title: heavy_control_controlECM_4

description: SAMPLE 13


title: total_control_controlECM_4

status: Public on Mar 04 2014

type: RNA

city: Minneaplois

first: Matthew

last: Parker

state: MINNESOTA

address: 420 Delaware St. SE

department: Department of Medicine

country: USA

institute: University of Minnesota

description: SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (illumina iScan)

data_processing: The data was normalized using the robust spline normalization (RSN) and log2 transformed in the statistical R package (v.2.15.3).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: control lung fibroblast_control-ECM

label_protocol: Illumina Total Pre-96 RNA Amp. Kit

extract_protocol: Cells were treated with cycloheximide to immobilize ribosomes on RNA. Total RNA was isolated using Tri Reagent. Polysome-associated RNA was obtained by centrifuging samples on sucrose gradient, fractionating, and isolating using Tri Reagent.

tag: cell type

value: control lung fibroblast

tag: ecm type

value: control

tag: cell line

value: control 4

tag: batch

tag: molecule subtype

value: total RNA


title: total_control_IPFECM_3

description: SAMPLE 12

source_name: control lung fibroblast_IPF-ECM

value: IPF

value: control 3


title: Heart sample 52

city: Cleveland

first: James

last: Hester

state: Ohio

address: 9500 Euclid Avenue

department: Genomic Medicine

institute: Cleveland Clinic

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Beadstudio

organism: Mus musculus

source_name: Mouse Heart

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

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

tag: tissue

value: heart

tag: Sex

value: M

tag: cage

tag: maternal diet

value: HF

tag: diet

tag: weight (g) 3 weeks

tag: weight (g) weaning

tag: glucose (mg/dl)

tag: length (mm)

tag: bmi

tag: genetic background


title: total_control_controlECM_5

description: SAMPLE 18

value: control 5


title: Heart sample 55

value: LF


title: total_control_IPFECM_4

description: SAMPLE 16


title: Heart sample 24


title: heavy_control_controlECM_3

description: SAMPLE 9

value: polysome-associated RNA


title: Heart sample 23


title: heavy_control_IPFECM_2

description: SAMPLE 7

value: control 2


title: Brain sample 227

source_name: Mouse Brain

value: brain


title: total_control_controlECM_2

description: SAMPLE 6


title: Heart sample 14


title: total_control_controlECM_3

description: SAMPLE 10


title: total_control_IPFECM_1

description: SAMPLE 4

value: control 1


title: total_control_IPFECM_2

description: SAMPLE 8


title: Brain sample 210


title: Brain sample 211


title: Brain sample 209


title: Brain sample 208


title: Heart sample 13


title: heavy_control_controlECM_2

description: SAMPLE 5


title: total_control_controlECM_1

description: SAMPLE 2


title: Heart sample 15


title: Brain sample 200


title: Brain sample 201


title: Brain sample 199


title: Brain sample 182


title: Brain sample 183


title: Brain sample 207


title: Brain sample 177


title: Brain sample 172


title: Brain sample 173


title: Brain sample 134


title: Brain sample 123


title: Brain sample 128


title: Brain sample 174


title: Brain sample 124


title: Brain sample 100


title: Brain sample 102


title: Brain sample 97


title: Brain sample 108


title: Brain sample 133


title: Brain sample 126


title: Brain sample 109


title: Brain sample 101


title: Brain sample 99


title: total_IPF_IPFECM_3

description: SAMPLE 32

source_name: IPF lung fibroblast_IPF-ECM

value: IPF lung fibroblast

value: IPF 3


title: heavy_control_IPFECM_3

description: SAMPLE 11

value: control lung fibroblast


title: Brain sample 122


title: Brain sample 55


title: Brain sample 54


title: Brain sample 14


title: Brain sample 13


title: Brain sample 52


title: Brain sample 23


title: Brain sample 24


title: Brain sample 15


title: Ecoli_DH1_6%1-4-butanediol rep2

city: Berkeley

first: Aindrila

last: Mukhopadhyay

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Lawrence Berkeley National Laboratory

description: This sample is of wild-type E. coli DH1 grown in M9 defined medium and treated with 6% BDO for one hour and represents one of three technical replicates

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

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

data_processing: Data summarization, normalization, and analysis were performed using ArrayStar (DNASTAR) with the RMA algorithm.

organism: Escherichia coli DH1

source_name: Escherichia coli DH1 in M9 medium with 6% 1,4 Butanediol

label_protocol: Direct Rapid Labeling and cDNA synthesis protocols (Ouellet, 2009, A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology) were used to prepare triplicate samples for hybridization

growth_protocol: All cultures were grown in M9 minimal media (per liter: 200 ml 5x M9 salts, 2 ml 1M MgSO4, 50 ml 20% glucose, 20 ml 5% Casamino acids, 100 μl 0.5% Thiamine, 100 μl 1M CaCl2) and with appropriate antibiotics

extract_protocol: Cultures were harvested, centrifuged (8,000 x g, 4°C, 5 min) and the pellet stored at -80°C.  total RNA was isolated using the Qiagen RNeasy Mini Kit and RNA integrity and quantity were verified via gel electrophoresis and NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) respectively

treatment_protocol: Cells were grown to mid log and then treated with either 0% or 6% 1,4 Butanediol for one hour before sample collection.

tag: genotype/variation

value: wild type

tag: agent

value: 6% Butanediol


title: Ecoli_DH1_6%1-4-butanediol rep1


title: Ecoli_DH1_0%1-4-butanediol rep1

description: This sample is of wild-type E. coli DH1 grown in M9 defined medium and represents one of three technical replicates

source_name: Escherichia coli DH1 in M9 medium

value: no treatment


title: Ecoli_DH1_6%1-4-butanediol rep3


title: Ecoli_DH1_0%1-4-butanediol rep3


title: Ecoli_DH1_0%1-4-butanediol rep2


title: Brain sample 181


title: Patient #48

type: genomic

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

country: Germany

institute: Hannover Medical School

hyb_protocol: According to manufacturer's instructions (Agilent)

scan_protocol: Microarray slides were scanned immediately after washing using an Agilent microarray scanner G2505B at a resolution of 2 µm

data_processing:
Feature extraction and Genomic Workbench (Agilent)
algorithm ADM2

molecule: genomic DNA

source_name: blood mononuclear cells

label_protocol: standard Agilent protocol

extract_protocol: none provided

tag: sample type

value: human DNA reference pool XY

tag: cell type

value: blood mononuclear cells

source_name: bone marrow mononuclear cells

tag: disease state

value: acute myeloid leukemia with complex karyotype

value: bone marrow mononuclear cells

value: tumor DNA


title: Patient #40

value: human DNA reference pool XX


title: GBM-6dd-EtOH

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

description:
Gene expression analysis.
GBM TICs were obtained from tumor samples of patients subjected to surgery at the Neurosurgery Department of the San Martino Hospital in Genova. An informed consent was obtained from all patients before surgery as required by the Ethic Board. Cell isolation was described in detail elsewhere (SOX2 Silencing in Glioblastoma Tumor-Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity. Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2009 (PMID 18948646)).

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays (Agilent Technologies) following the manufacturer's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 υg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 100 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4845A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm). Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%. Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were analyzed with Feature Extraction Software version 10 (Agilent) using default parameters (Agilent protocol GE1-v5_95_Feb07). The output of Feature Extraction was analyzed with the Agi4x44PreProcess package to obtain background subtracted (Agilent parameter gBGSubSignal). Raw data was analyzed using GeneSpring software from Agilent. Normalization of the data was done in GeneSpring using the Quantile normalization.

source_name: Glioblastoma tumor-initiating cells, ethanol, 6d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com). Dye incorporation and cRNA yield were checked with the NanoDrop.

growth_protocol: Proliferation medium was DMEM-F12/Neurobasal additioned with 1% v/v B27 supplement (Gibco Ltd, Paisley, Scotland), 2 mM L-glutamine (Gibco Ltd), recombinant human fibroblast growth factor (FGF-2, 10 ng/ml Peprotech, London, UK), and recombinant human epidermal growth factor (EGF, 20 ng/ml Peprotech). The medium was changed twice a week. Under these conditions, TICs were grown as a monolayer in flasks coated with Matrigel (BD Biosciences, San Jose, CA) and expressed stem cell markers, maintained intact self-renewal capacity, partial multilineage differentiation ability and gave rise to tumor when injected orthotopically in nude mice (SOX2 Silencing in Glioblastoma Tumor-Initiating Cells Causes Stop of Proliferation and Loss of Tumorigenicity. Gangemi RM, Griffero F, Marubbi D, Perera M, Capra MC, Malatesta P, Ravetti GL, Zona GL, Daga A, Corte G. Stem Cells. 2009 (PMID 18948646)).

extract_protocol: miRNeasy Mini Kit (Qiagen) with DNase treatment. RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: GBM TICs were treated with vehicle alone (ethanol) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

value: glioblastoma tumor-initiating cells (GBM TICs)

value: ethanol

tag: exposure time


title: Patient #41


title: GBM-6dd-Tiron

source_name: Glioblastoma tumor-initiating cells, tiron, 6d

treatment_protocol: GBM TICs were treated with the antioxidant reagent 4,5-Dihydroxy-1,3-benzenedisulfonic acid disodium salt monohydrate (Tiron) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (6dd).

value: tiron


title: Patient #39


title: AN-48h-NAC

description:
Gene expression analysis.
Human astrocytes were obtained from ScienCell (San Diego, CA).

source_name: Normal astrocytes, NAC, 48h

growth_protocol: Human astrocytes were cultured in human astrocyte medium (ScienCell).

treatment_protocol: Human astrocytes were treated with the antioxidant reagent N-Acetyl-L-Cysteine (NAC) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

value: normal astrocytes

value: NAC


title: AN-48h-H2O

source_name: Normal astrocytes, water, 48h

treatment_protocol: Human astrocytes were treated with vehicle alone (H2O) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: GBM-6dd-Trolox

source_name: Glioblastoma tumor-initiating cells, trolox, 6d

treatment_protocol: GBM TICs were treated with the antioxidant reagent 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (6dd).

value: trolox


title: GBM-6dd-NAC

source_name: Glioblastoma tumor-initiating cells, NAC, 6d

treatment_protocol: GBM TICs were treated with the antioxidant reagent N-Acetyl-L-Cysteine (NAC) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (6dd).


title: Patient #37


title: GBM-48h-Trolox

source_name: Glioblastoma tumor-initiating cells, trolox, 48h

treatment_protocol: GBM TICs were treated with the antioxidant reagent 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: Patient #36


title: heavy_control_controlECM_1

description: SAMPLE 1

tag: ecm type

value: control

tag: cell line

value: control 1

tag: batch

tag: molecule subtype

value: polysome-associated RNA


title: GBM-6dd-H2O

source_name: Glioblastoma tumor-initiating cells, water, 6d

treatment_protocol: GBM TICs were treated with vehicle alone (H2O) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (6dd).


