title: miR-CLUS-99b/let-7e/125a_rep6 (B)

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

institute: University Medical Center Groningen

description: CLUS-6 (B)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Quantile normalization was applied on log2 transformed data. Set (A) and set (B) were analyzed separately.
Normalized matrix: GeneSpring GX 11.0-computed normalized signal intensity. Non-normalized matrix: GenomeStudio-computed raw signal intensity.

source_name: miR-cluster-99b/let-7e/125a -transduced EGFP+ BM

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s specifications starting with 100 ng total RNA.

growth_protocol: Primary BM cells were isolated from B6 mice 4 days post intraperitoneal injection of 150 mg/kg 5-fluorouracil (Pharmachemie Haarlem), and cultured in StemSpan (StemCell Technologies) supplemented with FCS, mouse stem cell factor (rmSCF; Peprotech), rmIL11 (R&D systems), Flt3 ligand (Amgen), penicillin and streptomycin. BM cells were transduced by transfecting Phoenix ecotropic packaging cells with 1-2 μg of pDNA (MXW empty vector, MXW-miR-cluster 99b/let-7e/125a, MXW-miR-125a and MXW-miR-155) and 3-6 μl Fugene HD (Roche). Virus-containing supernatant harvested 48 and 72 hours later was used to transduce 4-6x105 BM cells per 3.5 cm well. Five days after the first transduction, viable (negative for propidium iodide) EGFP+ cells were collected in RNA lysis buffer (Qiagen) for gene expression studies.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol.

value: Bone Marrow

tag: dataset

value: B


title: miR-125a_rep1 (B)

status: Public on Dec 15 2011

type: RNA

country: Netherlands

description: 125a-1 (B)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: miR-125a -transduced EGFP+ BM

tag: strain

tag: tissue


title: miR-125a_rep3 (B)

description: 125a-3 (B)


title: HPafII

type: genomic

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

country: USA

institute: University of California San Francisco

description: Common reference pool consists of genomic DNA from 8 normal individuals.

hyb_protocol: Agilent factory protocols.

scan_protocol: Agilent G2505C Microarray Scanner.

data_processing: Lowess normalization using Agilent Feature Extraction Software.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor DNA, cell line

label_protocol: Genomic DNA was digested with DpnII, randomly primed, and labeled with direct Cy dye-incorporated molecules.

growth_protocol: Xenografts were established as described: B. Rubio-Viqueira et al., Clin Cancer Res 12, 4652-61, Aug 1, 2006 (PMID: 16899615). Cell lines were grown under the recommended conditions of ATCC.

extract_protocol: DNA/RNA Allprep Kit (Qiagen 80204).

tag: sample source

value: cell line

tag: cell line

value: HPafII

tag: tissue derivation

value: pancreatic tumor

tag: disease state

value: pancreatic ductal adenocarcinoma (PDAC)

source_name: Common reference

value: normal


title: miR-155_rep2 (A)

description: 155-2 (A)

source_name: miR-155 -transduced EGFP+ BM

value: A


title: Colo357


title: miR-CLUS-99b/let-7e/125a_rep5 (B)

description: CLUS-5 (B)


title: miR-155_rep1 (A)

description: 155-1 (A)


title: SU86.86


title: Panc1


title: miR-CLUS-99b/let-7e/125a_rep4 (B)

description: CLUS-4 (B)


title: miR-CLUS-99b/let-7e/125a_rep3 (A)

description: CLUS-3 (A)


title: miR-125a_rep2 (B)

description: 125a-2 (B)


title: Hpac

value: Hpac


title: Miapaca2


title: Capan2


title: BxPC3


title: miR-CLUS-99b/let-7e/125a_rep2 (A)

description: CLUS-2 (A)


title: Empty_vector_rep5 (B)

description: EV-5 (B)

source_name: Empty vetor-transduced EGFP+ BM


title: SW1990


title: Empty_vector_rep6 (B)

description: EV-6 (B)


title: miR-CLUS-99b/let-7e/125a_rep1 (A)

description: CLUS-1 (A)


title: Empty_vector_rep4 (B)

description: EV-4 (B)


title: Cbp deficient LSK 1

city: Cambridge

first: Wai-In

last: Chan

address: Wellcome Trust/MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

description: Flow sorted LSK population of bone marrow from Cbp Mx mice, 4 weeks after pIpC treatment.

data_processing: Probes were first selected using the R package Lumi based on their detection p-values (p-value< 0.01 in Lumi in at least one sample). The data were then transformed using variance stabilization, followed by normalization using quantile normalization.

label: Biotin

source_name: Cbp deficient LSK

label_protocol: RNA was amplified and labelled using the Ovation RNA amplification system V2 (Nugen) according to manufacture's instructions.

extract_protocol: Total RNA was extracted from the LSK cells using Trizol reagent.

treatment_protocol: Cbp wt control and Cbp Mx mice (6-10 weeks old) were treated with pIpC to induce Cbp deletion in the hematopoietic system in vivo. BM were harvested from these mice 4 weeks after pIpC treatment. The LSK population was isolated by flow sorting.

tag: cell type

tag: genotype

value: Cbp Mx


title: Cbp deficient LSK 2

value: Flow sorted LSK population of bone marrow


title: Panc2.03


title: Empty_vector_rep1 (A)

description: EV-1 (A)


title: PL45


title: Wild type LSK 1

description: Flow sorted LSK population of bone marrow from Cbp wt mice, 4 weeks after pIpC treatment.

source_name: Wild type LSK

value: Cbp wt


title: Wild type LSK 2


title: Empty_vector_rep2 (A)

description: EV-2 (A)


title: 354

source_name: Tumor DNA, xenograft

value: xenograft


title: 697/USLAM

status: Public on Dec 16 2011

city: Huntsville

first: Devin

last: Absher

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Genomic DNA extracted from blood was genotyped using Infinium Human1MDuo Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genotypes and other intensity data were called and exported with Illumina GenomeStudio software

label: C-Bio and A-DNP

source_name: Blood DNA

label_protocol: 500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from peripheral blood with QIAGEN kits

tag: gender

value: male

tag: age


title: 421


title: 374


title: 163


title: JH27


title: PL5


title: PL4


title: JH15


title: 286


title: JH24


title: IKK2 -/- tumor, biological replicate 4

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

description: From finely dissected end stage lung tumor nodules

hyb_protocol: Fragmented cRNA are hybridized using a GeneChip Fluidics Station 450 in aGeneChip Hybridization Oven 640.

scan_protocol: Gene chips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene chips were analyzed using affymerix power tools using MAS 5 background correction, RMA probeset summarization, and median normalization (-a mas5-bg,med-norm,pm-only,med-polish).

source_name: IKK2 KO tumor

label_protocol: total RNA was labeled with the Ambion Affymetrix WT expression kit for Affymetrix whole transcript arrays, product #4411974.  Product number 4411974

extract_protocol: total RNA was harvested with Trizol according to manufacturer's instructions

value: tumor nodule cells

tag: ikk2 status


title: 247


title: Empty_vector_rep3 (A)

description: EV-3 (A)


title: IKK2 -/- tumor, biological replicate 1


title: 185


title: 430


title: IKK2 -/- tumor, biological replicate 3


title: IKK2 WT tumor, biological replicate 2

source_name: IKK2 WT tumor

value: WT


title: IKK2 WT cell line, biological replicate 1

description: cell lines were subcloned from WT and IKK2-/- primary tumors by serial dilution

source_name: IKK2 WT cell line

value: tumor-derived cell line


title: 410


title: 420


title: IKK2 -/- tumor, biological replicate 2


title: IKK2 WT tumor, biological replicate 3


title: 253


title: IKK2 WT tumor, biological replicate 4


title: IKK2 -/- cell line, biological replicate 2

source_name: IKK2 -/- cell line


title: IKK2 WT tumor, biological replicate 1


title: IKK2 -/- cell line, biological replicate 1


title: JH10


title: 287


title: 194


title: 140


title: JH11


title: A6L


title: 198


title: 281


title: 219


title: D2_Erythrocytes_(Ter119+)_rep3

scan_protocol: Slides were scanned at 5 μm resolution utilizing the Agilent eXtended Dynamic range function combining data from scans at 5% and 100% PMT power.

data_processing: Data were extracted using Agilent Feature Extraction Software version 9.5.3.1 and thresholded at 1, log2-transformed and normalized to the 75th percentile using GeneSpring GX11.0 (Agilent).

source_name: primary bone marrow

label_protocol: 100 ng of total RNA was labeled and hybridized to Agilent 8x15K Mouse miRNA arrays, based on version 11 release of Sanger Inst miRBASE. Labeling, hybridization and washing were performed by Oxford Gene Technology using the Agilent Mouse microRNA Microarray Kit.

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s protocol.


title: D2_Erythrocytes_(Ter119+)_rep2

hyb_protocol: Labeling, hybridization and washing were performed by Oxford Gene Technology using the Agilent Mouse microRNA Microarray Kit.


title: D2_Erythrocytes_(Ter119+)_rep1


title: transgenic PLN (T4)

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

hyb_protocol: as per GE Healthcare protocols

scan_protocol: as per GE Healthcare protocols

data_processing: Good and Low flagged normalized signals from CodeLink expression analysis were imported to genesifter for further analysis.

source_name: transgenic PLN

label_protocol: biotin-labeled cRNA synthesis, using the CodeLink Expression Assay Reagent Kit (GE Healthcare, USA).

growth_protocol: male FVB/N mice at 11 weeks of age

extract_protocol: Trizol extraction from frozen tissue

treatment_protocol: wilde type and transgenic mice

value: FVB/N

value: 11 weeks

value: whole heart


title: 159


title: Hs700T

value: cell line


title: JH21

value: pancreatic tumor


title: B6_Erythrocytes_(Ter119+)_rep2


title: 215

value: pancreatic ductal adenocarcinoma (PDAC)


title: transgenic PLN (T1)


title: B6_Erythrocytes_(Ter119+)_rep3


title: transgenic PLN (T6)


title: transgenic PLN (T5)


title: wild type (W5)

source_name: wild type


title: transgenic PLN (T3)


title: transgenic PLN (T2)


title: wild type (W4)


title: wild type (W6)


title: wild type (W2)


title: wild type (W3)


title: D2_Granulocytes_(Gr1+)_rep3


title: B6_Erythrocytes_(Ter119+)_rep1


title: D2_Granulocytes_(Gr1+)_rep2


title: HPDE

value: HPDE

value: normal


title: wild type (W1)


title: D2_Granulocytes_(Gr1+)_rep1


title: B6_Granulocytes_(Gr1+)_rep3


title: B6_Granulocytes_(Gr1+)_rep2


title: Panc05.04

scan_protocol: Agilent G2505C Microarray Scanner

data_processing: Agilent Feature Extraction Software

source_name: Tumor RNA

label_protocol: Agilent factory protocol -- Quick Amp labeling kit. Briefly, RNA was reverse transcribed to cDNA and subsequently underwent a round of in vitro transcription directly incorporated labeled Cy dyes during the process.

