title: control, biological rep 10

source_name: Lung tissue, control, biological rep 10


title: CLL B-cell, patient M4_unstimulated cells_at 90min

status: Public on Jan 04 2013

type: RNA

city: Strasbourg

first: Laurent

last: Vallat

address: 1, Place de l'Hopital

department: Immunology

country: France

institute: Strasbourg University Hospital

hyb_protocol: standard affymetrix

scan_protocol: standard affymetrix

data_processing: Data were normalized with the invariant set method and the model based expression index (MBEI) obtained by the PM-MM model (Li et al., PNAS 2001) using dChip software (dChip v.2006; www.dchip.org). The obtained expression values are preprocessed by truncating the value to less than or equal to 1.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CLL B-cell_unstimulated cells_90min

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

extract_protocol: At each time point 10^7 control US and S cells were washed and resuspended in 1 mL TRIzol (Invitrogen, Carlsbad, CA). Total RNA was purified using Promega columns (SV total isolation system, Promega corp. Madison, WI).

treatment_protocol:
cell isolation: B-cells were negatively selected from fresh blood samples using the Rosettesep B-cell enrichment cocktail (Stemcell Biotechnologies, Vancouver, Canada) and isolated by density gradient centrifugation over Ficoll-Paque plus (Pharmacia, Upsala, Sweden). Quality of the selection was assessed by flow cytometry on a Cytomics FC500 system (Beckman-Coulter, Fullerton, CA) after CD5-PE / CD19-FITC staining (BD Biosciences, Palo Alto, CA) and in all cases was greater than 93%, range from 93-98% (med. 96%). Cells were starved for 4 hr at 37degree C / 5% CO2 in RPMI 1640 media supplemented with 2 nM L-glutamine and 24 ug/mL gentamicin.
B-cells at a density of 10^7cells/mL were divided in two. One was used as unstimulated (US) control and the other stimulated (S) by goat F(ab’)2 anti human IgM-BIOT (Southern biotech, Birmingham, AL) at 20 mg/mL and cross-linked by 20 mg/mL of avidin (Sigma-Aldrich, St Louis, MO) on ice during 5 min, follow by incubation at 37degree C for 15 min. After washing, cells were cultured at 37degree C / 5% CO2 in RPMI 1640 media supplemented with 10% FBS, 2 nM L-glutamine and 24 ug/mL gentamicin.

tag: cell classification

value: indolent leukemia

tag: cell type

value: chronic lymphocytic leukemia B-cell

tag: unstimulated (us)/stimulated (s)

value: US

tag: time point (min)

tag: transfected with


title: CLL B-cell, patient M1_unstimulated cells_at 210min

source_name: CLL B-cell_unstimulated cells_210min


title: CLL B-cell, patient M1_stimulated cells_at 60min

source_name: CLL B-cell_stimulated cells_60min

value: S


title: CLL B-cell, patient M1_unstimulated cells_at 60min

source_name: CLL B-cell_unstimulated cells_60min


title: CLL B-cell, patient M1_stimulated cells_at 390min

source_name: CLL B-cell_stimulated cells_390min


title: control, biological rep 11

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

country: USA

institute: University of Pittsburgh

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. miRNA expression data from a control lung.

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters. The normalization algorithm used is quantile normalization.

source_name: Lung tissue, control, biological rep 11

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

tag: tissue

value: whole lung

tag: gender

value: male

tag: age


title: CLL B-cell, patient M1_stimulated cells_at 210min

source_name: CLL B-cell_stimulated cells_210min


title: Healthy B-cell, subject N6_stimulated cells_at 390min

source_name: Healthy B-cell_stimulated cells_390min

value: healthy control

value: Healthy B-cell


title: Healthy B-cell, subject N6_stimulated cells_at 60min

source_name: Healthy B-cell_stimulated cells_60min


title: CLL B-cell, patient M1_unstimulated cells_at 390min

source_name: CLL B-cell_unstimulated cells_390min


title: Healthy B-cell, subject N6_stimulated cells_at 90min

source_name: Healthy B-cell_stimulated cells_90min


title: Healthy B-cell, subject N6_unstimulated cells_at 60min

source_name: Healthy B-cell_unstimulated cells_60min


title: Healthy B-cell, subject N6_unstimulated cells_at 210min


title: Healthy B-cell, subject N6_unstimulated cells_at 90min

source_name: Healthy B-cell_unstimulated cells_90min


title: Healthy B-cell, subject N5_stimulated cells_at 390min


title: control, biological rep 7

source_name: Lung tissue, control, biological rep 7

value: not available


title: control, biological rep 5

source_name: Lung tissue, control, biological rep 5

value: female


title: control, biological rep 6

source_name: Lung tissue, control, biological rep 6


title: control, biological rep 3

source_name: Lung tissue, control, biological rep 3


title: control, biological rep 2

source_name: Lung tissue, control, biological rep 2


title: control, biological rep 4

source_name: Lung tissue, control, biological rep 4


title: UIP, biological rep 12

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. miRNA expression data from a lung with usual interstitial pneumonia.

source_name: Lung tissue, UIP, biological rep 12


title: UIP, biological rep 13

source_name: Lung tissue, UIP, biological rep 13


title: CLL B-cell, patient M2_stimulated cells_at 60min

source_name: CLL B-cell_stimulated cells_60min

value: aggressive leukemia


title: UIP, biological rep 10

source_name: Lung tissue, UIP, biological rep 10


title: UIP, biological rep 11

source_name: Lung tissue, UIP, biological rep 11


title: UIP, biological rep 9

source_name: Lung tissue, UIP, biological rep 9


title: UIP, biological rep 8

source_name: Lung tissue, UIP, biological rep 8


title: control, biological rep 1

source_name: Lung tissue, control, biological rep 1


title: Healthy B-cell, subject N4_stimulated cells_at 210min

source_name: Healthy B-cell_stimulated cells_210min


title: Healthy B-cell, subject N5_stimulated cells_at 90min

source_name: Healthy B-cell_stimulated cells_90min


title: Healthy B-cell, subject N5_stimulated cells_at 60min

source_name: Healthy B-cell_stimulated cells_60min


title: Healthy B-cell, subject N4_unstimulated cells_at 390min


title: UIP, biological rep 6

source_name: Lung tissue, UIP, biological rep 6


title: Healthy B-cell, subject N4_unstimulated cells_at 60min

source_name: Healthy B-cell_unstimulated cells_60min


title: UIP, biological rep 5

source_name: Lung tissue, UIP, biological rep 5


title: UIP, biological rep 4

source_name: Lung tissue, UIP, biological rep 4


title: UIP, biological rep 7

source_name: Lung tissue, UIP, biological rep 7


title: UIP, biological rep 2

source_name: Lung tissue, UIP, biological rep 2


title: Healthy B-cell, subject N5_unstimulated cells_at 90min

source_name: Healthy B-cell_unstimulated cells_90min


title: Healthy B-cell, subject N5_unstimulated cells_at 390min


title: Healthy B-cell, subject N5_stimulated cells_at 210min


title: Healthy B-cell, subject N5_unstimulated cells_at 210min


title: Healthy B-cell, subject N5_unstimulated cells_at 60min


title: Healthy B-cell, subject N4_stimulated cells_at 90min


title: Healthy B-cell, subject N4_stimulated cells_at 60min


title: Healthy B-cell, subject N4_unstimulated cells_at 210min


title: Healthy B-cell, subject N4_unstimulated cells_at 90min


title: Healthy B-cell, subject N4_stimulated cells_at 390min

source_name: Healthy B-cell_stimulated cells_390min


title: UIP, biological rep 3

source_name: Lung tissue, UIP, biological rep 3


title: Healthy B-cell, subject N3_stimulated cells_at 390min


title: Healthy B-cell, subject N3_stimulated cells_at 90min


title: UIP, biological rep 1

source_name: Lung tissue, UIP, biological rep 1


title: Healthy B-cell, subject N3_unstimulated cells_at 210min


title: Healthy B-cell, subject N3_stimulated cells_at 210min


title: Healthy B-cell, subject N2_stimulated cells_at 390min


title: TAN_4

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hyb on Illumina Mouse Ref-8 v2 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Array data were processed by Illumina’s BeadStudio software and expression levels exported for analysis.  The gene-wise, median correlation of each array compared to all other arrays was computed to ensure that no outliers existed within the data. The expression levels were then quantile normalized using Matlab software (2010b) and non-informative probes (those with detection p-value >0.05 in all samples) were removed to reduce experimental noise. Ultimately, 16,322 probes were used in our analysis.

organism: Mus musculus

source_name: tumor-associated neutrophils (TAN)

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit (Cat #AMIL1791)

extract_protocol: Gene expression was analyzed in neutrophils from 3 different populations – 7 isolated from bone marrow of naïve mice (NN), 4 isolated from spleens of tumor bearing mice (Granulocytic myeloid derived suppressor cells, G-MDSC), and 4 isolated from flank AB12 tumors (Tumor associated neutrophils, TAN). All neutrophil populations were defined as Ly6G+. Neutrophils were isolated following preparation of single cell suspension, using CD11b-Miltenni beads for enrichment, followed by flow-sorting of the Ly6G+ cells. RNA was processed as previously described and hybridized on Illumina Mouse Ref-8 v2 microarray chips.

tag: strain background

value: BALB/c

tag: group

value: neutrophils from tumor

tag: control group

value: No

tag: replicates

value: yes

tag: class

value: clonal

tag: sample id


title: G-MDSC_2

source_name: granulocytic fraction of myeloid-derived suppressor cells (G-MDSC)

value: splenic neutrophils of tumor-bearing mice


title: G-MDSC_1


title: Healthy B-cell, subject N3_unstimulated cells_at 390min


title: G-MDSC_4


title: NHLF cells_2hrTGFB_biological rep1

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

description: Cultured NHLF cells treated with 5ng/ml TGFB or DMSO for 2hr

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55 C on Agilent-019118 Human miRNA microarray 2.0 G4470B. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides

data_processing: Agilent Feature Extraction v10.5.1.1 default parameters

source_name: NHLF Cells

label_protocol: pCp-Cy3  labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

growth_protocol: The cells were subcultured in fibroblast growth medium 2, supplemented with hFGF-B, insulin, GA-1000 and fetal bovine serum (FBS)

extract_protocol: Total RNA extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: Cultured NHLF cells treated with 5ng/ml TGFB or DMSO for 2 hours

tag: cells

value: normal human lung fibroblast cells

tag: agent

value: TGFB


title: NHLF cells_2hrTGFB_biological rep2


title: NHLF cells_2hrTGFB_biological rep3


title: G-MDSC_3


title: NHLF cells_2hrTGFB_biological rep6


title: NHLF cells_2hrTGFB_biological rep5


title: Healthy B-cell, subject N3_unstimulated cells_at 60min

value: US


title: NHLF cells_2hrTGFB_biological rep4


title: TAN_2


title: TAN_1


title: TAN_3


title: NHLF cells_0h control_biological rep6

value: control


title: Healthy B-cell, subject N3_stimulated cells_at 60min

value: S


title: Healthy B-cell, subject N2_stimulated cells_at 90min


title: Healthy B-cell, subject N3_unstimulated cells_at 90min


title: NHLF cells_0h control_biological rep4


title: Healthy B-cell, subject N2_stimulated cells_at 210min


title: Healthy B-cell, subject N2_stimulated cells_at 60min


title: NHLF cells_0h control_biological rep3


title: NN_7

source_name: Naïve mouse

value: BM naïve neutrophils


title: NHLF cells_0h control_biological rep1


title: Healthy B-cell, subject N2_unstimulated cells_at 390min

value: healthy control


title: NHLF cells_0h control_biological rep2


title: NN_3


title: NN_4


title: NN_6


title: Healthy B-cell, subject N2_unstimulated cells_at 210min

value: Healthy B-cell


title: NN_2


title: NN_5


title: liver_individual 2

city: Shanghai

first: Ning

last: Fu

address: 320# Yue-Yang Road

department: Shanghai Institute for Biological Sciences

country: China

institute: Chinese Academy of Sciences

hyb_protocol: The labeled RNA was purified and hybridized to Agilent Human miRNA Microarray following the manufacturer’s instructions

scan_protocol: The slides were scanned with the Agilent Microarray Scanner using one color scan setting for array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain TotalGeneSignal. microRNAs with features in SystematicName column begining with hsa- and in column IsGeneDetected as 1 remained, others were removed. This resulted in detecting expression of 429 human miRNA in at least one of the 9 samples studied.