title: GBM-48h-EtOH

source_name: Glioblastoma tumor-initiating cells, ethanol, 48h


title: Patient #35


title: GBM-48h-Tiron

source_name: Glioblastoma tumor-initiating cells, tiron, 48h

treatment_protocol: GBM TICs were treated with the antioxidant reagent 4,5-Dihydroxy-1,3-benzenedisulfonic acid disodium salt monohydrate (Tiron) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).


title: Brain sample 228

tag: Sex

value: M

tag: cage

tag: maternal diet

value: HF

tag: diet

value: LF

tag: tissue

value: brain


title: heavy_control_IPFECM_1

description: SAMPLE 3

source_name: control lung fibroblast_IPF-ECM

value: control lung fibroblast

value: IPF


title: IK13_MDA-MB-134; EGFP; pair 4

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 7.5 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA normalisation using GeneSpring GX11.5

source_name: human lobular breast cancer cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3´ IVT Labeling protocol from 50ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

value: lobular breast cancer

tag: genotype

value: EGFP


title: GBM-48h-H2O

source_name: Glioblastoma tumor-initiating cells, water, 48h

treatment_protocol: GBM TICs were treated with vehicle alone (H2O) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

value: glioblastoma tumor-initiating cells (GBM TICs)


title: Patient #31

value: human DNA reference pool XX

value: blood mononuclear cells

value: acute myeloid leukemia with complex karyotype

value: bone marrow mononuclear cells

value: tumor DNA


title: IK14_MDA-MB-134; EcadEGFP; pair 4

value: EcadEGFP


title: Patient #21

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells


title: Patient #27

value: human DNA reference pool XY


title: Patient #22


title: IK10-MDA-MB-134; EcadEGFP; pair 2


title: IK12-MDA-MB-134; EcadEGFP; pair 3


title: SOD1-G93A SOL muscle, mutant animal 1

city: Zaragoza

first: Janne

middle: M

last: Toivonen

address: Miguel servet 177

department: Departamento de Anatomía, Embriología y Genética Animal

country: Spain

institute: Universidad de Zaragoza

description: RNAlater-stored left leg muscle was pulverized in liquid nitrogen and total RNA was purified using mirVana miRNA isolation kit

hyb_protocol: Hybridization was at 48 degrees celsius at 60 rpm for 16 hours, using Affymetrix hybridization oven. The hybridized chips were processed using Hybridization, Wash and Stain Kit (Affymetrix) according to the manufacturers instructions.

scan_protocol: Core software used for chip processing was AGCC 3.0 (Affymetrix) and miRNA QCTool (Affymetrix).

data_processing: Primary analysis was done using Partek Genomics Suite and dChip.

source_name: soleus muscle, SOD1-G93A overexpresser, age 90 days

label_protocol: One microgram of total RNA from each sample was poly(A) tailed and biotin labelled using FlashTag Biotin HSR RNA labeling Kit for Affymetrix GeneChip miRNA Arrays (Genisphere).

growth_protocol: The transgenic mice B6SJL-Tg(SOD1-G93A)1Gur/J expressing a high copy number of the G93A mutant form of human SOD1 were obtained from the Jackson Laboratory (Bar Harbor,ME, USA) and were housed under a 12 h light: 12 h dark cycle in 21–23 degrees celsius with relative humidity of 55%. Food and water were available ad libitum. Transgenic animals were maintained by breeding hemizygous SOD1-G93A males with B6SJL wild type females. The genotype was determined from a tail sample as described (http://www.jax.org/). Hemizygous SOD1-G93A mice and their non-transgenic littermates were used for all experiments.

extract_protocol: Excess RNAlater was removed from a muscle sample and the tissue was pulverized in liquid nitrogen. Total RNA was purified using mirVana miRNA isolation kit according to the manufacturers instructions and was finally eluted in 100 microliters of nuclease-free water. The quality and quantity of the extracted RNA was estimated using Bioanalyzer and Nanorop. RNA integrity (RIN) values of all samples were between 8.6 and 9.5, and A260/280 ratio were between 1.90 and 2.20.

treatment_protocol: Directly after dissection and removal of connective tissue the entire muscles (EDL or SOL) were individually submerged in 0.5 ml RNAlater solution (Ambion), kept 24 hours in +4 degrees celcius and transferred to -80 degrees celsius until use.

value: soleus

tag: strain


title: SOD1-G93A SOL muscle, mutant animal 2


title: IK11_MDA-MB-134; EGFP; pair 3


title: IK7-MDA-MB-134; EGFP; pair 1


title: Patient #16

source_name: blood mononuclear cells


title: Patient #13

source_name: bone marrow mononuclear cells


title: Patient #18


title: Wild type SOL muscle, control animal 2

source_name: soleus muscle, wild type, age 90 days


title: SOD1-G93A EDL muscle, mutant animal 3

source_name: extensor digitorum longus muscle, SOD1-G93A overexpresser, age 90 days

value: extensor digitorum longus


title: Wild type SOL muscle, control animal 1


title: IK9-MDA-MB-134; EGFP; pair 2


title: IK8_MDA-MB-134; EcadEGFP; pair 1


title: IK6_IPH-926; EcadEGFP; pair 3


title: Patient #34


title: SOD1-G93A EDL muscle, mutant animal 2


title: SOD1-G93A SOL muscle, mutant animal 3


title: Wild type SOL muscle, control animal 3


title: Patient #9


title: Patient #7


title: Patient #12


title: IK5-IPH-926; EGFP; pair 3


title: ob/ob_1mg/L_mouse#6

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

description: Gene expression profiling of liver tissue from ob/ob mouse treated with 1 mg/L drug mixture during 4 months

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Microarrays were then washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile. Finally, fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2505C) using one color scan setting for 4x44k array slides (scan resolution 5µm).

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.5.1.1 (Agilent Technologies) using default parameters (protocol GE1_105_Jan09 and Grid: 014868_D_F_20070820). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Normalization was performed with the 75th percentile shift algorithm. A baseline transformation to the median of all samples was applied. Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 50% of the values had a detected flag (i.e. a positive and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which at least 50% of the values were within the range of interest (i.e. 40-100th percentile).

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #6

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting material was 1µg of total RNA. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Five-week-old male C57BL/6J-+/+ mice (wild-type, also referred to as lean mice) weighing 19 to 20 g and C57BL/6J-ob/ob mice, weighing 28 to 32 g, and were purchased from Janvier (Le-Genest-St-Isle, France) and housed in the animal house facility of Rennes 1 University under a 12 h light-dark cycle. All mice were fed ad libitum on a normal diet bringing 2820 kcal per kg of food (A04 biscuits; UAR, Villemoisson-sur-Orge, France).

extract_protocol: Mice were then sacrificed by cervical dislocation and liver was quickly removed. While a majority of the liver fragments were immediately frozen in liquid nitrogen some of them were rapidly processed for appropriate histological staining. Collected tissues frozen in liquid nitrogen were subsequently stored at -80°C until total RNA extraction. All experiments were performed according to national guidelines for the use of animals in biomedical research and approved by the local Ethics Committee in Animal Experiment of Rennes 1 University and Robert Debré Hospital. Total RNA was extracted from liver samples using a standard RNA extraction protocol (Trizol) and quality-checked with an Agilent 2100 Bioanalyzer platform. All RNA samples revealed RNA Integrity Number (RIN) values between 7.2 and 8.

treatment_protocol: After 1 week of acclimatization, mice were further split into 4 subgroups (n=6 mice per group) that were treated or not with a mixture of 11 drugs at a concentration of 1 mg/L (for each drug). All these drugs (acetaminophen, caffeine, carbamazepine, cotinine, diclofenac, erythromycin, ibuprofen, phenazone, roxithromycin, salicylic acid and sulfamethoxazole) were purchased from Sigma-Aldrich (St. Quentin-Fallavier, France). Considering the molecular weight of the molecules, 1 mg/L corresponded to concentrations ranging from 1.2 µmol/L for roxithromycin to 7.2 µmol/L for salicylic acid. Mice were exposed during 4 months to these drugs by way of the drinking water, which was renewed every week.

tag: background strain

value: liver

tag: gender

value: male

value: ob/ob

tag: dose

value: 1 mg/L

tag: treatment duration

value: 4 months


title: IK4-IPH-926; EcadEGFP; pair 2

tag: cell type

value: lobular breast cancer


title: SOD1-G93A EDL muscle, mutant animal 1


title: Wild type EDL muscle, control animal 3

source_name: extensor digitorum longus muscle, wild type, age 90 days


title: ob/ob_1mg/L_mouse#5

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #5


title: Wild type EDL muscle, control animal 2


title: Patient #2

tag: sample type

tag: disease state


title: T2, rep3

city: Gothenburg

first: Dina

last: Petranovic

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from 6 days

hyb_protocol: Samples were hybridized with GeneChip yeast2 Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G

data_processing: CEL files were normalized and the probe sets were summarized using PLIER.

organism: Saccharomyces cerevisiae

source_name: Yeast at stationary phase for 6 days

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: batch cultivation on glucose

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA).

value: CENPK 113-7D

tag: growth phase

value: stationary phase for 6 days


title: T3, rep3

description: Gene expression data from 10 days

source_name: Yeast at stationary phase for 10 days

value: stationary phase for 10 days


title: T3, rep2

description: Gene expression data from 10 days


title: T3, rep1

description: Gene expression data from 10 days


title: IK3_IPH-926; EGFP; pair 2

tag: cell line

value: EGFP


title: ob/ob_1mg/L_mouse#3

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #3


title: Wild type EDL muscle, control animal 1


title: IK2_IPH-926; EcadEGFP; pair 1


title: KOVB6_2

city: Kyoto

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Gene expression data of ovarian cancer sample obtained at operation

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

scan_protocol: GeneChips were analyzed with Affymetrix microarray scanner using AGCC software.

data_processing: The data were analyzed with R.

source_name: ovarian cancer

label_protocol: Labeling was performed according to Affymetrix GeneChip 3' IVT Express Kit protocol.

extract_protocol: Total RNA was extracted using the RNAeasy Kit (Qiagen).

value: ovarian cancer

tag: figo stage

tag: age

tag: histological subtype

value: serous


title: ob/ob_1mg/L_mouse#4

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #4


title: lean_1mg/L_mouse#5

description: Gene expression profiling of liver tissue from WT mouse treated with 1 mg/L drug mixture during 4 months

