title: high R/FR_mock spray, biological rep 1

source_name: Arabidopsis petioles, 2h control treatment

value: 4 weeks old

value: high R/FR (control), mock spray


title: REL10

status: Public on Apr 03 2013

type: genomic

city: Bronx

first: Christoph

last: Heuck

address: 1300 Morris Park Ave

department: Cancer Center

country: USA

institute: Albert Einstein College of Medicine

description:
LMM08065C
Methylation data from HELP assay

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

molecule: genomic DNA

organism: Homo sapiens

source_name: REL_CD138+ selected cells

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). Total More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers.Genomic DNA was isolated using Puregene Cell and Tissue Kit according to the manufacturer instructions (Qiagene).  Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol  Khulan B et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: subject condition

value: relapsed myeloma

tag: cell type

value: CD138+ selected cells from bone marrow aspirates

tag: restriction enzyme used

value: MspI

tag: gdna digeted with

value: HpaII


title: NL3

description:
CD138C
Methylation data from HELP assay

source_name: NL_CD138+ selected cells

value: normal donor


title: high R/FR_mock spray, biological rep 2

type: RNA

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner

data_processing: Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH, R/FR = 2.2), 15 h dark) where they were transferred to individual pots after 10 d and gwon until 4 weeks old.

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions

treatment_protocol: Plants were put in each of the four conditions (control light with mock spray, control light with 0.5 mM SA spray, low R:FR (0.2) with mock spray, low R:FR (0.2) with 0.5 mM SA spray) for 2h. One petiole (approx. 5 mm length) per plant was harvested in liquid N2. 3 petioles/biological replicate were pooled.

tag: organ

value: petiole

tag: age

tag: treatment


title: A549, H1N1, 24hpi (rep2)

city: Lyon

first: olivier

last: Terrier

address: Rue Guillaume Paradin

department: Laboratoire de Virologie et Pathologie Humaine

country: France

institute: Université Claude Bernard Lyon 1

description:
Human influenza-infected cells
Sample name: H1B

data_processing:
For each miRNA, the expression level was determined by the 2(-Delta Delta C(T)) method (Livak & Schmittgen, 2001). Data were normalized using the small nucleolar human RNA RNU48 as a control.
1st step of normalization: CT correction based on the global mean CT obtained between plates
2nd step of normalization: Target gene signal normalized to housekeeping gene RNU48

label: FAM

source_name: A549 cells (ATCC  number CCL-185)

label_protocol: Reverse transcription reactions contained 390 ng of purified RNAs, 1x Megaplex RT primers (Human pool A v2.1, Applied Biosystems), 1x RT buffer, 2.5 mM of each dNTP, 3 mM MgCl2, 1U/µL of Multiscribe reverse transcriptase (Applied Biosystems) and 0.3 U/µL of RNase inhibitor (Applied Biosystems). The RT reaction had a final volume of 7.5 µL and was incubated for 5 min on ice, followed by 40 cycles (16°C 2 min, 42°C 1 min, 50°C 1 sec), 85°C 5 min and then held at 4°C. The RT products were subsequently amplified with sequence-specific primers contained in a TaqMan array MicroRNA card (card A, Applied Biosystems), which enables the simultaneous quantification of 377 different human miRNAs plus several endogenous controls. Six µL of RT products were diluted in 444 µL of nuclease-free water and mixed with 450 µL of 2x TaqMan Universal PCR Master Mix with no Amperase (Applied Biosystems) and dispensed into the 384 wells by centrifugation. The plates were incubated at 95°C for 10 min, followed by 40 cycles (95°C 15 sec, 60°C 1 min). The data were collected and processed using the Plate Utility and Automation Controller software (Applied Biosystems).

growth_protocol: Confluent A549 cells were Mock-infected or infected with influenza viruses at an MOI of 1 or 10-3 for 1 h in a minimal volume of DMEM supplemented with 2 mM L-glutamine, 100 U/mL of penicillin, 100 µg/mL of streptomycin sulphate and 0.5 µg/mL of trypsin (infection medium) at 37°C. The cells were then overlaid with fresh infection medium and incubated at 37°C for 24 h.

extract_protocol: Total RNAs, including small RNAs, were isolated using Qiazol reagent (Qiagen) in combination with the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol. Purified RNAs were eluted in 30µL RNase-free water.

tag: cell line

value: A549 cells (ATCC  number CCL-185)

tag: infection

value: H1N1 (A/PuertoRico/8/34)


title: A549, H3N2, 24hpi (rep1)

description:
Human influenza-infected cells
Sample name: H3A


title: high R/FR_mock spray, biological rep 3


title: REL9

description:
LMM08028
Methylation data from HELP assay


title: NEWMM11

description:
LMM08057D
Methylation data from HELP assay

source_name: NEWMM_CD138+ selected cells

value: newly diagnosed myeloma


title: EGL082

city: Atlanta

first: Karen

middle: E

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

institute: Emory University School of Medicine

hyb_protocol: Labeled DNA and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on a GenePix 4000B scanner or an Agilent high-resolution C scanner.

data_processing: Signal intensities were evalutated using Feature Extraction software (log ratios from Feature Extraction files included in Sample tables) and Genomic Workbench was used to analyze array data and make breakpoint predictions (Genomic Workbench data and README file provided as supplementary files on the Series record).

source_name: patient genomic DNA

label_protocol: Genomic DNA, 0.5-1ug, from patient samples and controls were Cy3/Cy5 labeled with Agilent Genomic DNA Enzymatic Labeling Kit following manufacture's protocol

extract_protocol: Genomic DNA was extracted from peripheral blood or cell lines using Gentra Puregene DNA Extraction kit following manufacturers protocol

tag: gender

value: M

tag: array number

tag: chromosome affected

tag: cnv type

value: duplication adjacent to terminal deletion

source_name: Normal control DNA

value: F


title: A549, H1N1, 24hpi (rep1)

description:
Human influenza-infected cells
Sample name: H1A


title: dhx29KD replicate 2

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Dhx9.1241 shRNA replicate 2

hyb_protocol: The resulting labeled samples were hybridized to the Affymetrix Mouse Gene 1.0 ST Array from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data was extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

organism: Mus musculus

label_protocol: The 3’ IVT Express Kit (Affymetrix) using conditions recommended by the manufacturer.

growth_protocol: Lymphomas used in this study were maintained in B-cell Media (BCM; 45% DMEM, 45% Iscove’s Media, 55 mM b-mercaptoethanol, 10% Fetal Bovine Serum) on g-irradiated Arf-/- MEF feeder layers.  Feeder layers were comprised of ~25% confluent irradiated Arf-/- MEFs pre-incubated with BCM for 3 days prior to addition of lymphoma cells.  Lymphomas were routinely split 1:3 every 2-3 days and discarded after >3 weeks in culture.

extract_protocol: Total RNA was extracted using trizol.

treatment_protocol: Cells were transduced with either Rluc.713 or Dhx9.1241shRNA

tag: tumor type

value: Lymphoma

tag: shRNA

tag: genotype/variation

value: Arf-/-Eu-myc/Bcl-2 lymphomas


title: A549, Mock, 24h (rep2)

description:
Mock-infected A549 cells
Sample name: CtrlB

value: Mock-infected


title: SG_Tel_025


title: EGL081


title: A549, Mock, 24h (rep1)

description:
Mock-infected A549 cells
Sample name: CtrlA


title: NL2

description:
CD138B
Methylation data from HELP assay


title: SG_Tel_021


title: dhx29KD replicate 3

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Dhx9.1241 shRNA replicate 3


title: dhx29KD replicate 1

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Dhx9.1241 shRNA replicate 1


title: SG_Tel_012


title: NEWMM13

description:
LMM08074B
Methylation data from HELP assay


title: SG_Tel_011


title: control replicate 2

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Rluc.713 shRNA replicate 2

source_name: control


title: SG_Tel_013


title: control replicate 1

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Rluc.713 shRNA replicate 1


title: control replicate 3

description: Arf-/-Eu-myc/Bcl-2 lymphomas with Rluc.713 shRNA replicate 3


title: NL1

description:
CD138A
Methylation data from HELP assay


title: NL4

description:
CD138D
Methylation data from HELP assay


title: ML-2 Human Cell Line Replicate 1 of 1

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
acute myelomonocytic cell line established from the peripheral blood of a 26-year-old man with acute myeloid leukemia (AML M4) at diagnosis of AML (following T-non-Hodgkin lymphoma and T-ALL) in 1978; carries t(6;11)(q27;q23) leading to MLL-MLLT4 (MLL-AF6) fusion gene
Gene expression data from a MLL-AF6 positive human cell line

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

label: Biotin

source_name: ML2 human Leukemia cell line from DSMZ

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The MLL-AF6 positive ML2 cell line (obtained from DSMZ) was grown in RPMI 10%FBS supplemented with 2mM L-glutamine and penicillin/streptomycin

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were not subject to any treatment prior to RNA preparation.

tag: disease state

value: MLL-AF6 leukemia


title: EGL395


title: EGL014


title: PCC6803_WT_CT5.5_rep1

status: Public on Apr 02 2013

city: Berlin

first: Robert

last: Lehmann

address: Invalidenstrasse 43

department: Institute for Theoretical Biology

country: Germany

institute: Humboldt University Berlin

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.5 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed using R language. Signal intensity was probe-wise LOS normalized, using a oscillation threshold of 0.7.

