title: PGC_dev8_rep3

description: PGCs (AEL:11h20m - 13h20m), biological replicate 3


title: PGC_dev10_rep4

status: Public on Dec 25 2016

type: RNA

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description: PGCs (AEL:16h20m - 19h20m), biological replicate 4

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/5-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA)

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

molecule: total RNA

organism: Drosophila melanogaster

source_name: PGC, stage: 16h20m - 19h20m AEL

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng of total RNA was used.

growth_protocol: incubated at 25C

extract_protocol: Total RNA extracted using RNeasy (QIAGEN) manufacturer's instructions

treatment_protocol: Embryo cells were dissociated by Tripsin treatment and then subjected to FACS sorting

tag: tissue

value: primordial germ cells

tag: developmental stage

tag: strain

value: EGFP-vasa

source_name: poole whole embryos

value: whole embryos

value: 0 - 24h AEL


title: PGC_dev6_rep4

description: PGCs (AEL:7h20m - 9h20m), biological replicate 4

source_name: PGC, stage: 7h20m - 9h20m AEL

value: 7h20m - 9h20m AEL


title: PGC_dev9_rep3

description: PGCs (AEL:13h20m - 16h20m), biological replicate 3

source_name: PGC, stage: 13h20m - 16h20m AEL


title: PGC_dev11_rep4

description: PGCs (AEL:19h20m - 24h00m), biological replicate 4

source_name: PGC, stage: 19h20m - 24h00m AEL


title: PGC_dev3_rep4

description: PGCs (AEL:3h20m - 4h20m), biological replicate 4

source_name: PGC, stage: 3h20m - 4h20m AEL

value: 3h20m - 4h20m AEL


title: PGC_dev4_rep4

description: PGCs (AEL:4h20m - 5h20m), biological replicate 4

source_name: PGC, stage: 4h20m - 5h20m AEL

value: 4h20m - 5h20m AEL


title: PGC_dev11_rep3

description: PGCs (AEL:19h20m - 24h00m), biological replicate 3


title: PGC_dev5_rep3

description: PGCs (AEL:5h20m - 7h20m), biological replicate 3

source_name: PGC, stage: 5h20m - 7h20m AEL

value: 5h20m - 7h20m AEL


title: probiotic strain Z33

city: Granada

first: Julio

middle: Ramon

last: Plaza Diaz

state: Granada

address: Avda. del Conocimiento s/n

department: Biochemistry and Molecular Biology II

country: Spain

institute: University of Granada

description: Gene expression data from intestinal rat mucosa

hyb_protocol: Following fragmentation, 5,5 ug of cDNA were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: GeneChips were scanned using the GeneTitan™ from Affymetrix

data_processing: The data were analyzed with the Command Console (AGCC 3.1, Affymetrix®) and the Expression Console (EE 1.1, Affymetrix®)

organism: Rattus norvegicus

source_name: Zucker-Leprfa/fa male rats

label_protocol: The label process was performed using he WT Terminal Labeling kit de Affymetrix with deoxynucleotidyl transferase linked to biotin

extract_protocol:
RNA extraction was performed using the RNeasy Mini kit and Qiacube system according to the manufacturer's instructions.
300 mg of total RNA was utilized in the cDNA synthesis with the Ambion WT Expression kit according to the manufacturer's instructions.
The resulting cDNA was fragmented using Uracil DNA Glycosylase) and APE1 (Apurinic/apyrimidinic endonuclease 1)

treatment_protocol: 40 Zucker-Leprfa/fa rats were randomly assigned to receive 10^10 CFUs of one of the three probiotic strains (probiotic strains groups), or a placebo (obese placebo) by oral administration each day for 30 days. An additional group of 8 Zucker-lean+/fa rats (control placebo) received placebo, and other two groups of rats (8 Zucker-lean+/fa rats  and 8 Zucker-Leprfa/fa rats)  were used as reference (lean reference and obese reference).

value: intestinal mucosa

tag: animal sex

value: Male rats

tag: age

value: six weeks


title: probiotic strain Z56

label: deoxynucleotidyl transferase linked to biotin


title: probiotic strain Z46


title: PGC_dev2_rep3

description: PGCs (AEL:2h20m - 3h20m), biological replicate 3

source_name: PGC, stage: 2h20m - 3h20m AEL

value: 2h20m - 3h20m AEL


title: PGC_dev3_rep3

description: PGCs (AEL:3h20m - 4h20m), biological replicate 3


title: probiotic strain Z36


title: PGC_dev7_rep3

description: PGCs (AEL:9h20m - 11h20m), biological replicate 3

source_name: PGC, stage: 9h20m - 11h20m AEL


title: PGC_dev1_rep3

description: PGCs (AEL:1h20m - 2h20m), biological replicate 3

source_name: PGC, stage: 1h20m - 2h20m AEL

value: 1h20m - 2h20m AEL


title: PGC_dev4_rep3

description: PGCs (AEL:4h20m - 5h20m), biological replicate 3


title: PGC_dev6_rep3

description: PGCs (AEL:7h20m - 9h20m), biological replicate 3


title: PGC_dev6_rep2

description: PGCs (AEL:7h20m - 9h20m), biological replicate 2


title: PGC_dev7_rep2

description: PGCs (AEL:9h20m - 11h20m), biological replicate 2


title: PGC_dev5_rep2

description: PGCs (AEL:5h20m - 7h20m), biological replicate 2


title: probiotic strain Z57


title: probiotic strain Z26


title: probiotic strain Z23


title: PGC_dev9_rep2

description: PGCs (AEL:13h20m - 16h20m), biological replicate 2


title: PGC_dev11_rep2

description: PGCs (AEL:19h20m - 24h00m), biological replicate 2


title: PGC_dev10_rep2

description: PGCs (AEL:16h20m - 19h20m), biological replicate 2


title: PGC_dev8_rep2

description: PGCs (AEL:11h20m - 13h20m), biological replicate 2

source_name: PGC, stage: 11h20m - 13h20m AEL


title: probiotic strain Z43


title: obese reference Z4


title: control placebo C16

source_name: Zucker-lean+/fa male rats


title: obese reference Z2


title: obese placebo Z16


title: control placebo C13


title: obese placebo Z13


title: PGC_dev4_rep2

description: PGCs (AEL:4h20m - 5h20m), biological replicate 2


title: PGC_dev3_rep2

description: PGCs (AEL:3h20m - 4h20m), biological replicate 2


title: probiotic strain Z55


title: PGC_dev11_rep1

description: PGCs (AEL:19h20m - 24h00m), biological replicate 1


title: PGC_dev2_rep2

description: PGCs (AEL:2h20m - 3h20m), biological replicate 2


title: lean reference C2

description: Gene expression data from intestinal rat mucosa


title: lean reference C4


title: PGC_dev9_rep1

description: PGCs (AEL:13h20m - 16h20m), biological replicate 1


title: probiotic strain Z51


title: PGC_dev10_rep1

description: PGCs (AEL:16h20m - 19h20m), biological replicate 1


title: PGC_dev8_rep1

description: PGCs (AEL:11h20m - 13h20m), biological replicate 1


title: PGC_dev7_rep1

description: PGCs (AEL:9h20m - 11h20m), biological replicate 1


title: probiotic strain Z41


title: PGC_dev6_rep1

description: PGCs (AEL:7h20m - 9h20m), biological replicate 1


title: probiotic strain Z31


title: probiotic strain Z25


title: probiotic strain Z35


title: probiotic strain Z45


title: obese placebo Z11


title: probiotic strain Z21


title: control placebo C15


title: control placebo C11


title: PGC_dev2_rep1

description: PGCs (AEL:2h20m - 3h20m), biological replicate 1


title: obese placebo Z15


title: PGC_dev1_rep1

description: PGCs (AEL:1h20m - 2h20m), biological replicate #1


title: obese reference Z3


title: PGC_dev4_rep1

description: PGCs (AEL:4h20m - 5h20m), biological replicate 1


title: PGC_dev3_rep1

description: PGCs (AEL:3h20m - 4h20m), biological replicate 1


title: PGC_dev1_rep2

description: PGCs (AEL:1h20m - 2h20m), biological replicate 2


title: obese reference Z1


title: Mammary_normal_lean-control_rep3

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression of normal mammary tissue from a lean rat fed with a standard diet

hyb_protocol: Labeled RNA was hybridized to DNA microarrays (Whole Rat Genome Microarray Kit, Agilent) using the Gene Expression Hybridization Kit (Agilent) at 65°C for 17 h and washed with Gene Expression Wash Buffers 1 and 2 (Agilent).

scan_protocol: Microarrays were then scanned (DNA Microarray Scanner, Model G2565BA; Agilent) using one color scan setting for 4x44K array slides (scan area, 61x21.6 mm; scan resolution, 5 um; scanning mode, single pass; extended dynamic range, on; dye channel, Green; Green PMT for XDR-Hi, 100%; and Green PMT for XDR-Lo, 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and grid 014879_D_F_20100118) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: Mammary gland

label_protocol: Cyanine 3–labeled complementary RNA was generated from total RNA samples of tumors and normal mammary tissues from age-matched rats using the Low RNA Input Linear Amplification Kit Plus (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Total RNA was extracted from frozen carcinomas and from frozen normal mammary tissues using the Maxwell 16 Total RNA Purification kit (Promega Co., Madison, WI).

treatment_protocol: Female Sprague-Dawley (Jcl:SD) rats fed on a high fat diet (45 kcal% fat) were divided into obesity prone and resistant individuals based on the body weight at 7 weeks of age, when they were whole-body irradiated with 4 Gy of Cs-137 gamma rays at 0.5 Gy/min; lean control rats were fed on a standard diet (10 kcal% fat) and irradiated in the same manner; these groups of rats were observed for development of palpable mammary cancer, while kept on the same diet, for 30 weeks.

