title: genotype: Embrapa48 - time: 012 - Treated or untreated: SBR - rep2

source_name: (genotype: Embrapa48 - time: 012 - Treated or untreated: SBR)

value: SBR


title: 1-285

status: Public on Nov 22 2011

type: RNA

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: The Hy3-labelled samples were hybridized to miRCURY LNA arrays (v11.0) (Exiqon, Denmark), containing capture probes targeting all human miRNAs registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed overnight at 56°C according to manufacturer specifications using a Tecan HS4800 hybridization station (Tecan, Austria). Since it was not possible to hybridize all arrays in one go, samples were randomly split into 5 batches as to minimize day to day variation in the hybridization process.

scan_protocol: After hybridization the microarray slides were scanned using an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) at 5µm resolution, and the resulting TIFF images were analyzed using the ImaGene 8.0 software on standard settings (BioDiscovery, Inc., USA).

data_processing: Probe signals were background corrected by fitting a convolution of normal and exponential distributions to the foreground intensities using the background intensities as a covariate 4. Four technical replicate spots for each probe were combined to produce one signal by taking the logarithmic base-2 mean of reliable spots. If all four replicates for a given probe were judged unreliable that probe was removed from further analysis. A reference data vector R was calculated as the median signal of each probe across all samples. For all probe signals in a given sample, represented by the sample data vector S, a curve F was determined by locally weighted polynomial regression so as to provide the best fit between S and R. A normalized sample vector M was calculated from this by transforming it with the function F, so that M = F(S). In this manner, all samples were normalized to the reference R. This normalization procedure largely follows that outlined in Rosenfeld et al., 2008. Remote data points (probes in sparsely sampled intensity regions with less than 15 probes per signal unit) were considered unreliably adjusted by this method and removed before further analysis.

molecule: total RNA

organism: Homo sapiens

source_name: human skin

label_protocol: From each sample 100 ng of total RNA was labeled with Hy3 fluorescent dye using the miRCURY LNA Array power labeling kit (Exiqon, Denmark). All samples were labeled the same day with the same master mix, in order to minimize technical variation.

extract_protocol: Total RNA was isolated from six 10 µm tissue sections using the RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems/Ambion, USA) according to manufacturer guidelines. Total RNA quantity and quality were checked by spectrophotometer (Nanodrop ND-1000).

tag: malign

tag: tissue

value: skin

tag: diagnosis

value: CTCL


title: 1-101


title: Irradiated rat testes, with hormonal ablation, biological rep 7

city: Houston

first: Wei

last: Zhou

state: TX

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

country: USA

institute: M.D.Anderson Cancer Center

description: gene expression data from irradiated rat testes

hyb_protocol: cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner and quantified with Affymetrix GCOS 1.2.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. After normalization, the expression levels within each chip were divided by the median value for all the probes whose expression was regarded as present on the array, and then log base 2 transformed.

label: biotin

organism: Rattus norvegicus

source_name: Irradiated rat testes, with hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: Total RNA extraction by RNeasy Midi Kit (Qiagen, Valencia, CA)

treatment_protocol: 6 Gy irradiation to the lower abdomen of the rats

tag: treatment

value: testes

tag: genotype

value: LBNF1 rat

tag: age

value: 25~27 weeks old


title: genotype: Embrapa48 - time: 012 - Treated or untreated: SBR - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: at inoculation (Age); field soil (Growth Media).

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Glycine max

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  mix of natural soil from the field, cattle manure and sand (3:2:1)

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

value: whole organism

tag: time

tag: infection


title: BAG4_11_06_NA

city: Bergen

first: António

last: Pagarete

address: Thormøhlensgate 53 A & B

department: Department of Biology

country: Norway

institute: University of Bergen

description: Phosphate Limited

hyb_protocol: Total cRNA present in each sample was quantified using a NanoDrop ND 1000 (NanoDrop Technologies, Wilmington, DE). For each sample 7.5 µl 20 × SSC (Sigma), 1.0 µl 10% SDS and 100 ng of labelled cRNA were combined in a total volume of 45 µl. 33.3 µl of this dye-labelled target were added to 16.7 µl of pre-heated (50 °C ) 3 × Hybridisation buffer (consisting of 9 × SSC, 0.6% SDS), and incubated at 100 °C for 2 mins. of denaturation in the dark. Tubes were kept for a few minutes at 50 °C while waiting to be loaded onto microarray slide. 46 µl of target were loaded into an AO Maui mixer (BioMicro Systems, Inc.) and transferred to the preheated Maui hybridisation system (BioMicro Systems, Inc.).  Mixing was started and arrays incubated overnight for 16 h at 50°C. Microarray slides were then given three post-hybridisation washes. The first wash was in 50 ml of 1 × SSC, 2% SDS for 5 mins with constant agitation; followed by a second wash for a further 5 mins (with constant agitation) in  50 ml of 0.5 × SSC, 2% SDS; then a third wash for 10 secs in 50 ml of 0.5 × SSC. Residual liquid was removed by centrifugation at 1000 rpm for 5 mins at room temperature, and the slides stored in the dark prior to scanning.

scan_protocol: Hybridised arrays were scanned in an Agilent DNA Microarray Scanner with Surescan High-Resolution Technology with 5 µm resolution. Each array was scan at 20%, 50%, and 100% gain settings in order to determine and select the optimal scan setting producing a high dynamic signal range without saturation (Forster et al., 2003). Images from all scans were quantified and background corrected using BlueFuse for Microarrays v3.6 (7145).

data_processing: Overall fluorescence values between different microarray chips were normalized using the quantile method using R (Team RDC, 2009) and the limma package (Smyth, 2005). This method assumed that the distribution of gene abundances was nearly the same across arrays. Intensity values were first sorted and then each ranked among arrays, leading to the normalization to the same single mean value for all the arrays. For posterior analysis the 5 within-array technical replicate values were replaced by the respective median.

organism: marine metagenome

source_name: Mesosom Enclosure 4; Experimental day 11; Time 6h

label_protocol: Random amplification of the entire mRNA population was achieved using the Microarray Target Amplification Kit (Roche). This required the use of a special primer, containing a random sequence with no significant homology to any known sequences in public databases (Target Amplification Sequence, [TAS]) in addition to T7 promoter and oligo (dT) sequences, for first-strand cDNA synthesis. The TAS-region generates a 3´ anchor on the cDNA for subsequent PCR amplification with a TAS-PCR primer. First and second strand cDNA synthesis was performed from 250 ng of total RNA and purified using the Target Purification Kit (Roche).  For expression profiling, purified cDNA was randomly amplified in a 100 µl volume by 21 cycles of PCR using TAS primers according to the manufactures instructions. PCR products (produced after the appropriate number of PCR cycles) were purified using the Microarray Target Purification kit (Roche). The resulting PCR-amplified cDNA was then transcribed into Cy5 (for each sample) fluorescently labelled cRNA using the T7 Microarray RNA Target Synthesis Kit (Roche). The appropriate labelled cRNAs were combined and then purified using the Microarray Target Purification kit.

growth_protocol: Six transparent polyethylene enclosures (11 m3; 90% penetration of photosynthetically active radiation) purchased from ANI-TEX (Notodden, Norway) were mounted on floating frames moored along the south side of a raft and filled with unfiltered fjord water pumped from 10 m depth adjacent to the raft. Homogeneous water masses within the enclosures were ensured by pumping water from the bottom of the bag to the surface. The 6 enclosures (encs.) were divided in 2 treatment groups allowing triplication of each treatment: phosphate replete (encs. #1, #3 and #5) and phosphate deplete (encs. #2, #4 and #6). Nutrients were added approx 15:00 h daily at an N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4) to the phosphate replete enclosures and at a ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4) to the phosphate deplete enclosures.

extract_protocol: Total RNA extracted from biological material present in 2L of water and collected in 0.2um filters. The cells were resuspended from the filter using 2 ml PBS buffer, and transferred into an Eppendorff tube. Tubes were centrifuged for 1 min at 15500 × g, and the supernatant discarded. Total RNA was extracted with RNeasy Midi Kits (Qiagen) according to the manufacturer’s instructions. Briefly, the samples were resuspended in 2 ml RLT lysis buffer, vortexed for 1 min. (5 sec. bursts), and spun for 5 min at 15500 × g. The supernatant was transferred to a new tube, and the nucleic acids were precipitated using 2 ml of 70% ethanol. The samples were loaded onto an RNA-binding midiprep column (Qiagen). The column was washed with RW1 and RPE solutions, and RNA was eluted in 200 μl of RNase free water. To remove contaminating DNA, the samples were DNase treated twice for 25 min. at 37º C with 2 U of Turbo DNA-free kit (Ambion) according to the manufacturer’s instructions. The quality of the RNA samples was determined with a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). All samples tested negative for genomic DNA contamination. Samples were stored at -80º C until further use.

treatment_protocol: Four daily samples (06 h, 12 h, 18 h, and 24 h) were taken from the surface of each mesocosm with 20 l carboys. Samples were immediately brought to the lab where 2l of each sample was filtered onto 0.45-µm-pore-size 47-mm-diameter Supor-450 filters (PALL Corp.).