organism: Synechocystis sp. PCC 6803

source_name: 30 minutes before noon

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Liquid cultures of the Synechocystis 6803 WT strain were grown in BG11 medium (Rippka et al., 1979) at 30°C under continuous illumination with white light at 120 µmol photons•m–2•s– 1 and a continuous stream of air.

extract_protocol: Over a 24 h time course, 6 samples for RNA isolation were taken at the following time points: 30 minutes before and after light is switched off (sample 1 - CT 11.5 and sample 2 - CT 12.5), 30 minutes before midnight (sample 3 - CT 17.5), 348 30 minutes before and after light onset (sample 4 - CT 23.5 and sample 5 - CT 0.5) and 30 minutes before noon (sample 6 - CT 5.5). Cells were filtered rapidly through Supor 0.45µm membrane filters (PALL), immediately stowed with TRIzol reagent (Invitrogen) and frozen in liquid nitrogen. Total RNA samples stored at −20°C were transferred directly to a 65°C waterbath for 5 minutes, mixed with 0.2 ml chloroform  per ml of TRIzol and incubated for 15 minutes. The dissolving of the membrane and lyses of the cells were supported by vortexing. Centrifugation at maximum speed for 10 min at 4°C separated the phases. The RNA in the supernatant was precipitated by adding 0.5 ml of isopropanol per ml TRIzol used in the initial homogenisation.

treatment_protocol: The optical density of the culture was monitored by measuring the absorbance at 750 nm. Cultures were synchronized with three cycles of light/dark 12h:12h prior sampling. Aliquots were taken at OD750 ≈ 0.5.

tag: genotype

value: wildtype


title: PCC6803_WT_CT23.5_rep2

source_name: 30 minutes before light onset


title: PCC6803_WT_CT0.5_rep2

source_name: 30 minutes after light onset


title: SG_Tel_014


title: PCC6803_WT_CT5.5_rep2


title: CRPC_Sample 57

city: New York

first: Matthew

last: Galsky

address: 1 Gustave L Levy Place

institute: Mount Sinai School of Medicine

description: whole blood from patients with castration-resistant prostate cancer collected in PAXgene tubes

data_processing:
18s was used as an endogenous control for each gene expression assay. This allowed gene expression quantification for each cDNA sample relative to the 18s control and this is the data supplied in the Sample data table. We did not measure fold changes. Normalized CT values (ΔCT) for each amplified target gene replicate were calculated by taking the difference between the CT value of the target gene and its endogenous control.  Resulting triplicate ΔCT values for individual target genes were averaged yielding a final ΔCT value.
The 'raw data' prior to the delta Ct calculation were never provided by Source MDx. The 18s endogenous control was used as a quality control measure and all the delta Ct data supplied by Source MDx met the glp 18s quality control parameters (i.e., if the 'raw data' did not meet the 18s quality control, it would have been excluded by the quality control system from the delta Ct data sent to us).

label: TaqMan chemistry (FAM for target gene and VIC for endogenous control)

source_name: peripheral blood

label_protocol: First strand cDNA was synthesized from random hexamer-primed RNA templates using TaqMan® Reverse Transcription reagents.  Quantitative PCR (QPCR) analysis of the 18S rRNA content of newly synthesized cDNA, using the 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) served as a quality check of the first strand synthesis reaction.  Target gene amplification was performed in a QPCR reaction using Applied Biosystem’s TaqMan® Universal PCR Master Mix and Source MDx® proprietary primer-probe sets (Precision Profiles™).  Individual target gene amplification was multiplexed with the Eukaryotic 18S rRNA Endogenous Control  and run in triplicate in a 384-well format on the 7900HT Fast Real-Time PCR System

extract_protocol: whole blood samples were collected in PAXgene Blood RNA tubes and were processed to total RNA within 30 days of phlebotomy with the Qiagen PAXgene Blood RNA kit.

value: male

tag: tumor stage

value: stage IV

tag: clinical disease stage

value: castration-resistant prostate cancer

tag: vital status

value: Dead

tag: time from blood draw to last follow-up (days)


title: CRPC_Sample 56

value: Alive


title: CRPC_Sample 60


title: PCC6803_WT_CT12.5_rep2

source_name: 30 minutes after light is switched off


title: CRPC_Sample 62


title: CRPC_Sample 63


title: CRPC_Sample 61


title: CRPC_Sample 59


title: CRPC_Sample 58


title: PCC6803_WT_CT0.5_rep1


title: PCC6803_WT_CT17.5_rep2

source_name: 30 minutes before midnight


title: CRPC_Sample 55


title: PCC6803_WT_CT23.5_rep1


title: PCC6803_WT_CT11.5_rep1

source_name: 30 minutes before light is switched off


title: CRPC_Sample 54


title: PCC6803_WT_CT11.5_rep2


title: PCC6803_WT_CT12.5_rep1


title: CRPC_Sample 52


title: CRPC_Sample 53


title: CRPC_Sample 51


title: CRPC_Sample 50


title: PCC6803_WT_CT17.5_rep1


title: CRPC_Sample 49


title: CRPC_Sample 47


title: CRPC_Sample 48


title: CRPC_Sample 44


title: CRPC_Sample 45


title: CRPC_Sample 41


title: CRPC_Sample 42


title: CRPC_Sample 38


title: CRPC_Sample 40


title: CRPC_Sample 39


title: CRPC_Sample 46


title: CRPC_Sample 35


title: CRPC_Sample 37


title: CRPC_Sample 36


title: CRPC_Sample 32


title: CRPC_Sample 34


title: CRPC_Sample 33


title: CRPC_Sample 29


title: CRPC_Sample 30


title: CRPC_Sample 31


title: microRNA_NK cells_after exercise_11

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

description: microRNA expression after-exercise

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The results were analyzed using GeneSpring GX 10.0.2 Software (Agilent Technologies, Inc). All raw signal values lower than 1 were adjusted to 1 and normalized using percentile shift (90th percentile).

source_name: Human NK cells after 20 min bout of exercise

label_protocol: One hundred ng of total RNA was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the miRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol: NK cells were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Kit #130-092-657 and the autoMACSÂ® Pro Separator). Total RNA was extracted using TRIzol®.

treatment_protocol: Blood sample was drawn before and immediately after 20 min of exercise.

tag: age

value: 20-29 yr old

tag: tissue

value: blood

tag: cell type

value: NK cells


title: microRNA_NK cells_after exercise_13

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_13

description: microRNA expression before-exercise

source_name: Human NK cells before exercise


title: microRNA_NK cells_after exercise_12

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_14

description: microRNA expression before-exercise


title: microRNA_NK cells_after exercise_14

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_11

description: microRNA expression before-exercise


title: CRPC_Sample 28


title: CRPC_Sample 43


title: microRNA_NK cells_before exercise_12

description: microRNA expression before-exercise


title: microRNA_NK cells_after exercise_10

description: microRNA expression after-exercise


title: CRPC_Sample 27


title: microRNA_NK cells_before exercise_10

description: microRNA expression before-exercise


title: CRPC_Sample 25


title: CRPC_Sample 23


title: CRPC_Sample 24


title: microRNA_NK cells_after exercise_09

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_09

description: microRNA expression before-exercise


title: microRNA_NK cells_before exercise_08

description: microRNA expression before-exercise


title: microRNA_NK cells_after exercise_07

description: microRNA expression after-exercise


title: microRNA_NK cells_after exercise_08

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_07

description: microRNA expression before-exercise


title: microRNA_NK cells_before exercise_05

description: microRNA expression before-exercise


title: microRNA_NK cells_after exercise_05

description: microRNA expression after-exercise


title: CRPC_Sample 21


title: CRPC_Sample 19


title: CRPC_Sample 20


title: CRPC_Sample 18


title: CRPC_Sample 26


title: CRPC_Sample 17


title: CRPC_Sample 13


title: CRPC_Sample 16


title: CRPC_Sample 15


title: CRPC_Sample 14


title: microRNA_NK cells_after exercise_04

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_04

description: microRNA expression before-exercise


title: microRNA_NK cells_after exercise_03

description: microRNA expression after-exercise


title: microRNA_NK cells_before exercise_03

description: microRNA expression before-exercise


title: CRPC_Sample 12


title: CRPC_Sample 22


title: 37°C-3A, biological rep3

city: México D.F

first: Victoria

last: Grosso

address: Tercer circuito exterior C.U

department: Biología Molecular y Biotecnología

country: Mexico

institute: Instituto de Investigaciones Biomédicas UNAM

description:
PGAS_37_3A
Gene expression data from cells growth in PPGAS media at 37° C

hyb_protocol: Following fragmentation, 1 ug of cDNA were hybridized for 16 hr at 50°C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data analyses from three biological replicates for each of the conditions tested were performed after normalizing and summarizing probe level measurements using Robust Multiarray Average (RMA). All microarray data analysis was performed using microarray software package Partek Genomic Suite 6.5. Only genes that fit stringent criteria (expression cutoff: 50–100% stringency; p-value ≤0.01 of one-way ANOVA data corrected by Benjamini Hochberg FDR; fold-change ≥1.4) were selected for further analysis.

