title: Ripley Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep2


title: Ripley Leaves treated with Mock solution for 30 min Rep3

status: Public on Oct 06 2011

type: RNA

city: Columbia

first: Md Shakhawat

last: Hossain

state: Missouri

address: 201 Life Science Center 1201 Rollins Road

department: Plant Sciences

country: USA

institute: University of Missouri

description: Gene Expression data from Soybean leaves treated with Mock

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 45C on Soybean Gene 1.1 ST Array Strip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned with a GeneChip 7G Plus high-resolution scanner

data_processing: The gene level expression values were summarized by RMA by using Expressionist Refiner 6.1 (GeneData). Briefly, the signal intensity cel files from scanner were analyzed by a workflow with GC background subtraction, quantile normalization, and Median-Polish. The gene expression values from different samples were further used for gene differential statistic analysis

label: biotin

molecule: total RNA

organism: Glycine max

source_name: Soybean leaves treated with Mock

label_protocol: 500 ng of genomic-DNA free total RNA were used to produce fragmented and biotin-labeled cDNA using the Ambion WT Expression Kit (Applied Biosystems) and the Affymetrix WT Terminal Labeling and Hybridization Kit (Affymetrix).

growth_protocol: Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 mmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod).

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

treatment_protocol: Trifoliolate leaves from three-week-old plants were detached and then vacuumed infiltrated with ddiH2O for 2 min. Water-infiltrated trifoliolate leaves from five different plants of each genotype were pooled and cut into approximately 1 cm2 slices. Equal amount of leaf slices (~30 slices) were transferred into two different Petri dishes and then floated overnight on autoclaved ddiH2O. Water was removed from both Petri dishes and was replaced with 5 ml of MAMP solution [1 mM flagellin 22 (flg22) and 50 mg of crab shell chitin (called in this study as chitin)], or 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO). DMSO was included since it was contained in the solution used to dissolve the flg22 peptide]. After a 30 min treatment, mock- and MAMP-treated leaf slices were harvested into different tubes and immediately frozen in liquid nitrogen. Samples were stored at -80 until use. All procedures described above were performed under dark conditions.

tag: tissue

value: Leaves Trifoliate

tag: genotype

value: Ripley

tag: age

value: Three weeks-old plants

tag: treatment

value: mock solution for 30 min


title: 8 h after JA treatment replicate 2

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Biological replicate 2 of 2.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent)

organism: Oryza sativa

source_name: untreated rice cells

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice suspension cultured cells (Oryza sativa L. cv. Nipponnbare) used for total RNA extraction were maintained using N-6 medium and incubated on a rotary shaker at 25 C and 120 rpm in a dark. Cells were transferred to a fresh medium every week.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Rice cells 6 days after transfer to the new medium were used experiment and jasmonic acid (100uM) was added to the culture medium.

tag: cultivar

value: Oryza sativa L. cv. Nipponnbare

value: un-treated (control)

source_name: rice cells treated with JA for 8 h

value: Jasmonic acid (100uM) for 8 h


title: 12 h after JA treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with JA for 12 h

value: Jasmonic acid (100uM) for 12 h


title: LDX01-1-65 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep1

description: Gene Expression data from Soybean leaves treated with MAMPs

source_name: Soybean Leaves Treated with MAMPs

value: MAMP (flg22+chitin) solution for 30 min


title: LDX01-1-65 Leaves treated with Mock solution for 30 min Rep3


title: Ripley Leaves treated with Mock solution for 30 min Rep1


title: 12 h after JA treatment replicate 1

description: Biological replicate 1 of 2.


title: 8 h after JA treatment replicate 1

description: Biological replicate 1 of 2.


title: 4 h after JA treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with JA for 4 h

value: Jasmonic acid (100uM) for 4 h


title: Ripley Leaves treated with Mock solution for 30 min Rep2


title: LDX01-1-65 Leaves treated with Mock solution for 30 min Rep1


title: 6 h after JA treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with JA for 6 h

value: Jasmonic acid (100uM) for 6 h


title: 2 h after JA treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with JA for 2 h

value: Jasmonic acid (100uM) for 2 h


title: LDX01-1-65 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep3


title: LDX01-1-65 Leaves treated with Mock solution for 30 min Rep2


title: 2 h after JA treatment replicate 1

description: Biological replicate 1 of 2.


title: 4 h after JA treatment replicate 1

description: Biological replicate 1 of 2.


title: LD0-2817P Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep3


title: LDX01-1-65 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep2


title: LD0-2817P Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep2


title: Tsu-1 +Fe 24h, biological rep2

city: Lincoln

first: Brian

middle: M

last: Waters

state: Nebraska

address: 279 Plant Sciences Hall

department: Agronomy and Horticulture

institute: University of Nebraska-Lincoln

description:
BrW_ATH1_121410_02_TpR24.CEL
Gene expression data from roots after 24h in complete solution

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: The data was analyzed with GeneSpringX (Agilent) using the MAS5 algorithm

organism: Arabidopsis thaliana

source_name: Arabidopsis Tsu-1 roots after 24h in complete nutrient solution

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

growth_protocol: Seeds were planted onto rockwool loosely packed into 1.5 ml centrifuge tubes with the bottoms removed. The tubes were floated in foam rafts in containers of nutrient solution. After 10 days, seedlings were transferred to holes in lids of containers contain nutrient solution with constant aeration for an additional 14 days before treatments.

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

treatment_protocol: Roots were collected after 24 or 48 h of exposure to complete (with 50 micromolar of Fe-EDDHA) or –Fe (without added Fe) solutions.

value: roots

tag: ecotype

value: 30 days old plants

tag: growth protocol

value: complete solution

tag: time


title: Col(gl)_leaf_100mM NaCl_rep2 (wt + tg set)

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

country: China

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

description: Gene expression data in Col(gl) in the presence of salt

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: All the Affymetrix data files produced with Affymetrix GCOS software (*.CEL files) were analyzed using Bioconductor, a public source software for the analyses of genomic data rooted in the statistical computing environment R. The data were normalized by robust multioiarray normalization of probe-level data with RMA and analyzed using affylmGUI running on R software.

source_name: Col(gl) plant, 100mM NaCl, 6 d

label_protocol: Ten µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Seeds of both transgenic and wild type plants were sown as described above with two replicate pots for each genotype and salt combination. Plants were grown at 23/18 °C in the growth chamber under a short-day cycle (10h light/14 h dark) at 350 μmol m-2s-1 and 70% relative humidity in order to increase seedling leaf area and growth while not promoting bolting. Sampling time was performed at 20 DAS by collecting developed but not senescent leaves (about 0.5cm width × 1.5cm length) from at least 15 seedlings.

extract_protocol: Total RNA was extracted and purified using QIAGEN-RNeasy Mini Kit according to guidelines specified by the manufacturer.

treatment_protocol: Plants subjected to salt stress were watered with NaCl solution which was dissolved in ½ Strength Hoagland Solution. Salt treatment started at 14 DAS . Plants were watered from below to field capacity and then sprayed with the same concentration of NaCl solution from the top, ensuring adequate leaching and preventing excess salinity. The concentrations of NaCl supplementation were increased stepwise by 50 mM every 2 days for each line, to the indicated maximum (0, 100 mM). Plants were then watered every 2 days with or without NaCl at the indicated concentrations. The flats were rotated in the growth chamber everyday to minimize the effect of growth condition.

value: leaf

value: wt

value: 20 days after sowing

tag: genetic background

value: Col(gl)

value: 100mM NaCl


title: LD0-2817P Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep1

value: Leaves Trifoliate

value: Three weeks-old plants


title: 6 h after JA treatment replicate 1

description: Biological replicate 1 of 2.

value: Oryza sativa L. cv. Nipponnbare

value: un-treated (control)


title: LD0-2817P Leaves treated with Mock solution for 30 min Rep3

value: mock solution for 30 min


title: LD0-2817P Leaves treated with Mock solution for 30 min Rep2


title: Col(gl)_leaf_0mM NaCl_rep1 (wt + tg set)

description: Gene expression data in Col(gl) in the absence of salt

source_name: Col(gl) plant, 0mM NaCl, 6 d

value: 0mM NaCl


title: LD0-2817P Leaves treated with Mock solution for 30 min Rep1


title: Col_leaf_100mM NaCl_rep1 (wt + tg set)

description: Gene expression data in Col in the presence of salt

source_name: Col plant, 100mM NaCl, 6 d


title: Col(gl)_leaf_100mM NaCl_rep1 (wt + tg set)


title: Col(gl)_leaf_0mM NaCl_rep2 (wt + tg set)


title: SE2

city: corvallis

first: palitha

last: dharmawardhana

state: OR

address: 321 richarson hall,OSU

institute: OSU

hyb_protocol: Nimblegen pipeline

scan_protocol: Nimblegen pipeline

data_processing: Nimblegen pipeline, RMA normalization algorithm.

organism: Populus trichocarpa

source_name: Seed

label_protocol: Nimblegen pipeline

tag: tissue type

value: Seed


title: Col_leaf_100mM NaCl_rep2 (wt + tg set)


title: Xpi2

source_name: Developing xylem and pith

value: Developing xylem and pith


title: SE1

value: seed


title: ApL2

source_name: Leaves plastochron # 1

value: Leaves plastochron # 1


title: F2

source_name: Female catkin post pollination

value: Female catkin post pollination


title: gf Pituitary cells_3

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: slide 43

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS

organism: Carassius auratus

source_name: pituitary cells with SN incubation

extract_protocol: RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) per the manufacturer's protocol. Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada). RNA quantity was evaluated using the NanoDrop. RNA integrity was evaluated using the BioAnalyzer (Agilent);

treatment_protocol: Dispersed pituitary cells were treated with 10 nM gfSN for 12 hours in static incubation

value: male and female pituitaries

value: with SN incubation

source_name: pituitary cells with no incubation

value: with no incubation


title: gf Pituitary cells_4

description: slide 45

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)


title: Col_leaf_0mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Col in the absence of salt

source_name: Col plant, 0mM NaCl, 6 d

value: leaf

value: wt

value: 20 days after sowing


title: ML1

source_name: Mature leaves plastochron # 5

value: Mature leaves plastochron # 5


title: RTC2

source_name: Roots from tissue culture

value: Roots from tissue culture


title: FM2

source_name: Mature catkin

value: Mature catkin before seed release


title: Col_leaf_0mM NaCl_rep1 (wt + tg set)


title: gf Pituitary cells_2

description: slide 42


title: M1

source_name: Male catkin - 3 stages pooled

value: Male catkin - RNA from 3 stages of catkin development prior to pollen release were pooled


title: FM1

source_name: Mature catkin before seed release


title: F1

source_name: Female -post pollination

value: Female -post pollination


title: M2

source_name: Male catkin- 3 stages pooled


title: ML2


title: gf Pituitary cells_1

description: slide 13


title: Ws_leaf_100mM NaCl_rep1 (wt + tg set)

description: Gene expression data in Ws in the presence of salt

source_name: Ws plant, 100mM NaCl, 6 d

value: Ws

value: 100mM NaCl


title: Cyto_vs_Mito_5_RNAse

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

country: Germany

institute: Miltenyi Biotec GmbH

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore ™ microarrays was done with the Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 8.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Hy5/Hy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos.

