value: relapsing-remitting MS

value: female


title: CL superovulated -  biological rep2


title: 02-016

value: other neurological disease:sensory symptoms


title: 02-014

value: Avonex


title: CL stimulated -  biological rep2

description:
Nelore crossbred cows aged between 2 and 5 years
Gene expression data from corpus luteum on day 6 pos ovulation - eCG stimulated animals

source_name: Stimulated- Bovine CL- colected day 6 pos ovulation

value: 400 IU of eCG on day 8 after the beginning of synchronization


title: 02-013


title: 02-015

value: Rebif


title: CL stimulated -  biological rep3

source_name: Stimulated - Bovine CL- colected day 6 pos ovulation


title: 02-012


title: skin_involved_ls52

description: skin biopsy

source_name: Skin biopsy from affected psoriatic skin

value: Qiagen Rneasy

value: I


title: 02-010

value: other neurological disease:spinal stenosis in cervical spine & chronic pain


title: 02-096

value: other neurological disease:tension headache


title: 02-099


title: skin_involved_ls10

description: skin biopsy

value: F


title: CL control -  biological rep2

description:
Nelore crossbred cows aged between 2 and 5 years
Gene expression data from corpus luteum on day 6 pos ovulation - control animal

source_name: Non treated- Bovine CL- colected day 6 pos ovulation

value: control

value: Corpus luteum

value: Nelore crossbred

value: 2 - 5 yrs


title: CL stimulated -  biological rep1

source_name: Stimulated -Bovine CL- colected day 6 pos ovulation


title: CL control -  biological rep3


title: skin_control_normal2

description: skin biopsy

source_name: Skin biopsy from a person with no dermatologic disease

value: D


title: CL control -  biological rep1


title: 02-001

source_name: CSF, other neurological disease

value: cerebrospinal fluid (CSF)

value: other neurological disease:slipped disc s1


title: skin_uninvolved_gen001

description: skin biopsy

source_name: Skin biopsy from NPF family 1, individual 1, uninvolved skin

value: C


title: 01-190

source_name: CSF, relapsing-remitting MS

value: relapsing-remitting MS

value: female


title: skin_control_normal1

description: skin biopsy

value: L


title: skin_involved_pustular_psoriasis

description: skin biopsy

source_name: Skin biopsy from an individual with pustular psoriasis

value: A


title: RPK-59 exp.2

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

country: Japan

institute: Tohoku University School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RPK-59 gemcitabine resistant

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

growth_protocol: Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Studio City, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: Pancreatic cancer cell line

value: RPK-59 gemcitabine resistant


title: RPK-59 exp.1


title: PK-59 exp.1

source_name: PK-59 parental

value: PK-59 parental


title: HEK001-D285G_transfected

data_processing: Raw data (i.e. non_normalized) were imported into R using the Beadarray package. Data were log2 transformed and quantile normalized to create the normalized data.

source_name: HEK001 cells

growth_protocol: Grown at 37C and 5% CO2 in Gibco Keratinocyte SFM (#10724-011).

extract_protocol: Qiagen miRNeasy kit, per manufacturer protocol

treatment_protocol: Transfected with pReceiver-M11 containing wildtype CARD14sh or mutated CARD14sh (Stratagene QuikChange Site-Directed Mutagenesis).

value: Keratinocytes

tag: transfected with

value: pReceiver-M11 containing mutated CARD14sh_D285G


title: skin_involved_gen001

description: skin biopsy

source_name: Skin biopsy from NPF family 1, individual 1, involved skin

value: Qiagen Rneasy

value: G


title: PK-9 exp.2

source_name: PK-9 parental

value: PK-9 parental


title: HEK001-I593N_transfected

value: pReceiver-M11 containing mutated CARD14sh_I593N


title: HEK001-R547S_transfected

value: pReceiver-M11 containing mutated CARD14sh_R547S


title: 01-185

value: cerebrospinal fluid (CSF)

value: other neurological disease:vertigo

value: male


title: HEK001-R682W_transfected

value: pReceiver-M11 containing mutated CARD14sh_R682W


title: 02-095

value: other neurological disease:tension headache

value: female


title: 01-183


title: PK-59 exp.2


title: 01-182

value: relapsing-remitting MS


title: 01-184


title: RPK-9 exp.2

source_name: RPK-9 gemcitabine resistant

value: Pancreatic cancer cell line

value: RPK-9 gemcitabine resistant


title: RPK-1 exp.2

source_name: RPK-1 gemcitabine resistant

value: RPK-1 gemcitabine resistant


title: 01-188


title: 01-181


title: PK-9 exp.1


title: 01-189


title: HEK001-R179H_transfected

value: Keratinocytes

value: pReceiver-M11 containing mutated CARD14sh_R179H


title: RPK-9 exp.1


title: HEK001-S200N_transfected

value: pReceiver-M11 containing mutated CARD14sh_S200N


title: HEK001-H171N_transfected

value: pReceiver-M11 containing mutated CARD14sh_H171N


title: RPK1-1 exp.1


title: PBMC Atopic 5

type: genomic

city: Vancouver

first: Dorota

last: Stefanowicz

address: Rm 166 - 1081 Burrard St.

department: James Hogg Research Centre

country: Canada

institute: UBC

description: atopic peripheral blood mononuclear cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina GoldenGate Methylation Cancer Panel I Beadchip using standard Illumina protocol.

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

data_processing: To avoid gender bias, all CpG sites on the X chromosome (n=84) were removed from the analysis as well as probes containing single nucleotide polymorphisms (n=272).  Probes with detection P-values > 0.05 in more than 10% of samples (n=122) were also removed leaving 1027 CpG sites across 671 genes.  Any data points with a detection P-value > 0.05 in less than 10% of samples were imputed using the K-nearest neighbor algorithm. Raw data was background corrected and adjusted for color bias using the Bioconductor methylumi package and batch effects using distance weighted discrimination.  For each sample, the M-value: M = log2 ((Cy5+1)/ (Cy3+1)) was calculated, where Cy5 and Cy3 were the methylated and unmethylated sequences, respectively.  Batch effect correction was performed in MATLAB R2009a (7.8.0) (MathWorks Inc., MA). All other preprocessing was performed in R version 2.12.0 (http://www.R-project.org ( http://www.r-project.org/ )).

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from AEC and PBMC samples using Qiagen Flexi Gene DNA Kit and QIAamp columns according to standard instructions.

tag: disease state

value: atopic

value: peripheral blood mononuclear cells (PBMCs)


title: HEK001-V191L_transfected

value: pReceiver-M11 containing mutated CARD14sh_V191L


title: HEK001-E142G_transfected

value: pReceiver-M11 containing mutated CARD14sh_E142G


title: 01-180

tag: tissue

value: cerebrospinal fluid (CSF)


title: HEK001-E138A_transfected

value: pReceiver-M11 containing mutated CARD14sh_E138A


title: PBMC Non-Atopic Asthmatic 5

description: non-atopic asthmatic peripheral blood mononuclear cells

source_name: PBMC_non-atopic asthmatic

value: non-atopic asthmatic


title: 01-166

source_name: CSF, primary progressive MS

tag: diagnosis

value: primary progressive MS

value: male


title: 01-150

source_name: CSF, secondary progressive MS

value: secondary progressive MS

tag: age

value: female


title: PBMC Non-Atopic Asthmatic 2


title: 01-142

tag: gender


title: PBMC Non-Atopic Asthmatic 3


title: PBMC Non-Atopic Asthmatic 1


title: PBMC Healthy 6

description: healthy peripheral blood mononuclear cells

value: healthy


title: 01-136

tag: treatment


title: 01-168

value: relapsing-remitting MS


title: 01-133


title: HEK001-L150R_transfected

value: Keratinocytes

value: pReceiver-M11 containing mutated CARD14sh_L150R


title: PBMC Healthy 5


title: PBMC Healthy 3


title: HEK001-D176H_transfected

value: pReceiver-M11 containing mutated CARD14sh_D176H


title: HEK001-E142K_transfected

value: pReceiver-M11 containing mutated CARD14sh_E142K


title: PK-1 exp.1

source_name: PK-1 parental

value: Pancreatic cancer cell line

value: PK-1 parental


title: HEK001-R62Q_transfected

value: pReceiver-M11 containing mutated CARD14sh_R62Q


title: PBMC Healthy 1

value: peripheral blood mononuclear cells (PBMCs)


title: 01-120

value: cerebrospinal fluid (CSF)


title: 01-109


title: 01-123


title: 01-119


title: PBMC Healthy 2


title: HEK001-G117S_transfected

value: pReceiver-M11 containing mutated CARD14sh_G117S


title: HEK001-R38C_transfected

value: pReceiver-M11 containing mutated CARD14sh_R38C


title: 01-103


title: PBMC Healthy 4


title: 01-085

value: other neurological disease:fibromyalgia & alcoholic dementia


title: 01-093

value: Rebif


title: PBMC Atopic Asthmatic 3

description: atopic asthmatic peripheral blood mononuclear cells

source_name: PBMC_atopic asthmatic

value: atopic asthmatic


title: PBMC Atopic Asthmatic 2


title: PBMC Atopic Asthmatic 1


title: PBMC Atopic Asthmatic 4


title: 02-035

hyb_protocol: Lipid arrays were produced using a CAMAG automatic TLC sampler robot (ATS4) adapted to print lipids onto PVDF membranes (Invitrogen, CA) taped onto the surface of Gold Seal Microslides microscope slides (Redding, CA) using double-sided scotch tape (3M). The lipids are solubilized in chloroform-methanol-water mixture. 200 nl of each lipid, at a range of 10 to 100 pmol, is sprayed onto each slide under nitrogen gas to form individual features. Printed membranes are stored dry and can retain reactivity for several months. Slides are then blocked at 4°C overnight (1 X phosphate-buffered saline (PBS), 1% Fatty Acid Free Bovine Serum Albumin (FAF-BSA)) and incubated with individual human CSF diluted at 1:20 in PBS/1% FAF-BSA for 110 min at 4°C, no shaking. After washing once for 5 min in old blocking solution, the slides were washed twice with fresh PBS/1% FAF-BSA, 15 min each time, on a 45 rpm shaker at RT. The reactive antibodies were detected using HRP-conjugated donkey-anti-human IgG secondary antibody (1:8,000 dilution in PBS/1% FAF-BSA, Jackson Immunoresearch). After incubating with the secondary antibody for 60 minutes at 4°C, no shaking, the slides were washed, on a 45 rpm shaker at RT, once for 5 min in old wash solution, then twice with fresh PBS/1% FAF-BSA, 30 min each time; then twice with 1 X PBS, 20 min each time; then rinsed quickly twice with distilled water.