organism: Pseudomonas aeruginosa

source_name: Cells of Pseudomonas aeruginosa growth in PPGAS media at 37° C and harvested at O.D600 1.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Protocol-Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in 15 ml of LB at 37 °C with shaking for 16 hours. Overnight precultures were diluted to an O.D600 of 0.05 in PPGAS media and grown at 25 °C and 37 °C, respectively.

extract_protocol: Total RNA was purified using the RNAeasy spin column RNeasy columns (Qiagen) according to the manufacturer’s instructions and residual DNA was eliminated by DNase treatment using RNase-free DNaseI (Thermo Scientific).

treatment_protocol: Samples were harvested at O.D600 of 1.5 and cells from 2.0 ml of each culture, was suspended in 0.5 ml of fresh PPGAS media and added to 1.0 ml of RNA Protect bacteria solution (Qiagen).

tag: strain

tag: growth temperature

value: 37° C


title: CRPC_Sample 11

tag: gender


title: 37°C-2B, biological rep2

description:
PGAS_37_2B
Gene expression data from cells growth in PPGAS media at 37° C


title: CRPC_Sample 9


title: CRPC_Sample 10


title: 25°C-2A, biological rep2

description:
PGAS_25_2A
Gene expression data from cells growth in PPGAS media at 25° C

source_name: Cells of Pseudomonas aeruginosa growth in PPGAS media at 25° C and harvested at O.D600 1.5

value: 25° C


title: 25°C-1A, biological rep1

description:
PGAS_25_1A
Gene expression data from cells growth in PPGAS media at 25° C


title: CRPC_Sample 8


title: CRPC_Sample 7


title: 25°C-4A, biological rep3

description:
PGAS_25_4A
Gene expression data from cells growth in PPGAS media at 25° C


title: 37°C-1B, biological rep1

description:
PGAS_37_1B
Gene expression data from cells growth in PPGAS media at 37° C


title: CRPC_Sample 4


title: CRPC_Sample 3


title: CRPC_Sample 2


title: CRPC_Sample 1


title: CRPC_Sample 5


title: CRPC_Sample 6


title: Liver sample from Control group 6

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'gcrma' function of the Bioconductor package (v2.8) 'gcrma' in R.2.13.0

source_name: Liver biopsy sample

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: liver

value: control


title: Liver sample from Control group 3


title: Liver sample from Control group 4


title: Liver sample from Control group 2


title: RA-FLS_sample2_stimulated by DcR3-Fc

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

description: Gene expression data from RA-FLS sample2 stimulated by human DcR3-Fc

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

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 set to 500.

source_name: Fibroblast like synoviosytes from patient with rheumatoid arthritis, sample2, stimulated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: RA-FLS were cultured in Dulbecco’s modified Eagle’s medium (Gibco BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (BioWhittaker, Walkersville, MD) and 100 units/mL of penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted with a QIAshredder and RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.

treatment_protocol: RA-FLS were incubated with 1.0 μg/mL of recombinant human DcR3-Fc protein or control human IgG1 (R&D Systems, Minneapolis, MN) for 12 hours at 37°C with 5% CO2.

value: Fibroblast like synoviocytes

tag: ethnicity

value: Asian


title: RA-FLS_sample1_stimulated by DcR3-Fc

description: Gene expression data from RA-FLS sample1 stimulated by human DcR3-Fc

source_name: Fibroblast like synoviosytes from patient with rheumatoid arthritis, sample1, stimulated


title: RA-FLS_sample4_stimulated by DcR3-Fc

description: Gene expression data from RA-FLS sample4 stimulated by human DcR3-Fc

source_name: Fibroblast like synoviosytes from patient with rheumatoid arthritis, sample4, stimulated


title: RA-FLS_sample3_stimulated by DcR3-Fc

description: Gene expression data from RA-FLS sample3 stimulated by human DcR3-Fc

source_name: Fibroblast like synoviosytes from patient with rheumatoid arthritis, sample3, stimulated


title: RA-FLS_sample4_stimulated by control IgG1

description: Gene expression data from RA-FLS sample4 stimulated by control IgG1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4


title: Liver sample from Control group 7


title: Liver sample from Control group 5


title: Liver sample from Control group 1


title: RA-FLS_sample3_stimulated by control IgG1

description: Gene expression data from RA-FLS sample3 stimulated by control IgG1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3


title: Liver sample from NASH group 5

value: non-alcoholic steatohepatitis (NASH)


title: Liver sample from NASH group 8


title: RA-FLS_sample2_stimulated by control IgG1

description: Gene expression data from RA-FLS sample2 stimulated by control IgG1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2


title: Liver sample from NASH group 4


title: Liver sample from NASH group 7


title: RA-FLS_sample1_stimulated by control IgG1

description: Gene expression data from RA-FLS sample1 stimulated by control IgG1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1


title: Liver sample from NASH group 3


title: TS206_28Liv_High4

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

description: Biological replicate 4 of 4. Control samples were pooled.

hyb_protocol: 0.825 ug of each labelled cRNA (specific activity >9.0 pmol/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agi_Toxarray3_Ver2 (Design ID: 015749) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505A) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE2-v5_91_0806 and Grid: 015749_D_F_20070118) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Signal intensities of two colors were normalized by lowess normalization method, respectively.

organism: Rattus norvegicus

source_name: [REF] Total RNA from rat liver

label_protocol: Cyanine-3 (Cy3)　or Cyanine-5 (Cy5) labeled cRNA were prepared from 0.5 ug RNA using the Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 4 week-old male Fischer 344 rats were purchased from Charles River Japan. They were housed in an air-conditioned room at 22±2 deg C and 55±15% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (CRF-1, Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: Total RNA was extracted from liver using RNeasy mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Each group was composed of 4 rats. At each time point for each compound, there were a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for 28 days. Control animals received corresponding volumes of vehicle.

value: Male

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: treatment time

value: 28 days

tag: vehicle

value: Water

source_name: [EXPT] Total RNA from rat liver

value: Tetracycline hydrochloride

value: 1000 mg/kg/day


title: Liver sample from NASH group 6

tag: disease state


title: SKNAS_iCSC_rep2

city: Philadelphia

first: Eric

last: Rappaport

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133_P_2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe-level data in CEL files was normalized using GCRMA method implemented in Partek Genomics Suite to get gene-level expression measurements.

source_name: Neuroblastoma cell line

label_protocol: Biotinylated amplified RNA (aRNA) was prepared from 200 ng total RNA using the standard protocol of the Ambion MessageAmp Premier Kit.

growth_protocol: SKNAS Monolayer was grown as monolayer culture.  SKNAS Sphere was grown as spheroid culture in a serum free medium.  SKNAS iCSC was grown as spheroid culture in a serum free medium.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit.

treatment_protocol: SKNAS iCSC was first treated with 5AdC (2.5 uM) for five days as monolayer culture and then transferred to the serum free medium to form spheroid culture.

tag: cell origin

value: Neuroblastoma

tag: culture condition

value: Sphere

tag: pretreatment

value: 5AdC treatement for five days before sphere culture


title: SKNAS_iCSC_rep1


title: TS206_28Liv_High3

description: Biological replicate 3 of 4. Control samples were pooled.


title: Liver sample from NASH group 2


title: TS205_28Liv_High4

value: Corn oil

value: 300 mg/kg/day


title: SKNAS_Sphere_rep2


title: Liver sample from NASH group 1

value: liver


title: TS206_28Liv_High1

description: Biological replicate 1 of 4. Control samples were pooled.


title: palatal_shelf-mutant_(Tbx1-/-)-biological_replicate_3

city: London

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridised to MOE430A 2.0 microarrays for 16 hours at 45°C using standard protocols. Then arrays were washed and stained in the fluidics station 400 (Affymetrix), following standard procedures.

scan_protocol: Arrays were scanned using the GCS3000 array scanner (Affymetrix) and image data was collected and processed using GCOS v1.4

data_processing: CHP files were generated using the MAS5 algorithm in GCOS v1.4. Signal values were globally scaled to a target value of 100. Then the probesets were filtered according to absent call, fold change and intra-group standard deviation before applying a 1-way ANOVA across the three genotypes.

source_name: palatal shelf, mutant Tbx1-/-

label_protocol: One microgram of total RNA was amplified and converted into biotinylated cRNA using the MessageAmp II-Biotin Enhanced cRNA Amplification Kit from Ambion.

growth_protocol: Embryos were allowed to develop naturally in utero until E13.5

extract_protocol: Total RNA was extracted from homogenate derived from each shelf pair using an RNeasy Isolation Kit (Qiagen).

treatment_protocol: Secondary palatal shelves were carefully microdissected from embryos, stored as pairs from each embryo in RNAlater (Ambion) and then homogenized using a blunt 20-guage needle to an RNase-free syringe.

tag: developmental stage

value: E13.5 embryo

value: palatal shelf

tag: tbx1 genotype


title: SKNAS_Sphere_rep1


title: TS205_28Liv_High2

description: Biological replicate 2 of 4. Control samples were pooled.

tag: age

tag: tissue


title: palatal_shelf-heterozygote_(Tbx1+/-)-biological_replicate_3

source_name: palatal shelf, heterozygote Tbx1+/-

tag: strain


title: TS206_28Liv_High2


title: palatal_shelf-mutant_(Tbx1-/-)-biological_replicate_1


title: SKNAS_Monolayer_rep_1

value: Monolayer


title: palatal_shelf-mutant_(Tbx1-/-)-biological_replicate_2


title: TS205_28Liv_High1

value: Male


title: TS205_28Liv_High3

value: Liver


title: NK cells_before exercise_14

hyb_protocol: 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix U133 plus 2 arrays.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.  Arrays were scanned using GeneChip® Scanner 3000 7G and Command Console Software v 3.2.3. to produce *.CEL intensity files.