growth_protocol: Xenografts were established as described: B. Rubio-Viqueira et al., Clin Cancer Res 12, 4652 (Aug 1, 2006). Cell lines were grown under recommended conditions of ATCC

extract_protocol: DNA/RNA Allprep Kit (Qiagen 80204)

value: Cell Line

source_name: Common Reference

value: Pooled RNA from 11 diverse cancer cell lines


title: B6_Granulocytes_(Gr1+)_rep1


title: D2_Progenitors_(L-S-K+)_rep3


title: 235

value: Xenograft


title: D2_Progenitors_(L-S-K+)_rep2


title: 480


title: JH171


title: JH102


title: 443


title: JH82


title: 440


title: IKK2 WT cell line, biological replicate 2


title: 475


title: JH166


title: JH39


title: 472


title: D2_Progenitors_(L-S-K+)_rep1


title: 302


title: JH127


title: 486


title: JH131


title: B6_Progenitors_(L-S-K+)_rep2


title: PQ treated recG mutant Replicate 2

city: Seoul

first: Jinki

last: Yeom

address: Anam-Dong, Sungbuk-Gu

department: Life Science

country: South Korea

institute: Korea University

description: Biological replicate 2 of 2. P. putida KT2440 recG gene mutant cells, 0.5 mM PQ treated

hyb_protocol: Oligoarray control targets 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 an Agilent G2565AA scanner and Images were quantified using Agilent Feature Extraction Software (version A.7.5).

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

organism: Pseudomonas putida KT2440

source_name: Control

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: After growth at the early exponential (OD600 of approximately 0.2) phase at 30 ˚C with aeration, The cells were then untreated or treated with paraquat, 0.5 mM for 10 min

extract_protocol: Total RNA extracted using Qiagen RNA miniprep kit following manufacturer's instructions

tag: genotype/variation

value: wild type

tag: treatment

source_name: Total RNA from PQ treated P. putida KT2440 recG gene mutant cells

treatment_protocol: Cells are treated with PQ 0.5 mM

value: recG gene mutant

value: paraquat, 0.5mM


title: B6_Progenitors_(L-S-K+)_rep1


title: PQ treated recG mutant Replicate 1

description: Biological replicate 1 of 2. P. putida KT2440 recG gene mutant cells, 0.5 mM PQ treated


title: untreated recG mutant Replicate 2

description: Biological replicate 2 of 2. P. putida KT2440 recG gene mutant cells

source_name: Total RNA from untreated P. putida KT2440 recG gene mutant cells


title: D2_Stem cells_(LSK)_rep3

value: Stem cells_(LSK)


title: Aspc1


title: D2_Stem cells_(LSK)_rep2


title: Hs766T


title: JH29


title: JH161


title: D2_Stem cells_(LSK)_rep1


title: 470


title: JH51


title: PQ treated Replicate 1

description: Biological replicate 1 of 2. P. putida KT2440 cells, 0.5 mM PQ treated

growth_protocol: After growth at the early exponential (OD600 of approximately 0.2) phase at 30 ˚C with aeration, The cells were then treated with oxidative stress agents (paraquat, 0.5 mM; cumen hydroperoxide, 3 mM) for 10 min

source_name: Total RNA from PQ treated P. putida KT2440 cells

treatment_protocol: Cells are treated with PQ 0.5 mM; CHP, 3 mM for 10 min at 37 °C

value: paraquat, 0.5 mM


title: CHP treated Replicate 1

description: Biological replicate 1 of 1. P. putida KT2440 cells, 3mM CHP treated

source_name: Total RNA from CHP treated P. putida KT2440 cells

value: cumen hydroperoxide, 3mM


title: PQ treated Replicate 2

description: Biological replicate 2 of 2. P. putida KT2440 cells, 0.5 mM PQ treated


title: untreated recG mutant Replicate 1

description: Biological replicate 1 of 2. P. putida KT2440 recG gene mutant cells


title: B6_Stem cells_(LSK)_rep2


title: JH33

value: xenograft

source_name: Common reference


title: B6_Stem cells_(LSK)_rep1


title: 430


title: Panc3.27


title: Hpac

value: Hpac


title: B6_Stem cells_(LSK)_rep3


title: CFPAC1


title: HPafII

value: HPafII


title: 341


title: Capan1


title: Panc8.13


title: 479


title: Miapaca2


title: BxPC3


title: PL5


title: Panc1


title: SU86.86


title: Capan2


title: 421


title: Valproic_acid+Lithium_rep2

data_processing:
Quantile normalization was applied on log2-transformed data.
Normalized matrix: GeneSpring GX 11.0-computed normalized signal intensity on log2-transformed data. Non-normalized matrix: GenomeStudio-computed raw signal intensity.

source_name: 7-day cultured HSPCs with Lithium and Valproic Acid

growth_protocol: Freshly isolated hematopoietic stem/progenitor cells, defined by L-S+K+ phenotype, were differentiated in a liquid medium supplemented with fetal calf serum, murine stem cell factor and recombinant murine granulocyte/macrophage-colony stimulating factor. The cells were cultured for 7 days with or without 1mM VPA or 5mM LiCl or the combination. At day 7 the cells were collected in RNA lysis buffer (Qiagen) for gene expression studies.

value: Bone Marrow HSPC


title: 374

value: pancreatic tumor


title: Valproic_acid+Lithium_rep1


title: JH24

value: pancreatic ductal adenocarcinoma (PDAC)


title: Panc2.03


title: Valproic_acid_rep3

source_name: 7-day cultured HSPCs with Valproic Acid


title: 163


title: Valproic_acid+Lithium_rep3


title: JH27


title: 354


title: SW1990


title: Lithium_rep2

source_name: 7-day cultured HSPCs with Lithum


title: 420


title: 253


title: Lithium_rep3


title: JH15


title: 247


title: HL60 Gleevec-treated_F

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

country: Singapore

institute: National University of Singapore

scan_protocol: Scanner used: Illumina BeadArray Reader  Scanning protocol: Scan factor of 1, PMT525  Software: Illumina Beadscan version 3.0

data_processing: Data is extracted using Illumina Genomestudio version 2010.2, Expression Module version 1.7.0  Data were analyzed using Partek GS6.4 Ver 6.09.0922.   Normalization algorithm: RMA  Analysis was performed using ANOVA.

source_name: ATCC (CCL-240)

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in Roswell Park Memorial Institute medium (RPMI) supplemented with 10% heat inactivated fetal bovine serum (HIFBS) (Gibco, Invitrogen), 2mM L-glutamine (Gibco, Invitrogen) and 100U/ml penicillin and streptomycin (Gibco, Invitrogen).

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) with modifications. Cells were first washed with PBS twice and then lysed in TRIzol (Invitrogen) before purification using RNA extraction columns and buffers provided in the kit. The RNA concentration was quantified using Nanodrop (Thermo Scientific). 500ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion). Steps were carried out by following the instructional manual in the kit.

treatment_protocol: Gleevec-treated and non-treated cells.

value: Female

tag: disease

value: acute promyelocytic leukemia

value: BCR-ABL deficient

tag: agent

value: Gleevec


title: K562 Gleevec-treated_H

source_name: ATCC (CCL-243)

value: chronic myelogenous leukemia

value: BCR-ABL positive


title: Valproic_acid_rep1


title: Valproic_acid_rep2


title: 286

value: Xenograft

value: Pooled RNA from 11 diverse cancer cell lines

value: normal


title: 185


title: HL60 Control_E

value: Control


title: K562 Control_G


title: PL45

value: Cell Line


title: Growth_factors_only_rep3

source_name: 7-day cultured HSPCs with GFs only


title: Growth_factors_only_rep2


title: K562 Control_D


title: Lithium_rep1


title: HL60 Control_C


title: 410


title: Growth_factors_only_rep1


title: HL60 Gleevec-treated_A


title: Muscle_UnTrained_Male_Rep4

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

description:
PGEF-Untrained_1335
Gene expression data from a young healthy human subject.

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays (Santa Clara, CA) according to manufacturer's instructions. Following hybridization, the probe arrays were washed and stained.

scan_protocol: The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray Scanner, Agilent), and the stored images were analyzed using the GeneChip software Microarray Analysis Suite (MAS) 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Raw intensity values of all samples were preprocessed and normalized by RMA using Bioconductor. Differentially expressed genes were tested by using an intensity-based Bayesian moderated t-statistic.

source_name: Untrained biceps, male, 4h post-exercise

label_protocol: Total RNA was used as a template for double-stranded cDNA synthesis (Superscript Double-Stranded cDNA synthesis kit, Invitrogen, Carlsbad, CA). Biotin-labeledcDNA was synthesized (EnzoBioarray High Yield RNA transcription Labeling Kit, Affymetrix).

extract_protocol: Total RNA was extracted from frozen tissue with a polytron homogenizer (Brinkman, Westbury, NY) and Trizol reagent (Invitrogen, Rockville, MD), and purified with an RNAse kit (Qiagen, Santa Clara, CA).

value: biceps

value: male

value: healthy

tag: training status

value: untrained

tag: subject identifier


title: K562 Gleevec-treated_B


title: 287

value: pancreatic tumor


title: A6L

value: pancreatic ductal adenocarcinoma (PDAC)


title: 281


title: 215


title: JH11


title: Muscle_Trained_Male_Rep4

description:
Trained_1342
Gene expression data from a young healthy human subject.

source_name: Trained biceps, male, 4h post-exercise

value: trained


title: 159


title: JH33


title: Muscle_UnTrained_Male_Rep3

description:
UnTrained_1342
Gene expression data from a young healthy human subject.


title: 194


title: Muscle_Trained_Male_Rep3

description:
Trained_1330-1UP
Gene expression data from a young healthy human subject.


title: 219


title: 140


title: 198


title: Muscle_UnTrained_Male_Rep1

description:
UnTrained_1327
Gene expression data from a young healthy human subject.


title: P10014_3_rEDC

city: Gainesville

first: Peter

middle: J

last: Hansen

state: Florida

address: L.E. "Red" Larson Professor  Dept. of Animal Sciences  University of Florida

department: Animal Sciences

institute: University of Florida

description: in vitro produced embryos were transfered into receptors cows at Day 7 of development and recovered at Day 15 of embryo development - embrionic disc was isolated for global gene expression analysis

hyb_protocol: Hybridizations were set up using 2 µg of each sample (Cy3 and Cy5 components) for a total of 4 µg per array.  Volumes were brought to 44 µl with Diethylpyrocarbonate (DEPC)-water and then 11 µl of Agilent 10x GE Blocking Agent was added.  The mixtures were incubated at 98oC for 3 minutes and then cooled to room temperature for 5 minutes before adding 55 µl of Agilent 2x Hi-RPM Hybridization buffer.  Tubes were flash-spinned on a microfuge and lightly vortexed before loading 100 µl of the hybridization mixture onto each array. Hybridization was carried out for 17 h at 65°C and 10 rpm in a SureHyb gasket slide (Agilent). Washing and scanning procedures were carried out using standard Agilent guidelines for gene expression microarray processing.

scan_protocol: At the end of hybridization, microarray slides were sequentially washed using standard Agilent guidelines for gene expression microarray processing.  Microarray slides were scanned immediately using an Agilent G2505B scanner.