data_processing: GenePix Pro 5.0 software (Molecular Devices, Sunnyvale, CA) was used to extract the net median pixel intensities for individual lipid features from the digital images. The data were not normalized. The mean net digital chemiluminescence units were then generated as the mean of the F450 Median – B450 values from two identical lipid features on each array. A "secondary antibody only" slide and a healthy control slide were included to subtract out non-specific binding. Data analysis was performed using Significance Analysis for Microarrays (SAM) software, version 1.21, (http://www-stat-class. stanford.edu /SAM/servlet/ SAMServlet) to identify antigen features with statistically significant differences in reactivities between the patient groups. Cluster software was then used to hierarchically group the samples and antigen features on the basis of a pairwise similarity function, and TreeView software was used to display the data as a heat map (http://rana.lbl.gov/EisenSoftware.htm).

value: other neurological disease:vertigo

value: female


title: 02-041

value: other neurological disease:paresthesia


title: PBMC Atopic 3

value: atopic


title: PBMC Atopic 2


title: 01-055

value: secondary progressive MS

value: male


title: 01-073


title: 01-008

value: relapsing-remitting MS


title: 01-001


title: 01-107


title: PBMC Atopic 1


title: 02-036


title: 02-030

value: other neurological disease:sensory symptoms


title: AEC Atopic 7

description: atopic airway epithelial cells

value: airway epithelial cells (AECs)


title: PBMC Atopic 4


title: 02-028

source_name: CSF, other neurological disease (later developed RRMS)

value: **other neurological disease - later developed RRMS:sensory symptoms


title: AEC Healthy 6

description: healthy airway epithelial cells

value: healthy


title: PBMC Non-Atopic Asthmatic 4

value: non-atopic asthmatic

value: peripheral blood mononuclear cells (PBMCs)


title: 02-091

source_name: CSF, other neurological disease

value: cerebrospinal fluid (CSF)

value: other neurological disease:tension headache


title: AEC Atopic 6

description: atopic airway epithelial cells


title: 02-089

source_name: CSF, healthy control


title: 02-088


title: 02-027

source_name: CSF, relapsing-remitting MS


title: 02-022

value: other neurological disease:benign intracranial hypertension


title: AEC Atopic 5

description: atopic airway epithelial cells


title: 02-023


title: AEC Healthy 5

description: healthy airway epithelial cells


title: AEC Atopic Asthmatic 4

description: atopic asthmatic airway epithelial cells

source_name: AEC_atopic asthmatic

value: atopic asthmatic


title: AEC Atopic 4

description: atopic airway epithelial cells


title: 02-025


title: 02-016


title: 02-019

value: other neurological disease:vestibular neuritis


title: 02-014

value: female

value: Avonex


title: 02-013


title: 02-015

value: Rebif


title: 01-185

value: other neurological disease:vertigo


title: 01-184


title: 02-012


title: 02-001

value: other neurological disease:slipped disc s1


title: 01-183


title: 01-190

value: relapsing-remitting MS


title: 01-189


title: AEC Atopic Asthmatic 3


title: AEC Non-Atopic Asthmatic 4

description: non-atopic asthmatic airway epithelial cells

source_name: AEC_non-atopic asthmatic


title: AEC Healthy 1

description: healthy airway epithelial cells


title: AEC Non-Atopic Asthmatic 2


title: AEC Healthy 4

description: healthy airway epithelial cells


title: AEC Non-Atopic Asthmatic 3


title: AEC Healthy 3

description: healthy airway epithelial cells


title: AEC Healthy 2

description: healthy airway epithelial cells


title: AEC Atopic Asthmatic 2


title: AEC Atopic Asthmatic 1


title: Caco-2+NCFM1hr1

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description:
SOF4_NCFM_1hr_1
Replicate 1 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Intensity values were captured and normalized via the cubic spline method and background subtraction was performed using the Illumina Genome Studio. The data was then quantile normalized to uniformly distribute any value < 2 to values between 1 and 2 using a custom SAS program. Transcripts were removed where the detection p-value was >0.05 in 95% of the samples.

source_name: Caco-2 monolayer, L. acidophilus, 1hr

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

growth_protocol: Caco-2 cells were routinely grown in 95% air-5% CO2 atmosphere in Minimum Essential Medium (MEM) supplemented with 20% (v/v) heat-inactivated fetal bovine serum (FBS), 0.10 mM non-essential amino acids, 1.0 mM sodium pyruvate and antibiotics (100 mg/ml penicillin G, 100 mg/ml streptomycin sulfate and 0.25 mg/ml amphotericin).

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

treatment_protocol: Prior to exposure assays, Caco-2 monolayers were washed twice with phosphate-buffered saline (PBS), and 1 ml of MEM medium was added per well as described below but without the addition of antibiotics. Caco-2 cells were then exposed to the bacterium L. acidophilus for 1, 4 or 8 hours or PBS for 1 hour.

value: intestinal epithelial cells

value: 21 days

value: Lactobacillus acidophilus NCFM

tag: treatment duration

value: 1 hr


title: Caco-2+NCFM1hr3

description:
SOF6_NCFM_1hr_3
Replicate 3 of 3.


title: Caco-2+NCFM8hr2

description:
SOF11_NCFM_8hr_2
Replicate 2 of 3.

source_name: Caco-2 monolayer, L. acidophilus, 8hr

value: 8 hrs


title: Caco-2+NCFM4hr1

description:
SOF7_NCFM_4hr_1
Replicate 1 of 3.

source_name: Caco-2 monolayer, L. acidophilus, 4hr

value: 4 hrs


title: Caco-2+NCFM4hr3

description:
SOF9_NCFM_4hr_3
Replicate 3 of 3.


title: Caco-2+NCFM1hr2

description:
SOF5_NCFM_1hr_2
Replicate 2 of 3.


title: AEC Non-Atopic Asthmatic 1

value: non-atopic asthmatic

value: airway epithelial cells (AECs)


title: Caco-2+PBS3

description:
SOF3_PBS.3
Replicate 3 of 3.

source_name: Caco-2 monolayer, PBS, 1hr

value: PBS


title: 01-180

value: cerebrospinal fluid (CSF)

value: other neurological disease:tension headache

value: male


title: AEC Atopic 1

description: atopic airway epithelial cells

value: atopic


title: AEC Atopic 2

description: atopic airway epithelial cells


title: 01-181

value: female


title: Caco-2+NCFM4hr2

description:
SOF8_NCFM_4hr_2
Replicate 2 of 3.


title: 01-182


title: PK-1 exp.2

value: Pancreatic cancer cell line

value: PK-1 parental


title: Caco-2+PBS2

description:
SOF2_PBS.2
Replicate 2 of 3.


title: Caco-2+PBS1

description:
SOF1_PBS.1
Replicate 1 of 3.


title: 01-131

value: secondary progressive MS


title: K5-CreER Control 3

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description:
US82800149_251486833988_S01_GE2_107_Sep09_1_4
Biological replicate 3 of 3 K5-CreER forestomach epithelium

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: K5-CreER forestomach epithelium

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color( Agilent p/n 5188-5340) according to the provided protocol.

growth_protocol: 7 weeks old K5-CreER controls and K5-CreER;Rosa26Sox2/Sox2 mutants were injected with two doses of Tamoxifen and the epithelial sheets in the forestomach were harvested for RNA extraction.

extract_protocol: Total RNA extracted using Trizol and purified with Qiagen Rneasy mini kit following manufacturer's instructions.

value: 12 week old

value: forestomach epithelial sheets

tag: strain

value: 129/Sv and C57/BL6 mixture

source_name: Agilent's Universal Mouse Reference RNA

value: 11 mouse cell lines

tag: reference

value: Agilent's Universal Mouse Reference RNA


title: K5-CreER;Rosa26Sox2/Sox2 mutant 2

description:
US82800149_251486832115_S01_GE2_105_Dec08_1_2
Biological replicate 2 of 3 K5-CreER Rosa26Sox2/Sox2 forestomach epithelium


title: Caco-2+NCFM8hr1

description:
SOF10_NCFM_8hr_1
Replicate 1 of 3.