organism: Homo sapiens

source_name: HeLa cells cytosolic fraction

label_protocol: 2 µg of respective total RNA were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The corresponding total RNA samples were hybridized in a dual colour approach to microarrays.

extract_protocol: Total RNA was extracted from the cytosolic fraction using Trizol LS and from the mitochondrial fraction using Trizol following manufacturer's instructions

tag: cell type

value: HeLa

source_name: HeLa cells mitochondrial fraction; RNAse A treatment: 30 min at 4°C


title: ApL1

source_name: Young leaves at apex

value: Leaves -plastochron number 2


title: Cyto_vs_Mito_6_RNAse


title: Cyto_vs_Mito_3

source_name: HeLa cells mitochondrial fraction


title: Cyto_vs_Mito_4_RNAse

source_name: HeLa cells mitochondrial fraction; RNAse A treatment: 15 min at RT


title: PC1

source_name: Phloem and Cortex

value: Phloem and Cortex


title: Cyto_vs_Mito_2


title: Ws_leaf_0mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Ws in the absence of salt

source_name: Ws plant, 0mM NaCl, 6 d

value: 0mM NaCl


title: Ws_leaf_100mM NaCl_rep2 (wt + tg set)


title: PAO1, pH7.5, rep3

city: Chicago

first: Olga

middle: Y

last: ZABORINA

state: IL

address: 5841 S Maryland

department: Surgery

institute: University of Chicago

description: gene expresion data from lawns at pH 7.5

hyb_protocol: 1.5 µg of fragmented  and biotin labeled targets was hybridized to array for 16 h at 50°C and 60 rpm in an Affymetrix Hybridization Oven 640.

scan_protocol: After hybridization, arrays were washed and stained with Streptavidin Phycoerythrin. The fluorescent signals were amplified using a biotinylated antistreptavidin antibody in a Affymetrix GeneChip Fluidics Station (Affymetrix, Inc.) and the signals were detected in a GeneChip Scanner 3000 7G.

data_processing: The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix). ANOVA was used to identify differentially expressed genes

organism: Pseudomonas aeruginosa PAO1

label_protocol: Ten μg of each total RNA was processed  for biotin labeled target preparation for hybridization to Pseudomonas aeruginosa expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).

growth_protocol: P. aeruginosa PAO1 grew on agarized Nematode growth media at different pH for 20 hrs, 37C

extract_protocol: Cells were suspended in RNA protector solution (Bio-Rad), centrifuged 5,000 rpm, 10 min, 4C, lyzed in lysozyme TE solution followed by TRIzol. Total RNA was separated using PLG Phase lock gel followed by precipitation with isopropanol. DNA was removed with DNA-free kit

treatment_protocol: no additional treatment

tag: strain


title: PAO1, pH6.0, rep2

description: gene expresion data from lawns at pH 6.0


title: Cyto_vs_Mito_1


title: PAO1, pH7.5, rep1


title: PAO1, pH7.5, rep2


title: XPi1

source_name: Developing xylem and pith

value: Developing xylem and pith


title: Ws_leaf_0mM NaCl_rep1 (wt + tg set)


title: VYL2

source_name: Leaves -plastochron  number 2


title: PAO1, pH6.0, rep3


title: Sox2GFP+ckit- testis, biological rep 2

city: Boston

first: Katrin

last: Arnold

state: MA

address: 185 Cambridge Street

department: Cancer Center

institute: MGH

description: Gene expression data from mouse testis cells that are able to regenerate damaged testis tubules.

hyb_protocol: Following fragmentation, amplification and labeling, 5 ug of cDNA was hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix  GS 3000 Scanner with G7 upgrade using factory PMT settings.

data_processing: ExpressionAnalysisR with RMA normalization using Genesifter/Geospiza

organism: Mus musculus

source_name: Sox2GFP+ckit- Mouse testis cells

label_protocol: Biotinylated cDNA was prepared from 5 ng total RNA using the Ovation  Pico WTA System and Encore Biotin Module (NuGEN, San Carlos, California).

growth_protocol: 2 week old SoxGFP mice (129SvJae/BL6)

extract_protocol: Mouse testes of 2-week old Sox2GFP mice were isolated, and dissociated with collagenase. Single cell suspensions were generated and stained with FACS antibody for ckit. Cells were FACS sorted into Trizol, RNA was purified from approximately 20.000-90.000 cells per specimen using the RNeasy Mini-kit (Qiagen, Hilden, Germany)  following the manufacturer's recommended protocol utilizing DNase treatment.

value: 2 week old


title: mESCs, rep3

status: Public on Oct 05 2011

first: Kenneth

last: Chien

address: Richard B. Simches Research Center, CPZN 3208, 185 Cambridge Street

department: Cardiovascular Research Center

institute: Masschusetts General Hospital

hyb_protocol: The biotinylated complementary RNA (cRNA) was purified, fragmented and added to a hybridization solution containing several biotinylated control oligonucleotides, and hybridized to a microarray chip overnight at 45oC. The chips were transferred to a fluidics instrument that performed washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Raw data (.cel files) were normalized using the RMA method in affy (R/Bioconductor).

source_name: Genetically matched mouse ES cells

label_protocol: RNA was converted into cDNA using a T7 promoter-tailed olilgo-dT primer, and second cDNA systhesis was then carried out. The double-stranded cDNA was used as the template in an in vitro transcription reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the for unmodified ribonucleotide triphosphates.

growth_protocol: Mouse ES or iPS cells were maintained on irradiated MEF feeders in Dulbecco's Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and LIF suppliment.

extract_protocol: RNA MiniPrep kit (Qiagen) was used to extract total RNA for analysis.

treatment_protocol: To dislodge the ES or iPS cells from the culture dishes, the cells were treated with 0.25% trypsin for 5 minutes at 37oC. Culture medium was added to the dishes to stop trypsinization. The cells were dispersed into individual ones, transfered to uncoated cutlure dishes and incubated for 45 minutes for differential plating to remove MEF cells. The ES or iPS cells remaining in the suspension were collected for RNA extraction.  Mouse tail tip fibroblasts and ventricular myocytes are derived from postnatal day one pups using standard protocols.

value: C57/Bl and BlackSwiss mixed background

tag: developmental stage

value: undifferentiated pluripotent stem cells

value: Genetically matched mouse ES cells


title: Sox2GFP+ckit- testis, biological rep 1

extract_protocol: Mouse testes of 2-week old Sox2GFP mice were isolated, and dissociated with collagenase. Single cell suspensions were generated and stained with FACS antibody for ckit. Cells were FACS sorted into Trizol, RNA was purified from approximately 20.000-90.000 cells per specimen using the RNeasy Mini-kit (Qiagen, Hilden, Germany) following the manufacturer's recommended protocol utilizing DNase treatment.


title: mESCs, rep1


title: VYL1

source_name: Young leaf


title: Tail tip fibroblasts

source_name: Tail tip fibroblasts

value: postnatal day one

value: Tail tip fibroblasts


title: mESCs, rep2


title: TiPSCs, rep2

source_name: TTF-derived iPSCs

value: TTF-derived iPSCs


title: Ventricular cardiomyocytes

source_name: Ventricular cardiomyocytes

value: Ventricular cardiomyocytes


title: Sox2GFP+ckit+ testis, biological rep 1

description: Gene expression data from mouse testis cells that are NOT able to regenerate damaged testis tubules.

source_name: Sox2GFP+ckit+ Mouse testis cells


title: PAO1, pH6.0, rep1

data_processing: The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix). ANOVA was used to identify differentially expressed genes.


title: blood-saline-24h-3

city: Portland

first: Susan

middle: L

last: Stevens

address: 3181 SW Sam Jackson Pk Rd

department: Molecular Microbiology & Immunology

institute: Oregon Health & Science University

description: corresponds to brain sample IZ4

hyb_protocol: Labeled target was fragmented at 95o C in the presence of high magnesium concentration. Ten μg of target was hybridized with the GeneChip MOE430 2.0 array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 400 (Affymetrix).

scan_protocol: The distribution of fluorescent material on the processed array is determined using the Agilent GeneArray laser scanner (Affymetrix).  Image inspection is performed manually immediately following each scan. Software- Affymetrix GCOS v. 1.4.0.036. Scanning hardware- Agilent Gene Array Scanner

data_processing: Probe level measurements produced by GCOS (.cel files). The brain and blood data were normalized seperately using the Robust Multichip Average method.

source_name: blood, saline, 24h

label_protocol:
For brain samples: Fifty ng of each brain RNA sample were labeled with Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA).
For blood samples: Fifty ng of each blood RNA sample were prepared for hybridization using a modification of the standard Ovation protocol that has been optimized for working with whole blood RNA. This protocol, described as the Ovation Whole Blood Solution (NuGEN Technologies), uses the Ovation RNA Amplification System V2 with Ovation WB Reagent for the cDNA synthesis, RNA amplification steps of the target labeling protocol.

extract_protocol:
For brain samples: Total RNA was isolated using the Qiagen RNeasy Lipid tissue mini kit (Qiagen Inc.).
For blood samples: Total RNA was isolated from fresh blood using the QIAamp RNA Blood Mini Kit (Qiagen Inc.).

treatment_protocol: Groups of C57Bl6 mice (n=4/treatment/time for all except sham+ischemic challenge (n=3/treatment/time)) received either preconditioning alone, preconditioning plus ischemic challenge (45 min MCAO) or ischemic challenge alone. Preconditioning paradigms included: LPS (0.2 mg/kg; ip), CpG (0.8 mg/kg; ip), saline (ip), brief ischemia (MCAO, 12 min) or sham surgery (duplicates time and procedure for brief ischemia with out suture advancement). For groups receiving preconditioning alone, mice were euthanized for blood and tissue collection at 3, 24 and 72 hr post preconditioning. In groups receiving preconditioning plus ischemic challenge, MCAO was performed 72 hr following the preconditioning stimulus and mice were euthanized for blood and tissue collection at either 3 or 24 hr post occlusion. Groups receiving ischemic challenge alone received 45 min MCAO with no prior pretreatment and tissue was collected at 3 and 24 hr post occlusion. Blood and tissue were also collected from 6 unhandled mice to include as a baseline control group. At the time of euthanization all mice were anesthetized, then perfused with heparinized saline. Under RNase-free conditions the ipsilateral cortex region from the frontal 4 mm  of brain was isolated and snap frozen in liquid nitrogen.