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #5

value: wild type


title: KOVB6_1

value: endometrioid


title: ob/ob_1mg/L_mouse#2

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #2


title: ob/ob_1mg/L_mouse#1

source_name: liver tissue from treated ob/ob animal (1mg/L), mouse/replicate #1


title: T2, rep2

description: Gene expression data from 6 days


title: IK1_IPH-926; EGFP; pair 1

source_name: human lobular breast cancer cells


title: lean_1mg/L_mouse#4

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #4


title: lean_1mg/L_mouse#6

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #6


title: T2, rep1

description: Gene expression data from 6 days


title: T1, rep3

description: Gene expression data from 2 days

source_name: Yeast at stationary phase for 2 days

value: stationary phase for 2 days


title: Brain sample 127

source_name: Mouse Brain

tag: Sex

value: M

tag: cage

tag: maternal diet

value: HF

value: LF

tag: weight (g) 3 weeks

tag: weight (g) weaning

tag: glucose (mg/dl)

tag: length (mm)

tag: bmi

value: brain

tag: genetic background


title: KOVB5_8

tag: tissue


title: T1, rep2

description: Gene expression data from 2 days

tag: strain


title: KOVB5_7


title: T1, rep1

description: Gene expression data from 2 days


title: KOVB5_5


title: KOVB5_9

value: mucinous


title: lean_1mg/L_mouse#3

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #3

tag: background strain

value: liver

tag: gender

value: male

tag: genotype

tag: dose

value: 1 mg/L

tag: treatment duration


title: KOVB5_4

tag: figo stage

tag: age

tag: histological subtype

value: clear


title: T0, rep2

description: Gene expression data from log phase

source_name: Yeast at log phase

value: CENPK 113-7D

tag: growth phase

value: log phase


title: lean_1mg/L_mouse#2

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #2

value: 4 months


title: ob/ob_0mg/L_mouse#6

description: Gene expression profiling of liver tissue from untreated ob/ob mouse

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #6

value: ob/ob

value: 0 mg/L


title: KOVB5_2

value: ovarian cancer

value: serous


title: KOVB5_1


title: ob/ob_0mg/L_mouse#4

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #4


title: ob/ob_0mg/L_mouse#3

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #3


title: lean_1mg/L_mouse#1

source_name: liver tissue from treated lean animal (1mg/L), mouse/replicate #1

value: wild type


title: T0, rep1

description: Gene expression data from log phase


title: ob/ob_0mg/L_mouse#5

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #5


title: KOVB6_3

source_name: ovarian cancer


title: DP thymocytes_USP8ffCD4Cre_rep2

city: Freiburg im Breisgau

first: Klaus-Peter

last: Knobeloch

address: Breisacher Str. 64

department: Inst. for Neuropathology

institute: University Freiburg

hyb_protocol: For each sample, 1.65 ug of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F Design ID 014868) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using a DNA microarray scanner, Model G2565A (Agilent Technologies)

data_processing:
The raw data were analyzed using GeneSpring GX 10.0 (normalization: shift to 75th percentile, baseline transformation: median of all samples). The normalized data were filtered to exclude probes flagged absent in all samples.
The remaining probes were tested for statistical significance of expression using a two-sample Student’s t test (unpaired) with asymptotic p-value computation and a cut off of 0.05. Multiple testing correction was performed according to Benjamini Hochberg50 (P ≤ 0.05). The cutoff for the fold change is ≤ 2 (1 log2) up or down regulation. Matrix data include extended values (cutoff  for the fold change ≤ 1.45).

source_name: DP thymocytes

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from sorted DP thymocytes using the RNeasy Mini kit (Quiagen) and RNA integrity was verified with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were left untreated

tag: genotype/variation

value: 6-12 week old

tag: description

value: littermates, sex matched


title: GBM-48h-NAC

source_name: Glioblastoma tumor-initiating cells, NAC, 48h

treatment_protocol: GBM TICs were treated with the antioxidant reagent N-Acetyl-L-Cysteine (NAC) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (48h).

tag: cell type

value: glioblastoma tumor-initiating cells (GBM TICs)

tag: agent

value: NAC

tag: exposure time


title: HOSE_IFN, biological rep3

description: Gene expression data from HOSE cells incubated for 6 hours with adding IFN-gamma.

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

source_name: immortalized ovarian surface epithelial cells

treatment_protocol: HOSE cells were incubated with or without 500 IU/ml recombinant human IFN-gamma in the culture medium for 6 hours prior to the analysis.

tag: cell line

value: HOSE

tag: treatment

value: 500 IU/ml recombinant human IFN-gamma


title: ob/ob_0mg/L_mouse#2

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #2

tag: tissue

value: liver

value: male


title: lean_0mg/L_mouse#6

description: Gene expression profiling of liver tissue from untreated WT mouse

source_name: liver tissue from untreated lean animal, mouse/replicate #6

tag: background strain


title: ob/ob_0mg/L_mouse#1

source_name: liver tissue from untreated ob/ob animal, mouse/replicate #1

tag: gender


title: DP thymocytes_USP8ff_rep1


title: HOSE_IFN, biological rep2

value: immortalized ovarian surface epithelial cells


title: HOSE_IFN, biological rep1


title: DP thymocytes_USP8ff_rep2


title: HOSE_control, biological rep4

description: Gene expression data from HOSE cells incubated for 6 hours without adding IFN-gamma.


title: KOVB5_3


title: HOSE_IFN, biological rep4


title: T0, rep3

description: Gene expression data from log phase

tag: strain

value: CENPK 113-7D


title: DP thymocytes_USP8ff_CD4Cre_rep1


title: HOSE_control, biological rep3


title: KOVB5_6

value: clear


title: HOSE_control, biological rep1


title: lean_0mg/L_mouse#1

source_name: liver tissue from untreated lean animal, mouse/replicate #1

tag: genotype

tag: dose

value: 4 months


title: lean_0mg/L_mouse#4

source_name: liver tissue from untreated lean animal, mouse/replicate #4

tag: treatment duration


title: lean_0mg/L_mouse#3

source_name: liver tissue from untreated lean animal, mouse/replicate #3


title: lean_0mg/L_mouse#2

source_name: liver tissue from untreated lean animal, mouse/replicate #2


title: lean_0mg/L_mouse#5

source_name: liver tissue from untreated lean animal, mouse/replicate #5


title: HOSE_control, biological rep2


title: Patient #20

source_name: blood mononuclear cells

tag: sample type

value: human DNA reference pool XY

value: blood mononuclear cells

source_name: bone marrow mononuclear cells

tag: disease state

value: acute myeloid leukemia with complex karyotype

value: bone marrow mononuclear cells

value: tumor DNA


title: normal lung_6229050079_R03C01

status: Public on Mar 03 2014

city: Rockville

first: Jianxin

last: Shi

state: Maryland

address: 9609 Medical Drive, 7E596

institute: NCI/NIH

description:
6229050079_R03C01
normal lung tissue samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software; Unmethylated and methylated signal intensities are provided in the non_normalized.txt

label: Cy5 and Cy3

source_name: EAGLE_population-based study of lung cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: DNA from fresh-frozen human lung tissue

