title: Pheochromocytoma V-PH-33T

description: Hybridized to CytoScan HD

value: M

value: VHL


title: Pheochromocytoma V-PH-38T

status: Public on Sep 21 2014

type: genomic

city: Melbourne

first: Aidan

last: Flynn

state: Victoria

address: St Andrews Place, Melbourne East

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: Hybridized to CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Raw CEL files were processed using Affymetrix Chromosome Analysis Suite (ChAS) Software
CYCHP files generated by Affymetrix Chromosome Analysis Suite

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Adrenal phaeochromocytoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh frozen tumour samples using DNeasy Blood and Tissue kit from Qiagen

tag: tissue

value: Adrenal phaeochromocytoma

tag: Stage

value: Benign

tag: ageatdiagnosis

tag: Sex

value: F

tag: origin

value: Sporadic

tag: drivergene

value: H-RAS


title: Pheochromocytoma V-PH-39T

description: Hybridized to CytoScan HD


title: Pheochromocytoma V-PH-34T

description: Hybridized to CytoScan HD

source_name: Left adrenal phaeochromocytoma

value: Left adrenal phaeochromocytoma

value: Benign(Local)

value: Familial


title: Paraganglioma V-PH-19T

description: Hybridized to CytoScan HD

source_name: Right extra adrenal phaeochromocytoma

value: Right extra adrenal phaeochromocytoma

value: Unknown


title: Pheochromocytoma VCB-PH-13T

description: Hybridized to CytoScan HD

source_name: Right adrenal phaeochromocytoma

value: Right adrenal phaeochromocytoma


title: Rbfox3 shRNA for T2-P19 cells with neuronal differentiation, biological rep1

type: RNA

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

country: USA

institute: NIH

hyb_protocol: Hybridization of the affymetrix microRNA arrays was done overnight at 45C for 16 hours in a hybridization oven.

scan_protocol: Scanning of the washed, stained arrays was done using Affymetrix 3000 7G scanner

data_processing: the image data was analyzed using the miRNA QC tool software for quality control. The raw data was preprocessed by Affymetrix miRNA QC Tool (Version 1.1.1.0) with the workflow of global background correction, quantile normalization and median polish summarization (miRNA-2_0.cdf).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Rbfox3 shRNA_T2-P19 cells_with neuronal differentiation

label_protocol: microRNAs were labeled using the flashtag  biotin assay as per the manufacturer's (Genisphere)directions. In brief,  the process begins with a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

growth_protocol: P19 mouse embryonal carcinoma cells were purchased from ATCC and maintained in MEMa containing 7.5% calf serum and 2.5% fetal bovine serum.

extract_protocol: Trizol (Invitrogen)

treatment_protocol: Neuronal differentiation by retinoic acid treatment

tag: cell line

tag: cell type

value: embryonal carcinoma cells

tag: transfected with

value: Rbfox3 shRNA

tag: treated with

value: retinoic acid


title: Paraganglioma V-PH-36T

description: Hybridized to CytoScan HD

source_name: Para aortic  paraganglioma

value: Para aortic  paraganglioma

value: SDHA


title: Pheochromocytoma VCB-PH-01T

description: Hybridized to CytoScan HD

value: RET


title: hda9_dryseed_ Biological replicate_3

city: Freiburg

first: Yong

last: Li

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

country: Germany

institute: Medical Center - University of Freiburg

description: Gene expression data from dry hda9-1 mutant seeds, replicate 3

hyb_protocol: After fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained with Fluidics Script FS450_004 in the Affymetrix Fluidics Station 450

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

data_processing: The RMA algorithm implemented in R package AFFY was used for background correction, normalization and expression calculation. Statistical analysis of the normalized data were performed using R packages LIMMA and RankProd

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion protocol from 1 ug total RNA (MessageAmp II-Biotin Enhanced Kit, 2008, Ambion)

growth_protocol: Plants were grown on soil containing a mixture of substrate and vermiculite (3:1) in growth cabinets (Elbanton BV, Kerkdriel, The Netherlands) in 16h light at 22oC and 8h dark at 16oC

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

treatment_protocol: Dry seeds were used obtained from 18-19 day-old (days after polination) ripe siliques

tag: genotype/variation

value: hda9-1 mutant

value: dry seeds


title: Control shRNA for GFP-P19 cells with neuronal differentiation, biological rep3

source_name: Control GFP shRNA_P19 _with neuronal differentiation

value: Control GFP shRNA


title: Pheochromocytoma V-PH-40T

description: Hybridized to CytoScan HD

value: Adrenal phaeochromocytoma

value: Benign

value: M

value: Sporadic


title: Pheochromocytoma VCB-PH-05T

description: Hybridized to CytoScan HD


title: Pheochromocytoma V-PH-16T

description: Hybridized to CytoScan HD

value: Left adrenal phaeochromocytoma

value: F


title: hda9_dryseed_ Biological replicate_2

description: Gene expression data from dry hda9-1 mutant seeds, replicate 2


title: Pheochromocytoma V-PH-18T

description: Hybridized to CytoScan HD


title: Rbfox3 shRNA for T2-P19 cells with neuronal differentiation, biological rep2


title: Control shRNA for GFP-P19 cells with neuronal differentiation, biological rep1


title: hda9_dryseed_ Biological replicate_1

description: Gene expression data from dry hda9-1 mutant seeds, replicate 1


title: Control shRNA for GFP-P19 cells with neuronal differentiation, biological rep2


title: Col_dryseed_ Biological replicate_3

description: Gene expression data from dry Col wild-type seeds, replicate 3

value: Col wild type


title: Control shRNA for GFP-P19 cells without neuronal differentiation, biological rep3

source_name: Control GFP shRNA_P19_w/x neuronal differentiation


title: Pheochromocytoma V-PH-22T

description: Hybridized to CytoScan HD

value: Familial


title: Control shRNA for GFP-P19 cells without neuronal differentiation, biological rep1

value: embryonal carcinoma cells


title: Col_dryseed_ Biological replicate_2

description: Gene expression data from dry Col wild-type seeds, replicate 2


title: Col_dryseed_ Biological replicate_1

description: Gene expression data from dry Col wild-type seeds, replicate 1


title: Pheochromocytoma VCB-PH-14T

description: Hybridized to CytoScan HD

source_name: Bilateral phaeochromocytoma

value: Bilateral phaeochromocytoma

value: VHL


title: Pheochromocytoma VCB-PH-09T

description: Hybridized to CytoScan HD

value: Benign(Local)


title: S17-d4

status: Public on Sep 20 2014

type: mixed

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

hyb_protocol: Standard array containing 60-mer probes manufactured by NimbleGen Systems (Madison, WI), which contains ~385,000 60-mer probes, covering approximately 42,000 Mus musculus genome transcripts (mm8, NCBI Build 36) were used. Microarrays were hybridized and processed following previously published protocols (Yu et al., 2007).

scan_protocol: Scanning was performed by NimbleGen Systems, Inc. following their standard operating protocol. See www.nimblegen.com.Gene expression raw data were extracted using NimbleScan software v2.1.

data_processing:
Considering that the signal distribution of the RNA sample is distinct from that of the gDNA sample, the signal intensities from RNA channels in all six arrays were normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003). Separately, the same normalization procedure was performed on those from the mouse gDNA samples.
For a given gene, the median-adjusted ratio between its normalized intensity from the RNA channel and that from the gDNA channel was then calculated as follows: Ratio = intensity from RNA channel/(intensity from gDNA channel + median intensity of all genes from the gDNA channel).

source_name: S17 bone-marrow stromal cell line, day 4

label_protocol: Labeling was performed by NimbleGen Systems, Inc. following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were plated on gelatin-coated 10cm dishes and grown in alphaMEM/20%FBS. Cells were harvested either on day 4 or day 8, as indicated. Cells that were harvested at day 8 had half of the media changed to fresh media on day 4.

extract_protocol: Cells were collected using trypsin-EDTA and then lysed in TRIReagent. Subsequent RNA was isolated using Ambion's RiboPure RNA isolation kit and TURBO DNAfree reagents.

value: stromal cell line

tag: strain/background

value: BALB/cAN

tag: time point

value: day 4 (at confluence)

source_name: S17 bone-marrow stromal cell line


title: S17-d8

source_name: S17 bone-marrow stromal cell line, day 8

value: day 8 (4 days post-confluence)


title: MS5-d8

source_name: MS5 bone-marrow stromal cell line, day 8

source_name: MS5 bone-marrow stromal cell line


title: OP9-d4

source_name: OP9 bone-marrow stromal cell line, day 4

value: (C57BL/6 x C3H)F2 -op/op

source_name: OP9 bone-marrow stromal cell line


title: TYPE 1 SCOUTs 7

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: TYPE 1 SCOUTs7.CEL.pimg

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing:
Expression console, Partek Genome Suite 6.6
HuEx-1_0-st-v2.r2.pgf; HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: SCOUTs

label_protocol: Encore® Biotin Module (Nugen)

extract_protocol: RNeasy FFPE Kit (Qiagen)

tag: gender

value: female

value: Type I secretory cell outgrowths (SCOUTs)

tag: sample type

value: FFPE-LCM


title: TYPE 1 SCOUTs 6

description: TYPE 1 SCOUTs6.CEL.pimg

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)


title: MS5-d4

source_name: MS5 bone-marrow stromal cell line, day 4


title: OP9-d8

source_name: OP9 bone-marrow stromal cell line, day 8


title: TYPE 2 SCOUTs 1

description: TYPE 2 SCOUTs1.CEL.pimg

value: Type 2 secretory cell outgrowths (SCOUTs)


title: TE-8 [miRNA]

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

hyb_protocol: The microarrays were hybridized with the denatured (95℃, 2 min) labeled RNAs at 56℃ for 16 hours with rotation.

scan_protocol: Fluorescent signals were detected using a SureScan Microarray Scanner G4900DA (Agilent).