value: whole blood

value: saline 24h


title: blood-brief ischemia-24h-4

description: corresponds to brain sample IY7

source_name: blood, brief ischemia, 24h

value: brief ischemia 24h


title: blood-saline-24h-4

description: corresponds to brain sample IZ5


title: ViPSCs, rep1

source_name: VM-deirved iPSCs

value: VM-deirved iPSCs


title: blood-brief ischemia-24h-3

description: corresponds to brain sample IY6


title: ViPSCs, rep3


title: blood-saline-24h-1

description: corresponds to brain sample IZ1


title: blood-ischemic challenge-24h-2

description: corresponds to brain sample IW2

source_name: blood, ischemic challenge, 24h

value: ischemic challenge 24h


title: blood-brief ischemia-24h-2

description: corresponds to brain sample IY5


title: blood-ischemic challenge-24h-1

description: corresponds to brain sample IW1


title: blood-sham+ischemic challenge-24h-3

description: corresponds to brain sample IX4

source_name: blood, sham+ischemic challenge, 24h

value: sham+ischemic challenge 24h


title: blood-sham+ischemic challenge-24h-1

description: corresponds to brain sample IX2


title: Sox2GFP+ckit+ testis, biological rep 2


title: TiPSCs, rep1


title: blood-brief ischemia-24h-1

description: corresponds to brain sample IY4


title: blood-sham+ischemic challenge-24h-2

description: corresponds to brain sample IX20


title: blood-ischemic challenge-24h-4

description: corresponds to brain sample IW6


title: blood-saline-3h-2

description: corresponds to brain sample IV3

source_name: blood, saline, 3h

value: saline 3h


title: TiPSCs, rep3


title: blood-saline-3h-4

description: corresponds to brain sample IV5


title: blood-saline-3h-3

description: corresponds to brain sample IV4


title: blood-saline-3h-1

description: corresponds to brain sample IV1


title: blood-ischemic challenge-24h-3

description: corresponds to brain sample IW5


title: blood-sham+ischemic challenge-3h-1

description: corresponds to brain sample IU1

source_name: blood, sham+ischemic challenge, 3h

value: sham+ischemic challenge 3h


title: blood-ischemic challenge-3h-4

description: corresponds to brain sample IT6

source_name: blood, ischemic challenge, 3h

value: ischemic challenge 3h


title: ViPSCs, rep2


title: blood-sham+ischemic challenge-3h-3

description: corresponds to brain sample IU3


title: blood-ischemic challenge-3h-3

description: corresponds to brain sample IT5


title: blood-ischemic challenge-3h-1

description: corresponds to brain sample IT1


title: blood-ischemic challenge-3h-2

description: corresponds to brain sample IT2


title: blood-brief ischemia+ischemic challenge-3h-2

description: corresponds to brain sample IS3

source_name: blood, brief ischemia+ischemic challenge, 3h

value: brief ischemia+ischemic challenge 3h


title: blood-sham+ischemic challenge-3h-2

description: corresponds to brain sample IU2


title: blood-saline-24h-2

description: corresponds to brain sample IZ3


title: blood-brief ischemia+ischemic challenge-3h-3

description: corresponds to brain sample IS4


title: blood-brief ischemia+ischemic challenge-3h-4

description: corresponds to brain sample IS5


title: blood-brief ischemia-72h-4

description: corresponds to brain sample IQ4

source_name: blood, brief ischemia, 72h

value: brief ischemia 72h


title: blood-sham-72h-3

description: corresponds to brain sample IR4

source_name: blood, sham, 72h

value: sham 72h


title: blood-brief ischemia-72h-3

description: corresponds to brain sample IQ3


title: blood-brief ischemia-72h-2

description: corresponds to brain sample IQ2


title: blood-brief ischemia+ischemic challenge-3h-1

description: corresponds to brain sample IS2


title: blood-sham-24h-4

description: corresponds to brain sample IP6

source_name: blood, sham, 24h

value: sham 24h


title: blood-sham-24h-2

description: corresponds to brain sample IP2


title: blood-sham-72h-2

description: corresponds to brain sample IR3


title: blood-brief ischemia+ischemic challenge-24h-4

description: corresponds to brain sample IN6

source_name: blood, brief ischemia+ischemic challenge, 24h

value: brief ischemia+ischemic challenge 24h


title: blood-sham-24h-3

description: corresponds to brain sample IP5


title: blood-brief ischemia-72h-1

description: corresponds to brain sample IQ1


title: blood-brief ischemia+ischemic challenge-24h-2

description: corresponds to brain sample IN2


title: blood-sham-24h-1

description: corresponds to brain sample IP1


title: blood-brief ischemia+ischemic challenge-24h-1

description: corresponds to brain sample IN1


title: blood-sham-72h-4

description: corresponds to brain sample IR5


title: blood-sham-72h-1

description: corresponds to brain sample IR1


title: blood-brief ischemia+ischemic challenge-24h-3

description: corresponds to brain sample IN3


title: blood-sham-3h-4

description: corresponds to brain sample IM5

source_name: blood, sham, 3h

value: sham 3h


title: blood-sham-3h-3

description: corresponds to brain sample IM4


title: blood-sham-3h-1

description: corresponds to brain sample IM1


title: blood-sham-3h-2

description: corresponds to brain sample IM3


title: blood-brief ischemia-3h-3

description: corresponds to brain sample IL4

source_name: blood, brief ischemia, 3h

value: brief ischemia 3h


title: blood-CpG+ischemic challenge-24h-1

description: corresponds to brain sample IK10

source_name: blood, CpG+ischemic challenge, 24h

value: CpG+ischemic challenge 24h


title: blood-CpG+ischemic challenge-24h-3

description: corresponds to brain sample IK3

value: whole blood


title: blood-CpG+ischemic challenge-3h-3

description: corresponds to brain sample IJ6

source_name: blood, CpG+ischemic challenge, 3h

value: CpG+ischemic challenge 3h


title: ICI-resistant vs. Control 2

type: genomic

city: Indianapolis

first: Jaesik

last: Jeong

address: 410 West 10th Street, Suite 3000

institute: IUPUI

hyb_protocol: Differential methylation hybridization was done using a customized 60-mer oligonucleotide microarray.

scan_protocol: Scanned on a GenePix Pro 4.0 scanner.

data_processing: LOWESS-normalized, background-subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were processed using R program.

molecule: genomic DNA

source_name: Wild type

label_protocol: Genomic DNA was labeled with the fluorophores Cy3 (wild type) or Cy5 (resistant cell line).

growth_protocol: Cells were maintained in MEM with 2 mmol/L L-glutamine, 0.1 mmol/L non-essential amino acids, 50 units/mL penicillin, 50 ug/mL streptomycin, 6 ng/mL insuliln, and 10% FBS.

extract_protocol: Genomic DNA was isolated by using the Qiagen DNeasy Tissue kit.

tag: cell line

value: breast cancer

tag: phenotype

value: ICI sensitive

source_name: ICI-resistant

value: ICI resistant


title: blood-brief ischemia-3h-4

description: corresponds to brain sample IL6


title: MOUSE4_2.5mm_UV

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description: Dual color Nimblegen data.

hyb_protocol: Each hybridization mixture was made up from 1.1 µg Test (Cy3) and 1.1 µg Reference (Cy5) sample. Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Roche NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche NimbleGen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto the microarrays, and hybridized for 18 hours at 42°C with the Roche NimbleGen Hybridization System 4. Afterwards, the slides were washed according to the Roche NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0.

scan_protocol: Arrays were scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies), and feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen).

data_processing:
No processed data was generated.

In the raw *.FTR file:
SIGNAL_MEAN_433844A**_#1 column represents the Cy3 channel
SIGNAL_MEAN_433844A**_#2 column represents the Cy5 channel

source_name: Dorsal skin, UV treated

label_protocol: Per RNA sample, 200 ng total RNA was amplified according to the Agilent LRILAK kit manual (Agilent technologies). Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies). Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test aRNA samples were labeled with Cy3 and a Reference sample (made by pooling equimolar amounts of RNA from the Test samples) was labeled with Cy5. 5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: Four 3- to 4-month-old SKH1 hairless mice were used in this experiment.

extract_protocol: Biopsy samples were grinded individually with a liquid nitrogen pre-chilled metal micro-pestle (Carl Roth) to a fine powder. The powder was transferred to a 1.5ml tube containing 300 µl Qiazol (Qiagen). The homogenate was vortexed vigorously for 15 s, shaken for 10 min on a Heidolph REAX 2000 with a multi-test tube attachment (speed setting 6), and then spun down quickly for 15 s. 60 µl chloroform was added to the homogenate, vortexed for 15 s and kept at room temperature for 3 min. The partly separated mixture was transferred as a whole to a pre-prepared phase-lock gel heavy containing tube. The tubes were inverted and centrifuged for 15 min at 12,000xg. The aqueous phase was transferred to a new 1.5 ml tube. The RNA was purified by column precipitation according to the RNeasy MinElute Cleanup Handbook (version 2007) – Appendix D: RNA Cleanup after Lysis and Homogenization with Qiazol Lysis Reagent (Qiagen). At the end of the procedure, the RNA was eluted in 14 µl nuclease-free water.

treatment_protocol: Two mice were untreated controls and two mice were irradiated with 300 J/m2 UVB light. 24 hours after exposure, both treated and untreated mice were euthanized by cervical dislocation. This was followed directly by biopsy sampling from the back to prevent RNA decay. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80 °C until further processing.

tag: mouse identifier

value: 3-4 months

value: dorsal skin

tag: biopsy punch diameter

value: UVB radiation

source_name: Pooled common reference

tag: composition

value: pool from all samples

tag: sample type

value: reference


title: blood-brief ischemia-3h-1

description: corresponds to brain sample IL2

tag: tissue


title: blood-CpG+ischemic challenge-3h-1

description: corresponds to brain sample IJ3

tag: treatment


title: blood-brief ischemia-3h-2

description: corresponds to brain sample IL3


title: OHT-resistant vs. Control 1

value: OHT sensitive

source_name: OHT-resistant

value: OHT resistant


title: blood-CpG+ischemic challenge-3h-2

description: corresponds to brain sample IJ4


title: blood-CpG+ischemic challenge-24h-4

description: corresponds to brain sample IK6


title: MOUSE4_2.0mm_UV

description: Dual color Nimblegen data.

tag: age


title: blood-CpG+ischemic challenge-24h-2

description: corresponds to brain sample IK13


title: MOUSE4_1.5mm_UV

description: Dual color Nimblegen data.


title: blood-CpG-72h-2

description: corresponds to brain sample II2

source_name: blood, CpG, 72h

value: CpG 72h


title: MOUSE3_2.5mm_UV

description: Dual color Nimblegen data.


title: MOUSE3_2.0mm_UV

description: Dual color Nimblegen data.


title: blood-CpG+ischemic challenge-3h-4

description: corresponds to brain sample IJ7


title: MOUSE2_2.5mm_noUV

description: Dual color Nimblegen data.

source_name: Dorsal skin, untreated


title: blood-CpG-72h-4

description: corresponds to brain sample II4


title: MOUSE1_2.0mm_noUV

description: Dual color Nimblegen data.


title: blood-CpG-72h-3

description: corresponds to brain sample II3


title: MOUSE3_1.5mm_UV

description: Dual color Nimblegen data.


