title: PBMC genomic DNA_CFS2

description:
PBMC genomic DNA from CFS subject 2
7985#WG0153568-DNA#A02#G00062

value: CFS subject 2


title: Tumor regresed 6 days 3

status: Public on Aug 12 2014

type: RNA

city: Boston

first: Annie

last: Tremblay

address: 1 Blackfan Circle

department: Hematology/Oncology and Stem Cell program

country: USA

institute: Boston Childrens Hospital

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 6 days (via doxycycline withdrawal)
OFF6_3

hyb_protocol: Samples are hybridized onto arrays for approximately 18 hours in Affymetrix GeneChip Hybridization Oven 640. The arrays are then washed and stained with streptavidin phycoerythrin in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data were analysed using GenePattern with default analysis settings for RMA normalization. The analysis was performed using array files from the Affymetrix package.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: regressed tumor, 6 days

label_protocol: Total RNA undergoes a reverse transcription reaction to generate double-stranded cDNA. The cDNA then undergoes an in-vitro transcription reaction in which biotin-labeled cRNA is created.

growth_protocol: Myf5Cre: R26-LSL-rtTA : Col1a-Teto-hYAP1 S127A mice (on a C57BL/6 background) were induced with doxycycline for 4 weeks and the interstitial muscle cells from hindlimbs were transplanted into gastrocnemius muscle of doxycycline-treated NOD/SCID hosts. Control muscle samples are from hindlimbs of uninduced Myf5Cre: R26-LSL-rtTA : Col1a-Teto-hYAP1 S127A mice.

extract_protocol: Trizol extraction then purification with RNeasy kit according to manufacturer's instructions.

treatment_protocol: Donor mice were induced with doxycycline for 4 weeks and host mice received doxycycline prior to transplant. For tumor regression, doxycycline was removed from the tumor-bearing host mice for the indicated time.

tag: strain/background

tag: genotype

tag: tissue

value: allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells

tag: days of regression

tag: condition


title: prostate cancer sample P461

city: Porto

first: Manuel

middle: R.

last: Teixeira

address: Rua Dr. António Bernardino de Almeida

department: Department of Genetics

country: Portugal

institute: Portuguese Oncology Institute-Porto

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data was pre-processed at the gene level using the RMA approach implemented in Expression Console (Affymetrix; gene-core analysis).

organism: Homo sapiens

source_name: Primary prostate cancer sample

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue samples using TRIzol (Invitrogen by Life Technologies, Carlsbad, CA, U.S.A.)

value: Primary prostate cancer biopsy

tag: ets rearrangement

value: No ETS rearrangement


title: Tumor regresed 6 days 1

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 6 days (via doxycycline withdrawal)
OFF6_1


title: prostate cancer sample P467

value: ERG rearrangement


title: prostate cancer sample P451

value: ETV1 rearrangement


title: Tumor regresed 6 days 2

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 6 days (via doxycycline withdrawal)
OFF6_2


title: Tumor regressed 3 days 3

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 3 days (via doxycycline withdrawal)
OFF3_3

source_name: regressed tumor, 3 days


title: prostate cancer sample P356


title: Tumor regressed 3 days 2

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 3 days (via doxycycline withdrawal)
OFF3_2


title: Patient Visceral fat

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® Human Gene 1.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.5. RMA16 algorithm was used for normalization

source_name: Patient Visceral fat

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion). For cDNA fragmentation and labeling Affymetrix WT Terminal Labeling kit (Affymetrix) was used.

extract_protocol: TriZol reagent (Life Technologies)

value: Visceral fat


title: prostate cancer sample P307


title: Tumor Day0 2

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells
TUM2

source_name: tumor

value: TUM


title: prostate cancer sample P344


title: Tumor regressed 3 days 1

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells and regressed for 3 days (via doxycycline withdrawal)
OFF3_1


title: Patient SQ fat

description: Gene expression data

source_name: Patient SQ fat

value: SQ fat


title: Tumor Day0 3

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells
TUM3


title: PBMC genomic DNA_CFS3

type: genomic

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description:
PBMC genomic DNA from CFS subject 3
7985#WG0153568-DNA#A03#G00055

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.

molecule: genomic DNA

source_name: CFS PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols

tag: gender

value: female

tag: subject id

value: CFS subject 3

tag: disease state

value: Chronic Fatigue Syndrome (CFS)

tag: cell type

value: peripheral blood mononuclear cells (PBMC)


title: PBMC genomic DNA_CFS1

description:
PBMC genomic DNA from CFS subject 1
7985#WG0153568-DNA#A01#G00061

value: CFS subject 1


title: prostate cancer sample P351


title: Carotid atherosclerotic samples 564

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

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 High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Carotid atherosclerotic samples

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

treatment_protocol: Fresh frozen in RNAlater (Ambion)

value: Male

tag: health state

value: Diseased donor

tag: age

value: 71 years


title: Carotid atherosclerotic samples 547

value: Female

value: 62 years


title: Tumor Day0 1

description:
Allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells
TUM1

value: allograft tumor from doxycycline-induced Myf5cre YAP1 S127A donor cells


title: Carotid atherosclerotic samples 427

value: 64 years


title: prostate cancer sample P305

value: Primary prostate cancer biopsy


title: prostate cancer sample P301

value: ERG rearrangement


title: Control muscle 2

description:
Control muscle (hindlimbs)
CTL2

source_name: control muscle (hindlimbs)

value: muscle (hindlimb)

value: CTL


title: Control muscle 3

description:
Control muscle (hindlimbs)
CTL3


title: Carotid atherosclerotic samples 505

value: 68 years


title: PBMC genomic DNA_CFS6

description:
PBMC genomic DNA from CFS subject 6
7985#WG0153568-DNA#A06#G00200

value: female

value: CFS subject 6


title: prostate cancer sample P298


title: prostate cancer sample P300


title: Carotid atherosclerotic samples 490

value: 59 years


title: Carotid atherosclerotic samples 414


title: Carotid atherosclerotic samples 495

value: 75 years


title: Carotid atherosclerotic samples 517

value: 69 years


title: prostate cancer sample P303


title: Control muscle 1

description:
Control muscle (hindlimbs)
CTL1


title: prostate cancer sample P297

value: No ETS rearrangement


title: 344_2_3: CompT_Expo

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

country: France

institute: ANSES

description: MMW exposure (3 h, 60 GHz, 20 mW/cm²) with the heat increase compensated to maintain constant the physiological temperature (CompT_Expo)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary human keratinocytes, pooled and isolated from 3 neonatal foreskin circumcised patients, were maintained as advised by supplier (Invitrogen, Saint-Aubin, France). Briefly, cells were cultured onto collagen IV coated plates (Becton Dikinson Franklin Lakes, NJ), in supplemented Keratinocyte-SFM medium (Gibco, Carlsbad, CA) with antibiotics (Invitrogen, Saint-Aubin, France).

extract_protocol: RNA was prepared using the RNAeasy column purification (Qiagen, Hilden, Germany), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop technology, Cambridge, UK) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the overall RNA integrity numbers (RIN) were between 9.8 and 10.

treatment_protocol: For each exposure experiment, 250 000 cells per well within a 6-well collagen IV plate were used. Keratinocytes were exposed (Expo) and control cells (Sham) were cultured under the same conditions, but the MMW generator switched off. Cells were exposed during 3 hours at 60.4 GHz, with an average IPD of 20 mW/cm². In order to determine the importance of this heating effect on the cellular response, several controls were performed. Firstly, a heat shock control (HSC) was carried out by culturing unexposed cells at the same temperature as that obtained during the MMW exposure (43°C). Secondly, cells were exposed to MMW at the same steady-state temperature as observed in sham control (35°C). The temperature increase was compensated during the exposure by lowering the temperature of the cell incubator (CompT_Expo).

value: Primary culture Keratinocyte


title: 344_2_1: CompT_Expo


title: Carotid atherosclerotic samples 413

value: Male

value: Diseased donor

value: 73 years


title: Carotid atherosclerotic samples 423

value: 58 years


title: Carotid atherosclerotic samples 390

value: Female

value: 72 years


title: prostate cancer sample P456

value: Primary prostate cancer biopsy

value: ETV1 rearrangement


title: Carotid atherosclerotic samples 523


title: prostate cancer sample P294

value: ERG rearrangement


title: prostate cancer sample P291


title: 344_1_4: Sham

description: unexposed condition (Sham)

source_name: Sham


title: 344_1_3: HSC

description: Heat shock control (HSC) to mimicking the heat effect of MMW exposure

source_name: HSC


title: prostate cancer sample P289


title: Carotid atherosclerotic samples 220

value: 66 years


title: Carotid atherosclerotic samples 180

value: 76 years


title: Carotid atherosclerotic samples 172

value: 74 years


title: prostate cancer sample P288


title: prostate cancer sample P276


title: 343_2_4: Expo

description: 60 GHz-exposure at 20 mW/cm2, for 3 h (Expo)

source_name: Expo


title: 343_2_2: Expo


title: prostate cancer sample P281


title: prostate cancer sample P279


title: 343_2_1: Sham

description: unexposed condition (Sham)


title: prostate cancer sample P274


title: 341_2_3: Sham

description: unexposed condition (Sham)


title: 343_2_3: CompT_Expo


title: 344_1_2: HSC


title: prostate cancer sample P272


title: Carotid atherosclerotic samples 154

value: 65 years


title: 341_2_4: Expo


title: 341_2_2: CompT_Expo


title: Carotid atherosclerotic samples 30

value: 67 years


title: prostate cancer sample P263


title: 341_2_1: HSC


title: prostate cancer sample P264


title: prostate cancer sample P265


title: prostate cancer sample P262


title: 341_1_2: Sham

description: unexposed condition (Sham)


