title: Sarcoma tumor ML622

description: Soft-tissue sarcoma


title: Sarcoma tumor PL131

status: Public on Sep 02 2011

type: RNA

city: New York

first: Brian

last: Denton

state: NY

address: 307 E. 63rd Street

department: Epidemiology and Biostatistics

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description:
Soft-tissue sarcoma

Re-analysis of GSM528895

hyb_protocol: Per manufacturer's instructions.

scan_protocol: Fluorescence was measured by confocal scanner (Agilent, Palo Alto, CA).

data_processing: Signal intensity was generated with Affymetrix Microarray Suite v5 software, and expression was estimated with robust multi-array average (RMA).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: liposarcoma, pleomorphic

label_protocol: Per manufacturer's instructions.

growth_protocol: None.

extract_protocol: Total RNA was extracted from macro-dissected cryomolds and homogenized in QIAzol lysis reagent.

treatment_protocol: None.

tag: tissue

value: primary liposarcoma

tag: subtype

value: pleomorphic

tag: sample id

tag: trainingtest

value: Training

tag: drfs

value: TRUE


title: Sarcoma tumor PL3275

description: Soft-tissue sarcoma

value: FALSE


title: Sarcoma tumor ML593

description: Soft-tissue sarcoma

source_name: liposarcoma, myxoid

value: myxoid

value: Test


title: Sarcoma tumor ML709

description: Soft-tissue sarcoma


title: Sarcoma tumor ML283

description: Soft-tissue sarcoma


title: Sarcoma tumor PL299

description:
Soft-tissue sarcoma

Re-analysis of GSM528900


title: Sarcoma tumor ML304

description: Soft-tissue sarcoma


title: Sarcoma tumor ML257

description: Soft-tissue sarcoma


title: Sarcoma tumor ML298

description: Soft-tissue sarcoma


title: Sarcoma tumor ML165

description: Soft-tissue sarcoma


title: Sarcoma tumor WD499

description: Soft-tissue sarcoma

source_name: liposarcoma, well-differentiated

value: well-differentiated


title: Sarcoma tumor ML138

description: Soft-tissue sarcoma


title: Sarcoma tumor ML163

description: Soft-tissue sarcoma


title: Sarcoma tumor MRC608

description: Soft-tissue sarcoma

source_name: liposarcoma, myxoid/round cell

value: myxoid/round cell


title: Sarcoma tumor MRC643

description:
Soft-tissue sarcoma

Re-analysis of GSM528431


title: Sarcoma tumor ML161

description: Soft-tissue sarcoma


title: 3D7/cam_30-38hpi

city: Singapore

first: Yen Hoon

last: Luah

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: 3D7/cam TP4

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Parasites were cultured as described previously (Trager and Jenson, 1978)

extract_protocol: Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions

treatment_protocol: Parasites were synchronized by repeated sorbitol lysis (Lambros and Vanderberg, 1979) to obtain a eight-hour growth window

tag: construct

value: transgenic 3D7 with an active episomal cam promoter

tag: hours post invasion (hpi)

source_name: 3D7 reference RNA pool


title: Sarcoma tumor PL247

description:
Soft-tissue sarcoma

Re-analysis of GSM528896


title: 3D7/pfmc-2tm_30-38hpi

description: 3D7/pfmc-2tm TP4

value: transgenic 3D7 with an active episomal pfmc-2tm promoter


title: Sarcoma tumor ML292

description: Soft-tissue sarcoma


title: Sarcoma tumor MRC644

description:
Soft-tissue sarcoma

Re-analysis of GSM528432


title: 3D7/cam_14-22hpi

description: 3D7/cam TP2


title: 3D7/cam_6-14hpi

description: 3D7/cam TP1


title: Sarcoma tumor MRC288

description: Soft-tissue sarcoma


title: Sarcoma tumor ML253

description: Soft-tissue sarcoma


title: Sarcoma tumor MRC275

description:
Soft-tissue sarcoma

Re-analysis of GSM528420


title: 3D7/cam_22-30hpi

description: 3D7/cam TP3


title: 3D7/pfmc-2tm_22-30hpi

description: 3D7/pfmc-2tm TP3


title: Sarcoma tumor MRC239

description:
Soft-tissue sarcoma

Re-analysis of GSM528418


title: Sarcoma tumor MRC624

description:
Soft-tissue sarcoma

Re-analysis of GSM528428


title: Sarcoma tumor MRC676

description:
Soft-tissue sarcoma

Re-analysis of GSM528433


title: Sarcoma tumor MRC5397

description:
Soft-tissue sarcoma

Re-analysis of GSM528425


title: Sarcoma tumor MRC626

description:
Soft-tissue sarcoma

Re-analysis of GSM528429


title: 3D7/pfmc-2tm_14-22hpi

description: 3D7/pfmc-2tm TP2


title: Sarcoma tumor MRC139

description:
Soft-tissue sarcoma

Re-analysis of GSM528416


title: Sarcoma tumor DD3516

description: Soft-tissue sarcoma

source_name: liposarcoma, dedifferentiated

value: dedifferentiated


title: 3D7/phist_6-14hpi

description: 3D7/phist TP1

value: transgenic 3D7 with an active episomal phistb promoter


title: 3D7/phist_22-30hpi

description: 3D7/phist TP3


title: 3D7/pfmc-2tm_6-14hpi

description: 3D7/pfmc-2tm TP1


title: 3D7/phist_30-38hpi

description: 3D7/phist TP4


title: Sarcoma tumor WD432

description: Soft-tissue sarcoma


title: 3D7/phist_14-22hpi

description: 3D7/phist TP2


title: 3D7/rif_30-38hpi

description: 3D7/rif TP4

value: transgenic 3D7 with an active episomal rif promoter


title: 3D7/rif_22-30hpi

description: 3D7/rif TP3


title: 3D7/stevor_30-38hpi

description: 3D7/stevor TP4

value: transgenic 3D7 with an active episomal stevor promoter


title: Sarcoma tumor DD88

description: Soft-tissue sarcoma


title: 3D7/stevor_6-14hpi

description: 3D7/stevor TP1


title: 3D7/stevor_14-22hpi

description: 3D7/stevor TP2


title: Sarcoma tumor DD712

description: Soft-tissue sarcoma


title: Sarcoma tumor DD715

description: Soft-tissue sarcoma


title: Sarcoma tumor WD439

description: Soft-tissue sarcoma


title: 3D7/stevor_22-30hpi

description: 3D7/stevor TP3


title: Sarcoma tumor DD714

description: Soft-tissue sarcoma


title: Sarcoma tumor PL243

description: Soft-tissue sarcoma


title: Sarcoma tumor DD719

description: Soft-tissue sarcoma


title: Sarcoma tumor DD718

description: Soft-tissue sarcoma


title: 3D7/rif_14-22hpi

description: 3D7/rif TP2


title: Sarcoma tumor DD8379

description:
Soft-tissue sarcoma

Re-analysis of GSM528324


title: Sarcoma tumor DD672

description:
Soft-tissue sarcoma

Re-analysis of GSM528319


title: Sarcoma tumor DD69

description: Soft-tissue sarcoma


title: Sarcoma tumor DD7533

description: Soft-tissue sarcoma


title: 3D7/rif_6-14hpi

description: 3D7/rif TP1


title: Sarcoma tumor DD670

description:
Soft-tissue sarcoma

Re-analysis of GSM528318


title: Sarcoma tumor DD668

description:
Soft-tissue sarcoma

Re-analysis of GSM528317


title: Sarcoma tumor DD639

description:
Soft-tissue sarcoma

Re-analysis of GSM528315


title: 3D7/upsB_6-14hpi

description: 3D7/upsB TP1

value: transgenic 3D7 with an active episomal upsB promoter


title: Sarcoma tumor DD6213

description:
Soft-tissue sarcoma

Re-analysis of GSM528313


title: 3D7/upsC_6-14hpi

description: 3D7/upsC TP1

value: transgenic 3D7 with an active episomal upsC promoter


title: 3D7/upsC_14-22hpi

description: 3D7/upsC TP2


title: 3D7/upsB_30-38hpi

description: 3D7/upsB TP4


title: 3D7/upsC_30-38hpi

description: 3D7/upsC TP4


title: 3D7/upsA_22-30hpi

description: 3D7/upsA TP3

value: transgenic 3D7 with an active episomal upsA promoter


title: 3D7/upsA_30-38hpi

description: 3D7/upsA TP4


title: 3D7/upsB_14-22hpi

description: 3D7/upsB TP2


title: Sarcoma tumor DD610

description:
Soft-tissue sarcoma

Re-analysis of GSM528305

value: primary liposarcoma


title: 3D7/upsB_22-30hpi

description: 3D7/upsB TP3


title: Sarcoma tumor DD611

description:
Soft-tissue sarcoma

Re-analysis of GSM528306

value: Training


title: Sarcoma tumor DD597

description: Soft-tissue sarcoma

value: TRUE


title: 3D7/upsA_14-22hpi

description: 3D7/upsA TP2


title: 3D7/upsA_6-14hpi

description: 3D7/upsA TP1


title: 3D7/upsC_22-30hpi

description: 3D7/upsC TP3


title: 3D7_30-38hpi

description: 3D7 TP4


title: 3D7_14-22hpi

description: 3D7 TP2


title: 3D7_22-30hpi

description: 3D7 TP3


title: 3D7_6-14hpi

description: 3D7 TP1


title: Sarcoma tumor DD391

description: Soft-tissue sarcoma

value: FALSE


title: Sarcoma tumor DD595

description:
Soft-tissue sarcoma

Re-analysis of GSM528300


title: Sarcoma tumor DD442

description:
Soft-tissue sarcoma

Re-analysis of GSM528292


title: Sarcoma tumor DD456

description: Soft-tissue sarcoma


title: Sarcoma tumor DD474

description:
Soft-tissue sarcoma

Re-analysis of GSM528296


title: Sarcoma tumor DD344

description:
Soft-tissue sarcoma

Re-analysis of GSM528287


title: Sarcoma tumor DD172

description:
Soft-tissue sarcoma

Re-analysis of GSM528280


title: Sarcoma tumor DD188

description: Soft-tissue sarcoma


title: Sarcoma tumor DD454

description:
Soft-tissue sarcoma

Re-analysis of GSM528293


title: Sarcoma tumor DD226

description: Soft-tissue sarcoma


title: Sarcoma tumor DD103

description:
Soft-tissue sarcoma

Re-analysis of GSM528277


title: Sarcoma tumor DD330

description: Soft-tissue sarcoma


title: Sarcoma tumor DD112

description:
Soft-tissue sarcoma

Re-analysis of GSM528278


title: VN1203_24H_2

city: Portland

first: Armand

last: Bankhead III

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Depatartment of Medical Informatics and Clinical Epidemiology

institute: Oregon Health and Science University

description:
251485048465_1_4
VN1203 H.5N1 host response 24H.

