title: mouse lung_bleo_day3_rep2

source_name: mouse lung, bleomycin, day3


title: mouse lung_bleo_day3_rep1

status: Public on Apr 13 2012

type: RNA

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

country: USA

institute: Cedars-Sinai Medical Center

hyb_protocol: After labeling, RNA from each sample was hybridazed onto the microarray slides using the miRCURY™ LNA miRNA Array labeling kit according to the manufacture's instructions.

scan_protocol: Slides was scaned by GenePix 4000B scanner(Molecular Devices, Sunnyvale, CA), Data and images were acqusited using GenePix Pro 6.1(Molecular Devices, Sunnyvale, CA) according to the manufacture's instructions.

data_processing: thresholding: raw signal to 1.0, summarization: Treatment of on-chip replicates- The signal value of a probeset is the geometric mean of all its probes. normalization: lowess, ratio computation: Cy5/Cy3, lowess normalized, log transformation: log2, baseline transformation: didn’t do any.

molecule: total RNA

organism: Mus musculus

label_protocol: RNA from each sample was labeled with Cy5 and reference sample RNA labeled with Cy3 using the miRCURY™ LNA miRNA Array labeling kit according to the manufacture's instructions.

growth_protocol: All experiments were carried out using 8- to 12-week-old female C57BL/6J mice. All studies were conducted in accordance with NIH guidelines for the care and use of animals and with approval from the Duke University Animal Care and Use Committee.

extract_protocol: Total RNA from lung tissues was isolated using the mirVana miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer’s instructions.

treatment_protocol: Under anesthesia, 2.5 U/kg bleomycin dissolved in sterile PBS was administered via trachea as previously described. Lung tissues were harvested at the time point of day 0, 3, 7, 14, and 21 post bleomycin challenges.

tag: strain

tag: Sex

value: Female

tag: age

tag: tissue

value: lung

source_name: Mouse Lung Total RNA


title: mouse lung_bleo_day3_rep3


title: mouse lung_bleo_day7_rep2

source_name: mouse lung, bleomycin, day7


title: mouse lung_bleo_day0_rep2

source_name: mouse lung, untreated, day0


title: mouse lung_bleo_day0_rep3


title: mouse lung_bleo_day0_rep1


title: Hypocotyl_DMSO_2hr_wildtype_rep1

city: Hanover

first: Kathleen

last: Greenham

state: NH

address: 78 College St

institute: Dartmouth College

description: This sample is of wildtype DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #1.

hyb_protocol: Hybridization was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

scan_protocol: Scanning was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

data_processing: Annotation packages were built with pdInfoBuilder using raw data files (.xys) along with a Nimblegen microarray design file (.ndf).  The data was RMA normalized in oligo using the annotation package in R.  See www.R-project.org/  AND www.bioconductor.org/

organism: Arabidopsis thaliana

label_protocol: Labeling was performed according to NimbleGen standard protocol at the GeneChip Microarray Core facility at the University of California San Diego.

growth_protocol:
Arabidopsis seedlings were grown on nylon mesh under long day (16L:8D) conditions for 5d and transferred to 5uM picloram or a DMSO control at ZT2 for 2hrs.
Hypocotyls were dissected following the 2hr treatment.  Dissection time was limited to 30min.  Tissue was immediately frozen in liquid N2.

extract_protocol: Total RNA was extracted using the Invitrogen PureLink RNA mini kit.

tag: genotype

tag: phenotype

value: normal

tag: ecotype


title: mouse lung_bleo_day7_rep1


title: Hypocotyl_DMSO_2hr_wildtype_rep2

description: This sample is of wildtype DMSO treated hypocotyls dissected over a 30min period.  Roughly 700 hypocotyls were pooled for this replicate #2.


title: glutamine sensing

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Mutant vs Wild-type, Glutamine
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16561.gif
is_reverse: No

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the medians

source_name: wild type Arabidopsis thaliana

label_protocol: not provided

extract_protocol: not provided

value: wild type

source_name: Arabidopsis thaliana Gsr1 mutant

value: Gsr1 mutant


title: adipose tissue  early pregnancy E6

city: Cleveland

first: Veronica

last: Resi

state: Ohio

address: MetroHealth Drive 2500

department: Ob/Gyn Department

institute: MetroHealth Medical Center

description: gene expression data from white adipose tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HG U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: MAS 5.0

label: biotin

organism: Homo sapiens

source_name: human adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA after two-cycle target labeling (GeneChip® Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Adipose tissue was immediately processed for adipose cell isolation and the remaining tissue was snap frozen in liquid nitrogen and stored for RNA processing.

extract_protocol: Total RNA was isolated from intact adipose tissue using Trizol (Invitrogen, Carlsbad, CA) extraction method

treatment_protocol: Adipocytes were isolated by digestion with 1mg/ml collagenase (Worthington Biochemical, Lakewood, NJ) in Hanks Buffered Salt Solution for 45 min at 37oC.

tag: developmental stage

value: early pregnancy

tag: age (yrs)

tag: gender

value: F

tag: bmi (kg/m2)

value: while adipose tissue


title: adipose tissue  pre-pregnancy P6

value: pre-pregnancy


title: adipose tissue  early pregnancy E2


title: GD2-HMLER_2

city: Houston

first: Kurt

last: Evans

state: TX

address: 1515 Holcombe Blvd.

institute: MDACC

hyb_protocol: Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000

data_processing: The scanner is controlled  by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.

source_name: HMLER

label_protocol: By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371  for cDNA and cRNA purification) and fragmented before hybridization.

growth_protocol: The cells were culture in MEGM media mixed 1:1 with DMEM/F12.  Se Mani et al, Cell 2008

extract_protocol: Qiagen RNA easy kit was used for RNA isolation

treatment_protocol: No treatment

tag: cell line

value: Ras-transformed human mammary epithelial cells (HMLER cells)

tag: facs-sorted cell population


title: GD2-HMLER_1


title: 86823-2x

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

description: tumor driven by MYCN AND mutated ALK

hyb_protocol: Hybridisation to mouse 430_2 arrays was performed according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent).

data_processing: Signal intensities were RMA normalized using PARTEK Genomics Suite, with the .CEL files as input.

source_name: tumor

label_protocol: Biotin labelling was performed according the manufacturer's recommendations (Affymetrix).

growth_protocol: Mice transgenic for neural crest specific expression of MYCN, mutated ALK or both were monitored until tumor was palpable and sacrificed afterwards.

extract_protocol: RNA was extracted from tumors or control tissue using the QIAGEN Rneasy mini kit.

tag: background strain

value: tumor

tag: genotype/variation

value: MYCN AND mutated ALK


title: GD2-HMLER_3


title: adipose tissue  pre-pregnancy P2


title: adipose tissue  late pregnancy L2

value: late pregnancy


title: 77204-10

description: tumor driven by MYCN AND mutated ALK


title: adipose tissue  late pregnancy L3


title: Fz2-/-; Fz7-/- E8.5 whole embryo replicate 3

city: Baltimore

first: Huimin

last: Yu

state: MD

address: 725 N Wolfe Street, PCTB 805

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA (Bioconductor)

source_name: Fz2-/-; Fz7-/- E8.5 whole embryo

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol and RNeasy according to the manufacturer's instructions

value: whole embryo

value: mixed gender

tag: genetic backround

value: C57BL6/129 mixed background


title: adipose tissue  late pregnancy L6


title: 82743-lo

description: tumor driven by MYCN AND mutated ALK


title: Fz2+/+; Fz7-/- E8.5 whole embryo replicate 3

source_name: Fz2+/+; Fz7-/- E8.5 whole embryo


title: Fz2+/+; Fz7-/- E8.5 whole embryo replicate 2


title: adipose tissue  pre-pregnancy P3


title: Fz2-/-; Fz7-/- E8.5 whole embryo replicate 1


title: GD2+HMLER_3


title: adipose tissue pre-pregnancy P1


title: CD44high-3


title: CD44high-2


title: adipose tissue late pregnancy L1


title: adipose tissue  early pregnancy E3


title: Fz2-/-; Fz7-/- E8.5 whole embryo replicate 2


title: adipose tissue early pregnancy E1


title: GD2+HMLER_1


title: Fz2+/+; Fz7-/- E8.5 whole embryo replicate 1


title: Single cell profile of retinal cell E2

city: Boston

first: jeffrey

last: trimarchi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.

source_name: E14.5 single retinal cell E2

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: Single retinal cells were isolated using FDG to label LacZ-positive cells, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: cell type

value: retinal

value: embryonic day 14.5 (E14.5)


title: CD44high-1


title: Single cell profile of retinal cell D2

source_name: P5 single retinal cell D2

extract_protocol: Single retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

value: postnatal day 5 (P5)


title: Single cell profile of retinal cell MB2

source_name: E14.5 single retinal cell MB2


title: Mostra 7

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: Gene expression data from HUMAN MCF7 cells

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

source_name: MCF7 control-tnf 20

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: transfection

value: Ctrl

tag: time


title: CD24high-1


title: Mostra 11

value: 14-3-3 transduced


title: Mostra 8


title: WAT from Ahnak knockout fed high fat diet Replicate 3

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University

description: Gene expression data from WAT

hyb_protocol: The resultant labeled cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays.

scan_protocol: The microarray images were scanned with the Agilent microarray scanner.

data_processing: All analysis of microarray data was carried out in R software. The expression data was preprocessed with affy package from bioconductor.

source_name: KO fed  High Fat Diet

label_protocol: Extracted RNA was amplified and labeled according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript Sense Target Labeling protocol

growth_protocol: Mice were maintained in temperature-controlled (24±2C) facility with a 12h light/dark cycle, and fed regular chow diet (Lab Diets, IN, USA) ad libitum with tap water.

extract_protocol: Total RNA was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer's instruction

treatment_protocol: Male mice were established in weight-matched groups fed either regular chow diet and high fat diet (20% carbohydrate, 60% fat, 20% protein : D12492: Research Diets Inc., New Brunswick, NJ) for 12 weeks.