title: Aortic tissue 103

source_name: Aortic tissue

value: Healthy

value: 61 years


title: prostate cancer sample P261

value: ETV5 rearrangement


title: 341_1_4: HSC

value: Primary culture Keratinocyte


title: 341_1_1: Expo


title: prostate cancer sample P257

value: No ETS rearrangement


title: Aortic tissue 9

value: Male

value: 78 years


title: Aortic tissue 104

value: Female

value: 71 years


title: Carotid atherosclerotic samples 344

value: Diseased donor


title: Aortic tissue 5

value: 54 years


title: Aortic tissue 101

value: 45 years


title: prostate cancer sample P249

value: Primary prostate cancer biopsy

value: ERG rearrangement


title: Aortic tissue 102


title: prostate cancer sample P245


title: prostate cancer sample P268


title: prostate cancer sample P242


title: Aortic tissue 100

value: 73 years


title: prostate cancer sample P238


title: prostate cancer sample P241


title: Aortic tissue 99

value: 65 years


title: Aortic tissue 6

value: 46 years


title: prostate cancer sample P251


title: prostate cancer sample P230


title: prostate cancer sample P229


title: Aortic tissue 95

value: Healthy

value: 69 years


title: prostate cancer sample P228


title: Aortic tissue 93

value: 88 years


title: prostate cancer sample P209


title: Aortic tissue 96


title: prostate cancer sample P223


title: prostate cancer sample P227


title: Aortic tissue 97


title: Atherosclerotic lesion 9

source_name: Atherosclerotic lesion


title: Atherosclerotic lesion 102


title: Atherosclerotic lesion 6


title: soPS6

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
1 of 1 samples
6071838135
G

hyb_protocol: Hybridization according to Illumina protocols on Illumina HumanHT-12 v4 Expression BeadChip (GPL14951). Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal. Background was subtracted.

source_name: somatic cell genome and oocyte genome containing nuclear transfer pluripotent stem cell, cell line 6

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit.

growth_protocol: Pluripotent stem cells were grown on a mouse embryonic fibroblast feeder layer and grown in medium containing knockout serum replacement (Life Technologies)

extract_protocol: Qiagen Rneasy Plus Mini kit

treatment_protocol: human pluripotent stem cells were grown under standard conditions prior to RNA isolation

tag: Stage

value: embryonic


title: Aortic tissue 98

value: 55 years


title: soPS3

description:
1 of 1 samples
6004838015
I

source_name: somatic cell genome and oocyte genome containing nuclear transfer pluripotent stem cell, cell line 3


title: soPS5

description:
1 of 1 samples
6004838015
H

source_name: somatic cell genome and oocyte genome containing nuclear transfer pluripotent stem cell, cell line 5


title: Atherosclerotic lesion 7

value: Male

value: 72 years


title: Atherosclerotic lesion 5

value: Female


title: Carotid atherosclerotic samples 219

value: 67 years


title: Atherosclerotic lesion 99

value: Diseased donor


title: soPS4

description:
1 of 1 samples
6004838015
F

source_name: somatic cell genome and oocyte genome containing nuclear transfer pluripotent stem cell, cell line 4


title: T21

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description: Sample 1

hyb_protocol: Hybridization was performed according to manufactorers intructions

scan_protocol: Slides were scanned with the Agilent DAN microarray scanner (Model 2505B)

data_processing: NimbleScan 2.6

source_name: Mouse DNA from SCLC

label_protocol: Labeling was performed with 250ng of input DNA according to manufactorers intructions

extract_protocol: Genomic DNA was extracted with the DNeasy blood and tissue kit (Qiagen) according to manufacturer's instructions

tag: tumor type

value: SCLC

source_name: Mouse DNA from spleen

value: Reference from spleen


title: T24

description: Sample 4


title: T22

description: Sample 2


title: prostate cancer sample P254

source_name: Primary prostate cancer sample

value: Primary prostate cancer biopsy


title: Leaf of mild chlorosis 2

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

country: Japan

institute: Kobe University

description: Gene expression in 3-week-old seedling leaves.

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: leaf, hexaploid wheat hybrid, mild chlorosis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 23°C for 3 weeks.

extract_protocol: Total RNA was extracted from the leaf tissues of WT and chlorosis lines, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

treatment_protocol: No treatment.

value: first leaf

tag: phenotype

value: mild hybrid chlorosis

value: 3 weeks


title: Atherosclerotic lesion 101

value: 45 years


title: Leaf of severe chlorosis 2

source_name: leaf, hexaploid wheat hybrid, severe chlorosis

value: severe hybrid chlorosis


title: BREAST CANCER 69

status: Public on Aug 11 2014

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

institute: VHIO

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized using 5 HK genes.  Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: Tumor

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol

extract_protocol: Total RNA was isolated from macrodissected FFPE tissue using ROCHE High Pure FFPE Kit

tag: treatment

tag: tumor size

tag: nodal stage

value: Basal

tag: miller-payne response

tag: ki67 ihc


title: Atherosclerotic lesion 97

value: 69 years


title: Leaf of severe chlorosis 1

tag: tissue


title: Aortic tissue 7

value: Healthy


title: BREAST CANCER 68


title: Atherosclerotic lesion 96

value: 71 years


title: Atherosclerotic lesion 100

value: Male

value: 73 years


title: BREAST CANCER 67


title: BREAST CANCER 65

value: CARBOPLATIN

value: Claudin


title: Leaf of wild type 2

source_name: leaf, hexaploid wheat hybrid, wild type

value: wild type


title: BREAST CANCER 64

value: Normal


title: BREAST CANCER 63


title: soPS7

description:
1 of 1 samples
6004838015
J

source_name: somatic cell genome and oocyte genome containing nuclear transfer pluripotent stem cell, cell line 7

value: embryonic


title: Leaf of wild type 1


title: Atherosclerotic lesion 95

value: Female

value: Diseased donor


title: BREAST CANCER 62


title: T23

description: Sample 3

value: SCLC

value: Reference from spleen


title: Atherosclerotic lesion 98

value: 55 years


title: Atherosclerotic lesion 93

value: 88 years


title: BREAST CANCER 57

value: Basal


title: BREAST CANCER 55


title: BREAST CANCER 60


title: BREAST CANCER 49


title: BREAST CANCER 58


title: BREAST CANCER 59


title: BREAST CANCER 46


title: BREAST CANCER 56


title: BREAST CANCER 53


title: BREAST CANCER 52


title: BREAST CANCER 50


title: BREAST CANCER 61


title: T103Cell lines from human melanoma grown in PDX

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL files were processed with the R-package CRLMM as available through bioconductor. HapMap samples as provided by Affymetrix were used as reference.

label: Biotin

source_name: Melanoma cell line 6

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

value: melanoma cell line

tag: origin

value: PDX derived


title: BREAST CANCER 54


title: BREAST CANCER 48


title: BREAST CANCER 44


title: BREAST CANCER 45


title: Atherosclerotic lesion 103

value: 61 years


title: BREAST CANCER 43


title: BREAST CANCER 42


title: BREAST CANCER 40


title: BREAST CANCER 41


title: BREAST CANCER 39


title: BREAST CANCER 36


title: BREAST CANCER 37


title: BREAST CANCER 32


title: BREAST CANCER 34


title: BREAST CANCER 33


title: BREAST CANCER 31


title: BREAST CANCER 29


title: BREAST CANCER 30


title: BREAST CANCER 28


title: BREAST CANCER 35


title: BREAST CANCER 27


title: T100 Cell lines from human melanoma grown in PDX

source_name: Melanoma cell line 3


title: T99 Cell lines from human melanoma grown in PDX

source_name: Melanoma cell line 2


title: T101 Cell lines from human melanoma grown in PDX

source_name: Melanoma cell line 4


title: BREAST CANCER 38


title: T102 Cell lines from human melanoma grown in PDX

source_name: Melanoma cell line 5


title: BREAST CANCER 47


title: BREAST CANCER 26


title: BREAST CANCER 24


title: BREAST CANCER 25


title: BREAST CANCER 23


title: BREAST CANCER 22


title: BREAST CANCER 20


title: BREAST CANCER 19


title: BREAST CANCER 21


title: Leaf of mild chlorosis 1

value: first leaf

value: mild hybrid chlorosis

value: 3 weeks


title: Index patient 2

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

description: rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The background was subtracted and the data was quantile normalized using Illumina genome studio software version 2010.3. The negative values indicate that the observed signal intensity of the probe is not above background.
Quantile normalized average signal intensity values across the samples and the intensity values were averaged across 4 biological replicates for Normal adult Control

source_name: Skin

label_protocol: Illumina array HumanHT-12 v4.0 Expression BeadChip kit used according to the maufacturers instructions.

extract_protocol: RNA was extracted using the Ambion mirVana miRNA Isolation kit in accordance with the manufacturers instructions. Quality control was performed with an Agilent Bioanalyser.

tag: developmental stage

value: child

value: ectodermal dysplasia features associated with hearing loss in GRHL2

value: skin


title: BREAST CANCER 66

value: CARBOPLATIN


title: BREAST CANCER 16


title: BREAST CANCER 18


title: BREAST CANCER 17


title: BREAST CANCER 51


title: Breast.Tumour.IDC.3mLet.patient350

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

hyb_protocol: Labelled cDNA was hybridised to Human HT-12v4 whole-genome expression beadarrays (Illumina) according to the standard protocol for NuGEN amplified samples. Approximately half of the samples analysed were processed on Affymetrix GeneChips within a previous study (GSE20181).