source_name: Adult human liver:individual 2

label_protocol: For each sample, 100ng total of RNA was dephosphorylated and ligated with pCp-Cy3, following the manufacturer’s instructions, as described in the miRNA Complete Labeling and Hybridization Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from 50mg frozen sample using a mirVana RNA Isolation Kit (Ambion, AM1560), according to the manufacturer’s instructions.The quality of each sample was checked by using an Agilent 2100 Bioanalyzer.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used.

value: Adult human liver

value: male


title: liver_individual 3

source_name: Adult human liver:individual 3


title: Healthy B-cell, subject N2_unstimulated cells_at 90min


title: Healthy B-cell, subject N2_unstimulated cells_at 60min


title: Healthy B-cell, subject N1_stimulated cells_at 390min


title: liver_individual 1

source_name: Adult human liver:individual 1


title: Healthy B-cell, subject N1_stimulated cells_at 210min

source_name: Healthy B-cell_stimulated cells_210min


title: CD1 VIERGE

city: JOUY-EN-JOSAS

last: GALIO

address: Domaine de Vilvert

institute: INRA

hyb_protocol: Cy3-labeled RNA was added to a hybridization cocktail, heated to 99°C for 5 minutes, transfered to an ice water bath for 5 minutes, then added to the miRNA array to hybridize at 55°C for 20 hours.  Arrays were washed according to manufacturer's directions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for miRNA array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters for miRNA arrays to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were flagged.  Intensity data were normalized with Rosetta Resolver (ver. 7.2), using the Agilent/miRNA-Intensity Profile Builder.  This process starts from raw scan data and saves reporter and sequence-level intensity profiles.  This pipeline implements summarization from feature data as described in the Agilent Feature Extraction Software (v9.5) Reference Guide, 4th ed, 2007, 237–239.  Features’ signal values are summarized to their reporter as a gTotalProbeSignal sum, and reporters are summarized to their sequence as a sum.  This pipeline is not group dependent: replicates are not normalized as a group, with all operations performed scan-by-scan.    Following this step, the Agilent/miRNA-Intensity Experiment Builder was used to do the group-level normalization.  This pipeline starts from intensity-profile reporter data and builds sequence-level intensity experiments.  This pipeline uses group processing.  This pipeline differs from Agilent/Intensity Experiment builder pipeline by addition of 75th percentile scaling operation in the Normalize Intensities step (Inter-chip Scaling plug-in).  The Inter-chip scaling plug-in also includes the option Trim outlying values from baseline data.  This option is disabled in this pipeline, and should remain disabled because it can introduce biases in scaled profiles. The bias arises because outlier trimming excludes datapoints with negative values, and Agilent/miRNA data profiles can include many datapoints with small negative values.

source_name: mammary gland, virgin

label_protocol: Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) was used to generate fluorescently-labeled miRNA with a sample input of 100 ng of total RNA. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of an RNA molecule with greater than 90% efficiency.  Work was done according to the manufacturer's instructions.

growth_protocol: mouse or ewe either virgin, in cycle, in gestation or lactation

extract_protocol: 100 to 150 mg of snap-frozen mammary tissue samples were homogenized in 1 ml TRIZOL® Reagent (Invitrogen) using an Ultra-turrax, and then incubated for 5 minutes at room temperature to allow the complete dissociation of nucleoprotein complexes. An 0.2 ml volume of chloroform was added and the samples were shaken vigorously for 15 seconds, incubated at room temperature for 2 to 3 minutes and then centrifuged at 10,000 g for 15 minutes at 4°C. The aqueous phase was transferred to a fresh tube and the total volume of samples was measured. After the addition of 3 volumes of absolute ethanol, the RNA solution was purified using the NucleoSpin RNA clean-up kit (Macherey-Nagel), according to the manufacturer's guidelines. The quantity and integrity of RNA were estimated with a NanoDrop spectrophotometer (NanoDrop Technologies) and Agilent 2100 bioanalyser (Agilent Technologies). Only samples with an RNA integrity number ≥6 were used for subsequent miRNA expression analyses.

value: mammary gland

tag: physiological stage

value: virgin

tag: days


title: Healthy B-cell, subject N1_stimulated cells_at 90min

source_name: Healthy B-cell_stimulated cells_90min

tag: cell classification

tag: cell type


title: CD1 L2

source_name: mammary gland, 2 days of lactation

value: lactation


title: NN_1

value: BALB/c


title: prefrontal cortex_individual 2

source_name: Adult human prefrontal cortex:individual 2

value: Adult human prefrontal cortex


title: Neural progenitor cells_control biological rep 3

first: Leonardo

last: D'Aiuto

address: 3811 O’Hara Street

institute: UPMC

description:
Mock-infected Neural progenitor cells 3
5991368001_F.AVG_Signal

hyb_protocol: After purification aliquots of each sample were hybridized to Illumina platform HumanHT-12 v4 Expression.

scan_protocol: After hybridization, each array was sequentially washed, stained with CY3, and scanned on the Illumina HiScan

data_processing: For array readout we used Illumina Feature Extraction Software (Genome Studio 11.0)

source_name: Neural progenitor cells

label_protocol: The cDNA was used as a template to generate biotin-labeled cRNA that was used for hybridization accordung to Illumina standard protocol

growth_protocol: NPCs were cultured in NP expansion medium (DMEM/F12 medium supplemented with 1% N2, bFGF (20 ng ml-1), 1 mM L-glutamine, 1% nonessential amino acids, 50 U ml_1 penicillin, 50 mg ml-1 streptomycin and 0.1 mM 2-mercaptoethanol)

extract_protocol: RNA was extracted using and RNeasy kit (Qiagen). RNA quantity was determined by OD measurement using the Nanodrop 1000 at 260 nm and RNA integrity by. The integrity of the RNA was determined using the Agilent 2100 Bioanalyzer to calculate the RNA integrity Number (RIN).

treatment_protocol: NPCs were infected with HCMV Ad 169 at an MOI of 3

value: neural progenitor cell (NPC)

tag: infection


title: CD1 L10

source_name: mammary gland, 10 days of lactation


title: prefrontal cortex_individual 1

source_name: Adult human prefrontal cortex:individual 1


title: CD1 G17

source_name: mammary gland, 17 days of gestation

value: gestation


title: Neural progenitor cells_control biological rep 1

description:
Mock-infected Neural progenitor cells 1
5991368001_D.AVG_Signal


title: Healthy B-cell, subject N1_stimulated cells_at 60min

source_name: Healthy B-cell_stimulated cells_60min

tag: unstimulated (us)/stimulated (s)

tag: time point (min)

tag: transfected with


title: CD1 G10

source_name: mammary gland, 10 days of gestation

tag: tissue


title: cerebellum_individual 2

source_name: Adult human cerebellum:individual 2

value: Adult human cerebellum

tag: gender

tag: age


title: BREBIS L60

organism: Ovis aries

source_name: mammary gland, 60 days of lactation


title: cerebellum_individual 3

source_name: Adult human cerebellum:individual 3


title: Healthy B-cell, subject N1_unstimulated cells_at 390min


title: Neural progenitor cells_control biological rep 2

description:
Mock-infected Neural progenitor cells 2
5991368001_E.AVG_Signal


title: Healthy B-cell, subject N1_unstimulated cells_at 210min


title: prefrontal cortex_individual 3

source_name: Adult human prefrontal cortex:individual 3


title: Neural progenitor cells biological rep 3

description:
HCMV-infected Neural progenitor cells 3
5991368001_C.AVG_Signal

value: HCMV


title: cerebellum_individual 1

source_name: Adult human cerebellum:individual 1


title: Healthy B-cell, subject N1_unstimulated cells_at 60min

source_name: Healthy B-cell_unstimulated cells_60min

value: US


title: Healthy B-cell, subject N1_unstimulated cells_at 90min

source_name: Healthy B-cell_unstimulated cells_90min


title: BREBIS G64

source_name: mammary gland, 64 days of gestation


title: BREBIS J15

source_name: mammary gland, in cycle

value: cycle


title: DLBCL cell line OCI-Ly07 versus male control DNA

type: genomic

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

description: OCI-Ly07 vs maleControlDNA

hyb_protocol: NimbleGen Hybridization Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/hybridization/index.html)

scan_protocol: NimbleGen Scan Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/software/nimblescan/index.html)

data_processing: The unspecific binding intensity was estimated using the random control probes and subtracted. Outlier probes and probes with too low signal were detected and removed (set to NaN). [Note: (1) the two 'DNAPool vs maleControlDNA' replicates were averaged already on signal level to get more robust results (thus the processed log2(ratio)s for these two replicates are identical). (2) The normalized values of the random sequence probes (e.g. RANDOM00000001, RANDOM00000002 etc) were used to subtract the unspecific binding offsets and included in the full_normalized_data.txt file available on Series records.]

molecule: genomic DNA

source_name: DLBCL cell line OCI-Ly07

label_protocol: NimbleGen Labeling Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/labeling/index.html)

extract_protocol: Genomic DNA from DLBCL cell lines was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's recommendations.

tag: cell line

value: DLBCL cell line OCI-Ly07

value: diffuse large B-cell lymphoma (DLBCL)

source_name: male control DNA


title: DLBCL cell line OCI-Ly02 versus male control DNA

description: OCI-Ly02 vs maleControlDNA

source_name: DLBCL cell line OCI-Ly02

value: DLBCL cell line OCI-Ly02


title: DLBCL cell line SUDHL-10 versus male control DNA

description: SUDHL-10 vs maleControlDNA

source_name: DLBCL cell line SUDHL-10

value: DLBCL cell line SUDHL-10


title: DLBCL cell line K422 versus male control DNA

description: K422 vs maleControlDNA

source_name: DLBCL cell line K422

value: female

value: DLBCL cell line K422


title: Neural progenitor cells biological rep 2

description:
HCMV-infected Neural progenitor cells 2
5991368001_B.AVG_Signal

source_name: Neural progenitor cells

value: male


title: BREBIS G14

source_name: mammary gland, 14 days of gestation

value: mammary gland


title: WT-Fibro-01

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

hyb_protocol: Purified cRNA (12,5 µg) was labeled, fragmented and hybridized on the Affymetrix HG-U133 plus 2.0 microarray according to the protocol provided by manufacturer.

scan_protocol: Affymetrix RUO platform.

data_processing: RAW data were acquired using Affymetrix GCOS software. The results were normalized by the quantile method and background corrected using robust multi-array analysis (RMA) (Yu J et al., 2009). After normalization, the probe-level data were  summarized using median polish to obtain the probe set level measurement. We then collapsed 54,675 probe sets to 51,337 transcripts by taking the average log intensity values for probe sets that represent a common accession number.

label: Biotin

source_name: Fibroblasts, father

label_protocol: GeneChip IVT Express and GeneChip Hybridization wash and stain kits were employed according the instructions provided by Affymetrix. Briefly, 100ng of total RNA was used as a template in the synthesis of double-strand cDNA. After in vitro transcription, the obtained cRNA was purifed and quantified by Nanodrop.

growth_protocol: Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS). Fibroblasts were grown in DMEM+15%FBS.

extract_protocol: Total RNA from cells was isolated using RNeasy Mini Kit. The quality of extracted RNA was checked using Agilent 2000 analyzer.

tag: genotype/variation

value: fibroblasts


title: BREBIS G125

source_name: mammary gland, 125 days of gestation


title: SMA-Fibro-02

source_name: Fibroblasts, SMA patient


title: pombe_SD2,biological rep1

city: Nanjing

first: Rongpeng

last: Li

address: Wenyuan Rd 1

department: College of life science

institute: Nanjing normal university

description: Gene expression data from S. pombe SD2 in log phase cultured in YEPD medium

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

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

data_processing: The data were analyzed with PARTEK genomic suit 6.5 using RMA normalization

organism: Schizosaccharomyces pombe

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual  Affymetrix).

growth_protocol: The rpl32-1, rpl32-2 deleted and SPQ-01 yeast strains were cultured in YEPD medium at 30C, until the OD600 was  5.0.