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710014_S01_GE2-v5_10_Apr08_1_3.txt

organism: Bos taurus

source_name: 16638ED (Control - ED)

label_protocol: samples of RNA (1.5-3.0 pg/µl) were concentrated to 5 µl using Savant SpeedVac (Therno Scientific) at low heat and amplified into ss-cDNA using the NuGEN WT-Ovation Pico RNA amplification System (NuGen Technologies, Inc, San Carlos, CA, USA) following manufacturer's instructions. Amplified ss-cDNA was purified using Zymo Spin IIC columns (Zymo Research, Orange, California, USA) and stored at -20 oC overnight. Product yield and purity were determined by the Nanodrop 1000 spectrophotometer assuming that 1 absorbance unit at 260 nm of ss-cDNA is equal to 33 µg/ml.  All 260/230 values were greater than 2.    Aliquots containing 2 µg of ss-cDNA were labeled with the Agilent Genomic DNA Enzymatic Labeling kit to incorporate cyanine 3- or 5-labeled CTP.  For half the replicates, ss-cDNA from control embryos was labeled with Cy3 and ss-cDNA from CSF2-treated embryos was labeled with Cy5. For the other replicates, control embryos were labeled with Cy 5 and CSF2-treated embryos with Cy3.

growth_protocol: Production of conceptuses: Cumulus oocyte complexes (COCs) from ovaries from a mixture of beef and dairy cattle were collected in Tissue Culture Medium-199 (TCM-199) with Hank’s salts without phenol red supplemented with 2% (v/v) bovine steer serum containing 2 U/ml heparin, 100 U/ml penicillin-G, 0.1 mg/ml streptomycin, and 1 mM glutamine. Oocytes were allowed to mature for 20-22 h in groups of 10 in 50 µl microdrops of TCM-199 with Earle’s salts supplemented with 10% (v/v) bovine steer serum, 2 µg/ml estradiol 17-µ, 20 µg/ml bovine follicle stimulating hormone, 22 µg/ml sodium pyruvate, 50 µg/ml gentamicin sulfate, and 1 mM glutamine. Matured oocytes were then washed in HEPES-TALP and transferred in groups of 50 to four-well plates containing 600 µL of IVF-TALP supplemented with 25 µL PHE (0.5 mM penicillamine, 0.25 mM hypotaurine, and 25 µM epinephrine in 0.9% [w/v] NaCl), and fertilized with 30 µL Percoll-purified spermatozoa (~ 1x106 sperm cells). Embryos were cultured at 38.5oC in a humidified atmosphere of 5% CO2, 5% O2, and 90% N2 (v/v).  At Day 5 after insemination, 5 µl of KSOM-BE2 or 5 µl of KSOM-BE2 containing 100 ng/ml recombinant bovine CSF2 (a gift from Novartis, Basle Switzerland) were added to each drop to achieve a final CSF2 concentration of 0 or 10 ng/ml.   Transfer into recipients: Morula, blastocyst and expanded blastocyst stage conceptuses classified as Grade 1 were harvested on Day 7 after insemination were transfered to thirty-five multiparous lactating Holstein cows were used as recipients. A total of 4 replicates were completed between June and October 2009 with 5-11 recipients per replicate. For each replicate, eligible cows were synchronized for embryo transfer as described previously.   Conceptus recovery: At Day 15 after expected ovulation, the ovary ipsilateral to the uterine horn that received the conceptus was examined using ultrasonography to confirm the presence of the corpus luteum. Cows that did not have a visible CL were not flushed. Conceptuses were recovered transcervically by flushing the uterine horn ipsilateral to the CL was flushed with Dulbecco’s phosphate-buffered saline (DPBS) with 1% (v/v) polyvinyl alcohol (PVA). The flushings recovered from the first 60 ml flush were centrifuged at 1000xg for 10 min and stored at -20oC for analysis of antiviral activity.  Conceptuses were washed once in DPBS-PVA and the conceptus was dissected to produce a piece of tissue containing the embryonic disc and some nearby extraembryonic membranes (termed here as embryonic disc) and two pieces of extraembryonic membranes that were on either end of the embryonic disc. Tissues were immediately snap frozen separately in liquid nitrogen.

extract_protocol: Microarray analysis was performed using a subset of 8 samples of embryonic disc and 8 samples of extraembryonic membranes from filamentous conceptuses (4 per treatment). Total cellular RNA was extracted with the RNeasy Plus Micro kit (Qiagen-Inc) following manufacturer’s instructions. Concentration of the input RNA was determined by Nanodrop 2000 spectrophotometer and RNA integrity was determined by use of the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples that showed high RNA integrity (RIN > 7) were used for the microarray hybridization and quantitative PCR analysis. Extracted RNA was stored at -80oC until microarray analysis.

value: embryonic disc


title: Muscle_UnTrained_Male_Rep2

description:
UnTrained_1330-1UP
Gene expression data from a young healthy human subject.


title: Type III

city: Omaha

first: Gautam

last: Malhotra

state: NE

address: 985805 Nebraska Medical Center

institute: UNMC

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 +2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: human mammary epithelial cells (TERT immortalized) K5+K19-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol from 200 ng total RNA.

growth_protocol: hTERT immortalized hMEC  stem/progenitor and myoepithelial cells  were grown in the DFCI-1, and MEGM  medium

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

treatment_protocol: No treatment. Logarithmically growing cells were collected for RNA extraction.

value: female reduction mammoplasty

value: Type III- K5-/K19- cell


title: P10014_2_rTFC

description: in vitro produced embryos were transfered into receptors cows at Day 7 of development and recovered at Day 15 of embryo development - extraembryonic membranes were isolated for global gene expression analysis

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710014_S01_GE2-v5_10_Apr08_1_2.txt

source_name: 20616TF (Control - TF)

treatment_protocol: At Day 5 after insemination, 5 µl of KSOM-BE2 or 5 µl of KSOM-BE2 containing 100 ng/ml recombinant bovine CSF2 (a gift from Novartis, Basle Switzerland) were added to each drop to achieve a final CSF2 concentration of 0 or 10 ng/ml.   Transfer into recipients: Morula, blastocyst and expanded blastocyst stage conceptuses classified as Grade 1 were harvested on Day 7 after insemination were transfered to thirty-five multiparous lactating Holstein cows were used as recipients. A total of 4 replicates were completed between June and October 2009 with 5-11 recipients per replicate. For each replicate, eligible cows were synchronized for embryo transfer as described previously.   Conceptus recovery: At Day 15 after expected ovulation, the ovary ipsilateral to the uterine horn that received the conceptus was examined using ultrasonography to confirm the presence of the corpus luteum. Cows that did not have a visible CL were not flushed. Conceptuses were recovered transcervically by flushing the uterine horn ipsilateral to the CL was flushed with Dulbecco’s phosphate-buffered saline (DPBS) with 1% (v/v) polyvinyl alcohol (PVA). The flushings recovered from the first 60 ml flush were centrifuged at 1000xg for 10 min and stored at -20oC for analysis of antiviral activity.  Conceptuses were washed once in DPBS-PVA and the conceptus was dissected to produce a piece of tissue containing the embryonic disc and some nearby extraembryonic membranes (termed here as embryonic disc) and two pieces of extraembryonic membranes that were on either end of the embryonic disc. Tissues were immediately snap frozen separately in liquid nitrogen.

value: trophectoderm


title: Muscle_UnTrained_Female_Rep3

description:
PGEF-Untrained_1340
Gene expression data from a young healthy human subject.

source_name: Untrained biceps, female, 4h post-exercise

value: female


title: P10014_1_rEDC

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710014_S01_GE2-v5_10_Apr08_1_1.txt

source_name: 20616ED (Control - ED)


title: P10013_4_rEDT

description: in vitro produced embryos  that were treated with CFS2 at Day 5 of development for 24 h, transfered into receptors cows at Day 7 and recovered at Day 15 of embryo development - embrionic disc was isolated for global gene expression analysis

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710013_S01_GE2-v5_10_Apr08_1_4.txt

source_name: 18893ED (Treatment - ED)


title: P10013_2_rTFT

description: in vitro produced embryos  that were treated with CFS2 at Day 5 of development for 24 h, transfered into receptors cows at Day 7 and recovered at Day 15 of embryo development - extraembryonic membranes were isolated for global gene expression analysis

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710013_S01_GE2-v5_10_Apr08_1_2.txt

source_name: 19415TF (Treatment - TF)


title: JH10

source_name: Tumor RNA

value: Xenograft

source_name: Common Reference


title: Hs700T

value: Pooled RNA from 11 diverse cancer cell lines


title: Muscle_Trained_Female_Rep3

description:
PGEF-Trained_1340
Gene expression data from a young healthy human subject.

source_name: Trained biceps, female, 4h post-exercise


title: HPDE

value: HPDE

value: normal


title: Muscle_UnTrained_Female_Rep2

description:
PGEF-Untrained_1333
Gene expression data from a young healthy human subject.


title: P10013_3_rTFT

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710013_S01_GE2-v5_10_Apr08_1_3.txt

source_name: 18893TF (Treatment - TF)


title: P10014_4_rEDT

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710014_S01_GE2-v5_10_Apr08_1_4.txt

source_name: 20449ED (Treatment - ED)


title: Muscle_Trained_Male_Rep2

description:
Trained_1327
Gene expression data from a young healthy human subject.


title: JH21


title: Muscle_UnTrained_Female_Rep1

description:
PGEF-Untrained_1324
Gene expression data from a young healthy human subject.


title: P10014_3_gTFC

source_name: 16638TF (Control - TF)


title: Muscle_Trained_Female_Rep2

description:
PGEF-Trained_1333
Gene expression data from a young healthy human subject.


title: Muscle_Trained_Male_Rep1

description:
PGEF-Trained_1335
Gene expression data from a young healthy human subject.


title: cKit- Oct4- somatic rep 1

city: Los Angeles

first: John

last: Vincent

address: 621 Charles E Young Dr. S

department: MCDB

institute: UCLA

description: Gene expression of in vitro somatic cells

hyb_protocol: Hybridization to Afftmetrix mouse 430 v2 chips and was performed as recommended by manufacturer.  Arrays were washed and stained with streptavidin phycoerythrin in Affy Fluidics Station 450using Affymetrix GeneChip protocol.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 30007G using manufacturer's recommended protocol.