title: blood-CpG-24h-4

description: corresponds to brain sample IH9

source_name: blood, CpG, 24h

value: CpG 24h


title: MOUSE2_2.0mm_noUV

description: Dual color Nimblegen data.


title: blood-CpG-24h-3

description: corresponds to brain sample IH8


title: MOUSE1_2.5mm_noUV

description: Dual color Nimblegen data.


title: blood-CpG-72h-1

description: corresponds to brain sample II1


title: blood-CpG-24h-2

description: corresponds to brain sample IH6


title: MOUSE2_1.5mm_noUV

description: Dual color Nimblegen data.


title: blood-CpG-24h-1

description: corresponds to brain sample IH1


title: MOUSE1_1.5mm_noUV

description: Dual color Nimblegen data.


title: blood-CpG-3h-4

description: corresponds to brain sample IG5

source_name: blood, CpG, 3h

value: CpG 3h


title: blood-LPS+ischemic challenge-24h-4

description: corresponds to brain sample IF8

source_name: blood, LPS+ischemic challenge, 24h

value: LPS+ischemic challenge 24h


title: blood-CpG-3h-1

description: corresponds to brain sample IG1


title: blood-LPS+ischemic challenge-24h-2

description: corresponds to brain sample IF5


title: blood-LPS+ischemic challenge-24h-3

description: corresponds to brain sample IF7


title: blood-CpG-3h-3

description: corresponds to brain sample IG3


title: blood-LPS+ischemic challenge-24h-1

description: corresponds to brain sample IF3


title: blood-CpG-3h-2

description: corresponds to brain sample IG2


title: blood-LPS+ischemic challenge-3h-1

description: corresponds to brain sample IE1

source_name: blood, LPS+ischemic challenge, 3h

value: LPS+ischemic challenge 3h


title: blood-LPS+ischemic challenge-3h-4

description: corresponds to brain sample IE4

value: whole blood


title: C57MG cells treated with rRspo2/rWnt3a, biological rep1

city: Bethesda

first: Jeffrey

middle: S

last: Rubin

state: MD

address: 37 Convent Drive

department: CCR

institute: NIH/NCI

description: Gene expression in C57MG cells after 24h treatment with rRspo2 and rWnt3a

hyb_protocol: One µg of purified cRNA was fragmented to uniform size and hybridized at 37°C for 18h in a rotating incubator.

scan_protocol: G2565 Microarray Scanner (Agilent Technologies)

data_processing: Arrays were processed with Agilent Feature Extraction v9.5.3.1 software and data were analyzed with GeneSpring GX v7.3.1 software.

label_protocol: Alexa-555-labeled cRNA was prepared by linear amplification of the poly(A)+ RNA population within the total RNA sample from 1µg total RNA.

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and 10μg/ml insulin and maintained in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using Ribopure RNA isolation kit from Ambion according to the manufacturer's protocol.

treatment_protocol: 2.5x10^5 cells were seeded per well of 6-well plates. After an overnight incubation growth medium was replaced with plain DMEM, and cells were treated for 24h with recombinant human R-spondin2 (100 ng/ml) or recombinant mouse Wnt3a (100 ng/ml) alone or in combination. For the vehicle control, cells were treated with BSA.

value: mammary epithelial cells

value: Rspo2/Wnt3a treatment


title: blood-LPS+ischemic challenge-3h-3

description: corresponds to brain sample IE3


title: C57MG cells treated with rWnt3a, biological rep2

description: Gene expression in C57MG cells after 24h treatment with rWnt3a

value: Wnt3a treatment


title: blood-LPS+ischemic challenge-3h-2

description: corresponds to brain sample IE2


title: C57MG cells treated with rRspo2/rWnt3a, biological rep2


title: blood-LPS-72h-4

description: corresponds to brain sample ID4

source_name: blood, LPS, 72h

value: LPS treated 72h


title: C57MG cells treated with rWnt3a, biological rep1


title: blood-unhandled-5

description: corresponds to brain sample IC7

source_name: blood, non-treated


title: C57MG cells treated with rRspo2/rWnt3a, biological rep3


title: blood-saline+ischemic challenge-24h-4

description: corresponds to brain sample ICC6

source_name: blood, saline+ischemic challenge, 24h

value: saline+ischemic challenge 24h


title: blood-saline+ischemic challenge-24h-3

description: corresponds to brain sample ICC5


title: blood-saline+ischemic challenge-24h-2

description: corresponds to brain sample ICC3


title: blood-saline+ischemic challenge-24h-1

description: corresponds to brain sample ICC2


title: blood-LPS-72h-1

description: corresponds to brain sample ID1


title: blood-LPS-72h-2

description: corresponds to brain sample ID2


title: blood-LPS-72h-3

description: corresponds to brain sample ID3


title: C57MG cells treated with rWnt3a, biological rep3


title: blood-unhandled-6

description: corresponds to brain sample IC8


title: C57MG cells treated with rRspo2, biological rep2

description: Gene expression in C57MG cells after 24h treatment with rRspo2

value: Rspo2 treatment


title: C57MG cells treated with rRspo2, biological rep1


title: blood-unhandled-4

description: corresponds to brain sample IC6


title: C57MG cells treated with BSA, biological rep1

description: Gene expression in C57MG cells after 24h treatment with BSA

source_name: C57MG control

value: control


title: C57MG cells treated with BSA, biological rep2


title: p_tr_72_Rep1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description: gene expression in tap root tip of soybean seedlings in control and under aluminum stress

hyb_protocol: Hybridization of the GeneChips was carried out  following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridization was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: ArrayAssist Enterprise (Agilent, CA)

source_name: One centimeter long  tap root tip of soybean genotype PI 416937 treated with Al

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, Two microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Plants were grown in hydroponic in growth chamber at 28oC /16 hours light and 20oC/8 hours dark cycle

extract_protocol: Total RNA was extracted using Qiagen plant RNeasy extraction kit according to manufucturer's protocol

treatment_protocol: 10 µM Al  (treated) or 0 µM Al (control)

value: root

tag: stress

value: aluminum


title: blood-unhandled-2

description: corresponds to brain sample IC2


title: p_tr_72_Rep2


title: blood-unhandled-3

description: corresponds to brain sample IC5


title: blood-unhandled-1

description: corresponds to brain sample IC1


title: p_tr_12_Rep3


title: C57MG cells treated with BSA, biological rep3


title: p_tr_48_Rep3


title: blood-saline+ischemic challenge-3h-4

description: corresponds to brain sample IBB6

source_name: blood, saline+ischemic challenge, 3h

value: saline+ischemic challenge 3h


title: p_tr_48_Rep1


title: p_tr_12_Rep2


title: p_tr_2_Rep2


title: p_tr_2_Rep1


title: p_con_72_Rep2

source_name: One centimeter long  tap root tip of soybean genotype PI 416937


title: blood-saline+ischemic challenge-3h-1

description: corresponds to brain sample IBB2


title: p_tr_72_Rep3


title: C57MG cells treated with rRspo2, biological rep3


title: blood-saline+ischemic challenge-3h-3

description: corresponds to brain sample IBB5


title: blood-saline+ischemic challenge-3h-2

description: corresponds to brain sample IBB4


title: blood-LPS-24h-3

description: corresponds to brain sample IB5

source_name: blood, LPS, 24h

value: LPS treated 24h


title: blood-LPS-24h-1

description: corresponds to brain sample IB1


title: blood-LPS-24h-4

description: corresponds to brain sample IB6


title: blood-LPS-24h-2

description: corresponds to brain sample IB3


title: p_con_48_Rep3


title: p_con_48_Rep2


title: blood-saline-72h-4

description: corresponds to brain sample IAA4

source_name: blood, saline, 72h

value: saline 72h


title: p_con_12_Rep3


title: p_con_48_Rep1


title: p_con_12_Rep2


title: p_con_72_Rep3


title: p_con_12_Rep1


title: blood-saline-72h-3

description: corresponds to brain sample IAA3


title: p_con_2_Rep2


title: blood-saline-72h-1

description: corresponds to brain sample IAA1


title: blood-LPS-3h-4

description: corresponds to brain sample IA8

source_name: blood, LPS, 3h

value: LPS treated 3h


title: whole blood-MDD-LPS-± 6 h-MDD32

first: sabine

last: Spijker

address: De Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research

institute: Neuroscience Campus Amsterdam

description:
LPS-stimulated gene expression in MDD patient.
MDD32_LPS

hyb_protocol: From each subject, labeled cRNA (1.5 µg Cy3-labeled basal blood sample; 1.25 µg Cy-5 labeled LPS-stimulated blood sample) was hybridized for 15-17 h at 65 °C onto the 44K Human Agilent whole genome arrays according to the manufacturer’s protocol. After washing, the arrays were quick-dried using acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 1x44k array slides. Scan resolution 10 µm. PMT set to 100%.

data_processing: Signal intensities were extracted using Agilent Feature Extraction (v8.0). Data were analyzed with Limma (Bioconductor) using median signals and median background. Control spots were normalized, but were set not to influence normalization. Non-uniform signals were removed prior to further analysis. After background subtraction (Edwards, offset 30), within normalization (Loess) and between array normalization (Aquantile) data were exported to SPSS. Further data selection for inclusion consisted of the following criteria (in this order): 1) Signal intensities for any gene should be 1.3x background (> 6.8 (log2)), and have non-saturated levels (<15.7 (log2)); 2) In addition, for any gene the signal should be present in >80% of the control as well as in >80% of the MDD samples to avoid type-1 errors due to a limited number of participants in each group. Genes present in <80 % of MDD or control samples were given an absent-call. From the total of 41,675 spots, filtering resulted in 22,789 spots for the basal sample and 22,935 spots in the LPS-stimulated sample, with an overlap of 21,107 spots (>92%).

source_name: peripheral blood, LPS, ±6 h

label_protocol: Labeling of RNA (1 µg) was according to the Agilent protocol (Agilent technologies, Palo Alto, USA). Using spectrophotometry, cRNA concentration and labeling efficiency were determined (Nanodrop ND-1000 UV-Vis Spectrophotometer, Nanodrop Technologies). For all subjects, the same set-up has been used with the basal sample labeled with Cy3 (green) and the LPS-stimulated sample labeled with Cy5 (red), except for one subject (MDD31). This excludes the possibility that differences between subjects are due to a color bias for which two-color arrays are known.

growth_protocol: NA.

extract_protocol: RNA was prepared using PAX (PreAnalytiX; Qiagen) gene blood collection tubes following the manufacturer's recommendations (after thawing of the PAX tubes for 2 h at room temperature). The protocol includes lysis of blood cells, digestion of proteins (prot K treatment), and an on-column DNaseI digestion. The purity of RNA was first determined by spectrophotometry (NanoDrop ND–1000 UV-Vis Spectrophotometer, Nanodrop Technologies). Because of contaminants due to the isolation procedure, visible in the spectrophotogram at 200-230 nm, RNA samples were precipitated using ethanol, and NaAc with addition of 0.1 µg linear acryl-amide. Subsequently, RNA quality was determined by spectrophotometry and by using the RNA 6000 NanoChip kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA passing quality control criteria (RIN values > 8) was used for further analysis.

treatment_protocol:
Serial venous whole blood samples were obtained between 8:00 a.m. and 10:00 a.m., after overnight fasting, in one 7 ml heparin-coated tube (Greiner). Between 10-60 minutes after blood draw, 2.5 ml of blood was transferred into a PAXgene tube (Qiagen) and used as the basal (non-LPS stimulated) sample. This tube was kept at room temperature for a minimum of 2 h, and subsequently stored at –20 °C. The remaining blood (4.5 ml) was stimulated by addition of LPS (10 ng/ml blood; E. coli, Sigma). LPS-stimulated samples were laid flat and incubated at a slow rotation for 5-6 h at 37° C before a 2.5 ml sample of this LPS-stimulated blood was transferred into a PAXgene tube (Qiagen), and treated as described for the basal sample.