value: white adipose tissue (WAT)

value: Male

tag: age

value: 18-weeks old

tag: diet

value: High fat diet


title: CD24high-2


title: WAT from Ahnak knockout fed high fat diet Replicate 1

description: Gene expression data from WAT

tag: tissue


title: Mostra 2

source_name: MCF7 control-tnf 0


title: Mostra 16


title: CD24high-3


title: Mostra 5


title: WAT from Ahnak knockout fed high fat diet Replicate 2

description: Gene expression data from WAT


title: Mostra 4


title: Mostra 17


title: WAT from wild-type control fed high fat diet Replicate 3

description: Gene expression data from WAT

source_name: WT fed  High Fat Diet


title: WAT from wild-type control fed high fat diet Replicate 2

description: Gene expression data from WAT


title: Single cell profile of retinal cell D8

source_name: E16.5 single retinal cell D8

value: embryonic day 16.5 (E16.5)


title: Mostra 15

source_name: MCF7 control-tnf 90


title: Mostra 13


title: Mostra 1


title: GD2+HMLER_2

value: Ras-transformed human mammary epithelial cells (HMLER cells)


title: WAT from Ahnak knockout fed regular chow diet Replicate 3

description: Gene expression data from WAT

source_name: KO fed  regular chow

value: Regular chow diet


title: WAT from wild-type control fed high fat diet Replicate 1

description: Gene expression data from WAT


title: Mostra 10


title: WAT from Ahnak knockout fed regular chow diet Replicate 2

description: Gene expression data from WAT


title: WAT from Ahnak knockout fed regular chow diet Replicate 1

description: Gene expression data from WAT


title: PIO, subject 14

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affimetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (target intensity = 100 ) for quality control. gcRMA ( justgcRMA function in bioconductor in R v.2.7.1 ) was run on all chips simultaneously to generate probe set signal intensities.

label: Standard Affymetrix

source_name: mouse hippocampus

label_protocol: Standard Affymetrix

extract_protocol: Standard Affymetrix

treatment_protocol: PIO was incorporated in the diet at 84 ppm yellding approximately 18 mg/kg body weight/day

tag: mouse model

value: female

value: 14 months old


title: PIO, subject 13


title: PIO, subject 16


title: WAT from wild-type control fed regular chow diet Replicate 2

description: Gene expression data from WAT

source_name: WT fed  regular chow


title: PIO, subject 11


title: PIO, subject 15


title: WAT from wild-type control fed regular chow diet Replicate 3

description: Gene expression data from WAT


title: WAT from wild-type control fed regular chow diet Replicate 1

description: Gene expression data from WAT


title: PIO, subject 9


title: PIO, subject 12


title: control, subject 6


title: Cluster C  D8 Group2

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D3

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: Cluster C lysis at D8, treated with microRNA cluster C, Group2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: MEFs were infected with virus twice as described, then cultured in mESC medium. Medium was changed everyday. The day first infection was set as Day 0.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MicroRNA cluster B or C retrovius， was prepared for stable simultaneous delivery in reprogramming MEFs(Group1) or MEFs(Group2) .

value: MEFs from OG2 cross 129/sv

tag: treatment

value: 8 d


title: PIO, subject 10


title: control, subject 7


title: Cluster B  D4  Group2

source_name: Cluster B lysis at D4, treated with microRNA cluster B,Group2

value: 4 d


title: Control  D4 Group2

source_name: Control  lysis at D4, control in group2

value: Control  lysis at D4, control in group2


title: control, subject 5


title: Control  D8 Group2

source_name: Control  lysis at D8, control in group2

value: Control  lysis at D8, control in group2


title: control, subject 3


title: SKO+cluster C  D8

source_name: SKO+cluster C  lysis at D8, treated with microRNA cluster C


title: control, subject 8


title: control, subject 4


title: SKO+control  D8

source_name: SKO+control  lysis at D8, control in group1


title: Macrophage M-CSF replicate 3

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas

hyb_protocol: Standard Codelink protocols, as described in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

scan_protocol: Scanned on an GenePix 4000B scanner

data_processing: The data were processed using Codelink TM expression analysis (Codelink EXP) v4.1, and the Normalization method was a Median-Normalization, with a Spot Based Computation Method for Median.

source_name: M-CSF Macrophage

label_protocol: 2 ug of total RNA was used to obtain cRNA. 10 ug of cRNA was labeled with Cy5-Streptavidin. All experimental procedures were performed following manufacturer instructions. Now available in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

growth_protocol: Freshly isolated CD14+ monocytes were cultured for 24 hours in RPMI 10% FCS containing either GM-CSF or M-CSF

extract_protocol: Total RNA from each condition was extracted and purified using the RNasey kit (Qiagen).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Cells were were treated with GM-CSF (1000 U/ml) or M-CSF (10 ng/ml) every 48 hours

value: peripheral blood

value: CD14+ monocytes


title: FamilyC_Unaffected5_Untreated_rep2

status: Public on Apr 12 2012

city: Brisbane

first: Julie

middle: Kim

last: Johnson

state: Queensland

address: 300 Herston Road

department: Genetics and Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: SAMPLE 139

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data uploaded were normalised using quantile normalization in Gene Spring.

source_name: Lymphoblastoid cell line (LCL), Untreated

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: RPMI1640 plus 10% Serum Supreme (Gibco).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Fresh medium (RPMI-1640 + 10% fetal bovine serum) containing 10mM caffeine (Sigma-Aldrich) was added to one 25cm2 flask containing 3.5 x 10^6 LCLs, whilst fresh medium with no caffeine was added to the control flask containing the same number of LCLs. After four hours of incubation at 37°C in a humidified atmosphere containing 5% carbon dioxide, the medium from both flasks was removed and cells were washed twice with phosphate-buffered saline (PBS). Normal media was added to the untreated control flask and the other flask was further treated for another four hours with 10mM caffeine media. After which, all medium was removed from both flasks and cells were washed twice with PBS before being pelleted and stored at -80°C until RNA extraction.

tag: family

value: C

value: Female

tag: breast cancer

value: Unaffected

value: Lymphoblastoid cell line (LCL)

tag: agent

value: Untreated


title: Macrophage GM-CSF replicate 3

source_name: GM-CSF Macrophage


title: FamilyC_Unaffected6_Untreated_rep3

description: SAMPLE 143

tag: gender


title: FamilyC_Unaffected4_Untreated_rep3

description: SAMPLE 137

tag: cell line


title: FamilyC_Unaffected6_Untreated_rep1

description: SAMPLE 141


title: SKO+control  D4

source_name: SKO+control  lysis at D4, control in group1, SKO means in iPS process


title: Cluster B  D8 Group2

source_name: Cluster B lysis at D8, treated with microRNA cluster B, Group2


title: FamilyC_Unaffected6_Untreated_rep2

description: SAMPLE 142


title: Cluster C  D4  Group2

source_name: Cluster C lysis at D4, treated with microRNA cluster C, Group2


title: HaCat Cell treated

city: Jackson

first: udensi

middle: kalu

last: udensi

state: Mississippi

address: 1400 J R Lynch

department: Biology

institute: Jackson State University

hyb_protocol: Fragmented aRNA was hybridized at 42 0C overnight using the HybBag mixing system with 1X OneArray Hybridization Buffer (Phalanx Biotech, Palo Alto, CA), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GenePix Results (GPR) format.

data_processing: The data from all microarrays in each experimental set was then passed to Rosetta Resolver (Rosetta Biosoftware, Seattle, WA) for analysis. Pearson correlation tables (R values) for each technical repeats. R values were calculated from raw log2 intensity (R) and normalized log2 intensity (N) values for each dataset and compared to each other. Only probes with P value (detected) less than 0.05 were included in the calculation.

source_name: skin keratinocyte cell

label_protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription systems that included amino-allyl UTP, and the aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Life sciences, Pittsburgh, PA).

growth_protocol: 1.5 ×105 HaCaT cells were cultured in 7.5 ml of complete DMEM containing 10% Fetal Bovine Serum (FBS) and 1% penicillin, streptomycin in T-25 culture plate. Cells were incubated in a humidified atmosphere with 5% CO2 at 37 ºC. The treatment groups were exposed to 0.5µg/mL As2O3 (equivalent to LC 0.5), and passaged at 90% confluent.

extract_protocol: Total RNA was extracted from 4 technical replicates of unexposed HaCaT cells and HaCaT cells chronically exposed to arsenic trioxide up to passage 22 using RNA STAT-60 (TEL-TEST, INC, Friendswood, TX, USA).  A NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE) was used to quantify the RNA by optical density reading. Also, the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) was used to determine the purity and quality of the extracted RNA. Only high quality RNA, having a RNA Integrity Number (RIN) of >7.0, and an A260/280 absorbance ratio of >1.8, was utilized for microarray experiments.

treatment_protocol: The treatment groups were exposed to 0.5µg/mL As2O3 (equivalent to LC 0.5), and passaged at 90% confluent. The treatment group was sub-cultured up to passage 22 to establish a chronic exposure state.  The passage control group was also sub-cultured up to 22 passages but with no exposure to arsenic trioxide.

value: HaCaT

value: 0.5µg/ml of arsenic trioxide


title: FamilyC_Unaffected5_Untreated_rep1

description: SAMPLE 138


title: FamilyC_Unaffected5_Untreated_rep3

description: SAMPLE 140


title: SKO+cluster B  D8

source_name: SKO+cluster B  lysis at D8, treated with microRNA cluster B


title: FamilyC_Unaffected4_Untreated_rep1

description: SAMPLE 135


title: Macrophage GM-CSF replicate 2


title: Macrophage M-CSF replicate 2


title: control, subject 2


title: HaCat Cell untreated


title: FamilyC_Unaffected3_Untreated_rep3

description: SAMPLE 134


title: FamilyC_Unaffected3_Untreated_rep1

description: SAMPLE 132


title: FamilyC_Unaffected4_Untreated_rep2

description: SAMPLE 136


title: control, subject 1


title: FamilyC_Unaffected6_Caffeine_rep3

description: SAMPLE 125

source_name: Lymphoblastoid cell line (LCL), Caffeine

value: Caffeine


title: SKO+cluster C  D4

source_name: SKO+cluster C  lysis at D4, treated with microRNA cluster C


title: FamilyC_Unaffected6_Caffeine_rep1

description: SAMPLE 123


title: SKO+cluster B  D4

source_name: SKO+cluster B  lysis at D4, treated with microRNA cluster B


title: Macrophage GM-CSF replicate 1


title: FamilyC_Unaffected5_Caffeine_rep2

description: SAMPLE 121


title: FamilyC_Unaffected2_Untreated_rep2

description: SAMPLE 130


title: FamilyC_Unaffected2_Untreated_rep3

description: SAMPLE 131


title: Macrophage M-CSF replicate 1


title: FamilyC_Unaffected2_Untreated_rep1

description: SAMPLE 129


title: FamilyC_Unaffected3_Untreated_rep2

description: SAMPLE 133


title: FamilyC_Unaffected1_Untreated_rep3

description: SAMPLE 128


title: FamilyC_Unaffected6_Caffeine_rep2

description: SAMPLE 124


title: FamilyC_Unaffected5_Caffeine_rep3

description: SAMPLE 122


title: FamilyC_Unaffected1_Untreated_rep1

description: SAMPLE 126


title: FamilyC_Unaffected5_Caffeine_rep1

description: SAMPLE 120


title: FamilyC_Unaffected1_Untreated_rep2

description: SAMPLE 127


title: FamilyC_Unaffected4_Caffeine_rep2

description: SAMPLE 119


title: FamilyC_Unaffected4_Caffeine_rep1

description: SAMPLE 118


title: Mof null ESC

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: Rm 5215A, MS I, 1301 Catherine Rd,

department: Department of Pathology, Department of Biological Chemistry

institute: University of Michigan

description: Gene expression data from embryonic stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy mouse430_2 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with the affy package of bioconductor implemented in the R statistical environment. pakage R version 2.10.0 (2009-10-26), i386-pc-mingw32
Expression values for each gene is calculated using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. These data can be converted to the natural scale by exponentiating (e.g., convert by using 2x, where x is the expression value).
Rafael A. Irizarry, Bridget Hobbs, Francois Collin, et al. Exploration, normal-ization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64, 2003.