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

treatment_protocol: Cells were collected and frozen in liquid nitrogen quickly for extraction of total RNA.

tag: strain

value: SPQ-01 with rpl32-2 deleted


title: DLBCL cell line HT versus male control DNA

description: HT vs maleControlDNA

source_name: DLBCL cell line HT

value: DLBCL cell line HT


title: Neural progenitor cells biological rep 1

description:
HCMV-infected Neural progenitor cells 1
5991368001_A.AVG_Signal

value: neural progenitor cell (NPC)


title: iPS-19.9-03

source_name: iPS cells-CTR

value: induced pluripotent stem cells (iPS cells)


title: pombe_SD1,biological rep3

description: Gene expression data from S. pombe SD1 in log phase cultured in YEPD medium

value: SPQ-01 with rpl32-1 deleted


title: pombe_SD1,biological rep1

source_name: S. pombe SD1 in log phase cultured in YEPD medium


title: pombe_SD1,biological rep2


title: Low_sensitive_1

city: Santiago de Chile

first: Calixto

last: Dominguez

state: Región Metropolitana

address: Zanartu 1482

department: Center for Bioinformatics and Genome Biology

country: Chile

institute: Fundación Ciencia y Vida

description: A RNA pool from the head kidney of 5 fishes belonging to Family 4 without challenge against P. Salmonis were used as control

hyb_protocol: Labeled samples were hybridized on a 32K cDNA microarray. Before hybridization, slides were pre-treated with 3% BSA fraction V, 5 × SSC, 0.1% SDS for 90 min at 49°C and washed with 5 x Milli-Q water for 30 s at room temperature. Hybridization slides were washed fivefold with washing solution A (2× SSC, 0.2% SDS) for 10 min at 49°C, twice with washing solution B (1× SSC) for 10 min and fourfold with washing solution C (0.1× SSC) at room temperature. Slides were then rinsed in Milli-Q water and dried by centrifugation

scan_protocol: Microarrays were scanned using a Scan array Express system (PerkinElmer) and a group of measures including foreground (FG) and background (BG) values of intensity for each spot in both channels were stored as tab-separated text file for further analysis.

data_processing: Data were normalized using an intensity dependent normalization (loess) procedure and a linear model was fitted to the expression data for each gene across the microarrays in order to identify significant expression changes. A FDR of 0.05 was applied to report specific transcripts as differentially expressed between conditions using limma library running R software environment.

organism: Salmo salar

label_protocol: 12 μg of pooled kidney RNA were reverse transcribed using a SuperScript® Indirect cDNA Labeling System (Invitrogen)

growth_protocol: Fish were maintained in 7 m3, with seawater in a recirculation system at 14.7 ± 0.1 °C water temperature, 33.92 ± 0.04 ppm salinity, and 93.35 ± 1.28 oxygen saturation, sharing the same nutritional and environmental background.

extract_protocol: Total RNA was extracted from 50 to 100 mg of tissue using TRIZOL® Reagent (Invitrogen), and then purified with RNeasy mini kit (QIAGEN).

treatment_protocol: Two challenges with P.salmonis were performed. For the first challenge up to around twenty fish from each family were randomly transferred to ten tanks All fishes were infected by intraperitoneal injection with 0.2 mL Piscirickettsia salmonis. The fishes were observed daily and mortality per family group was recorded for 40 days post infection. After forty days, fish were harvested and the cumulative mortality (dead fish / total fish) for each family was calculated.

value: head kidney

tag: treatment


title: DLBCL cell line HBL-1 versus male control DNA

description: HBL-1 vs maleControlDNA

source_name: DLBCL cell line HBL-1

value: DLBCL cell line HBL-1


title: pombe_SD2,biological rep3

source_name: S. pombe SD2 in log phase cultured in YEPD medium


title: Low_sensitive_3

description: A RNA pool from the head kidney of 5 fishes belonging to Family 6 without challenge against P. Salmonis were used as control

value: intraperitoneal injection with 0.2 mL Piscirickettsia salmonis


title: iPS-19.9-02


title: DLBCL cell line BJAB versus male control DNA

description: BJAB vs maleControlDNA

source_name: DLBCL cell line BJAB

value: DLBCL cell line BJAB


title: DLBCL cell line TMD-8 versus male control DNA

description: TMD-8 vs maleControlDNA

source_name: DLBCL cell line TMD-8

value: DLBCL cell line TMD-8

value: diffuse large B-cell lymphoma (DLBCL)


title: pombe_WT,biological rep3

description: Gene expression data from S. pombe WT in log phase cultured in YEPD medium


title: High_sensitive_3

description: A RNA pool from the head kidney of 5 fishes belonging to Family 3 without challenge against P. Salmonis were used as control


title: SMA-iPS-01

source_name: iPS cells, SMA patient


title: DNA pool versus male control DNA, 2 replicates

description:
Note that the two 'DNAPool vs maleControlDNA' replicates were combined already on signal level to get more robust results;
DNAPool vs maleControlDNA #1 (439546A01_2uM_532.pair & 439546A01_2uM_635.pair) and #2 (439546A02_2uM_532.pair & 439546A02_2uM_635.pair)

source_name: DNA pool (7*male + 3*female)

value: 7*male :3*female

source_name: male control DNA


title: SMA-iPS-02


title: DLBCL cell line OCI-Ly01 versus male control DNA

description: OCI-Ly01 vs maleControlDNA

source_name: DLBCL cell line OCI-Ly01

value: DLBCL cell line OCI-Ly01


title: pombe_SD2,biological rep2


title: SMA-Fibro-01


title: RPE derived from 253G1 iPSC

status: Public on Jan 03 2013

city: Kobe

first: Shin

last: Kawamata

state: Hyogo

department: The Basic Reserch Group for Regenerative Medicine

country: Japan

institute: Foundation for Biomedical and Innovation

description:
Gene expression data from cells
human datasheet

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. 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 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 500.

label_protocol: Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer’s instructions from 250 ng total RNA.

growth_protocol:
(RPE-253G1) Human primary retinal pigment epithelium (RPE, Lonza) was maintained in Retinal Pigment Epithelial Cell Basal Medium (Lonza Biologics, Basel, Switzerland) containing supplements (L-glutamine, GA-1000 and bFGF; Lonza). Human iPS cell (iPSC) line 253G1 [1] [Riken Bio Resource Center (Tsukuba, Japan)] was maintained on feeder cell SNL [2] in human ES cell culture medium and 5 ng/ml bFGF (Peprotech). iPSC was cultured in ReproFF2 (ReproCELL) supplemented with 5 ng/ml bFGF medium. iPSC-derived RPE [3,4] was maintained in RPE maintenance medium [DMEM:F12 (7:3) (Sigma-Aldrich) supplemented with B-27 supplement (Invitrogen), 2 mM L-glutamine (Invitrogen), 0.5 mM SB431542 (Sigma-Aldrich) and 10 ng/ml bFGF (WAKO)] .
In an attempt to establish a robust differentiation protocol for pluripotent stem cells into Retinal Pigment Epithelium (RPE), the differentiation protocol . The detailed method for differentiation to RPE from iPSC was previously described [3,4]. Briefly, iPSC clone was seeded on gelatin-coated plate and cultured in human ES cell culture medium supplemented with 10 μM Y-27632 (TOCRIS Bioscience), 5 μM SB431542 (Sigma-Aldrich) and 3 μM CKI-7 (Sigma-Aldrich). After 24 hours incubation, cells were incubated in 20% KSR human differentiation medium [GMEM (GIBCO), 0.1 mM non-essential amino acids (GIBCO), 1 mM sodium pyruvate (Sigma-Aldrich), and 0.1 mM 2-mercaptoethanol (WAKO) containing of 20% KSR (Invitrogen)]. After 4 days incubation, cells were replaced into 15% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 10 days incubation, cells were cultured with 10% KSR human differentiation medium supplemented with Y-275632, SB431542 and CKI-7. After 18 days incubation, culture medium was replaced with 10% KSR human differentiation medium without supplementation. After 20 days incubation cells were dissociated with the CTK solution and incubated on low cell binding plate (Corning, Corning, NY) in RPE maintenance medium (DMEM:F12 [7:3] supplemented with B-27 supplement [Invitrogen] and 2 mM L-glutamine [Invitrogen]). After 10 days floating incubation, the resulting RPE cells were picked up and seeded on CELLstart (Invitorgen)-coated dishes in RPE growing medium [F-10 supplemented with 10% FBS]. When they reach confluence, medium was replaced to RPE maintenance medium supplemented with 0.5 uM SB431542 and 10 ng/ml bFGF. A cobblestone-like block monolayer cells with black color were RPE and harvested RPE with 0.25 % Trypsin-EDTA for further assessment

extract_protocol: Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.

treatment_protocol: Total RNA from primary RPE and 253G1iPS derived-RPE was isolated with RNAeasy Pus Mini Kit (Quiagen ) in accordance with manufacture’s instruction

value: retinal pigment epithelium (RPE)

value: RPE derived from 253G1 iPSC


title: DLBCL cell line OCI-Ly03 versus male control DNA

description: OCI-Ly03 vs maleControlDNA

source_name: DLBCL cell line OCI-Ly03

value: male

value: DLBCL cell line OCI-Ly03


title: WT-iPS-01

source_name: iPS cells father


title: pH1N1 infected A549 at 10H, biological rep1

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from pH1N1 infected A549 6 hpi rep 1

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.