Patients were arbitrarily selected from all patients to serve as primary cohort (nMDD = 21 (#MDD01-MDD21); nControls = 21 (#Con01-Con21)), or replication cohort (nMDD = 12 (#MDD22-35); nControls = 13 (#Con22-37)) using microarrays.

tag: gender

value: male

tag: smoking status

value: non-smoking

tag: disease

value: major depressive disorder (MDD)

value: patient

value: lipopolysaccharide (LPS)


title: p_tr_12_Rep1


title: blood-LPS-3h-2

description: corresponds to brain sample IA5

value: whole blood


title: whole blood-MDD-LPS-± 6 h-MDD35

description:
LPS-stimulated gene expression in MDD patient.
MDD35_LPS

value: quit smoking


title: blood-saline-72h-2

description: corresponds to brain sample IAA2


title: p_con_2_Rep1


title: whole blood-MDD-LPS-± 6 h-MDD30

description:
LPS-stimulated gene expression in MDD patient.
MDD30_LPS

value: female

value: smoking


title: blood-LPS-3h-1

description: corresponds to brain sample IA1


title: brain-saline-24h-3

description: corresponds to blood sample Z4

source_name: ipsilateral brain cortex, saline, 24h

value: brain cortex

value: saline 24h


title: whole blood-MDD-LPS-± 6 h-MDD28

description:
LPS-stimulated gene expression in MDD patient.
MDD28_LPS


title: whole blood-MDD-LPS-± 6 h-MDD29

description:
LPS-stimulated gene expression in MDD patient.
MDD29_LPS


title: p_con_72_Rep1

value: root

value: control


title: brain-saline-24h-2

description: corresponds to blood sample Z3


title: whole blood-MDD-LPS-± 6 h-MDD31

description:
LPS-stimulated gene expression in MDD patient.
MDD31_LPS


title: whole blood-MDD-LPS-± 6 h-MDD27

description:
LPS-stimulated gene expression in MDD patient.
MDD27_LPS


title: brain-brief ischemia-24h-4

description: corresponds to blood sample Y7

source_name: ipsilateral brain cortex, brief ischemia, 24h

value: brief ischemia 24h


title: brain-brief ischemia-24h-3

description: corresponds to blood sample Y6


title: whole blood-MDD-LPS-± 6 h-MDD26

description:
LPS-stimulated gene expression in MDD patient.
MDD26_LPS


title: whole blood-MDD-LPS-± 6 h-MDD25

description:
LPS-stimulated gene expression in MDD patient.
MDD25_LPS


title: brain-saline-24h-4

description: corresponds to blood sample Z5


title: blood-LPS-3h-3

description: corresponds to brain sample IA6


title: brain-saline-24h-1

description: corresponds to blood sample Z1


title: whole blood-MDD-LPS-± 6 h-MDD24

description:
LPS-stimulated gene expression in MDD patient.
MDD24_LPS


title: brain-brief ischemia-24h-2

description: corresponds to blood sample Y5


title: brain-brief ischemia-24h-1

description: corresponds to blood sample Y4


title: brain-sham+ischemic challenge-24h-3

description: corresponds to blood sample X4

source_name: ipsilateral brain cortex, sham+ischemic challenge, 24h

value: sham+ischemic challenge 24h


title: whole blood-MDD-LPS-± 6 h-MDD23

description:
LPS-stimulated gene expression in MDD patient.
MDD23_LPS


title: whole blood-MDD-LPS-± 6 h-MDD19

description:
LPS-stimulated gene expression in MDD patient.
MDD19_LPS


title: brain-ischemic challenge-24h-2

description: corresponds to blood sample W2

source_name: ipsilateral brain cortex, ischemic challenge, 24h

value: ischemic challenge 24h


title: whole blood-MDD-LPS-± 6 h-MDD21

description:
LPS-stimulated gene expression in MDD patient.
MDD21_LPS


title: whole blood-MDD-LPS-± 6 h-MDD20

description:
LPS-stimulated gene expression in MDD patient.
MDD20_LPS


title: brain-sham+ischemic challenge-24h-2

description: corresponds to blood sample X20


title: whole blood-MDD-LPS-± 6 h-MDD18

description:
LPS-stimulated gene expression in MDD patient.
MDD18_LPS


title: brain-ischemic challenge-24h-1

description: corresponds to blood sample W1


title: whole blood-MDD-LPS-± 6 h-MDD22

description:
LPS-stimulated gene expression in MDD patient.
MDD22_LPS


title: brain-sham+ischemic challenge-24h-1

description: corresponds to blood sample X2


title: whole blood-MDD-LPS-± 6 h-MDD14

description:
LPS-stimulated gene expression in MDD patient.
MDD14_LPS


title: brain-ischemic challenge-24h-3

description: corresponds to blood sample W5


title: brain-ischemic challenge-24h-4

description: corresponds to blood sample W6


title: brain-saline-3h-3

description: corresponds to blood sample V4

source_name: ipsilateral brain cortex, saline, 3h

value: saline 3h


title: brain-saline-3h-2

description: corresponds to blood sample V3


title: whole blood-MDD-LPS-± 6 h-MDD16

description:
LPS-stimulated gene expression in MDD patient.
MDD16_LPS


title: brain-saline-3h-4

description: corresponds to blood sample V5


title: whole blood-MDD-LPS-± 6 h-MDD15

description:
LPS-stimulated gene expression in MDD patient.
MDD15_LPS

value: male


title: brain-saline-3h-1

description: corresponds to blood sample V1


title: brain-sham+ischemic challenge-3h-3

description: corresponds to blood sample U3

source_name: ipsilateral brain cortex, sham+ischemic challenge, 3h

value: sham+ischemic challenge 3h


title: whole blood-MDD-LPS-± 6 h-MDD13

description:
LPS-stimulated gene expression in MDD patient.
MDD13_LPS

value: major depressive disorder (MDD)


title: brain-sham+ischemic challenge-3h-2

description: corresponds to blood sample U2


title: brain-sham+ischemic challenge-3h-1

description: corresponds to blood sample U1


title: brain-ischemic challenge-3h-4

description: corresponds to blood sample T6

source_name: ipsilateral brain cortex, ischemic challenge, 3h

value: ischemic challenge 3h


title: whole blood-MDD-LPS-± 6 h-MDD09

description:
LPS-stimulated gene expression in MDD patient.
MDD09_LPS

value: patient

value: lipopolysaccharide (LPS)


title: whole blood-MDD-LPS-± 6 h-MDD12

description:
LPS-stimulated gene expression in MDD patient.
MDD12_LPS

value: whole blood


title: brain-ischemic challenge-3h-3

description: corresponds to blood sample T5


title: brain-ischemic challenge-3h-2

description: corresponds to blood sample T2


title: whole blood-MDD-LPS-± 6 h-MDD11

description:
LPS-stimulated gene expression in MDD patient.
MDD11_LPS

value: female

value: non-smoking


title: whole blood-MDD-LPS-± 6 h-MDD07

description:
LPS-stimulated gene expression in MDD patient.
MDD07_LPS

value: quit smoking


title: whole blood-MDD-LPS-± 6 h-MDD10

description:
LPS-stimulated gene expression in MDD patient.
MDD10_LPS

value: smoking


title: whole blood-MDD-LPS-± 6 h-MDD06

description:
LPS-stimulated gene expression in MDD patient.
MDD06_LPS


title: brain-brief ischemia+ischemic challenge-3h-4

description: corresponds to blood sample S5

source_name: ipsilateral brain cortex, brief ischemia+ischemic challenge, 3h

value: brain cortex

value: brief ischemia+ischemic challenge 3h


title: whole blood-MDD-LPS-± 6 h-MDD05

description:
LPS-stimulated gene expression in MDD patient.
MDD05_LPS


title: brain-ischemic challenge-3h-1

description: corresponds to blood sample T1


title: brain-brief ischemia+ischemic challenge-3h-2

description: corresponds to blood sample S3


title: whole blood-MDD-LPS-± 6 h-MDD02

description:
LPS-stimulated gene expression in MDD patient.
MDD02_LPS


title: brain-brief ischemia+ischemic challenge-3h-1

description: corresponds to blood sample S2


title: whole blood-MDD-LPS-± 6 h-MDD04

description:
LPS-stimulated gene expression in MDD patient.
MDD04_LPS


title: whole blood-MDD-LPS-± 6 h-MDD01

description:
LPS-stimulated gene expression in MDD patient.
MDD01_LPS


title: whole blood-control-LPS-± 6 h-CON37

description:
LPS-stimulated gene expression in healthy control.
CON37_LPS

value: healthy

value: control


title: brain-sham-72h-2

description: corresponds to blood sample R3

source_name: ipsilateral brain cortex, sham, 72h

value: sham 72h


title: brain-sham-72h-4

description: corresponds to blood sample R5


title: brain-sham-72h-3

description: corresponds to blood sample R4


title: brain-brief ischemia+ischemic challenge-3h-3

description: corresponds to blood sample S4


title: whole blood-MDD-LPS-± 6 h-MDD08

description:
LPS-stimulated gene expression in MDD patient.
MDD08_LPS


title: brain-sham-72h-1

description: corresponds to blood sample R1


title: whole blood-control-LPS-± 6 h-CON32

description:
LPS-stimulated gene expression in healthy control.
CON32_LPS


title: brain-brief ischemia-72h-3

description: corresponds to blood sample Q3

source_name: ipsilateral brain cortex, brief ischemia, 72h

value: brief ischemia 72h


title: brain-brief ischemia-72h-4

description: corresponds to blood sample Q4


title: whole blood-MDD-LPS-± 6 h-MDD03

description:
LPS-stimulated gene expression in MDD patient.
MDD03_LPS


title: whole blood-control-LPS-± 6 h-CON29

description:
LPS-stimulated gene expression in healthy control.
CON29_LPS

value: male


title: whole blood-control-LPS-± 6 h-CON36

description:
LPS-stimulated gene expression in healthy control.
CON36_LPS


title: brain-brief ischemia-72h-2

description: corresponds to blood sample Q2


title: brain-sham-24h-4

description: corresponds to blood sample P6

source_name: ipsilateral brain cortex, sham, 24h

value: sham 24h


title: brain-brief ischemia+ischemic challenge-24h-2

description: corresponds to blood sample N2

source_name: ipsilateral brain cortex, brief ischemia+ischemic challenge, 24h

value: brief ischemia+ischemic challenge 24h


title: brain-sham-24h-1

description: corresponds to blood sample P1


title: brain-sham-24h-3

description: corresponds to blood sample P5


title: brain-brief ischemia+ischemic challenge-24h-4

description: corresponds to blood sample N6


title: ROC_deletion_characterization

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

description: Reference sample: Pool of six normal control DNAs from six healthy donors