tag: sample

value: natural planktonic community exiting on Raunefjorden, Western Norway coast

tag: enrichment treatment

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: genotype: Embrapa48 - time: 012 - Treated or untreated: Mock - rep2

source_name: (genotype: Embrapa48 - time: 012 - Treated or untreated: Mock)

value: Mock


title: Irradiated rat testes, with hormonal ablation, biological rep 5

value: Irradiated rat testes, with hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide)


title: genotype: Embrapa48 - time: 012 - Treated or untreated: SBR - rep1


title: genotype: Embrapa48 - time: 006 - Treated or untreated: Mock - rep3

source_name: (genotype: Embrapa48 - time: 006 - Treated or untreated: Mock)


title: genotype: Embrapa48 - time: 006 - Treated or untreated: Mock - rep2


title: genotype: Embrapa48 - time: 006 - Treated or untreated: Mock - rep1


title: BAG4_10_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 10; Time 6h


title: BAG4_16_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 16; Time 6h


title: Irradiated rat testes, with hormonal ablation, biological rep 2


title: BAG4_15_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 15; Time 6h


title: 1-100


title: Irradiated rat testes, with hormonal ablation, biological rep 1


title: BAG4_14_06_AP

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 14; Time 6h


title: BAG4_13_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 13; Time 6h


title: 1-80


title: Irradiated rat testes, with hormonal ablation, biological rep 3


title: Irradiated rat testes, with hormonal ablation, biological rep 4


title: genotype: Embrapa48 - time: 006 - Treated or untreated: SBR - rep3

source_name: (genotype: Embrapa48 - time: 006 - Treated or untreated: SBR)


title: genotype: Embrapa48 - time: 006 - Treated or untreated: SBR - rep1


title: genotype: Embrapa48 - time: 006 - Treated or untreated: SBR - rep2


title: Irradiated rat testes, with sham treatment, biological rep 13


title: genotype: PI230970 - time: 168 - Treated or untreated: Mock - rep3

source_name: (genotype: PI230970 - time: 168 - Treated or untreated: Mock)


title: Irradiated rat testes, with sham treatment, biological rep 14


title: BAG4_08_06_AV

description: Phosphate Limited

source_name: Mesosom Enclosure 4; Experimental day 8; Time 6h


title: 1-45


title: 1-51


title: Irradiated rat testes, with sham treatment, biological rep 12


title: 1-44


title: 1-35


title: genotype: PI230970 - time: 168 - Treated or untreated: Mock - rep2


title: Irradiated rat testes, with sham treatment, biological rep 10

description: gene expression data from control rat testes


title: BAG3_15_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 15; Time 18h

value: N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4)


title: Irradiated rat testes, with sham treatment, biological rep 11


title: 1-24


title: Irradiated rat testes, with sham treatment, biological rep 7


title: BAG3_16_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 16; Time 18h


title: BAG3_16_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 16; Time 12h


title: BAG3_16_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 16; Time 24h


title: Irradiated rat testes, with sham treatment, biological rep 6


title: genotype: PI230970 - time: 168 - Treated or untreated: Mock - rep1


title: BAG3_16_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 16; Time 6h


title: Irradiated rat testes, with sham treatment, biological rep 8


title: genotype: PI230970 - time: 168 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 168 - Treated or untreated: SBR)


title: 1-34

source_name: human skin


title: genotype: PI230970 - time: 168 - Treated or untreated: SBR - rep1


title: genotype: PI230970 - time: 168 - Treated or untreated: SBR - rep2


title: Irradiated rat testes, with sham treatment, biological rep 9


title: genotype: PI230970 - time: 120 - Treated or untreated: Mock - rep2

source_name: (genotype: PI230970 - time: 120 - Treated or untreated: Mock)


title: BAG3_15_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 15; Time 12h


title: 0-134

value: PP


title: 1-54


title: 0-4

value: AD


title: 1-43


title: genotype: PI230970 - time: 120 - Treated or untreated: Mock - rep1


title: genotype: PI230970 - time: 120 - Treated or untreated: Mock - rep3


title: BAG3_15_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 15; Time 6h


title: 0-3


title: 0-111

value: NN


title: 0-1


title: 0-2


title: Irradiated rat testes, with sham treatment, biological rep 5


title: Irradiated rat testes, with sham treatment, biological rep 4


title: BAG3_14_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 14; Time 24h


title: 0-133


title: BAG3_13_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 13; Time 18h


title: Irradiated rat testes, with sham treatment, biological rep 3


title: Irradiated rat testes, with sham treatment, biological rep 2


title: BAG3_14_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 14; Time 18h


title: BAG3_13_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 13; Time 12h


title: BAG3_14_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 14; Time 12h


title: genotype: PI230970 - time: 120 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 120 - Treated or untreated: SBR)


title: BAG3_13_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 13; Time 24h


title: genotype: PI230970 - time: 120 - Treated or untreated: SBR - rep1


title: Irradiated rat testes, with sham treatment, biological rep 1


title: genotype: PI230970 - time: 120 - Treated or untreated: SBR - rep2


title: BAG3_12_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 12; Time 24h


title: BAG3_13_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 13; Time 06h


title: 0-124


title: genotype: PI230970 - time: 096 - Treated or untreated: Mock - rep1

source_name: (genotype: PI230970 - time: 096 - Treated or untreated: Mock)


title: 0-131


title: genotype: PI230970 - time: 096 - Treated or untreated: Mock - rep3


title: genotype: PI230970 - time: 096 - Treated or untreated: Mock - rep2


title: genotype: PI230970 - time: 096 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 096 - Treated or untreated: SBR)


title: BAG3_12_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 12; Time 18h


title: 0-113


title: genotype: PI230970 - time: 096 - Treated or untreated: SBR - rep1


title: 0-132


title: BAG3_12_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 12; Time 12h


title: BAG3_12_06_AP

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 12; Time 06h


title: 0-85

source_name: human skin


title: 0-86

value: PN


title: 0-84


title: genotype: PI230970 - time: 096 - Treated or untreated: SBR - rep2


title: genotype: PI230970 - time: 072 - Treated or untreated: Mock - rep3

source_name: (genotype: PI230970 - time: 072 - Treated or untreated: Mock)


title: BAG3_11_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 11; Time 6h


title: BAG3_11_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 11; Time 18h


title: BAG3_11_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 11; Time 24h


title: genotype: PI230970 - time: 072 - Treated or untreated: Mock - rep1


title: 0-83


title: BAG3_10_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 10; Time 24h


title: genotype: PI230970 - time: 072 - Treated or untreated: SBR - rep2

source_name: (genotype: PI230970 - time: 072 - Treated or untreated: SBR)


title: BAG3_11_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 11; Time 12h


title: genotype: PI230970 - time: 072 - Treated or untreated: SBR - rep3


title: 0-82


title: BAG3_10_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 10; Time 18h


title: 0-81


title: genotype: PI230970 - time: 072 - Treated or untreated: Mock - rep2


title: BAG3_10_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 10; Time 12h


title: genotype: PI230970 - time: 072 - Treated or untreated: SBR - rep1


title: 1-283


title: BAG3_10_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 10; Time 06h


title: 0-279


title: 1-284


title: BAG3_09_24_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 9; Time 24h


title: genotype: PI230970 - time: 048 - Treated or untreated: Mock - rep3

source_name: (genotype: PI230970 - time: 048 - Treated or untreated: Mock)


title: genotype: PI230970 - time: 048 - Treated or untreated: Mock - rep1


title: genotype: PI230970 - time: 048 - Treated or untreated: Mock - rep2


title: BAG3_09_18_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 9; Time 18h


title: 1-98


title: BAG3_09_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 9; Time 12h


title: 1-50


title: 818 tumor TILN

city: Boston

first: Lukas

last: Baitsch

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

description:
Set 2
Gene expression ex vivo of tumor-specific T cells from tumor-infiltrated lymph node.

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarray 4 x 44K using Agilent’s recommended hybridization chamber and oven. Microarrays were washed once with 6x SSPE buffer containing 0.005% N- lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

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

data_processing: Raw intensities from the Feature Extraction files were used and analyzed using R and Bioconductor applying the Agi4x44PreProcess package.

source_name: tumor TILN

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling, which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Samples were processed ex vivo.

extract_protocol: Using a Vantage SE, 1000 cells from each cell population were sorted directly into lysis and storage buffer, as provided by Miltenyi Biotec. After sorting, the lysed cells were incubated for 10min at 45°C and then directly frozen at –80°C.

treatment_protocol: Mononuclear cells were purified by density gradient using Lymphoprep and immediately frozen. CD8+ T cells were enriched using magnetic bead sorting. Cells were stained on ice and then diluted at one million cells/ml for optimal sorting speed and high purity.

tag: patient code

tag: disease

value: melanoma

value: tumor-infiltrated lymph node (TILN)

tag: cell type

value: CD8+ T cells

tag: tcr specificity (or naive)

value: self/tumor (Melan-A/MART-1 26-35 A27L)

value: 59 years

tag: Sex

value: male


title: genotype: PI230970 - time: 048 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 048 - Treated or untreated: SBR)

value: SBR


title: genotype: PI230970 - time: 048 - Treated or untreated: SBR - rep2

value: whole organism


title: V 2 CMV PBMC

description:
Set 2
Gene expression ex vivo of CMV-specific T cells from blood.

source_name: CMV PBMC

value: V 2

value: peripheral blood

value: 74 years


title: BAG3_08_12_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 8; Time 12h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast


title: genotype: PI230970 - time: 048 - Treated or untreated: SBR - rep1


title: 1-49

source_name: human skin

value: skin

value: CTCL


title: 205 tumor PBMC, repl 2

description:
Set 2
Gene expression ex vivo of tumor-specific T cells from blood.

source_name: tumor PBMC

value: 36 years


title: BAG3_08_06_AV

description: High phosphate enrichment

source_name: Mesosom Enclosure 3; Experimental day 8; Time 6h

value: N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4)


title: BAG2_16_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 16; Time 24h

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: 1-42


title: 1-41


title: BAG2_16_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 16; Time 18h


title: 672 tumor TILN

value: melanoma

value: 38 years


title: 1-33


title: genotype: PI230970 - time: 036 - Treated or untreated: Mock - rep1

source_name: (genotype: PI230970 - time: 036 - Treated or untreated: Mock)

value: Mock


title: genotype: PI230970 - time: 036 - Treated or untreated: Mock - rep2


title: 972 tumor PBMC, repl 2

value: CD8+ T cells

value: self/tumor (Melan-A/MART-1 26-35 A27L)

value: 64 years

value: female


title: V 12 CMV PBMC

value: 95 years

value: male


title: Caucasian_controls_rep2

type: genomic

city: Créteil

first: Alice

last: Hadchouel

address: 8 rue du général Sarrail

country: France

institute: INSERM

description: equimolar amounts of genomic DNA extracted from corf blood leukocytes were pooled and genotyped using Infinium HumanHap300 Genotyping BeadChips (Illumina).