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. Data were normalized based on a quantile normalization method.

source_name: Esophageal squamous cell carcinoma-derived cell line

label_protocol: Total RNAs (250 ng) were 3’-labeled with Hy3 using the miRCURY LNA microRNA Hi-Power Labeling Kit (Exiqon) according to the manufacturer's instructions.

growth_protocol: TE-1, TE-5, and TE-8 were cultured in RPMI-1640 supplemented with 10% fetal bovine serum. Het-1A was cultured using the BEGM kit (Lonza, Basel, Switzerland).

extract_protocol: AGPC method

treatment_protocol: The cells underwent no treatment during culture.

value: esophageal squamous cell carcinoma-derived cell line

tag: gender of donor

value: male

tag: age of donor

tag: stage of escc

value: III

tag: differentiation of escc

value: moderate


title: TYPE 2 SCOUTs 2

description: TYPE 2 SCOUTs2.CEL.pimg

tag: tissue


title: High grade ovarian cancer 2

source_name: High grade ovarian cancer

value: High grade ovarian cancer


title: High grade ovarian cancer 3


title: Pheochromocytoma V-PH-35T

description: Hybridized to CytoScan HD

source_name: Right adrenal phaeochromocytoma

value: Right adrenal phaeochromocytoma

tag: Stage

value: Benign

tag: ageatdiagnosis

tag: Sex

value: M

value: Familial


title: TYPE 2 SCOUTs 3

description: TYPE 2 SCOUTs3.CEL.pimg


title: Control shRNA for GFP-P19 cells without neuronal differentiation, biological rep2

tag: cell line

value: embryonal carcinoma cells

value: Control GFP shRNA


title: TE-5 [miRNA]

tag: cell type

value: IV

value: poor


title: TYPE 1 SCOUTs 4

description: TYPE 1 SCOUTs4.CEL.pimg

value: female


title: TYPE 1 SCOUTs 5

description: TYPE 1 SCOUTs5.CEL.pimg

value: Type I secretory cell outgrowths (SCOUTs)


title: TE-1 [miRNA]

value: II

value: well


title: OVA+ CD8+ T-cells Tsc-/- replicate 5

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system

scan_protocol: HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: OVA+ CD8+ T-cells from Tsc1-/- mouse

label_protocol: Twelve (12) nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Lymphocytes were isolated from the spleen of mice at day 9 after Listeria monocytogenes infection, and OVA-specific T cells (OVA+ CD8+) were sorted by flow cytometry.

extract_protocol: RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

treatment_protocol: Mice were infected with Listeria monocytogenes, and 9 days later, lymphocytes were isolated from the spleen and subjected to sorting by flow cytometry.

tag: background strain


title: OVA+ CD8+ T-cells Tsc-/- replicate 4


title: High grade ovarian cancer 1

value: FFPE-LCM


title: Het-1A [miRNA]

source_name: SV40 large T antigen-harboring normal human esophageal squamous cell line

value: male


title: Pheochromocytoma V-PH-13T

description: Hybridized to CytoScan HD

source_name: Left adrenal  phaeochromocytoma

value: Left adrenal  phaeochromocytoma

value: F

tag: origin

value: Sporadic

tag: drivergene


title: OVA+ CD8+ T-cells Tsc-/- replicate 2

tag: genotype/variation


title: OVA+ CD8+ T-cells Tsc-/- replicate 3


title: Normal fallopian tube epithelium 6

description: Normal epithelium6.CEL.pimg

source_name: fallopian tube epithelium

value: fallopian tube epithelium


title: OVA+ CD8+ T-cells Tsc-/- replicate 1


title: Normal fallopian tube epithelium 7

description: Normal epithelium7.CEL.pimg


title: Pheochromocytoma V-PH-15T

description: Hybridized to CytoScan HD

source_name: Left adrenal phaeochromocytoma

value: Left adrenal phaeochromocytoma

value: Benign

value: Unknown


title: Normal fallopian tube epithelium 4

description: Normal epithelium4.CEL.pimg


title: OVA+ CD8+ T-cells WT replicate 2

source_name: OVA+ CD8+ T-cells from WT mouse

value: WT


title: Normal fallopian tube epithelium 3

description: Normal epithelium3.CEL.pimg


title: Normal fallopian tube epithelium 5

description: Normal epithelium5.CEL.pimg


title: OVA+ CD8+ T-cells WT replicate 3


title: Normal fallopian tube epithelium 2

description: Normal epithelium2.CEL.pimg


title: Normal fallopian tube epithelium 1

description: Normal epithelium1.CEL.pimg


title: OVA+ CD8+ T-cells WT replicate 1


title: Fetus900_d90_MSLW

status: Public on Sep 19 2014

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

description: Gene expression at 90 days of gestation in MSLW fetal skeletal muscle

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44368 rows each corresponding to a unique ProbeName (provided as data Matrix) and 61 columns (individuals).

organism: Sus scrofa

source_name: skeletal muscle Longissimus lumborum (LD)

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

extract_protocol: An aliquot of 100mg of the fine powder was then processed for total RNA isolation and purification using Trizol (Invitrogen, France) and the kit Nucleospin RNA II (Macherey-Nagel, France) according to the manufacturer's instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 300µl of RNase-free water and stored at -80°C.

treatment_protocol: Muscle samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 minute in a liquid-nitrogen cooled grinder with stainless steel beads. RNA samples were conserved at -80°C until extraction.

tag: day of gestation

tag: fetus genotype

value: MSLW

tag: maternal genotype

value: LW

tag: paternal genotype

value: MS


title: Fetus560_d110_MSLW

description: Gene expression at 110 days of gestation in MSLW fetal skeletal muscle


title: Fetus411_d110_LWMS

description: Gene expression at 110 days of gestation in LWMS fetal skeletal muscle

value: LWMS


title: Fetus449_d90_LWLW

description: Gene expression at 90 days of gestation in LWLW fetal skeletal muscle

value: LWLW


title: Fetus686_d110_LWLW

description: Gene expression at 110 days of gestation in LWLW fetal skeletal muscle


title: Fetus524_d90_MSMS

description: Gene expression at 90 days of gestation in MSMS fetal skeletal muscle

value: MSMS


title: Pheochromocytoma V-PH-12T

description: Hybridized to CytoScan HD

value: M

value: RET


title: Fetus575_d110_LWLW


title: OVA+ CD8+ T-cells WT replicate 4


title: Fetus895_d90_LWLW


title: Het-1A [gene]

hyb_protocol: cRNA (600 ng) was applied for hybridization using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to generate quantized raw data. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A global mean normalization method was used.

label_protocol: Total RNAs (100 ng) were Cy3-labeled using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

value: SV40 large T antigen-harboring normal human esophageal squamous cell line

tag: gender of donor

value: male

tag: age of donor


title: Fetus627_d110_MSMS

description: Gene expression at 110 days of gestation in MSMS fetal skeletal muscle


title: Fetus551_d90_MSMS


title: Fetus670_d110_LWLW


title: Fetus827_d90_MSMS


title: Fetus458_d90_LWLW


title: Fetus473_d110_LWLW


title: Fetus559_d110_LWLW


title: Fetus630_d110_LWMS


title: Fetus825_d90_LWMS

description: Gene expression at 90 days of gestation in LWMS fetal skeletal muscle


title: Fetus874_d110_LWMS


title: Fetus617_d110_MSMS


title: Fetus899_d90_MSLW


title: Pheochromocytoma V-PH-08T

description: Hybridized to CytoScan HD

value: Right adrenal phaeochromocytoma

value: Benign(Local)

value: Familial


title: Pheochromocytoma V-PH-04T

description: Hybridized to CytoScan HD

source_name: Recurrent phaeochromocytoma

value: Recurrent phaeochromocytoma

value: Metastatic

value: Sporadic

value: VHL


title: Fetus872_d110_LWMS


title: Fetus533_d90_LWMS


title: Fetus455_d90_MSLW

value: MSLW


title: Fetus826_d90_MSMS


title: Fetus607_d110_MSMS


title: Pheochromocytoma V-PH-01T

description: Hybridized to CytoScan HD


title: Fetus498_d90_MSLW

value: LW


title: Pheochromocytoma V-PH-07T

description: Hybridized to CytoScan HD

source_name: Left adrenal pheochromocyroma

value: Left adrenal pheochromocyroma

value: Unknown


title: TEC-R(high) replicate 3_Cy3

city: Storrs

last: Zappulla

state: CT

address: 61 North Eagleville Road

department: Pathobiology

institute: University of Connecticut

description:
R(high)4-3.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr

hyb_protocol: 1.5 ug of total cRNA (750 ng Cy3-labelled cRNA and 750 ng Cy-5-labelled) (specific activity >7 pmol Cy3/ug cRNA or >7 pmol Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B Laser Scanner using two color scan setting (Scan resolution 5um). PMT gains were adjusted to give equal ratio of Cy3 and Cy5 intensity while keeping saturated features to less than 1%.

data_processing: The scanned images were analyzed with GenePix Pro 7 for feature extraction (Molecular Devices) using default parameters to obtain background subtracted Signal intensities for each channel. Background intensity was calculated as the mean value of the 5 closest negative control features. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: Tracheal epithelial cell

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5)  labeled cRNA was prepared from 50 ng RNA using the Two-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Chicken tracheal epithelial cells were isolated from chicken trachea and cultured in ATE medium (described in manuscript) at 37C with 5% CO2 in a cell culture incubator for 96 hours. Mycoplasma gallisepticum strains were grown in Hayflicks media at 37C. All LAMPs were isolated using TX-114 phase seperation.

extract_protocol: Total RNA was extracted using a combination protocol of Trizol-Chloroform extraction followed by purification using Qiagen RNEasy Mini kit (Qiagen, Valencia, CA)

treatment_protocol: TECs were exposed to either 500 MOI live Mycoplasma gallisepticum Rlow or Rhigh or 5µg/mL LAMPs from either strain for 1.5 hours for microarray experiments.

