title: canola removed at V8 rep 2 and control rep 2 [Alexa 555]

description:
080409 209dR 212d B.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V8 rep 2 and control rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: SFM control cells (3hr), biological rep_1

status: Public on May 09 2011

type: RNA

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

description:
H1.3hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183421.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133A GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: log2 expression values estimated using GC RMA with Array analyzer software

label: biotin

molecule: total RNA

organism: Homo sapiens

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

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

tag: cell line

value: MCF-7 breast cancer cell line

tag: agent

value: SFM (control)

tag: time


title: canola removed at V4 rep 2 and canola removed at V8 rep 2 [Alexa 555]

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description:
073009 212dR 207dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

hyb_protocol: 46,000-element microarray chip developed by the University of Arizona was hybridized using their protocol (International Microarray Workshop Handbook, 2009; Gardiner et al. 2005).

scan_protocol: Intensities based on fluorescence for each probe were visualized and quantified with a GenePix scanner9 and GenePix Pro software.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V4 rep 2 and canola removed at V8 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

label: Alexa 555

organism: Zea mays

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of canola to V8 were harvested and pooled.

label_protocol: First strand cDNA synthesis was performed using 1900 ng total RNA and second strand cDNA synthesis was performed using the resulting first-strand cDNA sample to make double-stranded cDNA using the Aminoallyl Message Amp II kit7.  aRNA was synthesized using the resulting double-stranded cDNA. Technical replicates from each treatment were labeled with Alexa Fluor 6478 or Alexa Fluor 5558 dye. An Alexa Fluor 647-labeled sample from one treatment was mixed with an Alexa Fluor 555-labeled sample from another treatment.

growth_protocol: Corn was planted on May 10, 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls) (Clay et al. 2009). The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 (2008) and 41 (2009) kg N ha-1, respectively, from residual nitrate and legume credit. The experimental design was a randomized complete block design with four replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008, and April 28, 2009. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plant matrerial was harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

extract_protocol: Total RNA was extracted using Trizol reagent5 and purified using Qiagen RNeasy MinElute cleanup kit6, following the manufacturer’s protocol.

treatment_protocol: 8 cm of the top most fully expanded leaf was harvested directly into liquid nitrogen and stored at -80 until RNA extraction.

tag: tissue

tag: stress

value: grown in the presence of canola to V8


title: E2-treated cells (3hr), biological rep_1

description:
H4.3hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 3hr.

value: estradiol (E2)


title: shade removed at V4 rep 2 and low nitrogen  rep 2 [Alexa 555]

description:
073009 203dB 213dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V4 rep 2 and low nitrogen  rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown without added nitrogen to V8 were harvested and pooled.

value: grown without added nitrogen to V8


title: control rep 3 and shade removed at V8 rep 2 [Alexa 555]

description:
072309 208dR 312dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: control rep 3 and shade removed at V8 rep 2

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of shade to V8 were harvested and pooled.

value: grown in the presence of shade to V8


title: B12-B6 whole brain RNA

status: Public on May 10 2011

city: Portland

first: Ted

last: Laderas

state: OR

address: 3181 SW Sam Jackson Rd CR145

department: OHSU Knight Cancer Institute

institute: Oregon Health & Science University

hyb_protocol: Samples containing at least 10 μg of total RNA were sent to the Oregon Health & Science University Gene Microarray Shared Resource facility for further quality assessment using an Agilent 2100 BioAnalyzer and for GeneChip array analysis. Because two samples were scanned by a different scanner , the dataset reported here includes whole brain samples from 22 individual mice (10 B6 and 12 D2).  After ribosomal RNA reduction, amplification and labeling, whole-brain total RNA samples were each hybridized to AffymetrixGeneChip® Mouse Exon 1.0 ST Array (24 arrays total).  The procedures used follow the Affymetrix Whole Transcript Sense Target Labeling Assay, rev3, protocol. Additional details can be found at (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

scan_protocol: Standard Affymetrix protocol.

data_processing: All CEL files were processed using the Affy package (version 1.12.2) in the statistical programming environment R under the Bioconductor package [R version 2.6.0 (http://www.r-project.org), Bioconductor2.1 (http://www.bioconductor.org)]. All data was RMA [11] background corrected and normalized. Data were summarized at the probeset level using the median polish. The Mouseexonpmcdf package was utilized for summarization at the probeset-level (http://xmap.picr.man.ac.uk/download/). The data were SNP masked at the probe level. Prior to the summarization step at the probeset level described above, individual probes were masked (expression value replaced by 'null') if there was a known SNP within the boundaries of the probe.  The SNP mask was built by comparing the Affymetrix design time annotation files (GFF) files (based on NCBI mouse build 36) for each chromosome to known SNP locations in DBSNP. A total of 12,101 probesets were masked to some degree, representing 5.4% of the core probesets.

label: Biotin

organism: Mus musculus

source_name: B6 whole brain RNA

extract_protocol: Naïve, adult, male C57BL/6J (B6) (n=12) and DBA/2J (D2) (n=12) strain mice were euthanized by cervical dislocation, the whole brain was rapidly removed and flash frozen in liquid nitrogen.  Total RNA was isolated using TRIzol® reagent (Invitrogen, Carlsbad, CA) in a one-step guanidine isothiocyanate procedure. For microarray analyses, the extracted RNA was purified using RNeasy (Qiagen, Valencia, CA). RNA samples were evaluated by ultraviolet spectroscopy for purity and concentration.

value: whole brain

tag: strain

tag: gender

value: Male


title: shade removed at V4 rep 1 and shade removed at V8 rep 1 [Alexa 555]

description:
071009 109dB 111dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V4 rep 1 and shade removed at V8 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

value: top 8 cm of the topmost fully expanded leaf of four plants


title: shade removed at V8 rep 1 and control rep 1  [Alexa 555]

description:
070809 111dB 101dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: shade removed at V8 rep 1 and control rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four control plants were harvested and pooled.

value: control


title: canola removed at V8 rep 1 and Canola removed at V4 rep 1 [Alexa 555]

description:
070909 107dB 105dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  Herbicides were applied at V4 to control unwanted species (canola and all plots were thereafter maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V8 rep 1 and Canola removed at V4 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.

source_name: top 8 cm of the topmost fully expanded leaf of four plants grown in the presence of canola to V4 were harvested and pooled.

value: grown in the presence of canola to V4


title: endometrioma, patient M4

description: Endo M4

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: endometrioma

label_protocol: According to Illumina protocol.

extract_protocol: Total RNA was isolated from 50 to 100 mg of frozen tissue using the mirVana kit (Applied Biosystems, Foster City, CA). RNA quality control was performed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease state

value: endometrioma

tag: patient


title: endometrioma, patient M1


title: Healthy control 8

city: Prague

first: Katerina

last: Stechova

address: V Uvalu 84

department: Paediatric

country: Czech Republic

institute: Charles University 2nd Medical Faculty

hyb_protocol: Twenty five μg of aRNA was labeled by Cy5 dye and 3 to 6 μg of the labeled aRNA were hybridized to each microarray according to manufacturer´s protocols. Samples were processed on human whole genome expression microarray (HOA v4.3, Phalanx Biotech, Palo Alto, CA, U.S.A.) which contains 32050 probes with 30968 human genome targets and 1082 experimental control probes.

scan_protocol: The slides were scanned using InnoScan 700 (Innopsys, Carbonne, France) with 5 μm resolution. Artefacts were masked and raw data were extracted by using the Mapix software (Innopsys, Carbonne, France).

