title: A673_EWS/FLI_7/6_0.2ug

status: Public on Jan 31 2012

type: RNA

city: Salt Lake City

first: Wen

last: Luo

state: UT

address: 2000 Circle of Hope

country: USA

institute: Huntsman Cancer Institute

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_011

hyb_protocol: Five microgram or otherwise indicated amount of total RNA samples were used to combine with Agilent Hi-RPM GE Hybridization kit reagents and hybridized to the array slides at 65 °C for 17 h. The slides were washed in 6xSSPE, 0.005% N-lauroylsarcosine for 1 min at 20 °C and in 0.06xSSPE, 0.005% N-lauroylsarcosine for 1 min at 31 °C. The slides were then incubated with 0.025 mg/ml S9.6 antibody diluted in 500 ml of SB+BSA (100 mM MES, pH 6.6, 1 M NaCl, 0.05% Tween 20, and 1 mg/ml BSA) for 60 min at 25 °C. After washing four times for 3 min in NSWB (6xSSPE, 0.01% Tween 20), the slides were incubated with 3 ug/ml Cy3-labeled goat anti-mouse secondary antibody diluted in 500 ml of SB+BSA for 60 min at 25 °C. The slides were then washed four times for 3 min in NSWB at room temperature and scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software. Feature extraction of the scanned images was done using Agilent Feature Extraction Software version 9.5.1.

scan_protocol: Slides were scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software.

data_processing: Images obtained from the Agilent microarray scanner were processed using Agilent Feature Extraction software version 10.5.1.1. Features flagged as non-uniform or population outliers were discarded. The gProcessedSignal values (which have undergone a spatial detrending correction in the Feature Extraction software) from remaining features for each unique probe sequence were averaged and then log2 transformed.A 'normalized' value was obtained for each probe by calculating a log ratio of each probe in a test sample hybridization to the corresponding probe from a negative control hybridization. In essence this “subtracts” the background hybridization observed in the control from the values obtained in the test sample. Finally, these log ratios were shifted by the addition of the average log intensity from all probes on the control array. This yields a log ratio value within the same range as the original log intensities, which allows us to visualize log ratio and log intensity data on the same scale.In the experiment with overexpressed fusion transcripts in 293 cells, the negative control is wild-type 293 cells. In the experiment with Ewing sarcoma cell lines expressing endogenous fusion transcripts, a negative control data set was derived as followed because of the lack of a negative cell line. Total RNA was extracted individually from five Ewing cell lines (A673, TC466, ST97-894, TC32, RDES) containing different known fusion types and subjected to hybridization with the array.  A negative control value for each fusion probe was obtained by averaging the log intensities of that probe from the hybridization of RNA from the cell lines known to be absent of that fusion type. For example, the EWS/FLI 7/6 fusion is known to present in A673 and TC32 cells. When calculating the negative control value of probe for EWS/FLI 7/6 fusion, only the log intensities of this probe from TC466, ST97-894, and RDES hybridization was averaged and served as negative control for this probe. An Excel spreadsheet was designed to perform normalization and display of the data as a heatmap from these arrays.

molecule: total RNA

organism: Homo sapiens

source_name: cell line

label_protocol: standard label protocol

growth_protocol: Cell lines were grown in their respective media.

extract_protocol: RNeasy mini kit (Qiagen) and High Pure RNA Paraffin Kit (Roche) were used to extract total RNA from cells/frozen tumors and FFPE xenograft tumors, respectively.

tag: background cell line

value: A673 Ewing cell line

tag: variation/fusion type

tag: sample type

value: cell line


title: A673_EWS/FLI_7/6_0.05ug

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_012


title: ST97894_EWS/FLI_10/8

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_008

value: ST97894 Ewing cell line


title: Frozen_tumor2_EWS/ERG_7/8

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_014

source_name: tissue

value: tumor xenografts


title: A673_EWS/FLI_7/6_0.5ug

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_010


title: Frozen_tumor1_EWS/FLI_7/5

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_013


title: Met_wound at D3_biological rep2

city: Gainesville

first: James

middle: R

last: Monaghan

state: FL

address: 2033 Mowry Road

department: Biology

institute: University of Florida

description:
MD3WH2
Gene expression data from regenerating flank full thickness skin wounds

hyb_protocol: Following fragmentation, cRNA were hybridized for on 32 GeneChip Axolotl Microarrays (AMBY_002a520748F) in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.

data_processing: Microarray data was analyzed in the software system R using the Bioconductor package and oneChannelGUI. Microarray data was preprocessed and normalized using RMA and a linear model testing the effect of time for each morph type was fit for each gene across all 32 GeneChips using limma.

label: biotin

organism: Ambystoma mexicanum

source_name: Terrestrial axolotl 3 day flank wound

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

growth_protocol: Animals were housed individually in Aquatic Habitats flow-through systems (aquatics) or on wet paper towels (terrestrials) at 21-23˚C in 40% Holtfreter’s Solution.

extract_protocol: RNA was isolated using Trizol Reagent followed by Qiagen RNeasy Clean-up columns

treatment_protocol: Sterile 4mm biopsy punches were used to create full thickness epithelial wounds through the flank skin into the dorsal muscle.  The entire wound was harvested using a 6mm biopsy punch and iridectomy scissors.

tag: animal type

value: terrestrial

tag: tissue

value: flank skin wound

tag: days post injury

value: 3 days


title: FFPE_xenograft_EWS/FLI_7/6

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_015

value: FFPE primary tumors


title: FFPE_patient_EWS/FLI_7/6

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_016


title: Met_wound at D1_biological rep4

description:
MD1WH4
Gene expression data from regenerating flank full thickness skin wounds

source_name: Terrestrial axolotl 1 day flank wound

value: 1 day


title: Met_wound at D7_biological rep4

description:
MD7WH4
Gene expression data from regenerating flank full thickness skin wounds

source_name: Terrestrial axolotl 7 day flank wound

value: 7 days


title: RDES_EWS/FLI_7/5

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_007

value: RDES Ewing cell line


title: Met_wound at D0_biological rep4

description:
MD0WH4
Gene expression data from regenerating flank full thickness skin wounds

source_name: Terrestrial axolotl time 0 flank wound

value: 0 (uninjured)


title: Met_wound at D1_biological rep1

description:
MD1WH1
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D7_biological rep2

description:
MD7WH2
Gene expression data from regenerating flank full thickness skin wounds


title: A673_EWS/FLI_7/6_5ug

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_009


title: Met_wound at D1_biological rep2

description:
MD1WH2
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D3_biological rep3

description:
MD3WH3
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D1_biological rep3

description:
MD1WH3
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D7_biological rep3

description:
MD7WH3
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D3_biological rep4

description:
MD3WH4
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D3_biological rep1

description:
MD3WH1
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D0_biological rep3

description:
MD0WH3
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D0_biological rep2

description:
MD0WH2
Gene expression data from regenerating flank full thickness skin wounds


title: Met_wound at D7_biological rep1

description:
MD7WH1
Gene expression data from regenerating flank full thickness skin wounds


title: TC466_EWS/ERG_7/8

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_006

value: TC466 Ewing cell line


title: A673_EWS/FLI_7/6

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_005


title: 293_EWS/ERG_7/8

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_004

value: wild-type 293 cells


title: 293_EWS/FLI_7/7

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_003


title: Paed_wound at D7_biological rep3

description:
PD7WH3
Gene expression data from regenerating flank full thickness skin wounds

source_name: Aquatic axolotl 7 day flank wound

value: aquatic


title: Paed_wound at D7_biological rep4

description:
PD7WH4
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D3_biological rep2

description:
PD3WH2
Gene expression data from regenerating flank full thickness skin wounds

source_name: Aquatic axolotl 3 day flank wound


title: Met_wound at D0_biological rep1

description:
MD0WH1
Gene expression data from regenerating flank full thickness skin wounds


title: 293_EWS/FLI_7/6

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_002


title: Paed_wound at D3_biological rep3

description:
PD3WH3
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D1_biological rep3

description:
PD1WH3
Gene expression data from regenerating flank full thickness skin wounds

source_name: Aquatic axolotl 1 day flank wound


title: Paed_wound at D7_biological rep1

description:
PD7WH1
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D7_biological rep2

description:
PD7WH2
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D3_biological rep1

description:
PD3WH1
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D1_biological rep1

description:
PD1WH1
Gene expression data from regenerating flank full thickness skin wounds


title: 293_EMPTY

description:
Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion, and  Cy3-labeled anti-mouse IgG secondary antibody (instead of total RNA being labeled with Cy3)
ADOT_001

value: wild type


title: Paed_wound at D1_biological rep4

description:
PD1WH4
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D3_biological rep4

description:
PD3WH4
Gene expression data from regenerating flank full thickness skin wounds


title: Paed_wound at D0_biological rep4

description:
PD0WH4
Gene expression data from regenerating flank full thickness skin wounds

source_name: Aquatic axolotl time 0 flank wound


title: 48 hpf MES Rep 1

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: 48 hpf zebrafish embryo exposed to MES - Rep 1

hyb_protocol: Hybridization was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