source_name: pH1N1 infected A549 10 hpi rep 1

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with Influenza A virus (A/Singapore/478/2009 (pH1N1)) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

value: Human aveolar basal epithelial cells

tag: time

value: 10 hpi


title: DLBCL cell line OCI-Ly10 versus male control DNA

description: OCI-Ly10 vs maleControlDNA

source_name: DLBCL cell line OCI-Ly10

value: female

value: DLBCL cell line OCI-Ly10


title: DLBCL cell line U2932 versus male control DNA

description: U2932 vs maleControlDNA

source_name: DLBCL cell line U2932

value: DLBCL cell line U2932


title: High_sensitive_2

description: A RNA pool from the head kidney of 5 fishes belonging to Family 2 without challenge against P. Salmonis were used as control

value: head kidney


title: pombe_WT,biological rep1

source_name: S. pombe WT in log phase cultured in YEPD medium


title: pH1N1 infected A549 at 8H, biological rep2

description: Gene expression data from pH1N1 infected A549 6 hpi rep 2

source_name: pH1N1 infected A549 8 hpi rep 2

value: 8 hpi


title: Primary RPE

source_name: Primary RPE

value: Primary RPE


title: pH1N1 infected A549 at 8H, biological rep1

source_name: pH1N1 infected A549 8 hpi rep 1


title: pH1N1 infected A549 at 10H, biological rep2

source_name: pH1N1 infected A549 10 hpi rep 2


title: pH1N1 infected A549 at 8H, biological rep3

description: Gene expression data from pH1N1 infected A549 6 hpi rep 3

source_name: pH1N1 infected A549 8 hpi rep 3


title: pH1N1 infected A549 at 6H, biological rep1

source_name: pH1N1 infected A549 6 hpi rep 1

value: 6 hpi


title: pH1N1 infected A549 at 4H, biological rep2

description: Gene expression data from pH1N1 infected A549 4 hpi rep 2

source_name: pH1N1 infected A549 4 hpi rep 2

value: 4 hpi


title: pH1N1 infected A549 at 6H, biological rep2

source_name: pH1N1 infected A549 6 hpi rep 2


title: Low_sensitive_2

description: A RNA pool from the head kidney of 5 fishes belonging to Family 5 without challenge against P. Salmonis were used as control

value: intraperitoneal injection with 0.2 mL Piscirickettsia salmonis


title: pH1N1 infected A549 at 4H, biological rep3

description: Gene expression data from pH1N1 infected A549 4 hpi rep 3

source_name: pH1N1 infected A549 4 hpi rep 3


title: pH1N1 infected A549 at 2H, biological rep1

description: Gene expression data from pH1N1 infected A549 2 hpi rep 1

source_name: pH1N1 infected A549 2 hpi rep 1

value: 2 hpi


title: pH1N1 infected A549 at 6H, biological rep3

source_name: pH1N1 infected A549 6 hpi rep 3


title: High_sensitive_1

description: A RNA pool from the head kidney of 5 fishes belonging to Family 1 without challenge against P. Salmonis were used as control


title: pH1N1 infected A549 at 4H, biological rep1

description: Gene expression data from pH1N1 infected A549 4 hpi rep 1

source_name: pH1N1 infected A549 4 hpi rep 1


title: pH1N1 infected A549 at 2H, biological rep3

description: Gene expression data from pH1N1 infected A549 2 hpi rep 3

source_name: pH1N1 infected A549 2 hpi rep 3


title: pH1N1 infected A549 at 2H, biological rep2

description: Gene expression data from pH1N1 infected A549 2 hpi rep 2

source_name: pH1N1 infected A549 2 hpi rep 2


title: pH1N1 infected A549 at 0H, biological rep1

description: Gene expression data from mock infected A549 rep 1

source_name: Mock infected A549 rep 1

value: control


title: pH1N1 infected A549 at 0H, biological rep3

description: Gene expression data from mock infected A549 rep 3

source_name: Mock infected A549 rep 3


title: pH1N1 infected A549 at 0H, biological rep2

description: Gene expression data from mock infected A549 rep 2

source_name: Mock infected A549 rep 2


title: H5N3 infected A549 at 10H, biological rep3

description: Gene expression data from H5N3 infected A549 10h rep 3

source_name: H5N3 infected A549 10 hpi rep 3

treatment_protocol: The cells were infected with A/duck/Malaysia/F119/3/1997(H5N3) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2


title: H5N2-F189 infected A549 at 10H, biological rep2

description: Gene expression data from H5N2 (F189) infected A549 10 hpi rep 2

source_name: H5N2 (F189) infected A549 10 hpi rep 2

treatment_protocol: The cells were infected with A/duck/Malaysia/F189/07/2004(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2


title: H5N2-F189 infected A549 at 10H, biological rep1

description: Gene expression data from H5N2 (F189) infected A549 10 hpi rep 1

source_name: H5N2 (F189) infected A549 10 hpi rep 1


title: H5N3 infected A549 at 10H, biological rep2

description: Gene expression data from H5N3 infected A549 10h rep 2

source_name: H5N3 infected A549 10 hpi rep 2


title: H5N2-F118 infected A549 at 10H, biological rep3

description: Gene expression data from H5N2 (F118) infected A549 10 hpi rep 3

source_name: H5N2 (F118) infected A549 10 hpi rep 3

treatment_protocol: The cells were infected with A/duck/Malaysia/F118/08/2004(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2


title: pombe_WT,biological rep2

description: Gene expression data from S. pombe WT in log phase cultured in YEPD medium


title: H5N2-F118 infected A549 at 10H, biological rep2

description: Gene expression data from H5N2 (F118) infected A549 10 hpi rep 2

source_name: H5N2 (F118) infected A549 10 hpi rep 2


title: H5N2-F189 infected A549 at 10H, biological rep3

description: Gene expression data from H5N2 (F189) infected A549 10 hpi rep 3

source_name: H5N2 (F189) infected A549 10 hpi rep 3


title: H5N2-F118 infected A549 at 10H, biological rep1

description: Gene expression data from H5N2 (F118) infected A549 10 hpi rep 1

source_name: H5N2 (F118) infected A549 10 hpi rep 1


title: H5N3 infected A549 at 10H, biological rep1

description: Gene expression data from H5N3 infected A549 10h rep 1

source_name: H5N3 infected A549 10 hpi rep 1


title: H5N2-F118 infected A549 at 8H, biological rep2

description: Gene expression data from H5N2 (F118) infected A549 8 hpi rep 2

source_name: H5N2 (F118) infected A549 8 hpi rep 2


title: H5N2-F118 infected A549 at 4H, biological rep3

description: Gene expression data from H5N2 (F118) infected A549 4 hpi rep 3

source_name: H5N2 (F118) infected A549 4 hpi rep 3


title: H5N2-F118 infected A549 at 6H, biological rep1

description: Gene expression data from H5N2 (F118) infected A549 6 hpi rep 1

source_name: H5N2 (F118) infected A549 6 hpi rep 1


title: H5N2-F118 infected A549 at 6H, biological rep3

description: Gene expression data from H5N2 (F118) infected A549 6 hpi rep 3

source_name: H5N2 (F118) infected A549 6 hpi rep 3


title: H5N2-F118 infected A549 at 2H, biological rep2

description: Gene expression data from H5N2 (F118) infected A549 2 hpi rep 2

source_name: H5N2 (F118) infected A549 2 hpi rep 2


title: H5N2-F118 infected A549 at 4H, biological rep1

description: Gene expression data from H5N2 (F118) infected A549 4 hpi rep 1

source_name: H5N2 (F118) infected A549 4 hpi rep 1


title: iPS-19.9-01

source_name: iPS cells-CTR

value: induced pluripotent stem cells (iPS cells)


title: H9N2 infected A549 cells at 8H, biological rep1

description: Gene expression data from H9N2 infected A549 8 hpi rep 1

source_name: H9N2 infected A549 8 hpi rep 1

treatment_protocol: The cells were infected with A/Duck/Malaysia/01 (H9N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2


title: H5N2-F118 infected A549 at 6H, biological rep2

description: Gene expression data from H5N2 (F118) infected A549 6 hpi rep 2

source_name: H5N2 (F118) infected A549 6 hpi rep 2


title: H9N2 infected A549 cells at 10H, biological rep1

description: Gene expression data from H9N2 infected A549 10 hpi rep 1

source_name: H9N2 infected A549 10 hpi rep 1


title: H5N2-F118 infected A549 at 0H, biological rep2

description: Gene expression data from mock infected A549 rep 2

source_name: Mock infected A549 rep 2

value: mock


title: H5N2-F118 infected A549 at 2H, biological rep1

description: Gene expression data from H5N2 (F118) infected A549 2 hpi rep 1

source_name: H5N2 (F118) infected A549 2 hpi rep 1


title: H5N2-F118 infected A549 at 8H, biological rep1

description: Gene expression data from H5N2 (F118) infected A549 8 hpi rep 1

source_name: H5N2 (F118) infected A549 8 hpi rep 1


title: H9N2 infected A549 cells at 8H, biological rep3

description: Gene expression data from H9N2 infected A549 8 hpi rep 3

source_name: H9N2 infected A549 8 hpi rep 3


title: H5N2-F118 infected A549 at 0H, biological rep1

description: Gene expression data from mock infected A549 rep 1

source_name: Mock infected A549 rep 1


title: H5N2-F118 infected A549 at 0H, biological rep3

description: Gene expression data from mock infected A549 rep 3

source_name: Mock infected A549 rep 3


title: H9N2 infected A549 cells at 6H, biological rep1

description: Gene expression data from H9N2 infected A549 6 hpi rep 1

source_name: H9N2 infected A549 6 hpi rep 1


title: H9N2 infected A549 cells at 6H, biological rep3

description: Gene expression data from H9N2 infected A549 6 hpi rep 3

source_name: H9N2 infected A549 6 hpi rep 3


title: H5N2-F118 infected A549 at 2H, biological rep3

description: Gene expression data from H5N2 (F118) infected A549 2 hpi rep 3

source_name: H5N2 (F118) infected A549 2 hpi rep 3


title: H5N2-F118 infected A549 at 4H, biological rep2

description: Gene expression data from H5N2 (F118) infected A549 4 hpi rep 2

source_name: H5N2 (F118) infected A549 4 hpi rep 2


title: H9N2 infected A549 cells at 4H, biological rep2

description: Gene expression data from H9N2 infected A549 4 hpi rep 2

source_name: H9N2 infected A549 4 hpi rep 2


title: H9N2 infected A549 cells at 10H, biological rep3

description: Gene expression data from H9N2 infected A549 10 hpi rep 3

source_name: H9N2 infected A549 10 hpi rep 3


title: H9N2 infected A549 cells at 4H, biological rep3

description: Gene expression data from H9N2 infected A549 4 hpi rep 3

source_name: H9N2 infected A549 4 hpi rep 3


title: H5N2-F118 infected A549 at 8H, biological rep3

description: Gene expression data from H5N2 (F118) infected A549 8 hpi rep 3

source_name: H5N2 (F118) infected A549 8 hpi rep 3


title: H9N2 infected A549 cells at 8H, biological rep2

description: Gene expression data from H9N2 infected A549 8 hpi rep 2

source_name: H9N2 infected A549 8 hpi rep 2


title: H9N2 infected A549 cells at 6H, biological rep2

description: Gene expression data from H9N2 infected A549 6 hpi rep 2

source_name: H9N2 infected A549 6 hpi rep 2


title: H9N2 infected A549 cells at 4H, biological rep1

description: Gene expression data from H9N2 infected A549 4 hpi rep 1

source_name: H9N2 infected A549 4 hpi rep 1


title: pH1N1 infected A549 at 10H, biological rep3

description: Gene expression data from pH1N1 infected A549 6 hpi rep 3

source_name: pH1N1 infected A549 10 hpi rep 3


title: H9N2 infected A549 cells at 0H, biological rep2

description: Gene expression data from mock infected A549 rep 2

source_name: Mock infected A549 rep 2


title: H9N2 infected A549 cells at 2H, biological rep1

description: Gene expression data from H9N2 infected A549 2 hpi rep 1

source_name: H9N2 infected A549 2 hpi rep 1


title: H1N1 infected A549 cells at 2H, biological rep1

description: Gene expression data from H1N1 infected A549 2 hpi rep 1

source_name: H1N1 infected A549 2 hpi rep 1

treatment_protocol: The cells were infected with A/WSN/33 (H1N1) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2