data_processing: The raw microarray data processing and statistical analysis of the differential gene expression was performed using the limma package in the R statistical environment. Raw intensity data were corrected for background (by normexp method) and normalized (quantile normalization). The data was filtered to remove probes with saturated signal intensity and probes with SNR<5, leaving 19493 probes. The differential gene expression was tested using the Bayesian moderated t-test in the limma package and corrected for multiple comparison with the Benjamini-Hochberg´s method for false discovery rate (FDR).

source_name: PBMC

label_protocol: The amplification procedure included incorporation of 5-(3-aminoallyl)-UTP (aaUTP) into aRNA during the in vitro transcription, to enable coupling to N-hydroxysuccinimidyl ester-reactive Cy5 dyes.

extract_protocol: Approximately 8 ml of peripheral blood was obtained from tested subjects. Total RNA was extracted by using TRIzol reagent according to the manufacturer´s protocol (Invitrogen, Carlsbad, CA, U.S.A.). Extracted total RNA was dissolved in 60-120 μl nuclease-free water and stored at -80°C. The RNA concentration was measured by a spectrophotometer (Helios γ, Thermo Fisher Scientific, Waltham, MA, U.S.A.) and RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA, U.S.A.). For obtaining sufficient amount of RNA for microarray assays, total RNA was amplified (aRNA) by using Amino Allyl MessageAmp II aRNA amplification kit (Applied Biosystems - Ambion, Foster City, CA, U.S.A.).

tag: cell type

value: PBMC

value: Healthy volunteer

tag: antibody positivity

value: negative


title: Healthy control 9


title: canola removed at V4 rep 1 and low nitrogen rep 1 [Alexa 555]

description:
070909 105d B 108dR.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. No additional nitrogen was added. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: canola removed at V4 rep 1 and low nitrogen rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: control endometrium, patient 4

source_name: control endometrium


title: control endometrium, patient 32


title: shade removed at V8 rep 1 and control rep 1  [Alexa 647]

description:
070809 111dB 101dR.txt
Alexa 647: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Herbicides were applied at V2 to control unwanted species and all plots were maintained weed-free by hoeing or hand-pulling if plants survived or if new plants emerged after initial treatment. Shade tents were 3- by 3-m frames covered with commercially available 40% shade cloth that had extending poles to keep the cloth about 25-30 cm above the corn plants. Shade tents, placed during corn emergence (VE, covered four corn rows in the center of designated plots. The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

label: Alexa 647


title: endometrioma, patient 14


title: Healthy control 10


title: control endometrium, patient 3

description: Endometrium 3


title: Healthy control 6


title: control endometrium, patient 1

description: Endometrium 1


title: endometrioma, patient M2

description: Endo M2


title: endometrioma, patient M3

description: Endo M3


title: control endometrium, patient 20


title: control endometrium, patient 24


title: control endometrium, patient 25


title: Healthy control 7


title: endometrioma, patient 9


title: control endometrium, patient 12


title: control endometrium, patient 18


title: endometrioma, patient 7


title: Healthy control 2


title: hi559 Wild Type Repl3

city: Pittsburgh

first: Carsten

last: Stuckenholz

state: PA

address: 3501 Fifth Avenue, Room 5065.5B

department: Department of Medicine, Division of Hematology and Oncology

institute: University of Pittsburgh

hyb_protocol: Hybridization protocol used was EukGE-WS2v4 on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: GeneChips were scanned with an Affymetrix scanner according to the manufacturer's protocol.

data_processing: Expression values were extracted with RMA (Affy Library in R). Each array was normalized by log2-transformation, subtraction of median, and division with standard deviation.

organism: Danio rerio

source_name: Phenotyped whole wild type embryo at 5 dpf

label_protocol: Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents, manufacturer's protocol.

growth_protocol: Embryos from an incross of heterozygous cdipt^hi559Tg/+ parents were grown until 5 dpf in standard embryo media at 28° C.

extract_protocol: RNA was prepared from 25 embryos for each phenotype with RNeasy (QIAGEN).

treatment_protocol: Embryos were sorted based on phenotype into mutant and wild type embryos.

tag: phenotype

value: Wild Type

tag: age

value: 5 dpf

tag: replicate


title: Healthy control 5


title: Healthy control 4


title: endometrioma, patient 6


title: Healthy control 3


title: endometrioma, patient 2


title: hi559 Wild Type Repl2


title: hi559 Wild Type Repl1


title: control rep 2 and canola removed at V8 rep 1  [Alexa 555]

description:
071009 107dR 209dB.txt
Alexa 555: Field experiments were conducted in 2008 at South Dakota State Research Farm about 15 miles east of Brookings, SD. The soil parent materials were loess over glacial outwash, and the soil series was Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls (Clay et al. 2009. The water content at planting ranged from 22-24%, and soil pH ranged from 6.0-6.5. Soil N at the beginning of the season was 44.5 kg N ha-1, from residual nitrate and legume credit. Nitrogen application of 236 kg N ha-1 was applied at the beginning of the season. Canola was planted at 7 kg ha-1, drilled 10-cm from the corn row at corn planting.  The experimental design was a randomized complete block design with three replications. A commercially available 97-d corn hybrid that had glyphosate-resistance and corn rootworm/corn borer stacked traits was planted on May 10, 2008. The seeding rate was about 79,000 seeds ha-1. Row spacing was 76 cm. Plants were grown to the V8 stage of growth and harvested on July 2, 2008. Weather conditions at harvest were partly cloudy with temperatures in the low to mid 80sF, with an 18 mph wind.

data_processing:
Data from dual channel hybridization was treated as if it were from single channel hybridizations.  Dual channel hybn: control rep 2 and canola removed at V8 rep 1

GeneMaths XT software was used to log transform (log 2) the intensity readings and samples from each individual hybridizations were normalize against each other using default parameters in Genemaths XT software (data was treated as if it were from single channel hybridizations). Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted (Horvath et al., 2007) and technical replicates for each probe were averaged to reduce any dye bias that existed. GeneMaths XT software was then used to identify P values based on ANOVA and individual t tests between treatments. Probes were considered differentially expressed if P values for any test were ≤0.05.


title: Related 10

value: Related to diabetic patient


title: MB231-Numb5, Biological Rep 2

city: Bethesda

first: Robert

last: Cheng

state: MD

address: 10 Center Drive

department: CCR

institute: NCI

description:
0_Cheng_MB52_111808.CHP
0_Cheng_MB52_111808.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Genomic Command Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: breast cell

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol.

growth_protocol: MCF7 cells were cultured withDMEM/F12, plus 10% FBS and 0.01 mg/ml bovine insulin. MDA-MB-231 cells were cultured with alpha modified MEM medium plus 10% FBS. Both cells were add 1% penicollin/streptomycin. Both cells with stably transfections were added 0.5 mg/ml of G418. Atmosphere: air, 95%; carbon dioxide (CO2), 5% Temperature: 37.0°C

extract_protocol: Total RNA was isolated with Trizol. RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: cells were transfected with CMV-GFP vector inserted with null, Numb4, Numb5 or Numb6 plasmid.