value: intestinal epithelial cells

value: 21 days

value: Lactobacillus acidophilus NCFM

value: 8 hrs


title: K5-CreER Control 2

description:
US82800149_251486832116_S01_GE2_105_Dec08_1_4
Biological replicate 2 of 3 K5-CreER forestomach epithelium


title: K5-CreER;Rosa26Sox2/Sox2 mutant 3

description:
US82800149_251486832115_S01_GE2_105_Dec08_1_3
Biological replicate 3 of 3 K5-CreER Rosa26Sox2/Sox2 forestomach epithelium


title: HEK001-Cardsh_transfected

description: Cardsh

source_name: HEK001 cells

value: Keratinocytes

value: pReceiver-M11 containing wildtype CARD14sh


title: 01-188

description:
Antibody in CSF.
We used a CAMAG Automatic TLC Sampler (ATS4) robot to spray 200nl of 10 to 100 pmol of lipids onto PVDF membranes affixed to the surface of microscope slides.

value: cerebrospinal fluid (CSF)

value: relapsing-remitting MS


title: Hrp3_Alp13-deleted mutant

status: Public on May 08 2012

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

hyb_protocol: Labeled samples from mutant (Cy5) and wild-type (Cy3) were mixed and hybridized to the customized microarray (Agilent Custom Gene Expression  4 X 44K) as described previously (Zofall et al. Nature, 2009).

scan_protocol: The microarray contains 43,987 probes of 60-base oligonucleotides, which represent alternately the plus and minus strands. Microarray raw data were extracted with the Agilent Feature Extraction Software and processed by using the GeneSpring program. Probes with non-significant P values (PValueLogRatio ≥ 0.05) were set to 1 as described previously (Zofall et al. Nature, 2009).

data_processing: Agilent's GeneSpring GX software was used for background substraction and normalization.

organism: Schizosaccharomyces pombe

source_name: Hrp3 and Alp13 mutant

label_protocol: DNase-treated mRNA was amplified and labelled with Agilent’s Low RNA Input Linear Amplification kit PLUS

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YES) at 30˚C.

extract_protocol: RNA was purified as described ‘hot phenol’ method (Schmitt et al. Nucleic Acids Res., 1990). Purified RNA was treated with DNase (rDNase I, Ambion) and subjected to reverse transcription (ImProm-II Reverse transcription system, promega). RNA samples were incubated with primers complementary to either the forward or reverse transcripts in first strand cDNA synthesis reactions. Reverse transcribed cDNAs were amplified by either PCR or real-time PCR using gene-specific check primers.

tag: genotype/variation

value: hrp3Δ::hphMX6 x alp13?::hphMX6 ade6-M216 leu1-32 ura4-D18

source_name: Wild-type


title: Con_a_4_IL28B-2_09-30-10

city: Bethesda

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Samples collected from Human liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization method of software Parteck

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: Primary Human Hepatocytes Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. Stehphen Strom and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

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

value: primary hepatocyte


title: RD

city: Philadelphia

first: Zhongyi

last: Hu

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

description: Gene expression data from PC-3 cells treated with/without RD.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 plus 2 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PC-3 cells treated with RD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: PC-3 cells were cultured in RPMI 1640 medium (HyClone) supplemented with 10% fetal bovine serum (HyClone).

treatment_protocol: PC-3 cells were treated with RD for 24h or with DMSO vehicle for control.

value: prostate cancer cells

value: PC-3 cells


title: Clr3-deleted mutant

source_name: Clr3 mutant

value: clr3Δ::kanMX6 ade6-M210 leu1-32 ura4-D18


title: K5-CreER Control 1

description:
US82800149_251486832116_S01_GE2_105_Dec08_1_3
Biological replicate 1 of 3 K5-CreER forestomach epithelium

value: 12 week old

value: forestomach epithelial sheets


title: Caco-2+NCFM8hr3

description:
SOF12_NCFM_8hr_3
Replicate 3 of 3.


title: 09-30-10_IL28b-2

description: Samples collected from Human liver

treatment_protocol: RNA was isolated after recombinant IL28B (25 ng/mL for 24 hours) and JFH1 (MOI of 5 for 36 hours) with three replications.

value: recombinant IL28B (25 ng/mL)

tag: time

value: 24 hours


title: 09-30-10_IL28b-1

description: Samples collected from Human liver


title: Control

source_name: PC-3 cells without treated


title: Con_a_4_IL28B-3_09-30-10

description: Samples collected from Human liver


title: 09-30-10_IL28b-3

description: Samples collected from Human liver


title: Hrp3-deleted mutant

source_name: Hrp3 mutant

value: hrp3Δ::hphMX6 ade6-M216 leu1-32 ura4-D18


title: Alp13-deleted mutant

source_name: Alp13 mutant

value: alp13Δ::kanMX6 ade6-M216 leu1-32 ura4-D18


title: JFH_a-3

description: Samples collected from Human liver

value: MOI of 5

value: 36 hours


title: Con_a_4_IL28B-1_09-30-10

description: Samples collected from Human liver


title: AGS-EBV cells pBABE-LMP1DN replicate 1

city: Chapel Hill

first: Aron

last: Marquitz

address: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Biological Replicate 1 of 2

hyb_protocol: Hybridization was performed following Agilent's Two color hybridization protocol, version 5.0.

scan_protocol: Agilent DNA Microarray Scanner with Sure Scan High Resolution Technology for scanning

data_processing: Raw data was processed using Aglient Feature Extraction Software.  Data was analyzed using the Partek Genomics Suite 6.5

source_name: AGS-EBV cells with pBABE-LMP1DN vector

label_protocol: Agilent Quick Amp Labeling Kit was used for labeling

growth_protocol: Cells grown in F12 media with 500 ug/ml G418 to select for maintenance of EBV.  Stable cells lines with pBABE vectors were generated by transfection followed by several weeks of selection with 1ug/ml puromycin until cells became resistant

extract_protocol: Total RNA extracted from cell lines using Qiagen's RNeasy Plus mini kit according to manufacturer's protocol.

treatment_protocol: All cells were plated at and equal density and grown for 2 days to ~50% confluence prior to harvesting for RNA prep.  No G418 or puro was added to media during these two days.

value: AGS-EBV

tag: vector

source_name: AGS cells

value: AGS


title: AGS-EBV cells no vector replicate 3

description: Biological Replicate 3 of 4

source_name: AGS-EBV cells

tag: cell line


title: AGS-EBV cells pBABE replicate 2

description: Biological Replicate 2 of 2

source_name: AGS-EBV cells with pBABE vector

value: pBABE


title: AGS-EBV cells no vector replicate 4

description: Biological Replicate 4 of 4


title: JFH_a-2

description: Samples collected from Human liver


title: AGS-EBV cells pBABE replicate 1

description: Biological Replicate 1 of 2


title: AGS-EBV cells pBABE-LMP1DN replicate 2

description: Biological Replicate 2 of 2


title: AGS-EBV cells no vector replicate 2

description: Biological Replicate 2 of 4


title: Curcumin_Replicate 2

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

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

value: day 14

value: Intestinal IEL

value: Broiler


title: Con_a_4_JFHa-3

description: Samples collected from Human liver

value: primary hepatocyte


title: AGS-EBV cells no vector replicate 1

description: Biological Replicate 1 of 4


title: ΔaraRΔXlnR-SEB 12h Replicate 2

status: Public on May 07 2012

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

description: Biological replicate 2 of 2.ΔaraRΔXlnR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.
After data were processed using TIGR platform. Briefly, the files extracted from FE were used to upload the Express Converter (v. 2.1) file transformation tool, in order to convert FE files format to MeV files. MeV files were uploaded into Microarray Data Analysis System (MIDAS v2.22), where the resulting data were averaged from replicated genes on each array. For MIDAS software, the bad chanel tolerance policy was stringent, the siganl/noise threshold was 2.0 and the cross file cutoff pct (<1.0) was 0.5. The statistical analysis were made using MeV software with the one-class t-test (p. 0.001).
Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus niger

source_name: A. niger mycelia SEB-treated 12h, labeled with Cyanine-5

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: A. niger strains (ΔXlnR, ΔaraR and ΔaraRΔXlnR) ) were initially grown on minimal medium with fructose for 24 hours at 30 oC.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Mycelia from strains were transferred to minimal medium containing steam-exploded sugarcane with no additional carboun source for 12 and 24 h, at 30 oC.

value: ΔaraRΔXlnR

tag: agent

value: SEB

source_name: total RNA from ΔXlnR ΔaraR strain treated with fructose for 24 h, labeled with Cyanine-3

value: fructose


title: Con_a_4_JFHa-2

description: Samples collected from Human liver


title: ΔaraR-SEB 24h Replicate 2

description: Biological replicate 2 of 2. ΔaraR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source

source_name: A. niger mycelia SEB-treated 24h, labeled with Cyanine-5

value: ΔaraR

source_name: total RNA from  ΔaraR strain treated with fructose for 24 h, labeled with Cyanine-3


title: WT-XA 2h Replicate 2

description: Biological replicate 2 of 2. WT A niger strain treated with XA for 2h in minimal medium, no additional carbon source

source_name: A. niger mycelia XA-treated 2h, labeled with Cyanine-5

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for XA-treated samples) for 2 hours at 40 oC.

growth_protocol: A. niger strains (WT, ΔXlnR, ΔaraR and ΔaraRΔXlnR)  were initially grown on minimal medium with fructose for 24 hours at 30 oC.

treatment_protocol: Mycelia from strains were transferred to minimal medium containing 25mM xylose+ 25mM arabinose with no additional carboun source for 2 and 8 h, at 30 oC.