title: H9N2 infected A549 cells at 2H, biological rep3

description: Gene expression data from H9N2 infected A549 2 hpi rep 3

source_name: H9N2 infected A549 2 hpi rep 3


title: H1N1 infected A549 cells at 4H, biological rep2

description: Gene expression data from H1N1 infected A549 4 hpi rep 2

source_name: H1N1 infected A549 4 hpi rep 2


title: H1N1 infected A549 cells at 2H, biological rep3

description: Gene expression data from H1N1 infected A549 2 hpi rep 3

source_name: H1N1 infected A549 2 hpi rep 3


title: H9N2 infected A549 cells at 10H, biological rep2

description: Gene expression data from H9N2 infected A549 10 hpi rep 2

source_name: H9N2 infected A549 10 hpi rep 2


title: H9N2 infected A549 cells at 2H, biological rep2

description: Gene expression data from H9N2 infected A549 2 hpi rep 2

source_name: H9N2 infected A549 2 hpi rep 2


title: H1N1 infected A549 cells at 10H, biological rep2

description: Gene expression data from H1N1 infected A549 10 hpi rep 2

source_name: H1N1 infected A549 10 hpi rep 2


title: H1N1 infected A549 cells at 0H, biological rep2


title: H1N1 infected A549 cells at 10H, biological rep1

description: Gene expression data from H1N1 infected A549 10 hpi rep 1

source_name: H1N1 infected A549 10 hpi rep 1


title: H1N1 infected A549 cells at 0H, biological rep1

description: Gene expression data from mock infected A549 rep 1

source_name: Mock infected A549 rep 1


title: H1N1 infected A549 cells at 10H, biological rep3

description: Gene expression data from H1N1 infected A549 10 hpi rep 3

source_name: H1N1 infected A549 10 hpi rep 3


title: H1N1 infected A549 cells at 6H, biological rep2

description: Gene expression data from H1N1 infected A549 6 hpi rep 2

source_name: H1N1 infected A549 6 hpi rep 2


title: H9N2 infected A549 cells at 0H, biological rep1


title: H1N1 infected A549 cells at 0H (10 H), biological rep2


title: H1N1 infected A549 cells at 6H, biological rep1

description: Gene expression data from H1N1 infected A549 6 hpi rep 1

source_name: H1N1 infected A549 6 hpi rep 1


title: H1N1 infected A549 cells at 2H, biological rep2

description: Gene expression data from H1N1 infected A549 2 hpi rep 2

source_name: H1N1 infected A549 2 hpi rep 2


title: H1N1 infected A549 cells at 4H, biological rep1

description: Gene expression data from H1N1 infected A549 4 hpi rep 1

source_name: H1N1 infected A549 4 hpi rep 1


title: H1N1 infected A549 cells at 0H (10 H), biological rep1


title: H1N1 infected A549 cells at 0H, biological rep3

description: Gene expression data from mock infected A549 rep 3

source_name: Mock infected A549 rep 3


title: H1N1 infected A549 cells at 0H (10 H), biological rep3


title: H1N1 infected A549 cells at 6H, biological rep3

description: Gene expression data from H1N1 infected A549 6 hpi rep 3

source_name: H1N1 infected A549 6 hpi rep 3


title: H1N1 infected A549 cells at 4H, biological rep3

description: Gene expression data from H1N1 infected A549 4 hpi rep 3

source_name: H1N1 infected A549 4 hpi rep 3


title: Expression data of CC_BV_14

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0, PerChip/PerGene normalization

source_name: Colorecal Cancer, BV_P_14

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

value: Colorecal Cancer

tag: treatment response


title: pombe_YSM,biological rep3

description: Gene expression data from S. pombe YHL6381 and SPQ-01 mixtures cultured for 90min in YEPME medium

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

growth_protocol: The h+ YHL6381 and h- SPQ-01 yeast strains were cultured in YEPD medium at 30C, until the OD600 was  5.0. The cells was collected and mixture at a 1:1 ratio and resuspended in YEPD or YEPME medium for another 90min.

value: Diploid strain YHL6381/SPQ-01

tag: growth protocol

value: 90min in YEPME medium


title: Expression data of CC_BV_15

source_name: Colorecal Cancer, BV_P_15


title: Expression data of CC_BV_16

source_name: Colorecal Cancer, BV_P_16


title: pombe_YSM,biological rep2

source_name: S. pombe YHL6381 and SPQ-01 mixtures cultured for 90min in YEPME medium


title: Expression data of CC_BV_21

source_name: Colorecal Cancer, BV_P_21


title: pombe_YSD,biological rep2

description: Gene expression data from S. pombe YHL6381 and SPQ-01 mixtures cultured for 90min in YEPD medium

value: Haploid YHL6381 and SPQ-01 mixtures

value: 90min in YEPD medium


title: Expression data of CC_BV_13

source_name: Colorecal Cancer, BV_P_13


title: Expression data of CC_BV_09

source_name: Colorecal Cancer, BV_P_09


title: Expression data of CC_BV_17

source_name: Colorecal Cancer, BV_P_17


title: Expression data of CC_BV_06

source_name: Colorecal Cancer, BV_P_06


title: Expression data of CC_FL_9

description: BV_Responder, FL_Non_Responder

source_name: Colorecal Cancer, FL_P_9

value: BV_Responder, FL_Non_Responder


title: Expression data of CC_BV_04

source_name: Colorecal Cancer, BV_P_04


title: Expression data of CC_BV_12

source_name: Colorecal Cancer, BV_P_12


title: pombe_YSD,biological rep1

source_name: S. pombe YHL6381 and SPQ-01 mixtures cultured for 90min in YEPD medium


title: Expression data of CC_BV_05

source_name: Colorecal Cancer, BV_P_05


title: Expression data of CC_FL_38

description: FL_Non_responder BV_Responder

source_name: Colorecal Cancer, FL_P_38

value: FL_Non_responder, BV_Responder


title: pombe_YSD,biological rep3


title: Expression data of CC_BV_02

source_name: Colorecal Cancer, BV_P_02


title: pombe_YSM,biological rep1


title: Expression data of CC_FL_40

description: FL_Responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_40

value: FL_Responder, BV_Non_reponder


title: Expression data of CC_FL_37

description: FL_Responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_37


title: Expression data of CC_FL_31

source_name: Colorecal Cancer, FL_P_31


title: Expression data of CC_FL_36

description: FL_Responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_36


title: Expression data of CC_FL_35

source_name: Colorecal Cancer, FL_P_35


title: Expression data of CC_BV_11

source_name: Colorecal Cancer, BV_P_11


title: Expression data of CC_FL_28

description: FL_Responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_28


title: H9N2 infected A549 cells at 0H, biological rep3

source_name: Mock infected A549 rep 3

value: Human aveolar basal epithelial cells


title: Expression data of CC_FL_30

description: FL_Non_responder BV_Responder

source_name: Colorecal Cancer, FL_P_30


title: Expression data of CC_FL_24

source_name: Colorecal Cancer, FL_P_24


title: Expression data of CC_FL_20

source_name: Colorecal Cancer, FL_P_20


title: Expression data of CC_FL_27

source_name: Colorecal Cancer, FL_P_27


title: Expression data of CC_FL_16

source_name: Colorecal Cancer, FL_P_16


title: Expression data of CC_FL_25

source_name: Colorecal Cancer, FL_P_25


title: Expression data of CC_FL_22

source_name: Colorecal Cancer, FL_P_22


title: Expression data of CC_FL_23

description: FL_Non_responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_23

value: FL_Non_responder, BV_Non_reponder


title: Expression data of CC_FL_19

source_name: Colorecal Cancer, FL_P_19


title: Expression data of CC_FL_15

source_name: Colorecal Cancer, FL_P_15


title: H5N2-F189 infected CEF at 10H, biological rep1

description: Gene expression data from H5N2 (F189) infected CEF 10 hpi rep 1

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

organism: Gallus gallus

source_name: H5N2 (F189) infected CEF 10 hpi rep 1

growth_protocol: The cells were harvested from 9 day-old embryonated eggs, grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

value: Chicken embryo fibroblast cells

value: CEF

value: 10 hpi


title: Expression data of CC_FL_14

source_name: Colorecal Cancer, FL_P_14


title: H5N2-F189 infected CEF at 10H, biological rep3

description: Gene expression data from H5N2 (F189) infected CEF 10 hpi rep 3

source_name: H5N2 (F189) infected CEF 10 hpi rep 3


title: H5N2-F118 infected CEF at 10H, biological rep2

description: Gene expression data from H5N2 (F118) infected CEF 10 hpi rep 2

source_name: H5N2 (F118) infected CEF 10 hpi rep 2


title: H5N2-F189 infected CEF at 10H, biological rep2

description: Gene expression data from H5N2 (F189) infected CEF 10 hpi rep 2

source_name: H5N2 (F189) infected CEF 10 hpi rep 2


title: H5N2-F118 infected CEF at 10H, biological rep3

description: Gene expression data from H5N2 (F118) infected CEF 10 hpi rep 3

source_name: H5N2 (F118) infected CEF 10 hpi rep 3


title: Expression data of CC_FL_11

source_name: Colorecal Cancer, FL_P_11


title: H5N2-F118 infected CEF at 10H, biological rep1

description: Gene expression data from H5N2 (F118) infected CEF 10 hpi rep 1

source_name: H5N2 (F118) infected CEF 10 hpi rep 1


title: Expression data of CC_FL_09

description: FL_Non_responder, BV_Responder

source_name: Colorecal Cancer, FL_P_09


title: Expression data of CC_FL_08

source_name: Colorecal Cancer, FL_P_08


title: Expression data of CC_FL_10

source_name: Colorecal Cancer, FL_P_10


title: Expression data of CC_FL_07

description: FL_Responder BV_Responder

source_name: Colorecal Cancer, FL_P_07

value: FL_Responder, BV_Responder


title: H5N2-F118 infected CEF at 6H, biological rep3

description: Gene expression data from H5N2 (F118) infected CEF 6 hpi rep 3

source_name: H5N2 (F118) infected CEF 6 hpi rep 3

value: 6 hpi


title: H5N2-F118 infected CEF at 8H, biological rep2

description: Gene expression data from H5N2 (F118) infected CEF 8 hpi rep 2

source_name: H5N2 (F118) infected CEF 8 hpi rep 2

value: 8 hpi


title: Expression data of CC_FL_04

source_name: Colorecal Cancer, FL_P_04


title: Expression data of CC_FL_06

description: FL_Responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_06


title: Expression data of CC_FL_05

description: FL_Non_responder BV_Non_reponder

source_name: Colorecal Cancer, FL_P_05


title: pCAGGS-BLV low transactivation activity Tax(S240P) mutant-IRES-CFP transfected HeLa cells

city: Wako

first: Yoko

last: Aida

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

institute: RIKEN

description:
Btax-S
HeLa cells were transiently transfected with the pCAGGS-BLV Tax (S240P) gene.

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols.