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. Data were normalized using RMA.

source_name: calu3, vn1203 infected, 24H

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

growth_protocol: Calu-3 cells, a human lung adenocarcinoma cell line, were kindly provided by Dr. Raymond Pickles (University of North Carolina, Chapel Hill, NC) and were maintained in a 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F12 nutrient medium (DF12; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum. All cells were grown at 37°C in an atmosphere of 5% CO2, with an antibiotic/antimycotic mixture (Invitrogen).

extract_protocol: At 0, 3, 7, 12, 18 and 24 hours post-infection (hpi), triplicate wells of mock-infected and VN1203-infected Calu-3 monolayers were washed with 5 ml cold phosphate-buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen), according to the manufacturer’s recommendation. The resulting lysates were stored at -80°C until further processing.  All TRIzol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 cells were seeded in 6-well plates (1 x 10^6 cells/well) two days prior to infection.  Immediately preceding infection, monolayers were washed twice with DF12 supplemented with 0.3% bovine serum albumin (DF12-BSA), and inoculated with VN1203 (multiplicity of infection [MOI] of 1 plaque forming unit per cell) in DF12-BSA for 50 minutes at 37°C.  Mock-infected controls were inoculated with DF12-BSA only.  Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ) for the times indicated.

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: infection

value: VN1203 influenza virus

tag: infection duration


title: VN1203_18H_3

description:
251485048467_1_2
VN1203 H.5N1 host response 18H.

source_name: calu3, vn1203 infected, 18H


title: VN1203_24H_3

description:
251485048469_1_4
VN1203 H.5N1 host response 24H.


title: Sarcoma tumor DD216

description:
Soft-tissue sarcoma

Re-analysis of GSM528283

value: Test


title: Sarcoma tumor DD0728

description:
Soft-tissue sarcoma

Re-analysis of GSM528276


title: Sarcoma tumor DD382

description: Soft-tissue sarcoma


title: VN1203_24H_1

description:
251485048497_1_1
VN1203 H.5N1 host response 24H.


title: Sarcoma tumor DD176

description: Soft-tissue sarcoma


title: NK3

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: The scanned images of microarray chips were analyzed using the Affymetrix GenChip Operating Software (GCOS) and Expression Console with the default settings except that the target signal was set to 100.

label: biotin

source_name: culture of normal oral keratinocytes

label_protocol: The cDNA was synthesized, in vitro transcribed and labeled using standard Affymetrix protocols.

growth_protocol: Keratinocytes were cultured in keratinocyte serum free medium (KSFM) containing bovine pituitary extract, epidermal growth factor and calcium chloride.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Total
RNA Mini Kit (Qiagen, Crawley, West Sussex, UK).

treatment_protocol: Normal oral keratinocyte culture were established by single cell suspension from excess tissue originating from routine oral surgical procedures.

tag: disease state

value: Normal


title: NK2


title: VN1203_7H_3

description:
251485048497_1_3
VN1203 H.5N1 host response 7H.

source_name: calu3, vn1203 infected, 7H


title: VN1203_3H_3

description:
251485048498_1_1
VN1203 H.5N1 host response 3H.

source_name: calu3, vn1203 infected, 3H


title: VN1203_12H_3

description:
251485048466_1_2
VN1203 H.5N1 host response 12H.

source_name: calu3, vn1203 infected, 12H


title: PT 30 TO1

type: genomic

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5, Cy3

molecule: genomic DNA

source_name: tumor, day 1 (before treatment)

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood and biopsy samples using Qiagen QIAmp DNA blood Mini Kit according to standard instructions

tag: condition

value: ovarian cancer

value: tumor


title: PT 29 AO2

source_name: ascites, day 8 (after treatment)

value: ascites


title: PT 30 TO2

source_name: tumor, day 8 (after treatment)


title: VN1203_18H_2

description:
251485048496_1_3
VN1203 H.5N1 host response 18H.


title: VN1203_3H_2

description:
251485048497_1_4
VN1203 H.5N1 host response 3H.


title: VN1203_12H_2

description:
251485048495_1_3
VN1203 H.5N1 host response 12H.


title: VN1203_18H_1

description:
251485048468_1_1
VN1203 H.5N1 host response 18H.


title: VN1203_7H_2

description:
251485048469_1_2
VN1203 H.5N1 host response 7H.


title: VN1203_12H_1

description:
251485048466_1_4
VN1203 H.5N1 host response 12H.


title: VN1203_7H_1

description:
251485048498_1_4
VN1203 H.5N1 host response 7H.


title: VN1203_3H_1

description:
251485048469_1_3
VN1203 H.5N1 host response 3H.


title: VN1203_0H_2

description:
251485048496_1_2
VN1203 H.5N1 host response 0H.

source_name: calu3, vn1203 infected, 0H


title: VN1203_0H_1

description:
251485048496_1_4
VN1203 H.5N1 host response 0H.


title: PT 29 AO1

source_name: ascites, day 1 (before treatment)


title: Mock_24H_3

description:
251485048467_1_3
Mock host response 24H.

source_name: calu3, mock, 24H

value: mock


title: Mock_24H_2

description:
251485048467_1_4
Mock host response 24H.


title: VN1203_0H_3

description:
251485048497_1_2
VN1203 H.5N1 host response 0H.


title: Mock_18H_2

description:
251485048466_1_3
Mock host response 18H.

source_name: calu3, mock, 18H


title: Mock_18H_3

description:
251485048465_1_2
Mock host response 18H.


title: Sarcoma tumor DD506

description:
Soft-tissue sarcoma

Re-analysis of GSM528298

value: dedifferentiated


title: Mock_12H_3

description:
251485048465_1_3
Mock host response 12H.

source_name: calu3, mock, 12H


title: Mock_12H_1

description:
251485048496_1_1
Mock host response 12H.


title: PT 26 TO2


title: PT 24 TO2


title: Mock_18H_1

description:
251485048469_1_1
Mock host response 18H.


title: Mock_12H_2

description:
251485048468_1_4
Mock host response 12H.


title: PT 30 C1D1

source_name: PBMC, day 1 (before treatment)

value: PBMC


title: PT 26 TO1


title: Mock_7H_3

description:
251485048498_1_2
Mock host response 7H.

source_name: calu3, mock, 7H


title: Mock_24H_1

description:
251485048495_1_2
Mock host response 24H.


title: Mock_7H_2

description:
251485048495_1_4
Mock host response 7H.


title: PT 29 C1D8

source_name: PBMC, day 8 (after treatment)


title: Mock_3H_3

description:
251485048468_1_2
Mock host response 3H.

source_name: calu3, mock, 3H


title: PT 29 C1D1


title: Mock_7H_1

description:
251485048467_1_1
Mock host response 7H.


title: Mock_3H_1

description:
251485048468_1_3
Mock host response 3H.


title: Mock_3H_2

description:
251485048465_1_1
Mock host response 3H.


title: Mock_0H_2

description:
251485048498_1_3
Mock host response 0H.

source_name: calu3, mock, 0H


title: a17i_2 with array type Medicago from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: NFP is one of the putative Nod factor receptor and plays therefore a key role in the establishment of symbiosis. nfp allelic mutants are more susceptible to Aphanomyces euteiches (Ae), a root pathogen, than the A17 wild type (WT) line.  In this study we want to compare the early plant responses, 1 day post inoculation (dpi) between WT and the nfp2 mutant, in order to identify NFP-dependent gene networks during infection.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - In vitro conditions on M medium 16h light 8h dark 22°C

treatment_protocol: Name:A. euteiches - pathogen - pathogen infection,aphanomyces euteiches:time 1hour . Djebali et al, MPMI, 2009. 10e5 zoospores/mL

tag: strain

tag: harvest date


title: Mock_0H_3

description:
251485048495_1_1
Mock host response 0H.


title: PT 28 C1D1


title: a17ni_2 with array type Medicago from Affymetrix

treatment_protocol: Name:water  - pathogen - control,mock_water:time 1day . Djebali et al, MPMI, 2009.


title: nfpni_7 with array type Medicago from Affymetrix

value: nfp-2 allelic mutant


title: OPM1 DMSO control, replicate 1

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description:
Control cells exposed for 24hrs to DMSO
12ng of total RNA was amplified following the Ovation RNA amplification protocol (FLHSC).

hyb_protocol: 5.5ug of fragmented, biotinylated cDNA was hybridized according to the standard Affymetrix protocol for the Gene1.0ST array.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA probe summarization and normalization using the Bioconductor affy package (http://www.bioconductor.org).

source_name: OPM1 cells

label_protocol: 5.5ug of amplified single-stranded cDNA was fragmented and biotinylated using the Affymetrix Terminal Label and Control Kit.

extract_protocol: Total RNA was isolated by TRIzol extraction and further purified on a Qiagen RNeasy column according to manufacturer's directions. 100ng of RNA was converted into amplified single-stranded cDNA using the Ambion WT expression kit.

tag: treatment

value: DMSO

value: Multiple myeloma cell line


title: OPM1 DMSO control, replicate 2


title: OPM1 JQ1-treated, replicate 1

description:
Cells treated with JQ1 for 24hrs
12ng of total RNA was amplified following the Ovation RNA amplification protocol (FLHSC).


title: Sarcoma tumor DD513

description:
Soft-tissue sarcoma

Re-analysis of GSM528299

source_name: liposarcoma, dedifferentiated

value: primary liposarcoma


title: PT 27 C1D8


title: Mock_0H_1

description:
251485048466_1_1
Mock host response 0H.