scan_protocol: Scanning was performed on a Illumina scanner using the manufacturers protocol

data_processing: Illumina probe profiles were quantile normalised using the lumi package

label_protocol: RNA was reverse transcribed and amplified using the WT-Ovation FFPE System Version 2 (NuGEN), purified using the Qiaquick PCR Purification Kit (Qiagen), biotinylated using the IL Encore Biotin Module (NuGEN), purified using minElute Reaction Cleanup Kit (Qiagen) and quantified once again using the Nanodrop 2000c (Thermo Scientific).

growth_protocol: Tumour biopsies were taken with a 14-guage needle before and approximately 2 weeks and 3 months following commencement of continuous letrozole treatment. Samples were snap-frozen in liquid nitrogen and frozen sections taken, stained with haematoxylin and eosin (H&E) and the cellularity and percentage presence of cancerous tissue within each specimen was assessed by a pathologist.

extract_protocol: Biopsies were homogenised and RNA was extracted using the RNeasy Mini Kit with RNAse-free DNAse treatment (Qiagen). RNA quantity and quality was verified on a Bioanalyser 2100 with RNA 6000 Nano Kit (Agilent) and Nanodrop 2000c (Thermo Scientific).

treatment_protocol: Patients were treated within a neoadjuvant protocol in which letrozole (Femara, 2.5mg; Novartis Pharma AG, Basel, Switzerland) was given daily

tag: subject

value: patient 350

value: breat tumor IDC

value: 3 mo endocrine therapy

tag: gender

value: Female

tag: clinical response

value: Responder


title: BREAST CANCER 15


title: Index patient 1

description: rep 1

tag: disease state


title: Breast.Tumour.IDC.3mLet.patient334

value: patient 334


title: Breast.Tumour.IDC.3mLet.patient291

value: patient 291


title: Breast.Tumour.IDC.3mLet.patient322

value: patient 322


title: Atherosclerotic lesion 104

source_name: Atherosclerotic lesion

tag: health state

value: Diseased donor

value: 71 years


title: BREAST CANCER 13

tag: age

value: Basal


title: BREAST CANCER 12


title: BREAST CANCER 14


title: BREAST CANCER 10


title: BREAST CANCER 9

value: Claudin


title: BREAST CANCER 11


title: Breast.Tumour.IDC.3mLet.patient209

value: patient 209


title: BREAST CANCER 8


title: T98 Cell lines from human melanoma grown in PDX

source_name: Melanoma cell line 1

tag: cell type

value: melanoma cell line

value: PDX derived


title: BREAST CANCER 7


title: Breast.Tumour.ILC.3mLet.patient374

value: patient 374

value: breat tumor ILC


title: BREAST CANCER 6

value: CARBOPLATIN


title: Breast.Tumour.ILC.3mLet.patient325

value: patient 325


title: Breast.Tumour.ILC.3mLet.patient309

value: patient 309

value: 3 mo endocrine therapy


title: Breast.Tumour.ILC.3mLet.patient343

value: patient 343

value: Female

value: Responder


title: BREAST CANCER 5


title: Breast.Tumour.ILC.3mLet.patient289

value: patient 289


title: Breast.Tumour.IDC.2wLet.patient334

value: patient 334

value: breat tumor IDC

value: 2 wk endocrine therapy


title: Breast.Tumour.IDC.3mLet.patient200

value: patient 200


title: Breast.Tumour.ILC.3mLet.patient299

value: patient 299


title: Breast.Tumour.IDC.2wLet.patient291

value: patient 291


title: Breast.Tumour.IDC.2wLet.patient209

value: patient 209


title: Breast.Tumour.IDC.2wLet.patient350

value: patient 350


title: Breast.Tumour.IDC.2wLet.patient200


title: Breast.Tumour.ILC.3mLet.patient182

value: patient 182

value: breat tumor ILC


title: BREAST CANCER 4

value: Basal


title: BREAST CANCER 1

value: CARBOPLATIN


title: BREAST CANCER 2


title: BREAST CANCER 3


title: Breast.Tumour.ILC.2wLet.patient343


title: Breast.Tumour.ILC.2wLet.patient374

value: patient 374


title: Breast.Tumour.IDC.PreLet.patient322

value: patient 322

value: pre-treatment


title: Breast.Tumour.ILC.2wLet.patient299

value: Female

value: Responder


title: Breast.Tumour.IDC.PreLet.patient334

value: patient 334


title: Breast.Tumour.ILC.PreLet.patient343

value: patient 343


title: Breast.Tumour.IDC.PreLet.patient350

value: breat tumor IDC


title: Breast.Tumour.IDC.PreLet.patient209


title: Breast.Tumour.ILC.PreLet.patient374


title: Breast.Tumour.ILC.PreLet.patient289

value: patient 289


title: Breast.Tumour.ILC.PreLet.patient309

value: patient 309


title: Normal adult control 2

description: rep 2

data_processing: The background was subtracted and the data was quantile normalized using Illumina genome studio software version 2010.3. The negative values indicate that the observed signal intensity of the probe is not above background. Quantile normalized average signal intensity values across the samples and the intensity values was averaged across 4 biological replicates for Normal adult Control

value: skin

value: healthy control

tag: Stage

value: Adult


title: Breast.Tumour.IDC.PreLet.patient200

value: patient 200


title: Breast.Tumour.IDC.PreLet.patient291

value: patient 291


title: Normal adult control 4

description: rep 4

tag: phenotype


title: Breast.Tumour.ILC.2wLet.patient309

value: breat tumor ILC

tag: treatment

value: 2 wk endocrine therapy


title: Breast.Tumour.ILC.PreLet.patient182

value: patient 182


title: Breast.Tumour.ILC.PreLet.patient325

value: patient 325


title: Colonic EC in CRB mice fed with LFD, biological rep2

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

description: BALB/c germ-free mouse was inoculated orally with CRB and fed LFD for 4 weeks

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

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

data_processing: The data were analyzed with GeneSpring x11.  RMA.

source_name: 12-week-old male BALB/c mouse

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: 8-week-old male BALB/c germ-free mice were inoculated orally with CRB and fed LFD or HFD for 4 weeks.

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

treatment_protocol: The colon was dissected from each mice after 4 weeks and colonic epithelial cells were isolated.

value: low fiber diet

tag: genetic background

value: BALB/c

value: Colonic epithelial cell

tag: genotype

value: WT mouse

value: 12 week

value: M


title: Colonic EC in CRB mice fed with LFD, biological rep1


title: Colonic EC in CRB mice fed with HFD, biological rep1

description: BALB/c germ-free mouse was inoculated orally with CRB and fed HFD for 4 weeks

value: high fiber diet


title: Colonic EC in CRB mice fed with HFD, biological rep2


title: Breast.Tumour.ILC.PreLet.patient299

value: patient 299

value: pre-treatment

value: Female

value: Responder


title: dII_PSS_decayBvdII_Control_1

city: Ithaca

first: Cresten

last: Mansfeldt

address: 220 Hollister Hall

institute: Cornell University

hyb_protocol: For each experiment, Cy5-labeled cdNA from the mixed community mRNA pool was hybridized against an aliquot of common control of Cy3-labeled cdNA from a 3-day starved culture. The hybridization, washing, and scanning of the microarray samples was performed by the Cornell University Microarray Core facility (http://cores.lifesciences.cornell.edu/brcinfo/) and followed the methods outlined by the manufacturer (Agilent Technologies). The general procedure mixed 25 μl (~400 ng) of the labeled cdNA sample with 25 μl 2x Gene Expression (GEx) Hybridization Buffer HI-RPM (5), hybridized the sample to the microarray slide at 65° C for 17 hours, and washed with GEx Wash Buffer 1 and 2 at room and elevated (37° C) temperatures.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505C with a 5 μm resolution.

data_processing: Microarray image analysis was conducted using Agilent feature Extraction 10.5 Image Analysis Software. The feature Extraction Software was also utilized to perform a within array modified LOESS normalization between the Cy5 and Cy3 signals, to calculate a log ratio between the Cy5 and Cy3 channels, and to calculate a modified Student t-test p-value between the Cy5 and Cy3 signal distributions.

organism: Dehalococcoides mccartyi 195

source_name: dII containing dET, continuous fed - - μmol/(L/hr)

label_protocol: The Superscript I dNAse RNA cleanup, amino-allyl cdNA formation, cdNA cleanup, and cdNA labeling with Cy3 or Cy5 followed the method outlined (Waller 2010). The quality and quantity of the RNA was determined using the RNA 6000 Nano assay on an Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of resulting cdNA was determined by using the Quant-IT OliGreen ssdNA Assay Kit (Invitrogen). A common control RNA pool sampled from the main Donna II reactor after 3 days of starvation was labeled with Cy3.

growth_protocol: All subcultures studied in this experiment were 100 mL samples from a maintained 6L mixed community culture (Donna II) previously described (Rahm and Richardson 2006; Rahm and Richardson 2008; Rowe et al. 2009). The culture contains a dET population (near 5×10^8 cells/mL; 60% of total population on per cell basis) mixed with methanogens and organisms that ferment organic substrates.

extract_protocol: 50 mL of liquid culture samples were centrifuged-at 14190×g. The centrifuged sample was split into 8 individual RNA extractions with each sample following the RNeasy Mini Kit (Qiagen) extraction previously outlined (Rahm and Richardson 2008). The 8 distinct RNA extractions were recombined on the spin filter before the first RW1 buffer wash.

treatment_protocol: In brief, 160 mL glass serum bottles were filled with 100 mL of 3-day starved mixed community culture sampled from the main reactor (Donna II). Varying combinations of Pressure Lok syringe volumes (10 mL, 5 mL, 2.5 mL, 500 μL, and 100 μL; VICI Precision Sampling) and concentrations of electron acceptor and donor in media were loaded on a Cole Palmer 74900 Syringe Pump to deliver an expected continuous rate.  Rates of respiration and electron donor feed are given as conditions.