tag: transfection

value: GFP-Numb5 Transfected


title: Healthy control 1


title: MB231-Numb5, Biological Rep 3

description:
0_Cheng_MB53_111808.CHP
0_Cheng_MB53_111808.CEL


title: MB231-Numb6, Biological Rep 1

description:
0_Cheng_MB61_111808.CHP
0_Cheng_MB61_111808.CEL

value: GFP-Numb6 Transfected


title: Related 9


title: hi559 Mutant Repl3

source_name: Phenotyped whole mutant embryo at 5 dpf

value: Mutant


title: hi559 Mutant Repl2


title: Related 8

value: positive


title: hi559 Mutant Repl1


title: Skin_SKO_Rep3

city: Madison

first: Matthew

last: Flowers

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

description: Gene expression data of whole skin

hyb_protocol: Hybridization cocktail prepared acording to the protocols and procedures in the AFX Expression Analysis Technical Manual. 10 ug of aRNA applied to AFX array and hybridized overnight at 45C for 16 hours in AFX 640 Hybridization oven. AFX 430 2.0 gene chips were post processed on the AFX 450 Fluidics Station according to all AFX protocols and procedures defined for the array (EukGE_WS2v5_450)

scan_protocol: All AFX 430 2.0 gene chips scanned on AFX GC3000 G7 scanner using Command console. Data extracted from scanned images using Expression console. All recommended AFX control parameters ok.

data_processing: Expression measurements were pre-processed to provide background correction, normalization and log base 2 transformation using RMA (Robust Multi-array Average) (Irizarry RA, et al. Biostatistics 4: 249-264, 2003). We used two analytical approaches to generate lists of differentially expressed probe sets, loosely referred to as genes. First, we calculated an un-moderated t-statistic for every probe set by applying Welch’s t-test. The resulting p-values were used to calculate q-values, which account for multiple tests and provide thresholds so that lists can be generated for a target false discovery rate (FDR) (Storey JD, and Tibshirani R. Proc Natl Acad Sci U S A 100: 9440-9445, 2003). Using this method, we targeted a FDR of 5% and probe sets with q-values below 0.05 are considered to be of interest. We also applied EBarrays (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003; Newton MA, et al. J Comput Biol 8: 37-52, 2001), which along with RMA is implemented in R, a publicly available statistical analysis environment (R. Development Core Team. R: A language and environment for statistical computing. http://www.r-project.org. Vienna, Austria: R Foundation for Statistical Computing, 2005) and available at Bioconductor (Gentleman RC, et al Genome Biol 5: R80, 2004.). EBarrays is an empirical Bayes approach which models the probability distribution of a set of expression measurements (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003, 50). It accounts generally for differences among probe sets in their true underlying expression levels, measurement fluctuations and distinct expression patterns for a given probe set among conditions (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). An expression pattern is an arrangement of the true underlying intensities (u1) in each condition. The number of patterns possible depends on the number of conditions from which the expression measurements were obtained. For example, when measurements are taken from two conditions, two patterns of expression are possible: equivalent expression (EE; u1 = u2) and differential expression (DE; u1 ≠ u2). Since we do not know a priori which probe sets are in which patterns, the marginal distribution of the data is a mixture over the possible patterns with model parameters determined by the full set of array data. In this way, the approach utilizes information across a set of arrays to optimize model fit and is thus more efficient than a number of methods that make inferences one probe set at a time (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). The approach also naturally controls for both type I and type II errors (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). The fitted model parameters provide information on the number of probe sets expected in each expression pattern. Furthermore, the fitted model is used to assign posterior probability distributions to every probe set. Each probe set specific distribution gives the posterior probability of that probe set's individual expression pattern. The posterior expected FDR is controlled by thresholding the posterior probabilities. Two approaches were used as discussed in (Newton MA, et al. Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5: 155-176, 2004.). The most conservative approach to control the FDR at 5%, for example, is to only consider probe sets with specific posterior probability of EE less than 0.05 (hard threshold). We also report results from the less conservative approach that determines the exact threshold required (soft threshold) so that the average posterior probability of EE for all probe sets on a list is less than 0.05.

source_name: Dorsal Skin_SKO

label_protocol: Samples were labeled using the Ambion MessageAMP Biotin II-Enhanced IVT kit using 1.5 ug of RNA for all samples and processed according to kit instruction manual. 14 hour IVT reaction at 37C.

growth_protocol: Male Lox and SKO mice on a C57BL/6J background were weaned at 3 weeks of age and maintained on a standard rodent diet (Purina Formulab 5008) until 8-9 weeks of age

extract_protocol: RNA was extracted from skin with TRI reagent (Molecular Research Center), DNase treated with Turbo Dnase (Ambion), and re-extraced with TRI reagent to inactivate Dnase

treatment_protocol: Male mice were sacrificed in the non-fasted state by isoflurane overdose, shaved with electric clippers, and whole dorsal skin removed and flash frozen in liquid nitrogen

value: male

tag: genotype/variation

value: Scd1 knockout (SKO)

value: Dorsal skin

value: 8-9 wks old


title: MB231-Numb6, Biological Rep 3

description:
0_Cheng_MB63_111808.CHP
0_Cheng_MB63_111808.CEL


title: Patient 156

type: genomic

city: Cambridge

first: Xin Yi

last: Goh

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Hutchison-MRC Research Centre

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Genomic DNA extracted from esophageal adenocarcinoma tumors was genotyped using Illumina HumanCytoSNP-12 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: esophageal adenocarcinoma

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: Sex

value: Male

value: 72 years

tag: chemo-treated

value: No

tag: histological differentiation

value: Poorly

tag: days to death or last seen alive

value: esophageal adenocarcinoma


title: MB231-Numb4, Biological Rep 3

description:
0_Cheng_MB43_111808.CHP
0_Cheng_MB43_111808.CEL

tag: cell line

value: GFP-Numb4 Transfected


title: endometrioma, patient 19

value: endometrioma


title: 3333K6A_TVA

description:
Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H35__3333K6A_TVA_PyMT_MG_430A_2.0

hyb_protocol: Total of 15 µg biotin-labeled cRNA was fragmented, and 10 µg of the fragmented cRNA was prepared in the hybridization cocktail in a total volume of 200 µl, and 6.5 µg of them in 130 µl volume was hybridized onto the M430A 2.0 GeneChip in an Affymetrix Hybridization Oven 640 for 16-19 hours.  We used Affymetrix recommended procedures for prehybridization, hybridization, washing, and staining with streptavidin-phycoerythrin (SAPE).  Antibody amplification was employed with a biotin-linked antibody to streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: After automated staining and washing (Affymetrix protocol Midi_euk2v3 450) using the GeneChip Fluidics Station 450, the arrays were scanned by the Affymetrix GeneChip scanner 3000 using the GeneChip operating system (GCOS) v1.2.

data_processing: A low level quantification was done in the GCOS1.2, and the probe level data (CEL file) was saved for each array and analyzed subsequently by DNA chip analyzer (dChip v2006).

source_name: mouse mammary tumor, K6-tva RCAS-PyMT model

label_protocol: Double-strand cDNA was synthesized from 5 µg of total RNA for each sample, and an in vitro transcription reaction was carried out to produce biotin-labeled cRNA from the cDNA.  One-cycle target labeling and control reagents kit from Affymetrix (Part #900493) (Santa Clara, CA, USA) was used for the cDNA synthesis and biotin-labeling.

growth_protocol: The K6-tva BAC transgenic line was generating using the recombineering method. Briefly, the RP23-473O22 BAC clone (200-kb) containing the K6a gene was purchased from BACPAC Resources Center (Children’s Hospital Oakland Research Institute, Oakland, California). The Counter Selection BAC Modification Kit (Gene Bridges GmbH, Dresden, Germany) was used to modify the BAC following the manufacturer’s instructions. All mice were on the FVB/N background, and were kept on 2920X Teklad Global Extruded Rodent Diet (Soy Protein-Free) (Harlan Laboratories, Indianapolis, Indiana). All procedures using mice were performed in compliance with an Institutional Animal Care and Use Committee-approved animal protocol.