title: nfpni_9 with array type Medicago from Affymetrix


title: KMS11 JQ1-treated, replicate 2

source_name: KMS11 cells


title: PT 28 C1D8


title: KMS11 JQ1-treated, replicate 1


title: OPM1 JQ1-treated, replicate 2


title: a17ni_1 with array type Medicago from Affymetrix


title: PT 27 C1D1


title: PT 26 C1D8


title: a17i_3 with array type Medicago from Affymetrix


title: MM1.S JQ1-treated, replicate 2

source_name: MM1.S cells


title: PT 26 C1D1


title: KMS11 DMSO control, replicate 2


title: KMS11 DMSO control, replicate 1


title: PT 24 C1D1


title: a17ni_3 with array type Medicago from Affymetrix


title: a17i_1 with array type Medicago from Affymetrix


title: nfpni_8 with array type Medicago from Affymetrix


title: ESC Cells Day 15 rep 3

city: Perth

first: Munish

last: Mehta

state: WA

address: MRF Building, 50 Murray Street

country: Australia

institute: WAIMR UWA

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanning setting: 1.6 for Beadarray reader

data_processing: The data was normalised using RSN normalisation with Lumi moduleI in R

organism: Mus musculus

source_name: Mouse ESC cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent. Quality check performed with Agilent Bioanalyser 2100

tag: time

value: Day 15

value: differentiated in the presence of activin A, retinoid acid and retinoid acid plus fibroblast growth factor sequentially to generate pancreatic progenitor cells

value: ESC cells


title: nfpi_12 with array type Medicago from Affymetrix


title: PT 23 C1D8


title: MM1.S DMSO control, replicate 2


title: MM1.S JQ1-treated, replicate 1


title: nfpi_10 with array type Medicago from Affymetrix


title: PT 24 C1D8


title: ESC Cells Day 4 rep 3

description: replicate 3

value: Day 4


title: ESC Cells Day 0 rep 3

description: replicate 3

value: Day 0


title: PT 22 C1D8


title: PT 23 C1D1


title: ESC Cells Day 4 rep 2

description: replicate 2


title: nfpi_11 with array type Medicago from Affymetrix


title: ESC Cells Day 8 rep 2

description: replicate 2

value: Day 8


title: ESC Cells Day 8 rep 3

description: replicate 3


title: PT 22 C1D1


title: ESC Cells Day 15 rep 1

description: replicate 1


title: ESC Cells Day 4 rep 1

description: replicate 1


title: ESC Cells Day 8 rep 1

description: replicate 1


title: PT 20 C1D1


title: PT 19 C1D8


title: ESC Cells Day 0 rep 2

description: replicate 2


title: PT 24 TO1

source_name: tumor, day 1 (before treatment)


title: PT 20 C1D8


title: ESC Cells Day 0 rep 1

description: replicate 1


title: PT 19 C1D1


title: PT 30 C1D8


title: PT 15 C1D8


title: PT 16 C1D8


title: PT 16 C1D1


title: PT 15 C1D1


title: Bmi1 wild-type lung cells, biological replicate 3

city: Boston

first: Carla

last: Kim

state: MA

address: 300 Longwood Ave

department: Hem/Onc, Stem Cell Program

institute: Children's Hospital Boston

description: Gene expression data from wild-type lung cells

hyb_protocol: Fragmented, biotinylated cDNA was hybridized for 18 hours on Mouse 430_2 Affymetrix Mouse Genome 430 2.0 Arrays.  The arrays were then washed and stained with streptavidin-phycoerythrin, using the Affymetrix GeneChip Fluidics Station 450

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: The raw intensity data were preprocessed by Affymetrix's Expression Console (version 1.1)

source_name: Bmi1 wild-type lung cells

label_protocol: The purified cDNA (5ug per sample) was fragmented and biotinylated using FL-Ovation cDNA Biotin Module V2 (Nugen, cat# 4200-12)

growth_protocol: Primary lung cells were purified from 4 month old female mice; no ex vivo growth of cells prior to RNA extraction

extract_protocol: RNA was purified using an Absolutely RNA Purification Kit (Agilent Technologies), and amplified using the WT-Ovation Pico RNA Amplification System (Nugen) to generate cDNA

treatment_protocol: To make a total lung cell suspension, lungs were infused with dispase, then 1% agarose and lungs removed from animal; lungs were then minced, further digested with collagenase/dispase, treated with dnase, filtered, and red blood cells lysed.  Cells were then labeled with 7aad, anti-CD31 and anti-CD45 antibodies, and FACS-purified to exclude endothelial, hematopoietic, and dead cells (See Kim et al, 2005).

tag: source tissue

value: lung

tag: genetic background

value: Bl6/129 mixed background

tag: genotype

value: Bmi1 wild-type

value: primary lung cells (CD31-negative, CD45-negative)


title: Bmi1 mutant lung cells, biological replicate 2

description: Gene expression data from mutant lung cells

source_name: Bmi1 mutant lung cells

value: Bmi1 null


title: Bmi1 mutant lung cells, biological replicate 3


title: ESC Cells Day 15 rep 2

description: replicate 2


title: PT 13 C1D1

value: ovarian cancer


title: PT 13 C1D8

value: PBMC


title: PT 12 C1D8


title: PT 12 C1D1


title: Bmi1 wild-type lung cells, biological replicate 2


title: Bmi1 mutant lung cells, biological replicate 1


title: Wild caught prawn 1 wc2

city: Sippy Downs

first: Abigail

last: Elizur

state: Queensland

address: Sippy Downs Drive

department: Science and Education

institute: University of the Sunshine Coast

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_151206_375V_com_foc_110(1)_Array 1.txt

hyb_protocol: Pre-hybridisation steps (30 min) and hybridisations (16 h) were conducted in 30 µl volumes using hybridisation solution containing 6×SSPE, 0.05% Tween-20, 20 mM EDTA, 5×Denhardt’s solution, 100 ng/µl denatured salmon sperm DNA, 0.05% SDS, and 6×SSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionized formamide, 100 ng/µl denatured salmon sperm DNA, 0.04% SDS and 1 µg of target aRNA respectively, with microarrays loaded onto a rotisserie in a hybridisation oven and incubated at 45°C. Microarrays were then washed according to manufacturer’s instructions and scanned wet using supplied imaging solution with LifterSlips™ (Thermo Fisher Scientific Inc., Waltham, MA, USA) applied. After imaging, microarrays were stripped for subsequent re-hybridisation up to three times using the CombiMatrix CustomArray stripping kit (CombiMatrix Corporation, Mukilteo, USA) according to manufacturer’s instructions.

scan_protocol: Microarray slides were scanned using a fluorescent microarray scanner (GenePix 4000B, MDS Analytical Technologies, Toronto, Canada). Microarray Imager (CombiMatrix Corporation, Mukilteo, USA) was then used to create spot intensity reports, generate gene ID mapping files and assign gene identification. Final intensity reports were retrieved as raw spot intensities in tab-delimited files.

data_processing: Final intensity reports were then used for further data analysis using data mining software Acuity 4.0 (MDS Analytical Technologies, Toronto, Canada). Data were pre-processed and normalised by applying background and floor correction, and global means normalisation. Data was grouped and classified using hierarchical and non-hierarchical clustering analyses. Genes displaying significant differential expression were identified via Two-Sample Students t-Tests.

organism: Penaeus monodon

source_name: Wild Cephalothorax

label_protocol: Reverse transcription of total RNA, RNA amplification by in vitro transcription and aRNA labelling were conducted using the RNA ampULSe amplification and labelling kit (KREATECH Biotechnologies, Amsterdam, The Netherlands) according to manufacturer’s instructions. Briefly, reverse transcription reactions were performed using T7 Oligo(dT) primer with Arrayscript reverse transcriptase. Second strand synthesis was then performed and cDNA purified using cDNA filter cartridges and used as template for aRNA synthesis in in vitro transcription reactions. aRNA was then purified using aRNA filter cartridges and yield and quality of aRNA assessed by measuring the absorbance at 260 nm and 280 nm using a spectrophotometer (GeneQuant Pro, GE Healthcare UK Ltd., Buckinghamshire, England). One microgram of non-modified aRNA was labelled non-enzymatically using the Universal Linkage System (ULS) technology coupled with Cy5 fluorochrome. Unbound ULS label was removed using included KREApure columns and aRNA fragmentation conducted using RNA fragmentation reagents (Applied Biosystems/Ambion, Austin, TX, USA) according to manufacturer’s instructions. Labelled aRNA was then hybridised to the microarray slides according to manufacturer’s instructions. Briefly, slides were assembled with supplied hybridisation caps in hybridisation clamps and re-hydrated prior to use by adding nuclease-free water and incubating at 65°C for 10 minutes.

growth_protocol:
Sample collection
Wild-caught material: Wild-caught adult female P. monodon were obtained from commercial hatchery suppliers in Innisfail, Queensland and kept at the Queensland Department of Primary Industries and Fisheries, Bribie Island Aquaculture Research Centre (BIARC), Woorim, Queensland. Animals were stocked in 6 tonne tanks with flow-through sea water heated to 26oC and acclimated for 7 days whilst fed fresh diet (squid and mussels) twice daily. All animals were moult staged according to extent of epidermal retraction [57]. Animals/tissue samples were collected at various ovarian maturation stages based on in vivo observation of maturing ovaries [58] and kept for subsequent classification by histological analysis of developing oocytes as follows: whole ovaries, cephalothorax and eyestalk were collected from un-ablated inter-moult females (immature ovaries) euthanized in saline ice slurry, snap frozen in liquid nitrogen and stored at -80°C until processing. Additionally, seventy inter-moult females were unilaterally eyestalk ablated (to induce ovarian maturation), eye-tagged, carapace-tagged and maintained for a further 7 days as described above. In vivo ovarian maturation stage, moulting, mortality and other behaviour were recorded daily. Animals were sampled at 2 h and 24 h post ablation (immature ovaries) and further sampled during this period with tissues of interest collected from random animals representing each of four in vivo ovarian maturation stages: immature, early maturing, late maturing and mature. Gonadosomatic index (GSI) was also calculated (ovarian weight expressed as a percentage of total body weight) for all samples. All wild-caught animals were sampled during the first moult cycle after ablation.
Captive-reared material: Captive-reared adult female P. monodon were obtained from the Australian Institute of Marine Science (AIMS), Townsville, Queensland following grow-out (pond) culture at BIARC. As part of hatchery operations at AIMS, inter-moult animals were unilaterally eyestalk ablated and maintained in 5 tonne tanks with flow-through sea water heated to 26oC whilst fed fresh diet (squid and mussels) twice daily for up to one month. Ovary, cephalothorax and eyestalk samples were collected during this period as outlined above from random animals representing the same in vivo ovarian maturation stages as for the wild-caught animals. Captive-reared animals were sampled across several moult cycles after ablation.

extract_protocol: Total RNA was isolated individually from small pieces (100 mg) of the ovarian lobes, cephalothorax and eyestalk (initially ground under liquid nitrogen using mortar and pestle) from prawns of interest, using TRIZOL reagent as recommended by the manufacturer (Invitrogen, Carlsbad, CA, USA).  The samples were used for synthesis of cDNA, creation of cDNA libraries and for construction and screening of microarrays. Concentration and purity of the RNA were determined using a spectrophotometer (GeneQuant Pro, GE Healthcare UK Ltd., Buckinghamshire, England) at 260/280 nm.  RNA quality was assessed for all samples by visualisation on denaturing formaldehyde RNA gels (protocol recommended by Qiagen, Valencia, CA, USA) using ethidium bromide staining.  Total RNA was used for creation of cDNA for rapid amplification of cDNA ends (RACE) and for preparation of RNA probes for in situ hybridisation.