hyb_protocol: According to manufacturer's protocol

scan_protocol: According to manufacturer's protocol

data_processing: Caucasian cases and controls pools were genotyped using Infinium HumanHap300v2_A Genotyping BeadChips (Illumina). Raw data from micro-arrays were processed using BSGT Version 2.3.43.31247.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: cord blood

label_protocol: According to manufacturer's protocol

extract_protocol: Genomic DNA was extracted from cord-blood leukocytes by using the Nucleon kit (Amersham).

value: cord blood

value: leukocytes

tag: disease status

value: control

tag: race

value: Caucasian


title: BAG2_15_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 15; Time 24h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast


title: Caucasian_controls_rep3


title: Caucasian_controls_rep1


title: 1-31

tag: malign

value: skin

value: CTCL


title: 567 tumor TILN

tag: tissue

value: tumor-infiltrated lymph node (TILN)

value: 54 years


title: genotype: PI230970 - time: 036 - Treated or untreated: SBR - rep2

source_name: (genotype: PI230970 - time: 036 - Treated or untreated: SBR)

value: whole organism

value: SBR


title: BAG2_15_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 15; Time 18h

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: 706 CMV PBMC

value: melanoma

value: peripheral blood

value: CD8+ T cells

value: 66 years


title: genotype: PI230970 - time: 036 - Treated or untreated: SBR - rep3


title: 1-23

tag: diagnosis


title: 1-32


title: Caucasian_controls_rep4


title: genotype: PI230970 - time: 036 - Treated or untreated: Mock - rep3

value: Mock


title: BAG2_15_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 15; Time 12h


title: genotype: PI230970 - time: 036 - Treated or untreated: SBR - rep1


title: Caucasian_cases_rep2

value: cord blood

value: Bronchopulmonary dysplasia (BPD)


title: genotype: PI230970 - time: 024 - Treated or untreated: Mock - rep3

source_name: (genotype: PI230970 - time: 024 - Treated or untreated: Mock)


title: 618 tumor PBMC, repl 2

value: self/tumor (Melan-A/MART-1 26-35 A27L)

value: 75 years

value: female


title: genotype: PI230970 - time: 024 - Treated or untreated: Mock - rep2


title: 352 tumor TILN

value: 77 years

value: male


title: G 207 CMV PBMC

value: 95 years


title: Caucasian_cases_rep3

value: leukocytes

value: Caucasian


title: 1-21

value: skin

value: CTCL


title: BAG2_15_06_AP

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 15; Time 6h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: BAG2_14_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 14; Time 18h


title: genotype: PI230970 - time: 024 - Treated or untreated: Mock - rep1

value: whole organism


title: Caucasian_cases_rep1


title: BAG2_13_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 13; Time 24h


title: BAG2_14_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 14; Time 12h


title: 618 CMV PBMC

source_name: CMV PBMC

value: melanoma

value: peripheral blood

value: CD8+ T cells


title: 465 tumor PBMC

value: 58 years


title: genotype: PI230970 - time: 024 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 024 - Treated or untreated: SBR)

value: SBR


title: Chicken_Erythros_Poly(I:C) 3

city: Cerdanyola del Vallès

first: Davínia

middle: Morera

last: Capdevila

address: Edifici Biociències, ala sud

department: Biologia cel.lular, Immunologia i Fisiologia

country: Spain

institute: Universitat Autònoma de Barcelona

description: Chicken erythrocytes stimulated with Poly(I:C). Biological replicate 3 of 3

hyb_protocol: Each sample (1.65 μg) was hybridized to Gallus gallus array (Agilent ID 026441 v.2) at 65 ºC for 17 hours using Agilent's GE Hybridization kit. Washes were conducted as recommended by the manufacturer using Agilent's Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%). Spot intensities and other quality control features were extracted with Agilent's Feature Extraction software version 10.4.0.0

data_processing: Microarray data was analyzed using GeneSpring software version 10. The algorithm used to normalize our data is the shift to the 75th percentile.

organism: Gallus gallus

source_name: Primary culture isolated chicken erythrocytes

label_protocol: RNA labelling, hybridizations and scanning were performed according to manufacterer instructions. Briefly, total RNA (150 ng) was amplified and Cy3-labelled with Agilent's One Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling Kit) along with Agilent's One-Color RNA SpikeIn Kit. After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen) and quantified with the Nanodrop000.

growth_protocol: Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37 ºC and 5% CO2

extract_protocol: Total RNA was extracted with Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) following the manufacture instructions with minor modifications. The RNA was stored at -80 ºC in ethanol 70% until use. RNA was quantified using Nanodrop1000 (ThermoScientific), and RNA integrity and quality was assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Erythrocytes were stimulated/incubated 12 hours with lipopolysaccharide from E. coli (serotype 0111:B4, Sigma) or Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at  5 μg/ml.

tag: treatment


title: BAG2_14_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 14; Time 24h


title: Chicken_Erythros_Poly(I:C) 1

description: Chicken erythrocytes stimulated with Poly(I:C). Biological replicate 1 of 3


title: Chicken_Erythros_Poly(I:C) 2

description: Chicken erythrocytes stimulated with Poly(I:C). Biological replicate 2 of 3


title: BAG2_13_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 13; Time 12h


title: BAG2_12_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 12; Time 24h


title: 392 tumor TILN

source_name: tumor TILN

value: tumor-infiltrated lymph node (TILN)

value: self/tumor (Melan-A/MART-1 26-35 A27L)

value: 33 years


title: genotype: PI230970 - time: 024 - Treated or untreated: SBR - rep2

tag: genotype


title: genotype: PI230970 - time: 024 - Treated or untreated: SBR - rep1


title: Chicken_Erythros_PGN 2

description: Chicken erythrocytes stimulated with PGN. Biological replicate 2 of 3

value: Pepdidoglycan (PGN)


title: Chicken_Erythros_PGN 3

description: Chicken erythrocytes stimulated with PGN. Biological replicate 3 of 3


title: black African_cases_rep1

description: equimolar amounts of genomic DNA extracted from corf blood leukocytes were pooled and genotyped using Infinium HumanHap650Y Genotyping BeadChips (Illumina).

data_processing: Black African cases and controls pools were genotyped using Infinium HumanHap650Yv3_A Genotyping BeadChips (Illumina). Raw data from micro-arrays were processed using BSGT Version 2.3.43.31247.

source_name: cord blood

value: cord blood

value: Bronchopulmonary dysplasia (BPD)

value: black African


title: genotype: PI230970 - time: 018 - Treated or untreated: Mock - rep2

source_name: (genotype: PI230970 - time: 018 - Treated or untreated: Mock)

value: Mock


title: genotype: PI230970 - time: 018 - Treated or untreated: Mock - rep3


title: 969 tumor TILN

tag: age

value: 52 years

value: male


title: black African_controls_rep4

value: leukocytes

value: control


title: Chicken_Erythros_PGN 1

description: Chicken erythrocytes stimulated with PGN. Biological replicate 1 of 3


title: black African_controls_rep2


title: black African_controls_rep1


title: Caucasian_cases_rep4

value: Caucasian


title: BAG2_12_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 12; Time 6h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: BAG2_12_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 12; Time 12h


title: 465 tumor TILN

value: melanoma

value: CD8+ T cells

value: 48 years


title: genotype: PI230970 - time: 018 - Treated or untreated: Mock - rep1

value: whole organism

tag: time


title: black African_controls_rep3


title: genotype: PI230970 - time: 018 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 018 - Treated or untreated: SBR)

tag: infection

value: SBR


title: black African_cases_rep4


title: BAG2_12_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 12; Time 18h

tag: sample


title: black African_cases_rep3


title: 288 CMV PBMC

value: peripheral blood

value: 65 years


title: Chicken_Erythros_LPS 3

description: Chicken erythrocytes stimulated with LPS. Biological replicate 3 of 3

value: Lipopolysaccharide (LPS)


title: genotype: PI230970 - time: 018 - Treated or untreated: SBR - rep2


title: 1013 CMV PBMC

value: 59 years


title: 818 tumor PBMC

source_name: tumor PBMC

value: self/tumor (Melan-A/MART-1 26-35 A27L)


title: BAG2_11_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 11; Time 18h

tag: enrichment treatment


title: BAG2_11_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 11; Time 12h


title: BAG2_11_06_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 11; Time 6h


title: 1013 tumor PBMC, repl 1

description:
Set 1
Gene expression ex vivo of tumor-specific T cells from blood.