tag: gender

value: Female

tag: age

value: 5 weeks

value: Trachea


title: Fetus450_d90_MSLW

value: MS


title: Fetus557_d110_LWLW

value: LWLW


title: Fetus469_d110_LWLW


title: Pheochromocytoma V-PH-05T

description: Hybridized to CytoScan HD

tag: tissue

tag: Stage

value: F


title: Fetus894_d90_LWLW


title: Fetus688_d110_MSLW


title: Fetus578_d110_MSLW


title: TEC-R(high) replicate 2_Cy3

description:
R(high)4-2.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: Pheochromocytoma V-PH-03T

description: Hybridized to CytoScan HD

value: Right adrenal phaeochromocytoma

tag: ageatdiagnosis

tag: Sex


title: TEC-R(high) replicate 4_Cy3

description:
R(high)4-4.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: TEC-Media control biological replicate 8 technical replicate 2_Cy5

description:
R(high)4-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Pheochromocytoma P010-RPH Right Pole

description: Hybridized to CytoScan HD

value: Benign

value: RET


title: Fetus764_d90_LWMS

value: LWMS


title: Fetus744_d90_LWLW


title: Fetus622_d110_LWMS


title: TEC-R(high) replicate 1_Cy3

description:
R(high)4-1.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: TEC-Media control biological replicate 5 technical replicate 2_Cy5

description:
R(high)4-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 7 technical replicate 2_Cy5

description:
R(high)4-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 6 technical replicate 2_Cy5

description:
R(high)4-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 8 technical replicate 2_Cy3

description:
R(high)3-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(high) replicate 1_Cy5

description:
R(high)3-1.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: Fetus548_d90_LWMS


title: TEC-Media control biological replicate 6 technical replicate 2_Cy3

description:
R(high)3-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus481_d110_MSLW

description: Gene expression at 110 days of gestation in MSLW fetal skeletal muscle


title: Fetus624_d110_MSMS

value: MSMS


title: Fetus768_d90_MSMS


title: Fetus832_d90_LWMS


title: TEC-R(high) replicate 2_Cy5

description:
R(high)3-2.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: Fetus409_d110_MSMS


title: TEC-R(high) replicate 4_Cy5

description:
R(high)3-4.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: TEC-R(high) replicate 3_Cy5

description:
R(high)3-3.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rhigh for 1.5 hr


title: TEC-LAMP R(high) replicate 4_Cy3

description:
R(high)2-4.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: TEC-Media control biological replicate 8 technical replicate 1_Cy5

description:
R(high)2-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 5 technical replicate 2_Cy3

description:
R(high)3-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(high) replicate 3_Cy3

description:
R(high)2-3.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: TEC-Media control biological replicate 7 technical replicate 2_Cy3

description:
R(high)3-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Pheochromocytoma P010-RPH Left Pole

description: Hybridized to CytoScan HD

value: Familial


title: Fetus611_d110_LWMS

description: Gene expression at 110 days of gestation in LWMS fetal skeletal muscle


title: Fetus739_d90_MSLW

description: Gene expression at 90 days of gestation in MSLW fetal skeletal muscle


title: TEC-LAMP R(high) replicate 1_Cy3

description:
R(high)2-1.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: TEC-LAMP R(high) replicate 2_Cy3

description:
R(high)2-2.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: Fetus525_d90_LWMS

description: Gene expression at 90 days of gestation in LWMS fetal skeletal muscle


title: Fetus852_d110_LWLW

description: Gene expression at 110 days of gestation in LWLW fetal skeletal muscle


title: TEC-Media control biological replicate 7 technical replicate 1_Cy5

description:
R(high)2-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus485_d90_MSLW


title: Fetus609_d110_LWMS


title: TEC-Media control biological replicate 6 technical replicate 1_Cy5

description:
R(high)2-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(high) replicate 4_Cy5

description:
R(high)1-4.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: Fetus405_d110_LWMS


title: Fetus407_d110_MSMS

description: Gene expression at 110 days of gestation in MSMS fetal skeletal muscle


title: Fetus766_d90_MSMS

description: Gene expression at 90 days of gestation in MSMS fetal skeletal muscle


title: Fetus632_d110_MSMS


title: Fetus952_d90_MSMS


title: TEC-Media control biological replicate 5 technical replicate 1_Cy5

description:
R(high)2-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 8 technical replicate 1_Cy3

description:
R(high)1-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus736_d90_LWLW

description: Gene expression at 90 days of gestation in LWLW fetal skeletal muscle


title: Fetus738_d90_MSLW


title: TEC-LAMP R(high) replicate 3_Cy5

description:
R(high)1-3.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: TEC-LAMP R(high) replicate 2_Cy5

description:
R(high)1-2.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: Fetus484_d90_LWLW


title: Fetus500_d90_LWLW


title: Fetus954_d90_LWMS


title: TEC-Media control biological replicate 7 technical replicate 1_Cy3

description:
R(high)1-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(high) replicate 1_Cy5

description:
R(high)1-1.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rhigh LAMP for 1.5 hr


title: TEC-Media control biological replicate 6 technical replicate 1_Cy3

description:
R(high)1-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus850_d110_LWLW


title: Fetus476_d110_MSLW

description: Gene expression at 110 days of gestation in MSLW fetal skeletal muscle


title: TEC-Media control biological replicate 3 technical replicate 2_Cy5

description:
R(low)4-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(low) replicate 1_Cy3

description:
R(low)4-1.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-Media control biological replicate 2 technical replicate 2_Cy5

description:
R(low)4-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 4 technical replicate 2_Cy5

description:
R(low)4-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 5 technical replicate 1_Cy3

description:
R(high)1-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(low) replicate 4_Cy3

description:
R(low)4-4.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-R(low) replicate 3_Cy3

description:
R(low)4-3.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-Media control biological replicate 1 technical replicate 2_Cy5

description:
R(low)4-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(low) replicate 4_Cy5

description:
R(low)3-4.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-LAMP R(low) replicate 4_Cy3

description:
R(low)2-4.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: TEC-R(low) replicate 2_Cy3

description:
R(low)4-2.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-Media control biological replicate 4 technical replicate 1_Cy5

description:
R(low)2-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus773_d90_LWMS

description: Gene expression at 90 days of gestation in LWMS fetal skeletal muscle


title: TEC-Media control biological replicate 1 technical replicate 2_Cy3

description:
R(low)3-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(low) replicate 1_Cy5

description:
R(low)3-1.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-Media control biological replicate 3 technical replicate 2_Cy3

description:
R(low)3-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-R(low) replicate 2_Cy5

description:
R(low)3-2.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-R(low) replicate 3_Cy5

description:
R(low)3-3.gpr
Gene expression upon exposure to 500 MOI Mycoplasma gallisepticum Rlow for 1.5 hr


title: TEC-Media control biological replicate 2 technical replicate 2_Cy3

description:
R(low)3-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(low) replicate 3_Cy3

description:
R(low)2-3.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: TEC-Media control biological replicate 4 technical replicate 2_Cy3

description:
R(low)3-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: SK-BR-3 at 24hr

city: Kita-ku

first: Kazuteru

last: Fukasawa

state: Tokyo

address: 31-12, Shimo 3-Chome

department: Pharmaceutical Development Division

institute: Nippon Kayaku Co., Ltd.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human Genome Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix Microarray Suite version 5.0 (MAS 5.0) and GeneSpring 7.2 software for normalization and statistical analysis.  As for the control data (N=2) in each ell line, two independent data were averaged for further analysis.  The data were analyzed with Affymetrix Microarray Suite version 5.0 (MAS 5.0) and GeneSpring 7.2 software for normalization and statistical analysis.

source_name: SK-BR-3, treated with NK150460 for 24hr

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

growth_protocol: All cell lines were cultured at 37 degree C, 5% CO2 condition.

extract_protocol: Total RNA were extracted with ISOGEN (Nippon Gene) and Purified with Rneasy Mini Kit (Qiagen).

treatment_protocol: NK150460 were added to each culture dish, then incubated for 0hr (untreated), 3hr, 6hr and 24hr.

tag: cell line

tag: er status

tag: treated

value: treated with NK150460 for 24hr


title: MDA-MB-231 at 3hr

source_name: MDA-MB-231, treated with NK150460 for 3hr

value: treated with NK150460 for 3hr


title: MDA-MB-231 at 0hr-2

source_name: MDA-MB-231, untreated with NK150460

value: untreated


title: MDA-MB-231 at 6hr

source_name: MDA-MB-231, treated with NK150460 for 6hr

value: treated with NK150460 for 6hr


title: MDA-MB-231 at 0hr-1


title: MDA-MB-231 at 24hr

source_name: MDA-MB-231, treated with NK150460 for 24hr


title: SK-BR-3 at 6hr

source_name: SK-BR-3, treated with NK150460 for 6hr


title: Wildtype_2

city: Mizuho

first: Takeshi

last: Into

state: Gifu

address: Hozumi 1851-1

department: Department of Oral Microbiology

institute: Asahi University School of Dentistry

description: Control sample #2

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K, Design ID 028005) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: submandibular and sublingual glands

label_protocol: 100 ng of all RNA samples was used as template to produce Cy3-labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from thawed tissues using Trizol following manufacturer's instructions

treatment_protocol: Major salivary glands were collected and stereoscopically dissected to remove the lymph nodes and connective and fatty tissues and divided into the sublingual gland (SLG) and submandibular gland (SMG). These tissues were temporarily stored in ice-cold RNAlater solution (Life Technologies), and then quickly frozen in liquid nitrogen.

