title: SAMPLE 23_miRNA_Normal [FF]

description: SAMPLE 23


title: SAMPLE 25_miRNA_Normal [FF]

status: Public on Aug 03 2012

type: RNA

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

country: USA

institute: Mayo Clinic

description: SAMPLE 25

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol

scan_protocol: Scanned using the Illumina Bead Array Reader

data_processing: The data were normalized using quantile normalization with BeadStudio software. The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cDNA were prepared from 100-200ng total RNA using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser.

tag: tissue origin

value: uninvolved lung

tag: sample type

value: fresh-frozen (FF) normal tissue


title: SAMPLE 21_miRNA_Normal [FF]

description: SAMPLE 21


title: SAMPLE 19_miRNA_Normal [FF]

description: SAMPLE 19


title: SAMPLE 18_miRNA_Normal [FF]

description: SAMPLE 18


title: SAMPLE 20_miRNA_Normal [FF]

description: SAMPLE 20


title: SAMPLE 22_miRNA_Normal [FF]

description: SAMPLE 22


title: SAMPLE 16_miRNA_Normal [FF]

description: SAMPLE 16


title: SAMPLE 12_miRNA_Tumor [FF]

description: SAMPLE 12

value: lung adenocarcinoma

tag: cancer type

value: non-small-cell lung cancer (NSCLC)

value: fresh-frozen (FF) tumor tissue


title: SAMPLE 13_miRNA_Tumor [FF]

description: SAMPLE 13


title: SAMPLE 15_miRNA_Normal [FF]

description: SAMPLE 15


title: SAMPLE 14_miRNA_Normal [FF]

description: SAMPLE 14


title: SAMPLE 29_miRNA_Normal [FF]

description: SAMPLE 29


title: SAMPLE 17_miRNA_Normal [FF]

description: SAMPLE 17


title: SAMPLE 11_miRNA_Tumor [FF]

description: SAMPLE 11


title: SAMPLE 9_miRNA_Tumor [FF]

description: SAMPLE 9


title: SAMPLE 10_miRNA_Tumor [FF]

description: SAMPLE 10


title: SAMPLE 8_miRNA_Tumor [FF]

description: SAMPLE 8


title: SAMPLE 7_miRNA_Tumor [FF]

description: SAMPLE 7


title: SAMPLE 6_miRNA_Tumor [FF]

description: SAMPLE 6


title: SAMPLE 5_miRNA_Tumor [FF]

description: SAMPLE 5


title: SAMPLE 4_miRNA_Tumor [FF]

description: SAMPLE 4


title: SAMPLE 3_miRNA_Tumor [FF]

description: SAMPLE 3


title: 2hr flagellin exposure replicate2 vs 0hr untreatedpool

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

hyb_protocol: Labeled cDNA was hybridized to the Agilent arrays according to the Agilent protocol.

scan_protocol: Hybridizations were scanned on the Axon 4000B scanner with GenePix Pro software.

data_processing: Intensity values were extracted using Feature Extraction 9.5.3.1 from Agilent and then normalized and analyzed using MIDAS and MeV from the TM4 Suite.

organism: Mus musculus

source_name: RAW 264.7 cell line

label_protocol: A total of 2 ug of RNA in a mixture containing 6 ug of random hexamers, 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amini-allyl dUTP (aa-dUTP), reaction buffer, and 400 units of SuperScript III reverse transcriptase at 42C overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 65C for 15 min. Unincorporated aa-UTP was removed with a MinElute column. The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried and resuspended in 0.1 M sodium carbonate buffer (ph 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 was added at room temperature for 1 hour. Uncoupled label was removed using the Qiagen MinElute columns.

growth_protocol: RAW 264.7 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Cells were washed twice with PBS and then RNA was harvested according to the TriZol protocol.

treatment_protocol: Cells were treated with either flagellin or LPS for 1, 2, 4, or 24 hours.

tag: cell line

tag: treatment

value: 2hr flagellin exposure


title: PBMC_189_MED_final

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Affy'.

label: biotin

source_name: peripheral blood mononuclear cells (PBMCs), after intervention (final)

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Abdominally overweight subjects, both males and females aged between 45-60 years, participated in this study. All subjects gave written informed consent to participate in the study and the study protocol was approved by the Medical Ethical Committee of Wageningen University, the Netherlands.

extract_protocol: PBMCs were isolated from fasting whole blood samples by using the BD Vacutainer Cell Preparation Tubes. Total RNA was isolated of all PBMC samples by using the Qiagen RNeasy Micro kit (Qiagen, Venlo, Netherlands). The RNA yield was quantified with a Nanodrop ND 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and RNA integrity was checked on an Agilent 2100 bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom). Samples were only accepted for microarray analyzes if the RNA integrity number (RIN) was > 8.

treatment_protocol: Subjects consumed a completely controlled saturated fat (SFA)-rich diet, a SFA-by-MUFA-replaced diet (MUFA diet) or a MED diet for 8 weeks. Peripheral mononuclear cells PBMCs were collected before and after intervention.

tag: gender

value: female

tag: age

tag: health state

value: Abdominally overweight

tag: cell type

value: peripheral blood mononuclear cells

tag: diet

value: Mediterranean


title: SAMPLE 33_miRNA_Tumor [FF]

description: SAMPLE 33


title: PBMC_183_MED_final


title: PBMC_176_MED_baseline

source_name: peripheral blood mononuclear cells (PBMCs), before intervention (baseline)


title: PBMC_189_MED_baseline


title: PBMC_183_MED_baseline


title: PBMC_175_MED_final

value: male


title: PBMC_174_MED_final


title: PBMC_175_MED_baseline


title: PBMC_172_MED_final


title: PBMC_173_MED_baseline


title: PBMC_173_MED_final


title: SAMPLE 2_miRNA_Tumor [FF]

description: SAMPLE 2


title: PBMC_176_MED_final


title: SAMPLE 93_miRNA_normal [FFPE]

description: SAMPLE 93

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol.

data_processing: The data were normalized using quantile normalization with BeadStudio software

label_protocol: Biotinylated cDNA were prepared from 100-200ng total RNA using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation).

extract_protocol: RNA was extracted using the miRNeasy FFPE kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser.

tag: tissue type

value: formalin-fixed, paraffin-embedded (FFPE) normal tissues


title: SAMPLE 88_miRNA_normal [FFPE]

description: SAMPLE 88


title: SAMPLE 96_miRNA_Normal [FF]

description: SAMPLE 96


title: SAMPLE 92_miRNA_normal [FFPE]

description: SAMPLE 92


title: PBMC_172_MED_baseline


title: SAMPLE 90_miRNA_normal [FFPE]

description: SAMPLE 90


title: SAMPLE 91_miRNA_normal [FFPE]

description: SAMPLE 91


title: SAMPLE 94_miRNA_normal [FFPE]

description: SAMPLE 94


title: SAMPLE 87_miRNA_normal [FFPE]

description: SAMPLE 87


title: SAMPLE 89_miRNA_normal [FFPE]

description: SAMPLE 89


title: SAMPLE 86_miRNA_normal [FFPE]

description: SAMPLE 86


title: SAMPLE 1_miRNA_Tumor [FF]

description: SAMPLE 1


title: PBMC_174_MED_baseline


title: PBMC_161_MED_final


title: SAMPLE 83_miRNA_normal [FFPE]

description: SAMPLE 83


title: SAMPLE 84_miRNA_normal [FFPE]

description: SAMPLE 84


title: PBMC_161_MED_baseline


title: PBMC_149_MED_baseline


title: PBMC_154_MED_final


title: SAMPLE 81_miRNA_normal [FFPE]

description: SAMPLE 81


title: SAMPLE 82_miRNA_normal [FFPE]

description: SAMPLE 82


title: PBMC_153_MED_final


title: PBMC_153_MED_baseline


title: SAMPLE 79_miRNA_normal [FFPE]

description: SAMPLE 79


title: SAMPLE 76_miRNA_normal [FFPE]

description: SAMPLE 76


title: PBMC_154_MED_baseline


title: PBMC_118_MED_final


title: PBMC_112_MED_baseline


title: PBMC_115_MED_final


title: SAMPLE 80_miRNA_normal [FFPE]

description: SAMPLE 80


title: SAMPLE 78_miRNA_normal [FFPE]

description: SAMPLE 78


title: SAMPLE 77_miRNA_normal [FFPE]

description: SAMPLE 77


title: PBMC_112_MED_final


title: PBMC_190_MUFA_baseline

value: monounsaturated saturated fat


title: PBMC_118_MED_baseline


title: SAMPLE 72_miRNA_normal [FFPE]

description: SAMPLE 72


title: SAMPLE 71_miRNA_normal [FFPE]

description: SAMPLE 71


title: SAMPLE 75_miRNA_normal [FFPE]

description: SAMPLE 75


title: PBMC_115_MED_baseline


title: PBMC_180_MUFA_final


title: SAMPLE 73_miRNA_normal [FFPE]

description: SAMPLE 73


title: SAMPLE 70_miRNA_normal [FFPE]

description: SAMPLE 70


title: SAMPLE 69_miRNA_normal [FFPE]

description: SAMPLE 69


title: PBMC_111_MED_final


title: PBMC_149_MED_final


title: PBMC_111_MED_baseline


title: PBMC_177_MUFA_baseline


title: PBMC_190_MUFA_final


title: SAMPLE 74_miRNA_normal [FFPE]

description: SAMPLE 74


title: PBMC_162_MUFA_baseline


title: SAMPLE 67_miRNA_normal [FFPE]

description: SAMPLE 67


title: SAMPLE 66_miRNA_normal [FFPE]

description: SAMPLE 66


title: SAMPLE 65_miRNA_normal [FFPE]

description: SAMPLE 65


title: SAMPLE 63_miRNA_normal [FFPE]

description: SAMPLE 63


title: SAMPLE 64_miRNA_normal [FFPE]

description: SAMPLE 64


title: PBMC_180_MUFA_baseline


title: SAMPLE 62_miRNA_normal [FFPE]

description: SAMPLE 62


title: SAMPLE 58_miRNA_normal [FFPE]

description: SAMPLE 58


title: PBMC_177_MUFA_final


title: SAMPLE 59_miRNA_normal [FFPE]

description: SAMPLE 59


title: PBMC_146_MUFA_final


title: PBMC_146_MUFA_baseline


title: SAMPLE 57_miRNA_normal [FFPE]

description: SAMPLE 57


title: PBMC_144_MUFA_final


title: PBMC_162_MUFA_final


title: SAMPLE 68_miRNA_normal [FFPE]

description: SAMPLE 68


title: PBMC_136_MUFA_final


title: SAMPLE 56_miRNA_normal [FFPE]

description: SAMPLE 56


title: PBMC_125_MUFA_final


title: PBMC_144_MUFA_baseline


title: SAMPLE 60_miRNA_normal [FFPE]

description: SAMPLE 60


title: SAMPLE 61_miRNA_normal [FFPE]