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

organism: Danio rerio

source_name: 48 hpf Danio Rerio MES

label_protocol: Labeling was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Embryos were dechorionated at 4 hpf, and exposed to vehicle control, 50 ug/mL of 1.5nm MES AuNP, or 10 ug/mL of TMAT-AuNP from 6-24 or 6-48 hpf in 37C

extract_protocol: total RNA was isolated using Trizol protocol

treatment_protocol: Embryos were either exposed to vehicle control, 10ug/mL 1.5nm TMAT-AuNPs, or 50 ug/mL of 1.5nm MES-AuNPs

tag: agent

value: MES

tag: developmental stage

value: 48 hpf embryo


title: 48 hpf TMAT Rep 2

description: 48 hpf zebrafish embryo exposed to TMAT - Rep 2

source_name: 48 hpf Danio Rerio TMAT

value: TMAT


title: 48 hpf TMAT Rep 3

description: 48 hpf zebrafish embryo exposed to TMAT - Rep 3


title: Paed_wound at D1_biological rep2

description:
PD1WH2
Gene expression data from regenerating flank full thickness skin wounds


title: 48 hpf MES Rep 3

description: 48 hpf zebrafish embryo exposed to MES - Rep 3


title: 48 hpf MES Rep 2

description: 48 hpf zebrafish embryo exposed to MES - Rep 2


title: 48 hpf CON Rep 3

description: 48 hpf zebrafish embryo exposed to CON - Rep 3

source_name: 48 hpf Danio Rerio CON

value: CON


title: Paed_wound at D0_biological rep3

description:
PD0WH3
Gene expression data from regenerating flank full thickness skin wounds


title: 48 hpf TMAT Rep 1

description: 48 hpf zebrafish embryo exposed to TMAT - Rep 1


title: Paed_wound at D0_biological rep2

description:
PD0WH2
Gene expression data from regenerating flank full thickness skin wounds


title: GRTH KO 1

city: Bethesda

first: Chon-Hwa

last: Tsai-Morris

state: Md

address: Bldg. 49, Rm 6B03, 49 Convent Drive

department: PDEGEN, NICHD, NIH

description:
Test
KO.1

data_processing: The arrays were run on an ABI Prism 7900 HT Sequence Detection System (Applied Biosystems).  miRNAs were excluded from the analysis if cycle threshold (Ct) values were above 35 or high variation was found.

label: TaqMan MGB probe

organism: Mus musculus

source_name: Round spermatids of GRTH KO mice

label_protocol: Rodent TaqMan® Low Density miRNA Arrays A v2.0 (TLDA) was used to detect and quantify mature miRNAs expression level in accordance with the manufacturer’s instructions. 500 ng total RNA were reverse transcribed using the miRNA reverse transcription kit with the Megaplex pool containing about 380 stem-looped reverse transcription (RT) primers.

growth_protocol: Adult wild type (C57BL/6-SV129J) (Charles River Laboratories Inc.) and GRTH knock-out male mice (Tsai-Morris, et al, PNAS, 2004,101:6373) were housed in pathogen-free, temperature- and light-controlled conditions (20 °C; alternating light-dark cycle with 14 h of light and 10 h of darkness)

extract_protocol: Total RNA enriched for small RNAs was isolated from purified round spermatids either from wild type or GRTH knock-out mice by using the mirVanaTM miRNA isolation kit (Ambion)

treatment_protocol: Roudn spermatids were prepared from the tesits by collagenase/trypsin dispersion and purified by centrifugal elutriation

tag: strain

tag: genotype/variation

value: GRTH KO

tag: age

value: 3-4 month old


title: Wild type 2

description:
Control
WT.2

source_name: Round spermatids of adult wild type mice

value: Wild type


title: bovine monocyte-derived macrophage challenged with Mycobacterium avium subspecies paratuberculosis at T24 rep3

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description:
713_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep 3

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Following the hybridisation for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: All Affymetrix Bovine Genome Array microarrays were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing:
Affymetrix® GeneChip® Bovine Genome Array data were analysed using Bioconductor [http://www.bioconductor.org] contained within the R statistical package (http://www.r-project.org). Normalisation of raw data was performed using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm. In total, 89 arrays were used for normalisation, including 21 arrays from Mycobacterium bovis stimulated MDM across the same time course and 20 arrays from M. bovis (BCG) stimulated MDM across the same time course. The FARMS algorithm uses only perfect match probes and a quantile normalization procedure, which provides the signal intensities.
Microarray raw data quality control was assessed using the simpleaffy package in R (Wilson and Miller, 2005, Bioinformatics 21(18): 3683-3685 ). The microarray for  Mycobacterium avium subspecies paratuberculosis-infected MDM for animal 713 at 6hrs time point did not pass quality control and so was removed from the analysis

organism: Bos taurus

source_name: Bovine monocyte-derived macrophages cultured with Mycobacterium avium subspecies paratuberculosis for 24 hr

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

growth_protocol: For monocyte isolation, 300 ml of whole blood was collected in acid citrate dextrose buffer (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) in sterile bottles. Blood was layered onto Accuspin™ tubes containing Histopaque® 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and following density gradient centrifugation, peripheral blood mononuclear cells (PBMC) were collected. Contaminating red blood cells (RBC) were removed following resuspension and subsequent incubation of the PBMC in RBC lysis buffer (10mM KHCO3, 150mM NH4Cl, 0.1mM EDTA pH 8.0) for 5 minutes at room temperature. After incubation, PBMC were washed twice with phosphate-buffered saline (PBS) before resuspending cells in phosphate-buffered saline (PBS) containing 1% bovine serum albumin (BSA, Sigma-Aldrich Ireland Ltd., Dublin, Ireland). Monocytes were then isolated using the MACS protocol and a human anti-CD14 antibody (Miltenyi Biotec Ltd., Surrey, UK), which has been shown to be cross-reactive with bovine monocytes. All procedures were carried out according to the manufacturers’ instructions. The identity and purity of monocytes was confirmed by flow cytometry using an anti-CD14 FITC labelled antibody (data not shown). This method has been previously shown by us to yield a purity of CD14+ cells >= 99%. Purified monocytes were seeded at 1+E6/ml in 24-well tissue culture plates in RPMI 1640 medium (Invitrogen Ltd., Paisley, UK) containing 15% heat inactivated foetal calf serum (FCS; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), 1% non-essential amino acids (NEAA; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), gentamicin (5 µg/ml; Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and incubated at 37°C, 5% CO2. Following 24 hours incubation (day one) the media was replaced with 1ml fresh antibiotic-containing media to remove any non-adhered cells. On day three, media was replaced with 1 ml antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). To ensure that the same number of MDM were subjected to different treatments between experiments, cells were dissociated on day five using a non-enzymatic cell dissociation solution (Sigma-Aldrich Ireland Ltd., Dublin, Ireland), counted and then re-seeded at 2+E5 cells/well in 24-well tissue culture plates (Sarstedt, County Wexford, Ireland) using antibiotic-free culture media. By day eight, 80-100% confluent monolayers of MDM were generated that displayed the characteristic macrophage morphology as confirmed by Giemsa staining. Day eight MDM were used for the in vitro challenge experiments withMycobacterium avium subspecies paratuberculosis.

extract_protocol: All RNA extractions were performed in the CL3 laboratory using an RNeasy kit incorporating an on-column DNase treatment step (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 8.5. cDNA labelling, hybridisation and scanning for the microarray experiments were performed using a one-cycle amplification/labelling protocol on the Affymetrix GeneChip Bovine Genome Array (http://www.affymetrix.com). This array represents over 23,000 transcripts and includes approximately 19,000 UniGene clusters.

treatment_protocol: All challenge experiments including the preparation of non-challenge control samples were performed in the CL3 laboratory. Prior to the Mycobacterium avium subspecies paratuberculosis challenge experiments, MDMs from two adjacent culture plate wells were lysed using RLT buffer from the RNeasy Mini kit (Qiagen Ltd., Crawley, UK) supplemented with 1% Beta-mercaptoethanol (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and pooled. These samples constituted the 0 hour control MDM samples. MDM samples (seeded at 2E+5 cells per well) were challenged with Mycobacterium avium subspecies paratuberculosis (4E+5 cells/well; based on bacterial cell counts performed using a Petroff Hausser chamber (Fisher-Scientific, Dublin, Ireland) [multiplicity of infection 2:1] and incubated at 37°C, 5% CO2 for 2 hours, 6 hours and 24 hours. For the non-challenged control samples at each time-point, antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only) was added to each well. After 2 hours post-challenge, the media from all 6 hour and 24 hour challenge experiments was replaced with 0.5 ml fresh antibiotic-free culture media per well and re-incubated at 37°C, 5% CO2 until MDM were required for harvesting. Challenged and non-challenged control MDMs were lysed and harvested using RLT/1% Beta-mercaptoethanol buffer (Qiagen Ltd., Crawley, UK) at the designated time points. For each treatment, MDM lysates from two culture plate wells were pooled and stored at 80°C until required for RNA extraction.