value: WT

value: XA

source_name: total RNA from WT strain treated with fructose for 24 h, labeled with Cyanine-3


title: ΔaraRΔXlnR-SEB 12h Replicate 1

description: Biological replicate 1 of 2. ΔaraRΔXlnR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source


title: ΔXlnR-SEB 24h Replicate 2

description: Biological replicate 2 of 2. ΔXlnR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source

value: ΔXlnR

source_name: total RNA from ΔXlnR strain treated with fructose for 24 h, labeled with Cyanine-3


title: ΔaraR-SEB 12h Replicate 2

description: Biological replicate 2 of 2. ΔaraR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source


title: WT-XA 8h Replicate 1

description: Biological replicate 1 of 2. WT A niger strain treated with XA for 8h in minimal medium, no additional carbon source

source_name: A. niger mycelia XA-treated 8h, labeled with Cyanine-5


title: ΔaraR-SEB 12h Replicate 1

description: Biological replicate 1 of 2. ΔaraR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source

source_name: total RNA from ΔaraR strain treated with fructose for 24 h, labeled with Cyanine-3


title: 2cell embryo_matRing1/Rnf2 double mutant_alpha-amanitin treatment_rep2

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description: 2cell_matRing1-/Rnf2- dm_alpha-amanitin treatment_2

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Raw data was read into R (version 2.10.0) with the ReadAffy() command of the Bioconductor (version 2.5) package affy(). The data was normalized and probeset-level values calculated with the vsnrma() function of the vsn package. For probeset mapping and annotation the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file) were used.

label: Biotin

source_name: 2-cell embryo, matRing1/Rnf2 double mutant, alpha-amanitin treatment

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Mouse oocytes were derived from superovulated 5- to 10-week-old females according to standard procedures. Metaphase II (M-II)-arrested eggs were collected from PMSG- and hCG-primed (5 U each, Intervet) mice 14 h after hCG injection and fertilized in vitro by wild type sperm. Sperm was obtained from 10-16 week old control males. Sperm capacitation was carried out in human tubular fluid (HTF) containing 9 mg/ml BSA for 2h. IVF was performed in capacitation medium for 2 h, and thereafter, the embryos were cultured in KSOM medium plus amino acids (Chemicon) in a humidified atmosphere of 5% CO2 in air until required. For inhibiting de novo transcription, IVF embryos were transferred to KSOM containing 24 µg/ml α-amanitin at 6 hpf and harvested for expression profiling at 35 hpf.

extract_protocol: 2-cell embryos were pooled from several mice and RNA was isolated from batches of 40 oocytes, 3 (or 2) biological replicates per genotype/treatment. RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202) according to the manufacturer’s instructions (Stratagene). The quality of the RNA was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Pico Chip. The extracted RNA was converted into OmniPlex WTA cDNA libraries and amplified by WTA PCR using reagents supplied with the TransPlex Whole Transcriptome Amplification kit (WTA1, Sigma, USA) following the manufacturer’s instructions with minor modifications. The obtained cDNA was purified using the GeneChip cDNA Sample Cleanup Module (Affymetrix).

value: mixed 129/Sv and C57BL/6J

tag: genotype

value: maternal Ring1-Rnf2-

tag: developmental stage

value: 2-cell embryo

value: alpha-amanitin


title: Curcumin_Replicate 1

description: Biological replicate 1 of 2


title: ΔaraRΔXlnR-SEB 24h Replicate 1

description: Biological replicate 1 of 2.ΔaraRΔXlnR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source


title: ΔaraR-SEB 24h Replicate 1

description: Biological replicate 1 of 2. ΔaraR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source


title: ΔaraRΔXlnR-SEB 24h Replicate 2

description: Biological replicate 2 of 2. ΔaraRΔXlnR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source


title: ΔaraRΔXlnR-XA 8h Replicate 2

description: Biological replicate 2 of 2. ΔaraRΔXlnR A niger strain treated with XA for 8h in minimal medium, no additional carbon source

source_name: total RNA from ΔaraR ΔxlnR strain treated with fructose for 24 h, labeled with Cyanine-3


title: 2cell embryo_matRing1/Rnf2 double mutant_no treatment_rep1

description: 2cell_matRing1-/Rnf2- dm_no treatment_1

source_name: 2-cell embryo, matRing1/Rnf2 double mutant, no treatment

treatment_protocol: For inhibiting de novo transcription, IVF embryos were transferred to KSOM containing 24 µg/ml α-amanitin at 6 hpf and harvested for expression profiling at 35 hpf.


title: 2cell embryo_matRing1/Rnf2 double mutant_no treatment_rep2

description: 2cell_matRing1-/Rnf2- dm_no treatment_2


title: Con_a_4_JFHa-1

description: Samples collected from Human liver

tag: cell type


title: ΔXlnR-SEB 12h Replicate 2

description: Biological replicate 2 of 2. ΔXlnR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source


title: ΔXlnR-SEB 24h Replicate 1

description: Biological replicate 1 of 2. ΔXlnR A niger strain treated with SEB for 24h in minimal medium, no additional carbon source


title: WT-XA 2h Replicate 1

description: Biological replicate 1 of 2. WT A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: 2cell embryo_matRing1/Rnf2 double mutant_alpha-amanitin treatment_rep1

description: 2cell_matRing1-/Rnf2- dm_alpha-amanitin treatment_1


title: 2cell embryo_control_alpha-amanitin treatment_rep3

description: 2cell_control(matRing1-/Rnf2+)_alpha-amanitin treatment_3

source_name: 2-cell embryo, control, alpha-amanitin treatment

value: maternal Ring1-Rnf+


title: ΔXlnR-SEB 12h Replicate 1

description: Biological replicate 1 of 2. ΔXlnR A niger strain treated with SEB for 12h in minimal medium, no additional carbon source


title: 2cell embryo_control_alpha-amanitin treatment_rep1

description: 2cell_control(matRing1-/Rnf2+)_alpha-amanitin treatment_1


title: 2cell embryo_matRing1/Rnf2 double mutant_no treatment_rep3

description: 2cell_matRing1-/Rnf2- dm_no treatment_3


title: ΔaraRΔXlnR-XA 2h Replicate 2

description: Biological replicate 2 of 2.ΔaraRΔXlnR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: ΔaraRΔXlnR-XA 8h Replicate 1

description: Biological replicate 1 of 2.ΔaraRΔXlnR A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: ΔaraRΔXlnR-XA 2h Replicate 1

description: Biological replicate 1 of 2. ΔaraRΔXlnR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: ΔaraR-XA 8h Replicate 2

description: Biological replicate 2 of 2. ΔaraR A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: 2cell embryo_control_no treatment_rep3

description: 2cell_control(matRing1-/Rnf2+)_no treatment_3

source_name: 2-cell embryo, control, no treatment


title: ΔaraR-XA 8h Replicate 1

description: Biological replicate 1 of 2. ΔaraR A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: 2cell embryo_control_alpha-amanitin treatment_rep2

description: 2cell_control(matRing1-/Rnf2+)_alpha-amanitin treatment_2


title: AEC Atopic 3

description: atopic airway epithelial cells

tag: disease state

value: atopic

value: airway epithelial cells (AECs)


title: ΔaraR-XA 2h Replicate 2

description: Biological replicate 2 of 2. ΔaraR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: GV oocyte_Ring1/Rnf2 double mut_rep3

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (provided as a supplementary file on the Series record).

source_name: GV oocyte, Ring1/Rnf2 double mutant

growth_protocol: Mouse oocytes were derived from superovulated 5-10 week old females according to standard procedures. Fully-grown germinal vesicle (GV)-intact oocytes were collected 46 h after PMSG injection (5 U, Intervet) in M2 medium (Sigma) containing 2.5 μM milrinone (Sigma).

extract_protocol: GV oocytes were pooled from several mice and RNA was isolated from batches of 50 oocytes, 3 biological replicates per genotype. RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202) according to the manufacturer’s instructions (Stratagene). The quality of the RNA was assessed using the Agilent 2100 bioanalyzer and RNA 6000 Pico Chip. The extracted RNA was converted into OmniPlex WTA cDNA libraries and amplified by WTA PCR using reagents supplied with the TransPlex Whole Transcriptome Amplification kit (WTA1, Sigma, USA) following the manufacturer’s instructions with minor modifications. The obtained cDNA was purified using the GeneChip cDNA Sample Cleanup Module (Affymetrix).

tag: tissue

value: GV oocyte

value: Ring1-/-Rnf2F/FZp3-cre (Ring1/Rnf2 double mutant)


title: ΔXlnR-XA 2h Replicate 2

description: Biological replicate 2 of 2. ΔXlnR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: ΔXlnR-XA 8h Replicate 2

description: Biological replicate 2 of 2. ΔXlnR A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: GV oocyte_Rnf2 mut_rep3

source_name: GV oocyte, Rnf2 mutant

value: Ring1+/+Rnf2F/FZp3-cre (Rnf2 mutant)


title: ΔXlnR-XA 2h Replicate 1

description: Biological replicate 1 of 2. ΔXlnR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: GV oocyte_Ring1/Rnf2 double mut_rep2


title: ΔaraR-XA 2h Replicate 1

description: Biological replicate 1 of 2. ΔaraR A niger strain treated with XA for 2h in minimal medium, no additional carbon source


title: ΔXlnR-XA 8h Replicate 1

description: Biological replicate 1 of 2. ΔXlnR A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: GV oocyte_Ring1 mut_rep3

source_name: GV oocyte, Ring1 mutant

value: Ring1-/-Rnf2F/F (Ring1 mutant)


title: WT-XA 8h Replicate 2

description: Biological replicate 2 of 2. WT A niger strain treated with XA for 8h in minimal medium, no additional carbon source


title: GV oocyte_Rnf2 mut_rep2


title: GV oocyte_Ring1/Rnf2 double mut_rep1


title: 2cell embryo_control_no treatment_rep2

description: 2cell_control(matRing1-/Rnf2+)_no treatment_2


title: GV oocyte_Ring1 mut_rep2


title: K5-CreER;Rosa26Sox2/Sox2 mutant 1

description:
US82800149_251486832115_S01_GE2_105_Dec08_1_1
Biological replicate 1 of 3 K5-CreER Rosa26Sox2/Sox2 forestomach epithelium

value: 12 week old

value: forestomach epithelial sheets

value: 129/Sv and C57/BL6 mixture

source_name: Agilent's Universal Mouse Reference RNA

value: 11 mouse cell lines

value: Agilent's Universal Mouse Reference RNA


title: 2cell embryo_control_no treatment_rep1

description: 2cell_control(matRing1-/Rnf2+)_no treatment_1


title: GV oocyte_Rnf2 mut_rep1


title: FLASH siRNA 24 hrs flash.1.24.abh

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

description: aneuploid, colon adenocarcinoma cell line

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies, Cat. #: 5188-5242).  Hybridizations were performed on SureHyb chambers on a rotator oven at 65º C for 17 hours.