description: SAMPLE 61


title: PBMC_126_MUFA_final


title: SAMPLE 55_miRNA_normal [FFPE]

description: SAMPLE 55


title: PBMC_136_MUFA_baseline


title: SAMPLE 54_miRNA_normal [FFPE]

description: SAMPLE 54


title: SAMPLE 52_miRNA_normal [FFPE]

description: SAMPLE 52


title: PBMC_126_MUFA_baseline


title: SAMPLE 53_miRNA_normal [FFPE]

description: SAMPLE 53


title: SAMPLE 51_miRNA_normal [FFPE]

description: SAMPLE 51


title: PBMC_127_MUFA_baseline


title: SAMPLE 50_miRNA_normal [FFPE]

description: SAMPLE 50


title: PBMC_125_MUFA_baseline


title: SAMPLE 49_miRNA_normal [FFPE]

description: SAMPLE 49


title: SAMPLE 48_miRNA_normal [FFPE]

description: SAMPLE 48


title: SAMPLE 47_miRNA_tumor [FFPE]

description: SAMPLE 47

value: formalin-fixed, paraffin-embedded (FFPE) tumor tissues


title: PBMC_127_MUFA_final


title: PBMC_123_MUFA_final


title: SAMPLE 45_miRNA_tumor [FFPE]

description: SAMPLE 45


title: SAMPLE 46_miRNA_tumor [FFPE]

description: SAMPLE 46


title: PBMC_123_MUFA_baseline


title: SAMPLE 43_miRNA_tumor [FFPE]

description: SAMPLE 43


title: PBMC_109_MUFA_final


title: PBMC_109_MUFA_baseline


title: PBMC_110_MUFA_final


title: PBMC_108_MUFA_final


title: SAMPLE 42_miRNA_tumor [FFPE]

description: SAMPLE 42


title: PBMC_108_MUFA_baseline


title: SAMPLE 41_miRNA_tumor [FFPE]

description: SAMPLE 41


title: SAMPLE 40_miRNA_tumor [FFPE]

description: SAMPLE 40


title: SAMPLE 39_miRNA_tumor [FFPE]

description: SAMPLE 39


title: SAMPLE 38_miRNA_tumor [FFPE]

description: SAMPLE 38


title: PBMC_103_MUFA_baseline


title: SAMPLE 44_miRNA_tumor [FFPE]

description: SAMPLE 44


title: PBMC_106_MUFA_baseline


title: PBMC_110_MUFA_baseline


title: PBMC_103_MUFA_final


title: PBMC_187_SFA_final

value: saturated fat


title: PBMC_101_MUFA_final


title: PBMC_106_MUFA_final


title: PBMC_101_MUFA_baseline


title: PBMC_186_SFA_final


title: PBMC_186_SFA_baseline


title: SAMPLE 37_miRNA_tumor [FFPE]

description: SAMPLE 37


title: PBMC_187_SFA_baseline


title: SAMPLE 35_miRNA_tumor [FFPE]

description: SAMPLE 35


title: PBMC_185_SFA_final


title: SAMPLE 34_miRNA_tumor [FFPE]

description: SAMPLE 34


title: SAMPLE 31_miRNA_tumor [FFPE]

description: SAMPLE 31


title: SAMPLE 36_miRNA_tumor [FFPE]

description: SAMPLE 36


title: SAMPLE 33_miRNA_tumor [FFPE]

description: SAMPLE 33


title: SAMPLE 30_miRNA_tumor [FFPE]

description: SAMPLE 30


title: PBMC_181_SFA_baseline


title: SAMPLE 85_miRNA_normal [FFPE]

description: SAMPLE 85


title: SAMPLE 32_miRNA_tumor [FFPE]

description: SAMPLE 32


title: SAMPLE 28_miRNA_tumor [FFPE]

description: SAMPLE 28


title: SAMPLE 27_miRNA_tumor [FFPE]

description: SAMPLE 27


title: SAMPLE 29_miRNA_tumor [FFPE]

description: SAMPLE 29


title: PBMC_179_SFA_final


title: PBMC_181_SFA_final


title: SAMPLE 26_miRNA_tumor [FFPE]

description: SAMPLE 26


title: SAMPLE 25_miRNA_tumor [FFPE]

description: SAMPLE 25


title: PBMC_179_SFA_baseline


title: PBMC_145_SFA_final


title: PBMC_170_SFA_baseline


title: PBMC_185_SFA_baseline


title: SAMPLE 24_miRNA_tumor [FFPE]

description: SAMPLE 24


title: PBMC_170_SFA_final


title: SAMPLE 23_miRNA_tumor [FFPE]

description: SAMPLE 23


title: PBMC_169_SFA_baseline


title: PBMC_145_SFA_baseline


title: SAMPLE 22_miRNA_tumor [FFPE]

description: SAMPLE 22


title: PBMC_169_SFA_final


title: SAMPLE 21_miRNA_tumor [FFPE]

description: SAMPLE 21


title: SAMPLE 20_miRNA_tumor [FFPE]

description: SAMPLE 20


title: PBMC_140_SFA_final


title: SAMPLE 19_miRNA_tumor [FFPE]

description: SAMPLE 19


title: PBMC_129_SFA_final


title: SAMPLE 18_miRNA_tumor [FFPE]

description: SAMPLE 18


title: SAMPLE 17_miRNA_tumor [FFPE]

description: SAMPLE 17


title: SAMPLE 16_miRNA_tumor [FFPE]

description: SAMPLE 16


title: SAMPLE 14_miRNA_tumor [FFPE]

description: SAMPLE 14


title: PBMC_140_SFA_baseline


title: PBMC_129_SFA_baseline


title: PBMC_128_SFA_final


title: SAMPLE 13_miRNA_tumor [FFPE]

description: SAMPLE 13


title: SAMPLE 12_miRNA_tumor [FFPE]

description: SAMPLE 12


title: SAMPLE 10_miRNA_tumor [FFPE]

description: SAMPLE 10


title: SAMPLE 11_miRNA_tumor [FFPE]

description: SAMPLE 11


title: SAMPLE 9_miRNA_tumor [FFPE]

description: SAMPLE 9


title: PBMC_124_SFA_final


title: SAMPLE 8_miRNA_tumor [FFPE]

description: SAMPLE 8


title: SAMPLE 15_miRNA_tumor [FFPE]

description: SAMPLE 15


title: SAMPLE 6_miRNA_tumor [FFPE]

description: SAMPLE 6


title: PBMC_128_SFA_baseline


title: SAMPLE 5_miRNA_tumor [FFPE]

description: SAMPLE 5


title: SAMPLE 3_miRNA_tumor [FFPE]

description: SAMPLE 3


title: PBMC_119_SFA_baseline


title: PBMC_124_SFA_baseline


title: PBMC_120_SFA_baseline


title: PBMC_119_SFA_final


title: PBMC_113_SFA_final


title: PBMC_113_SFA_baseline


title: PBMC_122_SFA_baseline


title: PBMC_120_SFA_final


title: PBMC_114_SFA_final


title: PBMC_114_SFA_baseline


title: SAMPLE 7_miRNA_tumor [FFPE]

description: SAMPLE 7


title: PBMC_122_SFA_final


title: SAMPLE 1_miRNA_tumor [FFPE]

description: SAMPLE 1


title: SAMPLE 4_miRNA_tumor [FFPE]

description: SAMPLE 4


title: NuLi cell line treated at DMNQ biological rep2

city: Montréal

first: greg

last: VOISIN

state: QC

address: 3840 Saint-Urbain

department: Département de Médecine, Centre de Recherche

country: Canada

institute: Centre Hospitalier de l'Université de Montréal Hôtel Dieu

description: Gene expression data from normal CF cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment

hyb_protocol: Washing and staining with streptavidin-phycoerythrin (Invitrogen, Carlsbad, CA)

scan_protocol: 10 μg of the resulting cRNA were then loaded on each chip and scanned with a Genechip Scanner 3000 workstation

data_processing: For each hybridized chips, the probe intensity levels were extracted by the Affymetrix® Scanner 3000 7G and the data analyzed by the Microarray Analysis Suite (version 5.0) algorithm. Expression data files were generated for each chip to generate a CEL file

source_name: human normal cell lines airway with 24 hours of DMNQ treatment

label_protocol: The probes were labelled with biotin and fragmented using Affymetrix’s reagents following standard protocol

growth_protocol: Cultured in an air-liquid condition, cells were coated on collagen plastic dishes with serum-free bronchial epithelial cell growth medium with supplements (BEGM, Cambrex)

extract_protocol: RNAs were purified with the RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: After differentiation by cell culture at air-liquid interface, the cellular monolayer was treated on apical side with 15 μM DMNQ (2, 3-dimethoxy-1, 4-naphtoquinone) for a 24 hours period

value: DMNQ

value: NuLi

tag: genotype

value: no-Cystic Fibrosis deltaF508 mutation


title: NuLi cell line treated at DMNQ biological rep3

description: Gene expression data from normal cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment


title: SAMPLE 2_miRNA_tumor [FFPE]

description: SAMPLE 2


title: NuLi cell line biological rep3

description: Gene expression data from normalCF cell line cultivated on Air-liquid Interface

source_name: human normal cell lines airway

value: control


title: Nectary 1

city: Wuerzburg

first: Peter

last: Ache

address: Julius von Sachs Platz 2

country: Germany

institute: Julius von Sachs Institut

description: (clone T89)

hyb_protocol: Hybridized to the Gene Chip Poplar Genome (Affymetrix) according to the manufacture’s protocol

scan_protocol: Microarrays were scanned using the GCS3000 GeneChip scanner (Affymetrix) and GCOS software, version 1.4.

data_processing: Scanned images were subjected to visual inspection to control for hybridation artifacts and proper grind alignment. Files of quality control were generated using the program “Expression Console” (Affymetrix). The 'vsn normalized signal intensity on log scale' have been calculated using the vsn package (version 3.6.0) from Bioconductor (version 2.2).

organism: Populus tremula x Populus tremuloides

source_name: nectary, untreated

label_protocol: All samples were amplified using the “One-Cycle Target Labellig Assay” (Affymetrix) according to the manufacture’s protocol.

extract_protocol: Total RNA of leaves was extracted using the E.Z.N.A. Plant RNA Mini Kit (Omega bio-tek), nectaries total RNA with the RNeasy MicroKit (Qiagen,) according to the manufacturer’s protocols with minor modifications. The binding buffers were supplemented with 2% β- Mercaptoethanol, 1% PVP and 70 mM K-Ethylxantogenate and added to 30mg of homogenized leaf tissue or 120 homogenized nectaries, respectively. Afterincubation at room temperature for 30 min the sample were briefly centrifuged before transfer to the individual homogenation columns. 1 μg total RNA was used for RNA amplification based on the BD-SMART mRNA amplification kit (BD Bioscience). The mRNA was reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen). To pre-amplify full-length cDNAs prior to in vitro transcription, an additional 10 cycle PCR (95ºC for 30 sec, 60ºC for 1 min, and 68 º C for 10 min) was introduced using t7 extension and PCR primer IIA of the kit

value: nectary


title: NuLi cell line treated at DMNQ biological rep1


title: Leaf 1

description: (clone T89)

source_name: leaf, untreated

value: leaf


title: Leaf 3

description: (clone T89)


title: NuLi cell line biological rep1

description: Gene expression data from normal cell line cultivated on Air-liquid Interface


title: Leaf 2

description: (clone T89)


title: NuLi cell line biological rep2

description: Gene expression data from normal CF cell line cultivated on Air-liquid Interface


title: Myocyte treated with PE, biological rep2

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

description: Gene expression data from Myocyte treated with Phenylephrine

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChips were scanned using Scanner G3000.