tag: cell type

value: monocyte-derived macrophage

tag: breed

value: Holstein-Friesian

tag: Sex

value: Female

value: 3 years


title: Wild type 1

description:
Control
WT.1


title: GRTH KO 2

description:
Test
KO.2


title: bovine monocyte-derived macrophage challenged with Mycobacterium avium subspecies paratuberculosis at T24 rep7

description:
727R_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep 7


title: bovine monocyte-derived macrophage challenged with Mycobacterium avium subspecies paratuberculosis at T24 rep5

description:
721_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep 5


title: 24 hpf MES Rep 2

description: 24 hpf zebrafish embryo exposed to MES - Rep 2

source_name: 24 hpf Danio Rerio MES

value: 24 hpf embryo


title: 48 hpf CON Rep 1

description: 48 hpf zebrafish embryo exposed to CON - Rep 1


description:
706_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep2


title: bovine monocyte-derived macrophage challenged with Mycobacterium avium subspecies paratuberculosis at T24 rep4

description:
716_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep 4


title: 24 hpf TMAT Rep 2

description: 24 hpf zebrafish embryo exposed to TMAT - Rep 2

source_name: 24 hpf Danio Rerio TMAT


title: 24 hpf MES Rep 3

description: 24 hpf zebrafish embryo exposed to MES - Rep 3


title: 24 hpf CON Rep 2

description: 24 hpf zebrafish embryo exposed to CON - Rep 2

source_name: 24 hpf Danio Rerio CON


title: 24 hpf CON Rep 1

description: 24 hpf zebrafish embryo exposed to CON - Rep 1


title: bovine monocyte-derived macrophage challenged with Mycobacterium avium subspecies paratuberculosis at T24 rep6

description:
724R_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep 6


description:
724R_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep6

source_name: Bovine monocyte-derived macrophages cultured with Mycobacterium avium subspecies paratuberculosis for 6 hr


title: Paed_wound at D0_biological rep1

description:
PD0WH1
Gene expression data from regenerating flank full thickness skin wounds

value: flank skin wound

value: 0 (uninjured)


title: 24 hpf TMAT Rep 1

description: 24 hpf zebrafish embryo exposed to TMAT - Rep 1


title: 24 hpf CON Rep 3

description: 24 hpf zebrafish embryo exposed to CON - Rep 3


title: 24 hpf TMAT Rep 3

description: 24 hpf zebrafish embryo exposed to TMAT - Rep 3


title: 24 hpf MES Rep 1

description: 24 hpf zebrafish embryo exposed to MES - Rep 1


description:
700_Map_24Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T24 rep1


description:
716_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep4


description:
721_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep5


description:
727R_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep7


description:
700_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep1


title: 48 hpf CON Rep 2

description: 48 hpf zebrafish embryo exposed to CON - Rep 2


title: InvitroSpleen_UI14d_5

city: ADDLESTON

first: ELIHU

last: Aranday-Cortes

state: SURREY

address: Woodham Lane, New Haw

department: SEB 4

country: United Kingdom

institute: Central Veterinary Laboratories Agency-Weybridge

description: Infected with M.bovis after 14 days

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 825 ng Cy3- and Cy5-labeled fragmented cDNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values).

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using GeneSpring GX 11.5 (Agilent). After baseline transformation to mean of control samples (spleen and lung from uninfected mice), we decided to focus on those genes that reliably change their expression, then we filtered the microarrays following three conditions: 1) Filter by value. Genes that do not have normalized signal intensity values of more than -0.5 and 0.5 were disregarded. 2) Filter by flags. All the genes with flags values present in at least 100% of the values in any 1 out of the 3 conditions were considered. 3) Filter by percentile. All the genes with raw signal intensity values between 25 and 100 in any 1 out of the 3 conditions were also considered. Finally, all the genes in coincidence between filtering by flags group and filtering by percentile group were kept for statistical analysis. After filtering, parametric analysis of variance was applied to compare mean expression levels in each analysis. Data were considered significant when the Benjamini Hochberg false discovery rate (FDR) for the comparison under analysis was <0.05, and the significance level was <0.05. In order to focus on highly regulated genes, we also restricted the majority of the analysis to genes with changes in expression levels of at least 2.0-fold change (FC) in all the conditions.

source_name: Infected Spleen 14 days post infection with Mycobacterium bovis non-antigen stimulated

label_protocol: For the linear T7-based amplification step, 0.06 μg - 0.5 μg of each total RNA samples was used as starting material. To produce Cy3- and Cy5-labeled cDNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilente technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (Thermo Scientific). In general, control samples were labeled with Cy3 and experimental samples were labeled with Cy5.

growth_protocol: Two groups of 5 BALB/c mice each were infecetd with approx 600 CFU M. bovis via the intranasal route. At days 3 and 14 post challenge five mice per group were euthanized and spleens and lungs harvested. One group of 5 mice were used as a control. Their splenocytes and lung cells were stimulated in vitro for 3 days with M7 protein pool. Antigen cell culture stimulations in mice were performed using an equal pool of seven secreted, immunogenic recombinant mycobacterial proteins (Rv1886c, Rv3019c, Rv3763, Rv3804c, Rv0251, Rv0287 and Rv0288) common to M. bovis and BCG, referred here as M7 protein cocktail. Each protein was used at final concentration of 2μg/ml in 3-day culture.

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform

treatment_protocol: Five mice per group and time point were used. Spleen cells were prepared by passage through a 40μm cell strainer into DMEM supplemented with 10% (v/v) foetal calf serum (FCS) and antibiotics (100 U/ml penicillin and 100μg/ml streptomycin) (Gibco, UK) and suspended at 5 x 10^6/ml. Lung cell were isolated as follows. Briefly, thoracic cavities were opened, descending aorta transected and sterile HBSS gently injected into right heart ventricles to perfuse lungs. Lungs were excised, resuspended into digestion media (DMEM supplemented plus 10 U/ml DNAse (Sigma) and 150 U/ml collagenase type I (Gibco)) and incubated for 1 hour at 37ºC with gentle agitation (200 rpm). After digestion lungs were prepared by passage through 100 μm cell strainer into supplemented DMEM. Following washing at 1600 rpm for 5 minutes, cells were poured into another tube through a 40 μm cell strainer, washed and used at 5x10^5/well. After isolation splenocytes and lung cells were incubated for 3 days with M7 or ConA in 24-well tissue culture plates (Life Technologies). Their splenocytes and lung cells were stimulated in vitro for 3 days with M7 protein pool. Antigen cell culture stimulations in mice were performed using an equal pool of seven secreted, immunogenic recombinant mycobacterial proteins (Rv1886c, Rv3019c, Rv3763, Rv3804c, Rv0251, Rv0287 and Rv0288) common to M. bovis and BCG, referred here as M7 protein cocktail. Each protein was used at final concentration of 2μg/ml in 3-day culture. After stimulation, the plates were centrifuged (300 x g, 5 min at room temperature) and the supernatant was removed.

value: BALB/c

value: Spleen

source_name: Infected Spleen 14 days post infection with Mycobacterium bovis M7-antigen stimulated


title: InvitroSpleen_UI14d_4

description: Infected with M.bovis after 14 days


description:
727R_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep7

source_name: Bovine monocyte-derived macrophages cultured with Mycobacterium avium subspecies paratuberculosis for 2 hr


title: InvitroSpleen_UI3d_4

description: Infected with M.bovis after 3 days

source_name: Infected Spleen 3 days post infection with Mycobacterium bovis non-antigen stimulated

source_name: Infected Spleen 3 days post infection with Mycobacterium bovis M7-antigen stimulated


title: InvitroSpleen_UI14d_3

description: Infected with M.bovis after 14 days


title: InvitroSpleen_UI3d_5

description: Infected with M.bovis after 3 days


description:
706_Map_6Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T6 rep2


title: InvitroSpleen_UI14d_1

description: Infected with M.bovis after 14 days


description:
721_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep5


title: InvitroSpleen_UI3d_3

description: Infected with M.bovis after 3 days


title: InvitroSpleen_UI3d_2

description: Infected with M.bovis after 3 days


description:
700_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep1


title: 14054270 - wt1 vs invA1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system.

hyb_protocol: invA1 Cy5 / wt1 Cy3 : 30pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: invA1 infected