treatment_protocol: Abbreviations for the samples: w = wild, c = captive, o = ovary, e = eyestalk, p = preablation, 2 = 2 h postablation (previtelogenic) 24 = 24 h postablation (previtelogenic), v = vitellogenic, r = round cortical rod, e = elongated cortical rod, unless stated otherwise   For example, Wild caught prawn 1 wop1 = wild caught prawn, ovary, preablation experimental replicate 1 (wild samples have 2 experimental replicates for ovary and eyestalk samples)

tag: treatment stage

value: 2hrs postablation (previtellogenic)

tag: replicate number

tag: array number


title: Wild caught prawn 2 wc24

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_131206_375V_com_foc_110(1)_Array 2.txt

value: 24hrs postablation (previtellogenic)


title: Wild caught prawn 1 wcp

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_131206_375V_com_foc_110(1)_Array 1.txt
Note: From this point,  c = cephalothorax, ie. wild_cephalothorax_previtellogenic

value: preablation


title: Wild caught prawn 4 wce

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_131206_375V_com_foc_110(1)_Array 4.txt

value: elongated cortical rod


title: Wild caught prawn 2 wcr

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_151206_375V_com_foc_110(1)_Array 2.txt

value: round cortical rod


title: Captive bred prawn 3 cev

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_081206_375V_com_foc_110(1)_Array 3.txt

source_name: Captive Eyestalk

value: vitellogenic


title: Captive bred prawn 4 cee

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_081206_375V_com_foc_110(1)_Array 4.txt


title: PT 28 AO2

source_name: ascites, day 8 (after treatment)

value: ascites


title: Captive bred prawn 2 cepv

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_081206_375V_com_foc_110(1)_Array 2.txt

value: previtellogenic


title: Captive bred prawn 1 cep

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_081206_375V_com_foc_110(1)_Array 1.txt


title: Captive bred prawn 4 coe

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_061206_375V_com_foc_110(1)_Array 4.txt

source_name: Captive Ovary


title: PT 28 AO1

source_name: ascites, day 1 (before treatment)


title: Captive bred prawn 2 copv

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_061206_375V_com_foc_110(1)_Array 2.txt
Note: pv = previtellogenic


title: PT 23 AO2


title: PT 22 AO1


title: Bmi1 wild-type lung cells, biological replicate 1


title: Captive bred prawn 1 cop

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_061206_375V_com_foc_110(1)_Array 1.txt


title: PT 22 AO2


title: Wild caught prawn 3 wer2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_281106_375V_com_foc_110(1)_Array 3.txt

source_name: Wild Eyestalk


title: Wild caught prawn 4 wee2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_281106_375V_com_foc_110(1)_Array 4.txt


title: Wild caught prawn 2 wev2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_281106_375V_com_foc_110(1)_Array 2.txt


title: Captive bred prawn 3 cov

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_061206_375V_com_foc_110(1)_Array 3.txt


title: Wild caught prawn 2 wee1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_231106_375V_com(1)_Array 2.txt


title: Wild caught prawn 1 we242

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_281106_375V_com_foc_110(1)_Array 1.txt


title: Wild caught prawn 4 we22

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_231106_375V_com(1)_Array 4.txt


title: PT 13 AO2


title: Wild caught prawn 3 wep2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_231106_375V_com(1)_Array 3.txt


title: PT 13 AO1


title: PT 23 AO1


title: PT 12 AO2


title: PT 12 AO1


title: Wild caught prawn 1 wer1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_231106_375V_com(1)_Array 1.txt


title: Wild caught prawn 4 wev1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_211106_375V_com(1) Array 4.txt


title: PT 20 TO2

source_name: tumor, day 8 (after treatment)

value: tumor


title: MM1.S DMSO control, replicate 1

description:
Control cells exposed for 24hrs to DMSO
12ng of total RNA was amplified following the Ovation RNA amplification protocol (FLHSC).

value: DMSO

value: Multiple myeloma cell line


title: Wild caught prawn 3 we241

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_211106_375V_com(1) Array 3.txt


title: Wild caught prawn 2 we21

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_211106_375V_com(1) Array 2.txt


title: Wild caught prawn 4 woe2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_171106_375V_com(1) Array 4.txt

source_name: Wild Ovary


title: Wild caught prawn 1 wep1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_211106_375V_com(1) Array 1.txt


title: Wild caught prawn 3 wop2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_141106_375V_com(1)_Array 3.txt


title: Wild caught prawn 2 wov2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_171106_375V_com(1) Array 2.txt


title: Wild caught prawn 3 wor2

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_171106_375V_com(1) Array 3.txt


title: Wild caught prawn 4 wo22

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_141106_375V_com(1)_Array 4.txt


title: PT 19 TO1


title: Double knock out [1358:chd1∆,isw1∆]

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Biological replicates from Double knock out cells

hyb_protocol: 300ng of cy3 labeled samples and 300ng of cy5 labeled samples were fragmented and hybridized on the slides .  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C at 5 micron and Images were quantified using Agilent Feature Extraction Software (version10.7.3.1)

data_processing: Channel split analysis was performed. Probe signal intensities generated from feature extraction raw data were split based on channel type cy3 and cy5 [BMA B_Cy5, BMA A_Cy3, 3KO B_Cy5, 3KO A_Cy3 , 1358 B_Cy5 , 1358 A_Cy3]. Data analysis performed and ratios were obtained for the following: (1) 3KO B_Cy5 vs. BMA B_Cy5  (2)  1358 B_Cy5 vs. BMA B_Cy5 (3) 3KO A_Cy3 vs. BMA A_Cy3 (4) 1358 A_Cy3 vs. BMA A_Cy3 . Python programming language was used for the normalization and analysis. Gene based analysis is performed. [BMA is  yeast wild type strain as control in the analysis]

organism: Saccharomyces cerevisiae

source_name: Double knock out [1358:chd1∆,isw1∆]

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Liquid suspension cultures were inoculated from starter cultures and grown O/N in YPAD at 30C.

extract_protocol: Qiagen, Rneasy Mini Kit cat No.74104, As per the manufacturers instructions.

tag: genotype/variation

value: Double knock out [1358:chd1∆,isw1∆]


title: Wild caught prawn 2 woe1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_141106_375V_com(1)_Array 2.txt


title: Wild caught prawn 1 wo242

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_171106_375V_com(1) Array 1.txt


title: Wild caught prawn 1 wor1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_141106_375V_com(1)_Array 1.txt


title: Wild caught prawn 4 wov1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_021106_375V_com_Array 4.txt


title: PT 19 TO2


title: Wild caught prawn 1 wop1

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_021106_375V_com_Array 1.txt

source_name: Wild ovary


title: Wild caught prawn 2 wo21

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_021106_375V_com_Array 2.txt


title: PT 20 TO1


title: PT 17 TO2


title: Wild Type cells

description: Biological replicates of Wild type cells

source_name: WT cells

value: BMA wild-type


title: Wild caught prawn 3 wo241

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn1_021106_375V_com_Array 3.txt


title: PT 16 TO1


title: PT 16 TO2


title: PT 15 TO2


title: PT 17 TO1


title: Triple knock out [TKO:chd1∆,isw1∆, isw2∆]

description: Biological replicates from Triple knock out cells

source_name: Triple knock out [3KO:chd1∆,isw1∆, isw2∆]


title: adipose_168

status: Public on Sep 01 2011

city: Los Angeles

first: Blake

middle: Edwin

last: Haas

state: CA

address: 695 Charles E. Young Drive South

institute: UCLA

hyb_protocol: manufacturer's instructions

scan_protocol: manufacturer's instructions

data_processing: background subtraction and quantile normalization using Genome Studio (GenomeStudioV2010.1) with the Gene Expression Module version 1.6.0.

label_protocol: manufacturer's instructions

extract_protocol: manufacturer's instructions, miRNeasy (Qiagen)

tag: tissue

value: adipose

tag: Sex

value: male

tag: rs7575840 genotype

value: TX


title: adipose_173


title: adipose_165


title: adipose_167


title: adipose_172


title: adipose_174


title: adipose_158


title: adipose_164


title: adipose_159


title: adipose_170


title: adipose_161


title: adipose_154


title: adipose_157


title: adipose_162


title: adipose_163


title: adipose_166


title: adipose_171


title: Wild caught prawn 3 wcv

description:
2240 oligos were spotted on 4 fields.
Raw data file: prawn2_131206_375V_com_foc_110(1)_Array 3.txt


title: adipose_156


title: adipose_160


title: adipose_153


title: adipose_155


title: adipose_152


title: adipose_175


title: DG 4h after ECS, biological rep 2

city: Cambridge

first: Junjie

last: Guo

address: 9 Cambridge Center

institute: Whitehead Institute

description: Microdissected from whole hippocampus

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings.

data_processing: Data were preprocessed using the R package oligo. RMA and quantile normalization of all probeset values were performed. An in-house perl script was used to filter out non-exonic probesets and average across probesets for each Refseq transcript. [Gene-level averaged values of Log2-transformed intensity values for all exonic probesets within each Refseq transcript are provided as supplementary file on Series records.]

label_protocol: RNA from all samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Affymetrix. Briefly, ribosomal RNA was reduced from the samples using Ribominus Human/Mouse Transcriptome isolation kit (Invitrogen, Carlsbad, California) from 1 micrograms of total RNA.  The isolated RNA was then used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the product was purified using cDNA clean-up column, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  Sense strand cDNA was then purified using cDNA clean-up column, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: Wild-type C57/Black6 male mice were provided by Charles River Laboratory, and housed in Johns Hopkins BRB Animal Facility for two weeks before experiment.

extract_protocol: Total RNA were extrated from microdissected DG tissues using TRIzol reagent following the standard protocol.