tag: strain

value: strain 195 in the Donna II Mixed Community

tag: feed type

value: continuous

tag: electron acceptor

tag: electron donor

value: endogenous decay

tag: electron acceptor respiration rate (µeeq/(l-hr))

tag: electron donor/electron acceptor ratio on eeq basis

tag: length of experiment (hours)

source_name: dET containing dII, 3 day starved

value: batch

value: PCE

value: butyrate + yeast extract

tag: batch acceptor feed concentration (µeeq/l)


title: dII_PSS_d_INHIB_dCEvdII_Control_3

source_name: dII containing dET, continuous fed dCE 120 μmol/(L/hr)

value: dCE


title: dII_PSS_CpB_CpvdII_Control_1

source_name: dII containing dET, continuous fed dCP 0.56 μmol/(L/hr)

value: dCP


title: dII_PSS_d_INHIB_dCEvdII_Control_2

source_name: dII containing dET, continuous fed dCE 114 μmol/(L/hr)


title: dII_PSS_CpB_CpvdII_Control_2


title: Normal adult control 1

description: rep 1

tag: tissue

value: skin

value: healthy control

value: Adult


title: dII_PSS_decayBvdII_Control_2


title: Colonic EC in re-fed mouse treated with antibiotics, biological rep2

description:
Colonic EC in Refed with antibiotics_2
Gene expression data from colonic epithelial cells from starved and re-fed mouse treated with antibiotics.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were RMA normalized and analyzed with GeneSpring GX11.

source_name: 6-week-old male BALB/c mouse starved and re-fed, antibiotics

growth_protocol: 6-week-old male BALB/c mice were starved for 36 h, and then the mice were started to be re-fed. During the re-feeding, half of the mice were treated with antibiotics. The colon was dissected from each mouse after 24 h re-feeding.

treatment_protocol: EpCAM+CD45- colonic epithelial cells (ECs) were isolated from the starved and re-fed mice treated with or without antibiotics and were sorted by FACS.

value: BALB/c

value: WT

value: colon

value: EpCAM+CD45- epithelial cells

tag: gender

value: male

value: 6 weeks

tag: diet

value: starved for 36h, re-fed for 24h

value: antibiotics


title: dII_PSS_d3B_dCEvdII_Control_1

source_name: dII containing dET, continuous fed dCE 8.9 μmol/(L/hr)

value: strain 195 in the Donna II Mixed Community

value: continuous


title: dII_PSS_CpA_CpvdII_Control_1

source_name: dII containing dET, continuous fed dCP 0.31 μmol/(L/hr)

value: N/d

value: batch

value: PCE


title: Colonic EC in re-fed mouse, biological rep3

description:
Colonic EC in Refed_3
Gene expression data from colonic epithelial cells from starved and re-fed mouse.

source_name: 6-week-old male BALB/c mouse starved and re-fed, untreated

tag: cell type

tag: age


title: dII_PSS_d3A_dCEvdII_Control_1

source_name: dII containing dET, continuous fed dCE 18 μmol/(L/hr)

value: dCE

value: butyrate + yeast extract


title: dII_PSS_d3A_dCEvdII_Control_2

source_name: dII containing dET, continuous fed dCE 32 μmol/(L/hr)


title: dII_PSS_d_INHIB_dCEvdII_Control_1


title: dII_PSS_d3C_dCEvdII_Control_1

source_name: dII containing dET, continuous fed dCE 2.2 μmol/(L/hr)


title: Colonic EC in re-fed mouse, biological rep1

description:
Colonic EC in Refed_1
Gene expression data from colonic epithelial cells from starved and re-fed mouse.


title: Colonic EC in re-fed mouse, biological rep2

description:
Colonic EC in Refed_2
Gene expression data from colonic epithelial cells from starved and re-fed mouse.


title: Colonic EC in re-fed mouse treated with antibiotics, biological rep3

description:
Colonic EC in Refed with antibiotics_3
Gene expression data from colonic epithelial cells from starved and re-fed mouse treated with antibiotics.


title: dII_PSS_decayAvdII_Control_1

value: endogenous decay


title: dII_PSS_d3B_dCEvdII_Control_2

source_name: dII containing dET, continuous fed dCE 8.2 μmol/(L/hr)


title: dII_PSS_T3C_TCEvdII_Control_2

source_name: dII containing dET, continuous fed TCE 1.4 μmol/(L/hr)

value: TCE


title: Colonic EC in re-fed mouse treated with antibiotics, biological rep1

description:
Colonic EC in Refed with antibiotics_1
Gene expression data from colonic epithelial cells from starved and re-fed mouse treated with antibiotics.

value: BALB/c


title: dII_PSS_T3C_TCEvdII_Control_1

source_name: dII containing dET, continuous fed TCE 1.6 μmol/(L/hr)


title: dII_PSS_CpA_CpvdII_Control_2

value: dCP


title: dII_PSS_d3C_dCEvdII_Control_2

source_name: dII containing dET, continuous fed dCE 2.4 μmol/(L/hr)


title: Breast.Tumour.IDC.2wLet.patient322

tag: subject

value: patient 322

value: breat tumor IDC

value: 2 wk endocrine therapy

value: Female

tag: clinical response

value: Responder


title: dII_PSS_T3B_TCEvdII_Control_2

source_name: dII containing dET, continuous fed TCE 7.2 μmol/(L/hr)


title: whole lung, smoke&hypoxia-exposed, rep3

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

institute: University of Liverpool

description: US92200305_254066610008_S01_GE1_107_Sep09_1_3.txt

hyb_protocol: Cy3-labelled cRNA (600 ng/sample) was hybridized at 65C for 16 hours to our custom Cavia porcellus oligonucleotide microarray (manufactured by Agilent) in randomized sample order

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The data were analyzed with R/Bioconductor (v3.0.1), quantile normalized values were obtained with the 'marray' package.

organism: Cavia porcellus

source_name: whole lung_smoke&hypoxia-exposed

label_protocol: One hundred nanograms of total RNA from each sample was amplified and converted into labelled cRNA using Agilent’s Low Input Quick Amp Labelling Kit according to the manufacturer’s recommendations

extract_protocol: Total RNA was extracted using the RNeasy Mini extraction kits (Qiagen, USA) according to the manufacturer’s recommendations

value: Hartley guinea pigs

value: male

tag: condition

value: smoke&hypoxia-exposed

value: whole lung


title: whole lung, smoke&hypoxia-exposed, rep4

description: US92200305_254066610009_S01_GE1_107_Sep09_1_4.txt


title: dII_PSS_T3A_TCEvdII_Control_2

source_name: dII containing dET, continuous fed TCE 23.6 μmol/(L/hr)

value: strain 195 in the Donna II Mixed Community

value: continuous

source_name: dET containing dII, 3 day starved

value: batch


title: dII_PSS_P3A_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 22.8 μmol/(L/hr)

value: PCE

value: butyrate + yeast extract


title: dII_PSS_P3A_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 25.2 μmol/(L/hr)


title: dII_PSS_P3C_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 0.6 μmol/(L/hr)


title: whole lung, smoke-exposed, rep4

description: US92200305_254066610010_S01_GE1_107_Sep09_1_4.txt

source_name: whole lung_smoke-exposed

value: smoke-exposed


title: dII_PSS_P3C_PCEvdII_Control_1


title: whole lung, smoke-exposed, rep2

description: US92200305_254066610008_S01_GE1_107_Sep09_1_2.txt


title: whole lung, smoke&hypoxia-exposed, rep2

description: US92200305_254066610007_S01_GE1_107_Sep09_1_2.txt


title: dII_PSS_P0fYY_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 4.8 μmol/(L/hr)

value: yeast extract


title: dII_PSS_T3A_TCEvdII_Control_1

source_name: dII containing dET, continuous fed TCE 34.4 μmol/(L/hr)

value: TCE


title: dII_PSS_P0fYf_PCEvdII_Control_1

value: fermented yeast extract


title: whole lung, smoke&hypoxia-exposed, rep1

description: US92200305_254066610006_S01_GE1_107_Sep09_1_1.txt


title: dII_PSS_P3B_PCEvdII_Control_2


title: whole lung, sham control, rep3

description: US92200305_254066610007_S01_GE1_107_Sep09_1_3.txt

source_name: whole lung_sham control

value: sham control


title: whole lung, smoke-exposed, rep1

description: US92200305_254066610007_S01_GE1_107_Sep09_1_1.txt


title: whole lung, smoke-exposed, rep3

description: US92200305_254066610009_S01_GE1_107_Sep09_1_3.txt


title: dII_PSS_P3B_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 4.2 μmol/(L/hr)


title: whole lung, sham control, rep4

description: US92200305_254066610008_S01_GE1_107_Sep09_1_4.txt


title: whole lung, hypoxia, rep3

description: US92200305_254066610010_S01_GE1_107_Sep09_1_3.txt

source_name: whole lung_hypoxia

value: hypoxia


title: dII_PSS_P0fY0_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 3 μmol/(L/hr)

value: endogenous decay


title: dII_PSS_H2B_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 8.8 μmol/(L/hr)

value: hydrogen


title: dII_PSS_P0fYf_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 5.4 μmol/(L/hr)


title: dII_PSS_P0fY0_PCEvdII_Control_1


title: whole lung, sham control, rep1

description: US92200305_254066610001_S01_GE1_107_Sep09_1_1.txt

value: Hartley guinea pigs


title: whole lung, hypoxia, rep2

description: US92200305_254066610009_S01_GE1_107_Sep09_1_2.txt

value: male


title: dII_PSS_H2AvdII_Control_2

source_name: dII containing dET, continuous fed - - μmol/(L/hr)


title: dII_PSS_H2B_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 10 μmol/(L/hr)