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

tag: patient code


title: genotype: PI230970 - time: 018 - Treated or untreated: SBR - rep1


title: Chicken_Erythros_LPS 1

description: Chicken erythrocytes stimulated with LPS. Biological replicate 1 of 3


title: BAG2_10_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 10; Time 24h


title: black African_cases_rep2

value: cord blood

value: Bronchopulmonary dysplasia (BPD)

value: black African


title: BAG2_10_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 10; Time 18h


title: Chicken_Erythros_LPS 2

description: Chicken erythrocytes stimulated with LPS. Biological replicate 2 of 3

source_name: Primary culture isolated chicken erythrocytes


title: BAG2_10_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 10; Time 12h


title: 1106 tumor PBMC

tag: disease

value: 39 years

value: male


title: Chicken_Erythros_control 1

description: Chicken erythrocytes control. Biological replicate 1 of 3

value: Control


title: 1013 naive PBMC

description:
Set 1
Gene expression ex vivo of naive T cells from blood.

source_name: naive PBMC

tag: cell type

value: naive


title: genotype: PI230970 - time: 012 - Treated or untreated: Mock - rep1

description: at inoculation (Age); field soil (Growth Media).

source_name: (genotype: PI230970 - time: 012 - Treated or untreated: Mock)

value: Mock


title: 1106 naive PBMC

value: melanoma

value: CD8+ T cells

tag: tcr specificity (or naive)


title: Chicken_Erythros_control 2

description: Chicken erythrocytes control. Biological replicate 2 of 3


title: BAG2_09_24_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 9; Time 24h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast

value: N:P ratio of 75:1 (1.5 µM  NaNO3 and 0.02 µM KH2PO4)


title: Chicken_Erythros_control 3

description: Chicken erythrocytes control. Biological replicate 3 of 3


title: genotype: PI230970 - time: 012 - Treated or untreated: Mock - rep3

value: whole organism


title: BAG2_09_18_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 9; Time 18h


title: sre1_t=8_Fe+

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: All hybridizations used a pooled reference of all channel 1 samples (all 20 samples) for channel 2.

hyb_protocol: cDNA from each individual time point was labeled with Cy5 and competitively hybridized against a Cy3 labeled reference (generated by pooling all cDNA samples in the time-course), using H. capsulatum G217B 70-mer oligonucleotide microarrays

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments/Molecular Devices, www.moleculardevices.com ).

data_processing: Arrays were gridded using Spotreader (Niles Scientific, www.nilesscientific.com) and archived, normalized, and aggregated in NOMAD 2.0 (http://nomad2.ucsf.edu/NOMAD/nomad-cgi/login.pl).  For each array, median spot intensities were adjusted for local background and filtered for FLAG >= 0 (not manually or automatically flagged as bad) and for summed channel intensities >= 500.  Log2(Cy5/Cy3) ratios for spots passing the filters were median normalized and transformed relative to the wt_t=0_1 sample.  This transformed log ratio is reported in the VALUE column.

organism: Histoplasma capsulatum

source_name: H. capsulatum yeast, mRPMI+10 uM FeSO4, t=8

label_protocol: cDNA was synthesized from 30 ug of total RNA from strains HcLH120 (Control RNAi-1) and HcLH123 (SRE1 RNAi-2) and fluorescent labeling was performed as previously described (Mol. Biol. Cell 16:4792).

extract_protocol: Cultures of H. capsulatum were harvested by filtration, and total RNA was isolated using a guanidine thiocyanate lysis protocol as previously described (Mol. Biol. Cell 16:4792).

tag: background strain

tag: strain

tag: genotype/variation

value: SRE1-depleted (SRE1 RNAi)

source_name: Pooled reference of all samples.

value: HcLH120 (control RNAi) and HcLH123 (SRE1 RNAi) pooled


title: genotype: PI230970 - time: 012 - Treated or untreated: Mock - rep2


title: genotype: PI230970 - time: 012 - Treated or untreated: SBR - rep2

source_name: (genotype: PI230970 - time: 012 - Treated or untreated: SBR)

value: SBR


title: genotype: PI230970 - time: 012 - Treated or untreated: SBR - rep3


title: 1144 naive PBMC

value: peripheral blood

value: 74 years

tag: Sex


title: sre1_t=4_Fe+

source_name: H. capsulatum yeast, mRPMI+10 uM FeSO4, t=4


title: BAG2_08_12_NA

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 8; Time 12h


title: sre1_t=.5_Fe+

source_name: H. capsulatum yeast, mRPMI/10uM FeSO4, t=0.5


title: 1144 tumor PBMC

source_name: tumor PBMC

tag: tissue

value: self/tumor (Melan-A/MART-1 26-35 A27L)


title: genotype: PI230970 - time: 012 - Treated or untreated: SBR - rep1


title: BAG1_16_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 16; Time 6h

value: N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4)


title: BAG2_08_06_AV

description: Phosphate Limited

source_name: Mesosom Enclosure 2; Experimental day 8; Time 6h


title: BAG1_15_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 15; Time 6h


title: HD4 EBV PBMC

description:
Set 1
Gene expression ex vivo of EBV-specific T cells from blood.

source_name: EBV PBMC

value: 37 years


title: genotype: PI230970 - time: 006 - Treated or untreated: Mock - rep2

source_name: (genotype: PI230970 - time: 006 - Treated or untreated: Mock)


title: 1013 tumor PBMC, repl 2

description:
Set 2
Gene expression ex vivo of tumor-specific T cells from blood.

value: 59 years

value: male


title: sre1_t=4_Fe-

source_name: H. capsulatum yeast, mRPMI, t=4


title: BAG1_14_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 14; Time 6h


title: sre1_t=8_Fe-

source_name: H. capsulatum yeast, mRPMI, t=8


title: genotype: PI230970 - time: 006 - Treated or untreated: SBR - rep3

source_name: (genotype: PI230970 - time: 006 - Treated or untreated: SBR)


title: HD4 naive PBMC

source_name: naive PBMC

value: naive


title: HD3 EBV PBMC

value: 55 years


title: genotype: PI230970 - time: 006 - Treated or untreated: Mock - rep3

value: Mock


title: genotype: PI230970 - time: 006 - Treated or untreated: Mock - rep1


title: sre1_t=.5_Fe-

source_name: H. capsulatum yeast, mRPMI, t=0.5


title: sre1_t=0

source_name: H. capsulatum yeast, mRPMI, t=0

source_name: Pooled reference of all samples.


title: genotype: PI230970 - time: 006 - Treated or untreated: SBR - rep2


title: HD3 naive PBMC

value: melanoma

value: CD8+ T cells


title: HD2 EBV PBMC

value: 65 years

value: female


title: BAG1_13_06_AP

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 13; Time 6h

value: natural planktonic community exiting on Raunefjorden, Western Norway coast


title: sre1_t=1_Fe+

source_name: H. capsulatum yeast, mRPMI+10 uM FeSO4, t=1

value: SRE1-depleted (SRE1 RNAi)

value: HcLH120 (control RNAi) and HcLH123 (SRE1 RNAi) pooled


title: BAG1_12_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 12; Time 6h


title: HD1 EBV PBMC

value: peripheral blood

value: 22 years


title: sre1_t=1_Fe-

source_name: H. capsulatum yeast, mRPMI, t=1


title: HD2 naive PBMC


title: wt_t=4_Fe+

source_name: H. capsulatum yeast, mRPMI+10 uM FeSO4, t=4

value: wild type (control RNAi)


title: wt_t=8_Fe+

source_name: H. capsulatum yeast, mRPMI+10 uM FeSO4, t=8


title: genotype: PI230970 - time: 006 - Treated or untreated: SBR - rep1

value: whole organism

value: SBR


title: genotype: HiProt - time: >200-300 - rep3

description: ld04-15154 (germplasm name); po: 0009010 seed, (Organism Part); PO:0007010 6 ripening (Development Stage); field soil (Growth Media).

hyb_protocol: Affymetrix Basic Protocol

scan_protocol: Array scanning

source_name: seed (genotype: HiProt - time: >200-300)

label_protocol: synthesizing and biotin labeling total RNA samples

growth_protocol: Growth Description:  plants grown in growth chambers with photoperiod d/n range: 14/10h-13/11 hours and thermoperiod d/n range: 22/10-28/14 °C  Environmental Conditions:  soil supplemented with granular Bradyrhizobium japonicum inoculant and 14-14-14 fertilizer

extract_protocol: Trizol total RNA extraction, Qiagen RNeasy column purification

value: seed

value: HiProt


title: BAG1_11_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 11; Time 6h

value: N:P ratio of 15:1 (1.5 µM  NaNO3 and 0.1 µM KH2PO4)


title: BAG1_10_06_NA

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 10; Time 6h


title: BAG1_08_06_AV

description: High phosphate enrichment

source_name: Mesosom Enclosure 1; Experimental day 8; Time 6h


title: wt_t=8_Fe-


title: genotype: HiProt - time: >200-300 - rep1


title: genotype: HiProt - time: >200-300 - rep2


title: genotype: HiProt - time: >100-200 - rep2

source_name: seed (genotype: HiProt - time: >100-200)


title: genotype: HiProt - time: >100-200 - rep3


title: HD1 naive PBMC

value: naive


title: 392 EBV PBMC

source_name: EBV PBMC

value: 41 years


title: wt_t=4_Fe-

source_name: H. capsulatum yeast, mRPMI, t=4


title: 936 EBV PBMC

value: melanoma

value: 57 years


title: 392 tumor PBMC

source_name: tumor PBMC

value: CD8+ T cells

value: self/tumor (Melan-A/MART-1 26-35 A27L)


title: wt_t=1_Fe+


title: wt_t=.5_Fe+

source_name: H. capsulatum yeast, mRPMI/10uM FeSO4, t=0.5


title: genotype: HiProt - time: >50-100 - rep3

source_name: seed (genotype: HiProt - time: >50-100)


title: 392 naive PBMC

source_name: naive PBMC

value: female


title: genotype: HiProt - time: >100-200 - rep1


title: genotype: HiProt - time: >50-100 - rep2


title: 400956_LS180_24hr_dscDNA_1252_532

city: Madison

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

description: This sample was treated for 24 hrs with 1,25(OH)2D3. It is the second in the series of biological replicate experiments.