value: Normal

tag: obesity

value: Lean control

tag: diet

value: 10 kcal% fat


title: Mammary_normal_lean-control_rep2


title: lean reference C3


title: lean reference C1


title: PGC_dev5_rep1

description: PGCs (AEL:5h20m - 7h20m), biological replicate 1


title: HL60 DMSO 4h R1

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

country: USA

institute: Constellation Pharmaceuticals

hyb_protocol: The fragmented and labelled ST-cDNA was added to the hybridization cocktail in accordance with the NuGENΓäó guidelines for hybridization onto Affymetrix GeneChip┬« arrays. Following the hybridization for 18 hours at 45┬░C in an Affymetrix GeneChip┬« Hybridization Oven 640, the array was washed and stained on the GeneChip┬« Fluidics Station 450 using the appropriate fluidics script.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000.  Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
CEL files were processed by the Affymetrix Expression Console software package using the gene-level RMA algorithm on the core set of probesets and the annotation file Huex-1_0-st-v2_na31_hg19 provided by Affmyetrix.
HuEx-1_0-st-v2.r2.pgf

label: biotin

organism: Homo sapiens

source_name: Promyelocytic leukemia

label_protocol: Total RNA was amplified using the NuGEN ApplauseΓäó WT Amp Plus ST Amplification System. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity.  A modification step targeting the amplified single-stranded cDNA resulted in the generation of sense target (ST) cDNA product compatible with the Affymetrix  GeneChip┬« Exon arrays.  The ST-cDNA was purified for accurate quantitation and to ensure optimal performance during the fragmentation and labeling process. The ST- cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer.  The appropriate amount of amplified ST-cDNA was fragmented and labeled using the EncoreΓäó Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented ST-cDNA.

extract_protocol: Total RNA was prepared using a Qiagen RNEasy Mini Kit with on column DNAse digestion according to the manufacturer's instructions.

tag: cell line

tag: treatment

value: DMSO 1.25 pc

tag: timepoint


title: HL60 HMBA 4h R2

value: HMBA 2.5 uM


title: Mammary_normal_obesity-prone_rep1

description: Gene expression of normal mammary tissue from an obese rat fed with a high-fat diet

value: Obesity prone

value: 45 kcal% fat


title: Adult 18 (9879671086_H)

status: Public on Dec 26 2016

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalised using robust-spline normalisation

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

extract_protocol: RNA was extracted from PAXgene tubes using PAXgene RNA extraction kit, and globin depleted using GLOBINclear™

treatment_protocol: PAXgene tubes. Baseline is pre-vaccination. Post-vaccinatio is 7 days post first vaccination. Post-booster is 7 days post second (booster) vaccination. Vaccine group 1 is first vaccination with Menveo (intramuscular), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 3 is first vaccination with ACWYVax (subcutaneous), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 4 is first vaccination with ACWYVax (1/5th dose intramuscular), followed by Menveo (intramuscular) booster 28 days later.Vaccine group 2 is first vaccination with ACWYVax (intramuscular), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 3 is first vaccination with ACWYVax (subcutaneous), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 4 is first vaccination with ACWYVax (1/5th dose intramuscular), followed by Menveo (intramuscular) booster 28 days later.

tag: sample time

value: Baseline

tag: vaccine group

tag: adult


title: HL60 DMSO 4h R2


title: HL60 CPI203 4h R1


title: HL60 CPI203 4h R2


title: HL60 4h control R2

value: control


title: Mammary_normal_obesity-resistant_rep2

description: Gene expression of normal mammary tissue from a lean rat fed with a high-fat diet

value: Obesity resistant


title: Mammary_normal_obesity-prone_rep3


title: Mammary_normal_lean-control_rep1


title: HL60 4h control R1


title: HL60 HMBA 4h R1


title: Mammary_normal_obesity-resistant_rep1


title: Mammary_cancer_lean-control_rep2

description: Gene expression of mammary cancer from a lean rat fed with a standard diet

value: Cancer


title: Mammary_cancer_lean-control_rep3


title: Mammary_cancer_lean-control_rep1


title: Mammary_cancer_obesity-resistant_rep1

description: Gene expression of mammary cancer from a lean rat fed with a high-fat diet


title: Mammary_normal_obesity-prone_rep2


title: JDCaP_Relapse_ARv567es_2

city: Fujisawa

first: Daisuke

last: Nakata

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

institute: Takeda Pharmaceutical Company

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1.0.

source_name: Relapsed JDCaP xenograft expressing ARv567es

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: JDCaP prostate cancer xenografts were maintained under the renal capsule of male F344/N Jcl-rnu/rnu rats. Serum prostate-specific antigen (PSA) levels were monitored as a biomarker of JDCaP tumor growth.

extract_protocol: Relapsed JDCaP tumor xenografts were harvested after the serum PSA levels exceeded a threshold of 20 ng/mL. Extraction of total RNA was performed using RNeasy Mini Kit (QIAGEN).

treatment_protocol: The rats were subjected to surgical or medical castration when the average serum PSA levels reached 25.72 ng/mL (range, 9.98–51.67 ng/mL). Parent JDCaP tumor xenografts were harvested without castration.

tag: tissue type

value: Prostate cancer JDCaP xenograft

tag: tumor stage

value: Castration-resistant


title: Mammary_cancer_obesity-resistant_rep2


title: Mammary_cancer_obesity-resistant_rep3


title: Mammary_cancer_obesity-prone_rep5

description: Gene expression of mammary cancer from an obese rat fed with a high-fat diet


title: JDCaP_Relapse_ARv567es_1


title: Mammary_cancer_obesity-prone_rep6


title: JDCaP_Relapse_ARv567es_3


title: Mammary_cancer_obesity-prone_rep4


title: JDCaP_Relapse_ARhiV7hi_1

source_name: Relapsed JDCaP xenograft overexpressing full-length AR and AR-V7


title: NAA treatment, Biological Replicate 3

first: Ottoline

last: Leyser

address: Bateman Street

institute: Sainsbury Laboratory Cambridge University

description:
Gene expression data from isolated cauline bud, treated with apical auxin for 18 h
Col-0 wild-type, 3-4 weeks old, node 1 bud

hyb_protocol: Affymetrix GeneChip Experiment Information; Protocol EukGE-WS2v4_450  Wash A1 Recovery Mixes 0  Wash A1 Temperature (C) 25  Number of Wash A1 Cycles 10  Mixes per Wash A1 Cycle 2  Wash B Recovery Mixes 0  Wash B Temperature (C) 50  Number of Wash B Cycles 4  Mixes per Wash B Cycle 15  Stain Temperature (C) 25  First Stain Time (seconds) 600  Wash A2 Recovery Mixes 0  Wash A2 Temperature (C) 25  Number of Wash A2 Cycles 10  Mixes per Wash A2 Cycle 4  Second Stain Time (seconds) 600  Third Stain Time (seconds) 600  Wash A3 Recovery Mixes 0  Wash A3 Temperature (C) 30  Number of Wash A3 Cycles 15  Mixes per Wash A3 Cycle 4  Holding Temperature (C) 25  Station 1  Module 2  Hybridize Date Jun 12 2008 11:41AM

scan_protocol: Pixel Size 2.5  Filter 570  Scan Temperature   Scan Date Jun 12 2008 11:41AM  Scanner ID 50208380  Number of Scans 1  Scanner Type M10

data_processing: Statistical analyses of microarray data were performed using R software (version 2.15)  and the affy, affycoretools and Bioconductor Limma packages. Raw data was initially assessed and normalised using the robust multichip analysis (RMA) algorithm. Differential gene expression between groups was then determined by fitting a linear model to the data using lmFit  with subsequent comparisons made using the makeContrasts function. Transcripts with a q-value of less than 0.05 and a fold change of greater than 1.5 were classed as significantly differentially regulated.

label: Biotin

organism: Arabidopsis thaliana

source_name: Isolated cauline bud, treated with apical auxin for 18 h

label_protocol: Enzo Bioarray HighYield RNA Transcript Labelling Kit (Affymetrix 900181). Labelled cRNA was purified using using the IVT cRNA Cleanup Spin Columns and reagents in the GeneChip Sample Cleanup Module (Affymetrix). Purified cRNA was fragmented at 94C for 35 minutes using fragmentation buffer in the GeneChip Sample Cleanup Module.

growth_protocol: Arabidopsis thaliana plants grown axenically as per Bennett, T., Sieberer, T., Willett, B., Booker, J., Luschnig, C. and Leyser, O. (2006) The Arabidopsis MAX pathway controls shoot branching by regulating auxin transport. Curr. Biol., 16, 553-563.

extract_protocol: Total RNA extracted using Qiagen RNeasy Micro Kit. Double stranded cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, 900371).

treatment_protocol: Isolated nodal stem segments bearing the first cauline bud were treated in split agar plates with mock (70 % ethanol apically), 1 μM apical NAA (1-naphthaleneacetic acid), or 1 μM apical NAA plus 1 μM basal CK (6-benzylaminopurine) as per Chatfield, S.P., Stirnberg, P., Forde, B.G. and Leyser, O. (2000) The hormonal regulation of axillary bud growth in Arabidopsis. Plant J., 24, 159-169.

tag: ecotype

value: 3-4 weeks old

value: cauline bud


title: NAA + CK treatment, Biological Replicate 1

description:
Gene expression data from isolated cauline bud, treated with apical auxin and basal CK for 18 h
Col-0 wild-type, 3-4 weeks old, node 1 bud

source_name: Isolated cauline bud, treated with apical auxin and basal CK for 18 h


title: JDCaP_Relapse_ARhiV7hi_2


title: JDCaP_Parent_2

source_name: Parent JDCaP xenograft expressing full-length AR

value: Androgen-dependent


title: NAA + CK treatment, Biological Replicate 2


title: JDCaP_Relapse_ARhiV7hi_3


title: NAA treatment, Biological Replicate 2


title: NAA + CK treatment, Biological Replicate 3


title: Mammary_cancer_obesity-prone_rep3


title: JDCaP_Parent_3


title: Mammary_cancer_obesity-prone_rep2


title: Ethanol control, Biological Replicate 2

description:
Gene expression data from isolated cauline bud, mock treated for 18 h
Col-0 wild-type, 3-4 weeks old, node 1 bud

source_name: Isolated cauline bud, mock treated for 18 h


title: JDCaP_Parent_1


title: Mammary_cancer_obesity-prone_rep1


title: Ethanol control, Biological Replicate 1


title: Ethanol control, Biological Replicate 3


title: DC_mix_D_1

status: Public on Dec 24 2016

city: Philadelphia

first: Theresa

last: Busch

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

hyb_protocol: Hybridization took place for 16 h in an Affymetrix GeneChip ® Hybridization Oven 640. Affymetrix GeneChip® Fluidics Station 450 was then used to wash and stain the arrays with streptavidin-phycoerythrin according to the standard antibody amplification protocol for eukaryotic targets.