title: dII_PSS_H2AvdII_Control_1


title: gastrocnemius hindlimb muscle, smoke&hypoxia-exposed, rep3

description: US92200305_254066610006_S01_GE1_107_Sep09_1_3.txt

value: smoke&hypoxia-exposed

value: gastrocnemius hindlimb muscle


title: gastrocnemius hindlimb muscle, smoke&hypoxia-exposed, rep4

description: US92200305_254066610007_S01_GE1_107_Sep09_1_4.txt


title: whole lung, sham control, rep2

description: US92200305_254066610006_S01_GE1_107_Sep09_1_2.txt

value: whole lung


title: dII_PSS_PLL_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 45 μmol/(L/hr)

value: strain 195 in the Donna II Mixed Community

value: continuous

value: lactate + yeast extract


title: dII_PSS_PHB_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 102 μmol/(L/hr)

value: PCE

value: butyrate + yeast extract

value: batch


title: dII_PSS_PHB_PCEvdII_Control_3

source_name: dII containing dET, continuous fed PCE 108 μmol/(L/hr)

source_name: dET containing dII, 3 day starved


title: gastrocnemius hindlimb muscle, smoke-exposed, rep2

description: US92200305_254066610006_S01_GE1_107_Sep09_2_2.txt

value: smoke-exposed


title: dII_PSS_PLB_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 30 μmol/(L/hr)


title: gastrocnemius hindlimb muscle, smoke&hypoxia-exposed, rep1

description: US92200305_254066610010_S01_GE1_107_Sep09_1_1.txt


title: dII_PSS_PHB_PCEvdII_Control_2


title: gastrocnemius hindlimb muscle, smoke-exposed, rep3

description: US92200305_254066610007_S01_GE1_107_Sep09_2_3.txt


title: whole lung, hypoxia, rep1

description: US92200305_254066610008_S01_GE1_107_Sep09_1_1.txt


title: gastrocnemius hindlimb muscle, smoke&hypoxia-exposed, rep2

description: US92200305_254066610001_S01_GE1_107_Sep09_1_2.txt


title: dII_PSS_HLL_PCEvdII_Control_3

source_name: dII containing dET, continuous fed PCE 7.2 μmol/(L/hr)


title: dII_PSS_PLL_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 38 μmol/(L/hr)


title: gastrocnemius hindlimb muscle, smoke-exposed, rep1

description: US92200305_254066610001_S01_GE1_107_Sep09_2_1.txt


title: gastrocnemius hindlimb muscle, sham control, rep3

description: US92200305_254066610001_S01_GE1_107_Sep09_1_3.txt

source_name: gastrocnemius hindlimb muscle_sham control


title: gastrocnemius hindlimb muscle, sham control, rep4

description: US92200305_254066610006_S01_GE1_107_Sep09_1_4.txt


title: dII_PSS_PLB_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 58 μmol/(L/hr)


title: dII_PSS_HLL_PCEvdII_Control_2


title: Normal adult control 3

description: rep 3

source_name: Skin

value: skin

tag: phenotype

value: healthy control

tag: Stage

value: Adult


title: dII_PSS_HLL_PCEvdII_Control_1

tag: strain

tag: feed type


title: dII_PSS_HLH_PCEvdII_Control_INHIB_2

source_name: dII containing dET, continuous fed PCE 504 μmol/(L/hr)

tag: electron acceptor

tag: electron donor


title: gastrocnemius hindlimb muscle, hypoxia, rep3

description: US92200305_254066610008_S01_GE1_107_Sep09_2_3.txt

source_name: gastrocnemius hindlimb muscle_hypoxia

value: hypoxia


title: gastrocnemius hindlimb muscle, hypoxia, rep4

description: US92200305_254066610009_S01_GE1_107_Sep09_2_4.txt


title: dII_PSS_HLH_PCEvdII_Control_INHIB_1

source_name: dII containing dET, continuous fed PCE 456 μmol/(L/hr)

tag: electron acceptor respiration rate (µeeq/(l-hr))

tag: electron donor/electron acceptor ratio on eeq basis


title: soleus hindlimb muscle, smoke&hypoxia-exposed, rep4

description: US92200305_254066610001_S01_GE1_107_Sep09_2_4.txt

value: soleus hindlimb muscle


title: gastrocnemius hindlimb muscle, hypoxia, rep1

description: US92200305_254066610006_S01_GE1_107_Sep09_2_1.txt

value: Hartley guinea pigs


title: gastrocnemius hindlimb muscle, hypoxia, rep2

description: US92200305_254066610007_S01_GE1_107_Sep09_2_2.txt

value: male


title: soleus hindlimb muscle, smoke&hypoxia-exposed, rep2

description: US92200305_254066610009_S01_GE1_107_Sep09_2_2.txt

value: smoke&hypoxia-exposed


title: soleus hindlimb muscle, smoke&hypoxia-exposed, rep3

description: US92200305_254066610010_S01_GE1_107_Sep09_2_3.txt


title: dII_PSS_High_PCEvdII_Control_1

source_name: dII containing dET, continuous fed PCE 258 μmol/(L/hr)

tag: length of experiment (hours)

tag: batch acceptor feed concentration (µeeq/l)


title: gastrocnemius hindlimb muscle, sham control, rep1

description: US92200305_254066610009_S01_GE1_107_Sep09_1_1.txt

tag: gender

value: sham control

tag: tissue

value: gastrocnemius hindlimb muscle


title: Sesb1 mutant female flies biological replicate 4

city: Tampere

first: Suvi

last: Vartiainen

address: Biokatu 6

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

hyb_protocol: Following fragmentation,  cRNA were hybridized on GeneChip Drosophila Genome Array 2.0 in Affymetrix Hybridization oven 645. GeneChips were washed and stained in the Fluidics Station 450.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G with autoloader

data_processing: Genespring GX all genes were normalized and averaged to median

organism: Drosophila melanogaster

source_name: Drosophila whole fly total RNA

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

growth_protocol: at +25 degrees Celsius, virgin females and males separated and grown for 2 days before RNA extraction

treatment_protocol: Mutant versus wild type

tag: genotype/variation

value: Sesb1 mutation

value: female


title: Sesb1 mutant female flies biological replicate 3


title: Spleen and head kidney, 2d after injection of flagellin, biological replicate4

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50 ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, AgilentTechnologies) by the Agilent Feature ExtractionSoftware (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by the Agilent feature extraction

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other  replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

organism: Oncorhynchus mykiss

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Trout fingerlings were maintained at 18-19 ºC in aquaria with tap-dechlorinated carbon-filtered water provided with biological filters and fed with a commercial feed diet in a 50 l aquarium during two weeks

extract_protocol: RNA was extracted using the RNAeasyPlus kit  (Qiagen, Hilden, Germany).

treatment_protocol: Trouts were intraperitoneally injected with 10 µg of flagellin recombinant protein. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at  -70  ºC  until processed. All trouts  were anesthetized by immersion in 50 mg/mL buffered tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling

tag: developmental stage

value: trout fingerlings

tag: size

value: 10 cm

tag: weight

tag: tissues

value: spleen and head kidney

tag: treatment

value: flagellin


title: 3T3_6hA_replicate3

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

country: Germany

institute: Max Planck Institure for Biophysical Chemistry

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6h treatment with anisomycin (188.5 nM) (replicate3)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x GEx Agilent Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse 4x44k expression array (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent GE Wash Buffer 1 and 1 minute with 37°C Agilent GE Wash Buffer 2, followed by drying for 1 min with acetonitril.

scan_protocol: Slides were scanned with Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100617) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Swiss 3T3 fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labelling kit, One-color, according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  cRNA was quantified with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: Swiss 3T3 fibroblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% (vol/vol) fetal calf serum (FCS) in the presence of Penicillin and Streptomycin. The cells were serum-deprived for 72 h using DMEM containing 0.2% FCS (vol/vol).

extract_protocol: RNA was isolated using Trizol (Invitrogen) according to manufacturer'instructures.

treatment_protocol: Serum-straved (72 h) mouse 3T3 fibroblasts we treated with 188.5 nM of anisomycin (Sigma) for 1, 3 and 6h.

tag: cell line

tag: cell type

value: fibroblasts


title: Spleen and head kidney, 2d after injection of PBS, biological replicate3

treatment_protocol: Trouts were intraperitoneally injected with PBS. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at  -70  ºC  until processed. All trouts  were anesthetized by immersion in 50 mg/mL buffered tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling

value: PBS


title: Spleen and head kidney, 2d after injection of PBS, biological replicate1


title: soleus hindlimb muscle, smoke-exposed, rep4

description: US92200305_254066610006_S01_GE1_107_Sep09_2_4.txt

source_name: soleus hindlimb muscle_smoke-exposed

tag: strain

tag: condition

value: smoke-exposed


title: Spleen and head kidney, 2d after injection of flagellin, biological replicate3


title: Spleen and head kidney, 2d after injection of PBS, biological replicate2


title: Sesb1 mutant female flies biological replicate 2


title: dII_PSS_High_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 234 μmol/(L/hr)

value: strain 195 in the Donna II Mixed Community

tag: feed type

value: continuous

tag: electron acceptor

value: PCE

tag: electron donor

value: butyrate + yeast extract

value: batch


title: dII_PSS_High_PCEvdII_Control_3

source_name: dII containing dET, continuous fed PCE 282 μmol/(L/hr)

tag: electron acceptor respiration rate (µeeq/(l-hr))

tag: electron donor/electron acceptor ratio on eeq basis

tag: length of experiment (hours)


title: gastrocnemius hindlimb muscle, sham control, rep2

description: US92200305_254066610010_S01_GE1_107_Sep09_1_2.txt

value: Hartley guinea pigs

tag: gender

value: male

tag: tissue


title: 3T3_6hA_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6h treatment with anisomycin (188.5 nM) (replicate1)