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

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

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

source_name: LS180 colorectal cancer cells treated for 24hrs with 1,25(OH)2D3

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

growth_protocol: Human LS180 CRC cells were obtained from ATCC (Manassas, VA).  LS180 cells were cultured in minimum Eagle’s medium supplemented with 10% non-heat-inactivated fetal bovine serum from Hyclone (Logan, UT), 1% non-essential amino acids, 1% sodium pyruvate, and 1% penicillin-streptomycin

extract_protocol: RNA was isolated using the TRI-Reagent protocol (MRC, Cincinnati, OH) and amplification methods according Roche NimbleGen protocols.

treatment_protocol: Cells were treated with 10-7M 1,25(OH)2D3 for 0 and 24 hours

tag: cell line

value: LS180 cells


title: wt_t=1_Fe-

source_name: Pooled reference of all samples.

value: HcLH120 (control RNAi) and HcLH123 (SRE1 RNAi) pooled


title: 400952_LS180_24hr_dscDNA_1251_532

description: This sample was treated for 24 hrs with 1,25(OH)2D3. It is the first in the series of biological replicate experiments.

tag: treatment


title: wt_t=0_3

source_name: H. capsulatum yeast, mRPMI, t=0


title: wt_t=.5_Fe-

source_name: H. capsulatum yeast, mRPMI, t=0.5


title: 936 naive PBMC

value: peripheral blood


title: 936 tumor PBMC


title: 400960_LS180_24hr_dscDNA_1253_532

description: This sample was treated for 24 hrs with 1,25(OH)2D3. It is the third in the series of biological replicate experiments.


title: genotype: HiProt - time: >50-100 - rep1

tag: genotype


title: wt_t=0_2


title: 400949_LS180_0hr_dscDNA_Veh3_532

description: This sample was treated for 0 hrs with 1,25(OH)2D3. It is the third in the series of biological replicate experiments.

source_name: LS180 colorectal cancer cells treated for 0hrs with 1,25(OH)2D3

value: 0 h


title: 672 EBV PBMC

tag: age

value: 43 years

value: male


title: genotype: HiProt - time: 25-50 - rep3

source_name: seed (genotype: HiProt - time: 25-50)


title: 400948_LS180_0hr_dscDNA_Veh2_532

description: This sample was treated for 0 hrs with 1,25(OH)2D3. It is the second in the series of biological replicate experiments.

tag: time


title: wt_t=0_1

value: wild type (control RNAi)


title: 672 tumor PBMC

description:
Set 1
Gene expression ex vivo of tumor-specific T cells from blood.


title: 672 naive PBMC


title: 0 vs. 0, 13368856A

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description:
13368856 A
Hybridizations conducted using Interwoven Loop Design.

hyb_protocol: Products of the cDNA synthesis reactions were combined according to dye-swap assignments and hybridized onto microarrays.  Two µL of blocking agent, locked nucleic acid (LNA) dT Blocker (Genisphere) was included in each hybridization.  RNA sample probes were hybridized at 55ºC overnight (~16h), then washed for 20 min in 60ºC 2x SSC including 0.2% SDS, 20 min in 2x SSC at room temperature, and 20 min in 0.2x SSC also at room temperature.  Slides were then spin dried and subsequently hybridized to A647- and Cy3-labeled secondary hybridization probes in 100 µL hybridization buffer with 1 µL of Anti-Fade Reagent for 4h at 60ºC.  Microarrays were washed as described above only at 15 minute wash intervals and spin dried.  Slides were stored for no more than 1 week in a darkened desiccation chamber prior to microarray scanning.

scan_protocol: Microarrays were scanned at 5μm using a VersArray Chipreader™ (Bio-Rad, Hercules, CA). To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan. Independent statistical analyses were run on high- and low-intensity scan data, and significant targets were summed among analyses. Grids were manually fit to microarray spots for each image file and both positive and negative controls were flagged prior to spot analysis. Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from the analysis.

data_processing: Summary data consisted of LOWESS-normalized Cy3:A647 ratio values calculated using background-normalized median-signal intensities. The statistical analysis was conducted using Bayesian Analysis of Gene Expression Levels (BAGEL) software version 3.62 (Townsend and Hartl, 2002).  Non-overlapping 97.5% confidence intervals (C.I.) among treatments were established a priori as statistically significant differences in expression.  Only targets for which both technical replicates were found to be differentially expressed were considered to be true differentially expressed transcripts.

organism: Colinus virginianus

source_name: female brain, control

label_protocol: Probes for microarray hybridizations were prepared from 600 ng total RNA/sample following the Genisphere®, Array 900™ Alexa Fluor 647 and Cy3 secondary hybridization labeling protocol (Genisphere, Hatfield, PA) according to manufacturer’s instructions.

growth_protocol: Juvenile Northern bobwhite quail (age 12 weeks) were obtained from Trace Pheasantry. On arrival to the U.S. Army Center for Health Promotion and Preventive Medicine (CHPPM), birds were kept individually in 24-cage units; each cage was 28 cm wide by 30.5 cm tall by 38 cm deep and volume did not exceed 1.3 ml.

extract_protocol: RNeasy® Mini RNA extraction kits (Qiagen, Valencia, CA) were used for total RNA extractions.  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® RNA. Only samples with a 28s/18s ratio {greater than or equal to} 1.4 and RNA integrity number (RIN) {greater than or equal to} 6 were used for downstream applications.  The majority of RNA samples greatly exceeded these minimum requirements.  Total RNA was utilized for cDNA library construction, microarray analysis and RT-qPCR.

treatment_protocol:
A 14-day 2,6-DNT exposure in female Northern bobwhite administering 2,6-DNT at 0, 50, 100, 190, or 350 mg/kg/day with each treatment group included seven birds (at least three of each sex per treatment). The females were examined in this microarray assay.

The complete toxicology protocol is presented in: Johnson MS, Quinn MJ, Bazar MA, KA Gust, Escalon BL Perkins EJ. (2007) Subacute Toxicity of Oral 2,6-Dinitrotoluene and 1,3,5-trinitro-1,3,5-triazine (RDX) Exposure to the Northern Bobwhite (Colinus virginianus) Environ Toxicol Chem 26(7):1481–1487 (PMID 17665690).

tag: gender

tag: developmental stage

value: juvenile

value: brain


title: 1144 EBV PBMC

value: 74 years


title: 618 EBV PBMC

value: 79 years


title: 618 naive PBMC

value: naive


title: genotype: LoProt - time: >200-300 - rep3

description: ld04-15146 (germplasm name); po: 0009010 seed, (Organism Part); PO:0007010 6 ripening (Development Stage); field soil (Growth Media).

source_name: seed (genotype: LoProt - time: >200-300)

value: seed

value: LoProt


title: 0 vs. 60, 13368861A

description:
13368861 A
Hybridizations conducted using Interwoven Loop Design.

source_name: female brain, 2,6-DNT, 60mg/kg/d

value: 2,6-dinitrotoluene (2,6-DNT)

tag: treatment dosage

tag: treatment duration

value: 14 days


title: 60 vs. 0, 13368855A

description:
13368855 A
Hybridizations conducted using Interwoven Loop Design.

value: female


title: 100 vs. 0, 13368858A

description:
13368858 A
Hybridizations conducted using Interwoven Loop Design.

source_name: female brain, 2,6-DNT, 100mg/kg/d


title: 618 tumor PBMC, repl 1

tag: patient code

tag: disease

value: melanoma

value: CD8+ T cells

value: self/tumor (Melan-A/MART-1 26-35 A27L)


title: siRNA_PSMB5B

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

hyb_protocol: Hybridizations were performed on the GeneChip Hybridization oven 645 (Affymetrix) at45º C for 17 hours.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: log2 transformation of signal intensity, quantile normalization, R/Bioconductor

label: Biotin

source_name: aneuploid, breast adenocarcinoma cell line

label_protocol: Biotinylated cDNA were prepared according to the Nugen protocol from 300 ng total RNA using the Applause WT-Amp ST RNA amplification kit (Cat. N° 5500-24) and the Encore Biotin Module Kit (Cat. N° 4200-12). Wash and stain was performed by using the GeneChip Fluidic Station 450 from Affymetrix

growth_protocol: Cells were grown in phenol-red free DMEM containing 5% charcoal-dextran treated FBS for 48 hours prior to treatment with Bortezomib or estrogen.

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

treatment_protocol: Where indicated, cells were pretreated with 50 nM Bortezomib for 15 minutes followed by 10 nM 17-β-estradiol for 24 hours.

tag: group


title: 0 vs. 100, 13368857A

description:
13368857 A
Hybridizations conducted using Interwoven Loop Design.


title: 972 tumor PBMC, repl 1

value: peripheral blood

tag: cell type

tag: tcr specificity (or naive)

value: 64 years


title: siRNA_PSMB5A


title: genotype: HiProt - time: 25-50 - rep1

value: HiProt


title: genotype: LoProt - time: >200-300 - rep1


title: 60 vs. 0, 13368860A

description:
13368860 A
Hybridizations conducted using Interwoven Loop Design.


title: siRNA_PSMB3A


title: 400937_LS180_0hr_dscDNA_Veh1_532

description: This sample was treated for 0 hrs with 1,25(OH)2D3. It is the first in the series of biological replicate experiments.

value: LS180 cells

value: 0 h


title: genotype: HiProt - time: 25-50 - rep2


title: siRNA_PSMB5C


title: 100 vs. 60, 13368850A

description:
13368850 A
Hybridizations conducted using Interwoven Loop Design.

value: juvenile

value: brain


title: genotype: LoProt - time: >200-300 - rep2


title: genotype: LoProt - time: >100-200 - rep2

source_name: seed (genotype: LoProt - time: >100-200)


title: siRNA_PSMB3C


title: siRNA_PSMB3B


title: genotype: LoProt - time: >100-200 - rep3


title: 972 naive PBMC

description:
Set 1
Gene expression ex vivo of naive T cells from blood.


title: 0 vs. 100, 13368849A

description:
13368849 A
Hybridizations conducted using Interwoven Loop Design.