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

data_processing: Affymetrix GeneChip Operating Software (GCOS) were used for processing scanning data. Normalization was performed using the MAS5.0 (Algorithm: ExpressionStat 5.0) method.

source_name: HeLa cells transiently transfected with pCAGGS-BLV Tax (S240P) gene

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols.

extract_protocol: RNA from total cell extracts was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: HeLa cells were transiently transfected for 30 hours.

value: HeLa

tag: transfection

value: pCAGGS-BLV Tax (S240P)


title: H5N2-F118 infected CEF at 6H, biological rep2

description: Gene expression data from H5N2 (F118) infected CEF 6 hpi rep 2

source_name: H5N2 (F118) infected CEF 6 hpi rep 2


title: pCAGGS-wild type BLV Tax-IRES-CFP transfected HeLa cells

description:
Btax-wt
HeLa cells were transiently transfected with the pCAGGS-BLV Tax gene amplified from the BLV infectious molecular clone pBLV-IF vector.

source_name: HeLa cells transiently transfected with pCAGGS-wild type BLV Tax gene

value: pCAGGS-wild type BLV Tax


title: pCAGGS-BLV high transactivation activity Tax(D247G) mutant-IRES-CFP transfected HeLa cells

description:
Btax-D
HeLa cells were transiently transfected with the pCAGGS-BLV Tax (D247G) gene.

source_name: HeLa cells transiently transfected with pCAGGS-BLV Tax (D247G) gene

value: pCAGGS-BLV Tax (D247G)


title: H5N2-F118 infected CEF at 4H, biological rep3

description: Gene expression data from H5N2 (F118) infected CEF 4 hpi rep 3

source_name: H5N2 (F118) infected CEF 4 hpi rep 3

value: 4 hpi


title: H5N3 infected MDCK at 10H, biological rep1

description: Gene expression data from H5N3 infected MDCK 10 hpi rep 1

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Canine Genome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

organism: Canis lupus familiaris

source_name: H5N3 infected MDCK rep 1 10 hpi

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: Mardin-Darby Canine Kidney cells

value: MDCK


title: H5N2-F118 infected CEF at 8H, biological rep1

description: Gene expression data from H5N2 (F118) infected CEF 8 hpi rep 1

source_name: H5N2 (F118) infected CEF 8 hpi rep 1


title: H5N3 infected MDCK at 10H, biological rep3

description: Gene expression data from H5N3 infected MDCK 10 hpi rep 3

source_name: H5N3 infected MDCK rep 3 10 hpi


title: H5N2-F118 infected CEF at 8H, biological rep3

description: Gene expression data from H5N2 (F118) infected CEF 8 hpi rep 3

source_name: H5N2 (F118) infected CEF 8 hpi rep 3


title: pCAGGS-IRES-CFP transfected HeLa cells

description:
Control
HeLa cells were transiently transfected with the pCAGGS vector.

source_name: HeLa cells transiently transfected with pCAGGS vector

value: pCAGGS vector


title: H5N3 infected MDCK at 10H, biological rep2

description: Gene expression data from H5N3 infected MDCK 10 hpi rep 2

source_name: H5N3 infected MDCK rep 2 10 hpi


title: H5N2-F189 infected MDCK at 10H, biological rep3

description: Gene expression data from H5N2 (F59) infected MDCK 10 hpi rep 3

source_name: H5N2 (F189) infected MDCK 10 hpi rep 3


title: Expression data of CC_FL_02

description: FL_Non_responder BV_Responder

source_name: Colorecal Cancer, FL_P_02

value: Colorecal Cancer

value: FL_Non_responder, BV_Responder


title: Expression data of CC_FL_03

source_name: Colorecal Cancer, FL_P_03


title: H5N2-F118 infected CEF at 4H, biological rep1

description: Gene expression data from H5N2 (F118) infected CEF 4 hpi rep 1

source_name: H5N2 (F118) infected CEF 4 hpi rep 1


title: Expression data of CC_FL_01

source_name: Colorecal Cancer, FL_P_01


title: H5N2-F118 infected CEF at 4H, biological rep2

description: Gene expression data from H5N2 (F118) infected CEF 4 hpi rep 2

source_name: H5N2 (F118) infected CEF 4 hpi rep 2


title: H5N2-F118 infected CEF at 2H, biological rep3

description: Gene expression data from H5N2 (F118) infected CEF 2 hpi rep 3

source_name: H5N2 (F118) infected CEF 2 hpi rep 3

value: 2 hpi


title: H5N2-F189 infected MDCK at 10H, biological rep2

description: Gene expression data from H5N2 (F59) infected MDCK 10 hpi rep 2

source_name: H5N2 (F189) infected MDCK 10 hpi rep 2


title: GF120 RA/siRNF20

city: Rehovot

first: Gilad

last: Fuchs

address: Rehovot

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Plier + lowess

source_name: GF120 RA/siRNF20

label_protocol: standard Affymetrix protocol

growth_protocol: Biological duplicates of NTera2/D1 cells were grown as described (Gutekunst et al., 2011) with 1mM Sodium Pyruvate and 0.1mM nonessential amino acid.

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen)

treatment_protocol: RA 10 µM

value: 10 uM RA

tag: knockdown


title: H5N2-F189 infected MDCK at 10H, biological rep1

description: Gene expression data from H5N2 (F59) infected MDCK 10 hpi rep 1

source_name: H5N2 (F189) infected MDCK 10 hpi rep 1

tag: cell type


title: H5N2-F118 infected MDCK at 10H, biological rep1

description: Gene expression data from H5N2 (F118) infected MDCK 10 hpi rep 1

source_name: H5N2 (F118) infected MDCK 10 hpi rep 1

tag: infection


title: H5N2-F118 infected MDCK at 10H, biological rep2

description: Gene expression data from H5N2 (F118) infected MDCK 10 hpi rep 2

source_name: H5N2 (F118) infected MDCK 10 hpi rep 2


title: H5N2-F118 infected MDCK at 8H, biological rep2

description: Gene expression data from H5N2 (F118) infected MDCK 8 hpi rep 2

source_name: H5N2 (F118) infected MDCK 8 hpi rep 2


title: H5N2-F118 infected MDCK at 8H, biological rep3

description: Gene expression data from H5N2 (F118) infected MDCK 8 hpi rep 3

source_name: H5N2 (F118) infected MDCK 8 hpi rep 3


title: H5N2-F118 infected MDCK at 10H, biological rep3

description: Gene expression data from H5N2 (F118) infected MDCK 10 hpi rep 3

source_name: H5N2 (F118) infected MDCK 10 hpi rep 3


title: H5N2-F118 infected CEF at 2H, biological rep1

description: Gene expression data from H5N2 (F118) infected CEF 2 hpi rep 1

source_name: H5N2 (F118) infected CEF 2 hpi rep 1

value: Chicken embryo fibroblast cells

value: CEF


title: GF120 DMSO/siRNF20

source_name: GF120 DMSO/siRNF20

value: DMSO


title: H5N2-F118 infected CEF at 2H, biological rep2

description: Gene expression data from H5N2 (F118) infected CEF 2 hpi rep 2

source_name: H5N2 (F118) infected CEF 2 hpi rep 2


title: GF117  DMSO/siRNF20

source_name: GF117  DMSO/siRNF20


title: GF120  RA/siLacZ

source_name: GF120  RA/siLacZ

value: siLacZ


title: GF117  RA/siRNF20

source_name: GF117  RA/siRNF20


title: GF117  DMSO/siLacZ

source_name: GF117  DMSO/siLacZ


title: H5N2-F118 infected CEF at 0H, biological rep3

description: Gene expression data from mock infected CEF rep 3

source_name: Mock infected CEF rep 3

value: mock

value: control


title: H5N2-F118 infected MDCK at 6H, biological rep1

description: Gene expression data from H5N2 (F118) infected MDCK 6 hpi rep 1

source_name: H5N2 (F118) infected MDCK 6 hpi rep 1

value: 6 hpi


title: H5N2-F118 infected CEF at 0H, biological rep2

description: Gene expression data from mock infected CEF rep 2

source_name: Mock infected CEF rep 2


title: H5N2-F118 infected MDCK at 8H, biological rep1

description: Gene expression data from H5N2 (F118) infected MDCK 8 hpi rep 1

source_name: H5N2 (F118) infected MDCK 8 hpi rep 1

value: 8 hpi


title: GF120  DMSO/siLacZ

source_name: GF120  DMSO/siLacZ


title: H5N2-F118 infected MDCK at 6H, biological rep2

description: Gene expression data from H5N2 (F118) infected MDCK 6 hpi rep 2

source_name: H5N2 (F118) infected MDCK 6 hpi rep 2


title: H5N2-F118 infected MDCK at 6H, biological rep3

description: Gene expression data from H5N2 (F118) infected MDCK 6 hpi rep 3

source_name: H5N2 (F118) infected MDCK 6 hpi rep 3


title: H5N2-F118 infected MDCK at 4H, biological rep3

description: Gene expression data from H5N2 (F118) infected MDCK 4 hpi rep 3

source_name: H5N2 (F118) infected MDCK 4 hpi rep 3


title: H5N2-F118 infected CEF at 6H, biological rep1

description: Gene expression data from H5N2 (F118) infected CEF 6 hpi rep 1

source_name: H5N2 (F118) infected CEF 6 hpi rep 1


title: H5N2-F118 infected MDCK at 2H, biological rep1

description: Gene expression data from H5N2 (F118) infected MDCK 2 hpi rep 1

source_name: H5N2 (F118) infected MDCK 2 hpi rep 1


title: H5N2-F118 infected MDCK at 4H, biological rep2

description: Gene expression data from H5N2 (F118) infected MDCK 4 hpi rep 2

source_name: H5N2 (F118) infected MDCK 4 hpi rep 2


title: H5N2-F118 infected CEF at 0H, biological rep1

description: Gene expression data from mock infected CEF rep 1

source_name: Mock infected CEF rep 1


title: H9N2 infected CEF at 10H, biological rep3

description: Gene expression data from H9N2 infected CEF 10 hpi rep 3

source_name: H9N2 infected CEF 10 hpi rep 3

treatment_protocol: The cells were infected with A//Duck/Malaysia/01 (H9N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