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - MS 22°C Long day

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001) boyes

tag: infected with

value: Salmonella typhimurium invA1 mutant

source_name: wt1 infected

treatment_protocol: Plants were grown during 14 days in solid medium and were transfered to liquid medium during 16 h. at 9 am samonella was added to a final concentration of OD600=0.2.

value: Salmonella typhimurium wild type


description:
713_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep3


title: 14054273 - invA1 vs wt1

hyb_protocol: wt1 Cy5 / invA1 Cy3 : 30pmol.


title: 14054277 - invA2 vs wt2

hyb_protocol: wt2 Cy5 / invA2 Cy3 : 30pmol.

source_name: wt2 infected

source_name: invA2 infected

value: Salmonella typhimurium invA2 mutant


title: 14054276 - wt2 vs invA2

hyb_protocol: invA2 Cy5 / wt2 Cy3 : 30pmol.


title: Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys, replicate 4

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: Biological replicate 4 of 4. Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples (100µl per microarray slot) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Agilent Technologies Scanner G2505B US22502611. Images were quantified by Agilent Feature Extraction Software (protocol GE1‐v5_95_Feb 97 and Grid: 014868_D_20060807).

data_processing: An intensity-dependent normalization (Lowess) was applied to correct for artifacts caused by non-linear rates of dye incorporation, as well as inconsistencies in the relative fluorescence intensity between some red and green dyes. The GeneSpring 7.3 software (Agilent) was used to generate lists of selected genes and for different statistical and visualization methods.

source_name: Mouse embryonic kidneys (E13.5), mutant (UB HDAC1, 2-/-)

label_protocol: Fluorescently labeled cRNA (Cy3 and Cy5) was generated from 0.5 μg of total RNA, and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Embryonic kidneys were aseptically microdissected from timed-pregnant mice at E13.5.

extract_protocol: Total RNA was isolated from kidney rudiments using the RNeasy Micro Kit (Qiagen).

value: CD1 C57BL/6 mix

tag: genotype

value: mutant (UB HDAC1, 2-/-)

value: kidneys

source_name: Mouse embryonic kidneys (E13.5), wild type

value: wild type


title: Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-), replicate 4

description: Biological replicate 4 of 4, dye-swap. Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-).


description:
716_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep4


title: InvitroSpleen_UU_5

description: Uninfected

source_name: Naïve Spleen pre infection non-antigen stimulated

source_name: Naïve Spleen pre infection M7-antigen stimulated


description:
724R_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep6


title: Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-), replicate 3

description: Biological replicate 3 of 4, dye-swap. Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-).


title: InvitroSpleen_UI3d_1

description: Infected with M.bovis after 3 days


title: Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys, replicate 3

description: Biological replicate 3 of 4. Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys.


title: InvitroSpleen_UU_3

description: Uninfected


title: InvitroSpleen_UU_2

description: Uninfected


description:
706_Map_2Hr
gene expression data from bovine monocyte-derived macrophage challenged with  Mycobacterium avium subspecies paratuberculosis at T2 rep2


title: Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys, replicate 2

description: Biological replicate 2 of 4. Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys.


title: Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-), replicate 1

description: Biological replicate 1 of 4, dye-swap. Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-).


title: Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys, replicate 1

description: Biological replicate 1 of 4. Mutant kidneys (UB HDAC1,2-/-) vs. wild type kidneys.


title: InvitroSpleen_UU_1

description: Uninfected


title: InvitroSpleen_UU_4

description: Uninfected


title: Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-), replicate 2

description: Biological replicate 2 of 4, dye-swap. Wild type kidneys vs. mutant kidneys (UB HDAC1,2-/-).


title: InvitroLung_UI14d_5

description: Infected with M.bovis after 14 days

source_name: Infected Lung 14 days post infection with Mycobecterium bovis non-antigen stimulated

value: Lung

source_name: Infected Lung 14 days post infection with Mycobecterium bovis M7-antigen stimulated


title: InvitroLung_UU_4

description: Uninfected

source_name: Naïve Lung pre infection non-antigen stimulated

source_name: Naïve Lung pre infection M7-antigen stimulated


title: InvitroLung_UI14d_1

description: Infected with M.bovis after 14 days


title: InvitroLung_UU_5

description: Uninfected


title: HMEC_Tert_shp53_Ras_Mes_1

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

institute: Inserm U590

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing: CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software 1.1

source_name: HMEC mesenchymal

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA were extract with with the Qiagen RNeasy minikit (Qiagen), then 250 ng of total RNA were amplified using GeneChip 3' IVT Express Kit from Affymetrix.

tag: cell line

value: HMEC

tag: phenotype


title: InvitroLung_UU_2

description: Uninfected


title: InvitroLung_UU_1

description: Uninfected


title: HMEC_Tert_shp53_Ras_Mes_2


title: InvitroLung_UU_3

description: Uninfected


title: InvitroSpleen_UI14d_2

description: Infected with M.bovis after 14 days

source_name: Infected Spleen 14 days post infection with Mycobacterium bovis non-antigen stimulated

source_name: Infected Spleen 14 days post infection with Mycobacterium bovis M7-antigen stimulated


title: InvitroLung_UI14d_2

description: Infected with M.bovis after 14 days


title: HMEC_Tert_shp53_2

source_name: HMEC control

value: Tert/shp53 control


title: A. aceti_Mid-acetate-oxidation phase_#1

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at mid-acetate-oxidation phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed with Hybridization System 4 according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

scan_protocol: Array scanning was performed with MS200 Microarray Scanner according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software 2.5 (Roche NimbleGen).

organism: Acetobacter aceti NBRC 14818

source_name: A. aceti, Mid-acetate-oxidation phase replicate 1

label_protocol: Labeling of double stranded cDNA synthesized with the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) was performed according to the instructions for NimbleGen Arrays User’s Guide for Gene Expression Analysis by Roche NimbleGen using One-Color DNA Labeling Kit (Roche NimbleGen).

growth_protocol: A. aceti was cultivated in ethanol medium consisting of 1% yeast extract and 1% ethanol in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 1.2.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: growth phase

value: Mid-acetate-oxidation phase


title: HMEC_Tert_shp53_1


title: HMEC_Tert_shp53_Ras_Epi_1

source_name: HMEC epithelial


title: A. aceti_Pre-exponential phase_#2

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at pre-exponential phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Pre-exponential phase replicate 2

growth_protocol: A. aceti was cultivated in ethanol medium consisting of 1% yeast extract and 1% ethanol in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.1.

value: Pre-exponential phase


title: A. aceti_Early-ethanol-oxidation phase_#1

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at early-ethanol-oxidation phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Early-ethanol-oxidation phase replicate 1

growth_protocol: A. aceti was cultivated in ethanol medium consisting of 1% yeast extract and 1% ethanol in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.2.

value: Early-ethanol-oxidation phase


title: A. aceti_Late-transition phase_#2

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at late-transition phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Late-transition phase replicate 2

growth_protocol: A. aceti was cultivated in ethanol medium consisting of 1% yeast extract and 1% ethanol in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.6.

value: Late-transition phase


title: A. aceti_Late-transition phase_#1

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at late-transition phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Late-transition phase replicate 1


title: Leaf day1 susceptible aphids rep1

city: Ames

first: Matthew

last: Studham

state: IA

address: 2214 Molecular Biology Bldg.

institute: Iowa State University

hyb_protocol: 45C for 16 hours in the GeneChip hybridization oven 640 with constant rotation 60 rpm.

scan_protocol: Used GeneChip Scanner 7G and GeneChip software for image data collection and data file generation.

data_processing: Probe sets were normalized using the GC Robust Multi-array Average (GCRMA) method. The analysis was done in the R statistical software environment, using the limma package.

organism: Glycine max

source_name: third trifoliate leaves, aphid-susceptible cultivar, with aphids, 1 day of infestation

label_protocol: Labeling kit: One-cycle target labeling and control reagent package

growth_protocol: Growth chamber conditions: temperature was 25C, 16 hours of light per day

extract_protocol: Qiagen RNeasy Plant Mini Kit

treatment_protocol: For each aphid treated plant, ten aphids were applied, using a soft-tipped brush, to the adaxial surface of each leaflet of the third trifoliate, for a total of thirty aphids. At least 21 of the aphids were adults.

tag: time (d)

tag: cultivar

value: aphid-susceptible SD01-76R

tag: infestation

value: aphid

tag: tissue

value: third trifoliate leaves


title: Leaf day1 resistant control rep2

source_name: third trifoliate leaves, aphid-resistant cultivar, no aphids, 1 day of infestation

value: aphid-resistant LD05-16060


title: A287

type: genomic

city: Cambridge

first: Jun

last: Zhou

state: MA

address: 16 Divinity Ave. Rm2112

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Genomic DNA from Dark fly male genotype.