tag: strain

value: 10 weeks

value: salivary glands

value: wild type


title: Myd88-KO_2

description: KO sample #2

value: Female

tag: genotype/variation


title: Myd88-KO_1

description: KO sample #1


title: TEC-LAMP R(low) replicate 2_Cy3

description:
R(low)2-2.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr

value: 5 weeks

value: Trachea


title: SK-BR-3 at 3hr

source_name: SK-BR-3, treated with NK150460 for 3hr


title: TEC-Media control biological replicate 2 technical replicate 1_Cy5

description:
R(low)2-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-Media control biological replicate 3 technical replicate 1_Cy5

description:
R(low)2-3.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(low) replicate 1_Cy3

description:
R(low)2-1.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: SK-BR-3 at 0hr-1

source_name: SK-BR-3, untreated with NK150460


title: T-47D at 3hr

source_name: T-47D, treated with NK150460 for 3hr


title: Wildtype_1

description: Control sample #1


title: T-47D at 6hr

source_name: T-47D, treated with NK150460 for 6hr


title: TEC-Media control biological replicate 4 technical replicate 1_Cy3

description:
R(low)1-4.gpr
Gene expression upon exposure to media control for 1.5 hr


title: Fetus532_d90_MSMS

description: Gene expression at 90 days of gestation in MSMS fetal skeletal muscle

tag: day of gestation

value: MS


title: SK-BR-3 at 0hr-2


title: UT14 xenograft_Post irradiation_Day 21_Replicate 2

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description:
Gene expression data from UT14 xenografts at Day 21 after irradiation
XRT Day 21_29P

hyb_protocol: Target preparation for Affymetrix Human Exon 1.0 ST Arrays was performed using 5μg of amplified cDNA following the manufacturer’s recommendations. Hybridization, washing and staining performed with the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing:
The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.
probe group file: HuEx-1_0-st-v2
meta-probeset file: HuEx-1_0-st-v2

source_name: UT14 xenograft harvested 21 days after irradiation (15 Gy)

label_protocol: RNA was amplified and labeled using the Affymetrix WT terminal labeling kit  following the manufacturer’s recommendations

growth_protocol: Low passage head and neck squamous cancer cells (UT-14-SCC) were injected into the flanks of female nu/nu mice to generate xenografts. Tumors reached a size of 500mm3 before treatment.

extract_protocol: Laser capture microdissection was used to isolate cells from frozen tissue samples embedded in OCT. 8µm sections were cut and mounted onto PEN (polyethylene naphthalate) membrane glass slides (two sections per slide). The stained slides were microdissected within 2 hours of sectioning using an ArcturusXT™ Microdissection System (Molecular Devices) onto CapSure® Macro LCM Caps (Molecular Devices). RNA was isolated from the resh frozen tissue using the Qiagen Rneasy Plus Micro Kit according to the manufacturer's protocols.

treatment_protocol: They were treated with either sham RT or 15 Gy in one fraction. At different time points, days 0, 3, 10 and for controls and days 4, 7, 12, and 21 after irradiation, the tumors were harvested for global gene expression analysis and pathway analysis.

tag: growth conditions

value: xenograft (UT14 cells were injected into flanks of female nu/nu mice to generate xenografts)

tag: irradiation

value: 15 Gy

tag: harvest time

value: Day 21


title: T-47D at 24hr

source_name: T-47D, treated with NK150460 for 24hr


title: TEC-Media control biological replicate 2 technical replicate 1_Cy3

description:
R(low)1-2.gpr
Gene expression upon exposure to media control for 1.5 hr


title: TEC-LAMP R(low) replicate 3_Cy5

description:
R(low)1-3.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: TEC-LAMP R(low) replicate 4_Cy5

description:
R(low)1-4.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: UT14 xenograft_Post irradiation_Day 12_Replicate 2

description:
Gene expression data from UT14 xenografts at Day 12 after irradiation
XRT Day 12_13P

source_name: UT14 xenograft harvested 12 days after irradiation (15 Gy)

value: Day 12


title: T-47D at 0hr-1

source_name: T-47D, untreated with NK150460


title: T-47D at 0hr-2


title: UT14 xenograft_Post irradiation_Day 21_Replicate 1

description:
Gene expression data from UT14 xenografts at Day 21 after irradiation
XRT Day 21_19P


title: Asthmatic-5

city: Southampton

first: Victor Paky

last: Bondanese

address: Southampton General Hospital, Tremona Road

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton, UK

description: A 5

data_processing:
Real time amplification data were analyzed with Sequence Detection System v2.4 Enterprise Edition (Applied Biosystems). Threshold value was set to 0.2 for all plates and miRs. The unmodified microRNA Ct values are reported in the non-normalized_data.txt file.
MicroRNA Ct values were imported into Data Assist Software v2.0 (Applied Biosystems) in order to obtain the normalized values. Analysis settings were as follows: Maximum allowable CT value: 40.0; Include max CT values in calculations: Yes; Exclude outliers among replicates: Yes; Normalization method: Arithmetic Mean; Selected controls: RNU44-4373384.
Fold change values were calculated in excel for each microRNA and sample, using sample H 1 as calibrator.  See fold_change.txt file.
Normalized signals were calculated as follows: 2^-ΔCt, where -ΔCt = -(Ct_microRNA − Ct_RNU44).  Value of "null" if the microRNA was undetectable.

label: FAM

source_name: Primary human bronchial epithelial cells isolated from bronchial brushings obtained by fiberoptic bronchoscopy

label_protocol: The Applied Biosystems TaqMan Low Density Array system was used, following the manufacturer’s instructions. 400ng of total RNA from each sample were used to generate cDNA, using Megaplex RT Primers, Human Pool A v2.1. No preamplification was performed. TaqMan Array Human MicroRNA A Cards v2.0 were used for qPCR, on an Applied Biosystems 7900HT Real time PCR system.

growth_protocol: Primary human bronchial epithelial cells were cultured in complete Bronchial Epithelial Medium (BEGM, Cambrex cat.n. CC-3171). Cells at passage 1 were seeded at a density of 1x10^4 cells / square centimetre. When cells reached 80% confluency, they were placed in BEBM basal medium (Cambrex cat.n. CC-3171) supplemented with 0.1% (w/v) Bovine Serum Albumin (Sigma cat.n. A3059) and 1% (v/v) ITS (Sigma cat.n. I3146). Twenty-four hours later, cells were harvested in TRI-Reagent for total RNA isolation.

extract_protocol: Total RNA was extracted following TRI-Reagent manufacturer's instructions.

treatment_protocol: Cells were not subjected to any other treatment, besides the growth protocol outlined here.

tag: individual

value: Asthmatic subject

value: F

tag: % predicted fev1

tag: pc20 (mg/ml)

tag: cell type

value: Primary human Bronchial Epithelial cells (PBECs)


title: Asthmatic-4

description: A 4

tag: age

tag: gender

value: M


title: TEC-Media control biological replicate 1 technical replicate 1_Cy5

description:
R(low)2-1.gpr
Gene expression upon exposure to media control for 1.5 hr

source_name: Tracheal epithelial cell

tag: tissue


title: MCF-7 at 24 hr

source_name: MCF-7, treated with NK150460 for 24hr

value: treated with NK150460 for 24hr


title: Asthmatic-3

description: A 3


title: UT14 xenograft_Post irradiation_Day 12_Replicate 1

description:
Gene expression data from UT14 xenografts at Day 12 after irradiation
XRT Day 12_12P


title: TEC-LAMP R(low) replicate 2_Cy5

description:
R(low)1-2.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr


title: Asthmatic-1

description: A 1


title: Asthmatic-2

description: A 2


title: TEC-Media control biological replicate 1 technical replicate 1_Cy3

description:
R(low)1-1.gpr
Gene expression upon exposure to media control for 1.5 hr


title: MCF-7 at 3hr

source_name: MCF-7, treated with NK150460 for 3hr

value: treated with NK150460 for 3hr


title: Healthy-5

description: H 5

value: Healthy subject


title: UT14 xenograft_Post irradiation_Day 7_Replicate 2

description:
Gene expression data from UT14 xenografts at Day 7 after irradiation
XRT Day 7_15P

source_name: UT14 xenograft harvested 7 days after irradiation (15 Gy)

value: Day 7


title: UT14 xenograft_Post irradiation_Day 7_Replicate 1

description:
Gene expression data from UT14 xenografts at Day 7 after irradiation
XRT Day 7_14P


title: MCF-7 at 0hr-1

source_name: MCF-7, untreated with NK150460

value: untreated


title: UT14 xenograft_Post irradiation_Day 4_Replicate 2

description:
Gene expression data from UT14 xenografts at Day 4 after irradiation
XRT Day 4_3P

source_name: UT14 xenograft harvested 4 days after irradiation (15 Gy)

value: Day 4


title: MCF-7 at 6 hr

source_name: MCF-7, treated with NK150460 for 6hr

value: treated with NK150460 for 6hr


title: UT14 xenograft_Untreated Control_Day 10_Replicate 2

description:
Gene expression data from untreated UT14 xenografts at Day 10
Control Day 10_23P

source_name: UT14 xenograft harvested 10 days after sham irradiation

value: Control - sham irradiation

value: Day 10


title: UT14 xenograft_Post irradiation_Day 4_Replicate 1

description:
Gene expression data from UT14 xenografts at Day 4 after irradiation
XRT Day 4_1P

value: xenograft (UT14 cells were injected into flanks of female nu/nu mice to generate xenografts)


title: Healthy-2

description: H 2


title: Healthy-3

description: H 3


title: Healthy-1

description: H 1


title: UT14 xenograft_Untreated Control_Day 3_Replicate 2

description:
Gene expression data from untreated UT14 xenografts at Day 3
Control Day 3_20P

source_name: UT14 xenograft harvested 3 days after sham irradiation

value: Day 3


title: Control 2 H3K27me3

status: Public on Sep 18 2014

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

country: Canada

institute: SickKids Research Institute

hyb_protocol: Microarrays were hybridized at 42°C for four hours with 4μg of Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
scaled, log2 (ChIP/Input) ratio

source_name: H3K27me3 ChIP DNA from hippocampus

label_protocol: One μg of DNA from each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA.