treatment_protocol: Electroconvulsive stimulation (ECS) was administered with pulses consisted of 1.0 s, 100 Hz, 18 mA stimulus of 0.3 ms delivered using the Ugo Basile ECT unit (Model 57800)

value: wild type

tag: gender

tag: age

value: dentate gyrus


title: adipose_169


title: DG 4h after sham, biological rep 2

description: Microdissected from whole hippocampus


title: DG 4h after sham, biological rep 1

description: Microdissected from whole hippocampus


title: DG 4h after ECS, biological rep 1

description: Microdissected from whole hippocampus


title: adipose_144


title: adipose_148


title: adipose_151


title: adipose_145


title: adipose_146


title: adipose_149


title: adipose_131


title: adipose_142


title: adipose_147


title: adipose_150


title: adipose_140


title: adipose_138


title: adipose_136


title: adipose_133


title: adipose_143


title: adipose_128


title: adipose_130


title: adipose_134


title: adipose_135


title: adipose_139


title: adipose_132


title: adipose_126


title: adipose_127


title: adipose_129


title: adipose_141


title: PT 15 TO1

tag: condition

value: ovarian cancer

tag: cell type


title: adipose_137


title: adipose_125


title: adipose_124


title: adipose_123


title: adipose_122


title: adipose_121


title: adipose_120


title: adipose_115


title: adipose_116


title: adipose_118


title: adipose_114


title: adipose_97


title: adipose_119


title: adipose_117


title: adipose_108


title: adipose_110


title: adipose_112


title: adipose_106


title: adipose_99


title: adipose_100


title: adipose_103


title: adipose_98


title: adipose_104


title: adipose_111


title: adipose_101


title: adipose_107


title: adipose_113


title: adipose_109


title: adipose_105


title: adipose_96


title: adipose_92


title: adipose_102


title: adipose_94


title: adipose_95


title: adipose_93


title: adipose_91


title: adipose_87

value: GG


title: adipose_83


title: adipose_75


title: adipose_85


title: adipose_86


title: adipose_88


title: adipose_89


title: adipose_84


title: adipose_82


title: adipose_80


title: adipose_81


title: adipose_78


title: adipose_90


title: adipose_76


title: adipose_79


title: adipose_77


title: adipose_74


title: adipose_72


title: adipose_71


title: adipose_68


title: adipose_69


title: adipose_67


title: adipose_66


title: adipose_65


title: adipose_61


title: adipose_70


title: adipose_64


title: adipose_62


title: adipose_60


title: adipose_73


title: adipose_56


title: adipose_54


title: adipose_58


title: adipose_63


title: adipose_59


title: adipose_57


title: adipose_36


title: adipose_52


title: adipose_48


title: adipose_53


title: adipose_40


title: adipose_55


title: adipose_44


title: adipose_33


title: adipose_47


title: adipose_46


title: adipose_51


title: adipose_42


title: adipose_38


title: adipose_32


title: adipose_50


title: adipose_34


title: adipose_49


title: adipose_39


title: adipose_41


title: adipose_35


title: adipose_31


title: adipose_45


title: adipose_37


title: adipose_43


title: adipose_29


title: adipose_30


title: adipose_27


title: adipose_25


title: adipose_26


title: adipose_24


title: adipose_19


title: adipose_23


title: adipose_15


title: adipose_7


title: adipose_11


title: adipose_16


title: adipose_17


title: adipose_18


title: adipose_22


title: adipose_20


title: adipose_14


title: adipose_12


title: adipose_4


title: adipose_9


title: adipose_3


title: adipose_8


title: adipose_5


title: adipose_6


title: adipose_10


title: adipose_1


title: adipose_21


title: adipose_2


title: adipose_13


title: Fucose replicate 2

city: Amherst

first: Jeffrey

middle: L

last: Blanchard

address: 203 Morrill Science Center IVN

department: Biology

institute: University of Massachusetts Amherst

hyb_protocol: The labeled cDNA samples were hybridized with our Affymetrix GeneChip Arrays according to Affymetrix guidelines.

scan_protocol: The hybridized arrays were scanned with a GeneChip Scanner 3000.

data_processing: In addition expression values were calculated using the Robust Multichip Average method

organism: Lachnoclostridium phytofermentans

source_name: 0.3% fucose, mid-exponential phase

label_protocol: Ten μg total RNA from each sample was used as template to synthesize labeled cDNAs using Affymetrix GeneChip DNA Labeling Reagent Kits.

growth_protocol: C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20].  Growth on single carbon-source utilized anaerobic medium derived from GS-2CB and containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH.  This medium was supplemented with 0.3% (wt/vol) of the specific substrate (glucose, fucose and rhamnose) added as a filter-sterilized solution to the sterile medium.  Broth cultures were incubated at 30˚C under anaerobic conditions (100% N2) as described in by Hungate [30].  Growth was determined spectrophotometrically by monitoring changes in optical density at 660 nm.

extract_protocol: RNA was purified from mid-exponential phase cultures at 27 hr for glucose and 62 hrs for fucose and rhamnose.  Samples were flash-frozen by immersion in liquid nitrogen.  The cells were collected by centrifugation for 5 minutes at 8,000 rpm at 4°C.   Harvested cells were resuspended in 100 µl in TE buffer pH 8 (EMD Chemicals) containing 2 mg/ml lysozyme (Sigma-Aldrich) and incubated at 37°C for 40 minutes.  The total RNA was isolated using RNeasy RNA purification kit (QIAGEN) according to manufacturer’s instructions.  Contaminating DNA in total RNA preparations was removed with RNAse-free DNase I (QIAGEN).  The RNA concentration was determined by absorbance at 260/280 nm using a Nanodrop.


title: Glucose replicate 2

source_name: 0.3% glucose, mid-exponential phase

tag: Strain

value: ISDg


title: Fucose replicate 1


title: Rhamnose replicate 1

source_name: 0.3% rhamnose, mid-exponential phase


title: Rhamnose replicate 2


title: Glucose replicate 1


title: HELP_ID_20204302

first: Rita

last: Shaknovich

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medical Center

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: After QC processing, a median normalization was performed on each array by subtracting the median log-ratio (HpaII/MspI) of that array (resulting in median log-ratio of 0 for each array).

source_name: MspI representation of genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: Germinal center B cells (GCBs)

source_name: HpaII representation of genomic DNA


title: HELP_ID_20202002


title: HELP_ID_130587

value: Naive B cells (NBC)


title: HELP_ID_130062


title: HELP_ID_20200402


title: HELP_ID_20198202


title: HELP_ID_128811


title: HELP_ID_129166


title: HELP_ID_20201702


title: HELP_ID_129164


title: HELP_ID_20200702


title: HELP_ID_20195402


title: Umbilical cord blood_5290

city: Memphis

first: Ronald

middle: M

last: Adkins

state: TN

address: 50 N Dunlap, 308 West Patient Tower

department: Pediatrics

institute: Univ TN Health Science Center

hyb_protocol: Standard Illumina Humanmethylation27 array protocol

data_processing:
Default parameters in Illumina GenomeStudio version 1.7.0 software methylation module
Pairs of columns contain beta values (proportion of DNA molecules methylated at that site) and detection p values (indication of ability to distinguish measurements for that site from background)

label: Cy3 and Cy5

source_name: Buffy coat

extract_protocol: Promega Corp Maxwell 16 Blood DNA purification kit used with Maxwell 16 automated nucleic acids extractor

treatment_protocol: Umbilical cord blood samples were centrifuged, buffy coal drawn off by pipet and frozen until DNA extraction

value: Male

tag: maternal age (year)

tag: ethnicity

value: Caucasian


title: Umbilical cord blood_5316

scan_protocol: Standard Illumina Humanmethylation27 array protocol

value: Female


title: HELP_ID_20200602


title: HELP_ID_20209402


title: HELP_ID_20216902


title: HELP_ID_101693


title: HELP_ID_130502


title: Umbilical cord blood_5275

label_protocol: Standard Illumina Humanmethylation27 array protocol


title: adipose_28


title: Umbilical cord blood_5317


title: Umbilical cord blood_5320


title: Umbilical cord blood_5348


title: Umbilical cord blood_5286


title: Umbilical cord blood_5367


title: Umbilical cord blood_5280

value: African-American


title: Umbilical cord blood_5288


title: Umbilical cord blood_5272


title: Umbilical cord blood_5278


title: Umbilical cord blood_5247


title: Umbilical cord blood_5248


title: Umbilical cord blood_5246


title: Umbilical cord blood_5258


title: Umbilical cord blood_5239


title: Umbilical cord blood_5236


title: Umbilical cord blood_5188


title: Umbilical cord blood_5235


title: Umbilical cord blood_5225


title: Umbilical cord blood_5214


title: Umbilical cord blood_5204


title: Umbilical cord blood_5224


title: Umbilical cord blood_5216


title: Umbilical cord blood_5193


title: Umbilical cord blood_5207


title: Umbilical cord blood_5189


title: Umbilical cord blood_5219


title: Umbilical cord blood_5211


title: Umbilical cord blood_5213


title: Umbilical cord blood_5208


title: Umbilical cord blood_5237


title: Umbilical cord blood_5195


title: Umbilical cord blood_5223


title: Umbilical cord blood_5198


title: Umbilical cord blood_5186


title: Umbilical cord blood_5212


title: Umbilical cord blood_5190


title: Umbilical cord blood_5180


title: Umbilical cord blood_5185


title: Umbilical cord blood_5368


title: Umbilical cord blood_5177


title: Umbilical cord blood_5150


title: Umbilical cord blood_5154


title: Umbilical cord blood_5175


title: Umbilical cord blood_5151


title: Umbilical cord blood_5156


title: Umbilical cord blood_5158


title: Umbilical cord blood_5169


title: Umbilical cord blood_5170


title: Umbilical cord blood_5149


title: Umbilical cord blood_5140


title: Umbilical cord blood_5146


title: Umbilical cord blood_5131


title: Umbilical cord blood_5155


title: Umbilical cord blood_5152


title: Umbilical cord blood_5139


title: Umbilical cord blood_5137


title: Umbilical cord blood_5171


title: Umbilical cord blood_5157


title: Umbilical cord blood_5136


title: Umbilical cord blood_5142


title: Umbilical cord blood_5141


title: Umbilical cord blood_5126


title: Umbilical cord blood_5147


title: Umbilical cord blood_5135


title: Umbilical cord blood_5174


title: Umbilical cord blood_5125


title: Umbilical cord blood_5123


title: Umbilical cord blood_5124


title: Umbilical cord blood_5172


title: Umbilical cord blood_5120


title: Umbilical cord blood_5099


title: Umbilical cord blood_5107


title: Umbilical cord blood_5100


title: Umbilical cord blood_5104


title: Umbilical cord blood_5115


title: Umbilical cord blood_5103


title: Umbilical cord blood_5116


title: Umbilical cord blood_5079


title: Umbilical cord blood_5070


title: Umbilical cord blood_5091


title: Umbilical cord blood_5089


title: Umbilical cord blood_5094


title: Umbilical cord blood_5087


title: Umbilical cord blood_5073


title: Umbilical cord blood_5069


title: Umbilical cord blood_5086


title: Umbilical cord blood_5085


title: Umbilical cord blood_5098


title: Umbilical cord blood_5083


title: Umbilical cord blood_5074


title: Umbilical cord blood_5106


title: Umbilical cord blood_5077


title: Umbilical cord blood_5081


title: Umbilical cord blood_5110


title: Umbilical cord blood_5109


title: E.albidus_3 weeks_pH_rep3

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning was performed using an Agilent Microarray Scanner (Agilent Technologies) at 532 and 635 nm for Cy3 and Cy5 respectively. The images acquired were assessed using QuantArray (Packard Biochip Technologies) for spot identification and quantification of fluorescent signal intensities.

data_processing: The limmaGUI package (based on limma (Smyth 2005)) in the R (2.8.0) software environment (http://www.R-project.org) was used for background subtraction, normalization and succeeding statistical analysis of the microarray datasets. The Log2 transformed Cy3/Cy5 ratio data were normalized using the global loess (Yang et al., 2002), which is an intensity-based method.

organism: Enchytraeus albidus

source_name: E.albidus maintained for the same 3 weeks in clean LUFA 2.2 soil - Control RNA sample

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 7µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 150 pmol labelled target was vacuum dried.