data_processing: The results were analyzed using GeneSpring GX 10.0.2 Software (Agilent Technologies, Inc).

source_name: Human NK cells before exercise

label_protocol: First-strand cDNA is synthesized from 250ng of isolated total RNA using an oligo-dT primer with an attached T7 promoter sequence.  After making the complementary second strand, the double-stranded cDNA is used to generate biotin-tagged cRNA from an in- vitro transcription (IVT) using T7 RNA polymerase. 15ug of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® IVT 3’IVT Express Kit User Manual).

extract_protocol: NK cells were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Kit #130-092-657 and the autoMACS® Pro Separator). Total RNA was extracted using TRIzol®.

value: male

value: 20-29 yr old

tag: status

value: healthy

value: blood

tag: cell type

value: NK cells

tag: sample collection

value: before-exercise


title: TS204_28Liv_High4

tag: gender

tag: compound

value: Vehicle

value: gavage

value: 28 days

value: 250 mg/kg/day


title: NK cells_after exercise_14

source_name: Human NK cells after 20 min bout of exercise

value: after-exercise


title: palatal_shelf-heterozygote_(Tbx1+/-)-biological_replicate_1


title: palatal_shelf-wild_type_(Tbx1+/+)-biological_replicate_3

source_name: palatal shelf, wild-type Tbx1+/+


title: TS204_28Liv_High3

tag: dose

tag: administration

value: Corn oil


title: cerebrum, control, bio rep 3

city: Rehovoth

first: David

last: Zeevi

address: WIS

department: Computer Science

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GeneAtlas personal microarray system.

data_processing: Data processing was performed using the Affymetrix expression console.

source_name: Cerebrum tissue of mice treated with MCT

label_protocol: Labeling was performed using the Affymetrix GeneChip WT Terminal Labeling and Controls Kit by the TAU Bioinformatics Unit.

growth_protocol: at 4 months of age 3 FD mice and 3 wt mice were gavaged with PS (200mg/kg) or MCT every other day for a period of 3 months

extract_protocol: RNA was extracted from cerebrum and heart tissues using Qiagene RNeasy Plus mini kit according to the manufacturer`s protocol.

treatment_protocol: Each oral dosing was performed with 100 microliter of 200mg/kg or 100 microliter of medium-chain triglycerides (MCT).

tag: genotype

value: humanized knock-in IKBKAP FDloxP/+


title: NK cells_before exercise_13


title: NK cells_after exercise_13


title: TS204_28Liv_High1

tag: treatment time

tag: vehicle


title: NK cells_after exercise_12


title: palatal_shelf-wild_type_(Tbx1+/+)-biological_replicate_2

value: E13.5 embryo

value: palatal shelf


title: TS203_28Liv_High4

value: Male

value: 150 mg/kg/day


title: SKNAS_Monolayer_rep_2

tag: cell origin

value: Neuroblastoma

tag: culture condition

value: Monolayer


title: palatal_shelf-heterozygote_(Tbx1+/-)-biological_replicate_2

tag: developmental stage


title: palatal_shelf-wild_type_(Tbx1+/+)-biological_replicate_1

tag: tbx1 genotype


title: heart, treated, bio rep 3

source_name: Heart tissue of mice treated with PS (200 mg/ day)


title: TS204_28Liv_High2

tag: age

value: Liver


title: cerebrum, treated, bio rep 3

source_name: Cerebrum tissue of mice treated with PS (200 mg/ day)


title: NK cells_before exercise_12

value: male

value: 20-29 yr old

value: healthy

tag: tissue

value: blood


title: Arabidopsis Treated, biological rep2

city: Kolkata

first: Sharmila

last: Chattopadhyay

state: West Bengal

address: 4, Raja S.C. Mullick Road,

country: India

institute: CSIR-Indian Institute of Chemical Biology, Kolkata

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console and Gene springGX 12.1 using Affymetrix default analysis settings and RMA as normalization method used. The probes of intensities less than the 20.0 percentile in the raw data were excluded.

source_name: A. thaliana seedlings treated with GSH

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

growth_protocol: A. thaliana seedlings were grown for 15 days after germination and then used for experiment

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

treatment_protocol: A. thaliana seedlings were grown for 15 days after germination and then treated with GSH for 72 hrs befor used for array experiment

tag: ecotype

value: Columbia

value: seedlings

value: 15 days


title: NK cells_after exercise_11

tag: status

value: NK cells

value: after-exercise


title: heart, control, bio rep 3

source_name: Heart tissue of mice treated with MCT

tag: strain

value: humanized knock-in IKBKAP FDloxP/+


title: NK cells_before exercise_11

tag: cell type

tag: sample collection

value: before-exercise


title: TS203_28Liv_High3

tag: gender

tag: compound

value: Vehicle

value: gavage

value: 28 days

value: Corn oil


title: Arabidopsis control, biological rep1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: A. thaliana seedlings


title: cerebrum, treated, bio rep 2


title: TS203_28Liv_High2

value: Male

tag: dose

tag: administration

value: 150 mg/kg/day


title: Arabidopsis Treated, biological rep1


title: NK cells_after exercise_09

value: male


title: Arabidopsis control, biological rep2


title: cerebrum, control, bio rep 2

tag: genotype


title: NK cells_before exercise_09

value: 20-29 yr old


title: Ri17 treated with wound for 60min

city: Beijing

first: Daoxin

last: Xie

address: tsinghua univercity

country: China

institute: tsinghua univercity

description: Gene expression data from  wounding treated JAV1 RNAi plant

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Arabidopsis Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the SCAN3000.

data_processing: The data were analyzed with GCOS. Each experiment was represented by two biological replicates. The correction and normalization of the expression data were performed by calculating Pearson’s coefficient. Criteria for selection of differentially expressed genes at one time point were log ratio > 1. Only data from microarrays with very good technical quality were used for calculating and drawing cluster tree using Cluster Tree View soft (Alok Saldanha at Stanford University).

source_name: Ri17 treated with wound for 60min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 21-day-old Arabidopsis seedlings grown in MS medium.

treatment_protocol: For MeJA treatment, 21-day-old seedlings were treated with 100 μM MeJA for various time periods (0, 1, and 4 hours). treated leaves  were harvested at various time periods. For  wounding treatment, four rosette leaves from 21-day-old plants were crushed across the midrib with a forceps. About 30% of each leaf was damaged. Wounded leaves were harvested at various time periods (0, 0.5, and 1 hour) for RNA extraction.Control plants  were untreated and  leaves were harvested for RNA extraction.

value: Arabidopsis leaves

tag: cultivar

value: JAV1 RNAi transgenic plant (Ri17)


title: NK cells_after exercise_08

value: healthy

value: blood


title: TS202_28Liv_High1

value: Liver

tag: treatment time

tag: vehicle

value: 50 mg/kg/day


title: Ri17 treated with wound for 30min

source_name: Ri17 treated with wound for 30min


title: TS202_28Liv_High4


title: TS203_28Liv_High1


title: cerebrum, treated, bio rep 1


title: Ri17 treated with 100uM MeJA for 4 hour

description: Gene expression data from  JA treated JAV1 RNAi plant

source_name: Ri17 treated with 100uM MeJA for 4 hour


title: cerebrum, control, bio rep 1


title: TS202_28Liv_High2

source_name: [REF] Total RNA from rat liver


title: Ri17 treated with 100uM MeJA for 1 hour

source_name: Ri17 treated with 100uM MeJA for 1 hour


title: heart, control, bio rep 2


title: TS202_28Liv_High3

source_name: [EXPT] Total RNA from rat liver


title: TS201_28Liv_High3

value: Hexachloroethane

value: 500 mg/kg/day


title: NK cells_before exercise_08

value: NK cells

value: before-exercise


title: heart, treated, bio rep 1

value: humanized knock-in IKBKAP FDloxP/+


title: TS201_28Liv_High2

value: Vehicle

value: gavage

value: 28 days


title: NK cells_after exercise_06

value: after-exercise


title: NK cells_before exercise_06

value: male


title: Ri17 untreated

description: Gene expression data from  untreated JAV1 RNAi plant

source_name: Ri17 untreated


title: Col-0 treated with wound for 60min

description: Gene expression data from  wounding treated wild type

source_name: Col-0 treated with wound for 60min

value: Wild type


title: NK cells_after exercise_07

value: 20-29 yr old


title: heart, control, bio rep 1


title: TS201_28Liv_High4

value: Male

value: Corn oil


title: heart, treated, bio rep 2


title: fat bodies_control, rep2

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

description:
C-3
Gene expresion data from fat bodies (abdomen without midgut, ovaries and malpighian tubule) of mosquitoes injected with ODN elution buffer.