value: 10 hpi


title: H5N2-F118 infected MDCK at 2H, biological rep2

description: Gene expression data from H5N2 (F118) infected MDCK 2 hpi rep 2

source_name: H5N2 (F118) infected MDCK 2 hpi rep 2


title: GF117  RA/siLacZ

source_name: GF117  RA/siLacZ


title: H9N2 infected CEF at 10H, biological rep2

description: Gene expression data from H9N2 infected CEF 10 hpi rep 2

source_name: H9N2 infected CEF 10 hpi rep 2


title: H5N2-F118 infected MDCK at 0H, biological rep2

description: Gene expression data from mock infected MDCK rep 2

source_name: Mock infected MDCK rep 2


title: H5N2-F118 infected MDCK at 0H, biological rep1

description: Gene expression data from mock infected MDCK rep 1

source_name: Mock infected MDCK rep 1


title: H9N2 infected CEF at 8H, biological rep3

description: Gene expression data from H9N2 infected CEF 8 hpi rep 3

source_name: H9N2 infected CEF 8 hpi rep 3


title: H5N2-F118 infected MDCK at 2H, biological rep3

description: Gene expression data from H5N2 (F118) infected MDCK 2 hpi rep 3

source_name: H5N2 (F118) infected MDCK 2 hpi rep 3


title: H9N2 infected MDCK at 10H, biological rep3

description: Gene expression data from H9N2 infected MDCK 10 hpi rep 3

source_name: H9N2 infected MDCK 10 hpi rep 3


title: H5N2-F118 infected MDCK at 0H, biological rep3

description: Gene expression data from mock infected MDCK rep 3

source_name: Mock infected MDCK rep 3


title: H9N2 infected CEF at 8H, biological rep1

description: Gene expression data from H9N2 infected CEF 8 hpi rep 1

source_name: H9N2 infected CEF 8 hpi rep 1


title: H9N2 infected MDCK at 10H, biological rep1

description: Gene expression data from H9N2 infected MDCK 10 hpi rep 1

source_name: H9N2 infected MDCK 10 hpi rep 1


title: H9N2 infected MDCK at 8H, biological rep3

description: Gene expression data from H9N2 infected MDCK 8 hpi rep 3

source_name: H9N2 infected MDCK 8 hpi rep 3


title: H9N2 infected CEF at 10H, biological rep1

description: Gene expression data from H9N2 infected CEF 10 hpi rep 1

source_name: H9N2 infected CEF 10 hpi rep 1


title: H9N2 infected CEF at 8H, biological rep2

description: Gene expression data from H9N2 infected CEF 8 hpi rep 2

source_name: H9N2 infected CEF 8 hpi rep 2


title: H9N2 infected MDCK at 8H, biological rep1

description: Gene expression data from H9N2 infected MDCK 8 hpi rep 1

source_name: H9N2 infected MDCK 8 hpi rep 1


title: H9N2 infected MDCK at 10H, biological rep2

description: Gene expression data from H9N2 infected MDCK 10 hpi rep 2

source_name: H9N2 infected MDCK 10 hpi rep 2


title: H9N2 infected CEF at 6H, biological rep3

description: Gene expression data from H9N2 infected CEF 6 hpi rep 3

source_name: H9N2 infected CEF 6 hpi rep 3


title: H9N2 infected CEF at 6H, biological rep1

description: Gene expression data from H9N2 infected CEF 6 hpi rep 1

source_name: H9N2 infected CEF 6 hpi rep 1


title: H9N2 infected MDCK at 6H, biological rep3

description: Gene expression data from H9N2 infected MDCK 6 hpi rep 3

source_name: H9N2 infected MDCK 6 hpi rep 3


title: H9N2 infected CEF at 6H, biological rep2

description: Gene expression data from H9N2 infected CEF 6 hpi rep 2

source_name: H9N2 infected CEF 6 hpi rep 2


title: H9N2 infected MDCK at 8H, biological rep2

description: Gene expression data from H9N2 infected MDCK 8 hpi rep 2

source_name: H9N2 infected MDCK 8 hpi rep 2


title: H9N2 infected CEF at 4H, biological rep3

description: Gene expression data from H9N2 infected CEF 4 hpi rep 3

source_name: H9N2 infected CEF 4 hpi rep 3

value: 4 hpi


title: H9N2 infected MDCK at 6H, biological rep1

description: Gene expression data from H9N2 infected MDCK 6 hpi rep 1

source_name: H9N2 infected MDCK 6 hpi rep 1

value: Mardin-Darby Canine Kidney cells


title: H5N2-F118 infected MDCK at 4H, biological rep1

description: Gene expression data from H5N2 (F118) infected MDCK 4 hpi rep 1

source_name: H5N2 (F118) infected MDCK 4 hpi rep 1

value: MDCK


title: H9N2 infected MDCK at 6H, biological rep2

description: Gene expression data from H9N2 infected MDCK 6 hpi rep 2

source_name: H9N2 infected MDCK 6 hpi rep 2


title: H9N2 infected MDCK at 4H, biological rep3

description: Gene expression data from H9N2 infected MDCK 4 hpi rep 3

source_name: H9N2 infected MDCK 4 hpi rep 3


title: H9N2 infected CEF at 4H, biological rep1

description: Gene expression data from H9N2 infected CEF 4 hpi rep 1

source_name: H9N2 infected CEF 4 hpi rep 1


title: H9N2 infected CEF at 2H, biological rep3

description: Gene expression data from H9N2 infected CEF 2 hpi rep 3

source_name: H9N2 infected CEF 2 hpi rep 3


title: H9N2 infected CEF at 2H, biological rep2

description: Gene expression data from H9N2 infected CEF 2 hpi rep 2

source_name: H9N2 infected CEF 2 hpi rep 2


title: H9N2 infected MDCK at 4H, biological rep2

description: Gene expression data from H9N2 infected MDCK 4 hpi rep 2

source_name: H9N2 infected MDCK 4 hpi rep 2


title: H9N2 infected CEF at 4H, biological rep2

description: Gene expression data from H9N2 infected CEF 4 hpi rep 2

source_name: H9N2 infected CEF 4 hpi rep 2


title: H9N2 infected MDCK at 4H, biological rep1

description: Gene expression data from H9N2 infected MDCK 4 hpi rep 1

source_name: H9N2 infected MDCK 4 hpi rep 1


title: T256

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: DNAs were extracted using the QIAamp DNA mini kit (Qiagen, Courtaboeuf, France) from frozen tissue samples.

tag: sample id

tag: tissue type

value: Adenocarcinoma


title: T141

value: Bronchiolo-alveolar adenocarcinoma


title: H9N2 infected MDCK at 2H, biological rep3

description: Gene expression data from H9N2 infected MDCK 2 hpi rep 3

source_name: H9N2 infected MDCK 2 hpi rep 3


title: H9N2 infected CEF at 0H, biological rep3

description: Gene expression data from mock infected CEF rep 3

source_name: Mock infected CEF rep 3

value: Mock


title: H9N2 infected MDCK at 2H, biological rep1

description: Gene expression data from H9N2 infected MDCK 2 hpi rep 1

source_name: H9N2 infected MDCK 2 hpi rep 1

value: 2 hpi


title: T132

value: Large cell carcinoma


title: H9N2 infected CEF at 2H, biological rep1

description: Gene expression data from H9N2 infected CEF 2 hpi rep 1

source_name: H9N2 infected CEF 2 hpi rep 1

value: Chicken embryo fibroblast cells


title: H9N2 infected MDCK at 2H, biological rep2

description: Gene expression data from H9N2 infected MDCK 2 hpi rep 2

source_name: H9N2 infected MDCK 2 hpi rep 2


title: H9N2 infected MDCK at 0H, biological rep3

description: Gene expression data from mock infected MDCK rep 3

source_name: Mock infected MDCK rep 3


title: H1975

value: cell line


title: H9N2 infected MDCK at 0H, biological rep2

description: Gene expression data from mock infected MDCK rep 2

source_name: Mock infected MDCK rep 2


title: H9N2 infected CEF at 0H, biological rep2

description: Gene expression data from mock infected CEF rep 2

source_name: Mock infected CEF rep 2

value: CEF


title: T115


title: H9N2 infected MDCK at 0H, biological rep1

description: Gene expression data from mock infected MDCK rep 1

source_name: Mock infected MDCK rep 1


title: H1N1 infected MDCK at 10H, biological rep3

description: Gene expression data from H1N1 infected MDCK 10 hpi rep 3

source_name: H1N1 infected MDCK 10 hpi rep 3


title: H9N2 infected CEF at 0H, biological rep1

description: Gene expression data from mock infected CEF rep 1

source_name: Mock infected CEF rep 1


title: T355

value: Mucinous BAC


title: T143


title: T287


title: T251


title: H1650


title: T341


title: H1N1 infected MDCK at 10H, biological rep1

description: Gene expression data from H1N1 infected MDCK 10 hpi rep 1

source_name: H1N1 infected MDCK 10 hpi rep 1


title: H1N1 at 10H, biological rep3

description: Gene expression data from H1N1 infected CEF 10 hpi rep 3

source_name: H1N1 infected CEF 10 hpi rep 3

growth_protocol: The cells were harvested from 9 day-old embryonated eggs, grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at37˚C, 5% CO2


title: T252


title: H1N1 at 10H, biological rep2

description: Gene expression data from H1N1 infected CEF 10 hpi rep 2

source_name: H1N1 infected CEF 10 hpi rep 2


title: T340


title: H5N3 infected CEF at 10H, biological rep1

description: Gene expression data from H5N3 infected CEF 10h rep 1

source_name: H5N3 infected CEF 10 hpi rep 1


title: H1N1 infected MDCK at 10H, biological rep2

description: Gene expression data from H1N1 infected MDCK 10 hpi rep 2

source_name: H1N1 infected MDCK 10 hpi rep 2


title: H5N3 infected CEF at 10H, biological rep3

description: Gene expression data from H5N3 infected CEF 10h rep 3

source_name: H5N3 infected CEF 10 hpi rep 3


title: H1N1 at 10H, biological rep1

description: Gene expression data from H1N1 infected CEF 10 hpi rep 1

source_name: H1N1 infected CEF 10 hpi rep 1


title: H1N1 infected MDCK at 0H (10 H), biological rep3

value: mock


title: T246


title: T248


title: H1N1 infected MDCK at 0H (10 H), biological rep2

value: control


title: H1N1 H5N3 at 0H, biological rep3

description: Gene expression data from mock infected CEF rep 3

source_name: Mock infected CEF rep 3


title: H5N3 infected CEF at 10H, biological rep2

description: Gene expression data from H5N3 infected CEF 10h rep 2

source_name: H5N3 infected CEF 10 hpi rep 2


title: H1N1 infected MDCK at 0H (10 H), biological rep1


title: H1N1 H5N3 at 0H, biological rep2


title: H1N1 H5N3 at 0H, biological rep1


title: H1N1 infected MDCK at 6H, biological rep3

description: Gene expression data from H1N1 infected MDCK 6h rep 3

source_name: H1N1 infected MDCK 6 hpi rep 3

value: 6 hpi


title: H1N1 infected MDCK at 6H, biological rep2

description: Gene expression data from H1N1 infected MDCK 6h rep 2

source_name: H1N1 infected MDCK 6 hpi rep 2


title: H1N1 infected CEF at 8H, biological rep3

description: Gene expression data from H1N1 infected CEF 8 hpi rep 3

source_name: H1N1 infected CEF 8 hpi rep 3

value: 8 hpi


title: T236


title: H1N1 infected MDCK at 4H, biological rep3

description: Gene expression data from H1N1 infected MDCK 4h rep 3

source_name: H1N1 infected MDCK 4 hpi rep 3


title: H1N1 infected MDCK at 6H, biological rep1

description: Gene expression data from H1N1 infected MDCK 6h rep 1

source_name: H1N1 infected MDCK 6 hpi rep 1


title: H1N1 infected CEF at 8H, biological rep1

description: Gene expression data from H1N1 infected CEF 8 hpi rep 1

source_name: H1N1 infected CEF 8 hpi rep 1


title: T240


title: T245


title: H1N1 infected CEF at 8H, biological rep2

description: Gene expression data from H1N1 infected CEF 8 hpi rep 2

source_name: H1N1 infected CEF 8 hpi rep 2


title: H1N1 infected CEF at 6H, biological rep3

description: Gene expression data from H1N1 infected CEF 6 hpi rep 3

source_name: H1N1 infected CEF 6 hpi rep 3


title: H1N1 infected MDCK at 4H, biological rep1

description: Gene expression data from H1N1 infected MDCK 4h rep 1

source_name: H1N1 infected MDCK 4 hpi rep 1


title: H1N1 infected CEF at 6H, biological rep2

description: Gene expression data from H1N1 infected CEF 6 hpi rep 2

source_name: H1N1 infected CEF 6 hpi rep 2


title: T226


title: H1N1 infected MDCK at 2H, biological rep3

description: Gene expression data from H1N1 infected MDCK 2h rep 3

source_name: H1N1 infected MDCK 2 hpi rep 3


title: T237


title: H1N1 infected CEF at 6H, biological rep1

description: Gene expression data from H1N1 infected CEF 6 hpi rep 1

source_name: H1N1 infected CEF 6 hpi rep 1


title: H1N1 infected MDCK at 2H, biological rep2

description: Gene expression data from H1N1 infected MDCK 2h rep 2

source_name: H1N1 infected MDCK 2 hpi rep 2


title: H1N1 infected CEF at 4H, biological rep3

description: Gene expression data from H1N1 infected CEF 4 hpi rep 3

source_name: H1N1 infected CEF 4 hpi rep 3


title: T222


title: H1N1 infected MDCK at 2H, biological rep1

description: Gene expression data from H1N1 infected MDCK 2h rep 1

source_name: H1N1 infected MDCK 2 hpi rep 1


title: H1N1 infected MDCK at 4H, biological rep2

description: Gene expression data from H1N1 infected MDCK 4h rep 2

source_name: H1N1 infected MDCK 4 hpi rep 2


title: H1N1 infected CEF at 4H, biological rep2

description: Gene expression data from H1N1 infected CEF 4 hpi rep 2

source_name: H1N1 infected CEF 4 hpi rep 2


title: H1N1 infected MDCK at 0H, biological rep3

description: Gene expression data from mock infected MDCK rep 3

source_name: Mock infected MDCK rep 3


title: H1N1 infected CEF at 4H, biological rep1

description: Gene expression data from H1N1 infected CEF 4 hpi rep 1

source_name: H1N1 infected CEF 4 hpi rep 1


title: T229


title: H1N1 infected MDCK at 0H, biological rep2

description: Gene expression data from mock infected MDCK rep 2

source_name: Mock infected MDCK rep 2


title: T201


title: T198


title: T234


title: T202


title: Mu50 no Spm-60min

city: Atlanta

first: Xiangyu

last: Yao

state: Georgia

address: 100 piedmont ave., petit science center

department: Biology

institute: Georgia State University

scan_protocol: Affymetrix Protocol:Scan-M10

organism: Staphylococcus aureus subsp. aureus Mu50

source_name: Staphylococcus aureus no treatment 60min

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cDNA targets

growth_protocol: Overnight grown cultures of S. aureus Mu50 were used to inoculate 50 ml LB broth (pH8.0, Tris-Cl 20mM) and grown at 37ºC with shaking at 250rpm.