title: Spleen and head kidney, 2d after injection of flagellin, biological replicate2

tag: developmental stage


title: 3T3_6hA_replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6h treatment with anisomycin (188.5 nM) (replicate2)


title: Sesb1 mutant female flies biological replicate 1

tag: genotype/variation


title: soleus hindlimb muscle, smoke&hypoxia-exposed, rep1

description: US92200305_254066610008_S01_GE1_107_Sep09_2_1.txt

value: smoke&hypoxia-exposed

value: soleus hindlimb muscle


title: soleus hindlimb muscle, smoke-exposed, rep3

description: US92200305_254066610001_S01_GE1_107_Sep09_2_3.txt


title: dII_PSS_P0fYY_PCEvdII_Control_2

source_name: dII containing dET, continuous fed PCE 4.8 μmol/(L/hr)

value: yeast extract

tag: batch acceptor feed concentration (µeeq/l)


title: dII_PSS_T3B_TCEvdII_Control_1

source_name: dII containing dET, continuous fed TCE 6.8 μmol/(L/hr)

value: TCE

source_name: dET containing dII, 3 day starved


title: Sesb1 mutant male flies biological replicate 4

value: Sesb1 mutation


title: Sesb1 mutant male flies biological replicate 3


title: soleus hindlimb muscle, smoke-exposed, rep2

description: US92200305_254066610010_S01_GE1_107_Sep09_2_2.txt


title: 3T3_3hA_replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3h treatment with anisomycin (188.5 nM) (replicate2)


title: 3T3_3hA_replicate3

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3h treatment with anisomycin (188.5 nM) (replicate3)


title: Spleen and head kidney, 2d after injection of flagellin, biological replicate1

value: trout fingerlings

tag: size

value: 10 cm

tag: weight

tag: tissues

value: spleen and head kidney


title: Wild type female flies biological replicate 1

value: Wild type

value: female


title: Spleen and head kidney, 2d after injection of poliHis peptide, biological replicate3

hyb_protocol: The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50 ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, AgilentTechnologies) by the Agilent Feature ExtractionSoftware (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by the Agilent feature extraction.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other  replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

treatment_protocol: Trouts were intraperitoneally injected with 10 µg of polihistidine peptide. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at  -70  ºC  until processed. All trouts  were anesthetized by immersion in 50 mg/mL buffered tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

tag: treatment

value: poliHis peptide


title: Wild type female flies biological replicate 3


title: Wild type female flies biological replicate 2


title: 3T3_3hA_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3h treatment with anisomycin (188.5 nM) (replicate1)

tag: cell line

tag: cell type

value: fibroblasts


title: 3T3_1hA_replicate3

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate3)


title: Spleen and head kidney, 2d after injection of poliHis peptide, biological replicate4


title: Sesb1 mutant male flies biological replicate 1


title: soleus hindlimb muscle, smoke-exposed, rep1

description: US92200305_254066610009_S01_GE1_107_Sep09_2_1.txt

tag: strain

tag: condition

value: smoke-exposed


title: soleus hindlimb muscle, hypoxia, rep4

description: US92200305_254066610007_S01_GE1_107_Sep09_2_4.txt

source_name: soleus hindlimb muscle_hypoxia

value: hypoxia


title: Sesb1 mutant male flies biological replicate 2


title: Spleen and head kidney, 2d after injection of NV protein, biological replicate 4

growth_protocol: Trout fingerlings were maintained at 18-19 ºC in aquaria with tap-dechlorinated carbon-filtered water provided with biological filters and fed with a commercial feed diet in a 50 l aquarium during two weeks.

treatment_protocol: Trouts were intraperitoneally injected with 10 µg of NV recombinant protein. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at  -70  ºC  until processed. All trouts  were anesthetized by immersion in 50 mg/mL buffered tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

value: NV protein


title: 3T3_1hA_replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate2)


title: 3T3_1hA_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate1)


title: Spleen and head kidney, 2d after injection of poliHis peptide, biological replicate1

treatment_protocol: Trouts were intraperitoneally injected with 10 µg of polihistidine recombinant protein. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at  -70  ºC  until processed. All trouts  were anesthetized by immersion in 50 mg/mL buffered tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.


title: soleus hindlimb muscle, hypoxia, rep3

description: US92200305_254066610006_S01_GE1_107_Sep09_2_3.txt

value: Hartley guinea pigs


title: soleus hindlimb muscle, sham control, rep3

description: US92200305_254066610009_S01_GE1_107_Sep09_2_3.txt

source_name: soleus hindlimb muscle_sham control

value: male

value: sham control


title: 3T3_control_untreated_replicate3

description: Gene expression after 72h starvation in the medium containing 0.2% FCS (replicate3)


title: Spleen and head kidney, 2d after injection of NV protein, biological replicate3


title: soleus hindlimb muscle, sham control, rep1

description: US92200305_254066610007_S01_GE1_107_Sep09_2_1.txt

value: soleus hindlimb muscle


title: Spleen and head kidney, 2d after injection of poliHis peptide, biological replicate2


title: soleus hindlimb muscle, hypoxia, rep2

description: US92200305_254066610001_S01_GE1_107_Sep09_2_2.txt


title: Wild type male flies biological replicate 1


title: Spleen and head kidney, 2d after injection of NV protein, biological replicate2


title: soleus hindlimb muscle, hypoxia, rep1

description: US92200305_254066610010_S01_GE1_107_Sep09_2_1.txt


title: Wild type male flies biological replicate 3


title: Wild type male flies biological replicate 2


title: EB266_1h

status: Public on Aug 10 2014

city: Jena

last: Kupfer

address: Beutenbergstrasse 11a

institute: HKI Jena

description: SFB from RA treated with IL1

hyb_protocol: At each time point 4 the medium was removed and the cells were harvested after treatment with trypsin (0.25% in Versene; Invitrogen, Karlsruhe, Germany). After washing with phosphate-buffered saline, cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70◦C.

data_processing: The data were RMA normalized.

source_name: Fibroblasts of RA patient

growth_protocol: Negative purification of primary SFBs from RA patients (purity: > 98%) was performed as previously described by Kinne et al

treatment_protocol: At the end of the fourth passage, the SFB were washed in serum-free Dulbeccos modified Eagle’s medium (DMEM) and then stimulated with 10 ng/ml of either IL-1β or PDGF-D

value: PDGF

tag: patient

tag: time point


title: EB268_0h

description: SFB from RA treated with IL1


title: EB261_12h

description: SFB from RA treated with IL1


title: EB268_12h

description: SFB from RA treated with IL1


title: 3T3_control_untreated_replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS (replicate2)


title: 3T3_control_untreated_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS (replicate1)


title: EB266_0h

description: SFB from RA treated with IL1


title: EB268_4h

description: SFB from RA treated with IL1


title: EB266_4h

description: SFB from RA treated with IL1


title: EB266_12h

description: SFB from RA treated with IL1


title: Spleen and head kidney, 2d after injection of NV protein, biological replicate1


title: EB268_1h

description: SFB from RA treated with IL1


title: EB266_2h

description: SFB from RA treated with IL1


title: EB261_4h

description: SFB from RA treated with IL1


title: EB261_1h

description: SFB from RA treated with IL1


title: EB253_4h

description: SFB from RA treated with IL1


title: EB268_2h

description: SFB from RA treated with IL1


title: EB253_2h

description: SFB from RA treated with IL1


title: EB253_12h

description: SFB from RA treated with IL1


title: EB261_2h

description: SFB from RA treated with IL1


title: EB261_0h

description: SFB from RA treated with IL1


title: EB253_1h

description: SFB from RA treated with IL1


title: Spleen and head kidney, 2d after injection of PBS, biological replicate4

value: PBS


title: EB221_4h

description: SFB from RA treated with IL1


title: EB221_1h

description: SFB from RA treated with IL1


title: EB221_12h

description: SFB from RA treated with IL1


title: soleus hindlimb muscle, sham control, rep2

description: US92200305_254066610008_S01_GE1_107_Sep09_2_2.txt


title: EB253_0h

description: SFB from RA treated with IL1


title: RA6_SFbl_2h

description: SFB from RA treated with IL1


title: EB221_0h

description: SFB from RA treated with IL1


title: RA6_SFbl_1h

description: SFB from RA treated with IL1


title: RA6_SFbl_4h

description: SFB from RA treated with IL1


title: EB220_1h

description: SFB from RA treated with IL1


title: RA6_SFbl_0h

description: SFB from RA treated with IL1


title: RA5_SFbl_2h

description: SFB from RA treated with IL1


title: EB221_2h

description: SFB from RA treated with IL1


title: EB220_4h

description: SFB from RA treated with IL1


title: EB220_2h

description: SFB from RA treated with IL1


title: RA4_SFbl_1h

description: SFB from RA treated with IL1


title: RA4_SFbl_2h

description: SFB from RA treated with IL1


title: RA5_SFbl_0h

description: SFB from RA treated with IL1


title: EB220_12h

description: SFB from RA treated with IL1


title: RA4_SFbl_0h

description: SFB from RA treated with IL1


title: RA4_SFbl_4h

description: SFB from RA treated with IL1


title: RA6_SFbl_12h

description: SFB from RA treated with IL1


title: EB220_0h

description: SFB from RA treated with IL1


title: RA3_SFbl_12h

description: SFB from RA treated with IL1


title: RA4_SFbl_12h

description: SFB from RA treated with IL1


title: RA5_SFbl_12h

description: SFB from RA treated with IL1


title: RA3_SFbl_2h

description: SFB from RA treated with IL1


title: RA5_SFbl_1h

description: SFB from RA treated with IL1


title: RA2_SFbl_12h

description: SFB from RA treated with IL1


title: RA3_SFbl_1h

description: SFB from RA treated with IL1


title: RA3_SFbl_4h

description: SFB from RA treated with IL1


title: RA2_SFbl_4h

description: SFB from RA treated with IL1


title: RA2_SFbl_0h

description: SFB from RA treated with IL1


title: RA2_SFbl_1h

description: SFB from RA treated with IL1


title: RA1_SFbl_4h

description: SFB from RA treated with IL1


title: RA2_SFbl_2h

description: SFB from RA treated with IL1


title: RA3_SFbl_0h

description: SFB from RA treated with IL1


title: RA1_SFbl_12h

description: SFB from RA treated with IL1


title: RA1_SFbl_0h

description: SFB from RA treated with IL1


title: RA1_SFbl_1h

description: SFB from RA treated with IL1


title: CL_P150-160 of pregnancy_2

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description:
Gene expression in Pregnant CL d150-160
251896410051_2_4