growth_protocol: Mice housed and standard conditions prior to sacrafice

extract_protocol: Thawed hippocampal tissue samples were treated with 1% formaldehyde for five minutes and sonicated with the truChIPTM Tissue Prep Kit for SDS Chromatin Shearing (Covaris) and the Covaris® S2 Sonicator (Woburn, MA, USA) according the manufacturer’s protocol. The EpiQuik™ Tissue Chromatin Immunoprecipitation Kit (Epigentek) was used to perform ChIP. After sonication, samples were divided and immunoprecipitated with ChIP-grade polyclonal antibodies anti-H3K4me3 and anti-H3K27me3 (Millipore)

treatment_protocol: Mice injected with saline on PD 4 and 7

tag: treatment

value: Saline (control)

tag: Sex

value: male

tag: chip antibody

source_name: Input DNA from hippocampus


title: Control 1 H3K27me3


title: UT14 xenograft_Untreated Control_Day 3_Replicate 1

description:
Gene expression data from untreated UT14 xenografts at Day 3
Control Day 3_6P

tag: cell line


title: Control 3 H3K27me3

tag: strain


title: Ethanol 3 H3K27me3

treatment_protocol: Mice injected with 2.5g/kg ethanol on PD 4 and 7

value: Ethanol


title: Control 2 H3K4me3

source_name: H3K4me3 ChIP DNA from hippocampus


title: Control 3 H3K4me3


title: MCF-7 at 0hr-2

tag: er status

tag: treated


title: Ethanol 3 H3K4me3


title: Control 1 H3K4me3


title: Ethanol 2 H3K27me3


title: Ethanol 1 H3K27me3


title: Ethanol 1 H3K4me3


title: Ethanol 2 H3K4me3


title: UT14 xenograft_Untreated Control_Day 0_Replicate 2

description:
Gene expression data from untreated UT14 xenografts at Day 0
Control Day 0_24P

source_name: UT14 xenograft harvested at time of sham irradiation

tag: growth conditions

value: Day 0


title: UT14 xenograft_Untreated Control_Day 0_Replicate 1

description:
Gene expression data from untreated UT14 xenografts at Day 0
Control Day 0_10P

tag: irradiation


title: frontal cortex subject 11

city: London

first: Leonard

middle: C

last: Schalkwyk

address: De Crespigny Park

department: IOP-SGDP

institute: King's College London

hyb_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).

data_processing:
Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then  pre-processed in the R package wateRmelon using the dasen function. Array data for each of the tissues was normalized separately.
processed data: dasen normalized beta (dasen.csv)
raw data: Unmethylated and methylated signal intensities (signal_intensities.csv)

label: Cy5 and Cy3

source_name: frontal cortex, schizophrenia

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from ~100 mg of each dissected brain region or whole blood stored in EDTA collection tubes using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: subjectid

tag: barcode

tag: diagnosis

value: schizophrenia

tag: brainweight

tag: source tissue

value: frontal cortex


title: frontal cortex subject 32

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).

source_name: frontal cortex, control

value: normal

value: M

tag: age


title: frontal cortex subject 23


title: frontal cortex subject 14


title: frontal cortex subject 5

value: F


title: frontal cortex subject 24


title: UT14 xenograft_Untreated Control_Day 0_Replicate 3

description:
Gene expression data from untreated UT14 xenografts at Day 0
Control Day 0_30P

tag: harvest time


title: frontal cortex subject 38


title: frontal cortex subject 44


title: A375, biological rep2

city: Seongbuk-gu

first: Wooyoung

last: Hur

state: Seoul

address: 5 Hwarangro-14-gil, L2306

department: Chemical Kinomics Research Center

country: South Korea

institute: Korea Institute of Science and Technology

description: Transcriptome data from A375 cells

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: A375 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A375 cells and MAP4K5-KD A375 cells were cultured in DMEM supplemented with 10% FBS, penicllin/streptomycin.

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

treatment_protocol: No treatment

tag: tissue

value: Melanoma


title: A375-MAP4K5 knockdown, biological rep2

description: Transcriptome data from A375 cells where MAP4K5 is stably knocked down

source_name: A375 cells where MAP4K5 is stably knocked down by shRNA


title: frontal cortex subject 41


title: A375-MAP4K5 knockdown, biological rep3


title: A375, biological rep3

description: Transcriptome data from A375 cells


title: A375-MAP4K5 knockdown, biological rep1


title: frontal cortex subject 13


title: frontal cortex subject 33


title: TEC-Media control biological replicate 3 technical replicate 1_Cy3

description:
R(low)1-3.gpr
Gene expression upon exposure to media control for 1.5 hr

source_name: Tracheal epithelial cell

tag: gender

value: Female

value: 5 weeks

value: Trachea


title: LICR_HN1_CETU2

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

description:
replicate 1
LICR_HN1_CETU2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in limma 3.14.1 for R

source_name: Gift Prof Dr Olivier De Wever, Ghent University Hospital, Ghent, Belgium)

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: All HNSCC cell lines were grown as monolayers in Dulbecco's Modified Eagle's Medium (DMEM), supplemented with 10% fetal calf serum, 2 mM glutamine and 1% penicillin/streptomycin. All media and supplements were obtained from Life Technologies (Merelbeke, Belgium). Cultures were maintained in exponential growth in a humidified 5% CO2/95% air atmosphere at 37 °C. Cells were confirmed free of mycoplasma infection through regular testing (MycoAlertTM, Plus Mycoplasma detection kit, Lonza, Verviers, Belgium).

extract_protocol: RNA was isolated using the TRIzol-based method (Invitrogen, Merelbeke, Belgium). Concentration and purity were measured by Nanodrop ND-1000 spectrophotometry (Isogen, Sint-Pieters-Leeuw, Belgium). The RNA quality was assessed by capillary electrophoresis with an Agilent 2100 Bioanalyzer Series Nano kits (Agilent Technologies).

treatment_protocol: Cells were treated with either 15 nm Cetuximab or PBS during 13 hours

value: LICR HN1

tag: treatment

value: Cetuximab 15 nm Cetuximab for 13 hours


title: frontal cortex subject 9

tag: Sex


title: frontal cortex subject 30


title: LICR_HN1_PBS2

description:
replicate 1
LICR_HN1_PBS2

tag: cell line

value: PBS


title: LICR_HN2_PBS3

description:
replicate 2
LICR_HN2_PBS3

value: LICR HN2


title: LICR_HN1_CETU3

description:
replicate 2
LICR_HN1_CETU3


title: frontal cortex subject 19


title: frontal cortex subject 15


title: frontal cortex subject 10


title: A375, biological rep1

description: Transcriptome data from A375 cells


title: LICR_HN1_PBS3

description:
replicate 2
LICR_HN1_PBS3


title: frontal cortex subject 40


title: LICR_HN2_PBS2

description:
replicate 1
LICR_HN2_PBS2


title: LICR_HN1_CETU1

description:
replicate 3
LICR_HN1_CETU1


title: frontal cortex subject 7


title: frontal cortex subject 49


title: frontal cortex subject 52


title: LICR_HN1_PBS1

description:
replicate 3
LICR_HN1_PBS1


title: frontal cortex subject 53


title: frontal cortex subject 51


title: Healthy-4

description: H 4

source_name: Primary human bronchial epithelial cells isolated from bronchial brushings obtained by fiberoptic bronchoscopy

tag: individual

value: Healthy subject

tag: % predicted fev1

tag: pc20 (mg/ml)

tag: cell type

value: Primary human Bronchial Epithelial cells (PBECs)


title: LICR_HN2_PBS1

description:
replicate 3
LICR_HN2_PBS1


title: LICR_HN2_CETU1

description:
replicate 3
LICR_HN2_CETU1


title: frontal cortex subject 42


title: frontal cortex subject 47


title: SC263_PBS1

description:
replicate 1
SC263_PBS1

source_name: Gift Prof Dr Sandra Nuyts (University Hospital Leuven, Leuven, Belgium)


title: SC263_PBS3

description:
replicate 2
SC263_PBS3


title: SC263_CETU2

description:
replicate 2
SC263_CETU2


title: SC263_CETU1

description:
replicate 1
SC263_CETU1


title: LICR_HN2_CETU3

description:
replicate 2
LICR_HN2_CETU3


title: frontal cortex subject 16


title: SC263_PBS2

description:
replicate 2
SC263_PBS2


title: LICR_HN2_CETU2

description:
replicate 1
LICR_HN2_CETU2


title: SC263_CETU3

description:
replicate 3
SC263_CETU3


title: frontal cortex subject 20


title: UT14 xenograft_Untreated Control_Day 10_Replicate 1

description:
Gene expression data from untreated UT14 xenografts at Day 10
Control Day 10_22P

tag: growth conditions

value: xenograft (UT14 cells were injected into flanks of female nu/nu mice to generate xenografts)

tag: irradiation

value: Control - sham irradiation

value: Day 10


title: frontal cortex subject 35

tag: subjectid

tag: barcode

value: frontal cortex


title: frontal cortex subject 31

tag: diagnosis

value: normal

tag: brainweight


title: frontal cortex subject 18

value: schizophrenia

value: M

tag: age

tag: source tissue


title: frontal cortex subject 54


title: frontal cortex subject 46


title: frontal cortex subject 2


title: frontal cortex subject 34


title: frontal cortex subject 28

value: F


title: frontal cortex subject 1


title: frontal cortex subject 26


title: frontal cortex subject 37


title: frontal cortex subject 3


title: cerebellum subject 32

source_name: cerebellum, control

value: cerebellum


title: cerebellum subject 38


title: cerebellum subject 40


title: frontal cortex subject 22


title: frontal cortex subject 4


title: cerebellum subject 28


title: cerebellum subject 15

source_name: cerebellum, schizophrenia


title: frontal cortex subject 45


title: cerebellum subject 35


title: frontal cortex subject 6


title: cerebellum subject 2


title: cerebellum subject 53


title: frontal cortex subject 25


title: cerebellum subject 31


title: cerebellum subject 52


title: cerebellum subject 51


title: cerebellum subject 33


title: cerebellum subject 13


title: cerebellum subject 18


title: cerebellum subject 4


title: cerebellum subject 41


title: cerebellum subject 45


title: cerebellum subject 47


title: cerebellum subject 25


title: cerebellum subject 1


title: cerebellum subject 42


title: Cal27_PBS1

description:
replicate 3
Cal27_PBS1

source_name: cell line ATCC


title: cerebellum subject 16


title: Cal27_PBS3

description:
replicate 2
Cal27_PBS3


title: Cal27_PBS2

description:
replicate 1
Cal27_PBS2


title: cerebellum subject 44


title: cerebellum subject 20


title: Cal27_CETU3

description:
replicate 3
Cal27_CETU3

value: 15 nm Cetuximab for 13 hours


title: Cal27_CETU1

description:
replicate 1
Cal27_CETU1


title: cerebellum subject 6


title: Cal27_CETU2

description:
replicate 2
Cal27_CETU2


title: cerebellum subject 26


title: cerebellum subject 46


title: TEC-LAMP R(low) replicate 1_Cy5

description:
R(low)1-1.gpr
Gene expression upon exposure to 5µg/mL Mycoplasma gallisepticum Rlow LAMP for 1.5 hr

value: Female

value: 5 weeks

tag: tissue

value: Trachea


title: cerebellum subject 19


title: cerebellum subject 3


title: cerebellum subject 30


title: cerebellum subject 37


title: cerebellum subject 7


title: cerebellum subject 22


title: cerebellum subject 34


title: cerebellum subject 5


title: cerebellum subject 39


title: cerebellum subject 9


title: cerebellum subject 10


title: cerebellum subject 11


title: cerebellum subject 23


title: cerebellum subject 49


title: cerebellum subject 12


title: cerebellum subject 14


title: SAMPLE_110_Adult

city: Tartu

first: Lili

last: Milani

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: Bioconductor package’s minfi option ‘Raw’ pre-processing was used to convert the intensities from the red and the green channels from the original IDAT ﬁles extracted from the HiScanSQ scanner into methylated and unmethylated signals. Beta values were computed using Illumina’s formula [beta = M/(M+U+100)] and normalized using method SWAN. The beta-values were quantile normalized. The probe sequences were mapped to the human genome reference (build hg19); the bisulfite converted probe sequence were mapped to a similarly converted version of the human genome. All probes that mapped uniquely on both genomes with a minimal sequencing identity of 90% were retained. Probes that mapped to CpG sites with SNPs up to 3 bp upstream of the site or mapped to the X/Y chromosomes were discarded.