scan_protocol: Arrays were scanned on Affymetrix GeneChip ® Scanner 3000 at 570 nm. Images were acquired using the Affymetrix ® GeneChip ® Command Console ® Software (AGCC).

data_processing: Standard RMA algorithm steps were followed for background correction, quantile normalization and log summarization of probe sets. Subsequent analysis included differential gene expression analysis using ANOVA (p-value < 0.05). Each comparison was designed in a treated vs. untreated fashion. Probe sets with no annotation or mapping to the same gene were removed from the analysis.

organism: Mus musculus

source_name: bone marrow derived dendritic cells, cultured in the presence of rmGM-CSF

label_protocol: Approximately 300 ng of total RNA were used to generate biotinylated complementary RNA (cRNA) for each group using the GeneChip ® WT PLUS Reagent Kit protocol for Whole Transcript (WT) Expression Array, Rev3. Poly-A RNA control added to the RNA test samples as exogenous positive control and the RNA was reverse-transcribed to double stranded cDNA and biotinylated cRNA was synthesized and purified according to the protocol. A 2 nd cycle of cDNA synthesis followed along with a second purification step. Then, 6μg of the single-stranded DNA was fragmented, labeled with the appropriate labeling reagent and hybridized to GeneChip ® Mouse Gene 2.0 ST arrays (Affymetrix, UK).

growth_protocol: DCs were generated from pluripotent bone marrow stem cells obtained from HLA-A2.1 transgenic mice, that were cultured in the presence of rmGM-CSF for 7 days at 37°C and 5% CO2.

extract_protocol: DCs were harvested after 18 h of stimulation. Total RNA was isolated with Trizol Reagent (Invitrogen, Karlruhe, Germany) and purified on a Qiagen RNeasy column (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: DCs were stimulated with: (i) chimeric peptides derived from the L. infantum immunogenic proteins CPA, histone H1 and KMP-11 in particulate form (PLGA nanoparticles, mix A), (ii) chimeric peptides and MPLA adjuvant in particulate form (mix B), (iii) chimeric peptides in particulate form surface modified with an octapeptide targeting the TNFRII receptor on DCs surface (mix C), and (iv) chimeric peptides in soluble form (mix D). DCs cultured in medium alone were used as a reference group.

value: bone marrow derived dendretic cells (DCs)

tag: stimulation

value: stimulated with chimeric peptides in soluble form (mix D)


title: DC_mix_B_3

tag: tissue

value: stimulated with chimeric peptides and MPLA adjuvant in particulate form (mix B)


title: DC_mix_C_1

value: stimulated with chimeric peptides in particulate form surface modified with an octapeptide targeting the TNFRII receptor on DCs surface (mix C)


title: DC_mix_C_2


title: DC_mix_D_2


title: DC_mix_B_1


title: DC_mix_A_1

value: stimulated with chimeric peptides derived from the L. infantum immunogenic proteins CPA, histone H1 and KMP-11 in particulate form (mix A)


title: DC_mix_D_3


title: DC_mix_B_2


title: DC_untreated_3

value: unstimulated (control)


title: Patient-BE-091-PaxGenewholeblood-POD3-Rejection

city: Berlin

first: Nathanael

last: Raschzok

address: Augustenburger Platz 1

department: Department of Surgery; Campus Charite Mitte / Campus Virchow Klinikum

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3

hyb_protocol: The Hy3TM-labeled samples and a Hy5TM-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNATM microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0.

scan_protocol: miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing:
Image analysis was carried out using the ImaGene® 9 (miRCURY LNATM microRNA Array Analysis Software, Exiqon, Denmark).
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Peripheral Blood

label_protocol: 300 ng total RNA from both sample and reference (equal amounts of all samples pooled together according to the common reference design) was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark).

growth_protocol: The immunosuppression protocol consisted of calcineurin inhibitors (tacrolimus or cyclosporine), prednisolone, and mycophenolate mofetil in selected cases. Clinically significant ACR was defined as histopathologically proven ACR combined with biochemical graft dysfunction (6). Biopsies were performed based on clinical decisions in cases of an increase or delayed decrease of transaminases or cholestasis parameters.

extract_protocol: Total RNA was extracted from blood cells using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) and stored at -80°C.

treatment_protocol: Peripheral blood (2.5mL) was collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland). Blood samples were left at room temperature for 24 hours and then stored at -20°C until processing.

value: whole blood

tag: sample from pod

tag: group

value: Rejection

tag: sample type

value: reference pool of all samples


title: DC_mix_A_3


title: Patient-BE-002-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3

value: Control


title: Patient-BE-040-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-031-PaxGenewholeblood-POD1-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: ahr2_DMSO_mITP_3

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: Biological replicate 3 of 3, 48 hpf ahr2hu3335 embryos

hyb_protocol: Samples were hybridized to Agilent Whole Zebrafish Genome Oligo Microarrays 4x44K using the Gene Experssion Hybridization Kit (Agilent)

scan_protocol: Slides were scanned after hybridization using the Agilent DNA microarray scanner (Agilent)

data_processing: Scanned images were read and processed using Agilent Feature Extraction software and analzed using limma in R. We implemented the separate-channel analysis for two-color microarrays method in limma utilizing a 2x2 factorial statistical model. Data were background corrected, loess normalized, and the distribution of the average probe intensities for all arrays were quantile normalized. To control for the technical pairing between channels that originated from the same two-channel array, the probe-wise correlation between all array pairs was estimated prior to statistical testing. Data preprocessing identified seven probes on the arrays with aberrant intensity data, which were filtered from the analysis.

organism: Danio rerio

source_name: Whole embryo, 48 hpf, mITP treated

label_protocol: 0.1 ug of Cy3-labeled cRNA was generated using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

extract_protocol: Total RNA was exctracted using RNAzol RT according to manufacturers instructions. Whole embryos were homogenized in 500 uL RNAzol RT with 0.5 mm zirconium oxide beads using a bullet blender (Next Advance, Averill Park, NY) for 3 min at speed 8.

treatment_protocol: Dechorionated embryos were nominally exposed to statis aqueous concentrations of 0.2 or 0 uM mITP (0.1% DMSO) from 6-48 hpf. Embryos were maintained at 28 °C throughout exposure

tag: strain

value: whole embryo

value: mITP

source_name: Whole embryo, 48 hpf, DMSO control

value: DMSO


title: DC_mix_A_2


title: ahr2_DMSO_mITP_2

description: Biological replicate 2 of 3, 48 hpf ahr2hu3335 embryos


title: NAA treatment, Biological Replicate 1

description:
Gene expression data from isolated cauline bud, treated with 1 μM apical auxin for 18 h
Col-0 wild-type, 3-4 weeks old, node 1 bud

tag: age


title: DC_mix_C_3


title: Patient-BE-063-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: DC_untreated_1


title: ahr2_DMSO_mITP_1

description: Biological replicate 1 of 3, 48 hpf ahr2hu3335 embryos


title: wt_DMSO_mITP_3

description: Biological replicate 3 of 3, 48 hpf wild-type embryos

value: wild-type


title: wt_DMSO_mITP_1

description: Biological replicate 1 of 3, 48 hpf wild-type embryos


title: wt_DMSO_mITP_2

description: Biological replicate 2 of 3, 48 hpf wild-type embryos


title: DC_untreated_2


title: Patient-BE-028-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-099-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-044-PaxGenewholeblood-POD14-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-032-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-012-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-057-PaxGenewholeblood-POD14-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-076-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-LE-006-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-077-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-075-PaxGenewholeblood-POD5-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-099-PaxGenewholeblood-POD3-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-013-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-LE-042-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-058-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-030-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-021-PaxGenewholeblood-POD14-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-050-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-LE-032-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-LE-055-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-080-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-095-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-071-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-009-PaxGenewholeblood-POD14-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-BE-089-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: Patient-LE-007-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: 13_Blood_CD14+_rep2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Gene expression in human CD14+ monocytes in blood

hyb_protocol: The Cy3 labeled cDNAs were hybridized over night (17hrs, 65°C) to an Agilent whole human genome oligo microarray 8X60K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent gene expression wash buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent gene expression wash buffer 2 (37°C for 1 min). The last washing step was performed with acetonitrile.

scan_protocol: Fluorescent signals of the hybridized Agilent microarray were detected using Agilent's microarray scanner systems (Agilent technologies).

data_processing: The Agilent feature extraction software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidence.

source_name: Blood, CD14+ monocytes, rep2

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling, which was performed according to Miltenyi Biotec's undisclosed protocol.

growth_protocol: freshly isolated primary human immune cell populations

extract_protocol: Cell pellets lysed and frozen in SuperAmp Lysis Buffer, RNA was extracted and RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. Briefly, the amplification is based on a global PCR protocol usind mRNA-derived cDNA. mRNA was isloated via magnetic bead technology.