data_processing: RMA algorithm in GeneSpring.

organism: Rattus norvegicus

source_name: Neonatal Myocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Standard myocyte cell culture

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

treatment_protocol: Cells were treated with Uremic plasma (10%) before and after NHD

tag: tissue

value: Heart

value: ventricular myocytes

tag: strain

value: Sprague-Dawley

value: 5 days old myocyte culture


title: Nectary 3

description: (clone T89)


title: CuFi cell line treated at DMNQ biological rep3

description: Gene expression data from CF cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment

source_name: human CF cell lines airway with 24 hours of DMNQ treatment

value: CuFi

value: Cystic Fibrosis deltaF508 mutation


title: Myocyte treated with PE, biological rep1


title: Myocyte treated with plasma CT, biological rep3

description: Gene expression data from Myocyte treated with control plasma


title: CuFi cell line treated at DMNQ biological rep1


title: Nectary 2

description: (clone T89)


title: B-cell acute lymphoblastic leukemia patient 31

city: Kuala Lumpur

first: Zubaidah

last: Zakaria

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

hyb_protocol: Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was performed for 24 hours at 65°C using Agilent hybridization station. After hybridization, slides were washed sequentially.

scan_protocol: Slides were scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software v10.7.3.1. Data analysis were performed using GeneSpring version 12.0 software.

source_name: Blood

label_protocol: 100 ng of total RNA were primed with 0.8 µl of T7 promoter primer with the addition of 2 uL diluted spike (fluorescent dye dUTP-cyanine 3 (Reference DNA) and dUTP-cyanine 5 (Test DNA)) at 65°C for 10 min. The labeling reaction was done using Agilent Low Input Linear kit and Amplification Kit Plus for cDNA and cRNA synthesis and amplification.

extract_protocol:
Extraction of genomic RNA with high molecular weight was performed using QIAamp RNA extraction kit (Qiagen) according to the manufacturer's instructions.
Purification of cRNA sample was performed using QIAgen RNeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: Male

tag: age (y)

tag: risk assessment

value: Standard

tag: status

value: Alive

value: Blood

tag: disease state

value: B-cell acute lymphoblastic leukemia

source_name: Universal Human Reference RNA (Stratagene)


title: CuFi cell line treated at DMNQ biological rep2

value: DMNQ


title: B-cell acute lymphoblastic leukemia patient 35

source_name: Bone marrow

value: Medium

value: Bone marrow

tag: sample type

value: Universal Human Reference RNA (Stratagene)


title: Myocyte treated with plasma after NH, biological rep3

description: Gene expression data from Myocyte treated with plasma after NHD


title: Myocyte treated with plasma CT, biological rep2


title: Myocyte treated with plasma after NH, biological rep4


title: B-cell acute lymphoblastic leukemia patient 32

value: Female


title: Myocyte treated with plasma after NH, biological rep6


title: Myocyte treated with plasma CT, biological rep1


title: B-cell acute lymphoblastic leukemia patient 30


title: B-cell acute lymphoblastic leukemia patient 28


title: Myocyte treated with plasma after NH, biological rep5


title: Myocyte treated with plasma after NH, biological rep2


title: Myocyte treated with plasma after NHD, biological rep1


title: Myocyte treated with plasma before NHD, biological rep5

description: Gene expression data from Myocyte treated with plasma before NHD


title: CuFi cell line biological rep3

description: Gene expression data from CF cell line cultivated on Air-liquid Interface

source_name: human CF cell lines airway

value: control


title: B-cell acute lymphoblastic leukemia patient 37

value: Died


title: Myocyte treated with plasma before NHD, biological rep6

value: Heart

value: ventricular myocytes


title: B-cell acute lymphoblastic leukemia patient 27


title: Myocyte treated with plasma before NHD, biological rep1, biological rep3

value: Sprague-Dawley

value: 5 days old myocyte culture


title: CuFi cell line biological rep1

value: CuFi

value: Cystic Fibrosis deltaF508 mutation


title: B-cell acute lymphoblastic leukemia patient 26

value: Male


title: CuFi cell line biological rep2


title: B-cell acute lymphoblastic leukemia patient 19

value: Standard

value: Alive


title: Myocyte treated with plasma before NHD, biological rep4


title: Myocyte treated with plasma before NHD, biological rep1, biological rep2


title: Myocyte treated with plasma before NHD, biological rep1


title: B-cell acute lymphoblastic leukemia patient 21

value: B-cell acute lymphoblastic leukemia


title: B-cell acute lymphoblastic leukemia patient 17


title: B-cell acute lymphoblastic leukemia patient 12


title: B-cell acute lymphoblastic leukemia patient 23


title: B-cell acute lymphoblastic leukemia patient 16

value: Blood


title: B-cell acute lymphoblastic leukemia patient 11

value: Medium


title: B-cell acute lymphoblastic leukemia patient 05

value: Bone marrow


title: B-cell acute lymphoblastic leukemia patient 08

value: Universal Human Reference RNA (Stratagene)


title: B-cell acute lymphoblastic leukemia patient 10


title: B-cell acute lymphoblastic leukemia patient 03

value: Female


title: T-cell acute lymphoblastic leukemia patient 36

value: T-cell acute lymphoblastic leukemia


title: B-cell acute lymphoblastic leukemia patient 02


title: Eos_1

type: genomic

city: Huddinge

first: Lovisa

middle: E

last: Reinius

address: Novum, Halsovagen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: untouched protocol, Eosinophil Isolation kit II (Miltenyi Biotech, Germany)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation540 Beadchip using standard Illumina protocol

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

data_processing: The raw data from GenomeStudio software (v2011.1) methylation module (v1.9.0) were imported into R v. 2.13 and analyzed with the Bioconductor lumi package. Color channel imbalance adjusted, background corrected, and quantile normalized M values followed by fitting a Gamma distribution.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Eosinophils

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from all samples using QIAmp DNA Micro Kit (QIAGEN, Germany) according to standard instructions

tag: tissue/cell type

value: Eosinophils


title: Neu_6

description: anti-CD16 magnetic-activated cell sorting

source_name: Neutrophils

value: Neutrophils


title: Eos_5


title: T-cell acute lymphoblastic leukemia patient 34

value: Died


title: Eos_6


title: T-cell acute lymphoblastic leukemia patient 29

value: High


title: CD56+_4

description: anti-CD56 magnetic-activated cell sorting

source_name: CD56+ NK cells

value: CD56+ NK cells


title: EGI1_in_vitro.D

city: Biella

first: caterina

last: Peraldo Neia

state: Biella

address: via Malta 3

department: Laboratory of  Cancer Genomics

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Dye-swap

hyb_protocol: Hybridization with dye-swap duplication was performed to compare sample versus reference. The same quantity of differentially labelled sample and reference was put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing 60 K  human unique genes and transcripts. All steps were performed using the Gene Expression Hybridization kit (Agilent Technologies) following the 60-mer oligo microarray processing protocol (Agilent Technologies).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data were processed using the statistical computing software R and packages from Bioconductor (www.bioconductor.org); limma was used for preprocessing and differential expression analysis. Raw intensities were first background corrected (normexp method, with an offset value of 50 added to red and green intensities so that log-ratios are shrunk towards zero at lower intensities). In order to set log-ratios average to zero within each array and to have similar log-ratio distributions across all arrays, loess and Aquantile normalization were performed.

source_name: EGI-1 cells untreated

label_protocol: Labelling was performed using NHS ester Cy3 or Cy5 dyes (GE HealthCare, Buckinghamshire, UK) able to react with the modified RNA.

growth_protocol: RPMI + 10%FBS

extract_protocol: Total RNA was isolated from EGI-1 cells using TRIZOL (Life Technologies, Gathersburg, MD); in the case of frozen EGI-1 xenograft tissues, RNA was extracted with TriReagent (Sigma, St. Louis, MO, USA) and IKA T25 Digital ULTRA TURRAX homogenizer. For each sample and reference pair, equal amounts of mRNA were amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion Inc., Austin, TX) to obtain amino allyl antisense RNA. One round of amplification was performed and both dsDNA and aaRNA underwent a purification step using columns provided with the kit.

treatment_protocol: For in vitro experiment: 24 hours at 10 uM of Saracatinib. In Vivo: 21 days of treatement woth saracatinib at the dose of 25 mg/Kg/die

tag: cell line

value: Biliary tract carcinoma (BTC) cells

source_name: EGI-1 cells treated with Saracatinib

tag: treated with

value: 10 µM Saracatinib


title: Eos_2

tag: gender

value: Male


title: Neu_5


title: Eos_4


title: Eos_3


title: T-cell acute lymphoblastic leukemia patient 18


title: CD56+_1


title: T-cell acute lymphoblastic leukemia patient 15


title: EGI1_in_vivo.D

description: Dye-swap

source_name: EGI-1 xenograft untreated

value: Biliary tract carcinoma (BTC) xenograft

source_name: EGI-1 xenograft treated with Saracatinib

value: 25 mg/Kg/die Saracatinib


title: CD56+_5


title: CD56+_6


title: alveolar epithelial RelA mutant mice lungs with Sp pneumonia

city: Boston

first: Kazuko

last: Yamamoto

state: MA

address: 72 East Concord Street

department: Pulmonary Center

institute: Boston University School of Medicine

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://www.SABiosciences.com/pcrarraydataanalysis.php
For the normalization program automatically selected two housekeeping genes (Gusb and Hsp90ab1) from panel.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., wild-type / alveolar epithelial RelA mutant) ratios.

label: SYBR Green

label_protocol: PCR arrays were performed using the RT2 ProfilerTM Mouse Inflammatory Cytokines and Receptors PCR Array (PAMM-011, SABiosciences) following the Manufacturer's instructions. Reverse transcription was performed from 1μg total RNA using the SuperScript VILO cDNA Synthesis Kit (Applied Biosystems). Quantitative real-time PCR were performed (StepOne Plus Real-Time PCR Systems, Applied Biosystems) with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds.

extract_protocol: total RNA was extracted from mouse lung with RNeasy Mini Kit followed by DNase I treatment.