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Pregnant CL d150-160

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the CL using RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

tag: breed

value: Japanese Black

value: Corpus luteum

tag: study

value: In vivo

tag: group

value: Mid phase of pregnancy

tag: phase


title: CL_P150-160 of pregnancy_4

description:
Gene expression in Pregnant CL d150-160
251896410052_2_4

tag: tissue


title: RA1_SFbl_2h

description: SFB from RA treated with IL1


title: CL_P150-160 of pregnancy_3

description:
Gene expression in Pregnant CL d150-160
251896410052_2_3


title: CL_P150-160 of pregnancy_1

description:
Gene expression in Pregnant CL d150-160
251896410051_2_3


title: H5N3 H5N2-F59 F189 at 0H, biological rep1

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from mock infected MDCK rep 1

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

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

organism: Canis lupus familiaris

source_name: Mock infected MDCK rep 1

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

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

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

treatment_protocol: The cells were infected with A/duck/Malaysia/F59/04/1998(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

value: Mardin-Darby Canine Kidney cells

value: MDCK

tag: infection

value: mock

tag: time

value: control


title: H5N2-F59 infected MDCK at 10H, biological rep3

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

source_name: H5N2 (F59) infected MDCK 10 hpi rep 3

value: 10 hpi


title: H5N2-F59 F189 at 0H, biological rep1

description: Gene expression data from mock infected CEF rep 1

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

organism: Gallus gallus

source_name: Mock infected CEF rep 1

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

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

value: Chicken embryo fibroblast cells

value: CEF


title: CL_P40-45 of pregnancy_4

description:
Gene expression in Pregnant CL d40-45
251896410052_2_2

source_name: Pregnant CL d40-45

value: Early II phase of pregnancy


title: CL_P40-45 of pregnancy_3

description:
Gene expression in Pregnant CL d40-45
251896410052_2_1


title: 21d exposure to hyperglycemia+subsequent 48h TGF-β1 treatment rep3

city: Budapest

first: Gabor

last: Firneisz

address: Szentkiralyi St. 46

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

description: Cell culture (control cells and PSCs exposed to chronic hyperglycemia)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA semiautomated normalization procedure were applied

source_name: RLT-PSC, human pancreatic stellate cell (PSC) lineage

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: exposure to hyperglycemia+subsequent TGF-β1 treatment


title: H5N2-F59 infected MDCK at 10H, biological rep2

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

source_name: H5N2 (F59) infected MDCK 10 hpi rep 2


title: H5N3 H5N2-F59 F189 at 0H, biological rep2

description: Gene expression data from mock infected MDCK rep 2

source_name: Mock infected MDCK rep 2


title: H5N2-F59 infected CEF at 10H, biological rep1

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

source_name: H5N2 (F59) infected CEF 10 hpi rep 1


title: H5N2-F59 infected CEF at 10H, biological rep2

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

source_name: H5N2 (F59) infected CEF 10 hpi rep 2


title: H5N3 H5N2-F59 F189 at 0H, biological rep3

description: Gene expression data from mock infected MDCK rep 3

source_name: Mock infected MDCK rep 3


title: H5N2-F59 F189 at 0H, biological rep3

description: Gene expression data from mock infected CEF rep 3

source_name: Mock infected CEF rep 3


title: H5N2-F59 infected CEF at 10H, biological rep3

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

source_name: H5N2 (F59) infected CEF 10 hpi rep 3


title: H5N2-F59 F189 at 0H, biological rep2

description: Gene expression data from mock infected CEF rep 2

source_name: Mock infected CEF rep 2


title: 21d exposure to hyperglycemia rep4

value: RLT-PSC, human pancreatic stellate cell (PSC) lineage

value: exposure to hyperglycemia


title: H5N2-F59 infected MDCK at 10H, biological rep1

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

source_name: H5N2 (F59) infected MDCK 10 hpi rep 1


title: 21d exposure to hyperglycemia+subsequent 48h TGF-β1 treatment rep4


title: 21d exposure to hyperglycemia+subsequent 48h TGF-β1 treatment rep1


title: CL_P40-45 of pregnancy_1

description:
Gene expression in Pregnant CL d40-45
251896410051_2_1


title: 21d exposure to hyperglycemia+subsequent 48h TGF-β1 treatment rep2


title: CL_P40-45 of pregnancy_2

description:
Gene expression in Pregnant CL d40-45
251896410051_2_2


title: H5N2-F59 infected A549 at 10H, biological rep2

description: Gene expression data from H5N2 (F59) infected A549 10 hpi rep 2

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

source_name: H5N2 (F59) infected A549 10 hpi rep 2

value: Human aveolar basal epithelial cells


title: CL_P20-25 of pregnancy_4

description:
Gene expression in Pregnant CL d20-25
251896410052_1_4

source_name: Pregnant CL d20-25

value: Early I phase of pregnancy


title: 21d exposure to hyperglycemia rep3


title: CL_P20-25 of pregnancy_2

description:
Gene expression in Pregnant CL d20-25
251896410051_1_4

value: Japanese Black


title: H5N2-F59 infected A549 at 10H, biological rep3

description: Gene expression data from H5N2 (F59) infected A549 10 hpi rep 3

source_name: H5N2 (F59) infected A549 10 hpi rep 3


title: RA5_SFbl_4h

description: SFB from RA treated with IL1

source_name: Fibroblasts of RA patient


title: 21d exposure to hyperglycemia rep1


title: 48h TGF-β1 treatment rep3

value: TGF-β1 treatment


title: CL_D10-12 of the estrous cycle_3

description:
Gene expression in Cyclic CL d10-12
251896410052_1_1

source_name: Cyclic CL d10-12

value: Corpus luteum

value: In vivo

value: Non pregnant (estrous cycle)

value: NP


title: CL_P20-25 of pregnancy_1

description:
Gene expression in Pregnant CL d20-25
251896410051_1_3


description: Gene expression data from mock infected A549 rep 3

source_name: Mock infected A549 rep 3

value: mock


description: Gene expression data from mock infected A549 rep 1

source_name: Mock infected A549 rep 1

value: control


title: 48h TGF-β1 treatment rep2

description: Cell culture (control cells and PSCs exposed to chronic hyperglycemia)

source_name: RLT-PSC, human pancreatic stellate cell (PSC) lineage


title: CL_D10-12 of the estrous cycle_4

description:
Gene expression in Cyclic CL d10-12
251896410052_1_2


title: Control rep4

value: Control


title: CL_D10-12 of the estrous cycle_1

description:
Gene expression in Cyclic CL d10-12
251896410051_1_1


title: 48h TGF-β1 treatment rep1


title: CL_D10-12 of the estrous cycle_2

description:
Gene expression in Cyclic CL d10-12
251896410051_1_2


title: ATCC17978_OA_30min

status: Public on Aug 09 2014

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

country: South Korea

institute: Korea university

description: EtOH vs. OA64

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Acinetobacter_baumannii_ATCC-1797 30K 352926 microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The data quantification was performed using GenePix Pro 6.0 (Axon Instrument, CA). Lowess normalization conducted by using Genowiz 4.0TM (Ocimum Biosolutions, India) program.

organism: Acinetobacter baumannii ATCC 17978

source_name: EtOH

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: Overnight culture was diluted 1:100 in 5 mL LB medium at 37°C with aeration

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: 64μg/ml OA and ethanol were treated for 30min

tag: strain phenotype

value: multi-drug resistant pathogen

tag: treated with

value: vehicle (EtOH)

value: 64μg/ml OA


title: Control rep3


title: Control rep1


title: Control rep2


title: CL_P20-25 of pregnancy_3

description:
Gene expression in Pregnant CL d20-25
251896410052_1_3


title: 48h TGF-β1 treatment rep4


title: G1E-ER-GATA-1 - nontargeting siRNA - Replicate 3 of 3

city: Madison

last: DeVilbiss

state: WI

address: 1111 Highland Ave, WIMR 4028

department: Cell and Regenerative Biology

institute: UW-Madison

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Mouse GE 8x60 Microarray (GPL13912), microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), both containing 0.005% Triton X-102Slides were air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the 8x60K G3 one color Microarray format. Dye channel is green, scan area 61x21.65 mm, scan resolution 3 um, Tiff is 20 bit.

data_processing: Data was processed using Edge3 one color limma differential expression analysis. FDR = 10%

source_name: G1E-ER-GATA-1 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: G1E-ER-GATA-1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) containing 15% (vol/vol) FBS (Gemini), 1% penicillin-streptomycin (Gemini), 2 U/mL erythropoietin, 120 nM monothioglycerol (Sigma), 0.6% conditioned medium from a Kit-ligand producing CHO cell line, and 1 mg/mL puromycin (Gemini). ER-GATA-1 activity was induced by treating cells with 1 mM b-estradiol

extract_protocol: Total RNA from 1 million G1E-ER-GATA-1 cells was isolated using Trizol (Invitrogen). RNA was purified using Rneasy Micro Kit (Qiagen), per manufacture instructions.