tag: cell type

value: CD14+ monocytes

tag: organ

value: Blood

tag: gender

value: male

tag: donor

tag: age (years)

tag: array id


title: Patient-LE-037-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: 13_Blood_CD14+_rep1

source_name: Blood, CD14+ monocytes, rep1

value: female


title: 13_Blood_CD14+_rep3

source_name: Blood, CD14+ monocytes, rep3


title: 12_Blood_B_cells_rep1

description: Gene expression in human B cells in blood

source_name: Blood, B cell, rep1

value: B cells


title: 10_Blood_CD4+_T_cells_rep3

description: Gene expression in human CD4+ T cells in blood

source_name: Blood, CD4+ T cell, rep3

value: CD4+ T cells


title: 11_Blood_CD8+_T_cells_rep1

description: Gene expression in human CD8+ T cells in blood

source_name: Blood, CD8+ T cell, rep1

value: CD8+ T cells


title: Patient-BE-010-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: 10_Blood_CD4+_T_cells_rep2

source_name: Blood, CD4+ T cell, rep2


title: 12_Blood_B_cells_rep2

source_name: Blood, B cell, rep2


title: 12_Blood_B_cells_rep3

source_name: Blood, B cell, rep3


title: 11_Blood_CD8+_T_cells_rep3

source_name: Blood, CD8+ T cell, rep3


title: 09_Thymus_pDC_rep3

description: Gene expression in human pDCs in thymus

source_name: Thymus, pDC, rep3

value: pDC

value: Thymus


title: Patient-BE-085-PaxGenewholeblood-POD7-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3

value: whole blood


title: Patient-BE-067-PaxGenewholeblood-POD14-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3


title: 09_Thymus_pDC_rep2

description: Gene expression in human pDCs in thymus

source_name: Thymus, pDC, rep2


title: 10_Blood_CD4+_T_cells_rep1

source_name: Blood, CD4+ T cell, rep1


title: 09_Thymus_pDC_rep1

description: Gene expression in human pDCs in thymus

source_name: Thymus, pDC, rep1


title: 11_Blood_CD8+_T_cells_rep2

source_name: Blood, CD8+ T cell, rep2


title: Patient-BE-093-PaxGenewholeblood-POD3-Rejection

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3

source_name: Peripheral Blood

value: Rejection


title: Patient-BE-033-PaxGenewholeblood-POD7-Control

description: 0_Exiqon - Cy5, 1_Exiqon -Cy3

value: reference pool of all samples


title: 07_Blood_pDC_rep3

description: Gene expression in human pDCs in blood

source_name: Blood, pDC, rep3


title: 08_Spleen_pDC_rep1

description: Gene expression in human pDCs in spleen

source_name: Spleen, pDC, rep1

value: Spleen


title: 08_Spleen_pDC_rep2

description: Gene expression in human pDCs in spleen

source_name: Spleen, pDC, rep2


title: 07_Blood_pDC_rep2

description: Gene expression in human pDCs in blood

source_name: Blood, pDC, rep2


title: 06_Thymus_CD141+_rep3

description: Gene expression in human CD141+ DCs in thymus

source_name: Thymus, CD141+ DC, rep3

value: CD141+ DCs


title: 06_Thymus_CD141+_rep2

source_name: Thymus, CD141+ DC, rep2


title: 07_Blood_pDC_rep1

description: Gene expression in human pDCs in blood

source_name: Blood, pDC, rep1


title: 06_Thymus_CD141+_rep1

source_name: Thymus, CD141+ DC, rep1


title: 05_Spleen_CD141+_rep3

description: Gene expression in human CD141+ DCs in spleen

source_name: Spleen, CD141+ DC, rep3


title: 05_Spleen_CD141+_rep2

source_name: Spleen, CD141+ DC, rep2


title: 05_Spleen_CD141+_rep1

source_name: Spleen, CD141+ DC, rep1


title: 04_Blood_CD141+_rep3

description: Gene expression in human CD141+ DCs in blood

source_name: Blood, CD141+ DC, rep3


title: K562 cell line, treated with 50 µM hemin

city: Freiburg

first: Rainer

last: Claus

address: Hugstetter Str. 55

department: Hematology, Oncology and Stem Cell Transplantation

institute: University of Freiburg Medical Center

description: Gene expression data from hemin (high concentration) treated K562 myeloid leukemia cell line

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: Arrays were scanned using an Affymetrix laser confocal scanner.

data_processing: Scanned microarray images were quantitatively analyzed using background adjustment, normalization and summarization of  the gcrma algorithm (Wu et al, 2005) and processed to log2 transformed expression measures. Bioconductor packages simpleaffy, affy, affyPLM, and genefilter were used for data analysis.

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

growth_protocol: K562 and HEL cells (obtained and verified by DMSZ, Braunschweig, Germany) were cultured in RPMI1640 (Gibco BRL/Invitrogen) supplemented with 10% heat inactivated FCS (Gibco BRL/Invitrogen) and incubated at 37°C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: DAC (Sigma Aldrich), was dissolved in PBS, stored at -80°C and thawed directly before addition to the culture medium at final concentrations of 50 and 100 nM, respectively. Cells were treated with three 24 hour pulses of DAC and harvested 144 hours after the first pulse, as described previously (Claus et al, 2006). Hemin (Sigma Aldrich), as positive control for induction of erythroid differentiation in K562 cells (Miller CW et al., Blood 1984), was added to the culture medium at a final concentration of 50 µM(Rutherford et al, 1981)). Megakaryocytic differentiation was induced by treatment with phorbol ester (PMA), as first described by Guilbert et al.(Guilbert et al, 1983) PMA (Sigma Aldrich) was added to the culture medium at 5 nM for an incubation time of 48h.

value: myeloid leukemia cell line

tag: cell line

tag: treatment

value: hemin


title: K562 cell line, untreated

description: Gene expression data from untreated K562 myeloid leukemia cell line

value: untreated


title: 02_Spleen_CD1c+_rep3

description: Gene expression in human CD1c+ DCs in spleen

source_name: Spleen, CD1c+ DC, rep3

value: CD1c+ DCs


title: 01_Blood_CD1c+_rep2

description: Gene expression in human CD1c+ DCs in blood

source_name: Blood, CD1c+ DC, rep2

value: Blood


title: 01_Blood_CD1c+_rep1

source_name: Blood, CD1c+ DC, rep1


title: HEL cell line, treated with 20 nM DAC

description: Gene expression data from DAC treated HEL myeloid leukemia cell line

source_name: HEL

value: HEL

value: DAC


title: 04_Blood_CD141+_rep2

source_name: Blood, CD141+ DC, rep2

value: female


title: 02_Spleen_CD1c+_rep2

source_name: Spleen, CD1c+ DC, rep2

value: male


title: 03_Thymus_CD1c+_rep3

description: Gene expression in human CD1c+ DCs in thymus

source_name: Thymus, CD1c+ DC, rep3


title: K562 cell line, treated with 100 nM DAC

description: Gene expression data from DAC treated K562 myeloid leukemia cell line


title: 03_Thymus_CD1c+_rep2

source_name: Thymus, CD1c+ DC, rep2


title: K562 cell line, treated with 25 µM hemin

description: Gene expression data from hemin (low concentration) treated K562 myeloid leukemia cell line


title: 02_Spleen_CD1c+_rep1

source_name: Spleen, CD1c+ DC, rep1


title: 04_Blood_CD141+_rep1

source_name: Blood, CD141+ DC, rep1


title: 03_Thymus_CD1c+_rep1

source_name: Thymus, CD1c+ DC, rep1


title: HEL cell line, untreated

description: Gene expression data from untreated HEL myeloid leukemia cell line


title: K562 cell line, treated with 5 nM PMA

description: Gene expression data from PMA treated K562 myeloid leukemia cell line

value: PMA


title: HEL cell line, treated with 5 nM PMA

description: Gene expression data from PMA treated HEL myeloid leukemia cell line


title: willm-00144: INF_067_bone marrow

status: Public on Dec 23 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Peripheral Blood Cell/Bone Marrow

tag: diseasestate

value: leukemia

tag: agevalue

tag: histology

value: ALL

tag: Sex

tag: organismstatus

value: premortem

tag: organismpart

value: Peripheral Blood Cell/Bone Marrow


title: willm-00144: INF_061_bone marrow

scan_protocol: See mage-tab files linked to series entry for additional details

value: AML


title: K562 cell line, untreated replicate

tag: tissue


title: willm-00144: INF_109_bone marrow

data_processing: See mage-tab files linked to series entry for additional details


title: LncKdm2b WT

city: Beijing

first: Buqing

last: Ye

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: This sample is of wild-type embryonic stem cells

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

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing:
 Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
High quality expression values (for example, where at least 1 out of 2 samples have values within cut-off, cut-off =100) will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups. Hierarchical clustering was performed using R scripts. GO analysis and Pathway analysis were performed using the standard enrichment computation methods.

source_name: Wild-type ES cells

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

growth_protocol: Mouse ESCs were grown on CF-1 mouse MEFs treated with mitomycin C. mESCs were cultured in DMEM supplemented with 15% FBS (Invitrogen, USA), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM nucleotide, 0.1 mM non-essential amino acids and 103 units/ml mouse leukemia inhibitory factor (LIF).

extract_protocol: Total RNA was extracted using the TRIZOL reagent (TRIzol Plus RNA Purification Kit, Invitrogen life technologies) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: strain background

tag: genotype/variation

value: Wild-type

value: embryonic stem cells (ES cells)


title: willm-00144: INF_071_bone marrow

label_protocol: See mage-tab files linked to series entry for additional details


title: willm-00144: INF_060_bone marrow

extract_protocol: See mage-tab files linked to series entry for additional details


title: willm-00144: INF_055_bone marrow


title: willm-00144: INF_023_bone marrow


title: willm-00144: INF_118_bone marrow


title: willm-00144: INF_059_bone marrow


title: willm-00144: INF_084_bone marrow


title: willm-00144: INF_031_bone marrow


title: willm-00144: INF_078_bone marrow


title: willm-00144: INF_043_bone marrow


title: willm-00144: INF_044_bone marrow


title: willm-00144: INF_088_bone marrow


title: willm-00144: INF_028_bone marrow


title: willm-00144: INF_110_bone marrow


title: willm-00144: INF_077_bone marrow


title: willm-00144: INF_096_bone marrow


title: willm-00144: INF_019_bone marrow


title: willm-00144: INF_108_bone marrow


title: bovine somatic cells [SC P10]

city: Seoul

first: Daehwan

last: Kim

address: 1, Gwanak-ro, Gwanak-gu, Seoul

country: South Korea

institute: Seoul national university

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Bos taurus

source_name: bovine somatic cells, passage 10, replicate 1

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: All eSLCs were generated and cultured in 3i medium, which consists of equal volumes of DMEM/F12-GlutamaxTM and neurobasal media with 1% (v/v) N2 and 2% (v/v) B27 supplements plus the three inhibitors (3i): 0.8 μM PD184352 (Selleck Chemicals, Breda, Netherlands), 2 μM SU5402 (Tocris Bioscience, Ellisville, MO, USA), and 3 μM CHIR99021 (Tocris Bioscience). Somatic cells were cultured in growth medium, which consists of Dulbecco’s modified Eagle medium (DMEM) containing 10% FBS and antibiotics.