extract_protocol: 15 worms per replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C. All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1,5U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 50µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (15 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure

tag: time

value: 3 weeks

source_name: E.albidus exposed to OECD soil with lower pH for 3 weeks

value: OECD soil with lower pH


title: E.albidus_3 weeks_OM_rep3

source_name: E.albidus exposed to OECD soil with lower organic matter content for 3 weeks


title: E.albidus_3 weeks_OM_rep1

value: OECD soil with lower organic matter content


title: E.albidus_3 weeks_St_rep1

source_name: E.albidus exposed to standard OECD soil for 3 weeks

value: standard OECD soil


title: E.albidus_3 weeks_St_rep3


title: Umbilical cord blood_5093


title: E.albidus_3 weeks_St_rep2


title: Umbilical cord blood_5064


title: E.albidus_3 weeks_pH_rep1


title: Umbilical cord blood_5063


title: E.albidus_3 weeks_pH_rep2


title: Umbilical cord blood_5052


title: Umbilical cord blood_5051


title: Umbilical cord blood_5062


title: Umbilical cord blood_5044


title: E.albidus_3 weeks_Copper 320mg/kg_rep3

source_name: E.albidus exposed to 320 mg/Kg of Copper for 3 weeks

value: 320 mg Copper/Kg soil


title: Umbilical cord blood_5036


title: Umbilical cord blood_5049


title: E.albidus_3 weeks_Copper 320mg/kg_rep2


title: Umbilical cord blood_5057


title: E.albidus_3 weeks_OM_rep2


title: Umbilical cord blood_5042


title: Umbilical cord blood_5040


title: Umbilical cord blood_5030


title: E.albidus_3 weeks_Clay_rep3

source_name: E.albidus exposed to OECD soil with higher clay content for 3 weeks

value: OECD soil with higher clay content


title: Umbilical cord blood_5050


title: E.albidus_3 weeks_Clay_rep1


title: Umbilical cord blood_5038


title: Umbilical cord blood_5029


title: E.albidus_3 weeks_Phenmedipham 10mg/kg_rep3

source_name: E.albidus exposed to 10 mg/Kg of Phenmedipham for 3 weeks

value: 10 mg Phenmedipham/Kg soil


title: E.albidus_3 weeks_Phenmedipham 32mg/kg_rep1

source_name: E.albidus exposed to 32 mg/Kg of Phenmedipham for 3 weeks

value: 32 mg Phenmedipham/Kg soil


title: Umbilical cord blood_5027


title: E.albidus_3 weeks_Clay_rep2


title: E.albidus_3 weeks_Phenmedipham 10mg/kg_rep2


title: E.albidus_3 weeks_Phenmedipham 10mg/kg_rep1


title: E.albidus_4 days_St_rep3

source_name: E.albidus maintained for the same 4 days in clean LUFA 2.2 soil - Control RNA sample

value: 4 days

source_name: E.albidus exposed to standard OECD soil for 4 days


title: Umbilical cord blood_5018


title: Umbilical cord blood_5014


title: E.albidus_4 days_St_rep1


title: E.albidus_4 days_St_rep2


title: E.albidus_4 days_pH_rep2

source_name: E.albidus exposed to OECD soil with lower pH for 4 days


title: Umbilical cord blood_5022


title: E.albidus_4 days_pH_rep3


title: Umbilical cord blood_343

value: Other


title: Umbilical cord blood_334


title: Umbilical cord blood_5015


title: Umbilical cord blood_326


title: Umbilical cord blood_5002


title: Umbilical cord blood_341


title: Umbilical cord blood_5003


title: Umbilical cord blood_5007


title: Umbilical cord blood_312


title: E.albidus_4 days_OM_rep3

source_name: E.albidus exposed to OECD soil with lower organic matter content for 4 days


title: E.albidus_4 days_OM_rep2


title: E.albidus_4 days_pH_rep1


title: E.albidus_4 days_OM_rep1


title: E.albidus_4 days_Clay_rep1

source_name: E.albidus exposed to OECD soil with higher clay content for 4 days

value: OECD with higher clay content


title: E.albidus_4 days_Clay_rep2


title: E.albidus_4 days_Clay_rep3


title: E.albidus_4 days_Cu 320mg/kg_rep3

source_name: E.albidus exposed to 320 mg/Kg of Copper for 4 days


title: E.albidus_4 days_Cu 320mg/kg_rep1


title: E.albidus_4 days_Cu 320mg/kg_rep2


title: E.albidus_3 weeks_Phenmedipham 32mg/kg_rep3


title: E.albidus_3 weeks_Phenmedipham 32mg/kg_rep2


title: Umbilical cord blood_294


title: Umbilical cord blood_302


title: E.albidus_4 days_Phenmedipham 32mg/kg_rep3

description: The hybridization performed here was the control sample vs the 10 mg/Kg Phenmedipham exposure sample.

source_name: E.albidus exposed to 32 mg/Kg of Phenmedipham for 4 days


title: Umbilical cord blood_291


title: E.albidus_4 days_Phenmedipham 32mg/kg_rep2


title: E.albidus_4 days_Phenmedipham 32mg/kg_rep1


title: Umbilical cord blood_283

value: Male


title: E.albidus_4 days_Phenmedipham 10mg/kg_rep3

source_name: E.albidus exposed to 10 mg/Kg of Phenmedipham for 4 days


title: Umbilical cord blood_258

source_name: Buffy coat

value: Caucasian


title: Umbilical cord blood_256


title: E.albidus_4 days_Phenmedipham 10mg/kg_rep2


title: Umbilical cord blood_233

value: Female


title: Umbilical cord blood_242

value: African-American


title: Umbilical cord blood_260


title: Umbilical cord blood_259


title: Umbilical cord blood_285


title: Umbilical cord blood_278


title: Umbilical cord blood_232


title: E.albidus_4 days_Phenmedipham 10mg/kg_rep1

value: Whole body extracts (15 organisms)


title: Umbilical cord blood_252


title: S_aureus_delta_graSR_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: S. aureus delta graSR mutant, third biological replicate.

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

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

data_processing: An aggregated expression value was computed for each Genbank annotated CDS as the median log2 intensity of probes lying entirely within the corresponding region. To control for possible cross-hybridization artifacts, the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_delta graSR

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: Cultures of the parental strain S. aureus HG001 and a delta graSR mutant were grown with shaking (180 rpm) at 37°C in Tryptic Soy Broth (TSB; Difco) containing 50 µg/ml colistin until OD at 600 nm = 1.

extract_protocol: Cells were 2-fold diluted in ice-cold killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3), centrifuged and immediately frozen at -80°C. Total RNA was extracted as previously described (Even et al., 2006), followed by a DNase I treatment in order to eliminate residual genomic DNA and column purification using the RNA Clean-Up kit (Norgen Biotech Corp.). RNA quality was checked by electropherogram analysis (Agilent Bioanalyzer).

tag: genotype

value: delta graSR mutant


title: S_aureus_delta_graSR_rep2

description: S. aureus delta graSR mutant, second biological replicate.


title: S_aureus_delta_graSR_rep1

description: S. aureus delta graSR mutant, first biological replicate.


title: S_aureus_wild_type_rep2

description: S. aureus wild-type, second biological replicate.

source_name: Staphylococcus aureus_wild type

tag: strain

value: wild type


title: S_aureus_wild_type_rep3

description: S. aureus wild-type, third biological replicate.


title: Umbilical cord blood_198


title: Umbilical cord blood_211


title: S_aureus_wild_type_rep1

description: S. aureus wild-type, first biological replicate.


title: Umbilical cord blood_218


title: Umbilical cord blood_157


title: Umbilical cord blood_227


title: Umbilical cord blood_200


title: Umbilical cord blood_219


title: Umbilical cord blood_176


title: Umbilical cord blood_152


title: Umbilical cord blood_177


title: Umbilical cord blood_185


title: Umbilical cord blood_174


title: Umbilical cord blood_193


title: Umbilical cord blood_191


title: Umbilical cord blood_147


title: Umbilical cord blood_209


title: Umbilical cord blood_183


title: Umbilical cord blood_207


title: Umbilical cord blood_155


title: Umbilical cord blood_134


title: PFB_2 with array type rose from Affymetrix

description:
The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission.
For developmental stages, see Boyes et al. Plant Cell 2001.

hyb_protocol: labelled extract quantity: 10ug

organism: Rosa hybrid cultivar

source_name: PFB

growth_protocol: petal - Plants were cultivated in greenhouse conditions on soil (Klasmann) containing perlite and argil. Photoperiod (day/night): 16h/8h Temperature (day/night) : 21°C/18°C Humidity : 50 to 70%

extract_protocol: PFB_2:7ug. Plant RNA kit (Macherey Nagel).

treatment_protocol: no treatment

tag: flower type

value: scented

value: petals

tag: developmental stage

value: open flower stage, oocyte collected 24 hours before ovulation


title: RFB_2 with array type rose from Affymetrix

source_name: RFB

extract_protocol: RFB_2:8ug. Plant RNA kit (Macherey Nagel).

value: non-scented

tag: tissue


title: Umbilical cord blood_149


title: Umbilical cord blood_168


title: Umbilical cord blood_129


title: PFA_1 with array type rose from Affymetrix

source_name: PFA

extract_protocol: PFA_1:5ug. Plant RNA kit (Macherey Nagel).


title: Umbilical cord blood_104


title: Umbilical cord blood_131


title: SSA_2 with array type rose from Affymetrix

description:
The objective is to identify the genes involved in petal doubling in rose. In this study we are using two rosa gallica genotypes: wild-type (simple flower rose) and Cardinal de Richelieu (double flower rose) and two rosa hybrida genotypes : Souvenir de la Malmaison, which has about 110 petal and its bud sport cultivar, Souvenir de St Anne’s
For developmental stages, see Boyes et al. Plant Cell 2001.

source_name: SSA

growth_protocol: flowers - Open field experiment, ENS Lyon field, harvesting period : April 2007

extract_protocol: SSA_2:22ug. Plant RNA kit (Macherey Nagel).

value: Souvenir de St Anne's

value: floral bud

value: early stage of floral development


title: SSA_1 with array type rose from Affymetrix

extract_protocol: SSA_1:19ug. Plant RNA kit (Macherey Nagel).


title: Umbilical cord blood_107


title: Adipose tissue 238

city: Dublin

first: Helen

last: Roche

state: Belfield

address: UCD Conway Institute of Biomolecular and Biomedical Research

country: Ireland

institute: University College Dublin

description:
100678-238.CEL
Subcutaneous adipose tissue sample from volunteer 16

hyb_protocol: The labeled and fragmented cRNA was hybridized to Affymetrix nugohs1a520180 Genechips for 16 hr at 45C. Genechips were washed and stained using the Affymetrix fluidics Station 400.

scan_protocol: Affymetrix arrays were scanned using the Affymetrix 3000G scanner.