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post-hybridization wash and double-stain protocols (EukGE-WS2v4) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: Scanned arrays were analyzed first with Affymetrix MAS 5.0 software to obtain Absent/Present calls and for subsequent analysis with dChip 2006 (http://www.dchip.org, Wong Lab, Harvard). Using a probe set mask file that excluded all probes sets interrogating human and Plasmodium falciparum transcripts, the arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the four arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001).

organism: Anopheles gambiae

source_name: Adult females injected with elution buffer

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Plasmodium/Anopheles Genome Arrays, according to the manufacturer’s One-Cycle Target Labeling Assay. Briefly, 3.7 µg of total RNA containing spiked-in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (One-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Anopheles gambiae s.s. mosquitoes were reared at 25 ºC and 75% humidity with a 12-hour light/dark cycle. Adult mosquitoes were maintained on a 10% glucose solution.

extract_protocol: Batches of 20 to 30 fat bodies (abdomen without midgut, ovaries and malpighian tubule) were dissected in cold DEPC-treated phosphate-buffered saline (PBS). Trizol reagent (Invitrogen Life Technologies) was used to extract total RNA.

treatment_protocol: Three- to four-day-old female mosquitoes were cold-anaesthetized and inoculated intratoraxically with 69nl of a 0.1mM CpG-oligodeoxynucleotide (0604 -5’ TCCATGACGTTCCTGATGCT 3’) solution or with the same volume of elution buffer using a Nanoject micro-injector (Drummond Scientific). Mosquitoes were left to rest for 18h.

value: Yaounde

value: female

tag: developmental stage

value: adult

tag: treatment

value: control


title: Col-0 treated with 100uM MeJA for 4 hour

description: Gene expression data from  JA treated wild type

value: Arabidopsis leaves


title: NK cells_after exercise_05

source_name: Human NK cells after 20 min bout of exercise

tag: age

value: healthy

value: blood

value: NK cells


title: Col-0 treated with wound for 30min

source_name: Col-0 treated with wound for 30min

tag: tissue


title: NK cells_before exercise_07

source_name: Human NK cells before exercise

value: before-exercise


title: NK cells_before exercise_05


title: TS201_28Liv_High1

value: Liver

value: Vehicle

value: gavage

value: Hexachloroethane

value: 500 mg/kg/day


title: fat bodies_control, rep1

description:
C-1
Gene expresion data from fat bodies (abdomen without midgut, ovaries and malpighian tubule) of mosquitoes injected with ODN elution buffer.


title: NK cells_before exercise_04

value: male

value: 20-29 yr old


title: NK cells_after exercise_03

value: after-exercise


title: fat bodies_0604-ODN, rep2

description:
604-3
Gene expresion data from fat bodies (abdomen without midgut, ovaries and malpighian tubule) of mosquitoes injected with 0640-ODN.

source_name: Adult females injected with 0604-ODN

value: Yaounde


title: NK cells_after exercise_04


title: Col-0 treated with 100uM MeJA for 1 hour

value: Wild type


title: NK cells_after exercise_01


title: CKO keratinocytes treated with 4OHT

city: Taipei

first: Ming-Feng

last: Chiang

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia sinica

description:
CKO 4OHT
Tail skin keratinocytes from CKO mice were cultured in serum-free keratinocytes conditional medium with 4-hydroxytamoxifen (4OHT).

hyb_protocol: The biotinylated cRNAs were hybridized to GeneChip® Mouse Expression Array 430A.

scan_protocol: Microarray was scanned and images were acquired by GeneChip® Scanner 3000.

data_processing: Data were processed by the RMA algorithm using GeneSpring GX11.

source_name: Prdm1 floxed mice with CreER expression, 4OHT

label_protocol: Microarray was performed according to the protocol provided by the manufacturer (3' IVT express kit, Affymetrix). Total RNAs were used as the template to generate double-strand cDNAs. Total RNAs were degraded and double-strand cDNAs were purified by cDNA Cleanup Spin Column (Qiagen). cRNAs with biotin-conjugated nucleotide analog were generated and amplified by in vitro transcription using T7 RNA polymerase.

growth_protocol: Tail skin keratinocytes were cultured in serum-free medium, CnT-07 (CELLnTEC), and rat collagen I coated plates. Culture medium was refreshed on day 3 and cells were collected on day 5.

extract_protocol: Total RNA was isolated using the Qiagn RNeasy® Mini kit, followed by using the Qiagen RNase-Free DNase Set to remove DNA. The isolation procedure was performed per the manufacturer's instructions.

treatment_protocol: 4-hydroxytamoxifen (4OHT) or ethanol (EtOH, solvent control) were added to culture medium from day 1 to day 3.

tag: congenic strain

value: tail skin

value: primary cultured keratinocytes

value: 4-hydroxytamoxifen (4OHT)


title: Vehicle liver rep4

city: Cambridge

first: Peng

last: Yi

address: 7 Divinity Ave.

department: SCRB

institute: Harvard University

description:
replicate 4
SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: The data were normalized by average signal on chip with Illumina BeadStudio (v.3.1.3.0).

label_protocol: cRNA was labeled with biotin using Illumina TotalPrep RNA Amplification kit (Ambion)

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

treatment_protocol: The mice were treated with vehicle or S961 (10nMol/week) using Alzet osmotic pump for a week.

value: 8 weeks

tag: treated with

value: vehicle (PBS) for a week

value: liver


title: Control keratinocytes treated with EtOH

description:
control EtOH
Tail skin keratinocytes from control mice were cultured in serum-free keratinocytes conditional medium with solvent control ethanol (EtOH).

source_name: Prdm1 floxed mice without CreER expression, EtOH

value: ethanol (EtOH)


title: Col-0 untreated

description: Gene expression data from  untreated wild type

source_name: Col-0 untreated

value: Arabidopsis leaves


title: S961 liver rep4

description:
replicate 4
SAMPLE 8

tag: strain

value: S961 (10nMol/week) for a week


title: S961 liver rep2

description:
replicate 2
SAMPLE 6


title: S961 liver rep1

description:
replicate 1
SAMPLE 5


title: NK cells_before exercise_01

tag: status

value: healthy

value: blood

tag: cell type

value: NK cells

value: before-exercise


title: Neocortex_Eomes_KO.8

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 using the Affymetrix Expression Console,  version 1.1

label: Cy3 fluorescent label

source_name: Neocortex E14.5 mouse Eomes KO

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: E14.5 brains were removed, and neocortexes were immediately dissected.

value: neocortex

value: Eomes KO

tag: genetic background


title: CKO keratinocytes treated with EtOH

description:
CKO EtOH
Tail skin keratinocytes from CKO mice were cultured in serum-free keratinocytes conditional medium with solvent control ethanol (EtOH).

source_name: Prdm1 floxed mice with CreER expression, EtOH


title: Neocortex_Eomes_WT.6

source_name: Neocortex E14.5 mouse Eomes WT

value: Eomes WT


title: Neocortex_Eomes_WT.7


title: Neocortex_Eomes_WT.5


title: NK cells_before exercise_03

tag: gender

value: male

value: 20-29 yr old

tag: sample collection


title: Neocortex_Eomes_KO.4


title: fat bodies_0604-ODN, rep1

description:
604-1
Gene expresion data from fat bodies (abdomen without midgut, ovaries and malpighian tubule) of mosquitoes injected with 0640-ODN.

value: Yaounde

value: female

value: adult


title: S961 liver rep3

description:
replicate 3
SAMPLE 7

value: 8 weeks


title: Control keratinocytes treated with 4OHT

description:
control 4OHT
Tail skin keratinocytes from control mice were cultured in serum-free keratinocytes conditional medium with 4-hydroxytamoxifen (4OHT).

source_name: Prdm1 floxed mice without CreER expression, 4OHT

value: tail skin

value: primary cultured keratinocytes

value: 4-hydroxytamoxifen (4OHT)


title: Vehicle liver rep2

description:
replicate 2
SAMPLE 2

value: vehicle (PBS) for a week

value: liver


title: AKO-rep3

status: Public on Apr 01 2013

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description: batch 3

hyb_protocol: cRNA was hybridized to Illumina Sentrix® Murine Ref8_v2_R3 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol

scan_protocol: All signal intensity quantification was performed using an Illumina iScan scanner, using the standard Illumina scanning protocol.