title: genotype: LoProt - time: >100-200 - rep1


title: SiRNA treated cells_rep2

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

description: Biological replicate 2 of 2. cells treated with PRC SIRNA

hyb_protocol: Agilent hybridization protocol was used

scan_protocol: Agilent scanner

data_processing: The natural logarithms of the total gene signals for all genes expressing above 10 times x the background noise in both samples were regressed against each other, and the standard deviation of the residuals from the regression line were noted reported as the root mean square deviation.

source_name: XTC.UC1_PRc SIRNA_rep2

label_protocol: miRNA labeling with Cy3 dyes was made according to manufacturer’s recommendations (Agilent)

growth_protocol: growth medium consisted of Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal calf serum, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL fungizone, and 10 mU/mL thyrotropin (TSH) .

extract_protocol: Total RNA was isolated from cultured cells using Trizol reagent . The integrity of RNA was determined using a Bio-Analyzer 2100

treatment_protocol: The predesigned PRC siRNA (#121729) wa used at 30nM concentration. The knock-down of PRC was tested by comparison with a random negative control siRNA (scramble, #4635). The PRC siRNA was relevant for at least 70% knock-down of PRC mRNA expression knockdown after 48h of treatment.

value: cancer thyroid cell line


title: SiRNA treated cells_rep1

description: Biological replicate 1 of 2. cells treated with PRC SIRNA

source_name: XTC.UC1_PRc SIRNA_rep1


title: control cells_rep2

description: Biological replicate 2 of 2. cells treated with scramble


title: 100 vs. 60, 13368847A

description:
13368847 A
Hybridizations conducted using Interwoven Loop Design.


title: 205 EBV PBMC

description:
Set 1
Gene expression ex vivo of EBV-specific T cells from blood.

source_name: EBV PBMC

value: 36 years

value: male


title: 205 naive PBMC

value: naive


title: siRNA_Ctrl2B


title: siRNA_Ctrl2C


title: control cells_rep1

description: Biological replicate 1 of 2. cells treated with scramble


title: genotype: LoProt - time: >50-100 - rep3

source_name: seed (genotype: LoProt - time: >50-100)

value: seed

value: LoProt


title: genotype: LoProt - time: >50-100 - rep2


title: 60 vs. 0, 13368848A

description:
13368848 A
Hybridizations conducted using Interwoven Loop Design.

value: female

value: 2,6-dinitrotoluene (2,6-DNT)

value: 14 days


title: 205 tumor PBMC, repl 1

description:
Set 1
Gene expression ex vivo of tumor-specific T cells from blood.

source_name: tumor PBMC

value: melanoma

value: CD8+ T cells

value: self/tumor (Melan-A/MART-1 26-35 A27L)


title: siRNA_Ctrl2A


title: 0 vs. 100, 13368846A

description:
13368846 A
Hybridizations conducted using Interwoven Loop Design.


title: genotype: LoProt - time: >50-100 - rep1

description: ld04-15146 (germplasm name); po: 0009010 seed, (Organism Part); PO:0007010 6 ripening (Development Stage); field soil (Growth Media).


title: Bort+E2C


title: siRNA_Ctrl1A


title: 100 vs. 0, 13368858

description:
13368858
Hybridizations conducted using Interwoven Loop Design.

scan_protocol: Microarrays were scanned at 5μm using a VersArray Chipreader™ (Bio-Rad, Hercules, CA). To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the Low Intensity Scan. Independent statistical analyses were run on high- and low-intensity scan data, and significant targets were summed among analyses. Grids were manually fit to microarray spots for each image file and both positive and negative controls were flagged prior to spot analysis. Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from the analysis.


title: genotype: LoProt - time: 25-50 - rep3

source_name: seed (genotype: LoProt - time: 25-50)


title: siRNA_Ctrl1C


title: 0 vs. 0, 13368856

description:
13368856
Hybridizations conducted using Interwoven Loop Design.


title: genotype: LoProt - time: 25-50 - rep1


title: siRNA_Ctrl1B


title: genotype: LoProt - time: 25-50 - rep2


title: Bort+E2A


title: 60 vs. 0, 13368855

description:
13368855
Hybridizations conducted using Interwoven Loop Design.


title: cultured-MDA-MB-231-rep3

city: Miami

first: Jennifer

last: Clarke

state: FL

address: 1120 NW 14th Street

department: Epidemiology and Public Health

institute: University of Miami

description: MDA-MB-231 human breast carcinoma cell line was obtained from the American Type Culture Collection (ATCC) and maintained according to the supplier’s instructions. RNA was isolated from three independent cultures of sub-confluent MDA-MB-231 cells in the exponential phase of growth

hyb_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)

data_processing: Raw expression data from BeadStudio software was background corrected, normalized, and VST transformed using the lumi package v. 2.2.0 in Bioconductor. Probes with detection p-values < 0.05 in all three independent replicates were considered 'present' and included in further analyses.

extract_protocol: RNA was extracted from cultured MDA-MB-231 cells, MDA-MB-231 liver metastases and mouse liver using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions. Concentration and yield of RNA samples were determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s recommendations. Only samples with a RIN score >7.0 were used for microarray analysis.

tag: strain


title: 60 vs. 0, 13368860

description:
13368860
Hybridizations conducted using Interwoven Loop Design.


title: SV09121016Fsk

city: La Jolla

first: Sam

last: Van de Velde

address: 10010 North Torrey Pines Road

department: Peptide Biology Laboratories

institute: Salk Institute

description: Forskolin stimulation sample. 16 hour treatment with forskolin (10 uM) in vehicle (DMSO)

hyb_protocol: 17 hours at 45 degrees

scan_protocol: Chips were scanned using an Affymetrix genechip scanner 3000 7G (GPL6247)

data_processing: Data was processed using the Affymetrix Expression Console software v1.1.1.

source_name: Fsk 16h

label_protocol: Standard Affymetrix protocol

growth_protocol: RPMI with 10% serum

extract_protocol: Trizol/chloroform extraction. RNA cleanup with Qiagen Rneasy column.

treatment_protocol: 2 hour or 16 hour treatment with forskolin (10 uM) in DMSO

tag: agent

value: forskolin

tag: time point

value: INS-1 insulinoma cells

value: inbred albino rats of the NEDH (New England Deaconess Hospital)


title: E2D.2

tag: cell line


title: 0 vs. 60, 13368861

description:
13368861
Hybridizations conducted using Interwoven Loop Design.

value: juvenile

tag: tissue

tag: treatment


title: 100 vs. 60, 13368850

description:
13368850
Hybridizations conducted using Interwoven Loop Design.

value: brain


title: cultured-MDA-MB-231-rep1

scan_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)


title: 0 vs. 100, 13368857

description:
13368857
Hybridizations conducted using Interwoven Loop Design.


title: liver-mets-rep3

description: Metastatic liver xenografts of MDA-MB-231 cells were harvested by gross surgical dissection ~50 days following implantation into the abdominal mammary fat pads of eight week old female NOD scid gamma mice (The Jackson Laboratory). Mice were injected unilaterally with 2.5 x 106 cells in 200 μL of 50:50 Matrigel/Collagen I into the fourth abdominal fat pad by subcutaneous injection at the base of the nipple. Tumor growth was monitored externally using vernier calipers for 50 days and animals sacrificed when tumors reached 10% of body weight. Necropsies were performed to identify liver macro-metastases.

source_name: MDA-MB-231 liver metatasis

label_protocol: Samples were prepared according to the manufacturer’s instructions and analyzed using MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)

tag: age

value: 50 days


title: E2C


title: E2B


title: Bort+E2B


title: liver-mets-rep2


title: SV09121016Veh

description: Control sample. 16 hour treatment with vehicle (DMSO)

source_name: Con 16h


title: cultured-MDA-MB-231-rep2


title: 60 vs. 0, 13368848

description:
13368848
Hybridizations conducted using Interwoven Loop Design.


title: 0 vs. 100, 13368849

description:
13368849
Hybridizations conducted using Interwoven Loop Design.


title: ControlC

value: Control


title: 100 vs. 60, 13368847

description:
13368847
Hybridizations conducted using Interwoven Loop Design.


title: SV0912102Fsk

description: Forskolin stimulation sample. 2 hour treatment with forskolin (10 uM) in vehicle (DMSO)

source_name: Fsk 2h


title: SV0912102Veh

description: Control sample. 2 hour treatment with vehicle (DMSO)

source_name: Con 2h


title: 0 vs. 100, 13368846

description:
13368846
Hybridizations conducted using Interwoven Loop Design.

source_name: female brain, control


title: ControlA


title: ControlB


title: N2_Fibrosis stage 4_2

status: Public on Nov 21 2011

city: Lahore

first: Sajida

last: Hassan

address: 87-West Canal bank Road

department: CEMB

country: Pakistan

institute: University of the Punjab

description:
N2-F4-2
Sample 32

hyb_protocol: Equal amount of Cy3 and Cy5 (55pmol each) labeled targets was mixed with 45µl of OpArray Hyb Buffer. Pre-washing, array hybridization and post-washing of microarray labeled slides was performed according to manufacturer protocols at 42oC for 18 hours on fully automated workstation “GeneTAC TM HybStation”. A detailed protocol describing each step from start to microarray hybridization can be downloaded from (http://www.operon.com/products/microarrays/OpArray%20Protocol.pdf).

scan_protocol: Images were quantified using GeneTAC TM UC4×4 scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Midas software was used.

source_name: N2_Fibrosis stage 4

label_protocol: aRNA from HCV infected patients and normal were labeled with Cy5 (IA) and Cy3 (IB) respectively by using Oparray protocols.

extract_protocol: RNA isolation and preparation of cDNA and aRNA was carried out according to manufacturer protocols by using Qaigen kits.