value: normal


title: normal lung_6229050079_R05C01

description:
6229050079_R05C01
normal lung tissue samples


title: normal lung_6929726161_R06C01

description:
6929726161_R06C01
normal lung tissue samples

value: female


title: normal lung_6229050079_R05C02

description:
6229050079_R05C02
normal lung tissue samples


title: normal lung_6229050080_R06C02

description:
6229050080_R06C02
normal lung tissue samples


title: normal lung_6229050097_R03C01

description:
6229050097_R03C01
normal lung tissue samples


title: normal lung_6229050080_R06C01

description:
6229050080_R06C01
normal lung tissue samples


title: normal lung_6229050108_R01C01

description:
6229050108_R01C01
normal lung tissue samples


title: normal lung_6229050075_R05C01

description:
6229050075_R05C01
normal lung tissue samples


title: normal lung_6229050080_R02C01

description:
6229050080_R02C01
normal lung tissue samples


title: normal lung_6229050108_R05C01

description:
6229050108_R05C01
normal lung tissue samples


title: normal lung_6229050108_R03C02

description:
6229050108_R03C02
normal lung tissue samples


title: normal lung_6229050079_R03C02

description:
6229050079_R03C02
normal lung tissue samples


title: normal lung_6229050080_R04C02

description:
6229050080_R04C02
normal lung tissue samples


title: normal lung_6229050097_R01C02

description:
6229050097_R01C02
normal lung tissue samples


title: normal lung_6229050108_R01C02

description:
6229050108_R01C02
normal lung tissue samples


title: normal lung_6229050079_R02C02

description:
6229050079_R02C02
normal lung tissue samples


title: normal lung_6229050075_R03C02

description:
6229050075_R03C02
normal lung tissue samples


title: normal lung_6229050075_R05C02

description:
6229050075_R05C02
normal lung tissue samples


title: normal lung_6229050075_R01C02

description:
6229050075_R01C02
normal lung tissue samples


title: normal lung_6229050079_R01C02

description:
6229050079_R01C02
normal lung tissue samples


title: normal lung_6229050097_R05C01

description:
6229050097_R05C01
normal lung tissue samples


title: normal lung_6229050097_R03C02

description:
6229050097_R03C02
normal lung tissue samples


title: normal lung_6229050080_R02C02

description:
6229050080_R02C02
normal lung tissue samples


title: normal lung_6229050097_R05C02

description:
6229050097_R05C02
normal lung tissue samples


title: normal lung_6229050075_R03C01

description:
6229050075_R03C01
normal lung tissue samples


title: normal lung_6229050108_R05C02

description:
6229050108_R05C02
normal lung tissue samples


title: normal lung_6229050080_R04C01

description:
6229050080_R04C01
normal lung tissue samples


title: normal lung_6229050079_R01C01

description:
6229050079_R01C01
normal lung tissue samples


title: normal lung_6929689013_R05C01

description:
6929689013_R05C01
normal lung tissue samples


title: normal lung_6929689013_R01C01

description:
6929689013_R01C01
normal lung tissue samples


title: normal lung_6929671143_R06C02

description:
6929671143_R06C02
normal lung tissue samples


title: normal lung_6229050097_R01C01

description:
6229050097_R01C01
normal lung tissue samples


title: normal lung_6929671119_R01C02

description:
6929671119_R01C02
normal lung tissue samples


title: normal lung_6229050070_R06C02

description:
6229050070_R06C02
normal lung tissue samples


title: normal lung_6929689013_R05C02

description:
6929689013_R05C02
normal lung tissue samples


title: normal lung_6929671147_R01C01

description:
6929671147_R01C01
normal lung tissue samples


title: normal lung_6229050070_R01C01

description:
6229050070_R01C01
normal lung tissue samples


title: normal lung_6929671130_R01C02

description:
6929671130_R01C02
normal lung tissue samples


title: normal lung_6929671143_R02C01

description:
6929671143_R02C01
normal lung tissue samples


title: normal lung_6929671147_R01C02

description:
6929671147_R01C02
normal lung tissue samples


title: normal lung_6929671143_R04C01

description:
6929671143_R04C01
normal lung tissue samples


title: normal lung_6929671147_R03C01

description:
6929671147_R03C01
normal lung tissue samples


title: normal lung_6929671100_R05C01

description:
6929671100_R05C01
normal lung tissue samples


title: normal lung_6929671130_R05C01

description:
6929671130_R05C01
normal lung tissue samples


title: normal lung_6929671143_R03C01

description:
6929671143_R03C01
normal lung tissue samples


title: normal lung_6929671130_R03C01

description:
6929671130_R03C01
normal lung tissue samples


title: normal lung_6929671119_R05C02

description:
6929671119_R05C02
normal lung tissue samples


title: normal lung_6929671119_R05C01

description:
6929671119_R05C01
normal lung tissue samples


title: normal lung_6929671130_R05C02

description:
6929671130_R05C02
normal lung tissue samples


title: normal lung_6929671147_R05C02

description:
6929671147_R05C02
normal lung tissue samples


title: normal lung_6229050070_R04C01

description:
6229050070_R04C01
normal lung tissue samples


title: normal lung_6929671100_R01C01

description:
6929671100_R01C01
normal lung tissue samples


title: normal lung_6929671143_R04C02

description:
6929671143_R04C02
normal lung tissue samples


title: normal lung_6929671119_R03C02

description:
6929671119_R03C02
normal lung tissue samples


title: normal lung_6229050108_R03C01

description:
6229050108_R03C01
normal lung tissue samples


title: normal lung_6929671147_R05C01

description:
6929671147_R05C01
normal lung tissue samples


title: normal lung_6929671130_R01C01

description:
6929671130_R01C01
normal lung tissue samples


title: normal lung_6929689013_R01C02

description:
6929689013_R01C02
normal lung tissue samples


title: normal lung_6929689013_R03C02

description:
6929689013_R03C02
normal lung tissue samples


title: normal lung_6229050070_R02C02

description:
6229050070_R02C02
normal lung tissue samples


title: normal lung_6929671100_R05C02

description:
6929671100_R05C02
normal lung tissue samples


title: normal lung_6929671119_R01C01

description:
6929671119_R01C01
normal lung tissue samples


title: normal lung_6285625060_R05C02

description:
6285625060_R05C02
normal lung tissue samples


title: normal lung_6929671147_R03C02

description:
6929671147_R03C02
normal lung tissue samples


title: normal lung_6229050070_R06C01

description:
6229050070_R06C01
normal lung tissue samples


title: normal lung_6929671130_R03C02

description:
6929671130_R03C02
normal lung tissue samples


title: normal lung_6929726161_R04C02

description:
6929726161_R04C02
normal lung tissue samples


title: normal lung_6929671143_R06C01

description:
6929671143_R06C01
normal lung tissue samples


title: normal lung_6929689013_R03C01

description:
6929689013_R03C01
normal lung tissue samples


title: normal lung_6929671100_R01C02

description:
6929671100_R01C02
normal lung tissue samples


title: normal lung_6929671118_R06C02

description:
6929671118_R06C02
normal lung tissue samples


title: normal lung_6929726161_R06C02

description:
6929726161_R06C02
normal lung tissue samples


title: normal lung_6929671143_R02C02

description:
6929671143_R02C02
normal lung tissue samples


title: normal lung_6929726161_R02C01

description:
6929726161_R02C01
normal lung tissue samples


title: normal lung_6285625040_R01C01

description:
6285625040_R01C01
normal lung tissue samples


title: normal lung_6929671118_R04C02

description:
6929671118_R04C02
normal lung tissue samples


title: normal lung_6285625040_R02C02

description:
6285625040_R02C02
normal lung tissue samples


title: normal lung_6229050070_R04C02

description:
6229050070_R04C02
normal lung tissue samples


title: normal lung_6929671109_R02C02

description:
6929671109_R02C02
normal lung tissue samples


title: normal lung_6285625040_R03C01

description:
6285625040_R03C01
normal lung tissue samples


title: normal lung_6929671118_R04C01

description:
6929671118_R04C01
normal lung tissue samples


title: normal lung_6929726163_R04C01

description:
6929726163_R04C01
normal lung tissue samples


title: normal lung_6929726163_R04C02

description:
6929726163_R04C02
normal lung tissue samples


title: normal lung_6929671118_R02C01

description:
6929671118_R02C01
normal lung tissue samples


title: normal lung_6929671119_R03C01

description:
6929671119_R03C01
normal lung tissue samples


title: normal lung_6285625040_R06C01

description:
6285625040_R06C01
normal lung tissue samples


title: normal lung_6929671100_R03C02

description:
6929671100_R03C02
normal lung tissue samples


title: normal lung_6285625060_R01C02

description:
6285625060_R01C02
normal lung tissue samples


title: normal lung_6285625040_R05C01

description:
6285625040_R05C01
normal lung tissue samples


title: normal lung_6929671118_R02C02

description:
6929671118_R02C02
normal lung tissue samples


title: normal lung_6929726161_R04C01

description:
6929726161_R04C01
normal lung tissue samples


title: normal lung_6929671109_R06C01

description:
6929671109_R06C01
normal lung tissue samples


title: normal lung_6929726163_R06C01

description:
6929726163_R06C01
normal lung tissue samples


title: normal lung_6929671109_R04C02

description:
6929671109_R04C02
normal lung tissue samples


title: normal lung_6285625060_R05C01

description:
6285625060_R05C01
normal lung tissue samples


title: normal lung_6285625060_R03C01

description:
6285625060_R03C01
normal lung tissue samples


title: normal lung_6229050100_R02C02

description:
6229050100_R02C02
normal lung tissue samples


title: normal lung_6929671109_R04C01

description:
6929671109_R04C01
normal lung tissue samples


title: normal lung_6929726163_R02C01

description:
6929726163_R02C01
normal lung tissue samples


title: normal lung_6929726163_R06C02

description:
6929726163_R06C02
normal lung tissue samples


title: normal lung_6929671109_R02C01

description:
6929671109_R02C01
normal lung tissue samples


title: normal lung_6929671118_R06C01

description:
6929671118_R06C01
normal lung tissue samples


title: normal lung_6229050100_R06C01

description:
6229050100_R06C01
normal lung tissue samples


title: normal lung_6285625040_R06C02

description:
6285625040_R06C02
normal lung tissue samples


title: normal lung_6229050099_R04C01

description:
6229050099_R04C01
normal lung tissue samples


title: normal lung_6929726163_R02C02

description:
6929726163_R02C02
normal lung tissue samples


title: normal lung_6229050098_R02C02

description:
6229050098_R02C02
normal lung tissue samples


title: normal lung_6285625060_R01C01

description:
6285625060_R01C01
normal lung tissue samples


title: normal lung_6929671109_R06C02

description:
6929671109_R06C02
normal lung tissue samples


title: normal lung_6229050099_R06C01

description:
6229050099_R06C01
normal lung tissue samples


title: normal lung_6229050098_R06C02

description:
6229050098_R06C02
normal lung tissue samples


title: normal lung_6229050098_R02C01

description:
6229050098_R02C01
normal lung tissue samples


title: normal lung_6285625040_R04C02

description:
6285625040_R04C02
normal lung tissue samples


title: normal lung_6229050100_R04C02

description:
6229050100_R04C02
normal lung tissue samples


title: normal lung_6229050099_R04C02

description:
6229050099_R04C02
normal lung tissue samples


title: normal lung_6229050098_R04C02

description:
6229050098_R04C02
normal lung tissue samples


title: normal lung_6229050099_R06C02

description:
6229050099_R06C02
normal lung tissue samples


title: normal lung_6229050099_R02C01

description:
6229050099_R02C01
normal lung tissue samples


title: normal lung_6229050099_R02C02

description:
6229050099_R02C02
normal lung tissue samples


title: normal lung_6229041133_R02C01

description:
6229041133_R02C01
normal lung tissue samples


title: normal lung_6229050100_R06C02

description:
6229050100_R06C02
normal lung tissue samples


title: normal lung_6229050015_R05C01

description:
6229050015_R05C01
normal lung tissue samples


title: normal lung_6229050100_R02C01

description:
6229050100_R02C01
normal lung tissue samples


title: normal lung_6229041133_R03C01

description:
6229041133_R03C01
normal lung tissue samples


title: normal lung_6229041134_R03C01

description:
6229041134_R03C01
normal lung tissue samples


title: normal lung_6229041106_R03C02

description:
6229041106_R03C02
normal lung tissue samples


title: normal lung_6229041134_R01C01

description:
6229041134_R01C01
normal lung tissue samples


title: normal lung_6229041134_R05C02

description:
6229041134_R05C02
normal lung tissue samples


title: normal lung_6229041133_R01C02

description:
6229041133_R01C02
normal lung tissue samples


title: normal lung_6229050054_R06C01

description:
6229050054_R06C01
normal lung tissue samples


title: normal lung_6229041135_R06C01

description:
6229041135_R06C01
normal lung tissue samples


title: normal lung_6229041133_R05C01

description:
6229041133_R05C01
normal lung tissue samples


title: normal lung_6229050098_R04C01

description:
6229050098_R04C01
normal lung tissue samples


title: normal lung_6229041134_R05C01

description:
6229041134_R05C01
normal lung tissue samples


title: normal lung_6229041133_R03C02

description:
6229041133_R03C02
normal lung tissue samples


title: normal lung_6229041133_R05C02

description:
6229041133_R05C02
normal lung tissue samples


title: normal lung_6229050098_R06C01

description:
6229050098_R06C01
normal lung tissue samples


title: normal lung_6229041133_R01C01

description:
6229041133_R01C01
normal lung tissue samples


title: normal lung_6229041134_R01C02

description:
6229041134_R01C02
normal lung tissue samples


title: normal lung_6229041164_R02C01

description:
6229041164_R02C01
normal lung tissue samples


title: normal lung_6229050015_R01C01

description:
6229050015_R01C01
normal lung tissue samples


title: normal lung_6229041135_R02C01

description:
6229041135_R02C01
normal lung tissue samples


title: normal lung_6229050015_R03C02

description:
6229050015_R03C02
normal lung tissue samples


title: normal lung_6229041134_R03C02

description:
6229041134_R03C02
normal lung tissue samples


title: normal lung_6229041106_R03C01

description:
6229041106_R03C01
normal lung tissue samples


title: normal lung_6229050016_R05C01

description:
6229050016_R05C01
normal lung tissue samples


title: normal lung_6229050015_R01C02

description:
6229050015_R01C02
normal lung tissue samples


title: normal lung_6229041164_R06C01

description:
6229041164_R06C01
normal lung tissue samples


title: normal lung_6229041135_R02C02

description:
6229041135_R02C02
normal lung tissue samples


title: normal lung_6229050016_R03C02

description:
6229050016_R03C02
normal lung tissue samples


title: Liver_Tumor_2

city: Otsu

first: Masaki

last: Mori

state: Shiga

address: Tsukinowa-cho, Seta

department: Molecular Neuroscience Research Center

institute: Shiga University of Medical Science

hyb_protocol: Hybridization, blocking and washing were performed according to the manufacturer's protocol (nanoString nCounter analysis, nCounter® miRNA Expression Assays).

scan_protocol: nCounter Analysis system (nanoString) was used to analyze fluorophore signals.

data_processing: The miRNA expression in each condition was normalized to positive control probes and top 100 genes.

label: miRNA-specific probes

source_name: Liver tissue

label_protocol: Labeling was performed according to the manufacturer's protocol (nanoString nCounter analysis, nCounter® miRNA Expression Assays).

growth_protocol: For the liver tumorigenesis model, NF2fl/fl (Benhamouche et al., 2010) female mice (n=3) were administered PBS or AAV2/8-Cre (AV-8-PV1091, University of Pennsylvania Vector Core, MOI = 10^11) to induce hepatocyte-specific deletion of NF2 gene. Livers were inspected 50 weeks after the administration, and the tumors were dissected for gene expression analyses.