extract_protocol: All samples were collected fresh and snap-frozen in liquid nitrogen.  Frozen samples were ground into fine powder in liquid nitrogen and RNA was extracted by Trizol (Lift Technologies) with an additional step of the isopropanol precipitation following the regular isopropanol precipitation step recommended in the protocol.  This extra step cleans up the potential chemical contamination in the Trizol reagents.

tag: background

value: FVB/N

tag: tissue

value: mammary tumor

tag: transgenic

value: K6-tva RCAS-PyMT


title: MB231-Numb4, Biological Rep 2

description:
0_Cheng_MB42_111808.CHP
0_Cheng_MB42_111808.CEL


title: MB231-Numb4, Biological Rep 1

description:
0_Cheng_MB41_111808.CHP
0_Cheng_MB41_111808.CEL


title: MB231-Numb6, Biological Rep 2

description:
0_Cheng_MB62_111808.CHP
0_Cheng_MB62_111808.CEL

value: GFP-Numb6 Transfected


title: MB231-Numb5, Biological Rep 1

description:
0_Cheng_MB51_111808.CHP
0_Cheng_MB51_111808.CEL

value: GFP-Numb5 Transfected


title: Skin_SKO_Rep2

description: Gene expression data of whole skin

tag: gender

tag: strain


title: Patient 96

value: 63 years

value: Moderate


title: Patient 37

value: 68 years

value: Well


title: Patient 36

value: 81 years


title: Skin_SKO_Rep1

description: Gene expression data of whole skin

value: male

value: Scd1 knockout (SKO)

value: Dorsal skin

value: 8-9 wks old


title: Patient 118

value: Female

value: No

value: esophageal adenocarcinoma


title: MB231-GFP, Biological Rep 3

description:
0_Cheng_MB-GFP3_111808.CHP
0_Cheng_MB-GFP3_111808.CEL

value: GFP vector control


title: Patient 3


title: Patient 27

value: Male

value: 70 years

value: Poorly


title: Patient 138

value: 75 years

value: Yes


title: Related 4

tag: cell type

value: PBMC

tag: disease state

value: Related to diabetic patient

value: negative


title: Related 6

tag: antibody positivity


title: 3331K6A_TVA

description:
Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H34__3331K6A_TVA_PyMT_MG_430A_2.0

value: FVB/N

value: mammary tumor

value: K6-tva RCAS-PyMT


title: 3323K6A_TVA

description:
Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H31B__3323K6A_TVA_PyMT_MG_430A_2.0


title: Related 3

value: positive


title: Related 2


title: Skin_Lox_Control_Rep1

description: Gene expression data of whole skin

source_name: Dorsal Skin_Lox_Control

value: male

value: Scd1flox/flox (Lox) control

value: Dorsal skin

tag: age

value: 8-9 wks old


title: 3171MA

description:
Mouse mammary tumor, MMTV-tva RCAS-PyMT model.
YL6-H17__3171MA_PyMT_MG_430A_2.0

source_name: mouse mammary tumor, MMTV-tva RCAS-PyMT model

value: MMTV-tva RCAS-PyMT


title: 3166MA

description:
Mouse mammary tumor, MMTV-tva RCAS-PyMT model.
YL6-H16B__3166MA_PyMT_MG_430A_2.0


title: Related 7


title: MCF7-Numb6, Biological Rep 3

description:
0_Cheng_N63_012209.CHP
0_Cheng_N63_012209.CEL

value: GFP-Numb6 Transfected


title: MCF7-Numb6, Biological Rep 1

description:
0_Cheng_N61_012209.CHP
0_Cheng_N61_012209.CEL


title: 3176MA

description:
Mouse mammary tumor, MMTV-tva RCAS-PyMT model.
YL6-H18__3176MA_PyMT_MG_430A_2.0


title: MCF7-Numb6, Biological Rep 2

description:
0_Cheng_N62_012209.CHP
0_Cheng_N62_012209.CEL


title: Patient 2

value: Female

value: No

value: esophageal adenocarcinoma


title: Related 5


title: Diabetic patient 9

value: Diabetic patient


title: Related 1

value: PBMC


title: Skin_Lox_Control_Rep3

description: Gene expression data of whole skin


title: MB231-GFP, Biological Rep 2

description:
0_Cheng_MB-GFP2_111808.CHP
0_Cheng_MB-GFP2_111808.CEL

value: GFP vector control


title: 3186MA

description:
Mouse mammary tumor, MMTV-tva RCAS-PyMT model.
YL6-H24__3186MA_PyMT_MG_430A_2.0


title: MCF7-Numb5, Biological Rep 3

description:
0_Cheng_N53_012209.CHP
0_Cheng_N53_012209.CEL

value: GFP-Numb5 Transfected


title: Diabetic patient 6

value: negative


title: Diabetic patient 8


title: Diabetic patient 7


title: MCF7-Numb5, Biological Rep 2

description:
0_Cheng_N52_012209.CHP
0_Cheng_N52_012209.CEL


title: Skin_Lox_Control_Rep2

description: Gene expression data of whole skin


title: 3325K6A_TVA

description:
Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H33__3325K6A_TVA_PyMT_MG_430A_2.0

value: FVB/N

value: mammary tumor


title: 3324K6A_TVA

description:
Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H32__3324K6A_TVA_PyMT_MG_430A_2.0

value: K6-tva RCAS-PyMT


title: 6409MMTV

description:
Mouse mammary tumor, MMTV-PyMT model.
YL6-H27__6409MMTV_PyMT_MG_430A_2.0

source_name: mouse mammary tumor, MMTV-PyMT model

value: MMTV-PyMT


title: MCF7-Numb4, Biological Rep 2

description:
0_Cheng_N42_012209.CHP
0_Cheng_N42_012209.CEL

value: GFP-Numb4 Transfected


title: MCF7-Numb5, Biological Rep 1

description:
0_Cheng_N51_012209.CHP
0_Cheng_N51_012209.CEL


title: 6411MMTV

description:
Mouse mammary tumor, MMTV-PyMT model.
YL6-H29__6411MMTV_PyMT_MG_430A_2.0


title: Diabetic patient 2


title: MCF7-Numb4, Biological Rep 1

description:
0_Cheng_N41_012209.CHP
0_Cheng_N41_012209.CEL


title: MCF7-GFP, Biological Rep 3

description:
0_Cheng_GFP3_012209.CHP
0_Cheng_GFP3_012209.CEL


title: 6467MMTV

description:
Mouse mammary tumor, MMTV-PyMT model.
YL6-H30__6467MMTV_PyMT_MG_430A_2.0


title: Diabetic patient 5


title: Diabetic patient 4


title: MCF7-Numb4, Biological Rep 3

description:
0_Cheng_N43_012209.CHP
0_Cheng_N43_012209.CEL


title: MB231-GFP, Biological Rep 1

description:
0_Cheng_MB-GFP1_111808.CHP
0_Cheng_MB-GFP1_111808.CEL


title: 6410MMTV

description:
Mouse mammary tumor, MMTV-PyMT model.
YL6-H28__6410MMTV_PyMT_MG_430A_2.0


title: 6408MMTV

description:
Mouse mammary tumor, MMTV-PyMT model.
YL6-H26B__6408MMTV_PyMT_MG_430A_2.0


title: 3181MA

description:
Mouse mammary tumor, MMTV-tva RCAS-PyMT model.
YL6-H19__3181MA_PyMT_MG_430A_2.0


title: MCF7-GFP, Biological Rep 2

description:
0_Cheng_GFP2_012209.CHP
0_Cheng_GFP2_012209.CEL


title: Diabetic patient 3


title: Ex Vivo Stretched 4

status: Public on May 08 2011

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

scan_protocol: The GeneChip array was stained with phycoerythrin according to the Affymetrix Technical Manual and scanned with the GeneChip Scanner GS3000-G7.