data_processing: The data were quality checked and analyzed using the R programming language.  The GCRMA algorithm was used for background correction and normalization.

source_name: Subcutaneous adipose tissue

label_protocol: 2 μg of high quality total RNA was used with the Affymetrix Eukaryotic One-Cycle Target Labeling and Control reagents to generate Biotin-labeled antisense cRNA

extract_protocol: Total RNA was isolated using Qiagen RNeasy extraction kits

tag: individual

value: volunteer 16

tag: disease state

value: metabolic syndrome

tag: batch

tag: n-3 pufa intake g/day

value: F

value: subcutaneous adipose tissue


title: Umbilical cord blood_111

tag: gender

value: Male


title: SM_2 with array type rose from Affymetrix

source_name: SM

extract_protocol: SM_2:28ug. Plant RNA kit (Macherey Nagel).

value: Souvenir de la Malmaison


title: CDR_1 with array type rose from Affymetrix

organism: Rosa gallica

source_name: CDR

extract_protocol: CDR_1:12ug. Plant RNA kit (Macherey Nagel).

value: Cardinal de Richelieu (double flower rose)


title: SM_1 with array type rose from Affymetrix

extract_protocol: SM_1:23ug. Plant RNA kit (Macherey Nagel).


title: CDR_2 with array type rose from Affymetrix

extract_protocol: CDR_2:15ug. Plant RNA kit (Macherey Nagel).


title: E.albidus_3 weeks_Copper 320mg/kg_rep1

source_name: E.albidus maintained for the same 3 weeks in clean LUFA 2.2 soil - Control RNA sample

value: Whole body extracts (15 organisms)

value: Adult organisms with well developed clitellum

value: 3 weeks

source_name: E.albidus exposed to 320 mg/Kg of Copper for 3 weeks

value: 320 mg Copper/Kg soil


title: Adipose tissue 236

description:
100678-236.CEL
Subcutaneous adipose tissue sample from volunteer 15

value: volunteer 15


title: G2_2 with array type rose from Affymetrix

extract_protocol: G2_2:10ug. Plant RNA kit (Macherey Nagel).

value: WT (simple flower rose)


title: Adipose tissue 81

description:
100678-81.CEL
Subcutaneous adipose tissue sample from volunteer 19

value: volunteer 19


title: RFA_1 with array type rose from Affymetrix

source_name: RFA

extract_protocol: RFA_1:4.8ug. Plant RNA kit (Macherey Nagel).

value: non-scented

value: petals

value: open flower stage, oocyte collected 24 hours before ovulation


title: Adipose tissue 233

description:
100678-233.CEL
Subcutaneous adipose tissue sample from volunteer 14

value: volunteer 14


title: Adipose tissue 219

description:
100678-219.CEL
Subcutaneous adipose tissue sample from volunteer 12

value: volunteer 12

value: metabolic syndrome

value: M


title: Adipose tissue 43

description:
100678-43.CEL
Subcutaneous adipose tissue sample from volunteer 18

value: volunteer 18

value: subcutaneous adipose tissue


title: Adipose tissue 249

description:
100678-249.CEL
Subcutaneous adipose tissue sample from volunteer 17

value: volunteer 17


title: Adipose tissue 212

description:
100678-212.CEL
Subcutaneous adipose tissue sample from volunteer 11

value: volunteer 11

value: F


title: G1_1 with array type rose from Affymetrix

extract_protocol: G1_1:5ug. Plant RNA kit (Macherey Nagel).

value: floral bud

value: early stage of floral development


title: Adipose tissue 205

description:
100678-205.CEL
Subcutaneous adipose tissue sample from volunteer 09

value: volunteer 09


title: Adipose tissue 210

description:
100678-210.CEL
Subcutaneous adipose tissue sample from volunteer 10

value: volunteer 10


title: Adipose tissue 229

description:
100678-229.CEL
Subcutaneous adipose tissue sample from volunteer 13

value: volunteer 13


title: Adipose tissue 119

description:
100678-119.CEL
Subcutaneous adipose tissue sample from volunteer 08

value: volunteer 08


title: Adipose tissue 118

description:
100678-118.CEL
Subcutaneous adipose tissue sample from volunteer 07

value: volunteer 07


title: PS_1 with array type rose from Affymetrix

description:
The objective is to identify genes involved in petal development and senescence. R. chinensis cv Old Blush (OB) was used for the following reasons: it is a diploid Chinese rose that participated into the generation of modern roses (recurrent flowering, scent, etc.).
For developmental stages, see Boyes et al. Plant Cell 2001.

organism: Rosa chinensis

source_name: PS

growth_protocol: flowers - Plants were cultivated in greenhouse conditions on soil (Klasmann) containing perlite and argil. Photoperiod (day/night): 6h/8h Temperature (day/night) : 23°C/18°C Humidity : 50 to 70%

extract_protocol: PS_1:5ug. Plant RNA kit (Macherey Nagel).

tag: cultivar

value: Old Blush

value: senescing flowers


title: 1et2_2 with array type rose from Affymetrix

extract_protocol: 1et2_2:6.2ug. Plant RNA kit (Macherey Nagel).

value: floral meristem, petal primordia


title: FE_2 with array type rose from Affymetrix

source_name: FE

extract_protocol: FE_2:7.5ug. Plant RNA kit (Macherey Nagel).

value: open flowers, fully elongated petals


title: Adipose tissue 03

description:
100678-03.CEL
Subcutaneous adipose tissue sample from volunteer 03

value: volunteer 03

value: metabolic syndrome


title: FE_1 with array type rose from Affymetrix

extract_protocol: FE_1:8ug. Plant RNA kit (Macherey Nagel).


title: PS_2 with array type rose from Affymetrix

extract_protocol: PS_2:5.6ug. Plant RNA kit (Macherey Nagel).


title: Adipose tissue 110

description:
100678-110.CEL
Subcutaneous adipose tissue sample from volunteer 04

value: volunteer 04

value: M

value: subcutaneous adipose tissue


title: OSCC tumor_4155T

city: Taoyuan

first: Chien-Hua

last: Peng

address: No. 5, Fu-Hsing ST.

country: Taiwan

institute: Chang Gung Memorial Hospital

description: patient with OSCC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Data were processed using Partek software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: OSCC  specimens

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA was isolated from tissue using the Qiagen RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s protocol.

treatment_protocol: OSCC tissues were surgical dissected and immediately froze in liquid nitrogen until use

value: tumor


title: PA_1 with array type rose from Affymetrix

source_name: PA

extract_protocol: PA_1:4.9ug. Plant RNA kit (Macherey Nagel).

value: closed flower buds, petals just visible


title: OSCC tumor_4146T

description: patient with OSCC


title: Adipose tissue 113

description:
100678-113.CEL
Subcutaneous adipose tissue sample from volunteer 06

value: volunteer 06


title: 5_1 with array type rose from Affymetrix

extract_protocol: 5_1:5.2ug. Plant RNA kit (Macherey Nagel).

value: carpel primordia starting elongation


title: 3et4_2 with array type rose from Affymetrix

extract_protocol: 3et4_2:12ug. Plant RNA kit (Macherey Nagel).

value: stamen primordia


title: OSCC tumor_4130T

description: patient with OSCC


title: OSCC tumor_4145T

description: patient with OSCC


title: 5_2 with array type rose from Affymetrix

extract_protocol: 5_2:7ug. Plant RNA kit (Macherey Nagel).


title: 3et4_1 with array type rose from Affymetrix

extract_protocol: 3et4_1:6ug. Plant RNA kit (Macherey Nagel).


title: OSCC tumor_4081T

description: patient with OSCC


title: 1et2_1 with array type rose from Affymetrix

extract_protocol: 1et2_1:5ug. Plant RNA kit (Macherey Nagel).


title: OSCC tumor_4181T

description: patient with OSCC


title: OSCC tumor_4060T

description: patient with OSCC


title: PA_2 with array type rose from Affymetrix


title: OSCC tumor_4052T

description: patient with OSCC


title: OSCC tumor_4199T

description: patient with OSCC


title: W19_1

description: - Which genes are induced during floral initiation? - Are the genes involved in floral initiation identical between our 3 genotypes? - Which genes are involved in the control of recurrent blooming in rose? - Which genes are diferentially expressed between buds that will become floral and buds that will remain vegetative?

organism: Rosa lucieae

growth_protocol: shoot apex - Outdoor grown on KLASMANN RHP 15® (provided by RIPPERT), fertilized with LD10 (provided by COMPO France SAS)

tag: variety

value: Wichurana rosa

tag: days degrees

tag: developemental stage

value: floral


title: W26_1

value: vegetative


title: W19_2


title: W26_2


title: Adipose tissue 112

description:
100678-112.CEL
Subcutaneous adipose tissue sample from volunteer 05

extract_protocol: Total RNA was isolated using Qiagen RNeasy extraction kits

value: volunteer 05

value: F


title: LWP30_2

growth_protocol: shoot apex - Outdoor grown on KLASMANN RHP 15 (provided by RIPPERT), fertilized with LD10 (provided by COMPO France SAS)

value: rosa hybrida "Little White Pet"

value: vegetative, non recurrent


title: OSCC tumor_4058T

description: patient with OSCC


title: OSCC tumor_4041T

description: patient with OSCC


title: OSCC tumor_4043T

description: patient with OSCC


title: OSCC tumor_4032T

description: patient with OSCC


title: W10_2

value: vegetative, non-recurrent


title: OSCC tumor_4015T

description: patient with OSCC


title: LWP30_1


title: W03_2

value: pre-floral


title: WIII_2


title: W03_1


title: OSCC tumor_4004T

description: patient with OSCC


title: OSCC tumor_3306T

description: patient with OSCC


title: OSCC tumor_3383T

description: patient with OSCC


title: OSCC tumor_3283T

description: patient with OSCC


title: OSCC tumor_3294T

description: patient with OSCC


title: FP05_1

growth_protocol: shoot apex - Outdoor grown on KLASMANN RHP 15(provided by RIPPERT), fertilized with LD10 (provided by COMPO France SAS)

value: rosa hybrida "Fellicité and Perpetuates"


title: FP05_2


title: OSCC tumor_3326T

description: patient with OSCC


title: FP19_1


title: LWP05_1


title: WIII_1


title: FP19_2


title: OSCC tumor_3265T

description: patient with OSCC


title: OSCC tumor_3246T

description: patient with OSCC


title: OSCC tumor_3244T

description: patient with OSCC


title: OSCC tumor_3243T

description: patient with OSCC


title: W10_1


title: FP21_2


title: OSCC tumor_3268T

description: patient with OSCC


title: OSCC tumor_3234T

description: patient with OSCC


title: LWP16_1


title: FP30_1


title: FP30_2


title: LWP05_2


title: LWP16_2


title: OSCC tumor_3191T

description: patient with OSCC


title: OSCC tumor_3282T

description: patient with OSCC


title: OSCC tumor_3116T

description: patient with OSCC


title: OSCC tumor_3149T

description: patient with OSCC


title: FP21_1


title: OSCC tumor_3157T

description: patient with OSCC


title: OSCC tumor_3115T

description: patient with OSCC


title: FP13_1


title: OSCC tumor_3272T

description: patient with OSCC


title: OSCC tumor_3100T

description: patient with OSCC


title: FP13_2


title: OSCC tumor_3084T

description: patient with OSCC


title: OSCC tumor_3086T

description: patient with OSCC


title: OSCC tumor_3076T

description: patient with OSCC


title: OSCC tumor_2470T

description: patient with OSCC


title: OSCC tumor_2461T

description: patient with OSCC


title: half-sib-families G_FD_rep5

city: Brest

first: David

last: Mazurais

address: tecnopole Brest Iroise

institute: Ifremer

description: Gene expression after G half-sib family fed fish diet

hyb_protocol: Slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven, subsequently removed from the hybridization chamber, quickly submerged in GE Wash Buffer 1 to disassembly the slides and then washed in GE Wash Buffer 1 for approximately 1 minute followed by one additional wash in pre-warmed (37°C) GE Wash Buffer 2.