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.

source_name: Oct4-gfp derived somatic

label_protocol: RNA was prepared usng Nu-GEN Ovation Pico WTA System and FL-Ovation cDNA Biotin Module V2.

growth_protocol: Cells were grown for three to six days under 37C, 5% CO2  and harvest via FACS at room temperature.

extract_protocol: Cells were collected in RLT Buffer and RNA isolated with the Qiagen Rneasy micro Kit.

treatment_protocol: Cells were dissociated using 0.05% trypsin, subjected to FACS sorting

value: in vitro cKit- Oct4- somatic

tag: genetic background

value: mixed


title: cKit+ Oct4+ iPGC rep 2

description: Gene expression of in vitro PGC

source_name: Oct4-gfp derived PGC

value: in vitro cKit+ Oct4+ iPGC


title: cKit- SSEA- somatic rep 1

source_name: V6.5 derived somatic

value: in vitro cKit- SSEA- somatic


title: P10013_4_gTFC

source_name: 19871TF (Control - TF)

tag: tissue


title: cKit+ SSEA+ iPGC rep 2

description: Gene expression of in vitro PGC

source_name: V6.5 derived PGC

value: in vitro cKit+ SSEA+ iPGC


title: cKit+ SSEA+ iPGC rep 1

description: Gene expression of in vitro PGC


title: Muscle_Trained_Female_Rep1

description:
PGEF-Trained_1324
Gene expression data from a young healthy human subject.

value: biceps

value: healthy


title: P10014_4_gTFT

source_name: 20449TF (Treatment - TF)


title: P10013_1_rTFC

data_processing:
Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes.  The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed

raw data is green channel in US83800208_252364710013_S01_GE2-v5_10_Apr08_1_1.txt

source_name: 19474TF (Control - TF)


title: undifferentiated cKit+ SSEA+ ESC rep 2

description: Gene expression of undifferentiated ESCs

source_name: V6.5 ESC

value: undifferentiated cKit+ SSEA+ ESC


title: P10013_3_gEDC

source_name: 19871ED (Control - ED)

value: embryonic disc


title: P10014_1_gEDT

source_name: 21288ED (Treatment - ED)


title: cKit- Oct4- somatic rep 2

value: intro cKit- Oct4- somatic


title: P10014_2_gTFT

source_name: 21288TF (Treatment - TF)


title: cKit+ Oct4+ iPGC rep 1

description: Gene expression of in vitro PGC


title: P10013_2_gEDT

source_name: 19415ED (Treatment - ED)


title: undifferentiated cKit+ SSEA+ ESC rep 1


title: Time_24h_minus-C_v_Time_24h_plus-C

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis protocol version 6.0

scan_protocol: Scanned using an Agilent DNA Microarray Scanner according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol, version 6.0.

data_processing: Image analysis was performed with Agilent Feature Extraction. Data was normalized and differential expression statistics generated using the VERA/SAM pipeline (see http://db.systemsbiology.net/software/ArrayProcess/index.html)

label: Alexa 647

organism: Trypanosoma brucei

label_protocol: Labeled cDNA probes were created from 2μg of total RNA using the SuperScript indirect cDNA labeling kit. Unincorporated nucleotides were removed by QuickClean resin and the resulting cDNA was ethanol precipitated overnight at -20°C. Control and experimental samples were labeled with Alexa Fluor 555 and 647, respectively, and purified using the cDNA labeling purification module. Equal amounts of labeled control and experimental samples were combined. Microarray hybridization and washing were conducted as described previously (Wan et al., 2009).

growth_protocol: Expression of plasmid constructs was maintained using antibiotic selection at the following concentrations: G418 and hygromycin B at Trypanosoma brucei brucei MITat 1.2 (M221 strain) and PCF T. b. brucei MITat 1.2 (Lister 427) were grown at 37°C with 5% CO2 in Hirumi medium (HMI-9) or at 27°C in semi-defined medium (SDM-79) respectively with supplements as previously described (Brun and Schonenberger, 1979; Hirumi H, 1994). Single marker BSF (SMB) and PTT PCF lines were used for expression of tetracycline-inducible constructs (Wirtz et al., 1999).  1μg/ml and phleomycin at 0.1 μg/ml for BSF, G418 at 15 μg/ml, hygromycin B at 25 μg/ml, and phleomycin at 5 μg/ml for PCF.

extract_protocol: Cells were harvested at 800 × g for 10 min at 4°C, washed with cold PBS, and frozen in dry ice for 1 minute. RNA was purified using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA concentration was quantified using a ND-1000 spectrophotometer and Nanodrop software (Nanodrop Technologies).

treatment_protocol: RNAi line EATRO 795 2913 MVSG1.22->EGFP was obtained by consecutive transfections of EATRO795 PCF cells with pLew13, pLew29 and with the cassette replacing MVSG 1.22 open reading frame with eGFP. PLK, ATPaseAF, clathrin, and TbNUP-1 were depleted by RNAi in this line. 3 independent RNAi lines were examined for each gene.

tag: time point

value: 24 hour

value: untreated

label: Alexa 555

value: RNAi


title: Fg_24h_BR3_cy3

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: 24h SA treatment. Technical rep 2. Biorep 3 of 3

hyb_protocol: Hybridizations were incubated overnight at 65ºC in a Robbins 400 oven outfitted with a Hybridization Oven Rotator (Agilent G2530-60029). Slides were washed as described in the Supplemental Procedures: Wash with Stabilization and Drying Solution.

scan_protocol: Slides were scanned on the Genepix4200a (Molecular Devices) at 5µ resolution. Images were quantified using Genepix Pro 6.0 (Molecular Devices)

data_processing: Array results files (.gpr) were imported in Acuity 4.0 and Lowess M log ratio normalized. A dataset was formed with all arrays. Features that had Lowess A intensities lower that 7.5 in at least 50% of the arrays were removed. Spike-in controls were removed. Cy3 test array data were swapped to cy5. Candidate genes that were significantly differentially expressed were identifed using the following cut-off parameters: t-test p-value<0.05 and fold changes >2 in expression rations (SA vs control), and signal value>1000.

organism: Fusarium graminearum

source_name: Liquid Fg culture untreated for 24h biorep 3

label_protocol: 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.

growth_protocol: 100ml PDB (potato dextrose broth) media was inoculated with ground Fusarium graminearum mycelia (strain DAOM 180378; about 1/4 of the ground mycelia scrapped from a confluent PDA plate), grown for 40hrs at 28ºC and 170 rpm, then supplemented with salicylic acid (test samples) or not (reference samples) and grown for an additional 8h or 24h.

extract_protocol: Mycelia were harvested by vacuum filtration and ground in liquid nitrogen. Total RNA was extracted using the guanidine isothiocyanate-cesium chloride method (Ohan and Heikkila, 1995).

treatment_protocol: After initial 40h growth, 300 ul of 1 M Salicylic Acid in methanol was added to the test samples and 300 ul of methanol was added to the reference samples and the cultures grown for an additional 8h and 24h prior to sampling.

tag: strain

value: untreated, incubated for 24h

source_name: Liquid Fg culture treated with SA for 24h biorep 3

value: treated with SA for 24h


title: Time_48h_minus-C_v_Time_48h_plus-C

value: 48 hour


title: Time_24h_plus-B_v_Time_24h_minus-B


title: Fg_24h_BR3_cy5

description: 24h SA treatment. Technical rep 1. Biorep 3 of 3


title: Time_24h_minus-B2_v_Time_24h_plus-B2


title: STAT1-/- tumor, primary, mouse 4

city: St Louis

first: Szeman

middle: Ruby

state: MO

address: 425 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from a primary STAT1-/- mammary tumor.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000.

data_processing: The data was analyzed with dChip using default analysis settings.

source_name: primary STAT1-/- mammary tumor

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: Female STAT1-/- mice were monitored until palpable mammary adenocarcinomas developed. Tumors around 1 cm in diameters were harvested and processed for gene expression analysis.

value: 129 Sv/Ev

tag: cancer type

value: mammary adenocarcinoma


title: STAT1-/- tumor, primary, mouse 3


title: Time_12h_minus-C_v_Time_12h_plus-C

value: 12 hour


title: STAT1-/- tumor, primary, mouse 6


title: Time_12h_minus-B2_v_Time_12h_plus-B2


title: Time_48h_plus-B_v_Time_48h_minus-B


title: Time_12h_plus-B_v_Time_12h_minus-B


title: Time_6h_minus-C_v_Time_6h_plus-C

value: 6 hour


title: P10013_1_gTFC

source_name: 12077TF (Control - TF)

value: trophectoderm


title: Fg_24h_BR2_cy3

description: 24h SA treatment. Technical rep 2. Biorep 2 of 3

source_name: Liquid Fg culture untreated for 24h biorep 2

source_name: Liquid Fg culture treated with SA for 24h biorep 2


title: STAT1-/- tumor, primary, mouse 1


title: Fg_24h_BR1_cy5

description: 24h SA treatment. Technical rep 1. Biorep 1 of 3

source_name: Liquid Fg culture treated with SA for 24h biorep 1

source_name: Liquid Fg culture untreated for 24h biorep 1


title: STAT1-/- tumor, primary, mouse 2


title: genomic DNA of HCT116 DKO cells (r2)

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Colorectal cancer cell line knock-out for DNMT1 and DNMT3B
Sample_5.AVG_Beta

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD  Methylation Assay protocol.