extract_protocol: For RNA isolation, the cells from fresh cultures were harvested by centrifugation at 20 ºC for 2 min with 12,000 rpm. Cell pellets were suspended with 1 ml of suspension buffer (20mM Tris-Cl, pH7.5, 50mM NaCl, 10mM EDTA) and 2 ml of RNAprotect Bacteria Reagent (QIAGEN), and mixed immediately by vortexing for 5 seconds. The cell suspensions were then incubated for 5min at room temperature followed by centrifugation for 10min at 12,000 rpm. After decanting the supernatant, the cell pellets were resuspended in 3 ml of suspension buffer and added with 10 µl of lysostaphin (10mg/ml) to weaken cell wall. RNA extraction was then carried out using hot phenol extraction method. Contaminated genomic DNA was removed using RNase-Free DNase I (Pierce) coupled with DNase I buffer (USB). The treated sample was applied to an RNeasy Mini column (QIAGEN) to recover RNA. The quality of these RNA samples was monitored by agarose gel electrophoresis, and RNA quantity was measured by UV spectrophotometry.

treatment_protocol: Exogenous Spm (final conc.10mM) was added to the culture in log-phase (OD600 of 0.5) and RNA samples were collected in a time-course manner (15min, 30min, 60min).

value: 60 min


title: H1N1 infected CEF at 2H, biological rep3

description: Gene expression data from H1N1 infected CEF 2 hpi rep 3

source_name: H1N1 infected CEF 2 hpi rep 3


title: H1N1 infected MDCK at 0H, biological rep1

description: Gene expression data from mock infected MDCK rep 1

source_name: Mock infected MDCK rep 1


title: T230


title: H1N1 infected CEF at 2H, biological rep2

description: Gene expression data from H1N1 infected CEF 2 hpi rep 2

source_name: H1N1 infected CEF 2 hpi rep 2


title: Mu50 10mM Spm-60min

source_name: Staphylococcus aureus 10mM Spm 60min

value: 10 mM Spm


title: Mu50 10mM Spm-30min

source_name: Staphylococcus aureus 10mM Spm 30min

value: 30 min


title: H1N1 infected CEF at 2H, biological rep1

description: Gene expression data from H1N1 infected CEF 2 hpi rep 1

source_name: H1N1 infected CEF 2 hpi rep 1


title: Mu50 no Spm-0min

source_name: Staphylococcus aureus no treatment 0min

value: 0 min


title: Mu50 10mM Spm-15min

source_name: Staphylococcus aureus 10mM Spm 15min

value: 15 min


title: H1N1 infected CEF at 0H, biological rep1

description: Gene expression data from mock infected CEF rep 1

source_name: Mock infected CEF rep 1


title: T192

value: Adenocarcinoma


title: H1N1 infected CEF at 0H, biological rep3

description: Gene expression data from mock infected CEF rep 3

source_name: Mock infected CEF rep 3


title: T188


title: Hdh109/10cells9-DNRest-2

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

country: United Kingdom

institute: Kings College London

description: SAMPLE 12

hyb_protocol: Samples were hybridized on Sentrix Mouse Ref-6 Expression BeadChip microarrays (Illumina) using standard protocols

scan_protocol: Standard Illumina scanning protocols

data_processing:
Data were background corrected in Genespring so values below 10 were set to 10. Data were loaded into R, quantile normalised and log2 transformed using the beadarray package. Differential expression was assessed using the Bioconductor package limma.
Matrix non-normalized data contains raw illumina output.

source_name: RNA, cell line, striatum, Hdh109/109 mouse

label_protocol: RNA for microarray was labelled using a TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Hdh109/109 and Hdh7/7 cells were propagated in DMEM supplemented with 10% fetal calf serum at 33°C in a humidified 5% CO2 atmosphere

extract_protocol: Total RNA was extracted from Hdh109/109 and Hdh7/7 cells using Trizol (Invitrogen) and digested with DNAse I (Ambion).

treatment_protocol: Cells were not treated

tag: cell line origin

value: mouse striatum

tag: cell line type

value: immortalised

tag: genotype

value: from homozygous knock-in mouse with 109 CAG repeats in Hdh allele

value: DNRest


title: Hdh109/10cells9-DNRest-1

description: SAMPLE 11


title: T171


title: T187

value: Bronchiolo-alveolar adenocarcinoma


title: Hdh109/10cells9-emptyvec-2

description: SAMPLE 10

value: empty vector


title: T180


title: T177


title: Hdh109/10cells9-emptyvec-1

description: SAMPLE 9

source_name: RNA, cell line, striatum, Hdh7/7 mouse


title: H1N1 infected CEF at 0H, biological rep2

description: Gene expression data from mock infected CEF rep 2

source_name: Mock infected CEF rep 2

value: Chicken embryo fibroblast cells

value: CEF


title: Hdh109/10cells9-ctrl-2

description: SAMPLE 8


title: T181

value: Large cell carcinoma


title: T164


title: T178


title: Hdh7/7cells-DNRest-2

description: SAMPLE 6

value: from homozygous knock-in mouse with 7 CAG repeats in Hdh allele


title: T160


title: T148


title: Hdh7/7cells-DNRest-1

description: SAMPLE 5


title: Hdh7/7cells-emptyvec-2

description: SAMPLE 4


title: Hdh7/7cells-emptyvec-1

description: SAMPLE 3


title: T153


title: Hdh7/7cells-ctrl-1

description: SAMPLE 1


title: Hdh7/7cells-ctrl-2

description: SAMPLE 2


title: 3D-hESC-1

city: Randwick

first: Jaemin

last: Kim

state: NSW

address: High

department: UNSW

country: Australia

institute: SCL

hyb_protocol: Following fragmentation, cRNA was processed through second-cycle single stranded cDNA. Fragmented and labelled cDNA was then hybridized onto Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

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

data_processing: Gene array data is processed by Partek GenomeSuite software in which mean probeset signals for all probesets were analysed. A receiver operating curve (ROC) is generated by thresholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

source_name: Cell type: hESC, Culture type: 3D

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

extract_protocol: Total RNA was extracted from cell cultures using TRIZOL (Invitrogen) as per manufacturer instructions.

treatment_protocol: Human embryonic stem cells were differentiated on a monolayer of PA6 cells under 2D (using cell culture inserts) or 3D (microencapsulation) culture systems.

value: Human embryonic stem cells (hESC)

tag: culture type


title: D_HCC_TLR4 wt C3H/HeOuJ Abx_30

city: New York

first: Robert

middle: F

last: Schwabe

state: NY

address: Russ Berrie Pavilion, 1150 St. Nicholas Avenue

department: Medicine

institute: Columbia University

hyb_protocol: 10 μg of aRNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

source_name: HCC tissue of WT C3H/HeOuJ mice treated with antibiotics from weeks 10-54 and injected with DEN (100 mg/kg) at 12 weeks, CCl4 (0.5 ml/kg) at 13,15,17,19,21,23 weeks and sacrificed at 54 weeks

label_protocol: 100 ng RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by Trizol followed by column purification (Qiagen) and quantification by NanoDrop Spectrophotometer.

treatment_protocol: For all HCC mice, DEN (100 mg/kg) was administered by injection at 12 weeks. CCl4 (0.5 ml/kg) was administered by injection at weeks, 13,15,17.19,21,23. Antibotics (a combination of ampicillin (1 g/l), neomycin (1 g/l), metronidazole (1 g/l) and vancomycin (500 mg/l) were administered in drinking water for 2 weeks prior to the first DEN injection at continued up to week 54. After sacrifice, tissue from HCC lesions was dissected for the analysis. For control mice, normal liver tissue was used.

tag: gender

value: male

value: WT

tag: age

value: 54 weeks

tag: tissue

value: hepatocellular carcinoma


title: Hdh109/10cells9-ctrl-1

description: SAMPLE 7


title: 3D-hESC-2


title: T158


title: T134


title: D_HCC_TLR4 wt C3H/HeOuJ Abx_29

tag: genotype/variation

tag: strain


title: T135


title: T136


title: T112


title: 2D-hESC-2

source_name: Cell type: hESC, Culture type: 2D


title: 2D-hESC-1


title: D_HCC_TLR4 wt C3H/HeOuJ Abx_28


title: C_HCC_TLR4mut C3H/HeJ_27

source_name: HCC tissue of mutant C3H/HeJ mice (Tlr4P712H) treated with DEN (100 mg/kg) at 12 weeks, CCl4 (0.5 ml/kg) at 13,15,17,19,21,23 weeks and sacrificed at 54 weeks

value: TLR4 mutant (Tlr4P712H)


title: T124

value: Adenocarcinoma


title: C_HCC_TLR4mut C3H/HeJ_26


title: 2D-hESC-3


title: T127


title: T128


title: RiceShoot_VC60_2hr_nitrate_rep1

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

description: Gene expression in a vector control transgenic rice (line #60) 2 hours after treatment with 10 mM nitrate

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60｡C for 30 minutes in a reaction volume of 55 ｵl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ｵl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4x44k Microarrays (G1529F015241) for 17 hours at 65｡C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37｡C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (eXtended Dymanic range scan, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 015241_D_F_20110907) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Oryza sativa

source_name: Vector control #60 2hr 10 mM KNO3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked using a Spectrophotometer and the Agilent 2100 Bioanalyzer.

growth_protocol: Rice T1 seeds were germinated on agar plates containing 50 ug/ml hygromycin B and grown for 5 days. Resistant seedlings were transferred to a hydroponic setting and grown with distilled water for 9 days in a growth chamber set to 16 hr Light/8 hr Dark conditions at 25｡C.

extract_protocol: Total RNA was isolated using TRIzol reagent and then treated with DNase I. After phenol and phenol:chloroform:isoamylalcohol extraction followed by ethanol precipitation, RNA was further purified using the RNeasy mini kit (QIAGEN). The quality of RNA was checked by measuring absorbance at 230, 260 and 280 nm using a spectrophotometer and also using the Agilent 2100 Bioanalyzer.

treatment_protocol: Rice seedlings were transferred to 10 mM potassium nitrate at 3 hours into the light period and incubated for 2 hours. Shoots were collected.

tag: organ

value: shoot

tag: treatment

value: 10 mM nitrate


title: C_HCC_TLR4mut C3H/HeJ_25


title: RiceShoot_NIGT1ox51_2hr_nitrate_rep1

description: Gene expression in a NIGT1-overexpressing rice (line #51) 2 hours after treatment with 10 mM nitrate

source_name: NIGT1 overexpressor #51 2hr 10 mM KNO3

value: NIGT1-overexpressing rice (line #51)


title: T107


title: RiceShoot_NIGT1ox51_0hr_rep1

description: Gene expression in a NIGT1-overexpressing rice (line #51) before treatment with 10 mM nitrate

source_name: NIGT1 overexpressor #51 0hr


title: C_HCC_TLR4mut C3H/HeJ_24


title: C_HCC_TLR4mut C3H/HeJ_23


title: T83


title: RiceShoot_NIGT1ox55_2hr_nitrate_rep1

description: Gene expression in a NIGT1-overexpressing rice (line #55) 2 hours after treatment with 10 mM nitrate

source_name: NIGT1 overexpressor #55 2hr 10 mM KNO3

value: NIGT1-overexpressing rice (line #55)