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina GenomeStudio software with standard settings and no background correction.  The expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed.

source_name: bone marrow derived mast cells

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

growth_protocol: Bone marrow derived mast cells (BMMCs) from AhR null, AhR_d and normal control mice were cultured in 30% WEHI-3-conditioned medium

extract_protocol: RNA was extracted with RNeasy mini kits with DNase I treatment (Qiagen) in accordance with the prescribed protocol provided with the kit and stored at -80°C.  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: BMMCs were purified by negative selection with MicroBeads (Miltenyi Biotec) after 4 weeks in culture. The cells were further rested in cytokine free medium for 4h.

tag: mouse strain

tag: genotype/variation

value: AhR null


title: B6-rep2

description: batch 2

value: normal control


title: Vehicle liver rep1

description:
replicate 1
SAMPLE 1


title: AKO-rep2

description: batch 2


title: Ad-rep2

description: batch 2

value: AhR-d


title: Vehicle liver rep3

description:
replicate 3
SAMPLE 3


title: AKO-rep1

description: batch 1


title: Liver_LPS-treated_5

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Replicate 5

scan_protocol: Standard Illumina scanning protocol

data_processing:
The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.

source_name: mouse liver

label_protocol: Biotinylated cRNAs were prepared with the Illumina® TotalPrep™ RNA Amplification kit from Ambion.

extract_protocol: Total RNA was isolated using mirVana™ miRNA Isolation kit, followed by DNase treatment with Turbo DNA-free™ according to the protocol supplied by the manufacturer (Ambion, Austin, TX). Quality control was performed with the Agilent Bioanalyzer.

value: 2.5 months

tag: paradigm

value: 2 lipopolysaccharide injections (1 mg/kg i.p.) spaced one week apart


title: Neocortex_Eomes_KO.1

value: neocortex

tag: genotype

value: Eomes KO


title: Neocortex_Eomes_WT.2

value: Eomes WT


title: Liver_LPS-treated_7

description: Replicate 7


title: Liver_LPS-control_8

description: Replicate 8

value: water


title: Liver_LPS-treated_10

description: Replicate 10


title: Liver_LPS-treated_6

description: Replicate 6


title: Liver_LPS-treated_8

description: Replicate 8


title: Liver_LPS-treated_9

description: Replicate 9


title: Liver_LPS-treated_4

description: Replicate 4


title: B6-rep3

description: batch 3


title: Liver_LPS-control_7

description: Replicate 7


title: Liver_LPS-treated_3

description: Replicate 3


title: Liver_LPS-control_4

description: Replicate 4


title: Liver_LPS-control_6

description: Replicate 6


title: Liver_LPS-treated_1

description: Replicate 1


title: Ad-rep1

description: batch 1


title: Liver_LPS-control_10

description: Replicate 10


title: B6-rep1

description: batch 1


title: Liver_LPS-treated_2

description: Replicate 2


title: Liver_LPS-control_9

description: Replicate 9


title: Liver_LPS-control_5

description: Replicate 5


title: Liver_LPS-control_3

description: Replicate 3


title: Liver_LPS-control_2

description: Replicate 2


title: PFC_LPS-treated_9

description: Replicate 9

source_name: mouse prefrontal cortex

value: prefrontal cortex


title: Ad-rep3

description: batch 3


title: Liver_LPS-control_1

description: Replicate 1


title: PFC_LPS-treated_10

description: Replicate 10


title: PFC_LPS-treated_4

description: Replicate 4


title: PFC_LPS-treated_8

description: Replicate 8


title: PFC_LPS-treated_5

description: Replicate 5


title: PFC_LPS-treated_1

description: Replicate 1


title: PFC_LPS-treated_2

description: Replicate 2


title: PFC_LPS-control_10

description: Replicate 10


title: PFC_LPS-treated_7

description: Replicate 7


title: PFC_LPS-control_8

description: Replicate 8


title: PFC_LPS-treated_6

description: Replicate 6


title: PFC_LPS-control_4

description: Replicate 4


title: PFC_LPS-control_3

description: Replicate 3


title: PFC_LPS-treated_3

description: Replicate 3


title: PFC_LPS-control_6

description: Replicate 6


title: PFC_LPS-control_1

description: Replicate 1


title: Liver_DID-treated_10

description: Replicate 10

value: Drinking in the Dark -- limited access to one bottle of ethanol


title: PFC_LPS-control_7

description: Replicate 7


title: Liver_DID-treated_4

description: Replicate 4


title: Liver_DID-treated_5

description: Replicate 5


title: Liver_DID-treated_9

description: Replicate 9


title: Liver_DID-treated_6

description: Replicate 6


title: Liver_DID-treated_2

description: Replicate 2


title: Liver_DID-treated_3

description: Replicate 3


title: Liver_DID-treated_8

description: Replicate 8


title: PFC_LPS-control_5

description: Replicate 5


title: Liver_DID-treated_7

description: Replicate 7


title: Liver_DID-treated_1

description: Replicate 1


title: PFC_LPS-control_9

description: Replicate 9


title: Liver_DID-control_8

description: Replicate 8


title: Liver_DID-control_10

description: Replicate 10


title: Liver_DID-control_6

description: Replicate 6


title: PFC_LPS-control_2

description: Replicate 2


title: Liver_DID-control_9

description: Replicate 9


title: Liver_DID-control_4

description: Replicate 4


title: Liver_DID-control_5

description: Replicate 5


title: Liver_DID-control_3

description: Replicate 3


title: PFC_DID-treated_7

description: Replicate 7


title: PFC_DID-treated_5

description: Replicate 5


title: PFC_DID-treated_8

description: Replicate 8


title: PFC_DID-treated_10

description: Replicate 10


title: PFC_DID-treated_9

description: Replicate 9


title: Liver_DID-control_1

description: Replicate 1


title: Liver_DID-control_7

description: Replicate 7


title: PFC_DID-treated_6

description: Replicate 6


title: PFC_DID-control_8

description: Replicate 8


title: PFC_DID-control_7

description: Replicate 7


title: PFC_DID-control_4

description: Replicate 4


title: Liver_DID-control_2

description: Replicate 2


title: PFC_DID-control_3

description: Replicate 3


title: PFC_DID-control_5

description: Replicate 5


title: PFC_DID-control_10

description: Replicate 10


title: PFC_DID-treated_1

description: Replicate 1


title: PFC_DID-control_6

description: Replicate 6


title: PFC_DID-treated_2

description: Replicate 2


title: PFC_DID-control_1

description: Replicate 1


title: Liver_CI-treated_10

description: Replicate 10

value: Chronic Intermittent with two bottles choice every other day


title: PFC_DID-treated_4

description: Replicate 4


title: PFC_DID-control_2

description: Replicate 2


title: PFC_DID-treated_3

description: Replicate 3


title: Liver_CI-treated_9

description: Replicate 9


title: Liver_CI-treated_8

description: Replicate 8


title: Liver_CI-treated_7

description: Replicate 7


title: Liver_CI-treated_5

description: Replicate 5


title: Liver_CI-treated_4

description: Replicate 4


title: Liver_CI-treated_6

description: Replicate 6


title: Liver_CI-control_10

description: Replicate 10


title: Liver_CI-control_7

description: Replicate 7


title: Liver_CI-treated_1

description: Replicate 1


title: Liver_CI-control_4

description: Replicate 4


title: Neocortex_Eomes_WT.3


title: Liver_CI-control_5

description: Replicate 5


title: Liver_CI-control_9

description: Replicate 9


title: Liver_CI-control_6

description: Replicate 6


title: Liver_CI-control_8

description: Replicate 8


title: Liver_CI-treated_2

description: Replicate 2


title: Liver_CI-control_2

description: Replicate 2


title: Liver_CI-control_3

description: Replicate 3


title: Liver_CI-treated_3

description: Replicate 3


title: PFC_CI-treated_8

description: Replicate 8


title: Liver_CI-control_1

description: Replicate 1


title: PFC_CI-treated_9

description: Replicate 9


title: PFC_CI-treated_10

description: Replicate 10


title: PFC_CI-treated_4

description: Replicate 4


title: PFC_CI-treated_6

description: Replicate 6


title: PFC_CI-treated_7

description: Replicate 7


title: PFC_CI-treated_3

description: Replicate 3


title: PFC_CI-treated_2

description: Replicate 2


title: PFC_CI-control_10

description: Replicate 10


title: PFC_CI-treated_5

description: Replicate 5


title: PFC_CI-control_8

description: Replicate 8


title: PFC_CI-control_9

description: Replicate 9


title: PFC_CI-treated_1

description: Replicate 1


title: PFC_CI-control_5

description: Replicate 5


title: PFC_CI-control_6

description: Replicate 6


title: PFC_CI-control_7

description: Replicate 7


title: Liver_Chronic-treated_9

description: Replicate 9

value: continuous chronic two bottle choice


title: Liver_Chronic-treated_10

description: Replicate 10


title: Liver_Chronic-treated_7

description: Replicate 7


title: PFC_CI-control_4

description: Replicate 4


title: PFC_CI-control_3

description: Replicate 3


title: PFC_CI-control_1

description: Replicate 1


title: PFC_CI-control_2

description: Replicate 2


title: Liver_Chronic-treated_6

description: Replicate 6


title: Liver_Chronic-treated_2

description: Replicate 2


title: Liver_Chronic-treated_3

description: Replicate 3


title: Liver_Chronic-treated_8

description: Replicate 8


title: Liver_Chronic-treated_4

description: Replicate 4


title: Liver_Chronic-treated_1

description: Replicate 1


title: Liver_Chronic-treated_5

description: Replicate 5


title: Liver_Chronic-control_10

description: Replicate 10


title: Liver_Chronic-control_9

description: Replicate 9


title: Liver_Chronic-control_4

description: Replicate 4


title: Liver_Chronic-control_7

description: Replicate 7


title: Liver_Chronic-control_8

description: Replicate 8


title: Liver_Chronic-control_5

description: Replicate 5


title: Liver_Chronic-control_6

description: Replicate 6


title: PFC_Chronic-treated_10

description: Replicate 10


title: PFC_Chronic-treated_5

description: Replicate 5


title: Liver_Chronic-control_1

description: Replicate 1


title: PFC_Chronic-treated_6

description: Replicate 6


title: PFC_Chronic-treated_7

description: Replicate 7


title: PFC_Chronic-treated_9

description: Replicate 9


title: PFC_Chronic-treated_1

description: Replicate 1


title: Liver_Chronic-control_2

description: Replicate 2


title: PFC_Chronic-treated_3

description: Replicate 3


title: PFC_Chronic-control_7

description: Replicate 7


title: PFC_Chronic-treated_8

description: Replicate 8


title: PFC_Chronic-treated_2

description: Replicate 2


title: PFC_Chronic-control_8

description: Replicate 8


title: PFC_Chronic-treated_4

description: Replicate 4


title: PFC_Chronic-control_9

description: Replicate 9


title: PFC_DID-control_9

description: Replicate 9


title: PFC_Chronic-control_6

description: Replicate 6


title: PFC_Chronic-control_4

description: Replicate 4


title: PFC_Chronic-control_5

description: Replicate 5


title: PFC_Chronic-control_3

description: Replicate 3


title: Liver_Chronic-control_3

description: Replicate 3


title: RC84

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
4256290126_C.AVG_Signal
Illumina Human Ref-8 BeadArray

hyb_protocol: Standard Illumina probe synthesis for gene expression profiling (carried out UCLA Southern California Genotyping Consortium core laboratory).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out at UCLA Southern California Genotyping Consortium).