data_processing: Probe statistics were background-corrected, normalized and summarized using the rma method and affy package of Speed and coworkers.

source_name: mouse loose subcutaneous connective tissue of the trunk

label_protocol: Double-stranded cDNA was then synthesized followed by an in vitro transcription reaction and fragmentation reaction to produce biotin-labeled cRNA fragments

extract_protocol: Subcutaneous tissues were homogenized in Tri-Reagent (Sigma Product # T-9424).

tag: Strain

tag: Gender

value: male

tag: Weight


title: MCF7-GFP, Biological Rep 1

description:
0_Cheng_GFP1_012209.CHP
0_Cheng_GFP1_012209.CEL

tag: transfection


title: Diabetic patient 1


title: Ex Vivo Stretched 2


title: Ex Vivo Stretched 3


title: Ex Vivo Shortened 3


title: Ex Vivo Stretched 1


title: LPS-activated mature dendritic cell [TLR Array]

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

description: qPCR gene expression profiling

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:
http://sabiosciences.com/pcrarraydataanalysis.php

For the normalization it uses the average of five housekeeping genes:
B2M Beta-2-microglobulin
HPRT1 Hypoxanthine phosphoribosyltransferase 1
RPL13A Ribosomal protein L13a
GAPDH Glyceraldehyde-3-phosphate dehydrogenase
ACTB Actin, beta

The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The fold changes (mature dendritic cells vs. immature dendritic cells) and raw data (Ct values) are presented as supplementary files on the Series record.

label: SYBR Green

source_name: Monocyte-derived mature dendritic cell

label_protocol: PCR arrays were performed using the Dendritic Cell - Antigen Presenting Cell and the Toll-like Receptor Pathway PCR Arrays (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: Immature dendritic cells were differentiated from CD14-positive monocytes by culturing for five days in the presence of interleukin-4 (IL-4 100 ng/ml) and GM-CSF (100 ng/ml). Immature dendritic cells were activated with double-stranded DNA poly(dA:dT) (2.5 μg/ml) complexed with LyoVec transfection reagent. or LPS (500 ng/ml) or inflammatory cocktail containing 10 ng/ml TNF, 5 ng/ml IL-1β, 20 ng/ml IL-6, 75 ng/ml GM-CSF and 1 μg/ml PGE2, respectively.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: time

value: 5+1 days

tag: activation agent

value: LPS


title: Double-stranded DNA-activated mature dendritic cell [TLR Array]

description: qPCR gene expression profiling

value: Double-stranded DNA


title: In Vivo Stretched 6


title: Ex Vivo Shortened 1


title: In Vivo Stretched 5


title: In Vivo Shortened 7


title: Double-stranded DNA-activated mature dendritic cell [DC-APC Array]

description: qPCR gene expression profiling


title: Immature dendritic cell [TLR Array]

description: qPCR gene expression profiling

source_name: Monocyte-derived immature dendritic cell

value: 5 days

value: control


title: LPS-activated mature dendritic cell [DC-APC Array]

description: qPCR gene expression profiling


title: Inflammatory cocktail-activated mature dendritic cell [TLR Array]

description: qPCR gene expression profiling

value: Inflammatory cocktail (10 ng/ml TNF, 5 ng/ml IL-1β, 20 ng/ml IL-6, 75 ng/ml GM-CSF and 1 μg/ml PGE2)


title: Inflammatory cocktail-activated mature dendritic cell [DC-APC Array]

description: qPCR gene expression profiling


title: In Vivo Stretched 7


title: In Vivo Shortened 5


title: In Vivo Shortened 4


title: Immature dendritic cell [DC-APC Array]

description: qPCR gene expression profiling


title: In Vivo Stretched 2


title: In Vivo Stretched 3


title: In Vivo Stretched 4


title: In Vivo Shortened 3


title: In Vivo Shortened 6


title: In Vivo Shortened 2


title: In Vivo Stretched 1


title: HPB-ALL NBD 2

status: Public on May 07 2011

city: New York

first: Iannis

last: Aifantis

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Sch of Medicine

description: Twenty samples were analyzed: human T-ALL, CEM, KOPT-K, DND41, HPB-ALL cells lines have been treated at 100uM for 16 hours with control peptide or IKKγ Nemo binding domain (NBD) inhibitory peptide, that specifically block the canonical NF-κB activity by disrupting the interaction of IKKγ to IKKβ and IKKα

hyb_protocol: 15 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: NBD inhibitory peptide-treated HPB-ALL 100mM 16h

label_protocol: 20 ng total RNA converted to cDNA using Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: Rneasy (QIAGEN) according to manufacturer's protocol.

treatment_protocol: T-ALL1, CEM, KOPT-K, DND41 and HPB-ALL cells lines have been treated with control peptide or IKKg NEMO binding domain (NDB) inhibitory peptide at 100mM for 16 hours

value: ACC483 [HPB-ALL]

value: human T-ALL cell line

tag: agent


title: In Vivo Shortened 1


title: HPB-ALL NBD 1

tag: cell line

value: IKKγ Nemo binding domain (NBD) inhibitory peptide


title: 8_Mm_133m_1_Hyb20

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

description: M-, 133-, DDC-treated liver replicate 1

hyb_protocol: Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: The data were normalized by the quantile normalization method using the ‘‘normalizeBetweenArrays’’ function in the LIMMA (linear models for microarray data) package in R as described (Gentleman 2005).  Probes were considered present when their intensity as at least 2 times the inter-quartile range above the median intensity of negative control spots. For statistical analysis, genes were called differentially expressed using the Significance Analysis of Microarray (SAM) one-class response package with a false discovery rate of 10% and a minimum fold change of 1.53. Genes marked as absent (i.e., with expression levels near back- ground) were omitted.

source_name: M-, 133-, cell sorted from DDC-treated liver

label_protocol: Amplified cDNA was prepared using the WT-Ovation Pico Amplification System (NuGEN Technologies). Amplified cDNA was directly labeled using the BioPrime Array CGH Genomic Labeling System with Cy3-labeled nucleotides (GE Amersham Biosciences).

growth_protocol: c129/S3 mice, obtained from the Jackson Laboratory, were fed a Purina 5015 diet.

extract_protocol: Cell populations were sorted directly into Trizol LS (Invitrogen).

treatment_protocol: 0.1% (w/w) DDC (Sigma-Aldrich and Harlan Teklad) was added to diet for 2 wk. Hepatocytes and NPCs were isolated as described previously (Dorrell et al. 2008) with the following modifications. Accutase (Innovative Cell Technologies) was substituted for the published combination of 10 mg/mL Collagenase D and 10 mg/mL Pronase; although Pronase did not reduce cell viability, we observed that it selectively destroyed the MIC1-1C3 antigen and was therefore unsuitable for duct cell preparation. Erythrocytes present in the first NPC fraction were lysed by cell pellet resuspension in 0.2% NaCl for 1 min. Finally, once all three NPC fractions were collected and combined, these were resuspended in 35% Percoll (GE Health- care) and centrifuged at 900g for 10 min to exclude debris (which reduces the efficiency of FACS sorting).  Cells where then sorted using FACS.