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

tag: strain

value: HanWoo, korean native cattle


title: willm-00144: INF_002_bone marrow


title: willm-00144: INF_054_bone marrow


title: bovine embryo-derived stem-like cells from in vitro produced embryo [I9P30]

source_name: in vitro produced embryo of bovine, passage 30, replicate 1


title: bovine embryo-derived stem-like cells from in vitro produced embryo [I2P35]

source_name: in vitro produced embryo of bovine, passage 35, replicate 1


title: bovine embryo-derived stem-like cells from parthenogenetic embryo [P4P36]

source_name: parthenogenetic embryo of bovine, passage 36, replicate 1


title: bovine somatic cells [SC P5]

source_name: bovine somatic cells, passage 5, replicate 1


title: willm-00144: INF_093_bone marrow


title: bovine embryo-derived stem-like cells from somatic cell nuclear trasfer embryo [N2P36]

source_name: somatic cell nuclear transfer embryo of bovine, passage 36, replicate 1


title: willm-00144: INF_017_bone marrow


title: bovine embryo-derived stem-like cells from somatic cell nuclear trasfer embryo [N7P30]

source_name: somatic cell nuclear transfer embryo of bovine, passage 30, replicate 1


title: bovine embryo-derived stem-like cells from parthenogenetic embryo [P1P31]

source_name: parthenogenetic embryo of bovine, passage 31, replicate 1


title: willm-00144: INF_041_bone marrow


title: willm-00144: INF_048_bone marrow


title: willm-00144: INF_011_bone marrow


title: willm-00144: INF_117_bone marrow


title: willm-00144: INF_001_bone marrow


title: willm-00144: INF_032_bone marrow


title: willm-00144: INF_065_bone marrow


title: willm-00144: INF_020_bone marrow


title: willm-00144: INF_050_bone marrow


title: willm-00144: INF_070_bone marrow


title: willm-00144: INF_026_bone marrow


title: willm-00144: INF_119_bone marrow


title: willm-00144: INF_013_bone marrow


title: willm-00144: INF_021_bone marrow


title: willm-00144: INF_085_bone marrow


title: willm-00144: INF_004_bone marrow


title: willm-00144: INF_094_bone marrow


title: willm-00144: INF_063_bone marrow


title: willm-00144: INF_089_bone marrow


title: willm-00144: INF_025_bone marrow


title: willm-00144: INF_069_bone marrow


title: willm-00144: INF_090_bone marrow


title: willm-00144: INF_015_bone marrow


title: willm-00144: INF_097_bone marrow


title: willm-00144: INF_042_bone marrow


title: willm-00144: INF_035_bone marrow


title: willm-00144: INF_009_bone marrow


title: willm-00144: INF_105_bone marrow


title: willm-00144: INF_016_bone marrow


title: willm-00144: INF_007_bone marrow


title: willm-00144: INF_121_bone marrow


title: willm-00144: INF_095_bone marrow


title: willm-00144: INF_006_bone marrow


title: willm-00144: INF_045_bone marrow


title: willm-00144: INF_087_bone marrow


title: willm-00144: INF_022_bone marrow


title: willm-00144: INF_033_bone marrow


title: willm-00144: INF_034_bone marrow


title: willm-00144: INF_092_bone marrow


title: willm-00144: INF_024_bone marrow


title: willm-00144: INF_081_bone marrow


title: willm-00144: INF_075_bone marrow


title: willm-00144: INF_073_bone marrow


title: willm-00144: INF_046_bone marrow


title: willm-00144: INF_099_bone marrow


title: willm-00144: INF_079_bone marrow


title: willm-00144: INF_053_bone marrow


title: willm-00144: INF_052_bone marrow


title: willm-00144: INF_076_bone marrow


title: willm-00144: INF_064_bone marrow


title: willm-00144: INF_111_bone marrow


title: willm-00144: INF_057_bone marrow


title: willm-00144: INF_047_bone marrow


title: willm-00144: INF_018_bone marrow


title: willm-00144: INF_038_bone marrow


title: willm-00144: INF_058_bone marrow


title: willm-00144: INF_080_bone marrow


title: willm-00144: INF_037_bone marrow


title: willm-00144: INF_062_bone marrow


title: willm-00144: INF_123_bone marrow


title: willm-00144: INF_005_bone marrow


title: willm-00144: INF_104_bone marrow


title: willm-00144: INF_066_bone marrow


title: willm-00144: INF_125_bone marrow


title: willm-00144: INF_068_bone marrow


title: willm-00144: INF_120_bone marrow


title: willm-00144: INF_103_bone marrow


title: willm-00144: INF_072_bone marrow


title: willm-00144: INF_102_bone marrow


title: willm-00144: INF_098_bone marrow


title: willm-00144: INF_112_bone marrow


title: willm-00144: INF_122_bone marrow


title: Tcfeb KO, biological replicate3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Gene expression data from Tcfeb KO muscle
SAMPLE 6

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: muscle of Tcfeb KO mouse

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

extract_protocol: Total RNAs from either Tcfeb KO and wt mouse muscles were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The muscle from three Tcfeb KO mice (one month old) was isolated, while the muscle from other three wt mice (one month old) was used as control

value: muscle

tag: genotype

value: Tcfeb knockout

tag: age

value: 1 month


title: willm-00144: INF_027_bone marrow


title: willm-00144: INF_113_bone marrow


title: Tcfeb KO, biological replicate2

description:
Gene expression data from Tcfeb KO muscle
SAMPLE 5


title: injected, biological replicate2

description:
Gene expression data from muscle of mouse injected with AAV vector expressing Tcfeb
SAMPLE 5

source_name: Tcfeb overexpressing muscle mouse

extract_protocol: Total RNAs from either Tcfeb injected and control muscle were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The muscle from three wt mice (one month old) was injected with an AAV vector expressing the murine isoform of TFEB (Tcfeb), while the muscle  from other three wt mice (one month old) injected with an AAV vector expressing GFP was used as control


title: Tcfeb KO, biological replicate1

description:
Gene expression data from Tcfeb KO muscle
SAMPLE 4


title: willm-00144: INF_012_bone marrow


title: WT, biological replicate 3

description:
Gene expression data from wt muscle
SAMPLE 3

source_name: muscle of wt mouse

value: wildtype


title: WT, biological replicate 2

description:
Gene expression data from wt muscle
SAMPLE 2


title: injected, biological replicate3

description:
Gene expression data from muscle of mouse injected with AAV vector expressing Tcfeb
SAMPLE 6


title: injected, biological replicate1

description:
Gene expression data from muscle of mouse injected with AAV vector expressing Tcfeb
SAMPLE 4


title: willm-00144: INF_115_bone marrow


title: Control, biological replicate 1

description:
Gene expression data from muscle of mouse injected with AAV vector expressing GFP
SAMPLE 1

source_name: control muscle mouse


title: WT, biological replicate 1

description:
Gene expression data from wt muscle
SAMPLE 1


title: willm-00144: INF_083_bone marrow


title: Control, biological replicate 3

description:
Gene expression data from muscle of mouse injected with AAV vector expressing GFP
SAMPLE 3


title: Control, biological replicate 2

description:
Gene expression data from muscle of mouse injected with AAV vector expressing GFP
SAMPLE 2


title: willm-00144: INF_106_bone marrow


title: willm-00144: INF_014_bone marrow


title: willm-00144: INF_082_bone marrow


title: willm-00144: INF_040_bone marrow


title: willm-00144: INF_003_bone marrow


title: willm-00144: INF_056_bone marrow


title: willm-00144: INF_086_bone marrow


title: willm-00144: INF_126_bone marrow


title: Ang-II_kidney at 28 day, biological rep2

city: Louisville

first: Gregory

last: Weber

state: KY

address: 500 S. Preston St., Rm 802

institute: University of Louisville

description: miRNA expression data from kidney

hyb_protocol: Following Affymetrix protocol

scan_protocol: Following Affymetrix protocol

data_processing:
Cel files were imported to Partek 6.6 and normalized using RMA
Only probes interrogating M. Muculus transcripts were included for Multiple Test Correction
No transcripts passed a multiple Test correction (step-up FDR) with a significance up to 0.1. Further Analysis without multiple test correction is recommended.

source_name: Ang-II_kidney at 28 day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in cages on a 12 hour light:dark cycle

treatment_protocol: Mice were treated with Ang-II via mini osmotic pump and/or GYY4137 via i.p. injection for 28 days

tag: treated with

value: Ang-II via mini osmotic pump for 28 days

value: kidney


title: GYY-Ang-II_kidney at 28 day, biological rep1

description: miRNA expression data from kidney

source_name: GYY-Ang-II_kidney at 28 day

value: Ang-II via mini osmotic pump and GYY4137 via i.p. injection for 28 days


title: Ang-II_kidney at 28 day, biological rep1

description: miRNA expression data from kidney


title: GYY_kidney at 28 day, biological rep2

description: miRNA expression data from kidney

source_name: GYY_kidney at 28 day

value: GYY4137 via i.p. injection for 28 days


title: GYY_kidney at 28 day, biological rep1

description: miRNA expression data from kidney


title: control_kidney at 28 day, biological rep2

description: miRNA expression data from kidney

source_name: control_kidney at 28 day

value: none (control)


title: GYY-Ang-II_kidney at 28 day, biological rep3

description: miRNA expression data from kidney


title: GYY_kidney at 28 day, biological rep3

description: miRNA expression data from kidney


title: Ang-II_kidney at 28 day, biological rep3

description: miRNA expression data from kidney


title: control_kidney at 28 day, biological rep3

description: miRNA expression data from kidney


title: 60_promet_HiAg_rep6

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

hyb_protocol: MAGEX DNA array slides were briefly rinsed in a plastic coplin jar containing WB2 buffer (0.1x SSC, 0.1% (w/v) SDS) and subsequently incubated with 90 mL of PB1 buffer (5x SSC, 0.2% (w/v) BSA, and 0.2% (w/v) SDS) at 48°C for 45 min.  Each slide was dried by centrifugation in a 50 ml falcon tube for 3 min at 200x g.  Dried Lifterslip CS/3 coverslips (Erie Scientific Company) prerinsed with dH2O and 100% ethanol were placed over each DNA array region and the preheated cDNA/UDR samples added to each array. MAGEX array slides were placed in a slide rack and 300µL of dH2O was added to the humidity filter prior to chamber assembly. Hybridization was done for 18 h at 42°C in a Hybex Microsample Incubator (SciGene).  All buffers used in washing were prewarmed at 48°C prior to use. Following hybridization, coverslips were removed and each slide washed for 5 min with WB1 buffer (1x SSC and 0.1% (w/v) SDS). Two subsequent washes were performed with WB2 buffer followed by a wash with WB3 buffer (0.01x SSC and 0.1% (w/v) SDS). Slides were dried by centrifugation for 3 min at 200x g and stored in the dark in a Scienceware autodessicator.