scan_protocol: Agilent G2565BA

data_processing: log2 transformation of signal intensity, quantile normalization

label_protocol: Quick Amp Labeling Kit (Agilent Technologies, Cat. #: 5190-0442), including MMLV-RT and oligo dT-Promoter primers for cDNA sinthesis, and T7 RNA Polymerase, Cy3-CTP and NTPs for labeling.

extract_protocol: RNeasy Mini Kit (Qiagen) + RNase-Free DNase Set (Qiagen)

tag: time point

value: 24 hrs

value: FLASH siRNA


title: FLASH siRNA 72 hrs flash.6.72.abh

value: 72 hrs


title: negative control 24 hrs allstar.a.24.tlj

value: negative control


title: negative control 72 hrs allstar.b.72.tlj


title: GV oocyte_control_rep3

source_name: GV oocyte, control

value: mixed 129/Sv and C57BL/6J

value: Ring1+/+Rnf2F/F (control)


title: SCL006_icSARSCoV_72h_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 2B4 cells (a clonal derivative of Calu-3 cells) were infected with either icSARS CoV Urbani or the icSARS deltaORF6 mutant strain.  Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections. Calu-3 cells were seeded in 6-well plates (1.5 x 10^6 cells/well) two days prior to infection; immediately preceding infection, monolayers were washed twice with DF12 supplemented with 0.3% bovine serum albumin (DF12-BSA); and cells were inoculated with either the wild type SARS CoV virus or the mutant virus (multiplicity of infection [MOI] of 5 plaque forming unit [PFU] per cell) in DF12-BSA for 50 minutes at 37°C. Mock-infected controls were inoculated with DF12-BSA only. Cells were collected at 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. The end of the inoculation period was considered the “0” hour time point.

extract_protocol: All TRIzol lysates were processed for RNA isolation: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: At each time point, triplicate wells of mock-infected and virus-infected Calu-3 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen), according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.

tag: sample collection time post virus infection

tag: infection

value: SARS CoV Urbani infected

value: Calu -3 Cells


title: untreated 72 hrs untreated.c.72.abh

tag: treatment

value: untreated


title: SCL006_icSARSCoV_72h_2


title: SCL006_icSARSCoV_72h_1


title: FLASH siRNA 10 hrs flash.6.10.abh

value: 10 hrs


title: GV oocyte_control_rep2

value: GV oocyte


title: GV oocyte_control_rep1


title: FLASH siRNA 10 hrs flash.3.10.tlj


title: untreated 10 hrs untreated.b.10.abh


title: FLASH siRNA 48 hrs flash.3.48.abh

value: 48 hrs


title: FLASH siRNA 48 hrs flash.6.48.tlj


title: SCL006_icSARSCoV_54h_3


title: SCL006_icSARSCoV_54h_1


title: SCL006_icSARSCoV_60h_3_B


title: GV oocyte_Ring1 mut_rep1

value: Ring1-/-Rnf2F/F (Ring1 mutant)