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

data_processing: GenomeStudio software v2010.3, Methylation module v1.8.5

label: Cy5 and Cy3

source_name: Colon

label_protocol: Standard Infinium HD Methylation Assay protocol

growth_protocol: HCT116 cells were maintained in McCoy's 5A medium (Gibco BRL) supplemented with 10% fetal bovine at 37°C under 5% CO2.

extract_protocol: Genomic DNA was extracted and purified from HCT116 cells using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

tag: cell line

value: DNMT1 and DNMT3B double KO


title: Fg_24h_BR1_cy3

description: 24h SA treatment. Technical rep 2. Biorep 1 of 3


title: genomic DNA of HCT116 WT cells (r2)

description:
Colorectal cancer cell line
Sample_2.AVG_Beta

value: wild type


title: genomic DNA of HCT116 DKO cells (r3)

description:
Colorectal cancer cell line knock-out for DNMT1 and DNMT3B
Sample_6.AVG_Beta


title: Fg_24h_BR2_cy5

description: 24h SA treatment. Technical rep 1. Biorep 2 of 3


title: Nic 4.5mg/kg/day, biological rep2

city: Lincoln

first: Ali

last: Nawshad

address: 40th and Holdrege

department: Oral Biology

institute: Unviersity of Nebraska Medical Center

description: Gene expression data from 4.5mg/kg/day nicotine-treated fetuses

hyb_protocol: The GeneChip arrays are hybridized overnight in the Affymetrix hybridization oven at 42oC. The Affymetrix GeneChip Fluidics Station 450 performs the automated Affymetrix wash and stain protocols.

scan_protocol: The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image

data_processing: Scanned array images were analyzed by dChip applying a smoothing spline normalization method prior to obtaining model-based gene expression indices, a.k.a. signal values. There were no outliers identified by dChip, so all samples were carried on for subsequent analysis. When comparing two groups of samples to identify enriched genes in a given group, we used the lower confidence bound (LCB) of the fold change (FC) between the two groups as the cut-off criteria. If 90% LCB of FC between the two groups was above 1.2, the corresponding gene was considered to be differentially expressed.

source_name: Mouse newborn palate

label_protocol: The UNMC Microarray Core uses a variety of commercially available assays for generating biotin-labeled samples for hybridization to Affymetrix GeneChip

growth_protocol: A small incision of 0.5 cm was made in the skin posterior to the shoulder of pregnant mice and an osmotic mini-pump (Model 1004 - Alzet Corp, CA) was implanted subcutaneously. The incision was closed with a wound clip and covered with an antibiotic. The clip was removed after 14 days and dams were allowed to give birth naturally at/around 21 days

extract_protocol: Total RNA was isolated from the posterior one-third of palatal tissues from newborn pups (n=2) using the RNeasy spin column RNA purification kit (Qiagen)

treatment_protocol: Sterile physiological saline or nicotine (1.5 mg/kg/day, 3.0 mg/kg/day, or 4.5 mg/kg/day)

value: Newborn Palate

value: BALB/c

value: Newborn - P1

value: 4.5mg/kg/day nicotine-treated fetuses


title: Time_48h_plus-A_v_Time_48h_minus-A


title: Fg_8h_BR3_cy3

description: 8h SA treatment. Technical rep 2. Biorep 3 of 3

source_name: Liquid Fg culture untreated for 8h biorep 3

value: untreated, incubated for 8h

source_name: Liquid Fg culture treated with SA for 8h biorep 3

value: treated with SA for 8h


title: cKit- SSEA- somatic rep 2

source_name: V6.5 derived somatic

tag: cell type

value: in vitro cKit- SSEA- somatic


title: genomic DNA of HCT116 WT cells (r3)

description:
Colorectal cancer cell line
Sample_3.AVG_Beta

tag: genotype


title: Nic 3.0mg/kg/day, biological rep1

description: Gene expression data from 3.0mg/kg/day nicotine-treated fetuses

value: 3.0mg/kg/day nicotine-treated fetuses


title: genomic DNA of HCT116 WT cells (r1)

description:
Colorectal cancer cell line
Sample_1.AVG_Beta


title: genomic DNA of HCT116 DKO cells (r1)

description:
Colorectal cancer cell line knock-out for DNMT1 and DNMT3B
Sample_4.AVG_Beta


title: Nic 4.5mg/kg/day, biological rep1


title: Nic 3.0mg/kg/day, biological rep2


title: Time_24h_plus-A_v_Time_24h_minus-A

value: 24 hour

value: RNAi

value: untreated


title: Time_12h_plus-A_v_Time_12h_minus-A


title: Time_6h_plus-B_v_Time_6h_minus-B


title: Time_6h_plus-A_v_Time_6h_minus-A


title: MDM-LPS

status: Public on Dec 14 2011

city: Philadelphia

first: Julio

last: Martin-Garcia

state: PA

department: Microbiology and Immunology

institute: Drexel University College of Medicine

description: monocytes differentiated in vitro into MDMs with M-CSF for 7 days were treated with 10 mg/ml LPS for 16 hours before total RNA isolation

hyb_protocol: All hybridization was performed in automated hybridization stations with slow mixing mechanism. GenoExplorer microRNA arrays - human (GenoSensor Corporation, Tempe, AZ; containing probes in triplicate for most validated human mature miRNAs and validated human pre-miRNAs along with positive and negative control probes, all in triplicate) were used for hybridization. One miRNA microarray chip hybridization was performed per sample. The reaction was incubated at 42oC for 16 hours. The array was then stained by streptavidin-Cy5 dye. After washes, the arrays were dried and scanned.

scan_protocol: Arrays were scanned using Axon 4000B. Raw data with signal intensity were analyzed by GenePix software.

data_processing: Raw intensity values for each of the three probes for every miRNA or control were averaged and standard deviation was also calculated. Array background was calculated as the average of signal intensity of all negative controls and buffers, and a signal threshold was determined by array background + 2x background's standard deviation, for each array; only averaged miRNA intensities higher than the signal threshold were considered. Validated raw data were background subtracted and then normalized to account for the differences in individual hybridization intensities on each array chip dividing by the average of all positive control probe signals.

source_name: human MDMs from a healthy donor

label_protocol: Total RNA (a minimum of 1µg) was labeled using GenoExplorer microRNA labeling kit (GenoSensor, Tempe, AZ). Briefly, a biotinylated adaptor is labeled at the 5'end of miRNA and other non-capped small non-coding RNA. The reaction was incubated at 20oC for 2 hours. The labeled samples were then used for hybridization.

growth_protocol: monocytes were differentiated in vitro into MDMs with 16 U/ml M-CSF for 7 days, and then were either untreated or treated with a TLR ligand for 16 hours before total RNA isolation using Trizol

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) following manufacturer's instructions; total RNA samples were sent to GenoSensor Corp. for their GenoExplorer MicroRNA Expression full-analysis service

treatment_protocol: After differentiation, MDMs were either untreated or treated with a TLR ligand (Invivogen; used at their manufacturer's recommended optimal concentration) for 16 hours before total RNA isolation

value: primary monocyte-derived macrophages

value: LPS

tag: in vitro treatment

value: stimulation through TLR4


title: Fg_8h_BR1_cy3

description: 8h SA treatment. Technical rep 2. Biorep 1 of 3

source_name: Liquid Fg culture untreated for 8h biorep 1

source_name: Liquid Fg culture treated with SA for 8h biorep 1


title: MDM-Imiquimod

description: monocytes differentiated in vitro into MDMs with M-CSF for 7 days were treated with 5 mg/ml Imiquimod for 16 hours before total RNA isolation

value: Imiquimod

value: stimulation through TLR7


title: Time_0h-A1_v_Time_0h-B1

value: 0 hour


title: Fg_8h_BR2_cy5

description: 8h SA treatment. Technical rep 1. Biorep 2 of 3

source_name: Liquid Fg culture treated with SA for 8h biorep 2

source_name: Liquid Fg culture untreated for 8h biorep 2


title: MDM-unstimulated

description: monocytes differentiated in vitro into MDMs with M-CSF for 7 days were left untreated for 16 hours before total RNA isolation

value: unstimulated


title: Fg_8h_BR3_cy5

description: 8h SA treatment. Technical rep 1. Biorep 3 of 3


title: Nic 1.5mg/kg/day, biological rep2

description: Gene expression data from 1.5mg/kg/day nicotine-treated fetuses

value: Newborn Palate

value: BALB/c

tag: age

value: 1.5mg/kg/day nicotine-treated fetuses


title: Time_0h-B1_v_Time_0h-A1


title: Nic 1.5mg/kg/day, biological rep1

value: Newborn - P1


title: Saline control, biological rep1

description: Gene expression data from saline-treated fetuses

value: saline-treated fetuses


title: Fg_8h_BR2_cy3

description: 8h SA treatment. Technical rep 2. Biorep 2 of 3

value: untreated, incubated for 8h

value: treated with SA for 8h


title: Saline control, biological rep2


title: Pb01_M-to-Y_Control-untreated_216 h_flask1_rep1

city: San Jose

first: Jata

last: Shankar

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description:
13237616_C_216_F1
Flask1_rep1. Control, Pb01 M-to-Y, 216 h

hyb_protocol: Cy3-labeled samples were competitively hybridized against the Cy5-labeled reference sample on a pre-hybridized microarray slide (random shear gDNA microarray (Monteiro, Clemons et al. 2009)). cDNA labeling and pre-hybridization procedures were followed as previously described (Monteiro, Clemons et al. 2009). Samples of labeled cDNA for hybridization were concentrated using a Microcon® YM-30 Centrifugal Filter Device (Millipore) and suspended to 40 μl with 3X saline-sodium citrate buffer (SSC; Sigma-Aldrich, St. Louis, MO), 0.1% sodium dodecyl sulfate (SDS; Sigma-Aldrich).  These samples were preincubated at 100o C for 2 minutes, 37oC for 15-25 minutes, transferred onto a microarray slide, covered with a cover glass and placed in hybridization chambers. Hybridization was carried out at 50o C for 14 to 18 hours followed by washing, in order, with 2X SSC with 0.03%SDS, 2X SSC, 1X SSC and 0.2X SSC for 2-5 minutes in each solution. Slides were dried by centrifugation and scanned within 24 hours. All hybridization experiments were done in duplicate using samples from each of two independent cultures.