source_name: mouse embryonic stem cells

label_protocol: Microarray is processed using Ambion Premier Kit

growth_protocol: ES cells were derived from day 3.5dpc mice and were maintained on MEF feed cells in the presence of LIF, typically in 60mm plates.

extract_protocol: Total RNAs were extracted from ESCs by Trizol (Invitrogen) and further purified by RNA purification kit (Qiagen). The quality of RNA were tested by Nanodrop

treatment_protocol: Before the microarray experiments, ES cells were seeded in plates without feeder cells for two passages to remove MEF cells.

value: mouse embryonic stem cells

tag: genotype

value: MOF-/-

tag: strain

tag: passage


title: FamilyC_Unaffected3_Caffeine_rep3

description: SAMPLE 117


title: FamilyC_Unaffected3_Caffeine_rep2

description: SAMPLE 116


title: FamilyC_Unaffected3_Caffeine_rep1

description: SAMPLE 115


title: FamilyC_Unaffected2_Caffeine_rep3

description: SAMPLE 114


title: ESC

value: MOF +/+


title: wild type v-Myb, biological rep3

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

description: Gene expression data from chicken monoblasts transformed by wild type v-Myb.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite (version 6.4) using Affymetrix default annotation and GC-RMA as normalization method.

organism: Gallus gallus

source_name: wild type v-Myb

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

growth_protocol: Primary chicken monoblasts transformed by v-Myb were transferred to culture 16 days post infection and maintained in DMEM supplemented with antibiotics, biotin, hypoxanthine, amino acids, fetal bovine serum and chicken serum.

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

tag: breed

value: Brown Leghorn

value: monoblasts


title: FamilyC_Unaffected2_Caffeine_rep1

description: SAMPLE 112


title: wild type v-Myb, biological rep2

tag: cell type


title: FamilyC_Unaffected2_Caffeine_rep2

description: SAMPLE 113


title: deltaP v-Myb, biological rep3

description: Gene expression data from chicken monoblasts transformed by deltaP mutant of v-Myb.

source_name: deltaP v-Myb


title: wild type v-Myb, biological rep1


title: deltaP v-Myb, biological rep1


title: FamilyC_Unaffected1_Caffeine_rep3

description: SAMPLE 111


title: FamilyC_Unaffected1_Caffeine_rep1

description: SAMPLE 109


title: deltaP v-Myb, biological rep2


title: Muscle_AQM_CS_Treatment_1

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

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

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

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 800.

organism: Sus scrofa

source_name: porcine acute quadriplegic myopathy (AQM)_CS_treatment_Day5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup.

treatment_protocol: Eight female domestic piglets (Sus scrofa, average body weight 26.4 kg) were used in this study. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 - 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 - 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 - 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period. Bolus does of hydrocortisone is given for 5 days.

value: female

tag: disease

value: acute quadriplegic myopathy (AQM)

value: biceps femoris muscle

tag: treated with

value: corticosteroid (CS)


title: FamilyC_Unaffected1_Caffeine_rep2

description: SAMPLE 110

value: C


title: Muscle_AQM_CS_Treatment_3


title: FamilyC_Affected3_Untreated_rep3

description: SAMPLE 108

value: Female

value: Affected


title: Muscle_AQM_CS_Treatment_4


title: Muscle_AQM_CS_Treatment_2


title: HHUA treated with scytonemin rep 2

city: Yufu-shi

first: Noriyuki

last: Takai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Obstetrics and Gynecology

country: Japan

institute: Oita University Faculty of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HHUA treated with scytonemin

label_protocol: Cyanine-3 (Cy3)-labeled cRNA targets were generated using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: HHUA cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from scytonemin-treated and untreated HHUA cells using an RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: HHUA cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2, and treated with or without scytonemin for 48 hours.

value: HHUA

value: scytonemin


title: FamilyC_Affected3_Untreated_rep2

description: SAMPLE 107

value: Lymphoblastoid cell line (LCL)

value: Untreated


title: HHUA control rep 2

source_name: HHUA control

value: control


title: Control.Cy3_Msi1.Cy5_4

city: san antonio

first: raquel

last: abreu

address: 8403 Floyd Curl Drive

institute: CCRI

description: Biological Replicate 2, duplicate dye swap 2

hyb_protocol: Samples were hybridized using Agilent's Gene Expression Hybridization Kit.

scan_protocol: Scanned with Agilent G2565BA Scanner, 10 µm resolution.

data_processing: TIFF images were quantified using Agilent Feature Extraction Software 8.5. Microarrays were then analyzed by using the R project for statistical computing. Arrays were background corrected using “normexp” method. Within array normalization was achieved using “loess” normalization and a “quantile” normalization method was used for between array normalization.

source_name: U251 glioma cells

label_protocol: cRNA synthesis was carried out using Agilent's Low RNA Linear Amplification Kit Plus, two-color.

growth_protocol: Grown at 37°C in 5% CO2

extract_protocol: Phenol/chloroform extraction and isopropanol precipitation

treatment_protocol: The cell lysate and antibody (produced as previously described in PMCID: PMC2572071) coated sepharose beads were incubated at room temperature while tumbling end over end. Following incubation, the beads were spun down and washed 4 times with ice cold NT2 buffer. Subsequently, the material was digested with proteinase K, extracted with phenol/chloroform, and precipitated with isopropanol.

value: U251 glioma cells

tag: rip

value: RIP with Prebleed Antibody

tag: time

value: 48 hours

value: RIP with Msi1 Antibody [generated in-house]


title: FamilyC_Affected2_Untreated_rep3

description: SAMPLE 105

source_name: Lymphoblastoid cell line (LCL), Untreated


title: Control.Cy3_Msi1.Cy5_3

description: Biological Replicate 2, dye swap 2


title: Control.Cy5_Msi1.Cy3_4

description: Biological Replicate 2, duplicate dye swap 1


title: HHUA treated with scytonemin rep 1


title: FamilyC_Affected2_Untreated_rep1

description: SAMPLE 103


title: HHUA control rep 1


title: Control.Cy5_Msi1.Cy3_3

description: Biological Replicate 2, dye swap 1


title: FamilyC_Affected2_Untreated_rep2

description: SAMPLE 104


title: FamilyC_Affected3_Caffeine_rep2

description: SAMPLE 98

value: Caffeine


title: FamilyC_Affected1_Caffeine_rep2

description: SAMPLE 92


title: FamilyC_Affected1_Untreated_rep2

description: SAMPLE 101


title: Control.Cy3_Msi1.Cy5_1

description: Biological Replicate 1, dye swap 2


title: ABA control

city: Madison

first: Jamison

last: Wolfer

state: WI

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin

description:
The millichip used in this study has 4489 total spots. One quarter of these spots were left blank for background correction, labeling controls, hybridizaiton controls and Arabidopsis control probes were also included within the array.
millichip
*Raw data files are labeled as: Treatment_biological replicate#_technological replicate#
Raw data files are labeled as Treatment_biological replicate#_technological replicate#

hyb_protocol: MES-based pre-hybridization and hybridization buffers were made with the following final, standard component concentrations: 100 mM MES (2-(N-morpholino)ethanesulfonic acid), 1 M NaCl, 20 mM EDTA, 0.01% (v/v) Tween20, 0.1 μg μL-1 herring sperm DNA and 0.5 μg μL-1 bovine serum albumin (BSA). (All reagents were purchased from Sigma Aldrich with the exception of herring sperm DNA and BSA, which were purchased from Promega). Each millichip was placed in a dedicated 0.2 μL, flat-topped PCR tube and incubated for 15 minutes in 25 μL of pre-hybridization buffer using an MJ Research thermocycler (PTC-200) set at 45oC with lid temperature set at 50oC. At the conclusion of the 15 minutes, the pre-hybridization buffer was removed with a pipette and immediately replaced with 10 to 25 μL of hybridization solution per millichip. Total Cy3-labeled RNA per millichip was, on average, 2.7 μg. PCR tubes were loaded a second time into the thermocycler with their top covers left open and a low-density polyethylene plug cut to size with a razor blade was inserted into each PCR tube with the bottom of the plug approximately 3 mm above the surface of the hybridization buffer covering the millichip. The PCR tube top covers were then closed, the thermocycler lid was closed and the millichips were incubated overnight (16 to 20.5 hours) with the thermocycler set at 45oC with a constant lid temperature of 50oC. After hybridization individual millichips were washed with the Roche NimbleGen (Madison, WI) microarray wash buffer kit following the protocol specified with the kit. Each millichip was held with a reverse-acting tweezer in 250 mL beakers containing 120 mL of each wash buffer. Agitation was provided by magnetic stir bars in the beakers. After washing the millichips were dried with argon.

scan_protocol: Four fluorescent images of each millichip were captured with an upright Nikon E800 microscope equipped with a Nikon Plan APO 10X objective and Roper Scientific CCD camera. MetaMorph® version 6.2r4 was used to capture the four images per millichip and save them as 16-bit TIF files.

data_processing: Software was written to merge data from the four images into a single dataset and fluorescent measurements could be quantified and dropped into a spreadsheet file for evaluation by the user. This program is freely available for download at http://www.biotech.wisc.edu/sussmanlab/Downloads. This stand-alone software operates with Microsoft Windows® (i.e., requires no other software to run) and performs the following functions: accommodates images from a “standard” fluorescent microscope (e.g., 16-bit TIFF images); adjusts the angle, size and position of an image; automatically adjusts the spacing between spots to compensate for stretched images; gives the user the option of excluding damaged or contaminated areas of the millichip from further evaluation; and manipulates the raw pixel data to calculate minimum, maximum, average, median and standard deviation as well as background correct probe data.