label_protocol: 3DNA procedure

extract_protocol: QIAGEN DNeasy blood and tissue kit

value: Dark fly

value: male (XY)

value: adult

source_name: Genomic DNA from Ore-RS male genotype.

value: Ore-RS


title: Leaf day1 resistant aphids rep1

source_name: third trifoliate leaves, aphid-resistant cultivar, with aphids, 1 day of infestation


title: Leaf day7 susceptible control rep2

source_name: third trifoliate leaves, aphid-susceptible cultivar, no aphids, 7 days of infestation


title: Leaf day7 resistant aphids rep2

source_name: third trifoliate leaves, aphid-resistant cultivar, with aphids, 7 days of infestation


title: Leaf day1 resistant control rep1


title: Leaf day7 susceptible control rep3


title: A289

description: Biological replicate


title: Leaf day7 resistant control rep3

source_name: third trifoliate leaves, aphid-resistant cultivar, no aphids, 7 days of infestation


title: A286

description: Biological replicate


title: Leaf day1 susceptible control rep2

source_name: third trifoliate leaves, aphid-susceptible cultivar, no aphids, 1 day of infestation


title: HMEC_Tert_shp53_Ras_Epi_2


title: A288

description: Biological replicate


title: InvitroLung_UI14d_4

description: Infected with M.bovis after 14 days

source_name: Infected Lung 14 days post infection with Mycobecterium bovis non-antigen stimulated

tag: strain

value: BALB/c

source_name: Infected Lung 14 days post infection with Mycobecterium bovis M7-antigen stimulated


title: InvitroLung_UI14d_3

description: Infected with M.bovis after 14 days


title: A. aceti_Pre-exponential phase_#1

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at pre-exponential phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Pre-exponential phase replicate 1

value: wild type


title: Leaf day7 resistant aphids rep1


title: femaleE13.5PGC_rep1

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

description: MeDIP in PGCs isolated from female E13.5 embryos

hyb_protocol: Hybridization was performed according to standard procedures by Roche Nimblegen.

scan_protocol: Scanning was performed according to standard procedures by Roche Nimblegen.

data_processing: Data processing and calculations were performed with the R computing software (version 2.9.0) as described (Borgel et al. Nature Genetics 2010 42:1093-1100). First, we calculated MeDIP/Input log2 ratios for each oligonucleotide from raw fluorescence values provided by Roche Nimblegen. All datasets were then normalized using an intra-array loess normalization and an inter-array quantile normalization to have equal normal distributions between arrays using the limma package (version 2.18.2).

source_name: MeDIP DNA from E13.5 female PGCs

label_protocol: Labeling was performed according to standard procedures by Roche Nimblegen.

extract_protocol: Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction. Sonication of DNA was performed with a Diagenode Bioruptor apparatus. MeDIP was performed on 150 ng sonicated DNA as described (Borgel et al. Nature Genetics 2010 42:1093-1100), using anti-5mC antibodies from Abcam (catalog no. ab51552, monoclonal clone 3A3, 1mg/ml) or Serotec (catalog no. MCA2201, monoclonal clone 33D3, 1mg/ml) as indicated. We used 1/10 µl anti-5mC antibody for epiblasts and 1/30 µl for PGCs. Subsequently, 5ng input DNA and the entire MeDIP product were amplified with the Whole Genome Amplification kit (Sigma-Aldrich) following the manufacturer’s instructions.

tag: embryo stage

tag: gender

value: female

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog no

source_name: Input DNA from E13.5 female PGCs

value: None, input DNA


title: maleE13.5PGC_rep3

description: MeDIP in PGCs isolated from male E13.5 embryos

source_name: MeDIP DNA from E13.5 male PGCs

value: male

value: Serotec

source_name: Input DNA from E13.5 male PGCs


title: A284

description: Biological replicate

tag: genotype/variation

tag: Sex

tag: age

source_name: Genomic DNA from Ore-RS female genotype.

value: female (XX)


title: A283

description: Biological replicate


title: Leaf day1 resistant aphids rep3


title: A282

description: Biological replicate


title: Leaf day7 resistant aphids rep3


title: Leaf day7 susceptible control rep1


title: A. aceti_Early-ethanol-oxidation phase_#2

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at early-ethanol-oxidation phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Early-ethanol-oxidation phase replicate 2

tag: genotype

value: Early-ethanol-oxidation phase


title: Leaf day7 resistant control rep1


title: Leaf day7 susceptible aphids rep2

source_name: third trifoliate leaves, aphid-susceptible cultivar, with aphids, 7 days of infestation

value: aphid-susceptible SD01-76R


title: A. aceti_Mid-acetate-oxidation phase_#2

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol at mid-acetate-oxidation phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, Mid-acetate-oxidation phase replicate 2

value: Mid-acetate-oxidation phase


title: MIBP1 overexpression, biological rep3

city: Fukuoka

first: Yuji

last: Iwashita

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Reseach Center for Genetic Information

institute: Kyushu University, Medical Institute of Bioregulation

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. The cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes and centrifuged at max speed for 1 minute. The 80 μl of hyb solution was transfered to each array, then seal the holes with sticker. They were hybridized for 18 hours in 45°C hybridization oven at 60 rpm. Fluidics Script Protocol was FS450_0007

scan_protocol: Affymetrix GeneChiP Scanner 3000 7G

data_processing:
Cel files were summarized and normalized with Robust Multi-array Average (RMA) method in Expression Console software version 1.1.1 (Affymetrix). Logarithmic signal intensities were antilog-transformed to linear scale using Expression Console.
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuGene-1_0-st-v1.r3.mps

label: Biotin

source_name: HEK293 cell clone stably overexpressing MIBP1. Clone No.76

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HEK293 cells were obtained from Clontech (Mountain View, MO) and maintained in Dulbecco’s modified Eagle’s medium (D5796, Sigma-Aldrich, St. Louis, CA), supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin (15140-122, Invitrogen, Carlsbad, CA), in 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted from triplicated transfectants for each plasmid using RNeasy plus mini kit (74134, Qiagen, Hilden, Germany). RNA quality was checked using 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and RNA Integrity Number (RIN) was confirmed to be 9.4 or greater for all samples. Total RNA at 200 ng was amplified and reverse-transcribed using GeneChip WT Sense Target Labeling and Control Reagents (900652, Affymetrix).

treatment_protocol: HEK293 cells were transfected with pCI-neo (empty vector control) or pCI-neo-FLAG-HA-MIBP1 linearized with AclI and selected at 400 μg/ml G418 (345812, Calbiochem, San Diego, CA) for 2 weeks. Selected cells were cloned using cloning rings and maintained in the presence of G418. Genomic integration and protein expression of MIBP1 were confirmed by genomic PCR and immunoblotting using anti-FLAG M2 antibody (Sigma-Aldrich).

tag: cell line


title: adipose tissue, after weight maintenancs, biological rep7

city: Malmö

first: Anders

last: Danielsson

state: Skåne

address: Jan Waldenströms gata 35

department: Medical Faculty, Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Performed according to manufacturer’s recommendation at the SCIBLU Microarray Resource Centre, Lund University, Sweden

data_processing: We used AffyProbeMiner to regroup the individual probes into consistent probe sets and remap the probe sets to the correct sets of mRNA transcripts for HG-U133 Plus 2.0 array which resulted in 23,798 probe sets. We applied Robust Multi-array Average (RMA) method for normalization. We conducted filtering based on the MAS5.0 present/absent calls which classified each probe set as expressed above background (present call) or not (absent or marginal call). We included probe sets, which have detection call as present call in at least 50% arrays in one group, which left 13,463 probe sets out of 23,798 for further analysis. To identify differentially expressed genes for interclass paired comparisons we used a permutation based false discovery rate (FDR) approach calculated by the EOC function in the OCplus R package as well as Patterns from Gene Expression (PaGE) method for log (base 2) transformed data with the use of modified t statistics. We considered only those probe sets as differentially expressed between groups that fulfilled each of two requisites: (i) a global FDR less than 0.05 by the EOC function, and (ii) a confidence level of at least 0.95 (which is equivalent to 5% of false discovery rate by PaGE method. Gene lists were analyzed using WebGestalt for the enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using the hypergeometric test.

source_name: Subcutaneous adipose tissue

extract_protocol: RNA was extracted using Tri reagent (Sigma-Aldrich, St. Louis, MO) followed by RNeasy Midi kit (Qiagen, Düsseldorf, Germany). The RNA was further concentrated by RNeasy MiniElute (Qiagen, Düsseldorf, Germany) and SpeedVac (DNA 120 SpeedVac, Thermo Savant, Waltham, MA 02454).

treatment_protocol: Subcutaneous abdominal adipose tissue biopsies were obtained by needle aspiration under local anesthesia (2 ml 10% lidocain). Biopsies were immediately put in RNAlater (Ambion, Austin, TX) and after overnight incubation at 4C snap frozen at -80C until further processing.