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Patient and normal control DNAs (reference) were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 40 hours. The sandwiched slides were hybridized for 40 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).

data_processing: Log2 ratios were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s Genomic Workbench 5.0 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.

source_name: wholeblood leukocytes

label_protocol: Genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions (Protocol v6.3, October 2010, Agilent technologies). Patients’ DNA and pooled normal control DNAs (reference) were labeled with Cy5-dUTP and Cy3-dUTP, respectively.

extract_protocol:
High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from wholeblood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.

value: wholeblood leukocytes

tag: genotype/variation

tag: reference sample


title: whole blood-control-LPS-± 6 h-CON28

description:
LPS-stimulated gene expression in healthy control.
CON28_LPS


title: brain-sham-3h-4

description: corresponds to blood sample M5

source_name: ipsilateral brain cortex, sham, 3h

tag: strain

value: sham 3h


title: TIL_deletion_characterization

source_name: Pool of six normal control DNAs from six healthy donors


title: whole blood-control-LPS-± 6 h-CON25

description:
LPS-stimulated gene expression in healthy control.
CON25_LPS

value: lipopolysaccharide (LPS)


title: brain-sham-3h-3

description: corresponds to blood sample M4


title: brain-brief ischemia-72h-1

description: corresponds to blood sample Q1


title: brain-brief ischemia+ischemic challenge-24h-1

description: corresponds to blood sample N1


title: brain-brief ischemia+ischemic challenge-24h-3

description: corresponds to blood sample N3


title: brain-sham-3h-2

description: corresponds to blood sample M3


title: whole blood-control-LPS-± 6 h-CON24

description:
LPS-stimulated gene expression in healthy control.
CON24_LPS

value: whole blood


title: brain-brief ischemia-3h-3

description: corresponds to blood sample L4

source_name: ipsilateral brain cortex, brief ischemia, 3h

value: brief ischemia 3h


title: whole blood-control-LPS-± 6 h-CON31

description:
LPS-stimulated gene expression in healthy control.
CON31_LPS

source_name: peripheral blood, LPS, ±6 h

value: female

value: non-smoking


title: brain-sham-24h-2

description: corresponds to blood sample P2


title: brain-brief ischemia-3h-4

description: corresponds to blood sample L6


title: brain-sham-3h-1

description: corresponds to blood sample M1


title: whole blood-MDD-LPS-± 6 h-MDD17

description:
LPS-stimulated gene expression in MDD patient.
MDD17_LPS

value: smoking

value: major depressive disorder (MDD)

value: patient


title: whole blood-control-LPS-± 6 h-CON20

description:
LPS-stimulated gene expression in healthy control.
CON20_LPS

value: healthy


title: whole blood-control-LPS-± 6 h-CON26

description:
LPS-stimulated gene expression in healthy control.
CON26_LPS

value: control


title: whole blood-control-LPS-± 6 h-CON27

description:
LPS-stimulated gene expression in healthy control.
CON27_LPS


title: whole blood-control-LPS-± 6 h-CON22

description:
LPS-stimulated gene expression in healthy control.
CON22_LPS


title: brain-CpG-72h-4

description: corresponds to blood sample I4

source_name: ipsilateral brain cortex, CpG, 72h

value: brain cortex

value: CpG 72h


title: whole blood-control-LPS-± 6 h-CON18

description:
LPS-stimulated gene expression in healthy control.
CON18_LPS


title: whole blood-control-LPS-± 6 h-CON17

description:
LPS-stimulated gene expression in healthy control.
CON17_LPS


title: brain-CpG+ischemic challenge-24h-1

description: corresponds to blood sample K10

source_name: ipsilateral brain cortex, CpG+ischemic challenge, 24h

value: CpG+ischemic challenge 24h


title: brain-CpG+ischemic challenge-24h-4

description: corresponds to blood sample K6


title: brain-CpG+ischemic challenge-24h-3

description: corresponds to blood sample K3


title: brain-brief ischemia-3h-2

description: corresponds to blood sample L3


title: brain-CpG-72h-2

description: corresponds to blood sample I2


title: brain-CpG+ischemic challenge-3h-4

description: corresponds to blood sample J7

source_name: ipsilateral brain cortex, CpG+ischemic challenge, 3h

value: CpG+ischemic challenge 3h


title: whole blood-control-LPS-± 6 h-CON23

description:
LPS-stimulated gene expression in healthy control.
CON23_LPS


title: brain-CpG+ischemic challenge-3h-1

description: corresponds to blood sample J3


title: brain-CpG+ischemic challenge-24h-2

description: corresponds to blood sample K13


title: brain-CpG+ischemic challenge-3h-3

description: corresponds to blood sample J6


title: Liver_rat_male_PBDE_rep5

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description:
liver from PBDE treated male rat
X100809.30_.Rat230_2..CEL

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 Genechip Array. Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EuKGE_Ws2v5.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm.

organism: Rattus norvegicus

source_name: rat_male_50mg/kg DE71

label_protocol: Total RNA (50 ng) was used to synthesize double-stranded cDNA for each sample using Affymetrix  GeneChipExpression 3'amplication two-cycle target labeling and control reagents (Affymetrix Inc. Santa Clara, CA).  The cDNA served as a template to synthesize biotin-labeled antisense cRNA using an in vitro transcription (IVT) labeling kit. Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 Genechip Array.

growth_protocol: Time mated female Wistar/Han dams (CRL:WI (HAN)) were obtained from Charles River Laboratories (Raleigh, NC). Dams were dosed by gavage with 0 or 50 mg/kg DE71 in corn oil (dosing volume 5 ml/kg) from GD 6 through PND 21, 7 days per week.  Direct dosing of pups began on and continued through PND 21 for 7 days per week until weaning. Weaning occurred on PND 21, which was designated as Day 1 of the 13-week portion of the study, and the day the pups were assigned to the 13-week portion of the study. On day one of the 13-week portion of the study dosing began on a 5 days/week schedule.  Pups designated for toxicogenomic study were dosed through PND 21, the day prior to PND 22 liver sample collection. Tap water and NTP-2000 diet (Zeigler Brothers, Inc.  Gardners, PA) was made available ad libitum (National Toxicology Program 2005a, b).

extract_protocol: A section of the liver was collected at necropsy, frozen and sent to the microarray processing unit where the liver was placed into RNAlater (Ambion, Inc., Austin, TX). RNA was extracted from liver using the QIAGEN Rneasy (QIAGEN, Valencia, CA).   The RNA was analyzed for quantity and purity by UV analysis using the NanoDrop ND-1000 (NanoDropTechnologies, Wilmington, DE). Samples were concentrated using Microcon filters (Millipore, Billerica, MA).  All samples were evaluated for RNA integrity by gel electrophoresis using the Flash Gel RNA cassette system (Lonza, Rockland, ME).

treatment_protocol: On PND 22, livers from five male and five female pups culled from the control and high dose groups were collected for toxicogenomic analysis (each pup came from a different dam). These animals were dosed through the day (PND 21) before liver tissue collection (PND 22).  Liver samples were collected from 5 control female pups, 5 control male pups, 5 50 mg/kg female pups, and 5 50 mg/kg male pups. At week 13, 10 males from the 0 and 50 mg/kg groups were sacrificed and the liver tissue was collected for toxicogenomic analysis and histopathlogy (each animal came from a different dam in that dose group).

tag: strain background

value: Wistar/Han

value: rat (week 13)

value: male

value: liver

tag: pbde dose

value: high


title: brain-CpG+ischemic challenge-3h-2

description: corresponds to blood sample J4


title: whole blood-control-LPS-± 6 h-CON19

description:
LPS-stimulated gene expression in healthy control.
CON19_LPS

value: whole blood

value: quit smoking

value: lipopolysaccharide (LPS)


title: whole blood-control-LPS-± 6 h-CON15

description:
LPS-stimulated gene expression in healthy control.
CON15_LPS

value: non-smoking


title: whole blood-control-LPS-± 6 h-CON16

description:
LPS-stimulated gene expression in healthy control.
CON16_LPS

value: female


title: whole blood-control-LPS-± 6 h-CON14

description:
LPS-stimulated gene expression in healthy control.
CON14_LPS


title: brain-CpG-72h-3

description: corresponds to blood sample I3


title: brain-brief ischemia-3h-1

description: corresponds to blood sample L2

value: brief ischemia 3h


title: brain-CpG-72h-1

description: corresponds to blood sample I1


title: brain-CpG-24h-3

description: corresponds to blood sample H8

source_name: ipsilateral brain cortex, CpG, 24h

value: CpG 24h


title: whole blood-control-LPS-± 6 h-CON13

description:
LPS-stimulated gene expression in healthy control.
CON13_LPS

value: smoking

value: healthy

value: control


title: Liver_rat_male_PBDE_rep3

description:
liver from PBDE treated male rat
X100809.28_.Rat230_2..CEL


title: Liver_rat_male_PBDE_rep4

description:
liver from PBDE treated male rat
X100809.29_.Rat230_2..CEL


title: brain-CpG-24h-4

description: corresponds to blood sample H9

value: brain cortex


title: whole blood-control-LPS-± 6 h-CON12

description:
LPS-stimulated gene expression in healthy control.
CON12_LPS


title: brain-CpG-3h-4

description: corresponds to blood sample G5

source_name: ipsilateral brain cortex, CpG, 3h

value: CpG 3h


title: Liver_rat_male_PBDE_rep2

description:
liver from PBDE treated male rat
X100809.27_.Rat230_2..CEL

value: Wistar/Han


title: Liver_rat_male_PBDE_rep1

description:
liver from PBDE treated male rat
X100809.26_.Rat230_2..CEL

value: rat (week 13)