source_name: control

label_protocol: Total RNA was amplified and labeled with Cy3 dye using the Amino Allyle MessageAmp II aRNA Amplification Kit from Ambion followed by fragmentation with Ambion fragmentation reagents. The Affymetrix GeneChip Poly-A RNA Control Kit was used to monitor the target amplification and labeling process.

growth_protocol: Seeds of Arabidopsis thaliana, ecotype Columbia, were surface sterilized by agitation in 70% ethanol for 15 minutes, followed by 30% bleach and 0.1% Triton X-100 for 30 minutes.  Seeds were then rinsed 4 times with sterile water and stratified in fresh sterile water at 4 degrees C in the dark for 3 days.  Following stratification, seeds were transferred in a minimal volume of sterile water to 45 mL polypropylene flat bottom tubes with flip-top lids containing 15 mL of half-strength Murashige and Skoog salts, 0.05% (w/v) 2-(N-morpholino)ethanesulfonic acid (MES), and 0.5% (w/v) sucrose adjusted to pH 5.7 with 1M KOH.  Seedlings were germinated at room temperature under constant illumination (40 mmol m-2s-1,) with gentle shaking.

extract_protocol: Treated seedling tissue was blotted dry on tissue paper, weighed, flash frozen in liquid nitrogen, and stored at -80ºC until RNA could be isolated.  Total RNA was isolated from ground tissue using the RNeasy Plant Mini Kit (Qiagen), including the on-column DNase digestion step.

treatment_protocol: Following 10 days of hydroponic growth, seedlings were exposed to several single and combinatorial treatments intended to mimic environmental water-deficit conditions: (+)-abscisic acid (ABA), heat, cold, salt, dehydration and high light.  Treatments were carried out in a growth chamber (Enconair) under normal light conditions (80 µ at five-fold higher light conditions (400 µFor dehydration treatment, approximately 100 mg fresh weight of seedling tissue was removed from a polypropylene tube, blotted dry on tissue paper, and exposed to a water deficit treatments by placement on a piece of filter paper dampened with MS media in a polypropylene tube for 5h.  In parallel, non-drought control blotted seedlings were added to 10 mL of fresh MS media.  For the ABA treatment, seedlings were added to 10 mL fresh MS media containing 100 µa) in 10 µ For the ABA control treatment, seedlings were added to 10 mL of fresh MS media containing 10 µ (95% ethanol). Heat-treated seedlings were incubated in a growth chamber maintained at 37ºreated seedlings were incubated on ice in a growth chamber maintained at 10ºt treatment, seedlings were added to 10 mL of fresh MS media containing 200 mM NaCl.

value: control - ABA

tag: tissue

value: whole seedling

tag: ecotype

value: Columbia


title: Control.Cy5_Msi1.Cy3_2

description: Biological Replicate 1, duplicate dye swap 1


title: FamilyC_Affected2_Caffeine_rep1

description: SAMPLE 94


title: FamilyC_Affected2_Caffeine_rep3

description: SAMPLE 96


title: FamilyC_Affected3_Untreated_rep1

description: SAMPLE 106


title: Control.Cy5_Msi1.Cy3_1

description: Biological Replicate 1, dye swap 1


title: FamilyC_Affected1_Caffeine_rep3

description: SAMPLE 93


title: FamilyC_Affected1_Untreated_rep3

description: SAMPLE 102


title: FamilyC_Affected2_Caffeine_rep2

description: SAMPLE 95


title: FamilyC_Affected3_Caffeine_rep3

description: SAMPLE 99


title: FamilyC_Affected1_Caffeine_rep1

description: SAMPLE 91


title: FamilyC_Affected3_Caffeine_rep1

description: SAMPLE 97


title: FamilyC_Affected1_Untreated_rep1

description: SAMPLE 100


title: Responses to mycotoxin-Deoxynivalenol - Slide 3(replace)

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22172.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the medians

source_name: No DON treated control

label_protocol: not provided

extract_protocol: Promega total RNA isolation system

tag: reference

value: No DON treated control

source_name: 5ug DON treated for 24hrs

tag: test

value: 5ug DON treated for 24hrs


title: Fungus Inoculation 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27313.gif

source_name: control roots/leaves

extract_protocol: not provided

value: control roots/leaves

source_name: inoculated roots/leaves

value: inoculated roots/leaves

tag: infection

value: Yes


title: Control.Cy3_Msi1.Cy5_2

description: Biological Replicate 1, duplicate dye swap 2


title: heat

source_name: stress response

tag: treatment

value: Heat


title: FamilyB_Unaffected4_Caffeine_rep3

description: SAMPLE 78

source_name: Lymphoblastoid cell line (LCL), Caffeine

tag: family

value: B

tag: gender

value: Female

tag: breast cancer

value: Unaffected

value: Lymphoblastoid cell line (LCL)

tag: agent


title: FamilyB_Unaffected1_Untreated_rep1

description: SAMPLE 79

tag: cell line

value: Untreated


title: highlight heat

value: High light and Heat


title: highlight heat salt

value: High light and Heat and Salt


title: highlight cold dehydration

value: High light and Cold and Dehydration


title: dehydration

value: Dehydration


title: highlight heat dehydration

value: High light and Heat and Dehydration

value: whole seedling


title: ABA

value: ABA

value: Columbia


title: FamilyB_Unaffected4_Untreated_rep3

description: SAMPLE 90


title: FamilyB_Unaffected4_Untreated_rep2

description: SAMPLE 89


title: FamilyB_Unaffected4_Caffeine_rep2

description: SAMPLE 77

value: Caffeine


title: highlight

value: High light


title: salt

value: Salt


title: control

value: control - untreated


title: FamilyB_Unaffected3_Caffeine_rep3

description: SAMPLE 75

value: B


title: FamilyB_Unaffected4_Untreated_rep1

description: SAMPLE 88

value: Female


title: FamilyB_Unaffected3_Caffeine_rep2

description: SAMPLE 74

value: Unaffected


title: FamilyB_Unaffected4_Caffeine_rep1

description: SAMPLE 76

value: Lymphoblastoid cell line (LCL)


title: FamilyB_Unaffected3_Untreated_rep3

description: SAMPLE 87

value: Untreated


title: highlight cold salt

value: High light and Cold and Salt


title: FamilyB_Unaffected2_Caffeine_rep3

description: SAMPLE 72


title: FamilyB_Unaffected3_Caffeine_rep1

description: SAMPLE 73


title: FamilyB_Unaffected2_Caffeine_rep2

description: SAMPLE 71


title: Breast_primary_7001525

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Normalized log ratios (log10) were obtained using Agilent Feature Extraction software (version 9.5) using global lowess normalization.

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf] Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70

extract_protocol: RNA isolation. We used sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.

value: female

value: breast

tag: tumor type

value: primary tumor

tag: lymph node metastasis

tag: age at diagnosis

tag: days between diagnosis and blood collection

tag: metastatic

source_name: breast cancer reference pool (BRP)

tag: sample type

value: combined total RNA isolated from multiple breast cancer samples.


title: Breast_primary_7001524

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70

tag: tissue


title: highlight dehydration

value: High light and Dehydration

value: whole seedling

tag: ecotype


title: FamilyB_Unaffected2_Caffeine_rep1

description: SAMPLE 70


title: highlight salt

value: High light and Salt

value: Columbia


title: FamilyB_Unaffected3_Untreated_rep1

description: SAMPLE 85


title: Breast_primary_7001523


title: Breast_primary_7001521


title: FamilyB_Unaffected3_Untreated_rep2

description: SAMPLE 86


title: FamilyB_Unaffected1_Caffeine_rep3

description: SAMPLE 69

value: Caffeine


title: heat dehydraiton

value: Heat and Dehydration


title: cold dehydraiton

value: Cold and Dehydration


title: highlight cold

value: High light and Cold


title: heat salt

value: Heat and Salt


title: cold salt

value: Cold and Salt


title: cold

value: Cold


title: FamilyB_Unaffected2_Untreated_rep2

description: SAMPLE 83

value: B

value: Female

value: Unaffected

value: Lymphoblastoid cell line (LCL)

value: Untreated


title: FamilyB_Unaffected2_Untreated_rep3

description: SAMPLE 84


title: FamilyB_Unaffected1_Untreated_rep3

description: SAMPLE 81


title: FamilyB_Unaffected2_Untreated_rep1

description: SAMPLE 82


title: Breast_primary_7001520

value: female

value: breast

value: primary tumor

value: combined total RNA isolated from multiple breast cancer samples.