extract_protocol: Total RNA was extracted from mouse liver normal and tumor tissues with TRIzol (Ambion) and processed according to the manufacturer’s protocol.

tag: condition

value: tumors

value: Liver


title: Liver_Tumor_1


title: Liver_Normal_1


title: normal lung_6229041106_R05C02

description:
6229041106_R05C02
normal lung tissue samples


title: Liver_Normal_2


title: normal lung_6229041163_R04C02

description:
6229041163_R04C02
normal lung tissue samples


title: normal lung_6229041106_R01C02

description:
6229041106_R01C02
normal lung tissue samples


title: normal lung_6229041163_R04C01

description:
6229041163_R04C01
normal lung tissue samples


title: normal lung_6229041164_R06C02

description:
6229041164_R06C02
normal lung tissue samples


title: Skin_Tumor_2

data_processing: The miRNA expression in each condition was normalized to positive control probes and all miRNAs.

source_name: Epidermal cells

growth_protocol: Adult R26stoprtTA/+ Col-tetO-YAPS127A/+ K14-Cre (“+Cre” group) and R26stoprtTA/+ Col-tetO-YAPS127A/+ (“-Cre” control group, n=6) were treated for 8 days with doxycycline (1mg/ml) administered in drinking water to induce tumorigenic epidermal cells which form squamous cell carcinoma upon transplantation onto the nude mice skin

extract_protocol: After careful removal of fat tissues from the epidermal surface, the back skins were spread on petri dish and incubated with 0.25% Trypsin-EDTA overnight at 4C. The epidermal cells, which are enriched for the skin progenitor cells, were scraped off from the skin, minced, filtered sequentially with 70 μm and 40 μm strainers, collected by centrifugation at 600g for 8min, and used for gene expression analyses.Total RNA was extracted from cultured cells or mouse tissues with TRIzol (Ambion) and processed according to the manufacturer’s protocol.

value: oncogenic epidermal cells

value: Skin


title: normal lung_6229041164_R04C02

description:
6229041164_R04C02
normal lung tissue samples

value: male


title: Skin_Tumor_1


title: Skin_Normal_2

value: normal epidermal cells


title: normal lung_6229041135_R06C02

description:
6229041135_R06C02
normal lung tissue samples


title: normal lung_6229041106_R01C01

description:
6229041106_R01C01
normal lung tissue samples


title: normal lung_6229041163_R02C01

description:
6229041163_R02C01
normal lung tissue samples


title: normal lung_6229041164_R04C01

description:
6229041164_R04C01
normal lung tissue samples


title: normal lung_6229050015_R03C01

description:
6229050015_R03C01
normal lung tissue samples


title: normal lung_6229041163_R06C01

description:
6229041163_R06C01
normal lung tissue samples


title: normal lung_6229050016_R05C02

description:
6229050016_R05C02
normal lung tissue samples


title: normal lung_6229050016_R03C01

description:
6229050016_R03C01
normal lung tissue samples


title: Skin_Normal_1


title: siNF2/LATS2 + p72-2

source_name: HaCaT cells

growth_protocol: HaCaT immortalized human keratinocytes were cultured in DMEM + 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted from cultured cells with TRIzol (Ambion) and processed according to the manufacturer’s protocol.

treatment_protocol: p72 expression plasmid or control EGFP plasmid, in addition to siRNAs for NF2 and LATS2, were transfected in HaCaT human keratinocytes and maintained at high density prior to RNA sampling.

value: HaCaT

tag: transfection

value: siNF2/LATS2 + p72-1


title: normal lung_6229050015_R05C02

description:
6229050015_R05C02
normal lung tissue samples


title: normal lung_6229041106_R05C01

description:
6229041106_R05C01
normal lung tissue samples


title: normal lung_6229050016_R01C02

description:
6229050016_R01C02
normal lung tissue samples


title: normal lung_6229050046_R04C02

description:
6229050046_R04C02
normal lung tissue samples


title: normal lung_6229041163_R02C02

description:
6229041163_R02C02
normal lung tissue samples


title: siNF2/LATS2 + p72-1


title: siNF2/LATS2-1 (HaCaT,_p72)


title: siNF2/LATS2-2 (HaCaT,_p72)


title: siYAP-1

treatment_protocol: siRNAs (negative control RNA oligos or siRNA for YAP) were transfected in HaCaT human keratinocytes and maintained at high density prior to RNA sampling.

value: siYAP


title: siYAP-2


title: siCtrl-2

value: siCtrl


title: normal lung_6229050062_R03C01

description:
6229050062_R03C01
normal lung tissue samples


title: siCtrl-1


title: normal lung_6229050062_R03C02

description:
6229050062_R03C02
normal lung tissue samples


title: normal lung_6229050013_R02C01

description:
6229050013_R02C01
normal lung tissue samples


title: High density-1

extract_protocol: Total RNA was extracted from the equal number of cells with TRIzol (Ambion) and processed according to the manufacturer’s protocol.

treatment_protocol: HaCaT human keratinocytes were maintained at low and high densities prior to RNA sampling.

value: high density


title: normal lung_6229050011_R04C01

description:
6229050011_R04C01
normal lung tissue samples


title: normal lung_6229041164_R02C02

description:
6229041164_R02C02
normal lung tissue samples


title: Low density-2

value: low density


title: normal lung_6229050016_R01C01

description:
6229050016_R01C01
normal lung tissue samples


title: normal lung_6229050059_R01C02

description:
6229050059_R01C02
normal lung tissue samples


title: normal lung_6229050011_R06C01

description:
6229050011_R06C01
normal lung tissue samples


title: si p72-2

treatment_protocol: siRNAs (negative control oligos, siRNAs for NF2 and LATS2, siRNA for p72, siRNAs for DROSHA and DGCR8) were transfected in HaCaT human keratinocytes and maintained at high density prior to RNA sampling.

value: si p72


title: siDROSHA/DGCR8-1


title: normal lung_6229050013_R06C01

description:
6229050013_R06C01
normal lung tissue samples


title: siNF2/LATS2-2


title: si p72-1


title: Low density-1


title: Control-2


title: siNF2/LATS2-1


title: siDROSHA/DGCR8-2


title: Control-1


title: MTB at T360, biological rep4

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica NV

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 360 min

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mycobacterium tuberculosis ‘TB-All-Antisense’ 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 R (version 2.15.1) and BioConductor (package affy version 1.34.0). Preprocessing was done using the function expresso (settings: bg.correct = FALSE, normalize.method = vsn, pmcorrect.method = pmonly, summary.method = medianpolish) plus the CDF tballantisensecdf as provided by Affymetrix.

organism: Mycobacterium tuberculosis H37Rv

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

growth_protocol: Mycobacterium tuberculosis was Grown in Middlebrook 7H9 broth

extract_protocol: Bacteria were pelletted, resuspended in RLT-buffer with ß-mercaptoethanol and mechanically disrupted with Mixer Mill MM 310. Only the supernatant was used for RNA extraction using RNeasy Protect Bacteria Mini kit (Qiagen). RNA was eluted in RNAse free water.

treatment_protocol: Mycobacterium tuberculosis was treated with 1 µM Bedaquiline

value: 1 µM Bedaquiline

tag: timepoint


title: MTB at T360, biological rep3

source_name: Mycobacterium tuberculosis treated with bedaquiline and harvested after 360 min


title: normal lung_6229050062_R05C02

description:
6229050062_R05C02
normal lung tissue samples

value: DNA from fresh-frozen human lung tissue


title: MTB at T360, biological rep2


title: MTB at T180, biological rep4

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 180 min


title: MTB at T180, biological rep3

source_name: Mycobacterium tuberculosis treated with bedaquiline and harvested after 180 min


title: normal lung_6229050046_R04C01

description:
6229050046_R04C01
normal lung tissue samples

value: normal


title: normal lung_6229050046_R02C02

description:
6229050046_R02C02
normal lung tissue samples


title: normal lung_6229050059_R01C01

description:
6229050059_R01C01
normal lung tissue samples


title: normal lung_6229050046_R06C02

description:
6229050046_R06C02
normal lung tissue samples


title: normal lung_6229050011_R02C01

description:
6229050011_R02C01
normal lung tissue samples


title: normal lung_6229050013_R04C02

description:
6229050013_R04C02
normal lung tissue samples


title: normal lung_6229050059_R05C02

description:
6229050059_R05C02
normal lung tissue samples


title: MTB at T60, biological rep2

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 60 min


title: normal lung_6229050011_R04C02

description:
6229050011_R04C02
normal lung tissue samples


title: normal lung_6229050011_R02C02

description:
6229050011_R02C02
normal lung tissue samples


title: MTB at T60, biological rep1

source_name: Mycobacterium tuberculosis treated with bedaquiline and harvested after 60 min


title: normal lung_6229050059_R03C01

description:
6229050059_R03C01
normal lung tissue samples


title: MTB at T30, biological rep3

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 30 min


title: normal lung_6229050013_R04C01

description:
6229050013_R04C01
normal lung tissue samples

value: female


title: normal lung_6229050062_R01C02

description:
6229050062_R01C02
normal lung tissue samples


title: normal lung_6229050062_R05C01

description:
6229050062_R05C01
normal lung tissue samples


title: normal lung_6229050059_R02C02

description:
6229050059_R02C02
normal lung tissue samples


title: normal lung_6229050046_R02C01

description:
6229050046_R02C01
normal lung tissue samples


title: normal lung_6229050046_R06C01

description:
6229050046_R06C01
normal lung tissue samples


title: MTB at T180, biological rep1

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 180 min


title: MTB at T30, biological rep2

source_name: Mycobacterium tuberculosis treated with bedaquiline and harvested after 30 min


title: MTB at T30, biological rep1


title: MTB at T0, biological rep3

description: Gene expression data from Mycobacterium tuberculosis at T0

source_name: Mycobacterium tuberculosis at T0


title: MTB at T0, biological rep4


title: MTB at T180, biological rep2


title: normal lung_6229050011_R06C02

description:
6229050011_R06C02
normal lung tissue samples


title: MTB at T0, biological rep2


title: normal lung_6229050013_R06C02

description:
6229050013_R06C02
normal lung tissue samples


title: High density-2

tag: cell type


title: WT vs fpk1/2∆∆

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

institute: Kyoto Univ. Sch. of Medicine

description: Effect of fpk1/2∆ was monitored at transcriptome lebel to understand ISP-1 resistance and elevated LCB expression without ISP-1, phenotypes detected in fpk1/2∆ strain

hyb_protocol: Competitive hybridization was performed on the microarray (DNA CHIP RESEARCH INC, Yeast Chip Ver2). Supplier's condition was followed for hybridization and washing. In short, array was hybridized with 5xSSC-0.5% SDS at 65˚C for overnight and washed with 0.2xSSC-0.1% SDS at 55˚C.

scan_protocol: Data was obtained using an Affymetrix 428 array scanner. Scaning speed was of 0.5mm/sec.