scan_protocol: Scanner settings used 10 µm pixel size and photomultiplier tube gains for both detection channels, 635 nm (Cy5-red color) and 532 nm (Cy3-green color), were 540 and 500, respectively (GenePix® 4000B Microarray Scanner, Axon Instruments, Union City, CA).

data_processing:
Cited Bibliography: Stover, E. P., G. Schar, et al. (1986). Estradiol-binding proteins from mycelial and yeast-form cultures of Paracoccidioides brasiliensis. Infect. Immun. 51(1): 199-203. Clemons, K. V., D. Feldman, et al. (1989). Influence of oestradiol on protein expression and methionine utilization during morphogenesis of Paracoccidioides brasiliensis. J Gen Microbiol 135(6): 1607-17.                                                                                Monteiro, J. P., K. V. Clemons, et al. (2009). Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro. Microbiology 155(Pt 8): 2795-808.                                                                                Gentleman, R. C., V. J. Carey, et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10): R80.         Smyth, G. K. and T. Speed (2003). Normalization of cDNA microarray data. Methods 31(4): 265-73.                                                                                Ritchie, M. E., J. Silver, et al. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23(20): 2700-7. Kauffmann, A., R. Gentleman, et al. (2009). arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics 25(3): 415-6.  Huber, W., A. von Heydebreck, et al. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl 1: S96-104.
Microarray hybridizations were imaged using a GenePix scanner and images were processed using GenePix Pro 6.1.0.4 software.  GenePix files were imported into R/Bioconductor (Gentleman, Carey et al. 2004), using the limma package (Smyth and Speed 2003), removing spots having quality flags of -50 or less. Analysis of array backgrounds revealed evidence of spatial gradients, so background correction was applied to each array using the normexp method with an offset of 50 (Ritchie, Silver et al. 2007). We applied the arrayQualityMetrics package  (Kauffmann, Gentleman et al. 2009).  We normalized between arrays using variance stabilization from the vsn package (Huber, von Heydebreck et al. 2002), allowing for 20 percent outliers. We then normalized within arrays using loess to remove non-linearity from the MA curves (M and A are defined as: M = log2 (I1) - log2 (I2), A = 1/2 (log2 (I1) + log2 (I2)), where I1 and I2 are the intensities of the two channels).
We obtained standardized log2 ratios by dividing the log2 ratios of each array by its median absolute deviation (Cy3/Cy5=test/reference).

organism: Paracoccidioides lutzii Pb01

label_protocol: Total RNA (48 µg) was used for cDNA synthesis using anchored oligo-dT (5’ TTT TTT TTT TTT TTT TTT TTV N 3’). Fluorescently labeled cDNA was made by incorporating Cy5 or Cy3 labeled dUTP during reverse transcription of poly-adenylated (PolyA) mRNA. An equal amount of total RNA from untreated controls from each time-point was pooled to generate a Cy5-labeled cDNA reference sample.  Samples from each time point were individually labeled with Cy3.

growth_protocol: Mycelial (M) culture filtrate was filter sterilized from MVM broth cultures (Pb01) after 2-4 weeks of growth at 25°C on a gyrator shaker at 150 r.p.m. and stored at 4°C for use as a growth supplement. M spent culture medium used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as described previously for the growth of M liquid cultures (Stover, Schar et al. 1986; Clemons, Feldman et al. 1989). Two-week-old M slants were used to inoculate 300 ml of supplemented liquid MVM media and liquid cultures were grown for 8 d on a gyratory shaker at 150 r.p.m. at 25°C.

extract_protocol: Fungal cells were thawed in TRIzol reagent (Invitrogen, Carlsbad, CA) followed by cell disruption with 0.5 mm zirconia/silica beads (Biospec) using a BeadBeater apparatus (Biospec Products, Inc., Bartlesville, OK) using a high speed setting (3 pulses of 12-15 sec). Total RNA was extracted using TRIzol reagent per the manufacturer’s instructions. Contaminating gDNA was removed per the manufacturer’s instructions using an RNeasy mini spin column (RNeasy mini kit, Qiagen Science, MD, USA) and an RNase-free DNase set (50) (Qiagen, GmbH, Hilden). The quantity and quality of the extracted RNA were assessed by A260nm/A280nm ratio as well as by electrophoresis through a 1.5% agarose gel stained with ethidium bromide for the presence of intact 18S and 28S ribosomal RNA bands, visualized by UV transillumination at 302 nm.

treatment_protocol: After the 8 d growth period, E2 (17β-estradiol; Steraloids, Newport, RI, USA) at a final concentration of 2.6×10-7 M in 0.1% absolute ethanol or ethanol alone (final concentration 0.1%) was added to M-phase cultures.  Morphological transition from M-to-Y was induced by increasing the incubation temperature from 25°C to 37°C. Samples from 8 d old M cultures were collected, before adding E2 or ethanol alone and served as the 0 h time point. After temperature switch, samples were harvested from untreated controls, ethanol alone-treated controls or E2-treated cultures at 4 h, 12 h, 24 h, 72 h, 144 h, or 216 h time points by centrifugation at 1500 r.p.m. for 10 minutes followed by snap-freezing of the fungal mass in liquid nitrogen. These samples were stored at -80°C until RNA extraction was performed.

tag: isolate

value: Pb01 (ATCC:MYA-826)

tag: morphologic form

value: M-to-Y

tag: sample

value: M-to-Y, 216 h, Untreated-Control

tag: growth

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then, swtiched to 37°C

source_name: Pb01 (Mycelial form plus M-to-Y transition forms)

tag: morphology

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m

tag: rna source

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: Pb01_M-to-Y_E2-treated_144 h_flask2_rep2

description:
13235619_E2_144_F2
Flask2_rep2. E2-treated, Pb01  M-to-Y, 144 h

value: M-to-Y, 144 h, E2-treated


title: Pb01_M-to-Y_Control-untreated_216 h_flask1_rep2

description:
13237617_C_216_F1
Flask1_rep2. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_Control-untreated_216 h_flask2_rep2

description:
13237779_C_216_F2
Flask2_rep2. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_E2-treated_216 h_flask1_rep2

description:
13238425_E2_216_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 216 h

value: M-to-Y, 216 h, E2-treated


title: Pb01_M-to-Y_Control-untreated_216 h_flask2_rep1

description:
13235638_C_216_F2
Flask2_rep1. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_E2-treated_216 h_flask1_rep1

description:
13238424_E2_216_F1
Flask1_rep1. E2-treated, Pb01 M-to-Y, 216 h


title: Pb01_M-to-Y_E2-treated_216 h_flask2_rep1

description:
13235639_E2_216_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_Control-ethanol-treated_216 h_flask1_rep2

description:
13238421_OH_216_F1
Flask1_rep2. Control, Pb01  M-to-Y, 216 h

value: M-to-Y, 216 h, ethanol-treated-Control


title: Fg_8h_BR1_cy5

description: 8h SA treatment. Technical rep 1. Biorep 1 of 3

tag: treatment


title: Pb01_M-to-Y_E2-treated_144 h_flask1_rep2

description:
13237589_E2_144_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_Control-ethanol-treated_216 h_flask2_rep1

description:
13238018_OH_216_F2
Flask2_rep1. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_E2-treated_144 h_flask1_rep1

description:
13235555_E2_144_F1
Flask1_rep1. E2-treated, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_E2-treated_144 h_flask2_rep1

description:
13237684_E2_144_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_Control-ethanol-treated_216 h_flask2_rep2

description:
13238019_OH_216_F2
Flask2_rep2. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_Control-untreated_144 h_flask1_rep2

description:
13235552_C_144_F1
Flask1_rep2. Control, Pb01  M-to-Y, 144 h

value: M-to-Y, 144 h, Untreated-Control


title: Pb01_M-to-Y_Control-untreated_144 h_flask2_rep1

description:
13235575_C_144_F2
Flask2_rep1. Control, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_E2-treated_72 h_flask1_rep1

description:
13237595_E2_72_F1
Flask1_rep1. E2-treated, Pb01  M-to-Y, 72 h

source_name: Pb01 M-to-Y,72 h

value: M-to-Y, 72 h, E2-treated


title: Pb01_M-to-Y_E2-treated_72 h_flask1_rep2

description:
13238381_E2_72_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_Control-ethanol-treated_144 h_flask2_rep2

description:
13238227_OH_144_F2
Flask2_rep2. Control, Pb01  M-to-Y, 144 h

value: M-to-Y, 144 h, ethanol-treated-Control


title: Pb01_M-to-Y_E2-treated_72 h_flask2_rep2

description:
13235629_E2_72_F2
Flask2_rep2. E2-treated, Pb01 M-to-Y, 72 h


title: Pb01_M-to-Y_Control-ethanol-treated_144 h_flask2_rep1

description:
13238226_OH_144_F2
Flask2_rep1. Control, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_Control-ethanol-treated_144 h_flask1_rep2

description:
13237933_OH_144_F1
Flask1_rep2. Control, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_E2-treated_216 h_flask2_rep2

description:
13238022_E2_216_F2
Flask2_rep2. E2-treated, Pb01  M-to-Y, 216 h


title: MDM-poly(I:C)

description: monocytes differentiated in vitro into MDMs with M-CSF for 7 days were treated with 10 mg/ml poly(I:C) for 16 hours before total RNA isolation

value: primary monocyte-derived macrophages

tag: agent

value: stimulation through TLR3


title: Pb01_M-to-Y_Control-ethanol-treated_216 h_flask1_rep1

description:
13238243_OH_216_F1
Flask1_rep1. Control, Pb01  M-to-Y, 216 h


title: Pb01_M-to-Y_Control-untreated_144 h_flask2_rep2

description:
13235375_C_144_F2
Flask2_rep2. Control, Pb01  M-to-Y, 144 h


title: Pb01_M-to-Y_Control-ethanol-treated_144 h_flask1_rep1

description:
13237590_OH_144_F1
Flask1_rep1. Control, Pb01 M-to-Y, 144 h


title: Pb01_M-to-Y_E2-treated_72 h_flask2_rep1

description:
13235627_E2_72_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_Control-ethanol-treated_72 h_flask1_rep2