tag: genotype/variation

value: RelA mutant

value: lung

tag: time

value: 6 hours


title: CD19+_6

description: anti-CD19 magnetic-activated cell sorting

source_name: CD19+ B cells

value: CD19+ B cells


title: T-cell acute lymphoblastic leukemia patient 04

value: Medium

value: Alive

value: Bone marrow

value: Universal Human Reference RNA (Stratagene)


title: Neu_4

value: Neutrophils


title: Neu_2


title: T-cell acute lymphoblastic leukemia patient 14

value: Female

value: Died

value: T-cell acute lymphoblastic leukemia


title: Neu_3


title: EGI1_in_vitro.N

description: Normal

tag: cell type

value: Biliary tract carcinoma (BTC) cells


title: CD19+_5


title: EGI1_in_vivo.N

description: Normal


title: T-cell acute lymphoblastic leukemia patient 06


title: T-cell acute lymphoblastic leukemia patient 01


title: Neu_1


title: CD19+_4


title: CD56+_2

value: CD56+ NK cells


title: CD56+_3

value: Male


title: wild-type mice lungs with Sp pneumonia

source_name: wild-type mice lungs with Sp pneumonia

value: control


title: alveolar epithelial RelA mutant mice lungs with LPS inflammation


title: wild-type mice lungs with LPS inflammation


title: CD19+_1


title: CD14+_4

description: anti-CD14 magnetic-activated cell sorting

source_name: CD14+ Monocytes

value: CD14+ Monocytes


title: CD19+_2


title: Scl-/- PL31+ R1

city: LOS ANGELES

first: Hanna

last: Mikkola

state: CA

address: 621, Charles E. Young Drive South

department: MCDB

institute: UCLA

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: The data were normalized in 3 separate batches. Samples 1-6, 7-14 and 15-24 comprised three groups that were normalized separately according to the following description. The R package Limma provided through the open source project Bioconductor (version 2.7) was used for assessing differential expression. To calculate absolute mRNA expression levels, the RMA (Robust Multiarray Averaging) method (provided through R library affy) was used to obtain background adjusted, quantile normalized and probe level data summarized values for all probe sets. The Affymetrix Mouse Genome 430 2.0 Array GeneChip platform was used for the analysis. Official gene symbols for probe sets were obtained using the Bioconductor annotation database mouse4302.db. The 'mas5calls' algorithm through the R package affy was used for calculating PMA detection calls for each array sample. The algorithm employs a signed rank test to consider the significance of the difference between the PM and MM values for each probeset and returns a detection p-value that is used to flag a transcript as 'Present', 'Marginal' or 'Absent' (P/M/A). Probes that were ‘Absent’ for all samples analyzes were excluded from further analysis.

source_name: E9.25 Scl-/- Placenta total CD31+ cells

label_protocol: Affymetrix standard labeling kit

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Qiagen) and amplified by the UCLA Clinical Pathology Microarray Core using NuGEN Pico Kit

tag: developmental stage

value: E9.25 embryo

value: Placenta

value: CD31+ cells

value: Scl-/-


title: CD14+_6


title: Pt4_LatePassage

city: NEW BRUNSWICK

first: Ashwin

middle: R

last: Jadhav

address: 125 PATERSON STREET

department: OBGYN

institute: UMDNJ-RWJMS

description:
Ashwin 17 B+ 092311
Fetal cells.
Gene expression data.

hyb_protocol: Labeled and fragmented cRNA was hybridized to HG-U133 Plus 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix 7G GeneArray scanner.

data_processing: Feature intensity was extracted by the GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using the Agilent GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: Amniotic fluid-derived cells, late passage

label_protocol: The labeled target cRNA population was generated with the Affymetrix 3'-IVT Express kit.

growth_protocol: The amniotic fluid-derived cells were obtained from cytogenetics after karyotype analysis and then maintained in stem cell media using standard cell culture techniques.

extract_protocol: Total RNA extractions were performed by the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The cells were sorted at passage 2-3 (early passage) using the MACS separation protocol into c-kit-positive and -negative cells. Part of the c-kit-positive cells were maintained in culture and were resorted using the MACS separation protocol at passage 6-7 (late passage).

value: amniotic fluid

value: c-kit-positive cells

tag: passage

value: late


title: Scl-/- YS31+ R2

source_name: E9.25 Scl-/- Yolk Sac total CD31+ cells

value: Yolk Sac


title: Pt1_LatePassage

description:
Ashwin 14 B+ 091311
Fetal cells.
Gene expression data.


title: WT PL31+ R2

source_name: E9.25 WT Placenta total CD31+ cells

value: wild type


title: Pt3_LatePassage

description:
Ashwin 16 B+ 091311
Fetal cells.
Gene expression data.


title: CD19+_3

value: CD19+ B cells


title: WT PL31+ R1


title: CD14+_2


title: Pt5_EarlyPassage

description:
Ashwin 18 A+ 092311
Fetal cells.
Gene expression data.

source_name: Amniotic fluid-derived cells, early passage

value: early


title: Scl-/- YS31+ R1


title: Scl-/- PL31+ R2


title: Pt2_LatePassage

description:
Ashwin 15 B+ 091311
Fetal cells.
Gene expression data.


title: CD14+_3


title: CD14+_5


title: Pt5_LatePassage

description:
Ashwin 18 B+ 092311
Fetal cells.
Gene expression data.


title: WT YS41+ckit+ R1

source_name: E9.25 WT Yolk Sac CD41+ckit+ cells

value: CD41+ckit+ cells


title: Pt3_EarlyPassage

description:
Ashwin 16 A+ 091311
Fetal cells.
Gene expression data.


title: CD8+_6

description: anti-CD8 magnetic-activated cell sorting

source_name: CD8+ T cells

value: CD8+ T cells


title: CD14+_1


title: CD8+_3


title: Pt1_EarlyPassage

description:
Ashwin 14 A+ 091311
Fetal cells.
Gene expression data.


title: Pt2_EarlyPassage

description:
Ashwin 15 A+ 091311
Fetal cells.
Gene expression data.


title: CD8+_4


title: Pt4_EarlyPassage

description:
Ashwin 17 A+ 092311
Fetal cells.
Gene expression data.


title: CD8+_5


title: WT YS31+ R1

source_name: E9.25 WT Yolk Sac total CD31+ cells


title: WT YS41+ckit+ R2


title: WT YS31+ R2


title: CD8+_2


title: CD8+_1


title: RpoHII replicate 3

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

hyb_protocol: Labeled cDNA samples were hybridized to Rhodobacter sphaeroides GeneChip CustomExpress microarrays (Affymetrix) following product instructions, for 16 h at 45 C on a rotisserie spindle rotating at 60 rpm.

scan_protocol: Microarrays were washed, stained, and scanned using the Pseudomonas aeruginosa midi-array hybridization with amplification protocols.

data_processing: Microarray data sets were normalized by Robust Multichip Average (RMA) with background adjustment and quantile normalization. Statistical analysis of normalized data to identify differentially expressed genes used the limma package. Correction for multiple testing was done using Benjamini-Hochberg correction. Differentially expressed genes were defined as those having an adjusted p-value ≤ 0.01 and a fold-change ≥ 2 with respect to those in the reference data sets. All analyses were conducted in the R statistical programming environment (http://www.R-project.org).

organism: Cereibacter sphaeroides 2.4.1

source_name: Gene expression levels in R. sphaeroides expressing RpoHII

label_protocol: Fragmented cDNA was end-labeled with biotin-16-ddUTP using Terminal Transferase for 2 hr at 37 C.

growth_protocol: Cells were cultured in minimal succinate based medium under aerobic conditions at 30C until early-exponential growth phase when 100 uM IPTG was added to induce the expression of RpoHI_FLAG for 3 hours before harvesting cells.

extract_protocol: Cells were lysed by addition of 1/10 v 10% SDS at 64 C for 2 min. 1/10 v 1 M Na acetate (pH 5.2), then equal volume of H2O-saturated phenol, were added. Samples were incubated at 64 C for 6 min, with mixing every 30 s, then chilled on ice before centrifugation (16,000 X g for 10 min at 4 C). The aqueous phase was removed and extracted with equal volumes of phenol, then chloroform, then precipitated (1/10 v 3 M Na acetate, 1 mM EDTA, 2 volumes cold ethanol).

treatment_protocol: Cell culture was transferred to an ice-cold conical tube containing 1/8 volume of 5% water-saturated phenol in ethanol. Cells were collected by centrifugation (5,000 X g for 5 min at 4 C); cell pellets were frozen in dry ice/ethanol and stored at -80 C.

value: RSP_0601 mutant with plasmid containing RpoHII

tag: growth phase

value: mid-eponential

tag: grow conditions

value: aerobic in minimal medium


title: WT HT31+Pdgfra- R2

source_name: E9.25 WT Heart CD31+ Pdgfralpha- cells

tag: tissue

value: Heart

value: CD31+ Pdgfralpha- cells


title: WT HT31+Pdgfra+ R1

source_name: E9.25 WT Heart CD31+ Pdgfralpha+ cells

value: E9.25 embryo


title: control2

city: London

first: Bartlomiej

middle: Przemyslaw

last: Przychodzen

address: Coldharbour Lane

department: Department of Haematology

country: United Kingdom

institute: King's College

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mononuclear cells were separated from peripheral blood by density gradient sedimentation

label_protocol: Standard Affymetrix protocol

value: anti-VB and CD8 mAb sorted blood mononuclear cells

tag: patient


title: RpoHI_FLAG replicate 2

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The biological replicates were normalized to each others using quantile normalization. The data was smoothed using a moving median window of 100 bp.

source_name: RpoHI_FLAG ChIP DNA

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protocol.

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated with sepharose beads coated with monoclonal antibodies against the FLAG tag at 4°C for 3 hours. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

tag: strain

value: RSP_2410 deletion mutant complemented with a plasmid expressing RSP_2410 fused to a FLAG tag under the control of a lac promoter.

tag: antibody

value: commercial monoclonal antibody against the FLAG tag from Sigma-Aldrich.

tag: antibody manufacturer

value: Sigma-Aldrich

source_name: Input DNA

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

value: none.


title: control3


title: Scl-/- HT31+Pdgfra- R2

source_name: E9.25 Scl-/- Heart CD31+ Pdgfralpha- cells

value: Scl-/-


title: RpoHII replicate 2


title: RpoHII replicate 2

source_name: RpoHII ChIP DNA

growth_protocol: Cells were cultured in minimal succinate based medium under aerobic conditions at 30C until early-exponential growth phase when 100 uM IPTG was added to induce the expression of RpoHII for 3 hours before harvesting cells.