treatment_protocol: siRNA targeting Foxo3 or non-targeting siRNA (Dharmacon) was electroporated into 3 x 10^6 G1E-ER-GATA-1 cells using an Amaxa Nucleofector (Lonza) using Nucleofection Kit R (Lonza). G1E-ER-GATA-1 cells were treated with control or Foxo3-specific siRNA by nucleofection at t = 0 h and t = 24 h. At t = 24 h, cells were treated with ß-estradiol to activate ER-GATA-1. RNA was harvested at t = 48 h and processed for microarray analysis.

value: ß-Estradiol Treatment (24 h)

tag: sirna

value: nontargeting siRNA


title: G1E-ER-GATA-1 - nontargeting siRNA - Replicate 1 of 3

tag: treatment


title: WILDTYPE_3h_NaCl_rep2

city: Harbin

first: Yujia

last: Liu

state: Heilongjiang

address: 1 Xuehai Street

country: China

institute: Harbin University of Commerce

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of WILDTYPE

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s  instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with R-software (The R Project for Statistical Computing, http:// www. r-project.org/) of SAS system statistics to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: WILDTYPE, 3h, NaCl, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana seedlings grown in freshwater-irrigated pots filled with the artificial soil (Vermiculite: perlite: soil = 3:1:1, v/v) in a relative humidity of 55% under long-day conditions (16-h light/8-h dark)at 22°C (±2°C).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Four-week-old seedlings of T3 homozygous lines of the AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana with or without 150 mM NaCl treatment for 3 hours. The whole seedlings including root and shoot were harvested and pooled for each treatment before freezing in liquid nitrogen and storage at -80ºC for RNA isolation.

value: NaCl

tag: genotype

value: WILDTYPE

value: whole plant

tag: age

value: Four-week-old seedlings


title: Fetal Liver Erythroid Progenitors - shControl 03

source_name: Fetal Liver-Derived Erythroid Progenitor Cells

growth_protocol: Primary fetal liver erythroid progenitor cells were cultured in StemPro-34 (Gibco) supplemented with 10% nutrient supplement (Gibco), 2 mM L-glutamine (Cellgro), 1% penicillin-streptomycin (Cellgro), 100 M monothioglycerol (Sigma), 1 M dexamethasone (Sigma), 0.5 U/ml of erythropoietin, and 1% conditioned medium from a kit ligand producing CHO cell line.

extract_protocol: Total RNA from 1 million erythroid precursor cells was isolated using Trizol (Invitrogen). RNA was purified using Rneasy Micro Kit (Qiagen), per manufacture instructions.

treatment_protocol: Fetal liver erythroid progenitors were isolated using the EasySep Kit (Stem Cell Technologies) and treated with 100 mL viral supernatant produced from 293T cells. Virus expressed either Exosc8-specific shRNA or shRNA targeting luciferase (control). Cells were treated with 8 mg/mL polybrene and centrifuged at 1200 x g for 90 min at 30˚C.

value: Fetal Liver

value: shControl

tag: embryonic day


title: G1E-ER-GATA-1 - nontargeting siRNA - Replicate 2 of 3


title: G1E-ER-GATA-1 - Foxo3 siRNA - Replicate 2 of 3

value: Foxo3 siRNA


title: G1E-ER-GATA-1 - Foxo3 siRNA - Replicate 3 of 3


title: G1E-ER-GATA-1 - Foxo3 siRNA - Replicate 1 of 3


title: H5N3 H5N2-F59 F189 at 0H, biological rep2

description: Gene expression data from mock infected A549 rep 2

source_name: Mock infected A549 rep 2

tag: cell type

value: Human aveolar basal epithelial cells

tag: cell line


title: SALK_033618C_3h_NaCl_rep2

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of SALK_033618C

source_name: SALK_033618C, 3h, NaCl, replicate 2


title: WILDTYPE_3h_NaCl_rep3

source_name: WILDTYPE, 3h, NaCl, replicate 3


title: SALK_033618C_3h_NaCl_rep1

source_name: SALK_033618C, 3h, NaCl, replicate 1


title: WILDTYPE_3h_H2O_rep3

description: Gene expression after 3h in H2O-irrigated Arabidopsis seedlings of WILDTYPE

source_name: WILDTYPE, 3h, H2O, replicate 3


title: SALK_033618C_3h_NaCl_rep3

source_name: SALK_033618C, 3h, NaCl, replicate 3


title: AtbHLH112_3h_NaCl_rep1

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of AtbHLH112

source_name: AtbHLH112, 3h, NaCl, replicate 1


title: 21d exposure to hyperglycemia rep2

value: RLT-PSC, human pancreatic stellate cell (PSC) lineage

value: exposure to hyperglycemia


title: AtbHLH112_3h_NaCl_rep2

source_name: AtbHLH112, 3h, NaCl, replicate 2


title: WILDTYPE_3h_NaCl_rep1

source_name: WILDTYPE, 3h, NaCl, replicate 1


title: SALK_033618C_3h_H2O_rep3

description: Gene expression after 3h in H2O-treatmented Arabidopsis seedlings of SALK_033618C

source_name: SALK_033618C, 3h, H2O, replicate 3


title: WILDTYPE_3h_H2O_rep2

source_name: WILDTYPE, 3h, H2O, replicate 2


title: Fetal Liver Erythroid Progenitors - shExosc8 03


title: Fetal Liver Erythroid Progenitors - shExosc8 02


title: AtbHLH112_3h_NaCl_rep3

source_name: AtbHLH112, 3h, NaCl, replicate 3


title: SALK_033618C_3h_H2O_rep2

source_name: SALK_033618C, 3h, H2O, replicate 2


title: WILDTYPE_3h_H2O_rep1

source_name: WILDTYPE, 3h, H2O, replicate 1


title: Fetal Liver Erythroid Progenitors - shControl 01


title: H5N2-F59 infected A549 at 10H, biological rep1

description: Gene expression data from H5N2 (F59) infected A549 10 hpi rep 1

source_name: H5N2 (F59) infected A549 10 hpi rep 1

value: 10 hpi


title: Fetal Liver Erythroid Progenitors - shExosc8 01


title: AtbHLH112_3h_H2O_rep2

description: Gene expression after 3h in H2O-irrigated Arabidopsis seedlings of AtbHLH112

source_name: AtbHLH112, 3h, H2O, replicate 2


title: SALK_033618C_3h_H2O_rep1

source_name: SALK_033618C, 3h, H2O, replicate 1


title: AtbHLH112_3h_H2O_rep3

source_name: AtbHLH112, 3h, H2O, replicate 3


title: Fetal Liver Erythroid Progenitors - shControl 02

source_name: Fetal Liver-Derived Erythroid Progenitor Cells


title: AtbHLH112_3h_H2O_rep1

source_name: AtbHLH112, 3h, H2O, replicate 1


title: ICN1 T-ALL 3 2.10 TAM

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

institute: Institut Curie

description:
F3.2-10_TAM
Leukemic bone marrow.
Cell suspension.

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on Mouse GeneChip® 430 2.0 arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450 using the FS450_0004 script.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.

data_processing: The data was normalized using RMA.

source_name: bone marrow, leukemic cells, tamoxifen

label_protocol: Biotinylated cRNA targets were prepared from 200 ng of total RNA using the MessageAmp™ Premier RNA Amplification Kit from Ambion, according to the Instruction Manual # 4386269 Revision B, 18 September 2007.

growth_protocol: Bone collection on ice; bone crushing and bone marrow hematopoietic cells collected by flushing; leukemic cells (>50% of total BM cells) were flow cytometry sorted by virtue of expression of a GFP or similar marker.

extract_protocol: Total RNA was isolated using the RNeasy kit from QIAGEN.

treatment_protocol: Mouse ICN1-induced T-ALL were generated that include a ROSCreERT2 transgene and 2 copies of a CnB1 floxed alleles. Cohorts of secondary recipient mice were injected with these T-ALL cells, and when becoming leukemic, divided into 2 subgroups. Group 1 was treated with Tamoxifen (TAM), resulting in CnB1 gene deletion and inactivation of calcineurin. Group 2 was treated with carrier solvent (corn OIL), thus maintaining CnB1 and calcineurin activity.

value: ICN1-induced T-ALL leukemic cells

tag: genotype/variation

value: ROSCreERT2 transgene and 2 copies of CnB1 floxed alleles

value: tamoxifen

tag: calcineurin gene cnb1 deleted

value: yes


title: SS056

city: Bordeaux

first: céline

last: brulard

address: 229 cours de l'argonne

institute: Institut Bergonié

hyb_protocol: Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4112F; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.

scan_protocol: the scan was performed according to manufacturer’s recommendations with scanning resolution of 5µm

data_processing: For each series all microarrays were simultaneously normalized using the Quantile algorithm.

source_name: trunk

label_protocol: RNA was labeled according to manufacturer’s protocol.

extract_protocol: Total RNA were extracted from frozen tumor samples using the miRNeasy® Mini Kit (Qiagen) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Frozen tissue

tag: cinsarc group

tag: fusion transcrit

tag: metastasis

value: no

tag: age group

value: pediatric


title: SS042

source_name: member


title: SS052


title: SS055


title: SS054


title: SS045


title: SS039

value: adult


title: SS049


title: SS050


title: SS040


title: SS053

source_name: head and neck


title: SS047


title: SS046


title: SS058


title: SS044


title: SS043


title: SS037


title: SS057


title: SS051


title: SS041


title: SS048