title: SCL006_icSARSCoV_60h_2


title: SCL006_icSARSCoV_54h_2


title: negative control 24 hrs allstar.c.24.jcp


title: SCL006_icSARSCoV_60h_1


title: untreated 24 hrs untreated.a.24.abh


title: untreated 24 hrs untreated.b.24.tlj


title: FLASH siRNA 72 hrs flash.1.72.tlj


title: SCL006_icSARSCoV_36h_3


title: SCL006_icSARSCoV_48h_3


title: FLASH siRNA 48 hrs flash.3.48.jcp


title: FLASH siRNA 72 hrs flash.3.72.abh


title: FLASH siRNA 48 hrs flash.1.48.abh


title: SCL006_icSARSCoV_48h_2


title: untreated 10 hrs untreated.c.10.jcp


title: FLASH siRNA 72 hrs flash.6.72.jcp


title: JFH_a-1

description: Samples collected from Human liver

value: MOI of 5

value: 36 hours

value: primary hepatocyte


title: SCL006_icSARSCoV_36h_1


title: negative control 72 hrs allstar.a.72.jcp


title: FLASH siRNA 24 hrs flash.1.24.jcp


title: negative control 24 hrs allstar.a.24.jcp


title: SCL006_icSARSCoV_36h_2


title: negative control 24 hrs allstar.c.24.abh


title: SCL006_icSARSCoV_30h_3


title: SCL006_icSARSCoV_30h_1


title: SCL006_icSARSCoV_48h_1


title: FLASH siRNA 10 hrs flash.6.10.jcp


title: untreated 48 hrs untreated.c.48.tlj.1


title: SCL006_icSARSCoV_24h_3


title: FLASH siRNA 10 hrs flash.1.10.tlj


title: SCL006_icSARSCoV_12h_3_B


title: SCL006_icSARSCoV_12h_1


title: negative control 48 hrs allstar.c.48.abh


title: SCL006_icSARSCoV_12h_2


title: SCL006_icSARSCoV_24h_1


title: SCL006_icSARSCoV_7h_3


title: FLASH siRNA 24 hrs flash.3.24.tlj


title: SCL006_icSARSCoV_7h_2


title: SCL006_icSARSCoV_30h_2


title: SCL006_icSARSCoV_24h_2


title: negative control 10 hrs allstar.a.10.tlj


title: SCL006_BatSRBD_72h_3

value: SARS Bat SRBD infected


title: SCL006_icSARSCoV_7h_1


title: negative control 48 hrs allstar.a.48.jcp


title: SCL006_icSARSCoV_0h_1


title: SCL006_icSARSCoV_0h_3


title: FLASH siRNA 10 hrs flash.3.10.abh


title: SCL006_BatSRBD_72h_2


title: SCL006_icSARSCoV_0h_2


title: SCL006_BatSRBD_72h_1


title: negative control 72 hrs allstar.b.72.jcp


title: untreated 48 hrs untreated.c.48.tlj


title: FLASH siRNA 24 hrs flash.6.24.abh

value: 24 hrs


title: negative control 10 hrs allstar.c.10.abh


title: FLASH siRNA 10 hrs flash.1.10.jcp

value: FLASH siRNA


title: FLASH siRNA 48 hrs flash.6.48.jcp


title: SCL006_BatSRBD_60h_1


title: SCL006_BatSRBD_60h_3


title: SCL006_BatSRBD_60h_2


title: untreated 72 hrs untreated.a.72.tlj

value: 72 hrs


title: SCL006_BatSRBD_54h_1_B


title: SCL006_BatSRBD_54h_3


title: SCL006_BatSRBD_54h_2


title: negative control 48 hrs allstar.c.48.jcp

value: negative control


title: negative control 10 hrs allstar.a.72.abh


title: negative control 10 hrs allstar.b.10.jcp


title: FLASH siRNA 48 hrs flash.1.48.tlj


title: SCL006_BatSRBD_48h_3


title: untreated 48 hrs untreated.a.48.abh


title: SCL006_BatSRBD_48h_2


title: negative control 72 hrs allstar.a.10.jcp


title: FLASH siRNA 72 hrs flash.1.72.jcp


title: FLASH siRNA 24 hrs flash.6.24.tlj


title: FLASH siRNA 24 hrs flash.3.24.jcp


title: SCL006_BatSRBD_36h_2


title: SCL006_BatSRBD_36h_3


title: negative control 72 hrs allstar.c.72.tlj


title: negative control 10 hrs allstar.b.10.abh


title: SCL006_BatSRBD_48h_1_B


title: SCL006_BatSRBD_36h_1


title: negative control 24 hrs allstar.b.24.abh


title: untreated 48 hrs untreated.b.48.jcp


title: untreated 10 hrs untreated.b.10.tlj


title: negative control 48 hrs allstar.c.48.tlj


title: SCL006_BatSRBD_30h_2


title: FLASH siRNA 48 hrs flash.3.48.tlj


title: negative control 24 hrs allstar.b.24.tlj


title: SCL006_BatSRBD_24h_2


title: SCL006_BatSRBD_30h_3


title: untreated 24 hrs untreated.c.24.jcp


title: SCL006_BatSRBD_30h_1


title: SCL006_BatSRBD_24h_3


title: negative control 48 hrs allstar.b.48.abh


title: SCL006_BatSRBD_12h_3


title: negative control 10 hrs allstar.c.10.jcp


title: FLASH siRNA 72 hrs flash.6.72.tlj


title: SCL006_BatSRBD_12h_2


title: SCL006_BatSRBD_0h_3


title: SCL006_mock_72h_3

value: mock infected


title: negative control 72 hrs allstar.b.72.abh


title: FLASH siRNA 24 hrs flash.1.24.tlj


title: SCL006_mock_72h_2


title: SCL006_BatSRBD_0h_1


title: SCL006_BatSRBD_24h_1


title: FLASH siRNA 10 hrs flash.3.10.jcp


title: SCL006_mock_60h_3


title: FLASH siRNA 48 hrs flash.6.48.abh


title: SCL006_mock_60h_2


title: FLASH siRNA 72 hrs flash.1.72.abh


title: SCL006_BatSRBD_12h_1


title: NUP62 siRNA Set1_NUP62.3.3

value: NUP62 siRNA


title: SCL006_mock_60h_1


title: untreated 72 hrs untreated.b.72.jcp


title: SCL006_mock_72h_1


title: FLASH siRNA 24 hrs flash.3.24.abh


title: FLASH siRNA 10 hrs flash.1.10.abh


title: NUP62 siRNA Set1_NUP62.3.2


title: SCL006_mock_54h_3


title: SCL006_mock_54h_1


title: NUP62 siRNA Set1_NUP62.3.1


title: SCL006_mock_48h_3


title: SCL006_mock_54h_2


title: SCL006_mock_36h_3


title: NUP62 siRNA Set1_NUP62.2.1


title: SCL006_mock_48h_1


title: SCL006_mock_36h_2


title: NUP62 siRNA Set1_NUP62.2.3


title: NUP62 siRNA Set1_NUP62.2.2


title: FLASH siRNA Set1_FLASH.6.3


title: SCL006_mock_36h_1


title: FLASH siRNA Set1_FLASH.6.2


title: SCL006_mock_48h_2


title: SCL006_mock_30h_1


title: FLASH siRNA Set1_FLASH.3.2


title: SCL006_mock_24h_2


title: SCL006_mock_24h_1


title: negative control Set1_AllStar.1.7


title: negative control Set1_AllStar.3.10


title: FLASH siRNA Set1_FLASH.3.1


title: FLASH siRNA Set1_FLASH.6.1


title: negative control Set1_AllStar.3.8


title: FLASH siRNA Set1_FLASH.3.3


title: SCL006_mock_30h_3


title: SCL006_mock_30h_2


title: SCL006_mock_12h_3


title: SCL006_mock_24h_3


title: negative control Set1_AllStar.1.6


title: negative control Set1_AllStar.3.9


title: SCL006_mock_7h_3


title: negative control Set1_AllStar.1.5


title: negative control Set1_AllStar.0.3


title: SCL006_mock_0h_2


title: negative control Set1_AllStar.0.2


title: SCL006_mock_12h_1


title: SCL006_mock_7h_1


title: SCL006_mock_12h_2


title: negative control Set1_AllStar.1.4


title: SCL006_mock_7h_2


title: SCL006_mock_0h_1


title: MCF7_siRNA_ESR1_24h_AM0003_8.1

city: Auckland

first: Anita

last: Muthukaruppan

address: 85 Park Road, Grafton

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
ESR1_KD_AM0003

hyb_protocol: Following fragmentation, 15 ug of labelled cRNA was hybridized for 16 h at 45°C @ 60 RPM on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed with R using Affymetrix default analysis settings and RMA as the normalization method.

source_name: MCF7 cells that were transfected by siRNA targeting estrogen receptor alpha (ESR1).

label_protocol: Biotinylated cRNA was prepared from 1 ug total RNA according to the standard Affymetrix protocols (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF7 cells were grown in DMEM medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, 0.01 mg/ml bovine insulin, 2 mM L-Glutamine, 1 U/ml penicillin G and 1 ug/ml streptomycin sulfate, at 37˚C in a fully humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from Trizol homogenate using chloroform and purified using RNA affinity mini columns according to the manufacturers’ protocol (Invitrogen). RNA yields were determined by spectrophotometry using the NanoDrop (NanoDrop Technologies Inc, USA), and RNA integrity was assessed by capillary electrophoresis using the Experion (Bio-Rad Laboratories, CA, USA).

treatment_protocol: A transfection mix containing 2.5µl of RNAiMAX transfection reagent (Invitrogen) and 5nM siRNA in 500µl of OptiMEM media (Invitrogen) was incubated for 20 min at room temperature before added dropwise to 5.0 x 105 cells in 2.5ml of antibiotic-free media per well in a 6-well plate. The cells were incubated at 37°C for 24 h and harvested in 1ml of TRIzol Reagent (Invitrogen).

value: MCF7 breast cancer cells

value: estrogen receptor alpha (ESR1) knockdown


title: MCF7_siRNA_ESR1_24h_AM0009_9.1

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
ESR1_KD_AM0009


title: WT-2, control human MCF10A cells

city: GRENOBLE

first: Odile

last: FILHOL

address: 17, rue des martyrs

department: BIG

country: France

institute: INSERM-CEA

description:
WT-2
Parental MCF10A cells grown for 3 days (passage 16).

hyb_protocol: According to the Cogenics/Agilent protocol.

scan_protocol: Microarrays were scanned and raw data were extracted from the scanned images using Feature Extraction version 9.5.

data_processing: Raw data were normalized with the vsn method (R package limma, Smyth and Speed, 2003) and differential analysis was performed with the samr package (Tusher, 2001).  Regulated genes were selected based on the fdr value of the samr result genes list. Genes with an FDR lesser than  0.01 were declared as significantly differentially expressed.

source_name: MCF10A cells, control

label_protocol: Five hundred ng of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol:
MCF-10A is a spontaneously immortalized, but nontransformed human mammary epithelial cell line derived from the breast tissue of a 36-year-old patient with fibrocystic changes.
MCF-10A cells are grown on standard tissue culture plastic in a 5% CO2 humidified incubator at 37°C. The growth medium contains several additives and is composed of DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and antibiotics. MCF-10A cells should not be allowed to grow for more than 2 to 3 days without passage.

extract_protocol: Total RNA extraction was performed using the Absolutely RNA Miniprep kit (Agilent).

treatment_protocol:
MCF10A cells were grown as described for 3 days in the absence (WT) or presence of 4 ng/ml recombinant TGFβ1 (TGF).
Stable silencing of gene expression in MCF10A cells was accomplished by transduction with lentiviruses pLKO1 (SHVRCS-TRCN000003796, Sigma-Mission), followed by selection with puromycin (96). Specificity of the CK2β knockdown was checked by performing a complementation assay using a chicken CK2β, whose expression is not affected by the shRNA (F2).
-1' and '-2' correspond to two successive cell passages.

tag: gender

value: female

value: breast mammary gland epithelial cells

value: parental


title: MCF7_siRNA_ESR1_24h_AM0006_7.1

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
ESR1_KD_AM0006


title: 96-2, shRNA, human MCF10A cells

description:
96-2
Stable CK2β-knockdown MCF10A cells grown for 3 days (passage 16).

source_name: MCF10A cells, CK2beta depletion

value: stable CK2β-knockdown


title: negative control Set1_AllStar.0.1


title: F2-2, +rescue, human MCF10A cells

description:
F2-2
Stable CK2β-knockdown MCF10A cells rescued with chicken CK2β insensitive to shRNA, grown for 3 days (passage 16).

source_name: MCF10A cells, CK2beta depletion and rescue

value: rescued with chicken CK2β


title: 96-1, shRNA, human MCF10A cells

description:
96-1
Stable CK2β-knockdown MCF10A cells grown for 3 days (passage 15).


title: F2-1, +rescue, human MCF10A cells

description:
F2-1
Stable CK2β-knockdown MCF10A cells rescued with chicken CK2β insensitive to shRNA, grown for 3 days (passage 15).


title: MCF7_siRNA_GCMedControl_24h_AM0004_14.1

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
CONTROL_AM0004

source_name: MCF7 cells that were transfected by control siRNA.

value: control


title: TGF-2, +TGFbeta1, human MCF10A cells

description:
TGF-2
Parental MCF10A cells grown for 3 days (passage 16) in the presence of 4 ng/ml TGFβ1.

source_name: MCF10A cells, TGFbeta1


title: MCF7_siRNA_GCMedControl_24h_AM0011_97.1

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
CONTROL_AM0011


title: WT-1, control human MCF10A cells

description:
WT-1
Parental MCF10A cells grown for 3 days (passage 15).


title: TGF-1, +TGFbeta1, human MCF10A cells

description:
TGF-1
Parental MCF10A cells grown for 3 days (passage 15) in the presence of 4 ng/ml TGFβ1.