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated with polyclonal antibodies against RpoHII at 4°C over night. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours to capture antibodies. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

value: RSP_0601 deletion mutant complemented with a plasmid expressing wild type RSP_0601 under the control of a lac promoter.

value: custom rabbit polyclonal antibody against RSP_0601.


title: CD4+_5

description: anti-CD4 magnetic-activated cell sorting

source_name: CD4+ T cells

value: Male

value: CD4+ T cells


title: RpoHII replicate 3


title: WT HT31+Pdgfra- R1

value: wild type


title: control1


title: RpoHI_FLAG replicate 3


title: CD4+_3


title: CD4+_4


title: RpoHI_FLAG replicate 1


title: RpoHII replicate 1


title: WT HT31+Pdgfra+ R2


title: Y640F-LGL

value: Y640F-LGL; STAT3 mutation


title: WT-LGL

value: symptomatic WT-LGL


title: RpoHI replicate 2

source_name: Gene expression levels in R. sphaeroides expressing RpoHI

value: RSP_2410 mutant with plasmid containing RpoHI

value: mid-eponential

value: aerobic in minimal medium


title: CD4+_6


title: RpoHII replicate 1

value: RSP_0601 mutant with plasmid containing RpoHII


title: RpoHI replicate 1


title: RpoHI_FLAG replicate 3

source_name: Gene expression levels in R. sphaeroides expressing RpoHI_FLAG

value: RSP_2410 mutant with plasmid containing RpoHI_FLAG


title: Scl-/- HT31+Pdgfra- R1

value: E9.25 embryo

value: Heart

value: CD31+ Pdgfralpha- cells


title: CD4+_2


title: Gran_6

description: Obtained after Ficol separation and purification of pellet

source_name: Granulocytes

value: Granulocytes


title: D661Y-LGL

value: anti-VB and CD8 mAb sorted blood mononuclear cells

value: D661Y-LGL; STAT3 mutation


title: Scl-/- HT31+Pdgfra+ R2

source_name: E9.25 Scl-/- Heart CD31+ Pdgfralpha+ cells

value: Scl-/-


title: TP53 miR-34a [07KM4055]

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: not applicable

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: disease

value: AML

tag: karyotype

value: complex karyotype

tag: tp53 mutation status

value: p53 wildtype

tag: mir-34a expression

value: low


title: TP53 miR-34a [07KM4218]

value: high


title: TP53 miR-34a [06PB5792]

value: p53 biallelic aberration


title: Scl-/- YS31+Pdgfra- R1

source_name: E9.25 Scl-/- Yolk Sac CD31+ Pdgfralpha- cells

value: Yolk Sac


title: Scl-/- HT31+Pdgfra+ R1


title: TP53 miR-34a [08PB0892]


title: CD4+_1

tag: gender

value: Male

tag: tissue/cell type

value: CD4+ T cells


title: RpoHI_FLAG replicate 2

value: RSP_2410 mutant with plasmid containing RpoHI_FLAG

value: mid-eponential

value: aerobic in minimal medium


title: Gran_5


title: RpoHI_FLAG replicate 1


title: TP53 miR-34a [06KM2756]


title: Gran_4


title: Delta RpoHII replicate 1

source_name: Gene expression levels in R. sphaeroides lacking RpoHII

growth_protocol: R. sphaeroides cultures were grown aerobically to mid-exponential phase in Sistrom's Minimal Mediumat a temperature of 30 C.

value: RSP_0601 mutant with pIND4


title: Scl-/- YS31+Pdgfra- R2

value: E9.25 embryo

value: CD31+ Pdgfralpha- cells

tag: genotype/variation


title: TP53 miR-34a [05PB1095]


title: Delta RpoHII replicate 3


title: Delta RpoHI replicate 3

source_name: Gene expression levels in R. sphaeroides lacking RpoHI

value: RSP_2410 mutant with pIND4


title: Gran_2

value: Granulocytes


title: Gran_3


title: Gran_1


title: WT YS31+Pdgfra- R1

source_name: E9.25 WT Yolk Sac CD31+ Pdgfralpha- cells

tag: cell type

value: wild type


title: Scl-/- YS31+Pdgfra+ R2

source_name: E9.25 Scl-/- Yolk Sac CD31+ Pdgfralpha+ cells

tag: developmental stage

value: Scl-/-


title: TP53 miR-34a [04PB2464]

value: AML

value: complex karyotype


title: TP53 miR-34a [06KM0622]

value: low


title: Delta RpoHII replicate 2


title: Delta RpoHI replicate 2


title: Delta RpoHI replicate 1


title: TP53 miR-34a [03PB1033]

value: p53 wildtype

value: high


title: TP53 miR-34a [03KM556]

source_name: mononuclear cells from peripheral blood


title: PBMC_6

description: Obtained after Ficol separation and purification

source_name: PBMC

value: Male

value: PBMC


title: Flk1+Tie2+ cells, A2lox.Mesp1 day 5 EBs, treated with dox

city: St. Louis

first: Mi

last: Cai

state: MO

address: 660 S. Euclid Ave.

department: Immunology and Pathology

institute: Washington University School of Medicine

description:
Mesp1+dox_Flk1+Tie2+
Gene expression data from Flk1+Tie2+ cells purified from A2lox.Mesp1 day 5 embryoid bodies treated with doxycycline from day 2 to day 4.

hyb_protocol: The Affymetrix operating system (Command Console) was used to manage the washing and hybridization steps.

scan_protocol: The Affymetrix operating system (Command Console) was used for scanning. Affymetrix analysis software (Genotyping Console) was used to derive Quality Control metrics, create .CEL files and scaled expression data from the scanned expression array image files.

data_processing: The data was analyzed with dChip 2010 using default analysis settings. Both samples were normalized to a single baseline array of median intensity.

source_name: Flk1+Tie2+ cells purified from A2lox.Mesp1 day 5 embryoid bodies treated with doxycyline from day 2 to day 4

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express Kit protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit manual, 2008-2009, Affymetrix).

growth_protocol: A2lox.Mesp1 ES cells were differentiated as embryoid bodies in petri dishes at a density of 15,000 cells/mL in differentiation media consisting of 10% FCS for 5 days.

extract_protocol: RNA from sorted cell populations was extracted using Qiagen's RNeasy kits according to the manufacturer's instructions.

treatment_protocol: In dox-treated conditions, doxycycline was added at a final concentration of 250ng/mL on day 2. On day 5, EBs were trypsinized and stained with antibodies against Flk1 and Tie2. Flk1+Tie2+ endothelial cells were sorted using a MoFlo cytometer.

value: dox-inducible transgenic A2lox.Mesp1 mouse embryonic stem cells

tag: background strain

tag: day of differentiation

tag: treatment

value: doxycycline on day 2

tag: population


title: TP53 miR-34a [00KM1474]

value: p53 biallelic aberration


title: Flk1+Tie2+ cells, A2lox.Mesp1 day 5 EBs, untreated

description:
Mesp1-dox_Flk1+Tie2+
Gene expression data from Flk1+Tie2+ cells purified from A2lox.Mesp1 day 5 embryoid bodies without doxycycline.

value: untreated


title: WT YS31+Pdgfra- R2

value: E9.25 embryo

tag: tissue

value: Yolk Sac


title: TP53 miR-34a [03KM1194]


title: RpoHI replicate 3

tag: strain

value: RSP_2410 mutant with plasmid containing RpoHI

tag: growth phase

value: mid-eponential

tag: grow conditions

value: aerobic in minimal medium


title: PBMC_5


title: HD vs LD (Individual) 8, dye swap

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

hyb_protocol: Labelled cDNA was hybridised using the radiata pine 18K cDNA microarrays developed in CSIRO Plant Industry. Slides were placed in water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS) at 42 °C, 0.1x SSC (+0.1 % SDS), 0.1x SSC and 0.01x SSC at room temperature, each for 5 min prior to drying and scanning.

scan_protocol: Hybridized microarray slides were scanned using GenePix Personal 4100A microarray scanner (Axon Instruments, CA). Image pre-processing was performed using GenePix® Pro 4.0 and Acuity software (Axon Instruments, CA).

data_processing: Data analysis was carried out using GEPAS v3.1. The mean values from each channel were log2 transformed and normalized using print-tip lowess and slide scale normalization.

label: Alexa Fluor 555

organism: Pinus radiata

label_protocol: Equal amounts of total RNA (20 or 30 µg) of the two samples with contrasting wood density were reversely transcribed using Superscript reverse transcriptase, and generated fluorescently labelled cDNA using Alexa Fluor® 555-aha-dUTP and Alexa Fluor® 647-aha-dUTP, following the protocol of the SuperScriptTM Plus Direst cDNA Labelling System (Invitrogen, CA).

growth_protocol: Radiata pine trees used for microarray experiment were selected from a progeny trial planted at Flynn, Victoria (38º 14' S, 146º 45' E). The field trial included 250 half- or full-sib families. At time of sampling in autumn the cambial ages (ring numbers at breast height) of sampled trees were 7 yr, representing a developing stage at juvenile latewood formation in radiata pine.

extract_protocol: Developing xylem tissues were ground and total RNA was extracted using the method of Chang et al (1993) with a slight modification

treatment_protocol: Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

value: xylem

tag: wood density

value: HD

tag: replicate

label: Alexa Fluor 647

value: LD


title: Cancer_R1

first: Dylan

middle: Trefor

last: Jones

state: UK

address: Charterhouse square

department: Tumour Biology

institute: Barts Cancer Institute

description:
KHD.2.1
Hybridisation cocktail- NuGEN Cocktail PCR v1.0

hyb_protocol: Labelled cDNA Microarray hybridisations were performed on HG-U133 Plus 2 arrays (Affymetrix).

scan_protocol: PICR scanner 3000

data_processing: Data were processed using R/Bioconductor.  The RMA (Robust Multichip Average) expression measure was calculated for each probe set using the Affy package's “rma” function with default settings.

source_name: Invasive Ductal Caricoma of the breast tissue

label_protocol: RNA from LCM samples was amplified using the WT Ovation Pico RNA Amplification system (NuGEN) with a 2 cycle amplification following the manufacturer’s instructions, and cDNA was fragmented and labelled using the FL-Ovation cDNA Biotin Module V2 kit.

growth_protocol: Cells were not grown.  Cancer and normal tissues procured were from patients who gave appropriate informed consent. All tissue blocks were snap frozen in liquid nitrogen and stored until use. Normal breast tissue was obtained from patients undergoing mammoplasty and from pathologically normal tissue regions from breast IDC patients.

extract_protocol: RNA extraction was carried out using Qiagen RNeasy Mini or Micro Kit following the manufacturer’s instructions, and DNase treated (Qiagen). RNA concentration was initially tested with NanoDrop (ThermoScientific), followed by measurement with Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA) using Agilent Pico kit (RNA range 50-5000 pg) or Nano kit (RNA range 50-500 ng) for assessment of quality and concentration.