description:
13238062_OH_72_F1
Flask1_rep2. Control, Pb01  M-to-Y, 72 h

value: M-to-Y, 72 h, ethanol-treated-Control


title: Pb01_M-to-Y_Control-ethanol-treated_72 h_flask1_rep1

description:
13238061_OH_72_F1
Flask1_rep1. Control, Pb01  M-to-Y, 72 h

value: Pb01 (ATCC:MYA-826)


title: Pb01_M-to-Y_Control-untreated_144 h_flask1_rep1

description:
13235551_C_144_F1
Flask1_rep1. Control, Pb01 M-to-Y, 144 h

value: M-to-Y


title: Pb01_M-to-Y_Control-ethanol-treated_72 h_flask2_rep2

description:
13238070_OH_72_F2
Flask2_rep2. Control, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_Control-untreated_72 h_flask2_rep2

description:
13237613_C_72_F1
Flask2_rep2. Control, Pb01  M-to-Y, 72 h

value: M-to-Y, 72 h, Untreated-Control


title: Pb01_M-to-Y_E2-treated_24 h_flask1_rep1

description:
13238241_E2_24_F1
Flask1_rep1. E2-treated, Pb01  M-to-Y, 24 h

source_name: Pb01 M-to-Y,24 h

value: M-to-Y,24 h, E2-treated

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then, swtiched to 37°C


title: Pb01_M-to-Y_Control-untreated_72 h_flask1_rep1

description:
13237587_C_72_F2
Flask1_rep1. Control, Pb01 M-to-Y, 72 h

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h


title: Pb01_M-to-Y_E2-treated_24 h_flask2_rep2

description:
13237919_E2_24_F2
Flask2_rep2. E2-treated, Pb01  M-to-Y, 24 h

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: Pb01_M-to-Y_Control-untreated_72 h_flask1_rep2

description:
13237588_C_72_F2
Flask1_rep2. Control, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_E2-treated_24 h_flask1_rep2

description:
13238242_E2_24_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 24 h


title: Pb01_M-to-Y_Control-untreated_72 h_flask2_rep1

description:
13237612_C_72_F1
Flask2_rep1. Control, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_E2-treated_24 h_flask2_rep1

description:
13237918_E2_24_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 24 h


title: Pb01_M-to-Y_Control-ethanol-treated_72 h_flask2_rep1

description:
13238069_OH_72_F2
Flask2_rep1. Control, Pb01  M-to-Y, 72 h


title: Pb01_M-to-Y_Control-ethanol-treated_24 h_flask2_rep1

description:
13237585_24_OH_F2
Flask2_rep1. Control, Pb01  M-to-Y, 24 h

value: M-to-Y, 24 h, ethanol-treated-Control


title: Pit1dw/dw  biological rep 2

first: Amanda

last: Mortensen

address: 4909 Buhl Bld. 1241 E. Catherine St.

department: Human Genetics

description: Gene expression data from total pituitary RNA

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Pit1dw/dw mouse pituitary

label_protocol: Labeling, hybridization, scanning and data processing were performed by the University of Michigan Comprehensive Cancer Center Microarray Core facility (http://www.umich.edu/~caparray). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were fed high fat laboratory chow. (Purina #5020)

extract_protocol: Total RNA was isolated using the Ambion RNAqeuos  Micro kit ( #1931) according to the manufacture's protocol

tag: strain background

value: DW/J

tag: genotype/variation

value: P1 (newborn)

tag: tissue

value: pituitary


title: Pit1dw/dw  biological rep 5


title: Pb01_M-to-Y_Control-ethanol-treated_24 h_flask2_rep2

description:
13237920_OH_24_F2
Flask2_rep2. Control, Pb01  M-to-Y, 24 h


title: Pit1dw/dw  biological rep 4


title: Pb01_M-to-Y_Control-untreated_24 h_flask2_rep1

description:
13237916_C_24_F2
Flask2_rep1. Control, Pb01  M-to-Y, 24 h

value: M-to-Y, 24 h, Untreated-Control


title: Pb01_M-to-Y_Control-ethanol-treated_24 h_flask1_rep2

description:
13238328_OH_24_F1
Flask1_rep2. Control, Pb01  M-to-Y, 24 h


title: Pb01_M-to-Y_Control-untreated_24 h_flask1_rep2

description:
13237611_C_24_F1
Flask1_rep2. Control, Pb01  M-to-Y, 24 h


title: Pit1+/+ biological rep 3

source_name: Pit1+/+ P1 mouse pituitary

value: Pit+/+


title: Pit1+/+ biological rep 5


title: Pb01_M-to-Y_E2-treated_12 h_flask2_rep2

description:
13238329_E2_12_F2
Flask2_rep2. E2-treated, Pb01  M-to-Y, 12 h

source_name: Pb01 M-to-Y,12 h

value: M-to-Y,12 h, E2-treated


title: Pit1+/+ biological rep 2


title: Pb01_M-to-Y_Control-untreated_24 h_flask2_rep2

description:
13237917_C_24_F2
Flask2_rep2. Control, Pb01 M-to-Y, 24 h


title: Pb01_M-to-Y_Control-untreated_24 h_flask1_rep1

description:
13237556_C_24_F1
Flask1_rep1. Control, Pb01 M-to-Y, 24 h


title: Pb01_M-to-Y_Control-ethanol-treated_24 h_flask1_rep1

description:
13238327_OH_24_F1
Flask1_rep1. Control, Pb01  M-to-Y, 24 h


title: Pit1 dw/dw  biological rep 3


title: Prop1df/df biological rep 5

source_name: Prop1df/df P1 mouse pituitary

value: DF/B


title: Pb01_M-to-Y_E2-treated_12 h_flask2_rep1

description:
13238063_E2_12_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 12 h

value: Pb01 (ATCC:MYA-826)


title: Pit1dw/dw biological rep 1


title: Prop1df/df biological rep 1


title: Prop1df/df  biological rep 4


title: Prop1df/df biological rep 3


title: Prop1df/df biological rep 2


title: Pb01_M-to-Y_E2-treated_12 h_flask1_rep2

description:
13237937_E2_12_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 12 h

value: M-to-Y


title: Pit1+/+ biological rep 1


title: Pit1+/+  biological rep 4


title: Prop1+/+ biological rep 5

source_name: Prop1+/+  P1 mouse pituitary


title: Pb01_M-to-Y_E2-treated_12 h_flask1_rep1

description:
13237932_E2_12_F1
Flask1_rep1. E2-treated, Pb01  M-to-Y, 12 h


title: Prop1+/+ biological rep 4


title: Adult valve 3

city: Leuven

first: Geofrey

last: De Visscher

address: Minderbroedersstraat 12 Building P

institute: KULeuven

description: Gene expression from adult semilunar valves, steady-state tissue

hyb_protocol: The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.

scan_protocol: scanned with the GeneChip Scanner 3000

data_processing: The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.

organism: Rattus norvegicus

source_name: adult rat semilunar valves (aortic and pulmonary), male

label_protocol: The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit

extract_protocol: Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).

value: adult semilunar valve

tag: strain

value: Wistar


title: Pb01_M-to-Y_Control-untreated_12 h_flask1_rep2

description:
13237555_C_12_F1
Flask1_rep2. Control, Pb01  M-to-Y, 12 h

source_name: P. brasiliensis M-to-Y,12 h

value: M-to-Y, 12 h, Untreated-Control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C


title: Pb01_M-to-Y_Control-ethanol-treated_12 h_flask1_rep1

description:
13238325_OH_12_F1
Flask1_rep1. Control, Pb01  M-to-Y, 12 h

value: M-to-Y, 12 h, ethanol-treated-Control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then, swtiched to 37°C

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h


title: Prop1+/+ biological re 3


title: Pb01_M-to-Y_Control-ethanol-treated_12 h_flask1_rep2

description:
13238326_OH_12_F1
Flask1_rep2. Control, Pb01  M-to-Y, 12 h

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: Adult valve 2


title: Neonatal valve 1

description: Gene expression from adult aortas, steady-state tissue

source_name: neonatal rat semilunar valves (aortic and pulmonary), collected within 24h after birth

value: adult aorta


title: Prop1+/+  biological rep 2

description: Gene expression data from total pituitary RNA

value: P1 (newborn)

value: pituitary


title: Prop1+/+ biological rep 1


title: Adult valve 1


title: Adult aorta1

description: Gene expression from neonatal semilunar valves, early neonatal development (<24h after birth)

source_name: proximal part adult rat aorta, male

value: neonatal semilunar valve


title: Neonatal valve 2


title: Neonatal valve 3


title: Unstimulated

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

country: India

institute: Piramal Lifesciences India Limited

description: Single dye, indirect labelling protocol

hyb_protocol: The microarray slides were processed for pre-hybridization using the Pronto hybridization kit as described by the manufacturer. The slides were loaded onto the GeneTac automated hybridization station and primed with the labeled cDNA as per the manufacturer's instructions. A step down hybridization was performed for 18 hours with the following protocol – 6 hrs at 42 degree centigrade, 6 hours at 35 degree centigrade and 6 hours at 30 degree centigrade. At the end of the hybridization cycle, the slides were removed from the hybridization station, washed and processed for scanning as described by the manufacturer (Corning Pronto, USA). The slides were spun dry by centrifugation at 1600 rpm for 10 minutes and loaded onto a laser scanner for scanning the Cy3 intensities.

scan_protocol: The slides were scanned with the “autogain” function of the scanner (GeneTAC UC4) so as to optimize the laser power for amplifying the low intensity spots versus avoiding the over-saturation of the high intensity spots on the slide. The resultant scanned tiff image files were gridded using the GAL file generated from the spotting run with use of the GeneTac Integrator software.

data_processing: Foreground and background intensity values were recorded for every gene in the array using a fixed threshold boundary by GeneTAC Integrator software. Background intensity values were subtracted from the foreground and normalized using global normalization algorithm used by GeneTAC Integrator software. The resultant data with the background subtracted, globally normalized intensity values was used for statistical analysis.