title: FamilyB_Unaffected1_Caffeine_rep1

description: SAMPLE 67


title: FamilyB_Affected3_Untreated_rep2

description: SAMPLE 65

value: Affected


title: Breast_primary_7001514


title: FamilyB_Affected3_Untreated_rep1

description: SAMPLE 64


title: Breast_primary_7000482


title: Breast_primary_7001519


title: Breast_primary_7001515


title: FamilyB_Affected2_Untreated_rep3

description: SAMPLE 63


title: FamilyB_Affected2_Untreated_rep2

description: SAMPLE 62


title: FamilyB_Affected3_Untreated_rep3

description: SAMPLE 66


title: Breast_primary_7000480


title: Breast_primary_7000481


title: Breast_primary_7000465


title: Breast_primary_7000467


title: FamilyB_Affected3_Caffeine_rep3

description: SAMPLE 57

value: Caffeine


title: FamilyB_Affected3_Caffeine_rep2

description: SAMPLE 56


title: FamilyB_Unaffected1_Caffeine_rep2

description: SAMPLE 68


title: FamilyB_Affected1_Untreated_rep1

description: SAMPLE 58


title: Breast_primary_7000458


title: Breast_primary_7000459


title: FamilyB_Affected1_Untreated_rep3

description: SAMPLE 60


title: FamilyB_Affected2_Untreated_rep1

description: SAMPLE 61


title: FamilyB_Affected1_Untreated_rep2

description: SAMPLE 59


title: FamilyB_Affected3_Caffeine_rep1

description: SAMPLE 55


title: Breast_primary_7000461


title: Breast_primary_7000463


title: Breast_primary_7000460


title: FamilyB_Affected2_Caffeine_rep2

description: SAMPLE 53


title: FamilyB_Affected1_Caffeine_rep3

description: SAMPLE 51


title: Breast_primary_7000456


title: Breast_primary_7000457


title: FamilyB_Affected2_Caffeine_rep3

description: SAMPLE 54


title: Breast_primary_7000455


title: FamilyB_Affected2_Caffeine_rep1

description: SAMPLE 52


title: FamilyB_Affected1_Caffeine_rep2

description: SAMPLE 50


title: FamilyB_Affected1_Caffeine_rep1

description: SAMPLE 49


title: FamilyA_Unaffected3_Untreated_rep2

description: SAMPLE 47

value: A


title: FamilyA_Unaffected2_Untreated_rep3

description: SAMPLE 45


title: FamilyB_Unaffected1_Untreated_rep2

description: SAMPLE 80


title: Breast_primary_7000452


title: FamilyA_Unaffected3_Untreated_rep3

description: SAMPLE 48


title: Breast_primary_7000451


title: Breast_primary_7000454


title: FamilyA_Unaffected3_Untreated_rep1

description: SAMPLE 46


title: FamilyA_Unaffected1_Untreated_rep3

description: SAMPLE 42


title: FamilyA_Unaffected2_Untreated_rep1

description: SAMPLE 43


title: Breast_primary_7000449


title: Breast_primary_7000450


title: Breast_primary_7001516


title: FamilyA_Unaffected2_Untreated_rep2

description: SAMPLE 44


title: Breast_primary_7000446


title: Breast_primary_7000444


title: Breast_primary_7000442


title: FamilyA_Unaffected1_Untreated_rep1

description: SAMPLE 40


title: FamilyA_Unaffected2_Caffeine_rep3

description: SAMPLE 36


title: Breast_primary_7000431


title: Breast_primary_7000438


title: FamilyA_Unaffected3_Caffeine_rep1

description: SAMPLE 37


title: FamilyA_Unaffected2_Caffeine_rep2

description: SAMPLE 35


title: FamilyA_Unaffected1_Caffeine_rep2

description: SAMPLE 32


title: Breast_primary_7000433


title: Breast_primary_7000436


title: Breast_primary_7000434


title: FamilyA_Unaffected1_Caffeine_rep3

description: SAMPLE 33


title: FamilyA_Affected5_Untreated_rep3

description: SAMPLE 30


title: FamilyA_Affected5_Untreated_rep2

description: SAMPLE 29


title: Breast_primary_7000445


title: FamilyA_Unaffected1_Caffeine_rep1

description: SAMPLE 31


title: Breast_primary_7000432


title: Breast_primary_7000440


title: Breast_primary_7000447


title: Breast_primary_7000428


title: FamilyA_Unaffected1_Untreated_rep2

description: SAMPLE 41


title: Breast_primary_7000441


title: FamilyA_Affected5_Untreated_rep1

description: SAMPLE 28


title: Breast_primary_7000443


title: Breast_primary_7000435


title: Breast_primary_7000427


title: FamilyA_Unaffected3_Caffeine_rep3

description: SAMPLE 39


title: FamilyA_Affected4_Untreated_rep2

description: SAMPLE 26


title: Breast_primary_7000439


title: FamilyA_Affected4_Untreated_rep1

description: SAMPLE 25


title: FamilyA_Affected3_Untreated_rep2

description: SAMPLE 23


title: FamilyA_Affected3_Untreated_rep3

description: SAMPLE 24


title: Breast_primary_6001849


title: Breast_primary_6001851


title: FamilyA_Affected3_Untreated_rep1

description: SAMPLE 22


title: FamilyA_Affected4_Untreated_rep3

description: SAMPLE 27


title: Breast_primary_6001852


title: FamilyA_Unaffected2_Caffeine_rep1

description: SAMPLE 34


title: Breast_primary_6001848


title: Breast_primary_6001850


title: FamilyA_Unaffected3_Caffeine_rep2

description: SAMPLE 38


title: FamilyA_Affected2_Untreated_rep3

description: SAMPLE 21


title: Breast_primary_6001847


title: FamilyA_Affected2_Untreated_rep2

description: SAMPLE 20


title: Breast_primary_6001846


title: Control embryonic stem cell (6285449023_F)

city: Bonn

first: Frank

last: Edenhofer

address: Sigmund-Freud Str. 25

department: Institute of Reconstructive Neurobiology

institute: University of Bonn - Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using GenomeStudios average normalisation with background removal. Differential expression was computed by GenomeStudio using the Man-Whitney error model.

source_name: Oct4-GiP mouse embryonic fibroblasts (MEFs) (Ying et al., 2002)

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

tag: state

value: embryonic stem cell


title: Control embryonic stem cell (6285449023_D)


title: Breast_primary_6001844


title: Oct4-GFP neural stem cell clone 5 (6285449043_F)

value: induced neural stem cell clone 5


title: Control embryonic stem cell (6285449023_E)


title: Control neural stem cell (6285449043_C)

source_name: primary cells, mouse forebrain

value: neural stem cell


title: FamilyA_Affected2_Untreated_rep1

description: SAMPLE 19


title: Oct4-GFP neural stem cell clone 3 (6285449021_D)

value: induced neural stem cell clone 3


title: Oct4-GFP neural stem cell clone 3 (6285449021_F)


title: Oct4-GFP neural stem cell clone 3 (6285449043_E)


title: Oct4-GFP neural stem cell clone 5 (6285449023_B)


title: Control neural stem cell (6285449043_A)


title: FamilyA_Affected1_Untreated_rep1

description: SAMPLE 16


title: FamilyA_Affected1_Untreated_rep3

description: SAMPLE 18


title: Oct4-GFP neural stem cell clone 2 (6285449021_B)

value: induced neural stem cell clone 2


title: Breast_primary_6001845


title: Oct4-GFP neural stem cell clone 5 (6285449023_C)


title: Oct4-GFP neural stem cell clone 3 (6285449021_E)


title: Oct4-GFP neural stem cell clone 5 (6285449023_A)


title: Control neural stem cell (6285449043_B)


title: Oct4-GFP embryonic fibroblast (MEF) (6285449043_D)

value: fibroblast


title: Oct4-GFP neural stem cell clone 2 (6285449021_C)


title: FamilyA_Affected1_Untreated_rep2

description: SAMPLE 17

value: Female


title: Oct4-GFP neural stem cell clone 2 (6285449021_A)


title: Breast_primary_6001842


title: Breast_primary_6001843


title: Oct4-GFP embryonic fibroblast (MEF) (6285449005_C)


title: FamilyA_Affected5_Caffeine_rep3

description: SAMPLE 15


title: Oct4-GFP embryonic fibroblast (MEF) (6285449005_A)


title: Breast_primary_7000429


title: Oct4-GFP embryonic fibroblast (MEF) (6285449005_B)


title: Breast_primary_6001769


title: Breast_primary_6001770


title: Ad libitum fed Paneth cells, biological rep 1

city: Cambridge

first: Pekka

last: Katajisto

address: ) Cambridge center

institute: Whitehead Institute for Biomedical Research

description: expression data from isolated mouse paneth cells following ad libitum diet

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

scan_protocol: GeneChips were scanned using the affymetrix scanner

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: isolated Paneth cells

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

growth_protocol: analyzed cells were primary paneth cells

extract_protocol: Qiagen Rneasy column were used to isolate total RNA from sorted Paneth cells

treatment_protocol: Mice were euthanized and Paneth cells isolated by methods described in PMID:21113151

tag: age

value: 4 months

tag: diet

value: ad libitum diet

tag: cell type

value: paneth cells


title: Ad libitum fed Paneth cells, biological rep 3


title: Ad libitum fed Paneth cells, biological rep 2


title: Calorie restricted Paneth cells, biological rep 1

description: expression data from isolated mouse paneth cells following calorie restricted diet

value: calorie restricted diet


title: Calorie restricted Paneth cells, biological rep 3


title: FamilyA_Affected4_Caffeine_rep2

description: SAMPLE 11

tag: family

value: Lymphoblastoid cell line (LCL)


title: FamilyA_Affected5_Caffeine_rep1

description: SAMPLE 13

tag: gender


title: Breast_primary_6001767

value: female

value: breast

value: primary tumor


title: FamilyA_Affected5_Caffeine_rep2

description: SAMPLE 14

tag: breast cancer

value: Affected

value: Caffeine


title: FamilyA_Affected4_Caffeine_rep3

description: SAMPLE 12

value: A

tag: agent


title: Calorie restricted Paneth cells, biological rep 2


title: Breast_primary_6001768

value: combined total RNA isolated from multiple breast cancer samples.


title: Calorie restricted Paneth cells, biological rep 4


title: Ppar-beta null 1 uM GW0742 +hRas rep2

city: University Park

first: Combiz

last: Khozoie

state: PA

address: 312 Life Sciences Building

institute: The Pennsylvania State University

description: Affymetrix Mouse Gene 1.0 ST Array

hyb_protocol: Hybridization cocktail prepared using the GeneChip Hybridization Wash and Stain Kit (#702232).  Arrays hybridized according to the manufacturer’s instructions in the Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Arrays washed and stained using the Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol using the GeneChip Hybridization Wash and Stain Kit (#702232).  Stained arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Data was normalized using the Robust Multichip Average (RMA) approach as previously described (Do and Choi, 2006) with the CFM file provided by the manufacturer (mogene10stv1.r3cdf)

source_name: Ppar-beta null 1 uM GW0742 +hRas

label_protocol: FragmentED the sense strand cDNA according to the manufacturer’s instructions using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) and confirmed proper fragmentation using an RNA Nano Chip on the Agilent Bioanalyzer. Labeled the resulting fragmented cDNA using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) according to the manufacturer’s protocol. Assessed labeling efficiency with the gel shift assay described by the manufacturer but utilizing an Agilent Bioanalyzer RNA Nano Chip instead of PAGE.

growth_protocol: Primary keratinocytes were cultured as previously described (Dlugosz et al., 1995) for 2 days before transduced with Hras virus.

extract_protocol: Total RNA was extracted using TRIZOL reagent and subject to a further step of clean up using Rneasy kit.

treatment_protocol: Primary keratinocytes were treated with or without 1 uM GW0742 for 24 hours.