data_processing: Quantile normalization of Illumina raw expression data derived from GenomeStudio software

source_name: PBMC

label_protocol: Standard Illumina hybridization protocol for gene expression profiling (carried out UCLA Southern California Genotyping Consortium core laboratory).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

value: PBMC

tag: disease status

value: renal cell carcinoma

tag: cesd16 status


title: RC181

description:
4609526116_B.AVG_Signal
Illumina Human Ref-8 BeadArray


title: PFC_Chronic-control_2

description: Replicate 2


title: RC86

description:
4609526115_F.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC59

description:
4609526016_D.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC42

description:
4609526115_G.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC77

description:
4256290126_G.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC192

description:
4256290126_B.AVG_Signal
Illumina Human Ref-8 BeadArray


title: test

description:
4609526016_H.AVG_Signal
Illumina Human Ref-8 BeadArray

value: NA/test sample


title: control vector 3

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
The data were normalised using quantile normalisation with the lumi package in Bioconductor
not detected probes omitted (detection p-value where a probe is not detected in a sample if the p-value is above 0.01)

source_name: embryonic stem cell

label_protocol: The Illumina Total-prep 96-RNA amplification kit from Ambion was used.

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

treatment_protocol: Biological replicates were collected from consecutive passages, no additional treatment was performed.

value: embryonic stem cell

tag: treatment

value: control vector


title: control vector 1


title: Prdm14 overexpression 3

value: Prdm14 overexpression


title: PFC_Chronic-control_1

description: Replicate 1

tag: age


title: RC215

description:
4609526115_E.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC85

description:
4256290126_E.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC166

description:
4256290126_F.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC6

description:
4609526116_F.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC147

description:
4609526116_E.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC71

description:
4609526115_C.AVG_Signal
Illumina Human Ref-8 BeadArray


title: Prdm14 overexpression 1


title: Prdm14 knockout 1

growth_protocol: Prdm14-null and wild-type control cells were grown in 2i culture conditions as described by Ying et al. (Nature, 2008)

value: Prdm14 knockout


title: RC311

description:
4609526115_H.AVG_Signal
Illumina Human Ref-8 BeadArray


title: wild-type control 3

value: wild-type control


title: RC52

description:
4609526116_A.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC122

description:
4609526116_G.AVG_Signal
Illumina Human Ref-8 BeadArray


title: Prdm14 knockout 2


title: RC212

description:
4609526115_D.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC200

description:
4609526115_A.AVG_Signal
Illumina Human Ref-8 BeadArray


title: HC 3

city: Atlanta

first: Raul

last: Andero Gali

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

description: 1mm punch used

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse amygdala

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

extract_protocol: Total RNA was isolated and purified from the tissue with the RNeasy Mini Kit (Catalog #74106) following the manufacturer instructions (Qiagen)

tag: Sex

value: male

value: 10 weeks old

tag: tissue

value: Bilateral amygdala

value: Home caged


title: RC129

description:
4609526016_C.AVG_Signal
Illumina Human Ref-8 BeadArray


title: HC 1

description: 1mm punch used


title: control vector 2


title: Prdm14 overexpression 2


title: RC148

description:
4609526016_F.AVG_Signal
Illumina Human Ref-8 BeadArray


title: HC 2

description: 1mm punch used


title: FC, 2h after FC 1

description: 1mm punch used

value: Fear conditioning


title: RC103

description:
4609526115_B.AVG_Signal
Illumina Human Ref-8 BeadArray


title: FC, 2h after FC 4

description: 1mm punch used


title: wild-type control 2


title: IMO + FC, 2h after FC 4

description: 1mm punch used

value: Immobilization and fear conditioning


title: RC143

description:
4609526116_H.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC130

description:
4256290126_H.AVG_Signal
Illumina Human Ref-8 BeadArray


title: wild-type control 1


title: FC, 2h after FC 3

description: 1mm punch used


title: 129X1_heart_infected_rep2

city: Montreal

first: Jennifer

last: Marton

state: Quebec

address: 3649 Prom. Sir William Osler

department: Human Genetics

country: Canada

institute: McGill University

description: replicate 2

data_processing: The data were normalized using FlexArray

source_name: heart infected

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumine TotalPrep RNA Amplification Kit (IL1791)

extract_protocol: Hearts were perfused with PBS, removed and immediated snap frozen in liquid nitrogen.  Total RNA was extracted using TRIzol (Ambion) reagent according to the manufacturer's protocol and cleaned up using QIANGEN Rneasy columns.  Quality control by agilent bioanalyzer

treatment_protocol: Mice were infected with a dose of 500pfu per gram of CVB3 (H3) or left uninfected

value: Female

tag: infection

value: CVB3(H3) at 500pfu/g

value: 7 weeks


title: 129S1_heart_infected_rep2

description: replicate 2

tag: strain


title: IMO + FC, 2h after FC 2

description: 1mm punch used


title: RC116

description:
4256290126_A.AVG_Signal
Illumina Human Ref-8 BeadArray

value: PBMC


title: Prdm14 knockout 3


title: RC118

description:
4609526116_D.AVG_Signal
Illumina Human Ref-8 BeadArray

value: renal cell carcinoma


title: 129S1_heart_uninfected_rep2

description: replicate 2

source_name: heart uninfected


title: RC146

description:
4609526016_G.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC120

description:
4256290126_D.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC114

description:
4609526016_A.AVG_Signal
Illumina Human Ref-8 BeadArray


title: HC 4

description: 1mm punch used


title: RC104

description:
4609526116_C.AVG_Signal
Illumina Human Ref-8 BeadArray


title: RC113

description:
4609526016_E.AVG_Signal
Illumina Human Ref-8 BeadArray


title: 129X1_heart_uninfected_rep3

description: replicate 3


title: FC, 2h after FC 2

description: 1mm punch used


title: 129S1_heart_infected_rep3

description: replicate 3


title: 129S1_heart_uninfected_rep1

description: replicate 1


title: IMO + FC, 2h after FC 3

description: 1mm punch used


title: RC112

description:
4609526016_B.AVG_Signal
Illumina Human Ref-8 BeadArray


title: 129S1_heart_uninfected_rep3

description: replicate 3


title: 129X1_heart_uninfected_rep2

description: replicate 2


title: Line13_rep2

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

description: Rice leaf blades of linalool accumulating transgenic rice, replicate2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays for 17 hours at 65 ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

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

organism: Oryza sativa Japonica Group

source_name: linalool accumulating transgenic rice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rice plants were grown from seed in growthchamber [25 ºC, 60 - 80% relative humidity (RH)].

extract_protocol: Total RNA from rice was extracted from leaf blades using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: No treatment.

tag: cultivar

value: Nipponbare

tag: leaf-stage

value: four-leaf

value: linalool accumulating transgenic rice

value: fourth-leaf blade


title: 129S1_heart_infected_rep1

description: replicate 1


title: Line13_rep3

description: Rice leaf blades of linalool accumulating transgenic rice, replicate3


title: 129X1_heart_infected_rep3

description: replicate 3


title: Line13_rep1

description: Rice leaf blades of linalool accumulating transgenic rice, replicate1


title: 129X1_heart_uninfected_rep1

description: replicate 1


title: 129X1_heart_infected_rep1

description: replicate 1


title: IMO + FC, 2h after FC 1

description: 1mm punch used


title: WT_rep3

description: Rice leaf blades of wild type rice, replicate3

source_name: WT rice

value: wild type


title: WT_rep2

description: Rice leaf blades of wild type rice, replicate2


title: GSY2546-150genCloneA-VesselA

city: Stanford

first: Barbara

last: Dunn

department: Genetics

institute: Stanford University

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82556.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: GSY86-Rep1-g150-FRY883-MB1-61genomic DNA, Hae III cut, 450 ng

value: whole genome

tag: developmental stage

tag: replicate


title: Mono culture type 1_mixed culture type 1 [chemostat cultures]

city: Brabrand

first: Sander

last: Sieuwerts

address: rørdrumvej 2

department: Arla Scientific Innovation Centre

country: Denmark

institute: Arla Foods

description:
Mono over Mixed
Mono culture L. bulgaricus RNA compared to mixed culture L. bulgaricus + S. cerevisiae RNA (chemostat cultures)

hyb_protocol: For each array, 0.3 µg of cDNA labeled with either Cyanine 3 or Cyanine 5 was hybridized using the solutions and following the protocol delivered by Agilent (version 5.5) for 8x15K slides.