data_processing:
Raw data from each channel was evaluated by signal strength and spots giving reliable strength was collected. Median of each channel was used to compensate the difference. We used 428 Arrayscanner software version 1.1.0.100 by affymetrix to scan array. We used ImaGene version 4.0 (BioDiscovery) to quantify the signal strength of each spots. We used microsoft Excel 2004 for Mac for further calculation.
Difference in the expression each gene was expressed as fold difference against WT cells.

source_name: WT cells (log-phase) in SD medium

label_protocol: One μg of polyA+ RNA from these cells were  labeled using a CyScribe first-strand cDNA labeling kit (Amersham) where WT and fpk1/2∆ cells were labeled with Cy5 and Cy3, respectively.

growth_protocol: Overnight cultured yeast cells were diluted with pre-warm SD medium to achive logarithmic growth

extract_protocol: Total RNA was purified with hot-phenol method and mRNA was enriched with mTRAP mRNA isolation kit. Quality of mRNA was confirmed with Bioanalyzer2100 thus RNA quality of these two samples were reliable.

value: BY4741 cells with HIS3

source_name: fpk1/2∆ cells (log-phase) in SD medium


title: MTB at T0, biological rep1

tag: agent


title: MTB at T360, biological rep1

description: Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 360 min


title: normal lung_6229050059_R03C02

description:
6229050059_R03C02
normal lung tissue samples


title: normal lung_6229050003_R02C01

description:
6229050003_R02C01
normal lung tissue samples


title: Lesion_CL_40_CP73_1879

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

department: Department of Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

data_processing: Affymetrix CEL files were processed and normalized (across all samples) using the RMA algorithm from the 'affy' package in Bioconductor 2.13

label: Biotin

source_name: Drd1a dSPNs, hemi-parkinsonian condition (6-OHDA), Chronic low levodopa

growth_protocol: Mice were housed with food and water provided ad libitum. Experiments were conducted with Drd1::EGFP-L10a or Drd2::EGFP-L10a BAC transgenic, adult (9-14 weeks) male mice of the C57BL/6J strain background.

extract_protocol: Immediately following the last session of behavioral testing, mice were sacrificed by decapitation and the dorsal striatum ipsilateral to the lesion of each mouse was manually dissected for TRAP purification of mRNA. As noted above, to equalize the effects of stress and handling across all groups, including control groups, all mice were equally handled and thus received saline injections when not receiving levodopa injections. TRAP purifications were carried out as described in (Heiman, 2008), with the following modifications: purifications were conducted from single animal tissue; the affinity matrix consisted of anti-GFP monoclonal antibodies 19F7 and 19C8 (Memorial Sloan-Kettering Monoclonal Antibody Facility, New York, NY) bound to biotinylated Protein L (Thermo Scientific, Rockford IL)-coated Streptavidin MyOne T1 Dynabeads (Invitrogen, Carlsbad CA); affinity matrix was bound to clarified tissue lysate for 16-18 hours; TRAP-purified RNA was loaded directly onto Absolutely RNA Nanoprep Kit purification columns (Agilent Technologies, Santa Clara CA) and purified with on-column DNase digestion.

treatment_protocol: A hemi-parkinsonian condition was induced in mice by unilateral injection of 6-OHDA in the right medial forebrain bundle (MFB). Animals were anesthetized with a mixture of ketamine (Putney Inc., Portland, ME) and xylazine (Lloyd Inc., Shenandoah, IA) and mounted on a Kopf stereotaxic frame in a flat-skull position. 6-Hydroxydopamine (6- OHDA) hydrochloride (Sigma Chemical Co., St. Louis, MO) was dissolved at a concentration of 3.2 μg/μl free-base in 0.02% ice-cold ascorbate/saline and used within 2 hrs. One microliter of this solution was injected at the following coordinates (in mm relative to bregma, sagittal suture and dural surface): AP= -1.2, L= -1.3, DV= -4.75. Two weeks after the lesions, mice were evaluated with tests of spontaneous ipsilateral turning behavior and limb use asymmetry (cylinder test) in order to select animals with successful lesions (1). For TRAP studies of the effect of dopamine depletion alone, we compared animals that received an MFB lesion to animals that received a mock lesion (ascorbate/saline alone injected). Both of these groups went on to receive chronic saline  injections, so that the MFB group could also be used as a comparison group for those additional MFB-lesioned mice that received chronic levodopa injections.    L-DOPA methyl ester and the peripheral DOPA decarboxylase inhibitor benserazide- hydrochloride (Sigma Chemical Co., St. Louis, MO) were dissolved in physiological saline immediately prior to use. The drugs were injected at the volume of 0.1 ml/10 g body weight in a single intraperitoneal (i.p.) injection per day. Benserazide was always administered at a fixed dose (12 mg/kg per injection). Three weeks after lesion surgery,  mice with successful lesions were randomly allocated to receive treatment with ‘high- dose L-DOPA’, ‘low-dose L-DOPA’, or saline. The ‘high-dose’ L-DOPA regimen (3 mg/kg on days 1-3, followed by 6 mg/kg on days 4-9) was expected to induce severe dyskinesia in all MFB-lesioned mice (1, 3). The low-dose L-DOPA regimen (1 mg/kg on days 1-3, followed by 2 mg/kg on days 4-9) was expected to reverse limb use asymmetry without causing conspicuous dyskinesias. To equalize the effects of stress and handling across all groups, including control groups, all mice were equally handled and thus received saline injections when not receiving levodopa injections. Abnormal involuntary movements (AIMs) were rated using a validated scale, as previously described (1). Each mouse was observed individually for 1 min every 20 min for 3 hr, starting 20 min after L- DOPA/benserazide (or saline) administration. Only hyperkinetic and dystonic movements that could be clearly distinguished from naturally occurring behaviors (i.e. grooming, sniffing, rearing and gnawing) were considered in the ratings. The AIMs were classified into three subtypes: (i) axial AIMs, i.e. twisting of the neck and upper body towards the side contralateral to the lesion; (ii.) orolingual AIMs, i.e. jaw movements and contralateral tongue protrusion; (iii) forelimb AIMs, i.e. fluttering movements of the forelimb. Each AIMs subtype was rated on a severity scale from 0 to 4 (0, absent; 1, present during less than 50% of the observation time; 2, present during more than 50% of the observation time; 3, present all the time but suppressible by light visual-auditory stimuli; 4, continuous, severe and not suppressible).

value: spiny projection neurons

tag: lesion

tag: trap line

tag: drug treatment

value: Chronic low levodopa

tag: genetic background


title: normal lung_6229050003_R05C01

description:
6229050003_R05C01
normal lung tissue samples


title: Lesion_CH_24_CP73_1841

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

source_name: Drd1a dSPNs, hemi-parkinsonian condition (6-OHDA), Chronic high levodopa

value: Chronic high levodopa


title: Lesion_CH_23_CP73_1836

label_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.