value: Primary keratinocyte

tag: strain

tag: genotype

value: Ppar-beta NULL

tag: hras

value: hRAS transduced for 48h

tag: ligand


title: Breast_primary_6001765

tag: tumor type

tag: lymph node metastasis

tag: age at diagnosis

tag: days between diagnosis and blood collection


title: FamilyA_Affected4_Caffeine_rep1

description: SAMPLE 10

tag: cell line


title: Ppar-beta null 1 uM GW0742 +hRas rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001766

tag: tissue

tag: metastatic

tag: sample type


title: Ppar-beta null DMSO +hRas rep2

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Ppar-beta null DMSO +hRas

tag: cell type

value: Control (DMSO)


title: Ppar-beta null DMSO +hRas rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: FamilyA_Affected3_Caffeine_rep3

description: SAMPLE 9

tag: family

value: Female


title: Breast_primary_6001763

tag: gender


title: Ppar-beta null 1 uM GW0742 +hRas rep1

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001764


title: FamilyA_Affected3_Caffeine_rep2

description: SAMPLE 8

tag: breast cancer


title: Breast_primary_6001762


title: Wild-type 1 uM GW0742 +hRAS rep3

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Wild-type 1 uM GW0742 +hRAS

value: wild-type


title: FamilyA_Affected3_Caffeine_rep1

description: SAMPLE 7

tag: agent


title: Ppar-beta null DMSO +hRas rep1

description: Affymetrix Mouse Gene 1.0 ST Array

tag: strain


title: FamilyA_Affected2_Caffeine_rep2

description: SAMPLE 5


title: FamilyA_Affected2_Caffeine_rep1

description: SAMPLE 4


title: Wild-type DMSO +hRAS rep2

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Wild-type DMSO +hRAS

tag: genotype


title: Wild-type 1 uM GW0742 +hRAS rep2

description: Affymetrix Mouse Gene 1.0 ST Array

tag: hras


title: Breast_primary_6001760


title: Wild-type 1 uM GW0742 +hRAS rep1

description: Affymetrix Mouse Gene 1.0 ST Array

tag: ligand


title: FamilyA_Affected2_Caffeine_rep3

description: SAMPLE 6


title: Ppar-beta null 1 uM GW0742 rep2

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Ppar-beta null 1 uM GW0742

value: hRAS mock transduced


title: Wild-type DMSO +hRAS rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: FamilyA_Affected1_Caffeine_rep3

description: SAMPLE 3


title: Wild-type DMSO +hRAS rep1

description: Affymetrix Mouse Gene 1.0 ST Array


title: FamilyA_Affected1_Caffeine_rep2

description: SAMPLE 2


title: Ppar-beta null DMSO rep1

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Ppar-beta null DMSO


title: Ppar-beta null 1 uM GW0742 rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001044

tag: tumor type


title: Ppar-beta null DMSO rep2

description: Affymetrix Mouse Gene 1.0 ST Array


title: Ppar-beta null DMSO rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001043

tag: lymph node metastasis


title: FamilyA_Affected1_Caffeine_rep1

description: SAMPLE 1


title: Breast_primary_6001035

tag: age at diagnosis


title: Ppar-beta null 1 uM GW0742 rep1

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001761

tag: days between diagnosis and blood collection


title: Wild-type 1 uM GW0742 rep2

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Wild-type 1 uM GW0742


title: Wild-type 1 uM GW0742 rep3

description: Affymetrix Mouse Gene 1.0 ST Array


title: Wild-type 1 uM GW0742 rep1

description: Affymetrix Mouse Gene 1.0 ST Array


title: Breast_primary_6001030


title: dNC-PCs differentiated 1

city: Regensburg

first: Christian

last: Morsczeck

address: Franz-Josef Strauss Allee 11

institute: University of Regensburg

description:
SAMPLE 7
Gene expression of dNC-PCs at day 7 of differentiation

hyb_protocol: Hybridization to Affymetrix oligonucleotide microarray Human Gene 1.1 ST array was carried out overnight with 1biotin-labeled cRNA in a hybridization oven 640.

scan_protocol: GeneTitan scanner (Affymetrix)

data_processing: Affymetrix GeneChip Operating Software (GCOS) 1.4 and the Expression Console 1.1. Software. For the creation of the summarized log-signal the robust multi-chip analysis (RMA) algorithm was used.

source_name: dNC-PCs differentiated

label_protocol: Double-stranded cDNA was prepared from 5 μg of total cellular RNA (cDNA synthesis kit, Affymetrix Santa Clara, CA, USA), in vitro transcribed using an IVT labeling kit, and the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). All procedures according to the Affymetrix protocol.

growth_protocol: Cell were grown in DMEM medium (PAA, Pasching, Austria) and 10 % serum at 37°C in 5% CO2.

extract_protocol: Total RNAs were extracted using the kit NucleoSpin® RNA II kit (Macherey Nagel, Düren, Germany) and quality-controlled using the RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: After subconfluence cells at passage 6 were grown 7 days in the STEMPRO® Osteogenesis Differentiation Kit (Invitrogen).

value: dental neural crest progenitor cells (dNC-PCs)

tag: culture medium

value: differentiation medium


title: SHED differentiated 2

description:
SAMPLE 6
Gene expression of SHED at day 7 of differentiation

source_name: SHED differentiated

value: stem cells of exfoliated descidious teeth (SHED)


title: dNC-PCs differentiated 2

description:
SAMPLE 8
Gene expression of dNC-PCs at day 7 of differentiation


title: Fungus Inoculation 1 [strong spatial bias]

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15133.gif

tag: tissue

value: inoculated roots/leaves

tag: infection

value: Yes

source_name: control roots/leaves

value: control roots/leaves


title: anti H3K4me3 (Millipore 07-473) in Psip1 mutant

type: genomic

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

description: Chip-chip MEFs H3K4me3

hyb_protocol: Samples were hybridized according to standard protocol (NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: The mean signal intensity of the 4 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. The log enrichment for each group was calculated by subtracting the mean of log2 input intensities from the mean of log2 enriched intensities.

molecule: genomic DNA

source_name: Input ChIP DNA from Psip1 mutant MEFs

label_protocol: 0.6 to 1.5 µg ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Passage 4 Cells were used

extract_protocol: MEFs were harvested by trypsinizing and immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously(Johnson et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 200 µg chromatin was incubated with 4µg rabit IgG (Santa Cruz, sc-2025) or 4 µg Psip1 antibodies (A300-847) and washed and eluted as described in (Johnson et al 2007). Reverse cross-linked DNA was purified as described above.

value: embryonic fibroblast

tag: age

tag: chip antibody

tag: genetic background

value: 129/Ola C57BL/6 mixed

tag: sample type

value: Input ChIP DNA from Psip1 mutant MEFs

value: Psip1 mutant

source_name: H3K4me3ChIP DNA from Psip1 mutantMEFs

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

value: H3K4me3ChIP DNA from Psip1 mutantMEFs


title: 001-010

city: durham

first: Miao

last: yu

address: Laselle drive

institute: Duke

hyb_protocol: Hybridization of samples to  Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affymerix manual instructions

data_processing: Data is RMA normalized using R/Bioconductor

source_name: ovarian tissue biopsy

label_protocol: Prepared samples using the Affymetrix GeneChip ENZO one cycle labeling kit

extract_protocol: Qiagen RNeasy Mini Kit

tag: batch

value: FAIL

tag: patient identifier

tag: indicator of clinical response (cr=1/pr=2/sd=3)

tag: overall survival (years)

tag: status for overall survival (1=death, 0=censored)

tag: progression free survival (years)

tag: status for progression free survival (1=death, 0=censored)

tag: objective response (1 = cr or pr, 0= sd)


title: D107

value: PASS


title: Wild-type DMSO rep2

description: Affymetrix Mouse Gene 1.0 ST Array

source_name: Wild-type DMSO

tag: cell type

value: Primary keratinocyte

tag: strain

tag: genotype

tag: hras

tag: ligand

value: Control (DMSO)


title: 001-013


title: anti H3K4me3 (Millipore 07-473)

description: Chip-chip MEFs H3K4me3

source_name: Input ChIP DNA from MEFs

tag: age

tag: chip antibody

tag: genetic background

value: Input ChIP DNA from MEFs

value: wild type

source_name: H3K4me3 ChIP DNA from MEFs

value: H3K4me3 ChIP DNA from MEFs


title: Wild-type DMSO rep3

description: Affymetrix Mouse Gene 1.0 ST Array

value: wild-type

value: hRAS mock transduced


title: 002-004


title: Wild-type DMSO rep1

description: Affymetrix Mouse Gene 1.0 ST Array


title: dNC-PCs undifferentiated 2

description:
SAMPLE 4
Gene expression of dNC-PCs at day 0 of differentiation

source_name: dNC-PCs undifferentiated

value: dental neural crest progenitor cells (dNC-PCs)

tag: culture medium

value: standard medium


title: D103

tag: batch


title: SHED differentiated 1

description:
SAMPLE 5
Gene expression of SHED at day 7 of differentiation

value: stem cells of exfoliated descidious teeth (SHED)

value: differentiation medium


title: D104

tag: patient identifier


title: 001-012

tag: indicator of clinical response (cr=1/pr=2/sd=3)


title: dNC-PCs undifferentiated 1

description:
SAMPLE 3
Gene expression of dNC-PCs at day 0 of differentiation


title: H3K36me3 ChIP using anti H3K36me3 (Abcam Ab 9050-100)  rep4

description: Chip-chip MEFs H3K36me3

source_name: H3K36me3 ChIP DNA from MEFs

value: embryonic fibroblast

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: 129/Ola C57BL/6 mixed

tag: sample type

value: H3K36me3 ChIP DNA from MEFs

source_name: Input DNA from MEFs

value: Input DNA from MEFs


title: H3K36me3 ChIP using anti H3K36me3 (Abcam Ab 9050-100)  rep2

description: Chip-chip MEFs H3K36me3

source_name: H3K36me3 ChIPDNA from MEFs

value: H3K36me3 ChIPDNA from MEFs


title: 001-011

value: PASS

value: <NA>

tag: overall survival (years)

tag: status for overall survival (1=death, 0=censored)

tag: progression free survival (years)

tag: status for progression free survival (1=death, 0=censored)


title: H3K36me3 ChIP using anti H3K36me3 (Abcam Ab 9050-100)  rep3

description: Chip-chip MEFs H3K36me3

tag: cell type

tag: genotype


title: H3K36me3 ChIP using anti H3K36me3 (Abcam Ab 9050-100)  rep1

description: Chip-chip MEFs H3K36me3

value: Input ChIP DNA from MEFs

source_name: H3K36me3  ChIP DNA from MEFs

value: H3K36me3  ChIP DNA from MEFs


title: D106

value: FAIL

tag: objective response (1 = cr or pr, 0= sd)


title: Responses to mycotoxin-Deoxynivalenol - Slide 1

state: CA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21124.gif

source_name: No DON treated control

tag: reference

value: No DON treated control

source_name: 5ug DON treated for 6hrs

tag: test

value: 5ug DON treated for 6hrs

tag: time

value: 6 h


title: D101


title: Psip1 ChIP using A300-847 antibody (recognises p52 isoform of Psip1) rep4

description: Chip-chip MEFs Psip1 (A300-847)

source_name: Psip1 ChIP DNA from MEFs

tag: age

tag: chip antibody

value: Bethyl

tag: genetic background

value: Psip1 ChIP DNA from MEFs

value: wild type


title: M7780-liver-Chronic-non-tumor, 461097_A01

status: Public on Apr 11 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

description:
461097_A01
mRNA

hyb_protocol: Woodchuck Gene Expression HX3 Microarrays were hybridized with 6.7 μg Cy3-labelled cDNA for 16-20 hours at 42ºC and were washed and dried according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned using a Roche NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution. Features were extracted using NimbleScan Software.