value: HCV infected human liver biopsy samples

tag: liver fibrosis stage

source_name: normal human liver biopsy

tag: sample type

value: reference


title: liver-mets-rep1


title: N2_Fibrosis stage 4_3

description:
N2-F4-3
Sample 33


title: mouseliver-normal-rep3

organism: Mus musculus

source_name: mouse liver

value: eight weeks

tag: gender

value: NOD scid gamma (The Jackson Laboratory)


title: N1_Fibrosis stage 4_2

description:
N1-F4-2
Sample 29

source_name: N1_Fibrosis stage 4


title: mouseliver-normal-rep2

value: female


title: N3_Fibrosis stage 4_2

description:
N3-F4-2
Sample 35

source_name: N3_Fibrosis stage 4


title: N2_Fibrosis stage 4_1

description:
N2-F4-1
Sample 31


title: N1_Fibrosis stage 4_3

description:
N1-F4-3
Sample 30


title: N3_Fibrosis stage 3_1

description:
N3-F3-1
Sample 25

source_name: N3_Fibrosis stage 3


title: N3_Fibrosis stage 4_3

description:
N3-F4-3
Sample 36


title: mouseliver-normal-rep1


title: N2_Fibrosis stage 3_3

description:
N2-F3-3
Sample 24

source_name: N2_Fibrosis stage 3


title: N1_Fibrosis stage 4_1

description:
N1-F4-1
Sample 28


title: N1_Fibrosis stage 3_3

description:
N1-F3-3
Sample 21

source_name: N1_Fibrosis stage 3


title: N3_Fibrosis stage 3_2

description:
N3-F3-2
Sample 26


title: N3_Fibrosis stage 3_3

description:
N3-F3-3
Sample 27


title: N2_Fibrosis stage 3_1

description:
N2-F3-1
Sample 22


title: N1_Fibrosis stage 3_1

description:
N1-F3-1
Sample 19


title: N3_Fibrosis stage 4_1

description:
N3-F4-1
Sample 34


title: N1_Fibrosis stage 3_2

description:
N1-F3-2
Sample 20


title: N2_Fibrosis stage 3_2

description:
N2-F3-2
Sample 23


title: control 24 h replicate 3

city: Singapore

first: Chui Sun

last: Yap

address: 8, College Road

country: Singapore

institute: Duke-NUS

description:
control 24 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt

hyb_protocol: As described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

scan_protocol: Scanning was carried on a GCS3000 scanner

data_processing: The Probe Logarithmic Intensity Error (PLIER) algorithm, from the Affymetrix Power Tools (APT) software package, was used to generate gene and exon expression scores. Probes were filtered and remapped to rat genes with Entrez ID according to the tables provided by the Microarray Laboratory of the Molecular and Behavioral Neuroscience Institute, University of Michigan.

source_name: control

label_protocol: RNA was converted into biotinylated single stranded cDNA as described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: HOMycER12 cells were cultured, under exponential growth conditions, in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% calf serum (Hyclone) at 37°C and 5% CO2.

extract_protocol: Total RNA was harvested using the TRIZOL® reagent (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: Cells were plated at a density of 20% confluence 24 h prior to the addition of OHT (248 nM; for treated cells) or an equal volume of ethanol (for mock-treated cells).

value: fibroblasts

tag: genotype

value: c-Myc not active


title: control 16 h replicate 3

description:
control 16 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 20 h replicate 3

description:
OHT treated 20 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt

source_name: OHT treated

value: c-Myc active


title: OHT treated 24 h replicate 3

description:
OHT treated 24 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N3_Fibrosis stage 2_2

description:
N3-F2-2
Sample 17

source_name: N3_Fibrosis stage 2


title: N3_Fibrosis stage 2_1

description:
N3-F2-1
Sample 16


title: N3_Fibrosis stage 2_3

description:
N3-F2-3
Sample 18


title: OHT treated 16 h replicate 3

description:
OHT treated 16 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N2_Fibrosis stage 2_3

description:
N2-F2-3
Sample 15

source_name: N2_Fibrosis stage 2


title: OHT treated 12 h replicate 3

description:
OHT treated 12 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N1_Fibrosis stage 2_3

description:
N1-F2-3
Sample 12

source_name: N1_Fibrosis stage 2


title: OHT treated 10 h replicate 3

description:
OHT treated 10 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N2_Fibrosis stage 2_1

description:
N2-F2-1
Sample 13


title: OHT treated 8 h replicate 3

description:
OHT treated 8 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N1_Fibrosis stage 2_2

description:
N1-F2-2
Sample 11


title: Mucosa complete

city: Barcelona

first: Eduard

last: Batlle

state: Barcelona

address: Baldiri i Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine Barcelona

description: Comparison of human colonic mucosa-derived genomic DNA and white blood cell DNA from the same individual

hyb_protocol: 6 µg labeled DNA of test sample and reference sample were hybridized per microarray for 16 hours of hybridization at 42ºC; hybridization and washing was performed according to NimbleGen Array User Guide for CGH and CNV Arrays (Roche NimbleGen, http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a GenePix 4000B scanner (Molecular Devices)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan software for CGH-DNACopy Analysis.

source_name: Human colon mucosa genomic DNA

label_protocol: 500 ng genomic DNA was labeled with either Cy3 (Test sample) or Cy5 (Reference sample) according to NimbleGen Array User Guide for CGH and CNV Arrays (Roche NimbleGen, http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: Genomic DNA of human white blood cell fraction and human colonic tissue was isolated using the GenEluteTM Mammalian Genomic DNA MiniPrep Kit (Sigma-Aldrich)

treatment_protocol: Isolation of epithelial tissue and tissue disaggregation

value: human colonic mucosa

source_name: Human white blood cell DNA

treatment_protocol: white blood cell isolation

value: white blood cells


title: Spheres 6 weeks

description: Comparison of human colonic organoid-derived genomic DNA and white blood cell DNA from the same individual

source_name: Human colonic organoid genomic DNA

growth_protocol: Organoids embedded in matrigel were cultured for 6 weeks in the presence of Wnt3a, EGF1, Noggin, R-Spondin1, Gastrin, Nicotinamide, N-Acetylcystein, SB202190, and  LY2157299

treatment_protocol: In vitro tissue culture

value: In vitro human colon organoids


title: OHT treated 6 h replicate 3

description:
OHT treated 6 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N3_Fibrosis stage 1_2

description:
N3-F1-2
Sample 8

source_name: N3_Fibrosis stage 1


title: N2_Fibrosis stage 2_2

description:
N2-F2-2
Sample 14


title: OHT treated 4 h replicate 3

description:
OHT treated 4 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 3 h replicate 3

description:
OHT treated 3 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 5 h replicate 3

description:
OHT treated 5 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N3_Fibrosis stage 1_1

description:
N3-F1-1
Sample 7


title: OHT treated 1 h replicate 3

description:
OHT treated 1 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N2_Fibrosis stage 1_3

description:
N2-F1-3
Sample 6

source_name: N2_Fibrosis stage 1


title: N1_Fibrosis stage 2_1

description:
N1-F2-1
Sample 10

source_name: normal human liver biopsy


title: N2_Fibrosis stage 1_2

description:
N2-F1-2
Sample 5


title: Spheres 2 weeks

growth_protocol: Organoids embedded in matrigel were cultured for 14 days in the presence of Wnt3a, EGF1, Noggin, R-Spondin1, Gastrin, Nicotinamide, N-Acetylcystein, SB202190, and  LY2157299


title: OHT treated 2 h replicate 3

description:
OHT treated 2 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N3_Fibrosis stage 1_3

description:
N3-F1-3
Sample 9


title: control 24 h replicate 2

description:
control 24 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 0 h replicate 3

description:
control 0 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: N1_Fibrosis stage 1_3

description:
N1-F1-3
Sample 3

source_name: N1_Fibrosis stage 1


title: Blood male versus female

description: Reference experiment comparing male and female human white blood cell genomic DNA

value: male


title: N2_Fibrosis stage 1_1

description:
N2-F1-1
Sample 4


title: N1_Fibrosis stage 1_1

description:
N1-F1-1
Sample 1


title: N1_Fibrosis stage 1_2

description:
N1-F1-2
Sample 2


title: OHT treated 20 h replicate 2

description:
OHT treated 20 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 16 h replicate 2

description:
control 16 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 8 h replicate 2

description:
control 8 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 6 h replicate 2

description:
OHT treated 6 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 5 h replicate 2

description:
OHT treated 5 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 8 h replicate 2

description:
OHT treated 8 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 24 h replicate 2

description:
OHT treated 24 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 10 h replicate 2

description:
OHT treated 10 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 3 h replicate 2

description:
OHT treated 3 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 0 h replicate 2

description:
control 0 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 12 h replicate 2

description:
OHT treated 12 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 4 h replicate 2

description:
OHT treated 4 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 1 h replicate 2

description:
OHT treated 1 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 16 h replicate 2

description:
OHT treated 16 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 16 h replicate 1

description:
control 16 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 2 h replicate 2

description:
OHT treated 2 h replicate 2
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 8 h replicate 1

description:
control 8 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 24 h replicate 1

description:
OHT treated 24 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 12 h replicate 1

description:
OHT treated 12 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 20 h replicate 1

description:
OHT treated 20 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 10 h replicate 1

description:
OHT treated 10 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 16 h replicate 1

description:
OHT treated 16 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 4 h replicate 1

description:
OHT treated 4 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 5 h replicate 1

description:
OHT treated 5 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 6 h replicate 1

description:
OHT treated 6 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 1 h replicate 1

description:
OHT treated 1 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 8 h replicate 1

description:
OHT treated 8 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 3 h replicate 1

description:
OHT treated 3 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: OHT treated 2 h replicate 1

description:
OHT treated 2 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: control 0 h replicate 1

description:
control 0 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt


title: CD71+ cells Control 1

city: Memphis

first: Aisha

last: Walker

state: TN

address: 262  Danny Thomas Place; MS 313

institute: St Jude Children's Research Hospital

description: Biological replicate 1 of 2, non-SCA control from CD71+  cell

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent feature extraction software using the miRNA_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used, followed by  a log  transformation, percentile normalization across probes, and scaling through the samples, prior to actual analysis.