scan_protocol: MAGEX DNA array image data were collected at 5 µm from each slide using a Scan Array Express (Packard Bioscience Co.) as recommended by the manufacturer and at a PMT gain of 70% and laser level of 90% for both Cy5 and Cy3 channels.  Spot intensity levels were obtained via ImaGene Version 9.0 (BioDiscovery Inc.) as per the manufacturer’s protocol using the UDR to align the spot grid.

data_processing: Data normalization involved use of the geometric means derived from the total robust and high quality gene signals obtained for each sample. This resulted in normalization factors between 1.00 and 1.21. An appropriate background signal was determined by evaluating the empty and buffer-only spot positions interspersed throughout each array. The universal floor was set at 2 robust standard deviations greater than the highest median background signal across all arrays, helping to minimize false positives due to low signal intensities.  Data was log2 transformed to minimize heteroscedasticity.

organism: Xenopus laevis

source_name: liver, promet, HiAg

label_protocol: The DecaLabel DNA Labelling Kit was used to incorporate Cy3-dCTP (GE Healthcare Bio-Sciences Corp.) into cDNA according to manufacturer’s specification (Fermentas). To aid in microarray data collection, a universal DNA reference (UDR) containing amplicons representative of all gene sequences present on the MAGEX microarray was  labeled as above with Cy5-dCTP (GE Healthcare Bio-Sciences Corp.).  Labelled DNA was purified with the GeneJET PCR Purification Kit, and sufficient fluorophore incorporation was determined with the Nanodrop UV-Vis spectrophotometer (ND-1000, Thermo Scientific).  Labelled DNA was precipitated with sequential addition of 20 μg glycogen (ThermoFisher Scientific), 5 µl of 3 M sodium acetate (pH 5.2), and 150 µl of chilled 100% ethanol. Samples were incubated at -20 °C for a minimum of 60 min followed by centrifugation at 13,000 x g at 4 °C for 20 min. The DNA pellet was washed once with 300 µL 75% ethanol and air dried for 10 min prior to addition of 7 µl (samples) or 30 µl (UDR) dH2O, and stored at -20°C in 1.5 ml amber tubes. For hybridization, Cy5-labeled UDR (1 µL) was mixed with each Cy3-labeled cDNA (5.5 µL) and incubated at 95°C for 3 min followed by cooling on ice and a brief centrifugation to collect the denatured material. For each sample, a 33 µL hybridization solution was prepared that contained 5x SSC, 25% (v/v) deionized formamide, 0.02% (w/v) BSA, 1 µg A45 oligonucleotide, 0.1% (w/v) SDS, 5% (w/v) dextran, and 6.5 µL denatured labelled DNA and warmed briefly at 37°C prior to application onto the covered MAGEX array.

growth_protocol: Laboratory populations of X. laevis were housed at the Outdoor Aquatic Unit at the University of Victoria, BC.  All animals were treated and maintained in accordance with the guidelines of the Canadian Council on Animal Care and the Animal Care Committee guidelines of the University of Victoria.  Mature adults were bred by injection of human chorionic gonadotropin (Sigma-Aldrich, Oakville, ON, Cat#CG10) at 500 and 1000 IU into males and females, respectively.  Eggs and newly hatched tadpoles were kept in tadpole rearing water consisting of dechlorinated water treated with NaHCO3 and synthetic sea salts (Instant Ocean sea salt, Aquarium Systems Inc, Mentor, OH, USA) to a pH of 7.4-7.8 and salinity of 0.4 ppt.  A pump was used to circulate water and keep dissolved oxygen (DO) >90%.  After initiation of feeding behaviour and throughout the exposures tadpoles were fed Nasco frog brittle (Nasco, Modesto, CA, USA; Cat#:SA05961), ground and suspended at 10% (w/v) in untreated tap water.  Tadpoles were monitored until sufficient numbers reached the appropriate developmental stage for each exposure (n=200).  Conditions were based on the Organisation for Economic Co-operation and Development (OECD) guidelines for the Amphibian Metamorphosis Assay (AMA; Guideline 231, 2009).  In brief, four replicate exposure tanks (2 L glass beakers) were used within each treatment for a total of 20 tanks/exposure. Ten tadpoles were acclimated in each tank containing 2L tadpole rearing water for 24 h prior to treatment addition. Tadpole density was maintained at approximately 5 tadpoles/L, and water adjusted to 1.2L after removal of 4 tadpoles/tank on experimental day 2. Temperature was kept at 20.3 ±0.2°C with a photoperiod of 12/12 h light/dark. Glass pipettes were used as aerators to maintain high DO, prevent stagnation, and ensure treatments were thoroughly dispersed after chemical addition.  Nitrogenous wastes were monitored throughout the exposure with Aquacheck strips (Nitrate/Nitrite test strips; Ammonium test strips; Elkhart, IN, USA) to prevent toxic concentrations. Animals were euthanized with 0.1% (w/v) tricaine methanesulfonate (MS-222; Syndel Laboratories Ltd, Vancouver, BC) in tadpole rearing water with 25 mM NaHCO3.

extract_protocol: Total RNA was extracted from whole livers with TRIzol reagent (Invitrogen) according to manufacturer’s protocol. Premetamorphic tadpole livers were homogenized in 200 µl TRIzol manually with a micropestle, while prometamorphic livers were homogenized in 300 µl TRIzol using a 1mm tungsten-carbide bead and a Retsch MM301 mixer mill at 20 Hz for 6 min.  To increase RNA yield, 20 µg glycogen was added prior to isopropanol precipitation. Isolated RNA was resuspended in 40 and 60 µl diethyl pyrocarbonate (DEPC)-treated RNase-free water for the pre- and prometamorphic livers, respectively. Total RNA was quantified using Nanodrop UV- Vis spectrophotometer (ND-1000, Thermo Scientific), and stored at -80°C. cDNA was prepared using the SMARTer PCR cDNA Synthesis Kit as per manufacturer’s protocol (Clontech Laboratories Inc.) with subsequent purification of amplified cDNA with the GeneJET PCR Purification Kit (Fermentas), and stored at -20°C.

treatment_protocol: Two 48 h exposure sets were conducted with either pre- or prometamorphic tadpoles starting at NF51 and NF56 (Nieuwkoop and Faber, 1994), respectively. In each exposure, tadpoles were immersed in tadpole rearing water containing 1 of 5 treatments: negative control with 50 nM NaOH (Ctrl), T3 positive control (10 nM T3 in 50 nM NaOH), or 3 concentrations of nAg (0.018, 0.18 or 1.8 µg/L by Ag content), referred to here as Lo, Med or Hi nAg. After 48 h exposure tadpoles were euthanized in 0.1% (w/v) MS-222 and preserved whole in RNAlater (Life Technologies) as described by the manufacturer. The preserved tissue was stored at -20°C until dissection of tadpole liver prior to isolation of total RNA.

tag: developmental stage

value: Nieuwkoop and Faber stage 57

tag: unique animal number

tag: gender

value: Female

value: liver


title: willm-00144: INF_114_bone marrow

source_name: Peripheral Blood Cell/Bone Marrow

value: leukemia

value: female

value: premortem

value: Peripheral Blood Cell/Bone Marrow


title: 58_promet_HiAg_rep4

value: Male


title: 12_promet_HiAg_rep5


title: 24_promet_HiAg_rep3


title: 49_promet_HiAg_rep2


title: 35_promet_MedAg_rep6

source_name: liver, promet, MedAg


title: E13 p63-/- 1

city: Saskatoon

first: Julia

last: Boughner

state: Saskatchewan

address: 107 Wiggins Road

institute: University of Saskatchewan

description:
Sample 19 (BHN020)
5391709053_A

hyb_protocol: The labeled cRNA was then normalized at 1500 ng and hybridized on Mouse WG-6_v2 according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide. The BeadChips were incubated in an Ilumina Hybridization oven at 580oC for 14 to 20 hours at a rocking speed of 5. Beadchips were washed also according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide and scanned on an Illumina iScan Reader.

scan_protocol: BeadChips were imaged using iScan readers.

data_processing: Beadstudio software was used to generate the hybridization report that assessed signal against sample-independent and sample-dependent controls (e.g., housekeeping genes, noise-to-background and signal-to-noise, biotine/strep-Cy3, perfect-match and mismatch). Data were analyzed with FlexArray 1.5 software (Génome Québec Innovation Centre) and normalized using the lumi algorithm, a wrapper around the lumi Bioconductor package. Lumi is designed to pre-process and normalize Illumina microarray (BeadArray) data. Lumi includes many standard analysis options (e.g. log base 2 variance stabilization method, or quantile normalization), and it also contains several novel methods developed with Illumina microarrays in mind (the Variance-Stabilizing Transformation (VST) method, and the Robust Spline Normalization (RSN) method). Data were normalized with Robust Multi-Array Average (RMA) and the algorithm EB (Wright and Simon) was used for statistical analysis.

label_protocol: Double stranded cDNA was synthesized from 250 of total RNA, and in vitro transcription was performed to produce biotin-labeled cRNA using Illumina® TotalPrep RNA Amplification Kit, according to manufacturer’s instructions (Life Technologies).

extract_protocol: Uteri were removed, immersed in cold L-15 media, and embryos were dissected out. We excised mandibular prominences (MdPs) and tail clips from E10-E13 WT (p63+/+), heterozygote (p63+/-) and p63-/- embryos for gene expression assays and genotyping as per our earlier related study (Paradis et al. 2013). Samples were not pooled. Total RNA was extracted from each individual MdP using a Qiagen RNeasy blood & tissue kit and Qiagen DNase/RNase-free kit. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies). A TotalPrep RNA Amplification kit (Ambion) was used for one amplification of 50-500 ng of total RNA. Next, cDNA synthesis and in vitro transcription amplification were followed by hybridization.