title: MCF7_siRNA_GCMedControl_24h_AM0002_57.1

description:
Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
CONTROL_AM0002


title: SCL006_BatSRBD_0h_2

value: Calu -3 Cells


title: HSCC_Low_713

status: Public on May 06 2012

city: Portland

first: Ovidiu

middle: Dan

last: Iancu

state: OR

address: 3181 SW Sam Jackson Road

institute: OHSU

description: HSCC haloperidol response: Low

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: lumi R package quintile normalization

source_name: mouse striatum

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: striatum

tag: genetic background

value: HS-CC

tag: haloperidol response

value: Low


title: HSCC_Low_768

description: HSCC haloperidol response: Low


title: HSCC_Low_769

description: HSCC haloperidol response: Low


title: HSCC_Low_785

description: HSCC haloperidol response: Low


title: HSCC_Low_784

description: HSCC haloperidol response: Low


title: HSCC_Low_675

description: HSCC haloperidol response: Low


title: HSCC_Low_711

description: HSCC haloperidol response: Low


title: HSCC_Low_668

description: HSCC haloperidol response: Low


title: HSCC_Low_671

description: HSCC haloperidol response: Low


title: HSCC_Low_674

description: HSCC haloperidol response: Low


title: HSCC_Low_669

description: HSCC haloperidol response: Low


title: HSCC_Low_780

description: HSCC haloperidol response: Low


title: HSCC_Low_777

description: HSCC haloperidol response: Low


title: HSCC_Low_697

description: HSCC haloperidol response: Low


title: HSCC_Low_695

description: HSCC haloperidol response: Low


title: HSCC_Low_782

description: HSCC haloperidol response: Low


title: HSCC_Low_693

description: HSCC haloperidol response: Low


title: HSCC_Low_781

description: HSCC haloperidol response: Low


title: HSCC_Low_696

description: HSCC haloperidol response: Low


title: HSCC_Low_776

description: HSCC haloperidol response: Low


title: HSCC_Low_690

description: HSCC haloperidol response: Low


title: HSCC_Low_701

description: HSCC haloperidol response: Low


title: HSCC_Low_731

description: HSCC haloperidol response: Low


title: HSCC_Low_691

description: HSCC haloperidol response: Low


title: HSCC_Low_710

description: HSCC haloperidol response: Low


title: HSCC_Low_783

description: HSCC haloperidol response: Low


title: HSCC_Low_673

description: HSCC haloperidol response: Low


title: HSCC_Low_730

description: HSCC haloperidol response: Low


title: HSCC_Low_734

description: HSCC haloperidol response: Low


title: HSCC_Low_756

description: HSCC haloperidol response: Low


title: HSCC_Low_737

description: HSCC haloperidol response: Low


title: HSCC_Low_682

description: HSCC haloperidol response: Low


title: HSCC_Low_679

description: HSCC haloperidol response: Low


title: HSCC_Low_736

description: HSCC haloperidol response: Low


title: HSCC_Low_755

description: HSCC haloperidol response: Low


title: HSCC_Low_735

description: HSCC haloperidol response: Low


title: SCL006_mock_0h_3


title: HSCC_High_687

description: HSCC haloperidol response: High

value: High


title: HSCC_Low_759

description: HSCC haloperidol response: Low


title: HSCC_High_685

description: HSCC haloperidol response: High


title: HSCC_Low_681

description: HSCC haloperidol response: Low


title: HSCC_High_686

description: HSCC haloperidol response: High


title: HSCC_High_684

description: HSCC haloperidol response: High


title: HSCC_High_689

description: HSCC haloperidol response: High


title: HSCC_Low_754

description: HSCC haloperidol response: Low


title: HSCC_Low_758

description: HSCC haloperidol response: Low


title: HSCC_High_688

description: HSCC haloperidol response: High


title: HSCC_Low_676

description: HSCC haloperidol response: Low


title: HSCC_Low_772

description: HSCC haloperidol response: Low


title: HSCC_Low_788

description: HSCC haloperidol response: Low


title: HSCC_Low_677

description: HSCC haloperidol response: Low


title: HSCC_Low_680

description: HSCC haloperidol response: Low


title: HSCC_Low_773

description: HSCC haloperidol response: Low


title: HSCC_High_722

description: HSCC haloperidol response: High


title: HSCC_High_719

description: HSCC haloperidol response: High


title: HSCC_High_683

description: HSCC haloperidol response: High


title: HSCC_High_721

description: HSCC haloperidol response: High


title: HSCC_High_666

description: HSCC haloperidol response: High


title: HSCC_High_747

description: HSCC haloperidol response: High


title: HSCC_High_723

description: HSCC haloperidol response: High


title: HSCC_High_746

description: HSCC haloperidol response: High


title: HSCC_High_742

description: HSCC haloperidol response: High


title: HSCC_High_665

description: HSCC haloperidol response: High


title: HSCC_High_717

description: HSCC haloperidol response: High


title: HSCC_High_718

description: HSCC haloperidol response: High


title: HSCC_High_728

description: HSCC haloperidol response: High


title: HSCC_High_740

description: HSCC haloperidol response: High


title: HSCC_High_714

description: HSCC haloperidol response: High


title: HSCC_High_716

description: HSCC haloperidol response: High


title: HSCC_High_705

description: HSCC haloperidol response: High


title: HSCC_High_662

description: HSCC haloperidol response: High


title: HSCC_Low_708

description: HSCC haloperidol response: Low


title: HSCC_High_663

description: HSCC haloperidol response: High


title: HSCC_High_724

description: HSCC haloperidol response: High


title: HSCC_High_704

description: HSCC haloperidol response: High


title: HSCC_High_745

description: HSCC haloperidol response: High


title: HSCC_High_707

description: HSCC haloperidol response: High


title: HSCC_High_741

description: HSCC haloperidol response: High


title: HSCC_High_664

description: HSCC haloperidol response: High


title: HSCC_High_729

description: HSCC haloperidol response: High


title: HSCC_Low_760

description: HSCC haloperidol response: Low


title: HSCC_High_749

description: HSCC haloperidol response: High


title: HSCC_High_753

description: HSCC haloperidol response: High


title: HSCC_High_727

description: HSCC haloperidol response: High


title: HSCC_High_767

description: HSCC haloperidol response: High


title: HSCC_High_764

description: HSCC haloperidol response: High


title: HS4 Low_995_M_L10

description: HS4 Selection haloperidol response High or Low


title: HSCC_High_748

description: HSCC haloperidol response: High


title: HSCC_High_766

description: HSCC haloperidol response: High


title: HSCC_High_765

description: HSCC haloperidol response: High


title: HS4 Low_1017_M_L6


title: HSCC_High_750

description: HSCC haloperidol response: High


title: HSCC_High_751

description: HSCC haloperidol response: High


title: HSCC_High_763

description: HSCC haloperidol response: High


title: HS4 Low_961_M _L9


title: HSCC_High_726

description: HSCC haloperidol response: High


title: HS4 Low_1009_F_L13


title: HS4 Low_1020_F_L16


title: HSCC_High_725

description: HSCC haloperidol response: High


title: HSCC_High_752

description: HSCC haloperidol response: High


title: HSCC_High_762

description: HSCC haloperidol response: High


title: HS4 Low_942_M_L7


title: HS4 Low_978_F_L10


title: HSCC_High_720

description: HSCC haloperidol response: High


title: HS4 Low_863_F_L15


title: HS4 Low_1023_F_L6


title: HS4 Low_939_M _L7


title: HS4 Low_935_M_L5


title: HS4 Low_843_F_L11


title: HS4 Low_945_F_L7


title: HS4 Low_840_M _L11


title: HS4 Low_963_F_L9


title: HS4 Low_946_F_L8


title: HS4 Low_977_M _L16


title: HS4 Low_930_M _L3


title: HS4 Low_947_F_L8


title: HS4 Low_954_F_L1


title: HS4 Low_1006_F_L13


title: HS4 Low_994_M _L10


title: HS4 Low_943_F_L5


title: HS4 Low_890_F_L12


title: HS4 Low_814_M _L15


title: HS4 Low_896_F_L2


title: HS4 Low_899_F_L2


title: HS4 Low_952_M _L8


title: HS4 Low_847_F_L4


title: HS4 Low_1016_M _L6


title: HS4 Low_932_M_L3


title: HS4 Low_926_M _L2


title: HS4 Low_1001_F_L14


title: HS4 Low_864_F_L15


title: HS4 Low_998_F_L3


title: HS4 Low_842_M _L12


title: HS4 Low_929_M_L3


title: HS4 Low_1022_M _L13


title: HS4 Low_955_M _L1


title: HS4 Low_846_F_L11


title: HS4 Low_1002_F_L14


title: HS4 Low_969_F_L16


title: HS4 Low_958_M_L1


title: HS4 Low_966_F_L9


title: HS4 High_990_M_H11


title: HS4 High_835_F_H4


title: HS4 Low_851_F_L4


title: HS4 High_807_F_H7


title: HS4 High_1028_F_H15


title: HS4 High_822_F_H13


title: HS4 High_911_M _H10


title: HS4 High_882_F_H1


title: HS4 Low_1003_M _L14


title: HS4 High_1031_M_H15


title: HS4 High_878_M_H2


title: HS4 High_827_F_H5


title: HS4 High_1012_F_H14


title: HS4 High_801_M _H7


title: HS4 High_852_F_H16


title: HS4 High_868_F_H2


title: HS4 High_806_M _H9


title: HS4 Low_893_M_L12


title: HS4 High_982_M _H14


title: HS4 High_826_F_H5


title: HS4 High_906_M_H12


title: HS4 High_1029_M _H15


title: HS4 High_876_M_H3


title: HS4 High_993_M _H11


title: HS4 High_815_M _H13


title: HS4 High_881_M _H1


title: HS4 High_872_F_H3


title: HS4 High_904_F_H12


title: HS4 High_986_F_H8


title: HS4 High_862_F_H9


title: HS4 High_913_F_H6


title: HS4 High_819_F_H13


title: HS4 High_985_M_H8


title: HS4 High_1026_F_H11


title: HS4 High_831_M _H4


title: HS4 High_885_F_H1


title: HS4 High_836_F_H4


title: HS4 High_828_M _H5


title: HS4 High_855_F_H16


title: HS4 High_918_M _H6


title: HS4 High_900_F_H10


title: HS4 High_914_F_H6


title: HS4 High_925_M _H3


title: HS4 High_808_F_H7


title: HS4 High_1011_F_H14


title: HS4 High_912_M_H10


title: HS4 High_905_M _H12


title: HS4 High_983_M _H8


title: HS4 High_805_M_H9


title: Low_965

description: F2 haloperidol response: Low


title: Low_951

description: F2 haloperidol response: Low


title: HS4 High_875_M _H2


title: Low_960

description: F2 haloperidol response: Low