title: brain-CpG-24h-2

description: corresponds to blood sample H6


title: brain-CpG-24h-1

description: corresponds to blood sample H1


title: whole blood-control-LPS-± 6 h-CON09

description:
LPS-stimulated gene expression in healthy control.
CON09_LPS

value: male


title: brain-LPS+ischemic challenge-24h-2

description: corresponds to blood sample F5

source_name: ipsilateral brain cortex, LPS+ischemic challenge, 24h

value: LPS+ischemic challenge 24h


title: brain-CpG-3h-1

description: corresponds to blood sample G1


title: whole blood-control-LPS-± 6 h-CON10

description:
LPS-stimulated gene expression in healthy control.
CON10_LPS


title: whole blood-control-LPS-± 6 h-CON11

description:
LPS-stimulated gene expression in healthy control.
CON11_LPS


title: Liver_rat_male_CTL_rep4

description:
liver from untreated male rat
X100809.24_.Rat230_2..CEL

value: liver


title: brain-CpG-3h-3

description: corresponds to blood sample G3


title: brain-CpG-3h-2

description: corresponds to blood sample G2


title: Liver_rat_male_CTL_rep5

description:
liver from untreated male rat
X100809.25_.Rat230_2..CEL


title: Liver_rat_male_CTL_rep3

description:
liver from untreated male rat
X100809.23_.Rat230_2..CEL


title: brain-LPS+ischemic challenge-24h-4

description: corresponds to blood sample F8


title: brain-LPS+ischemic challenge-3h-3

description: corresponds to blood sample E3

source_name: ipsilateral brain cortex, LPS+ischemic challenge, 3h

value: LPS+ischemic challenge 3h


title: brain-LPS+ischemic challenge-24h-3

description: corresponds to blood sample F7


title: brain-LPS+ischemic challenge-3h-4

description: corresponds to blood sample E4


title: brain-LPS+ischemic challenge-24h-1

description: corresponds to blood sample F3


title: brain-LPS+ischemic challenge-3h-1

description: corresponds to blood sample E1


title: whole blood-control-LPS-± 6 h-CON06

description:
LPS-stimulated gene expression in healthy control.
CON06_LPS

value: whole blood

value: quit smoking


title: Liver_pup_female_PBDE_rep5

description:
liver from PBDE treated female pup
X100809.20_.Rat230_2..CEL

source_name: pup_female_50mg/kg DE71

value: pup (PND 22)

value: high


title: Liver_rat_male_CTL_rep2

description:
liver from untreated male rat
X100809.22_.Rat230_2..CEL


title: brain-LPS+ischemic challenge-3h-2

description: corresponds to blood sample E2


title: brain-LPS-72h-4

description: corresponds to blood sample D4

source_name: ipsilateral brain cortex, LPS, 72h

value: LPS treated 72h


title: whole blood-control-LPS-± 6 h-CON03

description:
LPS-stimulated gene expression in healthy control.
CON03_LPS

value: female

value: lipopolysaccharide (LPS)


title: whole blood-control-LPS-± 6 h-CON05

description:
LPS-stimulated gene expression in healthy control.
CON05_LPS

value: smoking

value: healthy


title: whole blood-control-LPS-± 6 h-CON08

description:
LPS-stimulated gene expression in healthy control.
CON08_LPS

value: control


title: brain-LPS-72h-2

description: corresponds to blood sample D2

value: brain cortex


title: brain-saline+ischemic challenge-24h-4

description: corresponds to blood sample CC6

source_name: ipsilateral brain cortex, saline+ischemic challenge, 24h

value: saline+ischemic challenge 24h


title: Liver_pup_female_PBDE_rep3

description:
liver from PBDE treated female pup
X100809.18_.Rat230_2..CEL

value: Wistar/Han


title: Liver_pup_female_PBDE_rep2

description:
liver from PBDE treated female pup
X100809.17_.Rat230_2..CEL


title: brain-LPS-72h-1

description: corresponds to blood sample D1


title: whole blood-control-LPS-± 6 h-CON07

description:
LPS-stimulated gene expression in healthy control.
CON07_LPS


title: Liver_pup_female_PBDE_rep4

description:
liver from PBDE treated female pup
X100809.19_.Rat230_2..CEL


title: whole blood-control-LPS-± 6 h-CON02

description:
LPS-stimulated gene expression in healthy control.
CON02_LPS

value: non-smoking


title: brain-saline+ischemic challenge-24h-1

description: corresponds to blood sample CC2


title: Liver_rat_male_CTL_rep1

description:
liver from untreated male rat
X100809.21_.Rat230_2..CEL

value: rat (week 13)

value: male


title: brain-saline+ischemic challenge-24h-3

description: corresponds to blood sample CC5


title: brain-saline+ischemic challenge-24h-2

description: corresponds to blood sample CC3


title: brain-unhandled-5

description: corresponds to blood sample C7

source_name: ipsilateral brain cortex, non-treated


title: whole blood-control-LPS-± 6 h-CON04

description:
LPS-stimulated gene expression in healthy control.
CON04_LPS


title: whole blood-control-LPS-± 6 h-CON01

description:
LPS-stimulated gene expression in healthy control.
CON01_LPS


title: brain-unhandled-6

description: corresponds to blood sample C8


title: brain-unhandled-4

description: corresponds to blood sample C6


title: Liver_pup_female_CTL_rep5

description:
liver from untreated female pup
X100709.9_.Rat230_2..CEL

value: liver


title: whole blood-MDD-basal-MDD32

description:
Basal gene expression in MDD patient.
MDD32_basal

source_name: peripheral blood, basal

value: whole blood

value: major depressive disorder (MDD)

value: patient


title: brain-LPS-72h-3

description: corresponds to blood sample D3


title: Liver_pup_female_PBDE_rep1

description:
liver from PBDE treated female pup
X100809.16_.Rat230_2..CEL

value: pup (PND 22)

value: high


title: brain-unhandled-1

description: corresponds to blood sample C1


title: whole blood-MDD-basal-MDD35

description:
Basal gene expression in MDD patient.
MDD35_basal

value: quit smoking


title: brain-saline+ischemic challenge-3h-1

description: corresponds to blood sample BB2

source_name: ipsilateral brain cortex, saline+ischemic challenge, 3h

value: saline+ischemic challenge 3h


title: brain-unhandled-2

description: corresponds to blood sample C2


title: brain-saline+ischemic challenge-3h-2

description: corresponds to blood sample BB4


title: brain-saline+ischemic challenge-3h-3

description: corresponds to blood sample BB5


title: brain-saline+ischemic challenge-3h-4

description: corresponds to blood sample BB6


title: whole blood-MDD-basal-MDD31

description:
Basal gene expression in MDD patient.
MDD31_basal

value: female


title: brain-LPS-24h-4

description: corresponds to blood sample B6

source_name: ipsilateral brain cortex, LPS, 24h

value: LPS treated 24h


title: brain-LPS-24h-3

description: corresponds to blood sample B5


title: brain-unhandled-3

description: corresponds to blood sample C5


title: Liver_pup_female_CTL_rep4

description:
liver from untreated female pup
X100709.8_.Rat230_2..CEL

value: control


title: Liver_pup_male_CTL_rep5

description:
liver from untreated male pup
X100709.5_.Rat230_2..CEL


title: whole blood-MDD-basal-MDD30

description:
Basal gene expression in MDD patient.
MDD30_basal

value: smoking


title: brain-LPS-24h-1

description: corresponds to blood sample B1

value: brain cortex


title: brain-saline-72h-4

description: corresponds to blood sample AA4

source_name: ipsilateral brain cortex, saline, 72h

value: saline 72h


title: Liver_pup_female_CTL_rep2

description:
liver from untreated female pup
X100709.6_.Rat230_2..CEL

value: Wistar/Han


title: brain-LPS-24h-2

description: corresponds to blood sample B3


title: whole blood-MDD-basal-MDD29

description:
Basal gene expression in MDD patient.
MDD29_basal


title: whole blood-MDD-basal-MDD27

description:
Basal gene expression in MDD patient.
MDD27_basal


title: whole blood-MDD-basal-MDD26

description:
Basal gene expression in MDD patient.
MDD26_basal


title: brain-saline-72h-3

description: corresponds to blood sample AA3


title: Liver_pup_female_CTL_rep3

description:
liver from untreated female pup
X100709.7_.Rat230_2..CEL


title: brain-saline-72h-2

description: corresponds to blood sample AA2


title: whole blood-MDD-basal-MDD28

description:
Basal gene expression in MDD patient.
MDD28_basal


title: brain-LPS-3h-4

description: corresponds to blood sample A8

source_name: ipsilateral brain cortex, LPS, 3h

value: LPS treated 3h


title: Liver_pup_male_CTL_rep4

description:
liver from untreated male pup
X100709.4_.Rat230_2..CEL

value: male


title: Liver_pup_male_CTL_rep3

description:
liver from untreated male pup
X100709.3_.Rat230_2..CEL

value: liver


title: whole blood-MDD-basal-MDD25

description:
Basal gene expression in MDD patient.
MDD25_basal

value: whole blood


title: U2OS_S134AGR_DEXrep3

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

description:
Gene expression after 6hr of 100nM Dexamethasone treatment
US23502387_251485042563_S01_H.tif
US23502387_251485042563_S01_L.tif

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

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: U2OS_S134AGR, 6hr, Dex

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

growth_protocol: U2OS cells were maintained in DMEM/F-12 media supplemented with 10% fetal calf serum. Geneticin (500 μg/ml)/ hygromyocin (200μg/ml) were used to establish U-2 OS cell lines stably expressing poly-clonal mixed population of WT- and S134A GR. Cells were washed with PBS and grown in DMEM/F-12 media supplimented with 10% charcoal/dextran stripped fetal bovine serum for 48 hours prior to hormone treatments

extract_protocol: The total RNA was harvested with RNeasy kits from QIIAGEN according to manufacturer's recommendations, including on-column DNase treatment. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and by RNA Gel electrophoresis.

treatment_protocol: U2OS cells were treated with vehicle (water) or 100nM Dexamethasone then incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: U2OS osteosarcoma


title: Liver_pup_male_CTL_rep2

description:
liver from untreated male pup
X100709.2_.Rat230_2..CEL


title: Liver_pup_male_PBDE_rep4

description:
liver from PBDE treated male pup
X100709.14_.Rat230_2..CEL

source_name: pup_male_50mg/kg DE71


title: brain-LPS-3h-2

description: corresponds to blood sample A5


title: brain-saline-72h-1

description: corresponds to blood sample AA1


title: Liver_pup_male_PBDE_rep5

description:
liver from PBDE treated male pup
X100709.15_.Rat230_2..CEL


title: whole blood-MDD-basal-MDD24

description:
Basal gene expression in MDD patient.
MDD24_basal

value: major depressive disorder (MDD)

value: patient


title: brain-LPS-3h-1

description: corresponds to blood sample A1


title: Liver_pup_female_CTL_rep1

description:
liver from untreated female pup
X100709.10_.Rat230_2..CEL

value: pup (PND 22)


title: whole blood-MDD-basal-MDD23

description:
Basal gene expression in MDD patient.
MDD23_basal


title: U2OS_S134AGR_vehrep1

description:
Gene expression after 6hr of vehicle treatment
US23502387_251485042562_S01_H.tif
US23502387_251485042562_S01_L.tif