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver samples using the AllPrep DNA/RNA/Protein Mini kit (QIAgen, Hilden, Germany) according to standard instructions

tag: group

value: Cancer

tag: agegroup

value: Adult

value: Male

value: liver

tag: slide

tag: array


title: cerebellum subject 8

tag: Sex


title: SAMPLE_108_Adult


title: SAMPLE_107_Adult


title: SAMPLE_106_Adult


title: SAMPLE_101_Adult


title: SAMPLE_102_Adult


title: SAMPLE_89_Adult


title: SAMPLE_92_Adult


title: SAMPLE_88_Adult


title: SAMPLE_95_Adult


title: SAMPLE_109_Adult


title: SAMPLE_105_Adult


title: SAMPLE_87_Adult


title: SAMPLE_93_Adult


title: SAMPLE_83_Adult


title: SAMPLE_99_Adult


title: SAMPLE_94_Adult


title: SAMPLE_103_Adult


title: SAMPLE_97_Adult


title: SAMPLE_13_Fetal_expression

data_processing: Probes with detectable expression (detection p-value < 0.05) in < 10% of the samples were discarded. Next, the expression data was log2 transformed and normalized using quantile normalization with package lumi in R. The sequences of the expression probes were mapped to the human genome reference (build hg19). The expression probes which mapped uniquely to the reference genome and corresponding transcripts with at least 90% identity were retained. All expression probes mapping to either the X or Y chromosomes were discarded.

label_protocol: Biotinylated cRNA were prepared with theTargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip (Epicentre, Chicago, Illinois, USA).

extract_protocol: RNA was extracted and purified using the AllPrep DNA/RNA/Protein Mini kit (QIAgen, Hilden, Germany), according to the standard protocol. Quality control was performed with Agilent Bioanalyser.

value: Liver

value: Fetal

value: D


title: SAMPLE_98_Adult


title: SAMPLE_14_Fetal_expression

value: K


title: SAMPLE_82_Adult


title: SAMPLE_96_Adult


title: SAMPLE_104_Adult


title: SAMPLE_11_Fetal_expression

value: B


title: SAMPLE_85_Adult


title: SAMPLE_10_Fetal_expression

value: C


title: SAMPLE_91_Adult


title: SAMPLE_9_Fetal_expression


title: SAMPLE_12_Fetal_expression

value: A


title: SAMPLE_86_Adult


title: SAMPLE_90_Adult


title: SAMPLE_8_Fetal_expression

value: E


title: SAMPLE_84_Adult


title: SAMPLE_100_Adult


title: SAMPLE_7_Fetal_expression

value: I


title: SAMPLE_81_Adult


title: SAMPLE_78_Adult


title: SAMPLE_75_Adult


title: SAMPLE_77_Adult


title: SAMPLE_80_Adult


title: SAMPLE_5_Fetal_expression


title: SAMPLE_4_Fetal_expression

value: H


title: SAMPLE_3_Fetal_expression

value: F


title: SAMPLE_76_Adult


title: SAMPLE_71_Adult

value: Female


title: SAMPLE_74_Adult


title: SAMPLE_73_Adult


title: SAMPLE_6_Fetal_expression

value: G


title: SAMPLE_72_Adult

value: Cancer


title: Liver_M520_rep2

city: Milwaukee

first: Leah

last: Solberg Woods

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from M520 rat liver

hyb_protocol: The Affymetrix GeneChip rat genome 230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log ratios.  Each sample was independently analyzed.

organism: Rattus norvegicus

source_name: M520 rat liver

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Male rats were maintained two per cage and fed ad libitum.  Rats were euthanized at 17 weeks of age after an overnight fast.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Rats were fasted overnight prior to being euthanized.  Rats were euthanized by decapitation and liver was immediately removed and place in liquid nitrogen.

tag: strain

tag: gender

value: male

value: 17 weeks


title: SAMPLE_1_Fetal_expression

value: Male

value: J


title: Liver_M520_rep1

value: liver


title: Liver_BN_rep2

description: Gene expression data from BN rat liver

source_name: BN rat liver

value: BN


title: SAMPLE_70_Adult

value: Adult


title: Liver_WKY_rep2

description: Gene expression data from WKY rat liver

source_name: WKY rat liver

value: WKY


title: SAMPLE_68_Adult


title: SAMPLE_67_Adult


title: SAMPLE_2_Fetal_expression

value: Liver

value: Fetal

value: L


title: Liver_F344_rep1

description: Gene expression data from F344 rat liver

source_name: F344 rat liver


title: SAMPLE_66_Adult

value: Accident


title: Liver_WKY_rep1

description: Gene expression data from WKY rat liver


title: Liver_BUF_rep2

description: Gene expression data from BUF rat liver

source_name: BUF rat liver

value: BUF


title: Liver_F344_rep2


title: SAMPLE_60_Adult


title: SAMPLE_69_Adult


title: SAMPLE_64_Adult


title: SAMPLE_62_Adult


title: SAMPLE_59_Adult


title: SAMPLE_79_Adult


title: SAMPLE_58_Adult


title: SAMPLE_63_Adult


title: Liver_BUF_rep1

description: Gene expression data from BUF rat liver


title: SAMPLE_56_Adult


title: SAMPLE_65_Adult


title: Liver_ACI_rep2

description: Gene expression data from ACI rat liver

source_name: ACI rat liver

value: ACI


title: Liver_ACI_rep1

description: Gene expression data from ACI rat liver


title: SAMPLE_54_Adult

value: Female


title: SAMPLE_61_Adult


title: SAMPLE_55_Adult


title: SAMPLE_52_Adult


title: Liver_HighGlucoseHS42

description: Gene expression data from liver of heterogenous stock rat with normal glucose intolerance

source_name: Heterogeneous stock rat liver

value: heterogeneous stock


title: SAMPLE_57_Adult


title: Liver_HighGlucoseHS43


title: Liver_LowGlucoseHS45

description: Gene expression data from liver of heterogenous stock rat with normal glucose tolerance


title: Liver_HighGlucoseHS46


title: SAMPLE_53_Adult


title: SAMPLE_51_Adult


title: Liver_HighGlucoseHS41


title: Liver_HighGlucoseHS40


title: Liver_LowGlucoseHS44


title: Liver_BN_rep1

description: Gene expression data from BN rat liver


title: SAMPLE_50_Adult


title: Liver_LowGlucoseHS39


title: SAMPLE_49_Adult


title: Liver_LowGlucoseHS38


title: Liver_LowGlucoseHS35


title: SAMPLE_48_Adult


title: SAMPLE_45_Adult


title: SAMPLE_44_Adult


title: SAMPLE_47_Adult


title: Liver_LowGlucoseHS37


title: SAMPLE_43_Adult


title: SAMPLE_46_Adult


title: Liver_LowGlucoseHS36


title: Liver_HighGlucoseHS34


title: Liver_HighGlucoseHS33


title: Liver_LowGlucoseHS32


title: Liver_HighGlucoseHS31


title: SAMPLE_41_Adult


title: SAMPLE_39_Adult


title: SAMPLE_38_Adult


title: Liver_HighGlucoseHS28


title: Liver_LowGlucoseHS30


title: Liver_LowGlucoseHS27


title: SAMPLE_40_Adult


title: SAMPLE_42_Adult


title: Liver_LowGlucoseHS26


title: Liver_HighGlucoseHS24


title: Liver_HighGlucoseHS22


title: SAMPLE_32_Adult


title: Liver_HighGlucoseHS23


title: SAMPLE_37_Adult


title: SAMPLE_30_Adult


title: SAMPLE_33_Adult


title: Liver_LowGlucoseHS29


title: Liver_LowGlucoseHS25


title: SAMPLE_34_Adult


title: Liver_LowGlucoseHS21


title: SAMPLE_35_Adult


title: Liver_HighGlucoseHS19


title: Liver_HighGlucoseHS18


title: Liver_HighGlucoseHS20


title: SAMPLE_36_Adult


title: SAMPLE_31_Adult


title: Liver_LowGlucoseHS15


title: Liver_LowGlucoseHS14


title: SAMPLE_28_Adult


title: SAMPLE_26_Adult


title: SAMPLE_29_Adult


title: Liver_LowGlucoseHS16


title: SAMPLE_25_Adult


title: SAMPLE_27_Adult


title: SAMPLE_22_Adult


title: SAMPLE_24_Adult


title: Liver_HighGlucoseHS11


title: Liver_HighGlucoseHS9


title: SAMPLE_20_Adult


title: SAMPLE_23_Adult


title: SAMPLE_21_Adult


title: Liver_HighGlucoseHS12


title: SAMPLE_18_Adult


title: SAMPLE_19_Adult


title: SAMPLE_15_Adult


title: SAMPLE_16_Adult


title: Liver_HighGlucoseHS7


title: SAMPLE_13_Fetal


title: SAMPLE_14_Fetal


title: Liver_LowGlucoseHS5


title: Liver_LowGlucoseHS10


title: Liver_LowGlucoseHS6


title: Liver_HighGlucoseHS17


title: SAMPLE_12_Fetal


title: Liver_HighGlucoseHS3


title: Med7 Grace+tet+FBS vs. Med7 grace-tet+FBS (replica 3)