source_name: Unstimulated

label_protocol: The RNA from THP-1 cells were labeled with fluorescent dyes (Cy3) using the indirect labeling method. Briefly, twenty micrograms of total RNA from THP-1 cells were converted to cDNA using modified amino-allyl dUTP. The resultant cDNA was purified using the silica columns provided by the kit and subsequently used for dye conjugation. The purified cDNA was eluted in binding buffer and incubated with the DMSO dissolved Cy3 dye suspension for 3 hours in a thermo mixer at room temperature. Excess dye was quenched using 20mM hydroxylamine and the resultant labeled cDNA was again purified using the silica columns as provided by the kit. The purified and labeled cDNA was eluted using 65μL elution buffer. The exultant was dried under vacuum and resuspended in 65μl of hybridization buffer. The resuspended cDNA was heated at 95 degree centigrade for 5 minutes, flash chilled on ice and microfuged on ice before use in hybridization.

growth_protocol: The human monocytic cell line THP-1 (ATCC, Manassas, VA) was maintained in RPMI-1640 supplemented with 10% FBS. Prior to cell-contact experiments, cells were cultured for 24 hours in the presence of 1 ng/ml of PMA to enhance their response to activation stimuli.

extract_protocol: On assay completion, THP-1 cells were harvested with chilled Trizol reagent (Invitrogen Corp, Carlsbad, USA). The volume of Trizol was maintained at 1 ml for every 1 x 106 cells. The cells with Trizol were stored at -80 degree centigrade until used for RNA extraction. The lysates were thawed at room temperature and passed through a 21-gauge needle for 10 times. This ensured that the lysates was uniformly homogenized. Post homogenization, the lysates were allowed to settle for 5 minutes at room temperature. The lysates were then spun at 12000 rpm for 15 minutes in a fixed angle rotor centrifuge at 4 degree centigrade. The upper aqueous phase was then transferred to a new microfuge tube and equal volumes of chilled 70% ethanol were added to the tubes. The ethanol-aqueous phase was mixed gently with a pipette and total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, USA). The lysates were then transferred to a purification column and spun at 10,000 rpm for 10 seconds. The flow-through is discarded and the column is filled with 500μl of RW1 buffer provided by the kit. The columns are spun at 10,000 rpm for 10 seconds and the flow-through is discarded. The columns are then filled with 500μl of RPE buffer and spun at 10,000 rpm for 10 seconds. The RPE buffer spin is repeated once more and a dry spin is performed by centrifugation of the empty column at 13,000 rpm for 2 minutes. The final elution step was performed by adding 32μl of nuclease free water and spinning the column for 5 minutes at 13,000 rpm. The concentration of the RNA is determined using 1μl of RNA with a Nanodrop spectro-photometer (ND-1000,).

treatment_protocol: THP-1 cells were differentiated with PMA (1ng/ml) for 2 hours and allowed to rest for 24 hours in normal growth medium. Subsequently, the cells were pre-treated with Dexamethasone (3µM); chlorojanerin (3µM) and or LPS (1µg/ml) for 12 hours. The treatment with the compounds was performed for 30 minutes prior to LPS stimulation.

tag: cell line


title: Chlorojanerin

description: Single dye, indirect labelling protocol

source_name: Chlorojanerin

value: LPS (1µg/ml) + Chlorojanerin (3µM)


title: LPS stimulated

description: Single dye, indirect labelling protocol

source_name: LPS stimulated

value: LPS (1µg/ml)


title: Pb01_M-to-Y_Control-untreated_12 h_flask1_rep1

description:
13237554_C_12_F1
Flask1_rep1. Control, Pb01 M-to-Y, 12 h

value: Pb01 (ATCC:MYA-826)

value: M-to-Y


title: Adult aorta3

value: Wistar


title: Adult aorta2


title: Neonatal aorta 2

description: Gene expression from neonatal aortas, early neonatal development (<24h after birth)

source_name: proximal part neonatal rat aorta, collected within 24h after birth

value: neonatal aorta


title: Pb01_M-to-Y_E2-treated_4 h_flask2_rep2

description:
13235641_E2_4_F2
Flask2_rep2. E2-treated, Pb01  M-to-Y, 4 h

source_name: Pb01 M-to-Y, 4 h

value: M-to-Y, 4 h, E2-treated

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C


title: Pb01_M-to-Y_Control-ethanol-treated_12 h_flask2_rep2

description:
13238067_OH_12_F2
Flask2_rep2. Control, Pb01  M-to-Y, 12 h

value: M-to-Y, 12 h, ethanol-treated-Control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then, swtiched to 37°C

source_name: Pb01 (Mycelial form plus M-to-Y transition forms)


title: Neonatal aorta 3


title: Neonatal aorta 1


title: Pb01_M-to-Y_E2-treated_4 h_flask2_rep1

description:
13237977_E2_4_F2
Flask2_rep1. E2-treated, Pb01  M-to-Y, 4 h

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h


title: Dexamethasone

description: Single dye, indirect labelling protocol

source_name: Dexamethasone

value: LPS (1µg/ml) + Dexamethasone (3µM)


title: Pb01_M-to-Y_Control-untreated_12 h_flask2_rep1

description:
13235602_C_12_F2
Flask2_rep1. Control, Pb01  M-to-Y, 12 h

value: M-to-Y, 12 h, Untreated-Control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: Day 70 T1 Control, Biological Rep2

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

description: miRNA expression data from day 70 matched control males during Trimester 1 (GD 8) via maternal injections of 0.15M saline with a dosage of 2.5g/kg. Saline was administered twice separated by two hours.

hyb_protocol: Samples were then hybridized to Affymetrix miRNA 2.0 arrays for 16 hours at 45°C

scan_protocol: Probe level (.CEL file) data was generated using Affymetrix Command Console v1.1.

data_processing: Probes were summarized to gene level data in Partek Genomics Suite v6.6 (Partek, St. Louis, MO, USA) using the RMA algorithm. Partek software was used to determine ANOVA p-values and fold changes.

source_name: Day 70 T1 Control

label_protocol: One microgram of total RNA was labeled using the Flash Tag Biotin HSR kit (Genisphere)

growth_protocol: C57BL/6J mice were prenatally exposed to ethanol either via Trimister 1,2, or 3, injections or continous preference drinking (Labelled T1, T2, T3, or CPD, respectively).

extract_protocol: TRIzol according to manufacturers protocol

treatment_protocol: Day 70 male mice were subjected to CO2 asphyxiation followed by cervical disolaction. Whole brain tissue was dissected in under five minutes and flash frozen liquid nitrogen.

tag: gender

value: Male

value: Whole Brain (with olfactory bulb)

tag: treament

value: Matched Control

tag: model

tag: # samples pooled


title: Day 70 T2 Control, Biological Rep2

description: miRNA expression data from day 70 matched control malesdu ring Trimester 2 (GD 14 and 16) via maternal injections of 0.15M saline with a dosage of 2.5g/kg. Saline was administered twice separated by two hours.

source_name: Day 70 T2 Control


title: Day 70 T1 Ethanol, Biological Rep2

description: miRNA expression data from day 70 males exposed prenatally to alcohol during Trimester 1 (GD 8) via maternal injections of  20% ethanol in 0.15M saline with a dosage of 2.5g/kg. Ethanol was administered twice separated by two hours.

source_name: Day 70 T1 Ethanol

value: Fetal alcohol exposed


title: Day 70 T1 Ethanol, Biological Rep1


title: Pb01_M-to-Y_Control-ethanol-treated_12 h_flask2_rep1

description:
13238066_OH_12_F2
Flask2_rep1. Control, Pb01  M-to-Y, 12 h

source_name: Pb01 M-to-Y,12 h

tag: isolate

value: Pb01 (ATCC:MYA-826)

value: M-to-Y


title: Day 70 T1 Control, Biological Rep1


title: SKOV3 ip1 Norepinephrine Rep1

city: Houston

first: Guillermo

middle: N

last: Armaiz-Pena

state: Texas

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Affymetrix U133A

hyb_protocol: Standard Affymetrix hybridization protocol for gen expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrixscan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: MAS 5.0

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Total RNA was extracted using Qiagen RNEasy.

value: Norepinephrine


title: SKOV3 ip1 Control Rep3

description: Affymetrix U133A

value: Control


title: SKOV3 ip1 Norepinephrine Rep3

description: Affymetrix U133A


title: SKOV3 ip1 Norepinephrine Rep2

description: Affymetrix U133A


title: Pb01_M-to-Y_E2-treated_4 h_flask1_rep2

description:
13238240_E2_4_F1
Flask1_rep2. E2-treated, Pb01  M-to-Y, 4 h

tag: morphologic form

value: M-to-Y, 4 h, E2-treated

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C


title: Day 70 T2 Control, Biological Rep1


title: SKOV3 ip1 Control Rep2

description: Affymetrix U133A


title: SKOV3 ip1 Control Rep1

description: Affymetrix U133A


title: Pb01_M-to-Y_Control-ethanol-treated_4 h_flask2_rep1

description:
13237594_OH_4_F2
Flask2_rep1. Control, Pb01  M-to-Y, 4 h

tag: sample

value: M-to-Y, 4 h, ethanol-treated-Control


title: Day 70 T3 Control, Biological Rep2

description: miRNA expression data from day 70 matched control males during Trimester 3 (PND 3 and 7) via injections of  0.15M saline with a dosage of 2.5g/kg. Ethanol was administered twice separated by two hours.

source_name: Day 70 T3 Control

value: Whole Brain (without olfactory bulb)


title: Pb01_M-to-Y_E2-treated_4 h_flask1_rep1

description:
13238239_E2_4_F1
Flask1_rep1. E2-treated, Pb01  M-to-Y, 4 h

source_name: Pb01M-to-Y, 4 h

tag: growth

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h


title: Day 70 T2 Ethanol, Biological Rep1

description: miRNA expression data from day 70 males exposed prenatally to alcohol during Trimester 2 (GD 14 and 16) via maternal injections of  20% ethanol in 0.15M saline with a dosage of 2.5g/kg. Saline was administered twice separated by two hours.

source_name: Day 70 T2 Ethanol


title: Pb01_M-to-Y_Control-ethanol-treated_4 h_flask2_rep2

description:
13235640_OH_4_F2
Flask2_rep2. Control, Pb01  M-to-Y, 4 h

tag: morphology


title: Pb01_M-to-Y_Control-untreated_4 h_flask2_rep2

description:
13238065_C_4_F2
Flask2_rep2. Control, Pb01  M-to-Y, 4 h

value: M-to-Y, 4 h, Untreated-Control

source_name: Pb01 (Mycelial form plus M-to-Y transition form)

tag: rna source


title: Day 70 T3 Control, Biological Rep1