tag: group

value: after weight maintenancs

value: Female

tag: bmi


title: E7.5Epiblast_rep2

description: MeDIP in epiblasts dissected from E7.5 embryos

source_name: MeDIP DNA from E7.5 epiblasts

value: mixed

source_name: Input DNA from E7.5 epiblasts


title: adipose tissue, after weight maintenancs, biological rep8

scan_protocol: Performed according to manufacturer’s recommendation at the SCIBLU Microarray Resource Centre, Lund University, Sweden

value: Male


title: adipose tissue, after weight maintenancs, biological rep9

label_protocol: Performed according to manufacturer’s recommendation at the SCIBLU Microarray Resource Centre, Lund University, Sweden


title: maleE13.5PGC_rep2


title: Leaf day1 susceptible control rep1

tag: time (d)

value: third trifoliate leaves


title: MIBP1 overexpression, biological rep2

source_name: HEK293 cell clone stably overexpressing MIBP1. Clone No.49


title: adipose tissue, after weight maintenancs, biological rep6


title: E7.5Epiblast_rep1


title: Leaf day1 susceptible control rep3

source_name: third trifoliate leaves, aphid-susceptible cultivar, no aphids, 1 day of infestation

tag: cultivar


title: adipose tissue, after weight maintenancs, biological rep5


title: maleE13.5PGC_rep1


title: empty vector control, biological rep3

source_name: HEK293 cell clone stably transformed with pCI-neo (empty vector). Clone No.11


title: Leaf day1 resistant aphids rep2

source_name: third trifoliate leaves, aphid-resistant cultivar, with aphids, 1 day of infestation

value: aphid-resistant LD05-16060

tag: infestation

value: aphid


title: adipose tissue, after weight maintenancs, biological rep2


title: empty vector control, biological rep1

source_name: HEK293 cell clone stably transformed with pCI-neo (empty vector). Clone No.3


title: Wild type GWAT 3

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: gonadal adipose tissue

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

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

treatment_protocol: The mice were anesthetized with Ketamine/Xylacine at 3PM and livers were collected in RNAlater.

value: 8 weeks

value: FVB

tag: tissue

value: gonadal adipose tissue

value: WT


title: MIBP1 overexpression, biological rep1

source_name: HEK293 cell clone stably overexpressing MIBP1. Clone No.31


title: adipose tissue, after weight maintenancs, biological rep4


title: Leaf day1 resistant control rep3

source_name: third trifoliate leaves, aphid-resistant cultivar, no aphids, 1 day of infestation


title: hematopoietic stem/precursor cells male 8 week biol rep 2

city: San Francisco

first: Miguel

last: Ramalho-Santos

state: CA

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

institute: UCSF

description: HSCs FACSorted for Sca-1+, c-Kit+, CD34-, Lin-, Side Population cells

hyb_protocol: Standard Affymetrix hybridization protocols

scan_protocol: Standard Affymetrix scanning protocols

data_processing: intensities of the Affymetrix CEL files were background subtracted, quantile normalized, and summarized for each probe set into a logarithm base two intensity value using the robust multi-array average method (RMA) implemented in the Affymetrix package. Subsequently we applied the mean center global adjustment to remove apparent batch effects across the experiments to facilitate between-experiment comparisons.

source_name: bone-marrow hematopoietic stem/precursor cells  8-week

label_protocol: mRNA was amplified using two-rounds of in vitro transcription, and lableled by incorporation of bio-UTP in the second round.

extract_protocol: total RNA was extracted with Qiagen RNeasy kit with in-column DNAse digestion.

tag: strain

tag: cell type

tag: source age

value: male


title: Caveolin-1 knockout GWAT 1

tag: gender

value: caveloin-1 KO


title: Leaf day7 susceptible aphids rep1


title: Leaf day1 susceptible aphids rep3

source_name: third trifoliate leaves, aphid-susceptible cultivar, with aphids, 1 day of infestation


title: hematopoietic stem/precursor cells male 8-week biol rep 1

value: HSCs FACSorted for Sca-1+, c-Kit+, CD34-, Lin-, Side Population cells


title: Caveolin-1 knockout GWAT 2


title: neural stem/precursor cells mixed 8-week biol rep 2

description: NSCs (neurospheres) passage 1 cultured in EGF

source_name: sub-ventricular zone-derived neural stem/precursor cells 8-week


title: Leaf day7 resistant control rep2

source_name: third trifoliate leaves, aphid-resistant cultivar, no aphids, 7 days of infestation


title: Caveolin-1 knockout GWAT 3


title: Leaf day7 susceptible aphids rep3

source_name: third trifoliate leaves, aphid-susceptible cultivar, with aphids, 7 days of infestation


title: adipose tissue, after weight loss, biological rep6

value: after weight loss


title: adipose tissue, after weight maintenancs, biological rep3


title: Wild type GWAT 1


title: Leaf day1 susceptible aphids rep2

value: aphid-susceptible SD01-76R


title: adipose tissue, after weight loss, biological rep7


title: Caveolin-1 knockout liver 3

source_name: Liver

value: 12 weeks

value: liver


title: adipose tissue, after weight maintenancs, biological rep1

source_name: Subcutaneous adipose tissue

value: after weight maintenancs


title: Wild type GWAT 2


title: adipose tissue, after weight loss, biological rep5

value: Female


title: adipose tissue, after weight loss, biological rep8


title: femaleE13.5PGC_rep3

source_name: MeDIP DNA from E13.5 female PGCs

tag: embryo stage

value: female

tag: antibody

tag: antibody vendor

value: Serotec

source_name: Input DNA from E13.5 female PGCs

value: None, input DNA


title: A285

description: Biological replicate

source_name: Genomic DNA from Ore-RS male genotype.

tag: genotype/variation

value: Ore-RS

tag: Sex

value: male (XY)

value: adult

source_name: Genomic DNA from Ore-RS female genotype.

value: female (XX)


title: neural stem/precursor cells mixed 8-week biol rep 1

value: NSCs (neurospheres) passage 1 cultured in EGF

value: mixed


title: embryonic fibroblasts mixed E13.5 biol rep 2

description: MEFs passage 2 cultured in Serum

source_name: embryonic fibroblasts E13.5

value: MEFs passage 2 cultured in Serum


title: embryonic fibroblasts mixed E13.5 biol rep 6

description: MEFs passage 2 cultured in Serum


title: somatic cells of gonad mesonephros mixed E11.5 biol rep 4

description: SGMs FACSorted for Oct4/GFP-

source_name: somatic cells of gonad mesonephros E11.5

value: SGMs FACSorted for Oct4/GFP-


title: embryonic fibroblasts mixed E13.5 biol rep 5

description: MEFs passage 2 cultured in Serum


title: somatic cells of gonad mesonephros mixed E11.5 biol rep 3

description: SGMs FACSorted for Oct4/GFP-


title: adipose tissue, after weight loss, biological rep3

value: after weight loss

tag: age


title: adipose tissue, baseline, biological rep8

value: baseline

value: Male


title: Caveolin-1 knockout liver 2

value: 12 weeks

value: FVB

value: liver

tag: genotype

value: caveloin-1 KO


title: Wild type liver 3

value: WT


title: adipose tissue, baseline, biological rep7

tag: group

value: Female


title: heart miR-214 KO adult

first: Arin

middle: B

last: Aurora

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing: Illumina bead studio software was used to analyze with quantile normalization

source_name: heart miR-214 KO

label_protocol: cRNA was generated and labeled according to the protocols outlined at: http://microarray.swmed.edu/protocols/protocol/illumina-gene-expression-probe-labeling/

growth_protocol: All animals were maintained in compliance with the Institutional Animal Care and Use Committee at University of Texas Southwestern Medical Center

extract_protocol: Total RNA was isolated from mouse tissues and cell lines using Trizol reagent according to the manufacturer’s protocol followed by clean-up with the Rneasy Kit (Qiagen).