treatment_protocol: RNA was extracted from immunostained blood vessels.  Immunochemistry staining of sections for LCM was optimised for maintenance of RNA quality. For endothelial-specific CD31 staining, sections were fixed in 100% acetone (5 min, -20C), and incubated with primary antibody anti-CD31 (WM59, BD Pharmingen) 1:5 for 5 min followed by two PBS (Ambion) washes, biotinylated secondary antibody (Vectastain Universal Quick kit PK8800 - Vector labs) for 5 min, two PBS washes, StreptABCcomplex/HRP (Vectastain Universal Quick kit PK8800 - Vector labs) for 5 min, two PBS washes, Amino-ethyl-carbazole (AEC, Dako K3464) for 5 min, two water washes (Ambion), Cresyl Violet 1:20 in water (Ambion, AM1935) for 30 sec, two water washes and finally air-dried for up to 1 min with a hair-dryer. All antibody steps and AEC contained the RNase inhibitor 0.4 U/μL RNase Protector (Roche; Indianapolis, IN), and all PBS and water were nuclease free. All steps were carried out in RNase-free conditions. LCM was carried out immediately on the slide after staining, using the Zeiss Axiovert 135 with PALM Microbeam 3 System and PALM RoboSoftware (Carl Zeiss Europe). Approximately 200 blood vessels were captured onto adhesive lids of PALM eppendorfs (PALM) per slide and lysed in 50 μl RNA extraction kit (Qiagen RNeasy Micro Kit).  Up to 3 hr of LCM was spent per slide. Blood vessels from up to 20 slides per patient were captured, combined and stored in -80C until RNA extraction.

tag: tissue source

value: Invasive Ductal Caricoma breast tissue

value: blood vessels


title: Cancer_R3

description:
KHD.2.4
Hybridisation cocktail- NuGEN Cocktail PCR v1.0


title: Tooth germ embryonic day 45 Replicate 1 vs. tooth germ embryonic day 60 Replicate 2

city: Beijing

first: Ang

address: Tian Tan Xi Li No.4

country: China

institute: Capital Medical University School of Stomatology

description:
E45G1_vs_E60G2
No treated tissues.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). The ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Sus scrofa

source_name: E60 tooth germ tissue

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore), and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

value: tooth germ

value: embryonic day 60

source_name: E45 tooth germ tissue

value: embryonic day 45


title: Normal_R3

description:
KHD.2.10
Hybridisation cocktail- NuGEN Cocktail PCR v1.0

source_name: Normal breast tissue

value: Normal breast tissue


title: HD vs LD (Individual) 8


title: Normal_R1

description:
KHD.2.9
Hybridisation cocktail- NuGEN Cocktail PCR v1.0


title: Normal_R2

description:
KHD.2.3
Hybridisation cocktail- NuGEN Cocktail PCR v1.0


title: Tooth germ embryonic day 60 Replicate 1 vs. tooth germ embryonic day 50 Replicate 3

description:
E60G1_vs_E50G3
No treated tissues.

source_name: E50 tooth germ tissue

value: embryonic day 50


title: Scl-/- YS31+Pdgfra+ R1

value: CD31+ Pdgfralpha- cells

value: Scl-/-


title: Cancer_R2

description:
KHD.2.2
Hybridisation cocktail- NuGEN Cocktail PCR v1.0


title: HD vs LD (Individual) 7, dye swap


title: HD vs LD (Individual) 7


title: PBMC_3

value: Male

value: PBMC


title: PBMC_4


title: PCB77, HK2 cells at T24, biological replicate 3

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from HK2 cell lines after 24 hours of PCB77 treatment.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed using GeneSpring GX 10.0 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 150.

source_name: HK2 (Human Kidney 2) cell line from ATCC at 8th generation.

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

growth_protocol: Grown for 48 hours in Keratinocyte-Serum Free Medium supplemented 5ng/ml recombinant epidermal growth factor and 0.05mg/ml bovinepituitary extract and 1X Pennicilllin-Streptromycin

treatment_protocol: Treated with 40 micro molar of PCB77 for 24hours

value: human kidney

tag: cell line

value: HK2 from ATCC

tag: cell passage

value: 8th generation

tag: sex

value: male

value: adult

tag: treatment group


title: PBMC_1

tag: gender

tag: tissue/cell type


title: Tooth germ embryonic day 50 Replicate 2 vs. tooth germ embryonic day 45 Replicate 3

description:
E50G2_vs_E45G3
No treated tissues.

tag: developmental stage


title: PCB77, HK2 cells at T24, biological replicate 2

tag: cell type

value: Treated with 40 micro molar of PCB77 for 24hours


title: WB_6

description: Whole blood obtained from blood donation

source_name: Whole blood

value: Whole blood


title: HD vs LD (Individual) 6, dye swap

value: xylem

value: HD

value: LD


title: HD vs LD (Individual) 5, dye swap


title: PCB77, HK2 cells at T6, biological replicate 3

description: Gene expression data from HK2 cell lines after 6 hours of PCB77 treatment.

treatment_protocol: Treated with 40 micro molar of PCB77 for 6 hours


title: HD vs LD (Individual) 6


title: CD41hi, A2lox.Meis1 and OP9-GFP co-culture, D8, treated with dox

description:
Meis1+dox_D8_CD41hi
Expression data from GFP-CD41hi cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture treated with doxycycline for 48 hours.

data_processing: The data was analyzed using DNASTAR ArrayStar 4 software. RMA was selected as the preprocessing method and Quantile was selected as the preprocessing parameters.

label_protocol: Amplified cDNA was prepared using NuGEN Ovation PicoSL WTA System from 50 ng total RNA. The cDNA product was then fragmented and labeled according to a validated NuGEN protocol.

growth_protocol: A2lox.Meis1 ES cells were differentiated as embryoid bodies (EBs) for 6 days. On day 6, EBs were dissociated and plated at a density of 100,000 cells/ml on irradiated OP9-GFP cell monolayers with cytokines (100 ng/ml SCF, 40 ng/ml TPO, 40 ng/ml VEGF, 5% Flt3-L conditioned media, 10 ng/ml IL-3 and 20 ng/ml IL-6).

treatment_protocol: ES cell and OP9-GFP cocultures were treated with (+) or without (-) doxycycline (dox) at a final concentration of 500 ng/ml on day 6. On day 7, ES cell and OP9-GFP cocultures were purified into GFP-CD41- and GFP-CD41+ populations by cell sorting on the FACS Aria II. On day 8, ES cell and OP9-GFP cocultures were purified into GFP-CD41-, GFP-CD41int and GFP-CD41hi populations by cell sorting on the FACS Aria II.

value: dox-inducible transgenic A2lox.Meis1 mouse embryonic stem cells

tag: background strain

tag: day of differentiation

tag: treatment

value: doxycycline on day 6


title: Tooth germ embryonic day 35 Replicate 2 vs. tooth germ embryonic day 50 Replicate 1

description:
E35G2_vs_E50G1
No treated tissues.

tag: tissue

value: tooth germ

value: embryonic day 50

source_name: E35 tooth germ tissue

value: embryonic day 35


title: Tooth germ embryonic day 60 Replicate 3 vs. tooth germ embryonic day 35 Replicate 3

description:
E60G3_vs_E35G3
No treated tissues.

value: embryonic day 60


title: PBMC_2

value: Male

value: PBMC


title: PCB77, HK2 cells at T24, biological replicate 1

value: human kidney

value: HK2 from ATCC


title: WB_5


title: WB_4


title: WB_3


title: Tooth germ embryonic day 45 Replicate 2 vs. tooth germ embryonic day 35 Replicate 1

description:
E45G2_vs_E35G1
No treated tissues.

value: embryonic day 45


title: CD41int, A2lox.Meis1 and OP9-GFP co-culture, D8, treated with dox

description:
Meis1+dox_D8_CD41int
Expression data from GFP-CD41int cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture treated with doxycycline for 48 hours.

tag: population


title: HD vs LD (Individual) 5


title: PCB77, HK2 cells at T6, biological replicate 2

value: 8th generation

value: male

value: adult

value: Treated with 40 micro molar of PCB77 for 6 hours


title: HD vs LD (Individual) 4, dye swap

value: xylem

value: HD


title: CD41-, A2lox.Meis1 and OP9-GFP co-culture, D8, treated with dox

description:
Meis1+dox_D8_CD41-
Expression data from GFP-CD41- cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture treated with doxycycline for 48 hours.

value: dox-inducible transgenic A2lox.Meis1 mouse embryonic stem cells


title: PCB77, HK2 cells at T6, biological replicate 1


title: 39FgVelB_kd3_2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: This sample is a FgVelB-deleted Fusarium graminearum strain. It is the second of two FgVelB-deleted biological replicates used in this experiment and was harvested from carrot agar cultures 3 days after sexual induction

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Fusarium graminearum

source_name: Fusarium graminearum FgVelB deletion strain derived from GZ03639 strain

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

growth_protocol: Both the wild-type and FgVelB-deleted-strains of F. graminearum were grown on carrot for 7 days at 25C under dark condition, then their aerial mycelia were removed for indcution of perithecia formation, and subseqeuntly were incublaed for 3 additional days at 25°C with 12 h light–dark cycle. Perithecia and/or ground mycelia on carrot agar  were collected by scarping with a spatula and frozen at -80°C.

extract_protocol: Frozen mycelia were pulverized with mortar and pestle using liquid nitrogen for nucleic acid extraction. Total RNAs were extracted by TRIZOL. Extracted total RNA was treated with DNase I (Takara, Japan) to remove genomic DNA according to instructions provided by the manufacturer. The total RNA sample were precipitated with ethanol and resuspended in DEPC-treated water finally.

treatment_protocol: There is no special treatment in F. graminearum.

tag: strain

tag: genotype/variation

value: FgVelB deletion

tag: fertility status

value: self-sterile

tag: appearance

value: albino

tag: virulence

value: avirulent on host plants


title: CD41hi, A2lox.Meis1 and OP9-GFP co-culture, D8, untreated

description:
Meis1-dox_D8_CD41hi
Expression data from GFP-CD41hi cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture without doxycycline.

value: untreated


title: PCB77, HK2 cells at T0.5, biological replicate 3

description: Gene expression data from HK2 cell lines after 30 minutes of PCB77 treatment.