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

description:
Med7 hyphae 37C
Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

hyb_protocol: The microarray slides were pre-hybridized for 1 hour at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1x SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1x SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1x SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: Med7 grace mutant - tet (YPD 37oC)

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174-1183, using the RNeasy Mini kit (Qiagen).

treatment_protocol: Saturated overnight cultures of all strains were diluted to a starting OD600 of 0.1 in 50 ml fresh YPD and grown at 30°C to an OD600 of 0.8. Hyphae were induced by growing Candida cells in YPD plus 10% fetal bovine serum at 37°C to an OD600 of 0.8. Cultures were harvested by centrifugation at 3,000 × g for 5 minutes, and the pellet rapidly frozen in liquid nitrogen.

tag: strain/background

tag: genotype/variation

value: Med7 grace mutant

tag: cell type

value: hyphae cells

tag: tetracycline

value: no

source_name: Med7 grace mutant + tet (YPD 37oC)

value: yes


title: Med7 Grace+tet+FBS vs. Med7 grace-tet+FBS (replica 2)


title: SAMPLE_10_Fetal


title: Liver_LowGlucoseHS1

value: male

value: 17 weeks


title: Liver_HighGlucoseHS4

value: liver


title: seedling,day_2_unirradiated,atm-1 rep2

city: Davis

first: Anne

last: Britt

state: CA

address: One Shields Drive

department: Plant Biology

institute: UC Davis

hyb_protocol: Subsequently, 10 μg of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix ATH1 array. The GeneChip arrays were washed and then stained with SAPE (streptavidin–phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.2 software (Affymetrix Inc.) with default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values).  The data was normalized using RMA from the R package affy.  To generate the matrix of expression values here, normalization was performed simultaneously across all samples.  NOTE: When generating the results reported in the paper itself, normalization was performed separately for each experimental condition/control condition pair, normalizing only across the 4 samples associated with that specific experimental or control condition.

label_protocol: Single-stranded and then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material for each sample reaction) using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) and poly(T) nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from the Affymetrix GeneChip IVT labeling kit, and 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

growth_protocol: Five days prior to irradiation, the plates were placed vertically in a 21°C growth chamber in the BNL Controlled Environment Facility, where plants grew under cool white lamps (16 h day) until the time of irradiation.

extract_protocol: Approximately 30-40 plants were harvested and pooled together for total RNA extraction (RNeasy Mini-Prep; Qiagen, Valencia, CA, USA). Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1.25 μg μl-1.

treatment_protocol: For irradiation, plates were moved either to the Controlled Environment Radiation Facility for exposure to gamma radiation (100 Gy at 7 Gy/min), or to the National Space Radiation Laboratory (NSRL) for exposure to accelerated 1 GeV/n 56Fe particles (30 Gy at 2.5 Gy/min).

value: 6 days old

tag: treated with

value: none (unirradiated control)

tag: sampling time

value: 9:15 am on Day #2


title: Med7 Grace+tet+FBS vs. Med7 grace-tet+FBS (replica 1)


title: Liver_LowGlucoseHS8


title: Liver_HighGlucoseHS23_genotype

description: Genome-wide 10K SNP array in heterogeneous stock rats

hyb_protocol: The Affymetrix 10K SNP array was selected for these studies for its overall comprehensive coverage.  Samples are hybridized overnight.

scan_protocol: After hybridization, arrays were washed and sarrays are washed and loaded onto the Affymetrix GeneChip Scanner 3000

data_processing: All SNPs were given a call rate.  Those that did not reach a sufficient call rate were removed.

source_name: heterogeneous stock rat tail

label_protocol: Targeted genotyping technology was used.  Two PCR reactions occur: the first is to amplify the targeted region and the second is to label the region for subsequent detection.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit

treatment_protocol: Rats were fasted overnight prior to being euthanized.

tag: phenotype

value: High Glucose

value: tail


title: SAMPLE_6_Fetal

value: Fetal

value: Male


title: seedling,day_1_unirradiated,atm-1 rep2

tag: age

value: 5 days old

value: 10:45 am on Day #1


title: seedling,day_1_unirradiated,atm-1 rep1


title: Med7 Grace+tet vs. Med7 grace-tet (replica 2)

description:
Med7 yeast 30C
Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

source_name: Med7 grace mutant - tet (YPD 30oC)

value: yeast-form cells

source_name: Med7 grace mutant + tet (YPD 30oC)


title: Med7 Grace+tet vs. Med7 grace-tet (replica 1)

value: Med7 grace mutant


title: Liver_HighGlucoseHS22_genotype

value: heterogeneous stock


title: SAMPLE_17_Adult

value: Accident

value: Adult


title: seedling,day_2_unirradiated,atm-1 rep1


title: Liver_LowGlucoseHS2

value: male


title: seedling,day_2_unirradiated,WT rep2

source_name: seedling_day 2_unirradiated control_WT

value: wild type


title: SAMPLE_8_Fetal

value: liver


title: SAMPLE_9_Fetal

value: Female


title: Liver_HighGlucoseHS13

value: 17 weeks


title: seedling,day_1_unirradiated,WT rep2

source_name: seedling_day 1_unirradiated control_WT

value: none (unirradiated control)


title: SAMPLE_3_Fetal


title: seedling,day_2_unirradiated,WT rep1

value: 6 days old

value: 9:15 am on Day #2


title: Liver_HighGlucoseHS20_genotype

value: High Glucose

value: tail


title: SAMPLE_2_Fetal

value: Fetal


title: SAMPLE_5_Fetal

value: Male


title: Liver_LowGlucoseHS21_genotype

value: Low Glucose


title: SAMPLE_7_Fetal


title: SAMPLE_1_Fetal


title: SAMPLE_4_Fetal


title: Liver_HighGlucoseHS17_genotype


title: Liver_LowGlucoseHS16_genotype


title: Liver_LowGlucoseHS15_genotype


title: Liver_HighGlucoseHS18_genotype


title: Liver_HighGlucoseHS12_genotype


title: seedling,24h_after_HZE,atm-1 rep2

source_name: seedling_24h after HZE irradiation_atm-1

value: 30 Gy of HZE

tag: treatment duration

value: approx. 12 minutes

value: 1:09 pm on Day #2

tag: time after treatment


title: Liver_LowGlucoseHS10_genotype

value: heterogeneous stock

tag: tissue


title: seedling,24h_after_HZE,atm-1 rep1


title: Liver_HighGlucoseHS11_genotype

value: male


title: seedling,12h_after_HZE,atm-1 rep2

source_name: seedling_12h after HZE irradiation_atm-1

value: 5 days old

value: 1:09 am on Day #2


title: seedling,1.5h_after_HZE,atm-1 rep1

source_name: seedling_1.5h after HZE irradiation_atm-1

value: 2:39 pm on Day #1


title: seedling,24h_after_Gamma,atm-1 rep2

source_name: seedling_24h after Gamma irradiation_atm-1

value: 100 Gy of Gamma radiation

value: 15 minutes

value: 8:40 am on Day #2


title: seedling,1.5h_after_HZE,atm-1 rep2


title: Liver_HighGlucoseHS9_genotype


title: seedling,day_1_unirradiated,WT rep1

value: wild type

value: none (unirradiated control)

value: 10:45 am on Day #1


title: seedling,6h_after_HZE,atm-1 rep1

source_name: seedling_6h after HZE irradiation_atm-1

value: 7:24 pm on Day #1


title: seedling,12h_after_HZE,atm-1 rep1


title: seedling,24h_after_Gamma,atm-1 rep1

value: 6 days old


title: HTR-8/Svneo SP cell

city: Tokyo

first: Tetsunori

last: Inagaki

address: Hongo 2-1-1, Bunkyo-ku,

department: Obstetrics and gynecology

institute: Juntendo University

description: gene expression of SP cells cultured for a week in HSM

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505A) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid:026652_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Parental and NSP cells were cultured in RPMI1640 containing 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL streptomycin (HTR-8/SVneo basal medium–[HBM]) providing differentiation conditions. To maintain the SP fraction, SP cells were cultured in 50% HBM and 50% MEF conditioned medium containing one μg heparin/mL and 25 ng /mL FGF2 ( HTR-8/SVneo SP medium [HSM]).

extract_protocol: RNA was isolated with Qiagen RNeasy Plus Mini kit (Qiagen, Hilden, Germany) as directed by the manufacturer. 5μg of total RNA was reverse-transcribed to cDNA using oligo dT primer and Superscript Ⅱreverse-transcriptase (Invitrogen, Carlsbad USA).

treatment_protocol: To identify and isolate HTR-8/SVneo SP and NSP cells, cultured cells were dislodged from dishes with trypsin and EDTA, washed, and suspended at a concentration of 1x 106 cells/mL in RPMI1640 containing 10% FBS, one mM Hepes and five mM EDTA . The cells were labeled in the same medium at 37℃ for 90 minutes with 2.5 μg/mL Hoechst 33342 dye (Moleular Probes Inc., Eugene, Oregon), either alone or in combination with 50 μmol/L verapamil (SIGMA-Aldrich, St.Louis, Missouri). Finally, the cells were counterstained with one μg/mL propidium iodide (PI) to label dead cells. The cells were then analyzed in a FACS Vantage fluorescence-activated cell sorter (BD Bioscience, San Jose, California) using dual wavelength analysis (blue, 424 - 444nm; red 675 nm) after excitation with 350 nm UV light. PI-positive dead cells were excluded from the analysis.