source_name: U2OS_S134AGR, 6hr, veh


title: Liver_pup_male_PBDE_rep1

description:
liver from PBDE treated male pup
X100709.11_.Rat230_2..CEL

value: high


title: whole blood-MDD-basal-MDD21

description:
Basal gene expression in MDD patient.
MDD21_basal


title: Liver_pup_male_PBDE_rep2

description:
liver from PBDE treated male pup
X100709.12_.Rat230_2..CEL


title: U2OS_S134AGR_DEXrep2

description:
Gene expression after 6hr of 100nM Dexamethasone treatment
US23502387_251485042762_S01_H.tif
US23502387_251485042762_S01_L.tif


title: whole blood-MDD-basal-MDD22

description:
Basal gene expression in MDD patient.
MDD22_basal


title: U2OS_S134AGR_vehrep3


title: U2OS_WTGR_vehrep2

description:
Gene expression after 6hr of vehicle treatment
US23502387_251485042563_S01_H.tif
US23502387_251485042563_S01_L.tif

source_name: U2OS_WTGR, 6hr, veh


title: Liver_pup_male_PBDE_rep3

description:
liver from PBDE treated male pup
X100709.13_.Rat230_2..CEL


title: whole blood-MDD-basal-MDD20

description:
Basal gene expression in MDD patient.
MDD20_basal

value: non-smoking


title: U2OS_S134AGR_vehrep2

description:
Gene expression after 6hr of vehicle treatment
US23502387_251485042762_S01_H.tif
US23502387_251485042762_S01_L.tif


title: U2OS_WTGR_DEXrep2

description:
Gene expression after 6hr of 100nM Dexamethasone treatment
US23502387_251485042562_S01_H.tif
US23502387_251485042562_S01_L.tif

source_name: U2OS_WTGR, 6hr, Dex


title: U2OS_WTGR_DEXrep1

description:
Gene expression after 6hr of 100nM Dexamethasone treatment
US23502387_251485042563_S01_H.tif
US23502387_251485042563_S01_L.tif


title: U2OS_WTGR_DEXrep3


title: U2OS_S134AGR_DEXrep1


title: brain-LPS-3h-3

description: corresponds to blood sample A6


title: whole blood-MDD-basal-MDD18

description:
Basal gene expression in MDD patient.
MDD18_basal

value: female


title: U2OS_WTGR_vehrep1


title: Cisplatin+Nimesulide_B

city: Vienna

first: Boban

last: Erovic

address: Waehringer Guertel 18-20

country: Austria

institute: MUW

description:
Experiments were done in triplicate; only two are included in this submission.

Detailed Sample protocols are available in the GSE15308_sample_protocols.txt file, which is linked as a supplementary file to the GSE15308 record.

hyb_protocol: Hybridization of the arrays was performed according to the manufacturer.

scan_protocol: Arrays were scanned using the GeneArray scanner (Affymetrix). Wavelength: 570nm for SAPE Pixel size: 3 μm for 24 μm Chip 6 μm for 50 μm Chip Number of scans: 2

data_processing: The Affymetrix chips were normalized using RMA (robust multi-array analysis). For the acquisition of reliable data, we used triplicate arrays although duplicate arrays are usually recommended. In a filtering step, all probe sets with inter-quartile range <0.3 were excluded, resulting in 300 probe sets for the analysis. A linear model for the comparison of the three treatment groups versus no treatment was calculated. However, due to the left-skewed distribution of the p-values (most likely induced by correlation between the probe sets), local false discovery rates were calculated for the three comparisons which give the probability of having no effect given the observed test statistics for each probe set. All probe sets with a local false discovery <0.2 were considered as "interesting". A heatmap with a dendogram of the arrays was plotted. All pre-processing steps and analyses were performed using R.2.6 and the Bioconductor environment (www.Bioconductor.org).

source_name: SSC9, cisplatin + nimesulide

label_protocol: Preparation of labeled cRNA was performed according to protocols of the manufacturer.

growth_protocol: The SCC9 cell line was cultured in RPMI 1640 medium containing 10% fetal bovine serum, 100U/mL penicillin and 100µg/mL streptomycin (all reagents from Life Technologies Ltd, Paisley, Scotland) and incubated at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA isolation was performed according to protocols of the manufacturer.

treatment_protocol: SCC9 cells were maintained in RPMI 1640 medium and seeded at equal densities of 5x10^5 cells in 10cm tissue culture dishes. 24 hours later, cells were harvested using Trypsin/EDTA (Life Technologies Ltd, Paisley Scotland) and treated with 100µmol/L nimesulide, 0.5µmol/L cisplatin or a combination of nimesulide/cisplatin. Control dishes were treated in exactly the same way without the addition of the respective compound. The concentration of 100µmol/L for nimesulide was chosen as this concentration is in a pharmacologically relevant range for humans.

tag: cell type

value: squamous carcinoma of the tongue

value: cisplatin + nimesulide


title: U2OS_WTGR_vehrep3


title: whole blood-MDD-basal-MDD19

description:
Basal gene expression in MDD patient.
MDD19_basal


title: Liver_pup_male_CTL_rep1

description:
liver from untreated male pup
X100709.1_.Rat230_2..CEL

value: control


title: whole blood-MDD-basal-MDD17

description:
Basal gene expression in MDD patient.
MDD17_basal

value: smoking


title: Cisplatin+Nimesulide_A


title: No70-3

city: Albany

first: Debbie

last: Laudencia-Chingcuanco

state: CA

address: 800 Buchanan Street

department: Western Regional Research Center

institute: USDA-ARS

description: SAMPLE 96

hyb_protocol: Microarray slides were hybridized to Biotin-labelled RNA using Affymetrix standard protocol

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

data_processing: The data were analyzed with GeneSpring GX using RMA as normalization method.

label: Biotin

organism: Triticum aestivum

source_name: Crown

label_protocol: The RNA was labelled with biotin according to standard Affymetrix protocol

extract_protocol: RNA was isolated using TRIZOL following the protocol recommended by the manufacturer

treatment_protocol: Wheat seedlings at 3-leaf stage were cold treated at 6 degree centigrade for 0, 2, 14, 28, 35, 42, 56 and 70 days.

value: winter Norstar

tag: developmental stage

value: seedling (3-leaf stage)

tag: biorep

value: low temperature

tag: time (duration of cold-treatment)

value: 70 days


title: Nimesulide_C

description:
Experiments were done in triplicate.

Detailed Sample protocols are available in the GSE15308_sample_protocols.txt file, which is linked as a supplementary file to the GSE15308 record.

source_name: SSC9, nimesulide

value: nimesulide


title: whole blood-MDD-basal-MDD16

description:
Basal gene expression in MDD patient.
MDD16_basal

tag: tissue

value: whole blood

tag: sample type


title: No56-2

description: SAMPLE 92

value: 56 days


title: whole blood-MDD-basal-MDD14

description:
Basal gene expression in MDD patient.
MDD14_basal

value: male

tag: age

value: major depressive disorder (MDD)

tag: treatment


title: whole blood-MDD-basal-MDD12

description:
Basal gene expression in MDD patient.
MDD12_basal

tag: gender

value: patient


title: No70-2

description: SAMPLE 95

tag: stress


title: No42-1

description: SAMPLE 88

value: 42 days


title: No42-2

description: SAMPLE 89


title: No56-3

description: SAMPLE 93


title: No35-3

description: SAMPLE 87

value: 35 days


title: No42-3

description: SAMPLE 90


title: whole blood-MDD-basal-MDD13

description:
Basal gene expression in MDD patient.
MDD13_basal

value: female

tag: smoking status

tag: disease


title: Cisplatin_C

source_name: SSC9, cisplatin

value: squamous carcinoma of the tongue

value: cisplatin


title: No35-2

description: SAMPLE 86

tag: genotype/variation


title: Cisplatin_A


title: Cisplatin_B


title: No21-3

description: SAMPLE 84

value: 21 days


title: No21-1

description: SAMPLE 82


title: No70-1

description: SAMPLE 94


title: whole blood-MDD-basal-MDD11

description:
Basal gene expression in MDD patient.
MDD11_basal

value: non-smoking


title: No56-1

description: SAMPLE 91

value: winter Norstar


title: No35-1

description: SAMPLE 85

value: seedling (3-leaf stage)


title: Nimesulide_B


title: Nimesulide_A


title: No21-2

description: SAMPLE 83

value: low temperature


title: No14-1

description: SAMPLE 79

value: 14 days


title: whole blood-MDD-basal-MDD10

description:
Basal gene expression in MDD patient.
MDD10_basal

value: smoking


title: whole blood-MDD-basal-MDD15

description:
Basal gene expression in MDD patient.
MDD15_basal

value: whole blood


title: Control_B

source_name: SSC9, control


title: Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-3

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM(400-648)+AF10 (677-758)

hyb_protocol: accoring to the recommended protocol followed by washing at a Fluidics Station 450 using fluidics script FS450_0003

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Data were processed using the miRNAQC tool from Affymetrix following the recommended workflow from Genisphere (Background Detection -> RMA Global Background Correction -> Quantile Normalization -> Median polish Summarization); Statistical analysis was done using BRB Array-Tools Software by Richard Simon

source_name: Adult mouse bone marrow

label_protocol: Samples were labeled using the FlashTag™ Biotin HSR Kit from Genisphere starting with 1µg of totel RNA according to the protocol of the manufaturer

growth_protocol: Adult C57/BL6/C3H mice were injected with 30µg/µl working solution of 5-Fluorouracil (100µl per 20gr of weight) to enrich for stem and progenitor cells. Four days post injection, total bone marrow

extract_protocol: Total RNA was extracted from FACS sorted GFP+ cells using the Qiagen miRNeasy Mini Kit For purification of microRNA and total RNA from tissues and cells per manufacturer's instructions

treatment_protocol: After 48 hours of pre-stimulation, the BM cells were transduced with different viruses, containing the relevent constructs, by overlaying them on virus-producing irradiated (40 Gy) GFP+E86 producers in the presence of cytokines and protamine sulfate (5ug/ml). The transduction was stopped by removing the BM cells from the GFP+E86 cells and plating them in BM medium with cytokines for another 48 hours to allow for GFP expression. Retrovirally transduced cells were FACS sorted based on expression of GFP.

tag: strain

value: bone marrow cells

tag: transducer


title: Bone marrow transduced with CALM-AF10 ΔOM-LZ, biological replicate-3

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM-AF10 ΔOM-LZ

value: CALM-AF10 ΔOM-LZ


title: No02-3

description: SAMPLE 78

value: 2 days


title: No14-3

description: SAMPLE 81


title: Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-2


title: Control_A


title: whole blood-MDD-basal-MDD04

description:
Basal gene expression in MDD patient.
MDD04_basal

value: major depressive disorder (MDD)

value: patient


title: No14-2

description: SAMPLE 80


title: No02-2

description: SAMPLE 77


title: No00-2

description: SAMPLE 74

value: control

value: 0 days


title: No00-1

description: SAMPLE 73


title: Control_C

value: squamous carcinoma of the tongue


title: whole blood-MDD-basal-MDD07

description:
Basal gene expression in MDD patient.
MDD07_basal

value: female

value: quit smoking


title: Ma70-1

description: SAMPLE 70

value: spring Manitou

value: 70 days