data_processing: The gene expression data was normalized by the Robust Multichip Average (RMA) algorithm implemented in Partek Genomics Suite 6.5 (Partek, St. Louis MO).

organism: Marmota monax

source_name: Woodchuck liver, chronic, non-tumor

label_protocol: 10 μg of total RNA was reverse-transcribed using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, Inc., Calsbad, CA). After precipitation, double-stranded cDNA was labelled with Cy3 by using the Roche NimbleGen One-color DNA Labelling Kit (Roche NimbleGen, Inc., Madison, WI).

extract_protocol: Total RNA was isolated from woodchuck liver tissues using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA).

tag: tissue

value: liver

tag: whv infection status

value: chronic

tag: tumor status

value: non-tumor

tag: sample identifier


title: M7777-liver-Chronic-non-tumor, 461119_A02

description:
461119_A02
mRNA


title: 002-005

tag: batch

tag: patient identifier

tag: indicator of clinical response (cr=1/pr=2/sd=3)

tag: overall survival (years)


title: SHED undifferentiated 1

description:
SAMPLE 1
Gene expression of SHED at day 0 of differentiation

source_name: SHED undifferentiated

tag: cell type

value: stem cells of exfoliated descidious teeth (SHED)

tag: culture medium

value: standard medium


title: M5616-liver-Chronic-Tumor, 460990_A03

description:
460990_A03
mRNA

source_name: Woodchuck liver, chronic, tumor

value: tumor


title: Psip1 ChIP using A300-847 antibody (recognises p52 isoform of Psip1) rep3

description: Chip-chip MEFs Psip1 (A300-847)

value: embryonic fibroblast

tag: chip antibody manufacturer

tag: chip antibody catalog #

value: 129/Ola C57BL/6 mixed

tag: sample type

tag: genotype

value: Input DNA from MEFs


title: SHED undifferentiated 2

description:
SAMPLE 2
Gene expression of SHED at day 0 of differentiation


title: M7777-liver-Chronic-Tumor, 461112_A02

description:
461112_A02
mRNA


title: M7777-liver-Chronic-Tumor, 460975_A03

description:
460975_A03
mRNA


title: M7777-liver-Chronic-non-tumor, 460970_A01

description:
460970_A01
mRNA


title: M7780-liver-Chronic-non-tumor, 460948_A03

description:
460948_A03
mRNA


title: M7780-liver-Chronic-Tumor, 461110_A02

description:
461110_A02
mRNA


title: M7780-liver-Chronic-non-tumor, 460808_A03

description:
460808_A03
mRNA


title: M7777-liver-Chronic-Tumor, 461103_A02

description:
461103_A02
mRNA


title: M5616-liver-Chronic-non-tumor, 460944_A02

description:
460944_A02
mRNA


title: M5616-liver-Chronic-non-tumor, 460971_A03

description:
460971_A03
mRNA


title: M7777-liver-Chronic-non-tumor, 460967_A01

description:
460967_A01
mRNA


title: M5616-liver-Chronic-non-tumor, 460968_A03

description:
460968_A03
mRNA


title: M7780-liver-Chronic-Tumor, 460878_A02

description:
460878_A02
mRNA


title: M5616-liver-Chronic-non-tumor, 460935_A03

description:
460935_A03
mRNA


title: M5616-liver-Chronic-Tumor, 460781_A01

description:
460781_A01
mRNA


title: M5616-liver-Chronic-non-tumor, 461116_A01

description:
461116_A01
mRNA


title: M5616-liver-Chronic-Tumor, 460808_A01

description:
460808_A01
mRNA


title: M7780-liver-Chronic-Tumor, 460969_A02

description:
460969_A02
mRNA


title: M5376-liver-Chronic-non-tumor, 461108_A02

description:
461108_A02
mRNA


title: Psip1 ChIP using A300-847 antibody (recognises p52 isoform of Psip1) rep2

description: Chip-chip MEFs Psip1 (A300-847)

tag: age


title: Psip1 ChIP using A300-847 antibody (recognises p52 isoform of Psip1) rep1

description: Chip-chip MEFs Psip1 (A300-847)

tag: chip antibody


title: liver-HIF-2a-rep2

city: Shanghai

first: Haixiang

last: Sun

address: Fenglin Road, 180

institute: Zhongshan Hospital

hyb_protocol: Labeled DNA was mixed and hybridized to NimbleGen HG18 RefSeq promoter array, which is single array design containing all known well-characterized 18028 RefSeq promoter regions (from about -2200bp to +500bp of the TSSs) totally covered by ~385, 000 probes.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner.

data_processing: Raw data were extracted and processed by NimbleScan 2.5.

source_name: HIF-2a(NB #100-122) chip DNA from MHCC97H cell

label_protocol: Purified Input (whole cell extract) and ChIP DNA were amplified by PCR and labeled with Cy3- and Cy5-labeled random 9-mers, respectively.

growth_protocol: cells were cultured in DMEM medium with 10% FBS

extract_protocol: Cells were chemically crosslinked by 1% formaldehyde, then lysed in lysis buffers and sonicated to solubilize and shear crosslinked DNA. The average length of DNA fragments was 400-500bp. The resulting whole cell extract was incubated overnight at 4°C with BioMag IgG magnetic beads that had been preincubated with the appropriate antibody. Bound complexes were eluted from the beads and crosslinking was reversed by overnight incubation at 65℃, and then purified. Whole cell extract DNA (reserved from the sonication step) was also treated for crosslink reversal.