title: Lesion_CL_37_CP73_1834


title: Lesion_CS_10_CP73_1833

source_name: Drd1a dSPNs, hemi-parkinsonian condition (6-OHDA), Chronic saline

value: Chronic saline


title: Lesion_CH_25_CP73_1876


title: Lesion_CH_21_CP73_1804


title: Lesion_CH_22_CP73_1832


title: Lesion_CL_38_CP73_1839


title: normal lung_6229050003_R01C02

description:
6229050003_R01C02
normal lung tissue samples

value: male


title: normal lung_6229050003_R05C02

description:
6229050003_R05C02
normal lung tissue samples


title: Lesion_CS_20_CP73_1767


title: Lesion_CL_36_CP73_1825


title: Lesion_CL_35_CP73_1784


title: normal lung_6229050002_R02C01

description:
6229050002_R02C01
normal lung tissue samples


title: normal lung_6229050013_R02C02

description:
6229050013_R02C02
normal lung tissue samples


title: normal lung_6229050034_R02C02

description:
6229050034_R02C02
normal lung tissue samples


title: Lesion_CH_34_CP73_1721


title: normal lung_6229050002_R02C02

description:
6229050002_R02C02
normal lung tissue samples


title: Lesion_CH_18_CP73_1665


title: Lesion_CS_7_CP73_1647


title: Lesion_CL_45_CP73_1655


title: Lesion_CL_33_CP73_1718


title: Lesion_CS_19_CP73_1755


title: Lesion_CS_9_CP73_1663


title: Asc_CS_6_CP73_1635

source_name: Drd1a dSPNs, mock lesion (Ascorbate), Chronic saline

value: Ascorbate


title: Lesion_CL_32_CP73_1710


title: Asc_CS_31_CP73_1642


title: Asc_CS_43_CP73_1631


title: normal lung_6229050034_R06C02

description:
6229050034_R06C02
normal lung tissue samples


title: normal lung_6229050034_R06C01

description:
6229050034_R06C01
normal lung tissue samples


title: Lesion_CS_17_CP73_1627


title: Lesion_CH_39_CP73_1857


title: normal lung_6229050002_R04C01

description:
6229050002_R04C01
normal lung tissue samples


title: Asc_CS_44_CP73_1634


title: Lesion_CL_30_CP73_1628


title: Asc_CS_29_CP73_1601


title: normal lung_6229050002_R06C02

description:
6229050002_R06C02
normal lung tissue samples


title: normal lung_6229050034_R02C01

description:
6229050034_R02C01
normal lung tissue samples


title: Asc_CS_41_CP73_1572


title: Lesion_CS_15_CP73_1578


title: Lesion_CH_16_CP73_1579


title: normal lung_6229050034_R04C01

description:
6229050034_R04C01
normal lung tissue samples


title: normal lung_6229050002_R04C02

description:
6229050002_R04C02
normal lung tissue samples


title: Lesion_CL_26_CP73_1535


title: Asc_CS_3_CP73_1570


title: normal lung_6229050052_R04C01

description:
6229050052_R04C01
normal lung tissue samples


title: Asc_CS_4_CP73_1598


title: Lesion_CL_28_CP73_1582


title: Lesion_CS_2_CP73_1562


title: normal lung_6229050002_R06C01

description:
6229050002_R06C01
normal lung tissue samples


title: Lesion_CS_13_CP73_1533


title: Lesion_CL_27_CP73_1561


title: Lesion_CS_12_CP73_1517


title: normal lung_6229050034_R04C02

description:
6229050034_R04C02
normal lung tissue samples


title: Asc_CS_5_CP73_1599


title: normal lung_6229050052_R02C02

description:
6229050052_R02C02
normal lung tissue samples


title: Lesion_CS_1_CP73_1513


title: normal lung_6229050064_R02C01

description:
6229050064_R02C01
normal lung tissue samples


title: Asc_CS_42_CP73_1600


title: Lesion_CH_67_CP101_1597

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic high levodopa


title: Lesion_CS_79_CP101_1615

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic saline


title: Lesion_CS_77_CP101_1505


title: normal lung_6229050064_R06C02

description:
6229050064_R06C02
normal lung tissue samples

source_name: EAGLE_population-based study of lung cancer


title: Lesion_CL_78_CP101_1577

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic low levodopa


title: normal lung_6229050053_R01C01

description:
6229050053_R01C01
normal lung tissue samples


title: Lesion_CH_14_CP73_1542


title: Lesion_CS_55_CP101_1483


title: Lesion_CS_65_CP101_1437


title: Lesion_CL_73_CP101_1436


title: Lesion_CL_76_CP101_1446


title: Lesion_CH_66_CP101_1557


title: Lesion_CL_74_CP101_1438


title: normal lung_6229050052_R06C02

description:
6229050052_R06C02
normal lung tissue samples


title: normal lung_6229050053_R05C01

description:
6229050053_R05C01
normal lung tissue samples


title: Lesion_CS_75_CP101_1439


title: normal lung_6229050064_R06C01

description:
6229050064_R06C01
normal lung tissue samples


title: Lesion_CS_64_CP101_1434


title: normal lung_6229050053_R06C02

description:
6229050053_R06C02
normal lung tissue samples


title: Lesion_CH_63_CP101_1428


title: Lesion_CH_11_CP73_1511


title: back muscle, control, P2 rep3

city: Baltimore

first: Saniya

last: Fayzullina

state: MD

address: 720 Rutland Avenue Ross Bldg., Room 558

department: Pathology

institute: Johns Hopkins School of Medicine

description: Control

data_processing:
Back muscle RNA samples from 3 mice (3 biological replicates) were assayed per group. One full RT-PCR array plate was run for each mouse sample. Raw ΔCt values for all genes of interest were normalized to Gapdh ΔCt. Other housekeeping genes were included in the array, but Gapdh resulted in the most consistent expression levels between mice and between groups, and Gapdh protein expression had been previously validated on samples from the same mice by Western blot. Array results were analyzed using an SABiosciences custom Microsoft Excel spreadsheet to calculate fold change (2^(-ΔCt)) and p values.
Matrix non-normalized worksheet - raw Ct values
Fold Change worksheet - Average Normalized ΔCt test/ Average Normalized ΔCt control

label: SYBR green

source_name: back muscle, control, P2

label_protocol: cDNA was synthesized using the RT2 First Strand kit (Qiagen). RNA quality was assessed by microarray on the Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RIN) between 9 and 10. Gene array plates were purchased from Qiagen (SABiosciences array PAMM-029ZD-12, “DNA Damage Signaling Pathway”). Biorad CFX-96 bioanalyzer was used to run quantitative PCR reactions with RT2 SYBR Green qPCR mastermix (Qiagen). All kits were used according to manufacturer instructions. Arrays included positive reverse transcription controls, positive qPCR controls, and genomic DNA contamination controls. All control results were valid within manufacturer specifications.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) from frozen mouse back muscles collected at P2.

value: FVB.Cg-Smn1tm1Hung Tg(SMN2)2Hung/J

tag: jax number

tag: developmental stage

value: postnatal day 2

tag: tissue

value: back skeletal muscle


title: back muscle, control, P2 rep2

description: Control

tag: strain


title: back muscle, control, P2 rep1

description: Control


title: back muscle, SMA, P2 rep3

description: test

source_name: back muscle, SMA, P2


title: back muscle, SMA, P2 rep2

description: test


title: Lesion_CH_62_CP101_1423

tag: genotype


title: normal lung_6229050053_R01C02

description:
6229050053_R01C02
normal lung tissue samples

tag: gender


title: normal lung_6229050041_R04C01

description:
6229050041_R04C01
normal lung tissue samples

tag: sample type


title: Asc_CS_54_CP101_1386

source_name: Drd2 iSPNs, mock lesion (Ascorbate), Chronic saline


title: normal lung_6229050052_R04C02

description:
6229050052_R04C02
normal lung tissue samples

tag: disease state


title: normal lung_6229050041_R04C02

description:
6229050041_R04C02
normal lung tissue samples


title: Asc_CS_52_CP101_1382


title: normal lung_6229050064_R04C02

description:
6229050064_R04C02
normal lung tissue samples


title: back muscle, SMA, P2 rep1

description: test


title: Asc_CS_53_CP101_1383


title: Asc_CS_61_CP101_1380


title: normal lung_6229050054_R06C02

description:
6229050054_R06C02
normal lung tissue samples


title: normal lung_6229050041_R02C01

description:
6229050041_R02C01
normal lung tissue samples


title: Asc_CS_51_CP101_1378


title: normal lung_6229050041_R06C01

description:
6229050041_R06C01
normal lung tissue samples


title: Δ2099 late stationary phase

city: Seattle

first: Elisabeth

last: Wurtmann

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Normalized log10 intensity of X_INT/Y_INT (sample/reference) averaged over dye flip between sample and reference RNA.

hyb_protocol: Whole-genome tiling arrays were designed using e-Array (Agilent Technologies) for the H. salinarum NRC-1 main chromosome (NC_002607), and pNRC100 (NC_001869) and pNRC200 (NC_002608) plasmids using a 60k feature design of 60-mer strand-specific probes spaced at 24 bp. Arrays included manufacturer’s control probes and were printed by Agilent Technologies. Hybridization and washing was performed as described (Turkarslan et al 2011), with dye flip experiments performed for each sample. See http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details.

scan_protocol: Arrays were scanned in ScanArray 5000 (Perkin Elmer) using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details.

data_processing:
Spot finding was performed using Feature Extraction (Agilent Technologies). See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
Normalization and statistical analysis were performed as described before (Koide et al, 2009). Values are normalized log10 ratios representing test/reference. Interarray comparisons were normalized relative to a reference RNA sample generated from unperturbed H. salinarum NRC-1 batch culture in rich medium at OD600 0.5-0.6.

label: Cy3, Cy5

organism: Halobacterium salinarum NRC-1

label_protocol: RNAs were direct labeled with Alexa547 and Alexa647 dyes (Kreatech). See Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35.

growth_protocol: The wild type (Dura3) and VNG2099C in-frame deletion strain (D2099) were batch cultured in flasks at 37°C with constant shaking (~220 rpm) in a complex media (CM: 250 g/l NaCl, 20 g/l MgSO4, 2 g/l KCl, 3 g/l sodium citrate, 10 g/l Oxoid brand bacteriological peptone). This standard CM was supplemented with 50mg/l uracil to compensate for the uracil deficiency caused by the Dura3 marker.

extract_protocol: Total RNA was prepared from the cell pellets using the mirVANA RNA kit (Ambion, Austin, TX) according to manufacturer's instructions and then treated with RNase-free DNase (Promega).

treatment_protocol: Culture aliquots (2 ml) were collected over mid-log (OD600: ~0.4), late-log (OD600: ~0.8), early stationary, and late stationary phases of growth (as the carrying capacity differs for the two strains, stationary phase points were determined as occurring after an equivalent proportion of the duration of stationary phase.) Cells were centrifuged (16 000 g, 60 s) and flash frozen.

tag: temperature

tag: od

label: Cy5, Cy3

source_name: Halobacterium salinarum NRC-1 reference sample

value: wild type


title: Lesion_CL_71_CP101_1343


title: Asc_CS_49_CP101_1310


title: Lesion_CH_59_CP101_1290


title: Asc_CS_50_CP101_1311


title: normal lung_6229050054_R02C02

description:
6229050054_R02C02
normal lung tissue samples


title: Biofilm +C. perfringens vs Mixed Reference 5_rep3

city: San Francisco

first: Emily

middle: Patricia

last: Fox

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

hyb_protocol: 0.4 mg Cy3-labelled cDNA and 0.4 mg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: Scanned on a 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R

organism: Candida albicans

source_name: Biofilm C. albicans +C. perfringens (replicate 3)

label_protocol: cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)

growth_protocol: C. albicans was grown alone or with bacteria, in biofilms or suspension cultures, in Bovine Heart Infusion Media +5% FBS, at 37degC

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: source strain background

source_name: Mixed reference pool#5: cDNA from 252016610086-blocks1 - 6


title: normal lung_6229050053_R03C02

description:
6229050053_R03C02
normal lung tissue samples


title: normal lung_6229050052_R06C01

description:
6229050052_R06C01
normal lung tissue samples


title: Δ2099 late-log phase


title: Lesion_CH_58_CP101_1288

tag: cell type


title: WP1130 treated rep3

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Slides were scanned using Illumina HiScan SQ

data_processing:
The data were extracted with GenomeStudio using Illumina default analysis settings. Data is background corrected and quantile normalized.
MBCB R package was used for background correction and quantile normalization

source_name: VCaP cells

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

growth_protocol: Cells were cultured in DMEM medium with 10% FBS.

extract_protocol: Total RNA was extracted from cells using the RNAeasy (Qiagen) Kit.

treatment_protocol: Cells were transfected with siERG for 72 hours or treated by WP1130 for 24 hours.

tag: treatment

tag: cell line

value: VCaP


title: Δ2099 early stationary phase


title: WP1130 treated rep2


title: normal lung_6229050041_R02C02

description:
6229050041_R02C02
normal lung tissue samples


title: normal lung_6229050064_R04C01

description:
6229050064_R04C01
normal lung tissue samples


title: wild type early stationary phase

source_name: Δura3 knockout at OD600 = 1.2401


title: Δ2099 mid-log phase


title: wild type late-log phase

source_name: Δura3 knockout at OD600 = 0.7986


title: normal lung_6229050054_R04C02

description:
6229050054_R04C02
normal lung tissue samples


title: Biofilm +media vs Mixed Reference 5_rep3

description: Biofilm vs Mixed Reference

source_name: Biofilm C. albicans +unbuffered media (replicate 3)


title: Lesion_CL_72_CP101_1426

tag: lesion

tag: trap line


title: Lesion_CL_70_CP101_1281

tag: drug treatment

tag: genetic background


title: wild type late stationary phase

source_name: Δura3 knockout at OD600 = 1.2614


title: WP1130 treated rep1


title: normal lung_6229050054_R02C01

description:
6229050054_R02C01
normal lung tissue samples


title: Biofilm +media vs Mixed Reference 5_rep2

description: Biofilm vs Mixed Reference

source_name: Biofilm C. albicans +unbuffered media (replicate 2)


title: DMSO treated rep2

value: DMSO


title: Biofilm +C. perfringens vs Biofilm

description: Biofilm +C. perfringens vs Biofilm

source_name: Biofilm C. albicans +C. perfringens (replicate 1)

source_name: Biofilm C. albicans +unbuffered media (replicate 1)


title: Biofilm +B. fragilis vs Biofilm

description: Biofilm +B. fragilis vs Biofilm

source_name: Biofilm C. albicans +B. fragilis (replicate 1)


title: DMSO treated rep3


title: ERG knockdown,siRNA2, rep3

value: ERG siRNA


title: 6 factor lentiviral hiPSC in Conv, rep2

city: San Diego

first: Dave

last: Robbins

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were normalized according to a log-scale robust multi-array analysis (RMA) method in Expression Console (Affymetrix).

source_name: induced pluripotent stem cells, conventional medium

label_protocol: Biotinylated cRNA were prepared using the Message Amp II kit two-round protocol from 100 ng total RNA.

growth_protocol: Pluripotent lines were cultured in FMM, SMC4 or Conventional medium as indicated above and in the manuscript. Cultures were maintained on either feeder cells or matrigel.