tag: mic status

value: M-

tag: 133 status

tag: ddc treatment

value: DDC-treated


title: 6_Mm_133m_2_Hyb16

description: M-, 133-, DDC-treated liver replicate 2


title: HPB-ALL Control 2

source_name: control peptide-treated HPB-ALL 100mM 16h


title: 6_Mp_133p_4_Hyb14

description: M+, 133+, DDC-treated liver replicate 4

source_name: M+, 133+, cell sorted from DDC-treated liver

value: M+


title: DND41 Control 2

source_name: control peptide-treated DND41 100mM 16h


title: 7_Mm_133m_4_Hyb18

description: M-, 133-, DDC-treated liver replicate 4


title: 5_Mm_133m_3_Hyb13

description: M-, 133-, DDC-treated liver replicate 3


title: DND41 Control 1


title: HPB-ALL Control 1


title: 7_Mp_133p_3_Hyb17

description: M+, 133+, DDC-treated liver replicate 3


title: DND41 NBD 1

source_name: NBD inhibitory peptide-treated DND41 100mM 16h


title: KOPT-K NBD 2

source_name: NBD inhibitory peptide-treated KOPT-K 100mM 16h

value: KOPT-K


title: KOPT-K control 1

source_name: control peptide-treated KOPT-K 100mM 16h


title: KOPT-K NBD 1


title: 5_Mp_133p_1_Hyb12

description: M+, 133+, DDC-treated liver replicate 1


title: KOPT-K control 2


title: 1B_Mm_133m_n2_2_Hyb8

description: M-, 133-, untreated liver replicate 2

source_name: M-, 133-, cell sorted from untreated liver

value: untreated


title: CEM NBD 1

source_name: NBD inhibitory peptide-treated CEM 100mM 16h

value: JCRB0033 [CEM]


title: 1B_Mm_133m_n1_3_Hyb6

description: M-, 133-, untreated liver replicate 2


title: CEM Control 2

source_name: control peptide-treated CEM 100mM 16h


title: 1_Mm_133m_1_Hyb2

description: M-, 133-, untreated liver replicate 1


title: 8_Mp_133p_2_Hyb19

description: M+, 133+, DDC-treated liver replicate 2


title: CEM NBD 2


title: 1B_Mp_133p_n2_5_Hyb7

description: M+, 133+, untreated liver replicate 1

source_name: M+, 133+, cell sorted from untreated liver


title: Ex Vivo Shortened 4


title: 1_Mp_133p_3_Hyb1

description: M+, 133+, untreated liver replicate 3


title: CEM Control 1


title: T-ALL1 NBD 2

source_name: NBD inhibitory peptide-treated T-ALL1 100mM 16h

value: JCRB0086 [TALL-1]


title: T-ALL1 NBD 1


title: whole blood mRNA from patients presenting with UA (MM_UA_28_5)

status: Public on May 06 2011

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

description: Gene expression data from whole blood 30 days post UA

hyb_protocol: 15µg of amplified RNA was fragmented (Gene Chip reagents, Affymetrix) and hybridized onto HGU133 Plus 2.0 GeneChips. After overnight hybridization at 42°C, the GeneChips underwent stringency washes and streptavidin staining in a GeneChip Fluidics Station 400 (Affymetrix)

scan_protocol: Fluorescent intensity of hybridized transcripts was determined with the GeneChip 3000 Scanner (Affymetrix).

data_processing: Gene expression was estimated using probabilistic models implemented in puma implemented in R (www.bioconductor.org) . These models provide estimates for the variance and credibility interval for probe level errors of each transcript and generate accurate estimates of low gene expression. FCs were calculated after combining gene expression values within groups using Bayesian hierarchical model, incorporating probe level errors into the variance estimate. Significance levels for differentially expressed genes were detected by calculating the probability of positive log ratio (PPLR). The higher is the probability the more confident is the estimate of that positive FC, conversely the lower is the probability the more confident is the estimate of that FC to be negative. This model is implemented in the pumaComb and pumaDE modules within puma.

source_name: whole blood mRNA 30 days post UA

label_protocol: Linear amplification and biotin labelling of RNA was carried out by the Two-Cycle Target Labelling Protocol (Affymetrix). Following input of 100ng RNA, approximately 120µg of biotin-labelled RNA was obtained.

growth_protocol: Venous blood (3ml) was collected into Tempus RNA blood tubes (Applied Biosystems)

extract_protocol: RNA was extracted according to manufactures instruction using Tempus spin RNA isolation kit (Applied Biosystems). NanoDrop Technologies ND-1000 spectrophotometer (Thermo Scientific) was used quantify RNA quality and quantity after extraction. Depletion of globin RNA was performed using GLOBINclear (Ambion). Quantity and quality of globin cleared RNA was reassessed using Agilent 2100 Bioanalyzer (Agilent) with a nanoRNA assay.

tag: disease

value: UA

tag: time point

value: day 30

tag: tissue

value: blood

tag: ethinicity

value: caucasian

tag: Sex

value: F


title: whole blood mRNA from patients presenting with UA (MM_UA_27_5)

tag: age

value: M


title: whole blood mRNA from patients presenting with UA (MM_UA_58_05)


title: whole blood mRNA from patients presenting with UA (MM_UA_70_05)


title: Low Bltitude, location B, mouse 1 liver

city: Reno

first: Monica

middle: M

last: Baze

state: NV

address: Dept. of Biology/ 314

department: Biology

institute: University of Nevada, Reno

description: Expression data set from wild mouse populations

hyb_protocol: GeneChip Mouse Genome 430 2.0 arrays were hybridized with 200 ul hybridization cocktail for 16 hours.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000

data_processing: Eighteen arrays were used for data analysis;  Affymetrix® microarray data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters settings. The Bioconductor 'affy' package from R [http://cran.r-project.org/] was used for data analysis. Probe values were normalized via quantile normalization, and a median polish was applied to compute one expression measure from all probe values. Resulting RMA expression values were log2-transformed; presence calls and detection p-values were calculated with the 'mas5calls' function using default parameters.

organism: Mus musculus domesticus

source_name: liver of low altitude wild mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from 30 mg of liver from mouse using Qiagen RNA Extraction Minikit (Qiagen, Inc.) per manufacturer protocols.

value: male

value: liver

tag: altitude

value: low

tag: location

value: B

tag: strain


title: whole blood mRNA from patients presenting with UA (MM_UA_70_04)

description: Gene expression data from whole blood 7 days post UA

source_name: whole blood mRNA 7 days post UA

value: day 7


title: T-ALL1 Control 1

source_name: control peptide-treated T-ALL1 100mM 16h

tag: cell type

value: human T-ALL cell line

value: control


title: whole blood mRNA from patients presenting with UA (MM_UA_29_05)


title: Low altitude, location C, mouse 1 liver

value: C


title: whole blood mRNA from patients presenting with UA (MM_UA_60_4)


title: 2_Mp_133p_4_Hyb3

description: M+, 133+, untreated liver replicate 4

value: M+

value: untreated


title: Low Bltitude, location B, mouse 2 liver


title: Low altitude, location C, mouse 2 liver


title: whole blood mRNA from patients presenting with UA (MM_UA_25_5)


title: whole blood mRNA from patients presenting with UA (MM_UA_22_5)


title: Low altitude, location A, mouse 3 liver

value: A


title: T-ALL1 Control 2

value: JCRB0086 [TALL-1]