value: mandibular prominence

tag: tissue source

value: single embryo - unpooled


title: E13 p63-/- 3

description:
Sample 21 (BHN024)
5391709053_C


title: Data 148 Area4

city: Québec

first: Florence

last: Pagé-Larivière

state: Québec

address: 2440, boulevard Hochelaga

institute: Laval University

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Sus scrofa

label_protocol:
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

treatment_protocol: Porcine zygotes were exposed to 0.2% ethanol in PZM3 medium for 7 days. Embryos developped in thilghly sealed glass vials.

tag: compound added

tag: number per pool

value: Ethanol


title: control_kidney at 28 day, biological rep1

description: miRNA expression data from kidney


title: E12 p63-/- 2

description:
Sample 14 (BHN015)
5391709037_B


title: Data 148 Area1


title: E12 p63-/- 3

description:
Sample 15 (BHN017)
5391709037_C


title: E13 p63-/- 2

description:
Sample 20 (BHN021)
5391709053_B


title: Data 148 Area2


title: GYY-Ang-II_kidney at 28 day, biological rep2

description: miRNA expression data from kidney


title: E13 p63+/- 2

description:
Sample 23 (BHN022)
5391709053_E


title: E13 p63+/- 1

description:
Sample 22 (BHN019)
5391709053_D


title: E12 p63+/- 1

description:
Sample 16 (BHN013)
5391709037_D


title: E12 p63+/- 3

description:
Sample 18 (BHN018)
5391709037_F


title: E12 p63+/- 2

description:
Sample 17 (BHN016)
5391709037_E


title: 52_promet_MedAg_rep5


title: 20_promet_MedAg_rep4


title: Data 148 Area3


title: 25_promet_MedAg_rep3


title: 42_promet_MedAg_rep2


title: 57_promet_HiAg_rep1


title: 40_promet_MedAg_rep1


title: E12 p63-/- 1

description:
Sample 13 (BHN014)
5391709037_A


title: E11 p63+/- 3

description:
Sample 12 (BHN012)
5391709009_F


title: E13 p63+/- 3

description:
Sample 24 (BHN023)
5391709053_F


title: willm-00144: INF_091_bone marrow

tag: diseasestate

tag: agevalue

tag: histology

value: AML

value: male


title: E11 p63-/- 3

description:
Sample 9 (BHN011)
5391709009_C


title: E11 p63+/- 2

description:
Sample 11 (BHN010)
5391709009_E


title: E11 p63+/- 1

description:
Sample 10 (BHN008)
5391709009_D


title: 16_promet_LoAg_rep6

source_name: liver, promet, LoAg


title: willm-00144: INF_049_bone marrow

value: ALL

tag: Sex

tag: organismstatus

tag: organismpart


title: 39_promet_LoAg_rep3

tag: tissue


title: 53_promet_LoAg_rep4


title: willm-00144: INF_036_bone marrow


title: willm-00144: INF_051_bone marrow


title: 10_promet_T3_rep4

source_name: liver, promet, T3


title: 28_promet_LoAg_rep1


title: 59_promet_LoAg_rep2


title: 29_promet_T3_rep6


title: E11 p63-/- 2

description:
Sample 8 (BHN009)
5391709009_B


title: 26_promet_T3_rep3


title: 4_promet_LoAg_rep5


title: 23_promet_T3_rep2


title: E11 p63-/- 1

description:
Sample 7 (BHN007)
5391709009_A


title: 9_promet_T3_rep1


title: E10 p63-/- 1

description:
Sample 1 (BHN002)
5391709007_B


title: E10 p63-/- 2

description:
Sample 2 (BHN003)
5391709007_C


title: E10 p63+/- 2

description:
Sample 5 (BHN004)
5391709007_D


title: E10 p63-/- 3

description:
Sample 3 (BHN005)
5391709007_E


title: E10 p63+/- 3

description:
Sample 6 (BHN006)
5391709007_F


title: E10 p63+/- 1

description:
Sample 4 (BHN001)
5391709007_A


title: willm-00144: INF_074_bone marrow


title: willm-00144: INF_101_bone marrow


title: willm-00144: INF_039_bone marrow


title: willm-00144: INF_107_bone marrow


title: willm-00144: INF_116_bone marrow


title: 38_promet_Ctrl_rep5

source_name: liver, promet, Ctrl


title: willm-00144: INF_124_bone marrow


title: willm-00144: INF_100_bone marrow


title: willm-00144: INF_029_bone marrow


title: willm-00144: INF_030_bone marrow


title: 54_promet_Ctrl_rep6


title: 50_promet_Ctrl_rep3


title: 7_promet_Ctrl_rep2


title: 32_promet_Ctrl_rep1


title: 5_premet_HiAg_rep4

source_name: liver, premet, HiAg

value: Nieuwkoop and Faber stage 53


title: 46_premet_HiAg_rep6


title: 27_premet_HiAg_rep5


title: 51_premet_HiAg_rep3


title: 43_premet_HiAg_rep2


title: 30_promet_Ctrl_rep4


title: willm-00144: INF_010_bone borrow


title: 33_premet_MedAg_rep4

source_name: liver, premet, MedAg


title: 31_premet_MedAg_rep5


title: 1_promet_T3_rep5


title: 56_premet_MedAg_rep3


title: 45_premet_MedAg_rep2


title: 21_premet_LoAg_rep5

source_name: liver, premet, LoAg


title: 15_premet_MedAg_rep1


title: 2_premet_LoAg_rep6


title: 17_premet_MedAg_rep6


title: Peripheral blood mononuclear cells from MTXAP after 34 days MTX&acupuncture therapy, replicate 1

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

institute: PICB

description:
RAT_MTXAP_repeat_34d_1
Gene expression data from RA rats after 34 days MTX&acupuncture therapy.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data Affymetrix .CEL files, were pre-processed using mas5 in the affy R package.

source_name: RAT Peripheral blood mononuclear cells, MTXAP

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Blood sampling was carried out before any therapy in RA (RA_T0) and NORA (NORA_T0) groups whereas in the other groups (AP, HAP and MTXAP) at 1hour and at 34 days after therapy. Animals were induced in deep general anesthesia and after total blood drawing (5ml), sacrificed by neck dislocation.

extract_protocol: Total RNA was extracted and purified using mirVanaTM mRNA and miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) checked for the RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were freshly isolated on Ficoll gradient (Histopaque®-1077, Sigma Aldrich, USA) according to the manufacture procedures. Separated cell were maintained in RNA Later (Ambion, USA) at -80ºC until the end of the study and then processed in a whole batch for the following extraction.

tag: strain/background

value: Wistar

tag: cell type

value: peripheral blood mononuclear cells

tag: subject group

value: rheumatoid arthritis rats after 34 days methotrexate & acupuncture therapy


title: 6_premet_LoAg_rep4


title: 36_premet_LoAg_rep2


title: 22_premet_LoAg_rep3

value: Female


title: Peripheral blood mononuclear cells from AP after 34 days acupuncture therapy, replicate 1

description:
RAT_AP_repeat_34d_1
Gene expression data from RA rats after 34 days acupuncture therapy.

source_name: RAT Peripheral blood mononuclear cells, AP

value: rheumatoid arthritis rats after 34 days acupuncture therapy


title: 8_premet_LoAg_rep1

value: liver


title: Peripheral blood mononuclear cells from MTXAP after 34 days MTX&acupuncture therapy, replicate 2

description:
RAT_MTXAP_repeat_34d_2
Gene expression data from RA rats after 34 days MTX&acupuncture therapy.

value: female


title: Peripheral blood mononuclear cells from AP after 34 days acupuncture therapy, replicate 3

description:
RAT_AP_repeat_34d_3
Gene expression data from RA rats after 34 days acupuncture therapy.


title: Peripheral blood mononuclear cells from MTXAP after 34 days MTX&acupuncture therapy, replicate 3

description:
RAT_MTXAP_repeat_34d_3
Gene expression data from RA rats after 34 days MTX&acupuncture therapy.


title: 14_premet_T3_rep6

source_name: liver, premet, T3


title: Peripheral blood mononuclear cells from RA before therapy, replicate 2

description:
RAT_RA_repeat_T0_2
Gene expression data from RA rats before therapy.

source_name: RAT Peripheral blood mononuclear cells, RA

value: rheumatoid arthritis rats before therapy


title: 48_premet_T3_rep4


title: 44_premet_T3_rep5


title: Peripheral blood mononuclear cells from HAP after 34 days acupuncture therapy, replicate 2

description:
RAT_HAP_repeat_34d_2
Gene expression data from healthy rats after 34 days acupuncture therapy.

source_name: RAT Peripheral blood mononuclear cells, HAP


title: Peripheral blood mononuclear cells from HAP after 34 days acupuncture therapy, replicate 1

description:
RAT_HAP_repeat_34d_1
Gene expression data from healthy rats after 34 days acupuncture therapy.


title: 19_premet_T3_rep2


title: Peripheral blood mononuclear cells from NORA before therapy, replicate 3

description:
RAT_NORA_repeat_T0_3
Gene expression data from healthy rats before therapy.

source_name: RAT Peripheral blood mononuclear cells, NORA

value: healthy rats before therapy


title: 11_premet_T3_rep3


title: Peripheral blood mononuclear cells from NORA before therapy, replicate 2

description:
RAT_NORA_repeat_T0_2
Gene expression data from healthy rats before therapy.


title: Peripheral blood mononuclear cells from NORA before therapy, replicate 1

description:
RAT_NORA_repeat_T0_1
Gene expression data from healthy rats before therapy.


title: 41_premet_Ctrl_rep4

source_name: liver, premet, Ctrl

value: Male


title: Peripheral blood mononuclear cells from RA before therapy, replicate 1

description:
RAT_RA_repeat_T0_1
Gene expression data from RA rats before therapy.


title: 34_premet_Ctrl_rep5


title: 47_premet_T3_rep1


title: RAT_PLA_34d_1

description:
Peripheral blood mononuclear cells from PLA after 34 days therapy, replicate 1
Gene expression data from RA rats after 34 days placebo therapy

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and  Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

data_processing: Raw data Affymetrix .CEL files, were pre-processed using robust multi-array average (rma)  in the affy R package.

source_name: RAT Peripheral blood mononuclear cells

growth_protocol: Blood sampling was carried out before any therapy in RA (RA_T0) and NORA  (NORA_T0) groups whereas in the other groups (AP/MEC, MTX,ANE, PLA and NORA) at 1hour and  at 34 days after therapy. Animals were induced in deep general anesthesia and after total blood drawing (5ml), sacrificed by neck dislocation.