value: placenta

value: trophoblast cell

tag: facs-isolated cell type

value: SP cell


title: Liver_HighGlucoseHS19_genotype

value: High Glucose

value: tail


title: seedling,12h_after_Gamma,atm-1 rep1

source_name: seedling_12h after Gamma irradiation_atm-1

value: 8:40 pm on Day #1


title: seedling,12h_after_Gamma,atm-1 rep2

value: 5 days old


title: HTR-8/Svneo NSP cell

description: gene expression of SP cells cultured for ａ week in HＢＭ

value: NSP cell


title: Liver_LowGlucoseHS8_genotype

value: heterogeneous stock

value: Low Glucose

value: male


title: Liver_HighGlucoseHS7_genotype


title: UWB1.289+BRCA1

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were processed using Affymetrix software Expression Console with default analysis settings and RMA as normalization method.

source_name: Ovarian cancer cell-line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions (RPMI-1640 glutamax-Gibco/Invitrogen- supplemented with 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin, 50 µg/ml gentamycin).

extract_protocol: Cells were directly lysed in the culture flasks and total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

tag: cell line

tag: description

value: pcDNA3 plasmid carrying wild-type BRCA1 was transfected into the UWB1.289 parent line, culture with selection marker G-418 to a final concentration of 200ug/ml

tag: morphology

value: Epithelial


title: Liver_LowGlucoseHS6_genotype

tag: strain


title: UWB1.289

value: carrier of a germline BRCA1 mutation within exon 11


title: Liver_LowGlucoseHS5_genotype

tag: gender


title: Liver_HighGlucoseHS4_genotype


title: seedling,6h_after_Gamma,atm-1 rep2

source_name: seedling_6h after Gamma irradiation_atm-1

value: 100 Gy of Gamma radiation

value: 15 minutes

value: 2:55 pm on Day #1


title: Liver_LowGlucoseHS14_genotype


title: TOV112D

value: Round


title: seedling,6h_after_Gamma,atm-1 rep1


title: Liver_HighGlucoseHS3_genotype


title: SKOV3


title: TOV21G


title: OVCAR3


title: Liver_LowGlucoseHS2_genotype


title: seedling,1.5h_after_Gamma,atm-1 rep1

source_name: seedling_1.5h after Gamma irradiation_atm-1

value: 10:10 am on Day #1


title: WN/N_Genotype

source_name: heterogeneous stock founder rat tail

value: WN/N


title: seedling,1.5h_after_Gamma,atm-1 rep2


title: Liver_LowGlucoseHS1_genotype


title: seedling,24h_after_HZE,WT rep2

source_name: seedling_24h after HZE irradiation_WT

value: wild type

value: 6 days old

value: 30 Gy of HZE

value: approx. 12 minutes

value: 1:09 pm on Day #2


title: WKY/N_Genotype

value: WKY/N

value: tail


title: seedling,24h_after_HZE,WT rep1


title: seedling,12h_after_HZE,WT rep2

source_name: seedling_12h after HZE irradiation_WT

value: 5 days old

value: 1:09 am on Day #2


title: OV7

value: Spindle


title: OV56


title: SKOV6

value: Epithelial


title: seedling,6h_after_HZE,WT rep2

source_name: seedling_6h after HZE irradiation_WT

value: 7:24 pm on Day #1


title: seedling,12h_after_HZE,WT rep1


title: OV90


title: OV17R


title: seedling,6h_after_HZE,WT rep1


title: MR/N_Genotype

value: MR/N

value: male


title: M520/N_Genotype


title: F344/N_Genotype


title: OAW42


title: seedling,6h_after_HZE,atm-1 rep2


title: IGROV1


title: seedling,3h_after_HZE,WT rep2

source_name: seedling_3h after HZE irradiation_WT

value: 4:09 pm on Day #1


title: seedling,3h_after_HZE,WT rep1


title: seedling,1.5h_after_HZE,WT rep2

source_name: seedling_1.5h after HZE irradiation_WT

value: 2:39 pm on Day #1


title: OAW28


title: seedling,1.5h_after_HZE,WT rep1


title: ACI/N_Genotype

value: ACI/N


title: BN/Ssn_Genotype

value: BN/Ssn


title: HOC7


title: BUF/N_Genotype

value: BUF/N


title: Liver_HighGlucoseHS46_genotype

source_name: heterogeneous stock rat tail

value: heterogeneous stock

value: High Glucose


title: SAMPLE_11_Fetal

source_name: Liver

tag: group

value: Fetal

tag: agegroup

tag: Sex

value: Female

value: liver

tag: slide

tag: array


title: Liver_LowGlucoseHS45_genotype

value: Low Glucose

value: tail


title: Liver_HighGlucoseHS43_genotype


title: Liver_HighGlucoseHS13_genotype


title: Liver_HighGlucoseHS42_genotype


title: seedling,12h_after_Gamma,WT rep2

source_name: seedling_12h after Gamma irradiation_WT

tag: genotype/variation

value: wild type

value: 5 days old

tag: treated with

value: 100 Gy of Gamma radiation

value: 15 minutes

tag: sampling time

value: 8:40 pm on Day #1


title: seedling,24h_after_Gamma,WT rep1

source_name: seedling_24h after Gamma irradiation_WT

tag: age

value: 6 days old

tag: treatment duration

value: 8:40 am on Day #2


title: COV413B

value: established from an intraperitoneal metastasis of the bladder dome. This cell line was derived from the same patient as the ovarian cell line COV413A

value: Spindle


title: Liver_LowGlucoseHS44_genotype

tag: phenotype

tag: tissue

value: male


title: seedling,12h_after_Gamma,WT rep1

tag: time after treatment


title: COV504

tag: cell line


title: COV644

tag: morphology

value: Epithelial


title: Liver_HighGlucoseHS41_genotype

tag: strain

value: heterogeneous stock

value: High Glucose


title: seedling,24h_after_Gamma,WT rep2


title: COV413A

tag: description

value: established from a metastasis of the sigmoid colon. This cell line was derived from the same patient as the ovarian cell line COV413B

value: Round


title: COV362


title: COV318


title: seedling,6h_after_Gamma,WT rep1

source_name: seedling_6h after Gamma irradiation_WT

value: 2:55 pm on Day #1


title: seedling,3h_after_Gamma,WT rep2

source_name: seedling_3h after Gamma irradiation_WT

value: 11:40 am on Day #1


title: jejunum_stressed 3-day_rep2

city: Beijing

first: peng

last: yin

state: Other

address: China Agricultural University (CAU), Beijing 100193, PR China

country: China

institute: CAU-BUA TCVM Teaching and Researching Team, College of Veterinary Medicine, China Agricultural University

description: Gene expression after 3 days heat and shake stressed jejunum. 2hr/day

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

source_name: jejunum, stressed 3 days, replicate 2

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

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

treatment_protocol: Sprague-Dawley rats weighing 200 ± 20 g were housed at 25°C and 60% relative humidity for 1 week. On the eighth day, the rats were randomly divided into control and 3day stress (S3d) groups. Ten rats in each group were housed in plastic cages (400 mm × 300 mm × 180 mm) with a layer of softwood chips and provided free access to food and water. Rats from each group were anesthetized by ether inhalational anesthesia, exsanguinated immediately after anesthesia, and then sacrificed. Sections of the jejunum were rapidly excised，a 3-cm section were washed using physiological saline (0.9%), then minced and separated into four sample tubes, frozen in liquid nitrogen, and stored at −80°C

value: Sprague-Dawley

value: jejunum

tag: gender

tag: age (weight)

tag: treatment


title: COV362.4

value: subline of an early passage of COV362 isolated by agar cloning


title: Liver_HighGlucoseHS40_genotype

value: tail


title: seedling,3h_after_Gamma,WT rep1

value: wild type

value: 5 days old

value: 100 Gy of Gamma radiation

value: 15 minutes


title: Genome-wide occupancy of Med7p in hyphae conditions (replica 2)

description:
Med7p-Hyphae(R2)
Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

data_processing: ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329.

source_name: WT under hyphae conditions (YPD 37oC) - Input sample

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174-1183, using the RNeasy Mini kit (Qiagen).

treatment_protocol: For ChIP-chip analysis, an overnight cultures in YPD were diluted to OD600nm =0.2 and grown to OD600nm=2 in 40 ml YPD at 30oC.

tag: strain/background

value: WT

tag: cell type

value: hyphae cells

tag: chip antibody

value: IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01)

source_name: Med7p-TAP under hyphae conditions (YPD 37oC) - ChIP sample


title: Genome-wide occupancy of Med7p in hyphae conditions (replica 1)

description:
Med7p-Hyphae(R1)
Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

tag: genotype/variation


title: jejunum_stressed 3-day_rep1

source_name: jejunum, stressed 3 days, replicate 1

value: male

value: 3 days heat and shake stressed jejunum. 2hr/day


title: COLO720E

source_name: Cancer cell-line

value: origin unclear, possibly contaminated or STR instability due to defective DNA mismatch repair


title: seedling,6h_after_Gamma,WT rep2

tag: treated with

tag: sampling time


title: Genome-wide occupancy of Med7p in yeast conditions (replica 2)

description:
Med7p-yeast (R2)
Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

source_name: WT under yeast conditions (YPD 30oC) - Input sample

value: yeast-form cells

source_name: Med7p-TAP under yeast conditions (YPD 30oC) - ChIP sample


title: jejunum_stressed 3-day_rep3

source_name: jejunum, stressed 3 days, replicate 3


title: Liver_LowGlucoseHS39_genotype

value: heterogeneous stock

value: Low Glucose


title: Liver_LowGlucoseHS37_genotype


title: Liver_LowGlucoseHS36_genotype


title: Liver_LowGlucoseHS35_genotype


title: CAOV4

source_name: Ovarian cancer cell-line

value: Epithelial


title: Liver_HighGlucoseHS34_genotype

value: High Glucose


title: seedling,1.5h_after_Gamma,WT rep1

source_name: seedling_1.5h after Gamma irradiation_WT

tag: age

tag: treatment duration

value: 10:10 am on Day #1


title: A2780 CIS (ECACC)

value: cisplatin resistant variant of A2780, once a month challenged with 1 µM cisplatin

value: Spindle


title: Liver_LowGlucoseHS38_genotype

tag: phenotype

tag: tissue

value: tail


title: A2780 ADR (ECACC)

tag: cell line

value: doxorubicin resistant variant of A2780, once a month challenged with 100 nM doxorubicin

value: Round


title: Liver_HighGlucoseHS33_genotype