title: Low Bltitude, location B, mouse 3 liver


title: Low altitude, location C, mouse 3 liver


title: 4B_Mp_133p_2_Hyb9

description: M+, 133+, untreated liver replicate 2


title: 1B_Mp_133p_n1_1_Hyb5

description: M+, 133+, untreated liver replicate 1


title: Low altitude, location A, mouse 2 liver


title: Ex Vivo Shortened 2

source_name: mouse loose subcutaneous connective tissue of the trunk

tag: Strain

tag: Gender

tag: Weight


title: whole blood mRNA from patients presenting with UA (MM_UA_28_4)

value: UA


title: High altitude, location B, mouse 3 liver

source_name: liver of high altitude wild mouse

value: high


title: whole blood mRNA from patients presenting with MI (MM_MI_75_05)

description: Gene expression data from whole blood 30 days post MI

source_name: whole blood mRNA 30 days post MI

value: MI

value: day 30

value: blood

value: caucasian


title: High altitude, location C, mouse 3 liver

value: male

value: liver


title: whole blood mRNA from patients presenting with UA (MM_UA_27_4)

value: M


title: whole blood mRNA from patients presenting with UA (MM_UA_58_04)

value: day 7


title: whole blood mRNA from patients presenting with MI (MM_MI_71_5)


title: whole blood mRNA from patients presenting with UA (MM_UA_22_4)


title: High altitude, location A, mouse 2 liver


title: whole blood mRNA from patients presenting with UA (MM_UA_29_04)


title: High altitude, location B, mouse 1 liver

value: B


title: whole blood mRNA from patients presenting with MI (MM_MI_77_05)


title: whole blood mRNA from patients presenting with MI (MM_MI_57_05)


title: Low altitude, location A, mouse 1 liver

value: low


title: High altitude, location B, mouse 2 liver


title: High altitude, location C, mouse 1 liver

value: C


title: whole blood mRNA from patients presenting with MI (MM_MI_55_5)


title: High altitude, location A, mouse 1 liver


title: High altitude, location C, mouse 2 liver


title: whole blood mRNA from patients presenting with UA (MM_UA_25_4)


title: DND41 NBD 2

tag: cell line

value: human T-ALL cell line

tag: agent

value: IKKγ Nemo binding domain (NBD) inhibitory peptide


title: whole blood mRNA from patients presenting with MI (MM_MI_74_05)


title: whole blood mRNA from patients presenting with MI (MM_MI_54_5)


title: WT Ly6D+CLP, biological rep2

city: Lund

first: Gudmundur

last: Norddahl

address: Tornavagen 10

country: Sweden

institute: Lund University

hyb_protocol: RNA hybridized to MOE430_2. Chips according to manufacturer manual

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

source_name: WT Ly6D+CLP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4000 to 7000 cell

growth_protocol: Primary Cells directly sorted for RNA extraction

extract_protocol: Total RNA extraction was performed with QIAGEN microRNeasy kit according to the manufacturer's instructions.

tag: background strain

tag: genotype

value: wild type

value: Mouse bone marrow

value: 8-12 weeks

tag: gender

value: female


title: whole blood mRNA from patients presenting with MI (MM_MI_30_5)

tag: disease

value: MI

tag: time point

value: F


title: WT Ly6D-CLP, biological rep1

source_name: WT Ly6D-CLP

tag: tissue


title: WT HSC, biological rep2

source_name: WT

value: 32 weeks


title: whole blood mRNA from patients presenting with MI (MM_MI_10_5)

value: day 30

value: blood

tag: ethinicity

value: caucasian

tag: Sex


title: WT Ly6D-CLP, biological rep2

tag: age


title: High altitude, location A, mouse 4 liver

value: male

value: liver

tag: altitude

value: high

tag: location

value: A


title: whole blood mRNA from patients presenting with MI (MM_MI_21_5)

value: M


title: WT HSC, biological rep1


title: Mutator, biological rep2

source_name: Mutator


title: whole blood mRNA from patients presenting with MI (MM_MI_26_5)


title: whole blood mRNA from patients presenting with MI (MM_MI_4_5)


title: WT Ly6D+CLP , biological rep1


title: whole blood mRNA from patients presenting with MI (MM_MI_24_5)


title: WT HSC, biological rep3


title: whole blood mRNA from patients presenting with MI (MM_MI_11_5)


title: whole blood mRNA from patients presenting with MI (MM_MI_7_5)


title: whole blood mRNA from patients presenting with MI (MM_MI_9_5)


title: whole blood mRNA from patients presenting with MI (MM_MI_77_04)

description: Gene expression data from whole blood7 days post MI

source_name: whole blood mRNA 7 days post MI

value: day 7


title: HSC old female , biological rep2

source_name: HSC old female

value: 24 months


title: whole blood mRNA from patients presenting with UA (MM_UA_60_5)

value: UA


title: HSC old female , biological rep1

value: wild type

value: Mouse bone marrow


title: whole blood mRNA from patients presenting with MI (MM_MI_74_04)


title: Mutator, biological rep3

value: female


title: whole blood mRNA from patients presenting with MI (MM_MI_5_5)

value: MI


title: whole blood mRNA from patients presenting with MI (MM_MI_3_5)


title: whole blood mRNA from patients presenting with MI (MM_MI_75_04)


title: Mutator, biological rep1


title: HSC old female, biological rep3


title: Genomic DNA from trisomy 18 fetal skin 3

city: Vancouver

first: Ryan

last: Yuen

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
PZLT2_t18_skin
Trisomy 18 skin sample.

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

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

data_processing: Data were background-normalized using BeadStudio software v3.1.3.0, which subtracts a background value derived by averaging the signals of built-in negative control bead types.

label: Cy5, Cy3

source_name: Fetal skin, trisomy 18

label_protocol: DNA was bisulfite converted, amplified, and fragmented.

extract_protocol: Genomic DNA was extracted using standard techniques and purified using the Qiagen DNeasy Kit according to standard instructions.

value: skin

tag: developmental stage

value: fetal

tag: disease state

value: trisomy 18


title: Genomic DNA from trisomy 18 fetal skin 4

description:
mT18-1_t18_skin
Trisomy 18 skin sample.


title: Genomic DNA from trisomy 18 fetal skin 2

description:
PYLT1_t18_skin
Trisomy 18 skin sample.


title: whole blood mRNA from patients presenting with MI (MM_MI_71_4)

value: blood


title: whole blood mRNA from patients presenting with MI (MM_MI_55_4)

value: caucasian


title: normal transitional zone prostate glands

city: Bonn

first: Andreas

last: Lindstrot

address: Sigmund-Freud-Str. 25

department: Molekular Patholoy

country: Germany

institute: University of Bonn

hyb_protocol: The hybridization was performed according to Agilent 60mer oligo Microarray processing protocol using Agilent gene expression hybridization kit. Briefly Cy3-labeled fragmented cRNA in hybridization buffer was hybridyzed over nigth (17h 65°C ) to Agilent whole human genome oligo Micrarray 4x44k using Agilent recommended hybridization chamber and oven. Finally the microarray was washed once with the agilent gene expression wash buffer 1 for 1 minute at Room temperature followed by a second wash with preheated Agilent gene expression wash buffer 2 (37° for 1 Minutes). The last washing step was performed with acetonitrile

scan_protocol: Fluorescence signals of the hydridysed agilent microarray were detected using the Agilent Microarray scanner system.