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

treatment_protocol: Treated with 40 micro molar of PCB77 for 30 minutes

tag: cell line

tag: cell passage


title: HD vs LD (Individual) 4

tag: wood density

tag: replicate

value: LD


title: WB_1

tag: gender

value: Male

tag: tissue/cell type

value: Whole blood


title: WB_2


title: CD41int, A2lox.Meis1 and OP9-GFP co-culture, D8, untreated

description:
Meis1-dox_D8_CD41int
Expression data from GFP-CD41int cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture without doxycycline.

tag: cell type


title: Gz3639_kd3_2

description: This sample is a wild-type Fusarium graminearum. It is the second of two wild-type biological replicates used in this experiment and was harvested from carrot agar culture 3 days after sexual induction

source_name: Fusarium graminearum wild-type GZ03639 strain

value: wild type

value: self-fertile

value: red-pigmented

value: virulent on host plants


title: PCB77, HK2 cells at T0, biological replicate 3

description: Gene expression data from HK2 cell lines before PCB77 treatment.

treatment_protocol: Treated with 40 micro molar of PCB77 for 0 minutes

value: human kidney

value: HK2 from ATCC

value: 8th generation

tag: sex

value: male

tag: developmental stage

value: adult

tag: treatment group


title: HD vs LD (Individual) 3, dye swap

tag: tissue

value: xylem

value: HD


title: HD vs LD (Individual) 3


title: HD vs LD (Bulk) 2, dye swap


title: PCB77, HK2 cells at T0.5, biological replicate 2

value: Treated with 40 micro molar of PCB77 for 30 minutes


title: PCB77, HK2 cells at T0.5, biological replicate 1


title: CD41-, A2lox.Meis1 and OP9-GFP co-culture, D8, untreated

description:
Meis1-dox_D8_CD41-
Expression data from GFP-CD41- cells purified on day 8 from A2lox.Meis1 and OP9-GFP co-culture without doxycycline.

value: dox-inducible transgenic A2lox.Meis1 mouse embryonic stem cells

tag: background strain

tag: day of differentiation

tag: treatment

tag: population


title: CD41+, A2lox.Meis1 and OP9-GFP co-culture, D7, treated with dox

description:
Meis1+dox_D7_CD41+
Expression data from GFP-CD41+ cells purified on day 7 from A2lox.Meis1 and OP9-GFP co-culture treated with doxycycline for 24 hours.

value: doxycycline on day 6


title: PCB77, HK2 cells at T0, biological replicate 2

value: Treated with 40 micro molar of PCB77 for 0 minutes


title: Berube_Stahl_N_europaea_starvation_recovery_Reco:Rep3

city: Cambridge

first: Paul

last: Berube

address: 15 Vassar Street

department: Civil and Environmental Engineering

institute: Massachusetts Institute of Technology

description:
Raw data file: 49941_532.ftr
Processed data file: 49941_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 recovering from 144 hours of ammonia starvation. Recovery was allowed to proceed for 20 minutes following ammonia addition. It is the third of three biological replicates used in this experiment.

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.2.14.

organism: Nitrosomonas europaea ATCC 19718

source_name: cells recovering from 144 hours of ammonia starvation (20 minutes post ammonia addition)

growth_protocol: Nitrosomonas europaea ATCC 19718 was grown to mid exponential phase in minimal salts medium with 12.5 mM ammonium sulfate and 50 mM HEPES as described in (Berube, P.M., Samudrala, R., and Stahl, D.A. (2007) J Bacteriol 189: 3935-3944).

extract_protocol: RNA was prepared using the hot acid phenol method as previously described (Sambrook, J., and Russell, D.W. (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press).  DNA was removed with Turbo DNA-free DNaseI (Ambion) by processing according to the manufacturer's directions. RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and concentration was determined by UV spectrophotometry using a Beckman-Coulter DU520 Spectrophotometer.

treatment_protocol:
Starvation of Nitrosomonas europaea ATCC was initiated by harvesting mid exponential phase cells by filtration and resuspending in medium without ammonia.  Samples were taken at 12 hours and 144 hours.
Recovery of cells starved of ammonia for 144 hours was initated by addition of 12.5 mM ammonium sulfate.  The recovery timepoint was 20 minutes following addition of ammonia to starved cells.

tag: strain

tag: accession

tag: protocol

value: 144 hours ammonia starvation plus 20 minutes recovery post-ammonia addition


title: 39FgVelB_kd3_1

description: This sample is a FgVelB-deleted Fusarium graminearum strain. It is the first of two FgVelB-deleted biological replicates used in this experiment and was harvested from carrot agar cultures 3 days after sexual induction

tag: genotype/variation

value: FgVelB deletion

tag: fertility status

value: self-sterile

tag: appearance

value: albino

tag: virulence

value: avirulent on host plants


title: CD41-, A2lox.Meis1 and OP9-GFP co-culture, D7, treated with dox

description:
Meis1+dox_D7_CD41-
Expression data from GFP-CD41- cells purified on day 7 from A2lox.Meis1 and OP9-GFP co-culture treated with doxycycline for 24 hours.


title: Berube_Stahl_N_europaea_starvation_recovery_Reco:Rep2

description:
Raw data file: 49801_532.ftr
Processed data file: 49801_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 recovering from 144 hours of ammonia starvation. Recovery was allowed to proceed for 20 minutes following ammonia addition. It is the second of three biological replicates used in this experiment.


title: Gz3639_kd3_1

description: This sample is a wild-type Fusarium graminearum. It is the first of two wild-type biological replicates used in this experiment and was harvested from carrot agar culture 3 days after sexual induction

value: wild type

value: self-fertile

value: red-pigmented

value: virulent on host plants


title: HD vs LD (Bulk) 1

tag: wood density

tag: replicate

value: LD


title: HD vs LD (Bulk) 2


title: Berube_Stahl_N_europaea_starvation_recovery_S144h:Rep3

description:
Raw data file: 49908_532.ftr
Processed data file: 49908_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 144 hours of ammonia starvation. It is the third of three biological replicates used in this experiment.

source_name: cells starved of ammonia for 144 hours

value: 144 hours ammonia starvation


title: PCB77, HK2 cells at T0, biological replicate 1

tag: cell type

value: human kidney

tag: cell line

value: HK2 from ATCC

tag: cell passage

value: 8th generation

tag: sex

value: male

value: adult


title: HD vs LD (Bulk) 1, dye swap

tag: tissue

value: xylem

value: HD


title: Berube_Stahl_N_europaea_starvation_recovery_S144h:Rep1

description:
Raw data file: 49350_532.ftr
Processed data file: 49350_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 144 hours of ammonia starvation. It is the first of three biological replicates used in this experiment.


title: CD41hi, A2lox.Meis2 and OP9-GFP co-culture, D8, treated with dox

description:
Meis2+dox_D8_CD41hi
Expression data from GFP-CD41hi cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture treated with doxycycline for 48 hours.

growth_protocol: A2lox.Meis2 ES cells were differentiated as embryoid bodies (EBs) for 6 days. On day 6, EBs were dissociated and plated at a density of 100,000 cells/ml on irradiated OP9-GFP cell monolayers with cytokines (100 ng/ml SCF, 40 ng/ml TPO, 40 ng/ml VEGF, 5% Flt3-L conditioned media, 10 ng/ml IL-3 and 20 ng/ml IL-6).

value: dox-inducible transgenic A2lox.Meis2 mouse embryonic stem cells

tag: background strain

tag: day of differentiation

value: doxycycline on day 6


title: Berube_Stahl_N_europaea_starvation_recovery_S012h:Rep3

description:
Raw data file: 49905_532.ftr
Processed data file: 49905_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 12 hours of ammonia starvation. It is the third of three biological replicates used in this experiment.

source_name: cells starved of ammonia for 12 hours

value: 12 hours ammonia starvation


title: CD41-, A2lox.Meis1 and OP9-GFP co-culture, D7, untreated

description:
Meis1-dox_D7_CD41-
Expression data from GFP-CD41- cells purified on day 7 from A2lox.Meis1 and OP9-GFP co-culture without doxycycline.

value: dox-inducible transgenic A2lox.Meis1 mouse embryonic stem cells

tag: treatment

value: untreated

tag: population


title: Berube_Stahl_N_europaea_starvation_recovery_S144h:Rep2

description:
Raw data file: 49742_532.ftr
Processed data file: 49742_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 144 hours of ammonia starvation. It is the second of three biological replicates used in this experiment.

tag: strain

tag: accession


title: Berube_Stahl_N_europaea_starvation_recovery_Reco:Rep1

description:
Raw data file: 49415_532.ftr
Processed data file: 49415_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 recovering from 144 hours of ammonia starvation. Recovery was allowed to proceed for 20 minutes following ammonia addition. It is the first of three biological replicates used in this experiment.

tag: protocol

value: 144 hours ammonia starvation plus 20 minutes recovery post-ammonia addition


title: CD41+, A2lox.Meis1 and OP9-GFP co-culture, D7, untreated

description:
Meis1-dox_D7_CD41+
Expression data from GFP-CD41+ cells purified on day 7 from A2lox.Meis1 and OP9-GFP co-culture without doxycycline.


title: CD41-, A2lox.Meis2 and OP9-GFP co-culture, D8, treated with dox

description:
Meis2+dox_D8_CD41-
Expression data from GFP-CD41- cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture treated with doxycycline for 48 hours.


title: HK2 cells at T24, biological replicate 3

description: Gene expression data from HK2 cell lines after 24 hours of PCB153 treatment.

treatment_protocol: Treated with 70uM PCB153 for 24 hours

tag: developmental stage

tag: treatment group


title: CD41int, A2lox.Meis2 and OP9-GFP co-culture, D8, treated with dox

description:
Meis2+dox_D8_CD41int
Expression data from GFP-CD41int cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture treated with doxycycline for 48 hours.


title: HK2 cells at T6, biological replicate 3

description: Gene expression data from HK2 cell lines after 6 hours of PCB153 treatment.

treatment_protocol: Treated with 70uM PCB153 for 6 hours


title: CD41-, A2lox.Meis2 and OP9-GFP co-culture, D8, untreated

description:
Meis2-dox_D8_CD41-
Expression data from GFP-CD41- cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture without doxycycline.


title: HK2 cells at T24, biological replicate 1


title: CD41hi, A2lox.Meis2 and OP9-GFP co-culture, D8, untreated

description:
Meis2-dox_D8_CD41hi
Expression data from GFP-CD41hi cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture without doxycycline.


title: HK2 cells at T0.5, biological replicate 3

description: Gene expression data from HK2 cell lines after 30 minutes of PCB153 treatment.

treatment_protocol: Treated with 70uM PCB153 for 30 minutes


title: HK2 cells at T24, biological replicate 2


title: Berube_Stahl_N_europaea_starvation_recovery_S012h:Rep2

description:
Raw data file: 49736_532.ftr
Processed data file: 49736_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 12 hours of ammonia starvation. It is the second of three biological replicates used in this experiment.


title: HK2 cells at T6, biological replicate 2


title: HK2 cells at T6, biological replicate 1


title: CD41int, A2lox.Meis2 and OP9-GFP co-culture, D8, untreated

description:
Meis2-dox_D8_CD41int
Expression data from GFP-CD41int cells purified on day 8 from A2lox.Meis2 and OP9-GFP co-culture without doxycycline.


title: Berube_Stahl_N_europaea_starvation_recovery_Expo:Rep3

description:
Raw data file: 49842_532.ftr
Processed data file: 49842_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 during exponential phase growth. It is the third of three biological replicates used in this experiment.

source_name: exponential phase cells

value: exponential growth


title: HK2 cells at T0.5, biological replicate 1


title: Berube_Stahl_N_europaea_starvation_recovery_S012h:Rep1

description:
Raw data file: 55416_532.ftr
Processed data file: 55416_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 following 12 hours of ammonia starvation. It is the first of three biological replicates used in this experiment. Note that this array file was incorrectly identified as sample Expo:Rep1 in the original NimbleGen data set (this error has been corrected for this submission).


title: HK2 cells at T0.5, biological replicate 2


title: CD41+, A2lox.Meis2 and OP9-GFP co-culture, D7, treated with dox

description:
Meis2+dox_D7_CD41+
Expression data from GFP-CD41+ cells purified on day 7 from A2lox.Meis2 and OP9-GFP co-culture treated with doxycycline for 24 hours.