source_name: CD71+ cells non-SCA control #1

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol

extract_protocol: Total RNA was isolated from a minimum of 50 million CD71+ cells freshly isolated from controls and patients using the miRNeasy kit according to manufactuer's protocol (Qiagen, Valencia, CA).

treatment_protocol: 3-9 ml venous  blood was collected in EDTA from controls and patients. CD71+ cells were isolated by first depleting samples of CD45+ cells followed by enrichment of CD71+ cells by autoMACS magnetic cell sorter (Miltnyi Biotec, Auburn, CA)

value: CD71+ erythroid cells

tag: disease state

value: control


title: CD71+ cells SCA 2

description: Biological replicate 2 of 3, SCA patient untreated with hydroxyurea

source_name: CD71+ cells SCA patient untreated #2

value: sickle cell anemia


title: CD71+ cells SCA 1

description: Biological replicate 1 of 3, SCA patient untreated with hydroxyurea

source_name: CD71+ cells  SCA patient untreated #1


title: CD71+ cells SCA 3

description: Biological replicate 3 of 3, SCA patient untreated with hydroxyurea

source_name: CD71+ cells SCA patient untreated #3


title: CD71+ cells SCA Hydroxyurea 1

description: Biological replicate 1 of 3, SCA patient treated with hydroxyurea

source_name: CD71+ cells SCA patient treated #1

value: hydroxyurea


title: CD71+ cells SCA Hydroxyurea 2

description: Biological replicate 2 of 3, SCA patient treated with hydroxyurea

source_name: CD71+ cell SCA patient treated #2


title: CD71+ cells Control 2

description: Biological replicate 2 of 2, non-SCA control from CD71+  cell

source_name: CD71+ cells non-SCA control #2


title: CD71+ cells SCA Hydroxyurea 3

description: Biological replicate 3 of 3, SCA patient treated with hydroxyurea

source_name: CD71+ cells SCA patient treated #3


title: in vitro-differentiated human NK cells, 6h, IL-15, replicate2

city: Daejeon

first: Tae-Don

last: Kim

address: 125 Gwahak-ro, Yuseong

department: Cell Therapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: miRNA expression upon activation

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray (15K) and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3.

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: In vitro differentiated mature NK cells (mNK) were generated and differentiated from a starting population of purified CD34+ cells isolated from human umbilical cord blood (UCB).

extract_protocol: Total RNA was extracted using Trizol (Invitrogene) according to the manufacture's recommendations

treatment_protocol: in vtro-differentiated human NK cells were freshly incubated in the presence of IL15 after 24h deprivation of IL-15. The cells were harvested at the times (0h, resting-Sample1 and2; 6h, activated-Sample 3 and 4) and analyzed by microarray.

value: in vitro-differentiated human NK cells


title: in vitro-differentiated human NK cells, 6h, IL-15, replicate1

description: miRNA expression upon activation


title: in vitro-differentiated human NK cells, 0 h, IL-15, replicate 1

description: miRNA expression at resting conditions


title: in vitro-differentiated human NK cells, 0 h, IL-15, replicate 2

description: miRNA expression at resting conditions


title: control 8 h replicate 3

description:
control 8 h replicate 3
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt

source_name: control


title: TES 4 4h

city: Tübingen

first: Gabriel

last: Willmann

address: Schleichstrasse 12-16

institute: University Eye Hospital and Centre for Ophthalmology Tübingen

hyb_protocol: 15 micrograms of labeled cRNA from retina was fragmented, and 10ug was hybridized to Affymetrix Rat Gene 1.0 ST Gene Chip arrays for 18-24h (Affymetrix Inc.). Gene chip was washed and stained with streptavidin-phycoerythrin.

scan_protocol: The chip was scanned at 6um resolution with Agilant model G2500A Gene Array scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing: For statistical analysis of microarray data all .cel files were imported to GeneSpring GX software (Agilent Technologies Inc.) where GC-RMA algorithm was applied to yield log signal values on each probe set. All transcripts with a minimum change of 1.2 fold together with a p value less than 0.05 were selected using Significance Analysis of Microarray (SAM) (Tusher VG, 2001).

source_name: retina

label_protocol: Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA, USA) as described by manufacturer. Briefly, total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.

extract_protocol: mRNA of retina was isolated 4h after transcornial electrical stimulation and compared to sham animals using RNAeasy Isolation Kit (Ambion, Austin, Texas, USA) according to manufacturers instructions.

value: Brown Norway Rat

value: 8 weeks


title: S4 vs. S3 (H04)

city: Beijing

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

hyb_protocol: HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The raw data were adjust by Rosetta Resolver® error model calculation. The statistic values were calculated after the replicated probes squeezing and median scaling normalization.

source_name: S4: HEK293-STAT6 stable cell line transfected with Poly(I:C) for 16 hours

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Cy3; Amershan).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: HEK293 stably expressing Stat6

value: poly(I:C) transfection for 16 hours

source_name: S3: HEK293-STAT6 stable cell line control


title: TES Control 2 4h


title: TES 3 4h


title: B cells WT vs CCR7-/- Replicate 2 (Pool2)

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7 (for details see http://www.agilent.com) except that 500ng of each labeled cRNA sample were used for hybridization. Microarrays were co-hybridized with differently-labeled material from CCR7 -/- versus wildtype animals in a dual-color setting.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml. To correct for systematic bias at the high end of the fluorescence intensity measurements, the highest ranking 2% of Processed Signals in the green channel (gPS) were further normalized according to an intensity-dependent, non-linear scaling strategy, to optimize fitting to their respective counterparts in the red channel.

source_name: B cells

label_protocol: 20ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the company.

growth_protocol: The cells were not cultured after isolation.

extract_protocol: Total RNA from sorted cell samples was extracted by use of the Nucleospin RNA XS kit (Macherey & Nagel).

treatment_protocol: The cells were sorted on a FACSAria (BD Biosciences) and immediately subjected to total RNA isolation.

tag: genotype/variation

value: wildtype

value: peripheral lymph nodes

value: Ccr7 knock-out


title: S1 vs. S2 (H01)

source_name: S1: HEK293 cells transfected with Poly(I:C) for 16hours

value: HEK293 cells

source_name: S2: HEK293 control


title: TES Control 1 4h


title: TES 1 4h


title: 2A 96hr Replicate 3

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

description: E2 treated sample vs. time-matched control pool

hyb_protocol: Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Cat#5188-5242) and protocol. Fragmented samples in 1X Hi-RPM Hybridization Buffer were hybridized to 4X44K Agilent oligonicleotide arrays (Cat# G2534-60011) in Agilent Stainless Chamber slides (Cat# G2534A). Hybridizations were performed in an Agilent Microarray Hybridization Oven (Cat# G2545A) for 17h at 65°C at 10rpm. Slides were washed using Agilent's Gene Expression Wash Buffer Kit and Protocol in an ozone-controlled environment at 5ppb ozone or less. A maximum of 4 slides were washed at a time prior to immediate scaning.

scan_protocol: Slides were scanned using an Agilent Scanner (G2505C) in an ozone controlled environment (less than 5ppb ozone) at 5um resolution, Single Pass, eXtended Dynamic Range (XDR), Green and Red PMT: XDR Hi 100% and XDR Lo 10% Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction v10.7 was used for background correction and dye-normalization

source_name: E2-treated 2A 96hr Replicate 3

label_protocol: 250 ng of total RNA from each E2-treated sample and 500ng of total RNA from each pooled reference sample were labeled using the protocol provided with the Agilent Quick Amp Labeling Kit (Cat# 5190-0447) using 1.2ul of T7 Promoter primer. Test samples were labeled with Cy3-dCTP (Perkin Elmer NEL580) and reference samples with Cy5-dCTP (Perkin Elmer NEL581). Labeled/amplified RNAs were purified using Qiaen's RNeasy spin columns (Qiagen# 74104). Purified cRNA was quantified on a Nanodrop ND-1000 Specrophotometer. 825 ng of each cRNA probe with a specific activity of at least 8.0 pmol Cy Dye per ug cRNA were used for hybridization.

growth_protocol:
Estrogen-dependent WS8 cells were maintained in fully-estrogenized media [phenol red-containing RPMI-1640 and 10% whole fetal bovine serum (FBS), supplemented with 6 ng/ml insulin, 2 mM glutamine, 100 μM non-essential amino acids, and 100 U of penicillin and streptomycin per ml], while 5C and 2A cells were maintained in estrogen-free medium (phenol red-free RPMI-1640 plus 10% dextran-coated charcoal-stripped FBS and the same supplements as for fully-estrogenized medium). Estrogen-dependent WS8 cells were switched to estrogen-free media for 3 days before all experiments.
MCF-7:WS8, MCF-7:2A, and MCF-7:5C cells were seeded at 2, 4, and 5 million cells per 15 cm plate, respectively, in estrogen-free RPMI-1640 + 10% dextran-coated charcoal-treated fetal bovine serum

extract_protocol:
Cells were harvested for RNA using TRIzol (Invitrogen) according to manufacturers instructions. RNA was further isolated using Total RNeasy purification columns (Qiagen).
RNA samples were controlled for purity and integrity using a Nanodrop 1000 spectrophotometer and an Agilent 2100 Bioanalyzer by requiring each sample to exhibit an RNA Integrity Number (RIN) of 9.8-10.0.

treatment_protocol: Cells were parsed into 2 groups of 6 replicate plates per treatment per time point, and then treated with either 0.1% ethanol (vehicle control) or 10-9 M E2 for 2, 6, 12, 24, 48, 72, and 96 h. At 48 h, media on the remaining cells was replenished.

tag: time (hr)

source_name: Control-treated RNA reference pool - 2A 96h

value: vehicle