treatment_protocol: MHCC97H cells are an established cell line

value: human liver cancer cell

tag: antibody

tag: antibody vendor

value: Novus Bio

tag: antibody catalog number

tag: cell line

source_name: Input DNA from same cells

tag: fraction

value: input DNA


title: M5376-liver-Chronic-non-tumor, 461099_A03

description:
461099_A03
mRNA

tag: tissue

tag: whv infection status

tag: tumor status

tag: sample identifier


title: M4790-liver-Chronic-Tumor, 461120_A03

description:
461120_A03
mRNA


title: liver-HIF-2a-rep1

tag: cell type


title: M5376-liver-Chronic-non-tumor, 460989_A02

description:
460989_A02
mRNA


title: M5616-liver-Chronic-non-tumor, 460828_A02

description:
460828_A02
mRNA


title: M4790-liver-Chronic-non-tumor, 460990_A02

description:
460990_A02
mRNA


title: M5376-liver-Chronic-non-tumor, 461105_A01

description:
461105_A01
mRNA


title: M4790-liver-Chronic-non-tumor, 460872_A01

description:
460872_A01
mRNA


title: M4790-liver-Chronic-Tumor, 460957_A02

description:
460957_A02
mRNA


title: M4765-liver-Chronic-Tumor, 461119_A03

description:
461119_A03
mRNA


title: M5376-liver-Chronic-Tumor, 460968_A02

description:
460968_A02
mRNA


title: M5376-liver-Chronic-Tumor, 461044_A03

description:
461044_A03
mRNA


title: M5376-liver-Chronic-non-tumor, 460781_A02

description:
460781_A02
mRNA


title: M4790-liver-Chronic-non-tumor, 461043_A03

description:
461043_A03
mRNA


title: M4790-liver-Chronic-Tumor, 460975_A02

description:
460975_A02
mRNA


title: M4790-liver-Chronic-non-tumor, 460968_A01

description:
460968_A01
mRNA


title: M4765-liver-Chronic-non-tumor, 461036_A03

description:
461036_A03
mRNA


title: M4765-liver-Chronic-Tumor, 460990_A01

description:
460990_A01
mRNA


title: M4765-liver-Chronic-non-tumor, 461061_A02

description:
461061_A02
mRNA


title: M4728-liver-Chronic-Tumor, 461112_A03

description:
461112_A03
mRNA


title: M4765-liver-Chronic-non-tumor, 460979_A03

description:
460979_A03
mRNA


title: M4790-liver-Chronic-non-tumor, 460829_A03

description:
460829_A03
mRNA


title: M4728-liver-Chronic-non-tumor, 461097_A03

description:
461097_A03
mRNA


title: M4728-liver-Chronic-non-tumor, 460830_A03

description:
460830_A03
mRNA


title: M4765-liver-Chronic-non-tumor, 461101_A01

description:
461101_A01
mRNA


title: M4728-liver-Chronic-non-tumor, 461043_A02

description:
461043_A02
mRNA


title: M4728-liver-Chronic-Tumor, 460961_A01

description:
460961_A01
mRNA


title: M4728-liver-Chronic-non-tumor, 460979_A02

description:
460979_A02
mRNA


title: M4765-liver-Chronic-non-tumor, 460828_A01

description:
460828_A01
mRNA


title: M4728-liver-Chronic-non-tumor, 460868_A01

description:
460868_A01
mRNA


title: M4765-liver-Chronic-Tumor, 460976_A03

description:
460976_A03
mRNA


title: M4727-liver-Chronic-Tumor, 461128_A02

description:
461128_A02
mRNA


title: M4727-liver-Chronic-non-tumor, 460948_A01

description:
460948_A01
mRNA


title: M4728-liver-Chronic-Tumor, 460771_A01

description:
460771_A01
mRNA


title: M4790-liver-Chronic-non-tumor, 460956_A02

description:
460956_A02
mRNA


title: M4727-liver-Chronic-non-tumor, 460868_A02

description:
460868_A02
mRNA


title: M4727-liver-Chronic-non-tumor, 461100_A02

description:
461100_A02
mRNA


title: M4727-liver-Chronic-non-tumor, 460894_A03

description:
460894_A03
mRNA


title: M4727-liver-Chronic-non-tumor, 461118_A03

description:
461118_A03
mRNA


title: M4727-liver-Chronic-Tumor, 460801_A02

description:
460801_A02
mRNA


title: M5376-liver-Chronic-non-tumor, 460950_A01

description:
460950_A01
mRNA


title: M4728-liver-Chronic-non-tumor, 461120_A02

description:
461120_A02
mRNA


title: M4727-liver-Chronic-Tumor, 461101_A02

description:
461101_A02
mRNA


title: M4727-liver-Chronic-non-tumor, 460941_A03

description:
460941_A03
mRNA


title: M4388-liver-Chronic-Tumor, 461108_A03

description:
461108_A03
mRNA


title: M4388-liver-Chronic-non-tumor, 460868_A03

description:
460868_A03
mRNA


title: M4388-liver-Chronic-Tumor, 460956_A03

description:
460956_A03
mRNA


title: M4388-liver-Chronic-non-tumor, 461059_A01

description:
461059_A01
mRNA


title: M4388-liver-Chronic-non-tumor, 460929_A01

description:
460929_A01
mRNA


title: M4324-liver-Chronic-non-tumor, 461059_A02

description:
461059_A02
mRNA


title: M5376-liver-Chronic-Tumor, 460892_A02

description:
460892_A02
mRNA


title: M4324-liver-Chronic-non-tumor, 460982_A03

description:
460982_A03
mRNA


title: M4388-liver-Chronic-Tumor, 460828_A03

description:
460828_A03
mRNA


title: M4324-liver-Chronic-Tumor, 460878_A03

description:
460878_A03
mRNA


title: M4324-liver-Chronic-Tumor, 460979_A01

description:
460979_A01
mRNA


title: M4191-liver-Chronic-Tumor, 460978_A01

description:
460978_A01
mRNA


title: M4191-liver-Chronic-non-tumor, 460949_A02

description:
460949_A02
mRNA


title: M4191-liver-Chronic-Tumor, 461109_A01

description:
461109_A01
mRNA


title: M4191-liver-Chronic-Tumor, 461058_A01

description:
461058_A01
mRNA


title: M4191-liver-Chronic-non-tumor, 461099_A01

description:
461099_A01
mRNA


title: M4171-liver-Chronic-Tumor, 460992_A03

description:
460992_A03
mRNA


title: M4171-liver-Chronic-Tumor, 461115_A02

description:
461115_A02
mRNA


title: M4171-liver-Chronic-Tumor, 460973_A01

description:
460973_A01
mRNA


title: M4171-liver-Chronic-Tumor, 460813_A02

description:
460813_A02
mRNA


title: M4171-liver-Chronic-non-tumor, 460988_A01

description:
460988_A01
mRNA


title: M4191-liver-Chronic-non-tumor, 460928_A02

description:
460928_A02
mRNA


title: M4171-liver-Chronic-Tumor, 461060_A02

description:
461060_A02
mRNA


title: M3134-liver-Chronic-Tumor, 461118_A02

description:
461118_A02
mRNA


title: M3134-liver-Chronic-non-tumor, 461113_A03

description:
461113_A03
mRNA


title: M4171-liver-Chronic-non-tumor, 461036_A02

description:
461036_A02
mRNA


title: M3134-liver-Chronic-non-tumor, 461059_A03

description:
461059_A03
mRNA


title: M4324-liver-Chronic-Tumor, 461104_A02

description:
461104_A02
mRNA


title: M3134-liver-Chronic-non-tumor, 460989_A01

description:
460989_A01
mRNA


title: M3134-liver-Chronic-non-tumor, 460987_A01

description:
460987_A01
mRNA


title: M4324-liver-Chronic-non-tumor, 460802_A01

description:
460802_A01
mRNA


title: M3134-liver-Chronic-Tumor, 460973_A02

description:
460973_A02
mRNA


title: M4171-liver-Chronic-non-tumor, 460961_A03

description:
460961_A03
mRNA


title: M3134-liver-Chronic-non-tumor, 460771_A03

description:
460771_A03
mRNA


title: M7780-spleen-Chronic, 461118_A01

description:
461118_A01
mRNA

source_name: Woodchuck spleen, chronic

extract_protocol: Total RNA was isolated from spleen.

value: spleen


title: M4765-liver-Chronic-non-tumor, 461125_A03

description:
461125_A03
mRNA


title: M3134-liver-Chronic-Tumor, 461104_A03

description:
461104_A03
mRNA


title: M3134-liver-Chronic-non-tumor, 460801_A03

description:
460801_A03
mRNA


title: M4324-spleen-Chronic, 461108_A01

description:
461108_A01
mRNA


title: M4075-spleen-Uninfected, 461110_A01

description:
461110_A01
mRNA

source_name: Woodchuck spleen, uninfected

value: uninfected


title: M4380-spleen-Resolved, 461042_A02

description:
461042_A02
mRNA

source_name: Woodchuck spleen, resolved

value: resolved


title: M4378-spleen-Resolved, 461034_A02

description:
461034_A02
mRNA


title: M4374-spleen-Resolved, 460976_A01

description:
460976_A01
mRNA


title: M4171-spleen-Chronic, 461114_A03

description:
461114_A03
mRNA


title: M4374-spleen-Resolved, 461105_A03

description:
461105_A03
mRNA


title: M4046-spleen-Uninfected, 460988_A03

description:
460988_A03
mRNA


title: M4301-spleen-Resolved, 460970_A02

description:
460970_A02
mRNA


title: M4075-spleen-Uninfected, 460982_A02

description:
460982_A02
mRNA


title: M4046-spleen-Uninfected, 460927_A03

description:
460927_A03
mRNA


title: M4374-spleen-Resolved, 460951_A03

description:
460951_A03
mRNA


title: M4380-spleen-Resolved, 461100_A01

description:
461100_A01
mRNA


title: M7777-spleen-Chronic, 461110_A03

description:
461110_A03
mRNA


title: M4046-spleen-Uninfected, 460948_A02

description:
460948_A02
mRNA


title: M4171-spleen-Chronic, 460830_A01

description:
460830_A01
mRNA


title: M7777-spleen-Chronic, 460951_A02

description:
460951_A02
mRNA


title: M7777-spleen-Chronic, 460894_A01

description:
460894_A01
mRNA


title: M7780-spleen-Chronic, 460969_A01

description:
460969_A01
mRNA


title: M4324-spleen-Chronic, 460987_A02

description:
460987_A02
mRNA


title: M4301-spleen-Resolved, 460944_A01

description:
460944_A01
mRNA


title: M4378-spleen-Resolved, 460813_A01

description:
460813_A01
mRNA


title: M4171-spleen-Chronic, 460829_A01

description:
460829_A01
mRNA


title: M4324-spleen-Chronic, 461107_A02

description:
461107_A02
mRNA


title: M4301-spleen-Resolved, 460974_A01

description:
460974_A01
mRNA


title: M4075-spleen-Uninfected, 460992_A01

description:
460992_A01
mRNA


title: M4380-spleen-Resolved, 460950_A02

description:
460950_A02
mRNA


title: M4380-kidney-Resolved, 461128_A01

description:
461128_A01
mRNA

source_name: Woodchuck kidney, resolved

extract_protocol: Total RNA was isolated using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA).

value: kidney


title: M7780-spleen-Chronic, 460878_A01

description:
460878_A01
mRNA


title: M7777-kidney-Chronic, 461128_A03

description:
461128_A03
mRNA

source_name: Woodchuck kidney, chronic


title: M4301-kidney-Resolved, 461114_A01

description:
461114_A01
mRNA


title: M7780-kidney-Chronic, 461104_A01

description:
461104_A01
mRNA


title: M4378-spleen-Resolved, 460768_A02

description:
460768_A02
mRNA


title: M4091-kidney-Uninfected, 461098_A01

description:
461098_A01
mRNA

source_name: Woodchuck kidney, uninfected


title: M4171-kidney-Chronic, 461125_A02

description:
461125_A02
mRNA


title: M4046-kidney-Uninfected, 461109_A02

description:
461109_A02
mRNA


title: M4374-kidney-Resolved, 461044_A02

description:
461044_A02
mRNA


title: M7777-kidney-Chronic, 461115_A03

description:
461115_A03
mRNA


title: M4324-kidney-Chronic, 461113_A02

description:
461113_A02
mRNA


title: M4171-kidney-Chronic, 461103_A01

description:
461103_A01
mRNA


title: M4191-kidney-Chronic, 461113_A01

description:
461113_A01
mRNA


title: M4378-kidney-Resolved, 461044_A01

description:
461044_A01
mRNA


title: M4324-kidney-Chronic, 461100_A03

description:
461100_A03
mRNA


title: M7780-kidney-Chronic, 460989_A03

description:
460989_A03
mRNA


title: M4191-kidney-Chronic, 460988_A02

description:
460988_A02
mRNA


title: M4171-liver-Chronic-Tumor, 460929_A03

description:
460929_A03
mRNA


title: M4075-kidney-Uninfected, 461042_A03

description:
461042_A03
mRNA


title: DLD1 5SA-Atoh1-3

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit. 1.65 μg of cRNA samples were subjected to fragmentation (30 min at 60°C) and then hybridized on a 4×44K Agilent Whole Human Genome Oligo DNA Microarray Ver2.0 in a rotary oven (10 rpm at 65°C for 17 h).

scan_protocol: Slides were scanned with Agilent DNA Microarray Scanner.

data_processing: Gene expression values measured with the microarrays for DLD1_GFP (N=3) and DLD1_5SA-Atoh1 (N=3) were normalized with GeneSpring software by using the 75th percentile value.The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:　026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: 5SA-Atoh1 expressing DLD1 cells

label_protocol: RNA samples were labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies). Labeling of 100 ng of total RNA was performed using Cyanine 3-CTP.

growth_protocol: Human sporadic colon cancer-derived DLD-1 cells were cultured in Dubecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent. All samples showed RNA Integrity Numbers (RIN) more than 9.5.

treatment_protocol: Either GFP or 5SA-Atoh1 was expressed in DLD1 cells by lenti virus infection system.

tag: genotype/variation

value: Mutated Atoh1 (5SA-Atoh1)


title: M4075-kidney-Uninfected, 460974_A03

description:
460974_A03
mRNA


title: DLD1 GFP-2

source_name: GFP expressing DLD1 cells

value: sporadic colon cancer-derived DLD-1 cells

value: control


title: M4324-kidney-Chronic, 461042_A01

description:
461042_A01
mRNA

value: chronic


title: DLD1 5SA-Atoh1-1