scan_protocol: Hybridized slides were scanned at 5 µm resolution using an Agilent G2565BA DNA microarray scanner. Default settings were modified to scan the same slide twice at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%). The two linked images generated were analysed together and data were extracted and background subtracted using the standard procedures contained in the Agilent Feature Extraction (FE) Software version 9.5.1.

data_processing: The software returns a series of spot quality measures in order to evaluate the goodness and the reliability of spot intensity estimates. All control features (positive, negative, etc.) except Spike-in data (Spike-In Viral RNAs) were excluded from subsequent analyses. Spike-in probe intensities were used to assess the performance of the normalization procedure for each dataset. After normalization, spike-in intensities are expected to be uniform across the experiments of a given dataset.microarray data were normalized across all arrays using the cyclic lowess approach

organism: Dicentrarchus labrax

source_name: half-sib-families G_FD_rep5

label_protocol: 200 ng of total RNA were linearly amplified and labeled with Cy3-dCTP according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Labeled cRNA was purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol Cy3/µg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer. A total of 1,650 ng of labeled cRNA was prepared for fragmentation adding 11 µl 10X Blocking Agent and 2.2 µl of 25X Fragmentation Buffer, heated at 60°C for 30 min, and finally diluted by addition with 55 µl 2X GE Hybridization buffer. A volume of 100 µl of hybridization solution was then dispensed in the gasket slide and assembled to the microarray slide (each slide containing four arrays).

growth_protocol: fish fed ad libitum during 9 months

extract_protocol: RNA was prepared using Trizol extraction protocole (Invitrogen)

treatment_protocol: FD consisted of fish oil and fish meal while VD consisted of vegetable oil and vegetable meal

value: liver

value: Male

value: adult

tag: group

value: half-sib-families G

tag: diet

value: fish


title: OSCC tumor_2449T

description: patient with OSCC

value: tumor


title: half-sib-families G_FD_rep1

source_name: half-sib-families G_FD_rep1

value: Female


title: half-sib-families G_FD_rep4

source_name: half-sib-families G_FD_rep4


title: half-sib-families G_VD_rep4

description: Gene expression after G half-sib family fed vegetable diet

source_name: half-sib-families G_VD_rep4

value: vegetable


title: OSCC tumor_2403T

description: patient with OSCC


title: OSCC tumor_2442T

description: patient with OSCC


title: OSCC tumor_2378T

description: patient with OSCC


title: half-sib-families G_FD_rep3

source_name: half-sib-families G_FD_rep3


title: half-sib-families G_VD_rep2

source_name: half-sib-families G_VD_rep2


title: OSCC tumor_2332T

description: patient with OSCC


title: half-sib-families G_VD_rep3

source_name: half-sib-families G_VD_rep3


title: half-sib-families G_FD_rep2

source_name: half-sib-families G_FD_rep2


title: half-sib-families G_VD_rep1

source_name: half-sib-families G_VD_rep1


title: OSCC tumor_2451T

description: patient with OSCC


title: half-sib-families g_FD_rep7

description: Gene expression after g half-sib family fed fish diet

source_name: half-sib-families g_FD_rep7

value: half-sib-families g


title: half-sib-families G_VD_rep5

source_name: half-sib-families G_VD_rep5


title: half-sib-families g_FD_rep8

source_name: half-sib-families g_FD_rep8


title: OSCC tumor_2328T

description: patient with OSCC


title: OSCC tumor_2309T

description: patient with OSCC


title: OSCC tumor_2343T

description: patient with OSCC


title: half-sib-families g_FD_rep3

source_name: half-sib-families g_FD_rep3


title: OSCC tumor_2266T

description: patient with OSCC


title: half-sib-families g_FD_rep2

source_name: half-sib-families g_FD_rep2


title: half-sib-families g_FD_rep6

source_name: half-sib-families g_FD_rep6


title: half-sib-families g_FD_rep4

source_name: half-sib-families g_FD_rep4


title: OSCC tumor_2341T

description: patient with OSCC

source_name: OSCC  specimens


title: half-sib-families g_VD_rep5

description: Gene expression after g half-sib family fed vegetable diet

source_name: half-sib-families g_VD_rep5


title: half-sib-families g_VD_rep6

source_name: half-sib-families g_VD_rep6


title: half-sib-families g_FD_rep5

source_name: half-sib-families g_FD_rep5


title: OSCC tumor_2237T

description: patient with OSCC


title: OSCC tumor_2193T

description: patient with OSCC


title: ACC S9

city: Ube

first: Atsunori

last: Oga

state: Yamaguchi

address: Minami-Kogushi 1-1-1

department: Pathology

country: Japan

institute: Yamaguchi University

description: without PCR

hyb_protocol: For hybridization, labeled DNA was mixed with Cot-1 DNA (50 mg, Gibco BRL, Gaithersburg, MD, USA) and ethanol precipitated. The precipitated DNA was dissolved in 40 µl hybridization  mix. The probe mixture was denatured at 75 ◦C for 5 min and incubated at 37 ◦C for 60 min for blocking of repetitive sequences. The arrays were prehybridized with salmon sperm DNA to reduce non-specific back-ground staining. The probe mixture was applied to the array. The arrays were placed in a moist chamber at 37 ◦C for 72 h for hybridization. The array slides were washed twice in 2 × standard saline citrate (2 ×SSC), 50% formamide, pH 7.0, at 45 ◦C. Then the array slides were washed well in phosphate buffer with 0.1% NP-40, pH 8.0, in 2 × SSC at room temperature.

scan_protocol: After hybridization, the slides were scanned on a GenePix 4000A scanner (Axon Instruments, Union City, CA, USA) and the 16-bit TIFF images were captured using GenePix Pro 5.0 software. The fluorescence images were analyzed using a software (MacViewer, Macrogen Inc.) optimized for analysis of the array. The fluorescence spots were defined using the automatic grid feature and adjusted manually.

data_processing:
Then the ratio of the green:red channel of each clone was calculated and all CGH ratios were converted to log base 2 (log2 ratios). The clones with log2 ratios that exceeded ± 0.25 were considered gain and loss of the copy number.
Because the chromosomal region showing high-level gain often contain an important oncogene, the high-level gain was marked and defined a log2 (green/red) ratio >1.0 as an amplification.
In order to define chromosomal regions with DCNAs, the adaptive weights smoothing (AWS) procedure with the gain and loss analysis of DNA (GLAD) algorithm was applied to the ratio data.

source_name: ACC case 9 cells

label_protocol: Test DNA and sex-matched reference DNA (Promega, Madison, WI) were labeled with Cy3 and Cy5-dCTP, (Perkin-Elmer Life Science), respectively, with a random primer labelling kit (BioPrime, DNA Labelling System, Invitrogen Co.).

extract_protocol: using a commercial kit, DNeasy Tissue Kit, (Qiagen Co., Hilden, Germany) according to the manufacturer’s instructions

treatment_protocol: no chemotherapy, no radiation therapy

value: adenoid cystic carcinoma (ACC)

tag: case

value: frozen cancer tissue

source_name: human normal cell (reference)

tag: reference provider

value: Promega Co.


title: OSCC tumor_1458T

description: patient with OSCC


title: OSCC tumor_2133T

description: patient with OSCC


title: half-sib-families g_VD_rep3

source_name: half-sib-families g_VD_rep3


title: OSCC tumor_1427T

description: patient with OSCC


title: half-sib-families g_VD_rep1

source_name: half-sib-families g_VD_rep1


title: ACC S8

description: without PCR

source_name: ACC case 8 cells


title: ACC S7

description: without PCR

source_name: ACC case 7 cells


title: ACC S5

description: without PCR

source_name: ACC case 5 cells


title: ACC S6

description: without PCR

source_name: ACC case 6 cells


title: half-sib-families g_FD_rep1

source_name: half-sib-families g_FD_rep1


title: B. subtilis_RNaseY depletion_replicate C_hyb1

description: B. subtilis_RNase Y depletion_third biological replicate

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B. subtilis GP193_with xylose

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: The B. subtilis strain GP193 expressing the essential gene rny (encoding RNase Y) under a xylose inducible promoter was grown under vigorous agitation at 37 °C in CSE minimal medium (Wacker et al., 2003, Microbiology 149: 3001-3009) in the presence and absence of xylose.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002, J. Bacteriol. 184: 2500-2520).

treatment_protocol: Cells were harvested immediately after the first detectable change in growth rate of the culture without xylose due to the reduced amounts of RNase Y.

tag: strain

tag: treatment

value: with xylose

source_name: B. subtilis GP193_without xylose

value: no xylose


title: ACC S10

description: without PCR

source_name: ACC case 10 cells


title: half-sib-families g_VD_rep4

source_name: half-sib-families g_VD_rep4

tag: developmental stage


title: B. subtilis_RNaseY depletion_replicate C_hyb2

description: B. subtilis_RNase Y depletion_third biological replicate_dye swap


title: half-sib-families g_VD_rep2

source_name: half-sib-families g_VD_rep2

tag: tissue


title: OSCC tumor_1058T

description: patient with OSCC

source_name: OSCC  specimens


title: ACC S3

description: without PCR

source_name: ACC case 3 cells


title: ACC S2

description: without PCR

source_name: ACC case 2 cells


title: ACC S4

description: without PCR

source_name: ACC case 4 cells


title: B. subtilis_RNaseY depletion_replicate B_hyb2

description: B. subtilis_RNase Y depletion_second biological replicate_dye swap


title: Normal oral tissue_89N

description: normal person

source_name: Normal oral tissue

value: normal


title: B. subtilis_RNaseY depletion_replicate B_hyb1

description: B. subtilis_RNase Y depletion_second biological replicate