tag: strain background

value: miR-214 KO

value: male

value: heart

value: adult (8 weeks)


title: adipose tissue, after weight loss, biological rep2

tag: bmi


title: tibialis anterior miR-214 KO adult

source_name: tibialis anterior miR-214 KO

value: tibialis anterior


title: embryonic fibroblasts mixed E13.5 biol rep 1

description: MEFs passage 2 cultured in Serum

value: mixed


title: tibialis anterior WT adult

source_name: tibialis anterior WT

value: wildtype


title: Wild type liver 2


title: embryonic fibroblasts mixed E13.5 biol rep 3

description: MEFs passage 2 cultured in Serum

value: MEFs passage 2 cultured in Serum


title: Wild type liver 1


title: somatic cells of gonad mesonephros mixed E11.5 biol rep 2

description: SGMs FACSorted for Oct4/GFP-

value: SGMs FACSorted for Oct4/GFP-


title: femaleE13.5PGC_rep2

value: female

value: Serotec

tag: antibody catalog no

value: None, input DNA


title: embryonic fibroblasts mixed E13.5 biol rep 4

description: MEFs passage 2 cultured in Serum


title: adipose tissue, after weight loss, biological rep4

value: after weight loss

value: Male


title: adipose tissue, baseline, biological rep9

value: baseline


title: adipose tissue, baseline, biological rep3


title: embryonic germ cells male E12.5 biol rep 2

description: EGCs passage 19 cultured in LIF and Serum

source_name: embryonic germ cells derived from E12.5 PGCs


title: heart miR-214 KO P14


title: heart WT adult

source_name: heart WT


title: adipose tissue, after weight loss, biological rep1


title: heart WT P14


title: adipose tissue, baseline, biological rep6


title: Caveolin-1 knockout liver 1

value: 12 weeks

value: FVB

value: liver

value: caveloin-1 KO


title: adipose tissue, baseline, biological rep5


title: 13832518 - wt-Col0-FGL22-1 vs wt-Col0-1

hyb_protocol: wt-Col0-1 Cy5 / wt-Col0-FGL22-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

growth_protocol: seedling - 1/2MS, 1% Sucrose 22°C

extract_protocol: wt-Col0-1:27.85ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: wild type

tag: dev.stage (boyes et al. plant cell 2001) boyes

treatment_protocol:
Flagellin22 (FLG22)- biotic stress - elicitor+pathogen infection
quantity 0.001mM
time 1hour .
Seedlings have been transferred from agar medium to liquid medium and let stand for 5 hours in order to erase any possible stress that could have activated MAPK proteins. After this time the liquid was carefully removed and replaced with fresh one containing 1 µM Flagellin22. After 1 hour samples have been collected and deep frozen in liquid nitrogen.


title: 13832517 - wt-Col0-1 vs wt-Col0-FGL22-1

hyb_protocol: wt-Col0-FGL22-1 Cy5 / wt-Col0-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol:
Flagellin22 (FGL22) - biotic stress - elicitor+pathogen infection
quantity 0.001mM
time 1hour .
Seedlings have been transferred from agar medium to liquid medium and let stand for 5 hours in order to erase any possible stress that could have activated MAPK proteins. After this time the liquid was carefully removed and replaced with fresh one containing 1 µM Flagellin22. After 1 hour samples have been collected and deep frozen in liquid nitrogen.


title: adipose tissue, baseline, biological rep2

value: Female


title: adipose tissue, baseline, biological rep4


title: embryonic germ cells male E12.5 biol rep 1

tag: strain

value: EGCs passage 19 cultured in LIF and Serum

value: male


title: adipose tissue, baseline, biological rep1


title: embryonic germ cells male E12.5 biol rep 3

tag: cell type


title: inner cell mass cells E3.5 mixed biol rep 3

description: ICMs dissected by immunosurgery

source_name: inner cell mass of the blastocyst

value: C57Bl/6 x C3H F1

value: ICMs dissected by immunosurgery

tag: source age

value: mixed


title: somatic cells of gonad mesonephros mixed E11.5 biol rep 1

description: SGMs FACSorted for Oct4/GFP-

value: SGMs FACSorted for Oct4/GFP-

tag: gender


title: inner cell mass cells E3.5 mixed biol rep 2

description: ICMs dissected by immunosurgery


title: inner cell mass cells E3.5 mixed biol rep 1

description: ICMs dissected by immunosurgery

value: [C57Bl/6 x C3H F1] x CD1 F1


title: Tumor tissue 5 sl43

city: New Delhi

first: Rakhshan

last: Ihsan

state: Delhi

address: Safdurjung Hospital Campus

country: India

institute: Institute of Pathology(ICMR)

description: Gene expression data of tumor tissue of lung cancer patient

hyb_protocol: 10.0 µg of the labeled aRNA in 100 µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and was used for hybridization with the Human 40 K A chip and printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hrs on Tecan HS 4800 automated Hyb station. Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains (40, 50, 60).

scan_protocol: Scanner Used: AFFYMETRIX, 428 Array. Define scan area: Always set size Y to 0. Use array finder to define the size height (1mm on the array finder » 1mm on the OciChip). Height means the distance from the top of the slide to the end of the spotted array (plus safe distance of 2 mm).Set scan settings: The PMT gain settings of the multiple scanning have to be increased with the same distance (usually a distance of 10 between the settings is used). Set the range of the increasing PMT gain setting to achieve both to avoid saturation of the strongest spots at lowest value and to receive reliable signals from the weak spots at the highest PMT gain setting. Scanning was performed at 40, 50 and 60 PMT gain for the hybridized chips.

data_processing: Initially, the data consisted of 20,160 probes including empty spots and control spots (GPL9365 is a 2 x 20K array). These spots were eliminated, leaving 19,700 genes, which were retained in the downstream analysis. The missing values were imputed by K-nearest neighbor (KNN) method. The resulting data was subjected to normalization. Normalization is performed to overcome the systematic bias incorporated in the experiment while handling multiple arrays. There was differences within control and tumor sample profiles. In order to facilitate comparison across arrays, median centering followed by scale adjustment for each array was performed. Median Absolute Deviation (MAD) scaling technique was used to rescale the data on each array

source_name: primary lung cancer

label_protocol: Five microgram of total RNA was used for amplification using Express Art® mRNA amplification Kit by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed followed by second strand synthesis priming with a oligo (dT) primer bearing T7 promoter in a thermal cycler using the conditions described in the manual. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA is then labelled with Cy3TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3 molecules were removed by purification process.

extract_protocol: Isolation Kit: RNeasy mini Kit (Qiagen). RNA concentration was evaluated by using a NanoDrop (NanoDrop, USA) and RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA that met the quality standards was released for probe generation.

tag: tissue

value: primary lung cancer

tag: patient id

tag: age (y)

tag: smoking

value: YES

tag: tobacco chewing

value: NO

tag: betelquid chewing

tag: alcohol

tag: histopathology

value: Squamous cell carcinoma


title: embryonic stem cells male biol rep 2

description: ESCs passage 9-14 cultured in LIF and Serum

source_name: embryonic stem cells


title: embryonic stem cells male biol rep 3

value: ESCs passage 9-14 cultured in LIF and Serum


title: 13832499 - wt-Col0-1 vs mpk3-1

description: Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. Flagellin is a protein present in the flagellum of almost all bacteria and triggers Innate Immunity in plants, mediated by a MAPK phosphorylation signal cascade. To better understand the changes occuring in the mpk3, mpk4, mpk6 mutants upon flagellin treatment at the gene expression level, we would like to perform a microarray transcriptomic analysis.

hyb_protocol: mpk3-1 Cy5 / wt-Col0-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seedling - 1/2 MS 1%sucrose, 22°C

extract_protocol: mpk3-1:21.2ug. (Qiagen_RNeasy.pdf)

tag: genotype/variation

value: mpk3 mutant

tag: age

tag: arabidopsis thaliana (col-0)


title: Sante_OrgCropProtection_ConvFertilizer_rep4

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT, institute of food safety

description: Biological replicate 4 of 4

hyb_protocol: 1 μl of luciferase RNA (Invitrogen) was added to each sample. Labeled cDNA was dissolved in 80 μl MiliQ water, to which 20 μl Cy3-labelled universal control cDNA was added as well as 4 μl denatured herring sperm DNA and 4 μl dentarued blocker (Agilent, USA). This mix was combined with 100 μl 2x hybridization buffer (Agilent) and hybridization was performed for 17 hrs at 60 degrees Celcius with the Agilent gasket/chamber system in an agilent hybridization oven with rotor. After hybridisation the slides were washed with wash buffer 1, 2 and 3 (Agilent, USA) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned after excitation of Cy5 dye with 633 nm laser and Cy3 dye with 543 nm laser using scanner ScanArray® Express HT (Perkin Elmer, USA). The microarrays were scanned at constant laser power (90 %) and 10 μm resolution settings.Tiff images were imported into the ArrayVision software (Imaging Research, Waalwijk, The Netherlands) and the fluorescent intensity, background and signal-to-noise ratio were determined for each spot. Photo mulitplier tube (PMT) settings were 80 for the Cy3 channel and 55 for the Cy5 channel.

data_processing: Quality was checked, removal of control and empty spots. The Cy5/Cy3 ratio was calculated and log2 transformed. Normalization was done per array by subtraction from all 3725 remaining spots the median value of the log2(cy3/Cy5) signal of 1080 spots with a target/background ratio of more than 2 on all 16 arrays. R statistical software and Genemaths XT®s software (Applied Maths, St-Martens-Latem, Belgium) were used for analysis.