extract_protocol: Total RNA was isolated post incubation with the PicoPure RNA Isolation kit.

treatment_protocol: Somatic cells were reprogrammed by either lentiviral- or episomal-induced ectopic expression of various genes including OCT4, NANOG and SOX2. The reprogrammed cells were selected by FACS and directly sorted into 96-well plates. Each clone was expanded in various culture conditions and asessed for pluripotent properties.

value: induced pluripotent stem cells

tag: culture medium

value: conventional


title: Lesion_CL_69_CP101_1272

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic low levodopa


title: Asc_CS_47_CP101_1247


title: Asc_CS_48_CP101_1266


title: 6 factor lentiviral hiPSC in Conv, rep3


title: Lesion_CH_57_CP101_1280

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic high levodopa


title: normal lung_6229050054_R04C01

description:
6229050054_R04C01
normal lung tissue samples

source_name: EAGLE_population-based study of lung cancer

value: DNA from fresh-frozen human lung tissue

value: normal


title: 6 factor lentiviral hiPSC in Conv, rep1


title: DMSO treated rep1


title: ERG knockdown,siRNA2, rep2


title: Asc_CS_46_CP101_1245

source_name: Drd2 iSPNs, mock lesion (Ascorbate), Chronic saline

value: spiny projection neurons


title: Lesion_CH_56_CP101_1205


title: Lesion_CS_68_CP101_1222

source_name: Drd2 iSPNs, hemi-parkinsonian condition (6-OHDA), Chronic saline


title: Biofilm +K. pneumoniae vs Mixed Reference 4

source_name: Biofilm C. albicans +K. pneumoniae (replicate 3)

source_name: Mixed reference pool#4: cDNA from 252016610066-blocks11 - 16


title: 4 factor lentiviral hiPSC in SMC4

source_name: induced pluripotent stem cells, SMC4


title: ERG knockdown,siRNA1, rep3

source_name: VCaP cells


title: ERG knockdown,siRNA1, rep1


title: Biofilm +B. fragilis vs Mixed Reference 5_rep3

description: Biofilm +B. fragilis vs Mixed Reference

source_name: Biofilm C. albicans +B. fragilis (replicate 3)

source_name: Mixed reference pool#5: cDNA from 252016610086-blocks1 - 6


title: wor1∆/∆ (TF176) +media vs Mixed Reference 4

source_name: Biofilm C. albicans wor1∆/∆ (TF176) +media


title: Biofilm +B. fragilis vs Mixed Reference 5_rep2

description: Biofilm +B. fragilis vs Mixed Reference

source_name: Biofilm C. albicans +B. fragilis (replicate 2)


title: 3 factor lentiviral hiPSC in Conv, rep1


title: wor1∆/∆ (TF176) +K. pneumoniae vs Mixed Reference 4

source_name: Biofilm C. albicans wor1∆/∆ (TF176) +K. pneumoniae


title: ERG knockdown,siRNA1, rep2


title: wor1∆/∆ (SN881) +media vs Mixed Reference 4

source_name: Biofilm C. albicans wor1∆/∆ (SN881) +media


title: ERG knockdown,siRNA2, rep1


title: RNA from H1 hESC in Conv


title: mouse cerebellar granule cells wild type 7

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: Haartmaninkatu 8 (PO Box 63)

department: Folkhälsan Institute of Genetics

country: Finland

institute: Folkhälsan Research Center

description:
CGC_WT7.CEL
Gene expression data from wild type mouse cerebellar granule cells.

hyb_protocol: The sample preparation and hybridzation of each cRNAs on Affymetrix GeneChip® Mouse Genome 430 2.0 arrays based on manufacturer's instruction.

scan_protocol: The quality control of each microarray was inspected using the Affymetrix GeneChip® Operating Software (GCOS) v1.4.

data_processing: The raw data were imported to GeneSpring GX software and expression signal values were generated using the RMA (Robust Multiarray Average) algorithm (Irizarry et al., 2003) for background adjustment, quantile-normalization and summarization. Filtering of the probe sets was based on the expression with lower and upper cutoff 20 and 100 percentile, and on the fold-change (FC) with cutoff 1.3. In overall statistics of differentially expressed genes, t-test unpaired equal variance with corrected p-value ≤ 0.05 (cerebella) and p-value ≤ 0.01 (CGCs), with Benjamini and Hochberg multiple testing correction was used.

source_name: WT_cerebellar granule cells at P5+2 DIV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Cstb-/- and wild type mice were grown under standard conditions in animal facilities. Cerebella from P5 pups were dissected and meninges removed in HHGN (1x HBSS, 2.5 mM HEPES, 35 mM glucose, 4 mM NaCO3). Intact cerebella were trypsinated in 10 mg/ml trypsin, 200 U/ml DNase in HHGN for 20 min at RT and triturated in 200 U/ml DNase in BME (Basal Medium Eagle). Cells were cultured in BME, 10% calf serum, 25 mM HCl. After 16-20 h from plating, 10 μM AraC (cytosine 1-β-d-arabinofuranoside) was added to prevent glial proliferation. Cells were harvested at DIV2.

extract_protocol: Total RNA was extracted using the ABI Prism 6100 Nucleic Acid PrepStation and PerfectPure RNA Cultured Cell kit according to the manufacturer’s instructions from cerebella and CGCs, respectively.

treatment_protocol: Mice were anesthetized with CO2 and sacrificed by decapitation. The dissected cerebella were homogenized using Lysing Matrix D tubes and FastPrep® FP120 Instrument with Proteinase K digestion (20 mg/ml, >30U/mg) according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: P5+2 DIV

tag: tissue

value: cerebellar granule cells


title: 3 factor lentiviral hiPSC in Conv, rep2

source_name: induced pluripotent stem cells, conventional medium


title: mouse cerebellar granule cells wild type 8

description:
CGC_WT8.CEL
Gene expression data from wild type mouse cerebellar granule cells.

tag: gender

value: female


title: RNA from HUES9 hESC in Conv


title: normal lung_6229050053_R03C01

description:
6229050053_R03C01
normal lung tissue samples

value: male

tag: sample type

tag: disease state


title: 3 factor lentiviral hiPSC in SMC4


title: normal lung_6229050064_R02C02

description:
6229050064_R02C02
normal lung tissue samples


title: Non-targeted rep3

value: non-targeted siRNA


title: mouse cerebellar granule cells wild type 5

description:
CGC_WT5.CEL
Gene expression data from wild type mouse cerebellar granule cells.


title: Biofilm +media vs Mixed Reference 4

description: Biofilm +media vs Mixed Reference

source_name: Biofilm C. albicans +media (replicate 3)

tag: strain


title: normal lung_6229050052_R02C01

description:
6229050052_R02C01
normal lung tissue samples


title: 6 factor lentiviral hiPSC adapted from Conv to SMC4, rep2


title: wor1∆/∆ (SN881) +K. pneumoniae vs Mixed Reference 4

source_name: Biofilm C. albicans wor1∆/∆ (SN881) +K. pneumoniae

tag: source strain background


title: mouse cerebellar granule cells wild type 4

description:
CGC_WT4.CEL
Gene expression data from wild type mouse cerebellar granule cells.


title: Biofilm +5mM GlcNAc vs Mixed Reference 3

description: Biofilm +5mM GlcNAc vs Mixed Reference

source_name: Biofilm C. albicans +5mM GlcNAc

source_name: Mixed reference pool#3: cDNA from 252016610064-blocks13 - 16


title: Non-targeted rep1


title: Biofilm +1mM GlcNAc vs Mixed Reference 3

description: Biofilm +1mM GlcNAc vs Mixed Reference

source_name: Biofilm C. albicans +1mM GlcNAc


title: Non-targeted rep2


title: mouse cerebellar granule cells knockout 3

description:
CGC_KO3.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellar granule cells.

source_name: CSTB KO_cerebellar granule cells at P5+2 DIV

value: cystatin B (CSTB)-deficient (Cstb-/-)


title: Episomal hiPSC adapted from FMM to Conv

tag: cell type


title: Biofilm +E. faecalis vs Mixed Reference 2

description: Biofilm +E. faecalis vs Mixed Reference

source_name: Biofilm C. albicans +E. faecalis (replicate 2)

source_name: Mixed reference pool#2: cDNA from 252016610051-blocks1 - 6


title: 6 factor lentiviral hiPSC adapted from Conv to SMC4, rep1

source_name: induced pluripotent stem cells, SMC4


title: Biofilm vs Mixed Reference 3

description: Biofilm vs Mixed Reference

source_name: Biofilm C. albicans


title: Biofilm +10mM GlcNAc vs Mixed Reference 3

description: Biofilm +10mM GlcNAc vs Mixed Reference

source_name: Biofilm C. albicans +10mM GlcNAc


title: mouse cerebellar granule cells knockout 2

description:
CGC_KO2.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellar granule cells.


title: Biofilm +K. pneumoniae vs Mixed Reference 2

source_name: Biofilm C. albicans +K. pneumoniae (replicate 2)


title: Biofilm +C. perfringens vs Mixed Reference 5_rep2

source_name: Biofilm C. albicans +C. perfringens (replicate 2)

source_name: Mixed reference pool#5: cDNA from 252016610086-blocks1 - 6


title: Neural_Crest_Cells_rep3

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

institute: Turku Centre for Biotechnology

description: Total RNA isolated from Neural Crest Cells

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.14.1). It was vst transformed and quantile normalized.

label_protocol: standard as recommended by illumina

extract_protocol: Qiagen's AllPrep DNA/RNA/Protein Mini kit

value: Human embryonic stem cells derived Neural Crest Cells


title: mouse cerebellum at P30 wild type 2

description:
P30 WT2.CEL
Gene expression data from wild type mouse cerebellum.

source_name: WT_cerebellum at P30

value: postnatal day 30 (P30)

value: cerebellum


title: Biofilm +E. coli clinical vs Mixed Reference 2

source_name: Biofilm C. albicans +E. coli clinical isolate (replicate 2)


title: mouse cerebellum at P30 wild type 3

description:
P30 WT3.CEL
Gene expression data from wild type mouse cerebellum.

value: wild type


title: Episomal hiPSC in FMM, rep3

source_name: induced pluripotent stem cells, small molecule medium FMM

value: FMM


title: 3 factor lentiviral hiPSC adapted from Conv to FMM


title: 6 factor lentiviral hiPSC adapted from Conv to FMM


title: mouse cerebellar granule cells knockout 1

description:
CGC_KO1.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellar granule cells.


title: Episomal hiPSC in FMM, rep2


title: mouse cerebellum at P30 wild type 1

description:
P30 WT1.CEL
Gene expression data from wild type mouse cerebellum.


title: Neural_Stem_Cells_rep3

description: Total RNA isolated from Neural Stem Cells

value: Human embryonic stem cells derived Neural Stem Cells


title: Neural_Crest_Cells_derived_under_NOTCH_inhibitor_rep1

description: Total RNA isolated from Neural Crest Cells derived under NOTCH inhibitor

value: Human embryonic stem cells derived Neural Crest Cells differentiated under NOTCH inhibitor