title: Low_948

description: F2 haloperidol response: Low


title: Low_950

description: F2 haloperidol response: Low


title: Low_870

description: F2 haloperidol response: Low


title: Low_945

description: F2 haloperidol response: Low


title: Low_848

description: F2 haloperidol response: Low


title: Low_849

description: F2 haloperidol response: Low


title: Low_835

description: F2 haloperidol response: Low


title: Low_946

description: F2 haloperidol response: Low


title: Low_879

description: F2 haloperidol response: Low


title: Low_964

description: F2 haloperidol response: Low


title: Low_813

description: F2 haloperidol response: Low


title: Low_766

description: F2 haloperidol response: Low


title: Low_949

description: F2 haloperidol response: Low


title: Low_761

description: F2 haloperidol response: Low


title: Low_755

description: F2 haloperidol response: Low


title: Low_751

description: F2 haloperidol response: Low


title: Low_748

description: F2 haloperidol response: Low


title: Low_757

description: F2 haloperidol response: Low


title: Low_809

description: F2 haloperidol response: Low


title: Low_961

description: F2 haloperidol response: Low


title: Low_808

description: F2 haloperidol response: Low


title: Low_736

description: F2 haloperidol response: Low


title: Low_747

description: F2 haloperidol response: Low


title: Low_657

description: F2 haloperidol response: Low


title: Low_704

description: F2 haloperidol response: Low


title: Low_737

description: F2 haloperidol response: Low


title: Low_697

description: F2 haloperidol response: Low


title: High_953

description: F2 haloperidol response: High


title: Low_661

description: F2 haloperidol response: Low


title: High_943

description: F2 haloperidol response: High


title: Low_688

description: F2 haloperidol response: Low


title: Low_724

description: F2 haloperidol response: Low


title: High_956

description: F2 haloperidol response: High


title: Low_686

description: F2 haloperidol response: Low


title: HS4 High_856_M _H16


title: Low_699

description: F2 haloperidol response: Low


title: Low_690

description: F2 haloperidol response: Low


title: High_894

description: F2 haloperidol response: High


title: High_942

description: F2 haloperidol response: High


title: Low_703

description: F2 haloperidol response: Low


title: Low_658

description: F2 haloperidol response: Low


title: High_944

description: F2 haloperidol response: High


title: High_875

description: F2 haloperidol response: High


title: High_947

description: F2 haloperidol response: High


title: Low_662

description: F2 haloperidol response: Low


title: Low_687

description: F2 haloperidol response: Low


title: Low_713

description: F2 haloperidol response: Low


title: Low_700

description: F2 haloperidol response: Low


title: High_878

description: F2 haloperidol response: High


title: High_869

description: F2 haloperidol response: High


title: High_868

description: F2 haloperidol response: High


title: High_826

description: F2 haloperidol response: High


title: High_799

description: F2 haloperidol response: High


title: High_801

description: F2 haloperidol response: High


title: High_802

description: F2 haloperidol response: High


title: High_778

description: F2 haloperidol response: High


title: High_797

description: F2 haloperidol response: High


title: High_720

description: F2 haloperidol response: High


title: High_831

description: F2 haloperidol response: High


title: High_819

description: F2 haloperidol response: High


title: High_759

description: F2 haloperidol response: High


title: High_828

description: F2 haloperidol response: High


title: Compression Xylem vs. Opposite Xylem Replicate 4

city: Malaga

first: Rocio

last: Bautista

address: Edificio de Bioinnovación, C/ Severo Ochoa, 34

country: Spain

institute: Plataforma Andaluza de Bioinformatica, Universidad de Malaga

description: Biological replicate 4 of 4. Compression xylem vs. opposite xylem

hyb_protocol: Prehybridization, hybridization, and posthybridization washes were carried out using Pronto!™ Universal Hybridization Kit (Corning) in a HS 400 Pro hybridization station (Tecan Trading AG, Switzerland). Five micrograms of each of the labeled aRNA targets was added to the hybridization solution and denatured at 95°C for 5 min in a thermal block. The slides were hybridized for 16 h at 42°C.

scan_protocol: Scanned with 5 µm resolution on a Q-Scan scanner (Genetix).

data_processing: Spots flagged below 0 using GenePix v6.0 software (Axon Instruments) and those whose signal intensity did not surpass 2X their background signal in both channels were discarded. Background correction was performed with the “normexp” method of the limma library. M value was defined as the base two logarithm of every expression ratio, computed as the ratio between the background-corrected foreground intensities of the Cy3 and Cy5 channels. Raw expression data were normalized for all sources of systematic variation with the print-tip loess. using the common assumption of considering the whole microarray expression as invariant. The Biobase v 2.0.1 of the Bioconductor package [Gentleman RC et al. Genome Biol 2004, 5:R80] was installed under R version 2.7.1 for all statistical analysis, mainly the limma v 2.14.5 [Smyth G. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York: Springer; 2005: 397–420] and marray v 1.18.0 (http://www.bioconductor.org/packages/release/bioc/html/marray.html) libraries.

organism: Pinus pinaster

source_name: Total RNA from compression xylem tree 4

label_protocol: Dye labeled aRNA was synthesized with the Amino allyl MessageAmp II aRNA amplification kit (Ambion Inc., Austin, TX)

growth_protocol: Field-grown adult trees from Sierra Bermeja (Estepona, Spain).

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

treatment_protocol: Compression wood was induced by bending the stem at an angle of 45° away from the vertical during two months.

tag: age

value: 28 years old

value: Developing Secondary Xylem

tag: xylem type

value: compression xylem

tag: harvesting date

source_name: Total RNA of opposite xylem from tree 4

value: opposite xylem


title: Opposite Xylem vs. Compression Xylem Replicate 2

description: Biological replicate 2 of 4. Dye-Swap. Opposite xylem vs. compression xylem

source_name: Total RNA from opposite xylem of tree 2

value: 35 years old

source_name: Total RNA of compression xylem from tree 2


title: Opposite Xylem vs. Compression Xylem Replicate 1

description: Biological replicate 1 of 4. Dye-Swap. Opposite xylem vs. compression xylem

source_name: Total RNA from opposite xylem of tree 1

value: 25 years old

source_name: Total RNA of compression xylem from tree 1


title: Compression Xylem vs. Opposite Xylem Replicate 2

description: Biological replicate 2 of 4. Compression xylem vs. opposite xylem

source_name: Total RNA from compression xylem tree 2

source_name: Total RNA of opposite xylem from tree 2


title: Compression Xylem vs. Opposite Xylem Replicate 3

description: Biological replicate 3 of 4. Compression xylem vs. opposite xylem

source_name: Total RNA from compression xylem tree 3

source_name: Total RNA of opposite xylem from tree 3


title: High_722

description: F2 haloperidol response: High


title: High_734

description: F2 haloperidol response: High


title: High_725

description: F2 haloperidol response: High


title: High_727

description: F2 haloperidol response: High


title: HS4 Low_934_M _L5


title: High_708

description: F2 haloperidol response: High


title: High_768

description: F2 haloperidol response: High


title: High_726

description: F2 haloperidol response: High


title: High_711

description: F2 haloperidol response: High


title: Opposite Xylem vs. Compression Xylem Replicate 4

description: Biological replicate 4 of 4. Dye-Swap. Opposite xylem vs. compression xylem

source_name: Total RNA from opposite xylem of tree 4

source_name: Total RNA of compression xylem from tree 4


title: High_728

description: F2 haloperidol response: High


title: Opposite Xylem vs. Compression Xylem Replicate 3

description: Biological replicate 3 of 4. Dye-Swap. Opposite xylem vs. compression xylem

source_name: Total RNA from opposite xylem of tree 3

source_name: Total RNA of compression xylem from tree 3


title: Compression Xylem vs. Opposite Xylem Replicate 1

description: Biological replicate 1 of 4. Compression xylem vs. opposite xylem

source_name: Total RNA from compression xylem tree 1

source_name: Total RNA of opposite xylem from tree 1


data_processing:
Spots flagged below 0 using GenePix v6.0 software (Axon Instruments) and those whose signal intensity did not surpass 2X their background signal in both channels were discarded. Background correction was performed with the “normexp” method of the limma library. M value was defined as the base two logarithm of every expression ratio, computed as the ratio between the background-corrected foreground intensities of the Cy3 and Cy5 channels. Raw expression data were normalized for all sources of systematic variation with the print-tip loess. using the common assumption of considering the whole microarray expression as invariant. The Biobase v 2.0.1 of the Bioconductor package [Gentleman RC et al. Genome Biol 2004, 5:R80] was installed under R version 2.7.1 for all statistical analysis, mainly the limma v 2.14.5 [Smyth G. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York: Springer; 2005: 397–420] and marray v 1.18.0 (http://www.bioconductor.org/packages/release/bioc/html/marray.html) libraries.
Only differential expressed genes between compression xylem and opposite xylem (10 %) were sequenced and annotated.  The others genes weren´t showing information in our experiment and then they weren´t sequenced.


title: High_668

description: F2 haloperidol response: High

source_name: mouse striatum