organism: Solanum tuberosum

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_Comcat

label_protocol: 25 µg of total RNA was primed with 2 µl 21-mer oligo-dT primer (1ug/ml) at 25°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 150 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dTTP, dGTP, with 40 µM dCTP Cy5-labeled

growth_protocol: Potatoes were grown at Nafferton Experimental Farm (University of Newcastle) under organic farming practices in a completely randomised block design with 4 replicate blocks; with all combinations of fertilisation and crop protection being established on one plot in each block (size of individual plots 15 x 6 m)

extract_protocol: Total RNA extraction following a protocol for extraction of RNA from polysaccharide rich tissues  (Chang et al.,2003,Plant Molecular Biology Reporter, 11: 113–116)

treatment_protocol: Organic fertilizer consisted of composted cattle manure, equivalent to 170 kg N/ha. Conventional fertilizer consisted of ammonium nitrate (Nitram), equivalent to 180 kg N/ha and superphosphate and KCl as a compound (0:20:300 fertilizer equivalent to 134 kg P/ha and 200 kg K/ha. Organic crop protection consisted of 2 times mechanical rigging of potato rows (weed control), 2 foliar sprays of copperoxychloride (product: Headland Copper, 15l/ ha + 6 kg Cu/ha) (disease control) and mechanical removal of foliage by flailing to avoid tuber blight. Conventional crop protection consisted of 1 spray of linuron (product: Linuron, 3.5 l/ha) (weed control), pre-planting soil application of aldicarp granules (product: Temik 10G, 67 kg/ha) (pest control), 2 foliar sprays of a mixture of fluazinam (product: Fubol Gold, 2.85 l/ha) and copperoxychloride (product: Headland Copper, 15l/ ha + 6 kg Cu/ha) (disease control) and 1 foliar spray of Oiquat (product: Reglone, 4 l/ha) for removal of foliage to avoid tuber blight.

tag: cultivar

value: Sante

tag: input regime

tag: sample size

value: 4-5 tubers

value: tuber

tag: treatment

value: Organic Crop Protection

tag: growth condition

value: Conventional Fertilizer

source_name: Universal control

tag: sample type

value: mixture of PCR products spotted on the microarray in vitro transcribed to RNA


title: 13832515 - wt-Col0-2 vs mpk3-2

hyb_protocol: mpk3-2 Cy5 / wt-Col0-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: mpk3-2:27.8ug. (Qiagen_RNeasy.pdf)

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001) boyes

extract_protocol: wt-Col0-2:43.7ug. (Qiagen_RNeasy.pdf)

value: wild type


title: Sante_OrgCropProtection_ConvFertilizer_rep2

description: Biological replicate 2 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_Compost_CopperOxychloride

tag: tissue


title: embryonic stem cells male biol rep 1

tag: strain

tag: cell type

tag: gender

value: male


title: Sante_OrgCropProtection_ConvFertilizer_rep3

description: Biological replicate 3 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_Compost_Comcat

value: mixed


title: 13832500 - mpk3-1 vs wt-Col0-1

hyb_protocol: wt-Col0-1 Cy5 / mpk3-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Tumor tissue 2 sl19

tag: patient id

tag: age (y)

value: Female

tag: smoking

tag: tobacco chewing

tag: betelquid chewing

tag: alcohol

value: adenocarcinoma


title: 13832516 - mpk3-2 vs wt-Col0-2

hyb_protocol: wt-Col0-2 Cy5 / mpk3-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (col-0)

tag: genotype/variation

tag: age


title: primordial germ cells male E13.5 biol rep 2

description: PGCs FACSorted for Oct4/GFP+

source_name: primordial germ cells E13.5

value: PGCs FAC Sorted for Oct4/GFP+

tag: source age


title: Tumor tissue 4 sl24

value: primary lung cancer

value: Male

value: YES

tag: histopathology


title: primordial germ cells male E13.5 biol rep 3

description: PGCs FACSorted for Oct4/GFP+


title: Sante_OrgCropProtection_OrgFertilizer_rep4

description: Biological replicate 4 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_Compost_Comcat

tag: cultivar

tag: input regime

value: organic

tag: sample size

tag: treatment

tag: growth condition

value: Organic Fertilizer

tag: sample type


title: empty vector control, biological rep2

source_name: HEK293 cell clone stably transformed with pCI-neo (empty vector). Clone No.6

tag: cell line


title: Tumor tissue 3 sl20

tag: tissue

tag: patient id

tag: age (y)

tag: gender

value: NO

value: Squamous cell carcinoma


title: primordial germ cells male E13.5 biol rep 1

description: PGCs FACSorted for Oct4/GFP+

tag: strain

tag: cell type


title: DosR OE, DMSO rep B

city: Seattle

first: Kyle

last: Minch

state: WA

address: 307 Westlake Ave N.

institute: Seattle BioMed

description: DosR-uninduced Rep. B

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

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all arrays.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

organism: Mycobacterium tuberculosis H37Rv

source_name: DMSO-treated DosR overexpression control in M. tuberculosis

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: M. tuberculosis strain H37Rv:deltaRv3133c::pEXNF-3133c cultures were grown in 7H9+GAT+50ug/mL Hygromycin B.  Samples for microarray were harvested in mid-log phase (OD600 = 0.3)

extract_protocol: Total RNA was extracted TRIzol chloroform:isopropanol phase separation using phaselock gels to separate the aqueous phase.  Samples were isolated by immobilization on Qiagen RNeasy columns as per manufacturer's instructions.  On- and off-column DNase treatments were performed to minimuze genomic or plasmid nucleic acid contamination of the final sample.

treatment_protocol: To ectopically induce expression of plasmid-based Rv3133c, cultures were treated with 10ng/mL anhydrotetracycline for 24 hours prior to RNA isolation.  Uninduced control samples were treated with equivalent amounts of dimethyl sulfoxide (DMSO) as a vehicle control

value: 10ng/mL dimethyl sulfoxide (DMSO)


title: DosR OE, DMSO rep C

description: DosR-uninduced Rep. C


title: Control pool 2 sl53

description: Gene expression data of normal lung tissue pooled from last two lung cancer patients

source_name: Normal human lung tissue

value: Normal human lung tissue

value: Control pool 2 sl53

value: Normal lung tissue


title: Sante_OrgCropProtection_OrgFertilizer_rep3

description: Biological replicate 3 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_CopperOxychloride

value: Sante

value: 4-5 tubers

value: tuber

value: Organic Crop Protection

value: mixture of PCR products spotted on the microarray in vitro transcribed to RNA


title: DosR OE, 10ng Atc, rep C

description: DosR-Induced Rep. C

source_name: Atc-treated DosR overexpression in M. tuberculosis

value: 10ng/mL anhydrotetracycline for 24 hours


title: Sante_OrgCropProtection_ConvFertilizer_rep1

description: Biological replicate 1 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_ChickenPellets_Water

value: mixed

value: Conventional Fertilizer


title: Sante_OrgCropProtection_OrgFertilizer_rep2

description: Biological replicate 2 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_ChickenPellets_Water


title: DosR OE, DMSO, rep A

description: DosR-uninduced Rep. A


title: primordial germ cells female E13.5 biol rep 2

description: PGCs FACSorted for Oct4/GFP+

value: PGCs FAC Sorted for Oct4/GFP+

value: female


title: primordial germ cells mixed E11.5 biol rep 5

description: PGCs FACSorted for Oct4/GFP+

source_name: primordial germ cells E11.5


title: DosR OE, 10ng Atc, rep B

description: DosR-Induced Rep. B


title: Control pool 1 sl70

description: Gene expression data of normal lung tissue pooled from first three lung cancer patients

value: Control pool 1 sl70


title: primordial germ cells mixed E11.5 biol rep 4

description: PGCs FACSorted for Oct4/GFP+


title: Sante_OrgCropProtection_OrgFertilizer_rep1

description: Biological replicate 1 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_Compost_Water

value: organic

value: Organic Fertilizer


title: Sante_ConvCropProtection_ConvFertilizer_rep4

description: Biological replicate 4 of 4

value: conventional

value: Conventional Crop Protection


title: Sante_ConvCropProtection_ConvFertilizer_rep2

description: Biological replicate 2 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment LadyBalfour_Compost_Water


title: primordial germ cells female E13.5 biol rep 1

description: PGCs FACSorted for Oct4/GFP+


title: DosR OE, 10ng Atc, rep A

description: DosR-Induced Rep. A


title: Sante_ConvCropProtection_ConvFertilizer_rep3

description: Biological replicate 3 of 4

source_name: Total RNA, Cy5 labeled, isolated from potato tubers, treatment Sante_ChickenPellets_CopperOxychloride


title: primordial germ cells mixed E11.5 biol rep 2

description: PGCs FACSorted for Oct4/GFP+


title: primordial germ cells mixed E11.5 biol rep 3

description: PGCs FACSorted for Oct4/GFP+