scan_protocol: Slides were scanned using an Agilent microarray scanner (G2565BA). Lasers of wavelengths at 532 and 635 nm were used to excite Cyanine3 and Cyanine5 dyes, respectively. Fluorescent images were captured as multi-image-tagged image file format and analyzed with Imagene software (Axon) (BioDiscovery, Marina del Rey, USA).

data_processing: The extent of hybridization was derived from a median value of pixel-by-pixel ratios. Spots were normalized using Lowess. Differential regulation was determined by false-discovery rate (FDR) from the Cyber-T p-values by means of multiple testing connections. Differential regulation was defined as a two-fold or higher differential expression with a FDR cut-off value of 0.05 or lower. Biological replicates were pooled in the analysis.

source_name: Mono

label_protocol: Processing of RNA, labeling and hybridization were performed as in Appl.Environ.Microbiol. 76:7775-7784. Each sample was split in two after purification and the halves were labeled with cyanine3 and cyanine 5.

extract_protocol: L. bulgaricus total RNA from pure and mixed cultures was isolated as previously described (Appl.Environ.Microbiol. 76:7775-7784). 500 mg of 0.1 mm zirconium beads (Biospec Products Inc., OK, USA) were added to the extraction tubes to ensure efficient mechanical lysis of cells.

treatment_protocol: Sampling for transcriptome analysis from pure and mixed cultures was performed as previously described, using liquid nitrogen for rapid quenching of metabolism (J.Biol.Chem. 283:23524-23532). Samples were stored at -80°C in a mixture of phenol/chloroform and TEA buffer until further processing for total RNA extraction.

tag: culture type

value: Mono culture

tag: cultivation type

value: Chemostat

tag: experiment

value: Co-fermentation experiment

organism:
Lactobacillus delbrueckii subsp. bulgaricus
Saccharomyces cerevisiae

source_name: Mixed

value: Mixed culture


title: Mono culture type 2_mixed culture type 2 [batch cultures]

description:
Lbul mono over Lbul/Scer
Mono culture L. bulgaricus RNA compared to mono culture L. bulgaricus RNA mixed with mono culture S. cerevisiae RNA (batch cultures)

organism: Lactobacillus delbrueckii subsp. bulgaricus

source_name: Lbul mono

value: Batch

value: Reference to test cross-hybridisation

source_name: Lbul/Scer

value: Combined mono cultures of L. bulgaricus and S. cerevisiae


title: WT_rep1

description: Rice leaf blades of wild type rice, replicate1

tag: genotype/variation


title: Mixed culture type 1_mono culture type 1 [chemostat cultures]

description:
Mixed over Mono
Mixed culture L. bulgaricus + S. cerevisiae RNA compared to mono culture L. bulgaricus RNA (chemostat cultures)


title: GSY2535-200genCloneA-VesselC

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82534.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY86-Rep3-g200-FRY999-MB1-80genomic DNA, Hae III cut, 450 ng

tag: genotype


title: Mixed culture type 2_mono culture type 2 [batch cultures]

description:
Lbul/Scer over Lbul mono
Mono culture L. bulgaricus RNA  mixed with mono culture S. cerevisiae RNA compared to mono culture L. bulgaricus RNA (batch cultures)


title: GSY2552-200genCloneB-VesselC

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82551.gif

source_name: GSY86-Rep3-g200-FRY1000-MB1-81genomic DNA, Hae III cut, 450 ng


title: GSY2547-200genCloneB-VesselA

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82526.gif

source_name: GSY86-Rep1-200b-MB1-63genomic DNA, Hae III cut, 450 ng


title: miR-205 EB lli004

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene Chips (version 1.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were RMA summarized with Partek Genomics Suite 6.6

source_name: Arf-null ES cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: ES cell lines were derived from E3.5 embryos. EBs were generated by trypsinizing undifferentiated mouse ES cells and placing 300 cells into 50 ul hanging drops.  Two days later, aggregates were collected and cultured in ultralow attachment Petri dishes with EB culture medium, consisting of 90% Dulbecco’s modified Eagle’s medium (DMEM), 10% fetal bovine serum, 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine (all from Invitrogen), and 0.1 mM mercaptoethanol (Gibco). The medium was changed every other day.

extract_protocol: Used Trizol to extract RNA

treatment_protocol: Arf-null ES cells infected with a retroviral vector co-expressing miR-205 and GFP, or with a control vector expressing GFP alone, were maintained in the presence of LIF to forestall differentiation and sorted for GFP expression. Later cell lines infected with each vector were then deprived of LIF and cultured for four days to form EBs.  All ES and EB samples were collected for RNA extraction by Trizol method.

tag: day

tag: cell type

value: EB


title: GSY86-TimeZeroInoculum-VesselC

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82550.gif

source_name: GSY86-Rep3-Inoc-MB1-73genomic DNA, Hae III cut, 450 ng


title: miR-205 ES lli002

value: ES

tag: treatment

value: infected with a retroviral vector co-expressing miR-205 and GFP


title: adenocarcinoma-293

city: San Francisco

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

data_processing: Data normalized by quantile normalization with limma in R. Probes with present/absent call ≥ 0.05 assessed by Illumina Beadstudio software were treated as absent in analysis.

source_name: adenocarcinoma

label_protocol: Biotin-NTP mix with T7 enzyme mix was used to make biotinylated cRNAs. The labeled cRNAs were purified, quantified, and checked again with Bioanalyzer.

extract_protocol:
Samples were extracted from human patients during surgical resection of lung tumors.
RNA was extracted with Trizol followed by DNAse I treatment and purification (RNeasy RNA purification kit, Qiagen). The purified RNA was quantified with Nanodrop and checked by Bioanalyzer for the quality.

tag: Sex

value: M


title: GSY2532-200genCloneA-VesselA

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82530.gif

source_name: GSY86-Rep1-200a-MB1-62genomic DNA, Hae III cut, 450 ng


title: GSY2551-150genCloneB-VesselC

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82547.gif

source_name: GSY86-Rep3-150b-MB1-78genomic DNA, Hae III cut, 450 ng


title: adenocarcinoma-418

value: F


title: adenocarcinoma-338


title: GSY2533-200genCloneA-VesselB

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82604.gif

source_name: GSY86-Rep2-g200-19a-PB3-24 genomic DNA, Hae III cut, 450 ng


title: GSY86-TimeZeroInoculum-VesselsAandB

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82529.gif

source_name: GSY86-Rep1-2-Inoc-MB1-55genomic DNA, Hae III cut, 450 ng


title: GSY2548-150genCloneA-VesselB

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82606.gif

source_name: GSY86-Rep2-g150-14a-PB3-19 genomic DNA, Hae III cut, 450 ng


title: GSY2550-200genCloneC-VesselB

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82602.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY86-Rep2-g200-19c-PB3-26 genomic DNA, Hae III cut, 450 ng


title: adenocarcinoma-470


title: GFP control EB lli003

value: infected with a control vector expressing GFP alone


title: adenocarcinoma-195


title: adenocarcinoma-493


title: GFP control ES lli001


title: adenocarcinoma-753


title: adenocarcinoma-585


title: adenocarcinoma-373


title: GSY2549-150genCloneB-VesselB

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82605.gif

source_name: GSY86-Rep2-g150-14b-PB3-20 genomic DNA, Hae III cut, 450 ng


title: adenocarcinoma-544


title: Src-overexpression - replicate 2

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: mouse ventral prostate

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99C for 2 min. and then 45C for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

source_name: mouse ventral prostate

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: the transformed cell lines are already stable prostate cancer cell lines, so growing transformed cells in DMEM medium with 10% FBS, while control PEC cells were cultured in prostate epithelial primary culture medium, change to normal DMEM medium with 10% FBS one night before harvest.

treatment_protocol: no special treatment to the cells before harvest, collected the cells when the confluence 85-90%

value: FVB

tag: transduction

value: transformed by v-src gene

tag: tissue

value: Primary prostate epithelial cell culture, oncogene-transduced


title: Src-overexpression - replicate 3

description: mouse ventral prostate

tag: strain


title: adenocarcinoma-583

first: David


title: adenocarcinoma-312


title: adenocarcinoma-146


title: adenocarcinoma-267


title: adenocarcinoma-304


title: E14.5_male_gonad_Cyp26b1 knockout_rep1and2

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

institute: National Institute of Genetics

description: Gene expression E14.5 mouse male gonad Cyp26b1 knockout

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
All gene list of E12.5-15.5 wild type and E12.5-14.5 Cyp26b1-targeted male gonad
The following normalization steps were applied: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median.
Averaged normalized signal intensities and flag calling for all genes of wild type and Cyp26b1-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).

source_name: embryonic male gonad

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Embryonic gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: gonad

value: male

tag: embryonic day

tag: mouse line

value: MCH


title: adenocarcinoma-471


title: Ras-overexpression - replicate 1

description: mouse ventral prostate

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

value: transformed by ha-ras gene


title: E15.5_male_gonad_wild type_rep1and2

description: Gene expression E15.5 mouse male gonad wild type

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The following normalization steps were applied: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median.
Averaged normalized signal intensities and flag calling for all genes of wild type and Cyp26b1-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).

value: wild type


title: adenocarcinoma-102