value: RAT Peripheral blood mononuclear cells

tag: strain

value: Wistar rat

value: RA rats after 34 days placebo therapy


title: RAT_PLA_34d_2

description:
Peripheral blood mononuclear cells from PLA after 34 days therapy, replicate 2
Gene expression data from RA rats after 34 days placebo therapy


title: RAT_ANE_34d_2

description:
Peripheral blood mononuclear cells from ANE after 34 days therapy, replicate 2
Gene expression data from RA rats after 34 days ANE therapy

value: RA rats after 34 days ANE therapy


title: RAT_MTX_34d_1

description:
Peripheral blood mononuclear cells from MTX after 34 days therapy, replicate 1
Gene expression data from RA rats after 34 days MTX therapy

value: RA rats after 34 days MTX therapy


title: 18_premet_Ctrl_rep1

tag: developmental stage


title: RAT_MTX_34d_2

description:
Peripheral blood mononuclear cells from MTX after 34 days therapy, replicate 2
Gene expression data from RA rats after 34 days MTX therapy


title: RAT_NORA_34d_1

description:
Peripheral blood mononuclear cells from NORA after 34 days therapy, replicate 1
Gene expression data from healthy rats at 34 days after therapy

value: healthy rats at 34 days after therapy


title: 55_premet_Ctrl_rep6

value: Nieuwkoop and Faber stage 53

tag: unique animal number


title: RAT_NORA_34d_2

description:
Peripheral blood mononuclear cells from NORA after 34 days therapy, replicate 2
Gene expression data from healthy rats at 34 days after therapy

tag: gender


title: 13_premet_Ctrl_rep3


title: RAT_AP_34d_2

description:
Peripheral blood mononuclear cells from AP after 34 days therapy, replicate 2
Gene expression data from RA rats after 34 days acupuncture therapy


title: RAT_ANE_34d_1

description:
Peripheral blood mononuclear cells from ANE after 34 days therapy, replicate 1
Gene expression data from RA rats after 34 days ANE therapy


title: RAT_PLA_1h_2

description:
Peripheral blood mononuclear cells from PLA after 1 hour therapy, replicate 2
Gene expression data from RA rats after 1 hour placebo therapy

value: RA rats after 1 hour placebo therapy


title: RAT_ANE_1h_2

description:
Peripheral blood mononuclear cells from ANE after 1 hour therapy, replicate 2
Gene expression data from RA rats after 1 hour ANE therapy

value: RA rats after 1 hour ANE therapy


title: RAT_AP_34d_1

description:
Peripheral blood mononuclear cells from AP after 34 days therapy, replicate 1
Gene expression data from RA rats after 34 days acupuncture therapy


title: RAT_PLA_1h_1

description:
Peripheral blood mononuclear cells from PLA  after 1 hour therapy, replicate 1
Gene expression data from RA rats after 1 hour placebo therapy


title: RAT_MTX_1h_2

description:
Peripheral blood mononuclear cells from MTX  after 1 hour therapy, replicate 2
Gene expression data from RA rats after 1 hour MTX therapy

value: RA rats after 1 hour MTX therapy


title: RAT_ANE_1h_1

description:
Peripheral blood mononuclear cells from ANE  after 1 hour therapy, replicate 1
Gene expression data from RA rats after 1 hour ANE therapy

value: Female


title: B. breve UCC2003 grown on RCM v. B. breve UCC2003 grown on RCM and stressed with 700µM Dipyridyl for 30 minutes

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) resuspended in deminerilised water. The RCM media was filtered to remove the agarose to allow cells to be collected by centrifugation this filtration was carried out with the aid of Watt man paper.   Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.6.  Iron limitation was then imposed by the addition of 700µM Dipyridyl for 30 minutes.

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Cells were collected by centrifugation at 10,000rpm for 2 minutes at room temperature prior to storage in the -80 degree freezer.

tag: genotype

value: wild type

source_name: B. breve UCC2003 grown in filtered RCM until OD.600 of 0.6, iron limitation was imposed by adding 700µM Dipyridyl for 30 minutes


title: B. breve UCC2003 grown on RCM and stressed with 700µM Dipyridyl for 30 minutes vs B. breve UCC2003 grown on RCM

description: Gene expression array

source_name: B. breve UCC2003 grown in filtered RCM until OD.600 of 0.6


title: RAT_MTX_1h_1

description:
Peripheral blood mononuclear cells from MTX after 1 hour therapy, replicate 1
Gene expression data from RA rats after 1 hour MTX therapy


title: RAT_AP_1h_1

description:
Peripheral blood mononuclear cells from AP after 1 hour therapy, replicate 1
Gene expression data from RA rats after 1 hour acupuncture therapy


title: 769-P_control_rep1

city: beijing

first: zhang

last: fan

address: beijing china

department: Department of Urology

institute: 301 hospital

description: Gene expression data from 769-P cell line transfected with plv-EGFP empty vector

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. The raw data were normalized by Expression Console.

source_name: Human ccRCC cell line 769-P transfected with plv-EGFP empty vector

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: The 769-P cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and incubated in a humidiﬁed atmosphere of 5% CO2 at 37 °C

treatment_protocol: The full-length of FOXK2 coding sequence was inserted into lentiviral vector pLV-EGFP-(2A) Puro between the sites of XbaI and EcoRI to generate pLV-EGFP-FOXK2 (plv-FOXK2). The constructed sequence was verified through DNA sequencing. plv-FOXK2 and plv-EGFP empty vector (EV) were transfected into 769-P cells by lentivirus to synthesize FOXK2 overexpressed and control cells.

value: clear-cell renal cell carcinoma

tag: cell line

tag: tumor

value: Non-metastatic


title: 769-P_plvFOXK2_rep1

description: Gene expression data from 769-P cell line transfected with pLV-EGFP-FOXK2

source_name: Human ccRCC cell line 769-P transfected with pLV-EGFP-FOXK2


title: RAT_NORA_1h_1

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 1
Gene expression data from healthy rats at 1 hour after therapy

value: healthy rats at 1 hour after therapy


title: RAT_NORA_1h_2

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 2
Gene expression data from healthy rats at 1 hour after therapy


title: A30-Low responder

city: Tokyo

first: Fumika

last: Shigiyama

address: 6-11-1, Omori Nishi, Otaku

department: Internal Medicine

institute: Toho University

scan_protocol: GeneChip were scaned by GeneChip Scaner 3000(Affymetrix 690036) using GeneChip Command Console Software ver3.2(Affymetrix 702569). The procedure of scan is followed by  Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

data_processing: Data is processed by RMA-Skech algorythm using Expression ConsoleTM Softwere ver.1.3（Affymetrix 702387）

source_name: Low responder_liver biopsy sample

label_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）. 100ng Total RNA was used for this assay.

extract_protocol: Total RNA was extracted from flash frozen ~10 mg liver biopsy using the RNeasy mini kit (Qiagen, Tokyo, Japan). RNA was reverse-transcribed into cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany).

tag: subject status

value: Nonalcoholic fatty liver disease (NAFLD)

tag: insuline response

value: Low responder

value: liver biopsy


title: RAT_AP_1h_2

description:
Peripheral blood mononuclear cells from AP after 1 hour therapy, replicate 2
Gene expression data from RA rats after 1 hour acupuncture therapy

value: RAT Peripheral blood mononuclear cells

value: Wistar rat


title: A28-Low responder

hyb_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

value: Male


title: A21-Low responder


title: A19-High responder

source_name: High responder_liver biopsy sample

value: High responder


title: A17-Low responder


title: A14-High responder


title: RAT_RA_T0_2

description:
Peripheral blood mononuclear cells from RA before therapy, replicate 2
Gene expression data from RA rats before therapy

value: RA rats before therapy


title: A15-High responder


title: RAT_ANE_34d_2

description:
Peripheral blood mononuclear cells from ANE after 34 days therapy, replicate 2
small RNA expression data from RA rats after 34 days ANE therapy

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned the image were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data were normalized by robust  multiple array average (RMA) using R package  Agi MicroRna.

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

value: Wistar


title: RAT_PLA_34d_1

description:
Peripheral blood mononuclear cells from PLA after 34 days therapy, replicate 1
small RNA expression data from RA rats after 34 days placebo therapy


title: RAT_PLA_34d_2

description:
Peripheral blood mononuclear cells from PLA after 34 days therapy, replicate 2
small RNA expression data from RA rats after 34 days placebo therapy


title: RAT_NORA_T0_2

description:
Peripheral blood mononuclear cells from NORA before therapy, replicate 2
Gene expression data from healthy rats before therapy

value: healthy rats before therapy


title: RAT_RA_T0_1

description:
Peripheral blood mononuclear cells from RA before therapy, replicate 1
Gene expression data from RA rats before therapy


title: Peripheral blood mononuclear cells from AP after 34 days acupuncture therapy, replicate 2

description:
RAT_AP_repeat_34d_2
Gene expression data from RA rats after 34 days acupuncture therapy.

value: female

value: peripheral blood mononuclear cells

value: rheumatoid arthritis rats after 34 days acupuncture therapy


title: RAT_NORA_T0_1

description:
Peripheral blood mononuclear cells from NORA before therapy, replicate 1
Gene expression data from healthy rats before therapy

value: Female


title: A20-High responder


title: 20mGyT1/ reference male mouse4

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse4


title: A10-Low responder


title: A11-High responder


title: RAT_MTX_34d_2

description:
Peripheral blood mononuclear cells from MTX after 34 days therapy, replicate 2
small RNA expression data from RA rats after 34 days MTX therapy


title: RAT_ANE_34d_1

description:
Peripheral blood mononuclear cells from ANE after 34 days therapy, replicate 1
small RNA expression data from RA rats after 34 days ANE therapy


title: A12-High responder


title: Peripheral blood mononuclear cells from HAP after 34 days acupuncture therapy, replicate 3

description:
RAT_HAP_repeat_34d_3
Gene expression data from healthy rats after 34 days acupuncture therapy.


title: RAT_MTX_34d_1

description:
Peripheral blood mononuclear cells from MTX after 34 days therapy, replicate 1
small RNA expression data from RA rats after 34 days MTX therapy