title: Definitive endoderm at day 5

first: Chenhuan

last: Xu

address: 1 Beichen West Road

institute: Beijing Institute of Genomics

description: Gene expression data from cells differentiated at day 5 from mES cells.

hyb_protocol: Cy3-labeled cRNA were hybridized according to the standard Agilent protocol (Agilent One-Color Microarray-Based Gene Expression Analysis, 2006, Agilent).

scan_protocol: The arrays were scanned according to the standard Agilent protocol (Agilent One-Color Microarray-Based Gene Expression Analysis, 2006, Agilent).

data_processing: The data were extracted using Agilent Feature Extraction Software. Raw data were normalized by the quantile algorithm, GeneSpring Software 11.0 (Agilent).

label_protocol: Cy3-labeled cRNA were prepared according to the standard Agilent protocol (Agilent One-Color Microarray-Based Gene Expression Analysis, 2006, Agilent).

growth_protocol: Mouse ES cells E14.1 were used in this study. Before induction of differentiation, cells were dissociated with Enzyme-Free Solution (Millipore) and passed to a 1:1 mixture of Neurobasal (Gibco) and DMEM/F12 (Gibco) medium supplemented with N2 (0.5x) (Gibco), B27 (0.5x) (Gibco), 0.05% BSA solution (Gibco), 0.15mM MTG (Sigma), 10ng/ml BMP4 (R&D) and 1000U/ml LIF (Millipore) on gelatin-coated plates. The medium was changed daily. After 2-3 passages in this medium, ES cells were dissociated and seeded onto mouse collagen IV-coated plates in the medium described above but 30ng/ml activin A (R&D) was added instead of BMP4 and LIF. The medium was changed every other day. For hepatic differentiation, DE cells were cultured for 2 more days in the same medium except that 30ng/ml BMP4 and 10ng/ml bFGF (R&D) were added besides activin A.

tag: days of differentiation

value: ES cell-derived definitive endoderm


title: Early hepatic cells at day 7

description: Gene expression data from cells differentiated at day 7 from mES cells.

value: ES cell-derived early hepatic cells


title: mES cells

description: Gene expression data from mES cells.

source_name: mouse embryonic stem cells

value: embryonic stem (ES) cells


title: Berube_Stahl_N_europaea_starvation_recovery_Expo:Rep2

description:
Raw data file: 57080_532.ftr
Processed data file: 57080_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 during exponential phase growth. It is the second of three biological replicates used in this experiment.


title: Berube_Stahl_N_europaea_starvation_recovery_Expo:Rep1

description:
Raw data file: 49359_532.ftr
Processed data file: 49359_532_RMA_calls.txt
This sample is of Nitrosomonas europaea ATCC 19718 during exponential phase growth. It is the first of three biological replicates used in this experiment. Note that this array file was incorrectly identified as sample S012h:Rep1 in the original NimbleGen data set (this error has been corrected for this submission).


title: CD41-, A2lox.Meis2 and OP9-GFP co-culture, D7, treated with dox

description:
Meis2+dox_D7_CD41-
Expression data from GFP-CD41- cells purified on day 7 from A2lox.Meis2 and OP9-GFP co-culture treated with doxycycline for 24 hours.


title: HK2 cells at T0, biological replicate 3

description: Gene expression data from HK2 cell lines before PCB153 treatment.

treatment_protocol: Treated with 70uM PCB153 for 0 hours

value: human kidney


title: CD41-, A2lox.Meis2 and OP9-GFP co-culture, D7, untreated

description:
Meis2-dox_D7_CD41-
Expression data from GFP-CD41- cells purified on day 7 from A2lox.Meis2 and OP9-GFP co-culture without doxycycline.


title: mac-2

status: Public on Aug 02 2012

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data acquisition and image processing were performed using GCOS (Gene Chip Operating Software, Affymetrix). Raw data were collected and analyzed using GeneSpring GX software.  Additional processing of data was performed using dChip software (v 1.3, Harvard University).  Data normalization and background corrections were performed using GC-RMA.

source_name: matching blood monocyte derived macrophages

label_protocol: Affymetrix standard protocol

extract_protocol: RNAeasy

tag: tissue source

value: peripheral blood monocytes

value: blood monocyte derived macrophage


title: HK2 cells at T0, biological replicate 1

value: HK2 from ATCC

value: 8th generation

value: male


title: CD41+, A2lox.Meis2 and OP9-GFP co-culture, D7, untreated

description:
Meis2-dox_D7_CD41+
Expression data from GFP-CD41+ cells purified on day 7 from A2lox.Meis2 and OP9-GFP co-culture without doxycycline.


title: mac-1


title: WMAC-3

source_name: human wound macrophages

value: human subjects with chronic wounds

value: wound macrophages


title: HK2 cells at T0, biological replicate 2

value: adult


title: WMAC-2


title: NNI-8 rep2

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

description:
Date: Feb 1, 2011
AFG1133-27

scan_protocol: Affymetrix scanning protocol

data_processing: The data were processed using mas5 normalized scaled and log2 scaleded in R2.14

source_name: Primary neurosphere

label_protocol: Affymetrix standard labelling protocol

growth_protocol: Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the SingHealth Centralised Institutional Review Board A. GPC lines were described in our previous work.5 Briefly, cells were seeded as free-floating spheres at a density of 2,500 cells per cm2 in chemically defined serum-free growth medium containing basic fibroblast growth factor (bFGF; 20 ng/ml; PeproTech, New Jersey), epidermal growth factor (EGF; 20 ng/ml; PeproTech), heparin (5 ug/ml; Sigma-Aldrich, St Louis), and serumfree supplement (B27; 1x; Gibco, Grand Island, NY) in a 3:1 mix of Dulbecco's modified Eagle's medium (DMEM; Sigma-Aldrich) and Ham's F-12 Nutrient Mixture (F-12; Gibco). Neurospheres were mechanically triturated with a flame-drawn glass Pasteur pipette twice weekly and re-seeded in fresh culture medium

extract_protocol: Total RNA was isolated from tumor neurospheres using TRI Reagent (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array using 3' IVT express kit (Affymetrix Inc, Santa Clara, California).

value: brain tumor

tag: histology

value: Anaplastic oligoastrocytoma

tag: grade

value: III


title: NNI-12 rep2

description:
Date: Feb 1, 2011
AFG1133-31

value: Glioblastoma multiforme

value: IV


title: NNI-5 rep2

description:
Date: Feb 1, 2011
AFG1133-26


title: NNI-11 rep2

description:
Date: Feb 1, 2011
AFG1133-30


title: NNI-9 rep2

description:
Date: Feb 1, 2011
AFG1133-28


title: WMAC-1

tag: cell type


title: NNI-13 rep2

description:
Date: Feb 1, 2011
AFG1133-32


title: NNI-4 rep2

description:
Date: Feb 1, 2011
AFG1133-25


title: NNI-10 rep2

description:
Date: Feb 1, 2011
AFG1133-29


title: mac-3


title: NNI-3 rep2

description:
Date: Feb 1, 2011
AFG1133-24


title: NNI-13 rep1

description:
Date: Feb 1, 2011
AFG1133-11


title: NNI-8 rep1

description:
Date: Feb 1, 2011
AFG1133-6


title: NNI-1 rep1

description:
Date: Feb 1, 2011
AFG1133-1


title: NNI-4 rep1

description:
Date: Feb 1, 2011
AFG1133-4


title: NNI-12 rep1

description:
Date: Feb 1, 2011
AFG1133-10


title: NNI-10 rep1

description:
Date: Feb 1, 2011
AFG1133-8


title: NNI-5 rep1

description:
Date: Feb 1, 2011
AFG1133-5


title: RL_siRNA_LIF1h_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Following fragmentation, 15 microgram of cRNA were hybridized for 17 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.28.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: MCF7 cells, RL silenced, LIF 1h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 nanogram total RNA.

extract_protocol: Cell lysates were homogenized with the QiaShredder Column (Qiagen), and total cellular RNA was extracted with the Rneasy Mini kit (Qiagen) following manufacturer’s instructions.

treatment_protocol: Transfected with 50nM Renilla Luciferase siRNA. 72h later, cells were cutured 4h without FCS and stimulated with 10ng/ml LIF 1h

tag: cell line

value: MCF7 breast cancer

value: RL silenced and LIF-stimulated


title: NNI-2 rep2

description:
Date: Feb 1, 2011
AFG1133-23


title: SIN3A_siRNA_LIF1h_rep1

source_name: MCF7 cells, SIN3A silenced, LIF 1h

treatment_protocol: Transfected with 50nM SIN3A siRNA. 72h later, cells were cutured 4h without FCS  and stimulated with 10ng/ml LIF 1h

value: SIN3A silenced and LIF-stimulated


title: NNI-1 rep2

description:
Date: Feb 1, 2011
AFG1133-22


title: SIN3A_siRNA_NS_rep2

source_name: MCF7 cells, SIN3A silenced, NS

treatment_protocol: Transfected with 50nM SIN3A siRNA. 72h later, cells were cutured 4h without FCS

value: SIN3A silenced


title: NNI-11 rep1

description:
Date: Feb 1, 2011
AFG1133-9


title: Mock_cells_rep2

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

hyb_protocol: The biotinylated cRNA targets are were cleaned up, fragmented, and hybridized to GeneChip expression arrays according to standard Affymetrix protocols.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R/Bioconductor version 2.10 using Affy package default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: pLenti transduced cell lines Mock (empty vector)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA using GeneChip IVT Labeling Kit.

extract_protocol: RNA Isolation was performed using the Tripure Isolation Reagent (Roche).Quality control was performed with Agilent Bioanalyser.

value: human gastric tubular adenocarcinoma

tag: tissue origin

value: stomach (70 year-old female)


title: RL_siRNA_NS_rep3

source_name: MCF7 cells, RL silenced, NS

treatment_protocol: Transfected with 50nM Renilla Luciferase siRNA. 72h later, cells were cutured 4h without FCS

value: RL silenced


title: RL_siRNA_LIF1h_rep3


title: SIN3A_siRNA_NS_rep3


title: NNI-2 rep1

description:
Date: Feb 1, 2011
AFG1133-2

tag: tissue


title: RL_siRNA_NS_rep2


title: NNI-3 rep1

description:
Date: Feb 1, 2011
AFG1133-3


title: SIN3A_siRNA_LIF1h_rep2


title: RL_siRNA_NS_rep1


title: WT_cells_rep2

source_name: pLenti transduced cell lines overexpressing canonical CDH1


title: WT_cells_rep1


title: RL_siRNA_LIF1h_rep1


title: WT_cells_rep3


title: SIN3A_siRNA_NS_rep1


title: Mock_cells_rep3


title: Ex1_cells_rep3

source_name: pLenti transduced cell lines overexpressing CDH1a


title: Ex1_cells_rep2