data_processing: the Agilent feature extraction software FES was used to read out and process the microarray image file. For the determination of differential gene expression FES derived output data files were further analyzed using the Rosetta resolver gene expression data analysis system (Rosetta biosoftware). All samples were labeled with Cy3, the ratio experiments are designated as control vs experiments. The ratios are always calculated by dividing sample signal intensity through control signal intensity.

source_name: prostate glands

label_protocol: For the linear T7 based amplification step, 0.26 - 0.3µg of total RNA sample was used. To produce Cy3-labeld cRNA, the RNA samples were amplified and labeld using Agilent low RNA input linear Amp Kit (Agilent Technologies) following manufactures protocol.

extract_protocol: The extraction of the laser microdissected glands was performed according to the manual of the Qiagen Rneasy Micro Kit including a recommend DNAse digestion

tag: tumor stage

value: Gleason 0


title: Genomic DNA from trisomy 21 fetal muscle 4

description:
FT12_t21_muscle
Trisomy 21 muscle sample.

source_name: Fetal muscle, trisomy 21

value: muscle

value: trisomy 21


title: Genomic DNA from trisomy 21 fetal muscle 2

description:
FT8_t21_muscle
Trisomy 21 muscle sample.

value: male


title: whole blood mRNA from patients presenting with MI (MM_MI_57_04)

value: M


title: whole blood mRNA from patients presenting with MI (MM_MI_26_4)

value: day 7


title: Genomic DNA from trisomy 21 fetal muscle 3

description:
FT9_t21_muscle
Trisomy 21 muscle sample.


title: Genomic DNA from trisomy 18 fetal skin 1

description:
FT2_t18_skin
Trisomy 18 skin sample.


title: Genomic DNA from trisomy 18 fetal brain 3

description:
mT18-1_t18_brain
Trisomy 18 brain sample.

source_name: Fetal brain, trisomy 18

value: brain


title: normal peripheral zone prostate stroma


title: whole blood mRNA from patients presenting with MI (MM_MI_30_4)

value: F


title: normal transitional zone prostate stroma


title: whole blood mRNA from patients presenting with MI (MM_MI_54_4)


title: Genomic DNA from trisomy 18 fetal brain 1

description:
FT2_t18_brain
Trisomy 18 brain sample.


title: whole blood mRNA from patients presenting with MI (MM_MI_24_4)


title: Genomic DNA from trisomy 21 fetal muscle 1

description:
FT1_t21_muscle
Trisomy 21 muscle sample.


title: whole blood mRNA from patients presenting with MI (MM_MI_10_4)


title: Genomic DNA from trisomy 21 fetal skin 4

description:
FT12_t21_skin
Trisomy 21 skin sample.

source_name: Fetal skin, trisomy 21


title: Genomic DNA from trisomy 18 fetal brain 2

description:
PYLT1_t18_brain
Trisomy 18 brain sample.


title: Genomic DNA from trisomy 21 fetal skin 5

description:
mT21-5_t21_skin
Trisomy 21 skin sample.


title: whole blood mRNA from patients presenting with MI (MM_MI_11_4)


title: whole blood mRNA from patients presenting with MI (MM_MI_9_4)


title: whole blood mRNA from patients presenting with MI (MM_MI_7_4)


title: whole blood mRNA from patients presenting with MI (MM_MI_21_4)


title: dorsal root ganglion_axotomised_7day_rep3

type: other

city: Bristol

first: Liang-Fong

last: Wong

address: Whitson Street

institute: University of Bristol

description: Biological 3 of 3

hyb_protocol: Labelled RNAs were hybridised to dual-channel microarray μParaflo™ microfluidic chips comprising mouse annotated miRNAs in the miRBase Release 9.0 (LC Sciences, USA).

scan_protocol: Scanned by Axon GenePix 4000B Microarray Scanner and analysed by TIGR MIDAS software (LC Sciences, USA).

data_processing: Background subtraction and normalized using a cyclic LOWESS (Locally-weighted Regression) method

molecule: other

source_name: dorsal root ganglion, axotomised, 7 days

label_protocol: Purified small RNAs were labelled with Cy3 or Cy5 fluorescent dyes (proprietry labelling performed by LC Sciences, USA).

extract_protocol: Total RNA was extracted from control and axotomised L4-L5 DRGs using the miRVANA™ miRNA isolation kit following the manufacturer’s instructions (Ambion, UK).

treatment_protocol: In adult C57/Bl mice under general anaesthesia, the left sciatic nerve was ligated at approximately 1 cm proximal to the nerve trifurcation with a 5/0 silk suture and severed distal to the ligation. Animals were killed at 7 days postoperatively to collect the ipsilateral and contralateral (control) L4-L5 DRGs.

value: Male

tag: strain

value: Adult

source_name: dorsal root ganglion, control, 7 days


title: dorsal root ganglion_axotomised_7day_rep1

description: Biological 1 of 3


title: whole blood mRNA from patients presenting with MI (MM_MI_4_4)


title: Muscle_saline injected chicken fed VIRG (antibiotic)_ replica 3

city: Ste Anne de Bellevue

first: Bushansingh

middle: Shyam

last: Baurhoo

state: Quebec

address: 21111, Lakeshore Road

department: Animal Science

institute: McGill University

description:
raw data file: Muscle Array_7.DAT
Slide 7_saline chicken_prebiotic group_ replica 3 (Cy3) vs saline chicken_antibiotic group_ replica 3 (Cy5)

hyb_protocol: mix of 33 pmol of both samples was resuspended with 33 µl Pronto! Long Oligo Hybridization solution and applied to pre-hybrydized microarray slides with spotted area coved with a 25 X 40 mm glass coverslip; slides were hybridized in Corning Hybridization Chambers immersed in 42C water bath, protected from light, for 16h. After hybridization, slides were sequencenly washed according to manufacturer's instructions (Pronto! Universal Microarray Hybridization Kit, Corning Inc.)

scan_protocol: scanned on ScanArray Gx Plus (PerkinElmer) set to 65% lazer power Images were quantified using ScanAlyze Software (version 2.50).

data_processing: Log2 transformed data was submitted to ratio analysis and LOWESS normalization using JMP Genomics Software (SAS Institute)

organism: Gallus gallus

source_name: Total RNA from skeletal muscles of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).

label_protocol: 5µg of total RNA were primed with 3µg of random primers and 2µg of oligo(dt) primer, heated at 70 oC for 10 min, then reverse transcribed at 42 oC for 2h with 3.2 µl ChipShot Reverse Transcriptase and 4 µl aminoallyl-sNTPs; cDNA was indirectly labeled with CyDye NHS Esters (Cy3 or Cy5) by adding 60 µl of cDNA eluted to dried 40,000 pmol CyDye aliquot and hybrydized at room temperature for 1h, followed by purification steps as indicated by manufacturer's instructions (ChipShot Indirect Labeling System and Membrane Clean-Up System, Promega Corp)

growth_protocol: broiler chicks raised under standard conditions and fed prebiotic or antibiotic diet ad libitum

extract_protocol: Total RNA from liver, intestine and skeletal muscle tissues was extracted using Trizol reagent and Prelink RNA Mini Kit following manufacturer's instructions (Invitrogen)

treatment_protocol: at 14 d of age, chicks were injected i.p. with saline or Salmonella LPS. At 24 h post-injection, liver, intestine (jejunum) and skeletal muscle (breast) tissue samples were snap frozen in liquid nitrogen and stored at -80 oC for later RNA extraction and microarray analysis.

value: skeletal breast muscle

tag: status

value: VIRG birds

tag: breed

value: cobb 500 broiler chicken

value: 14 days


title: Muscle_saline injected chicken fed (VIRG (antibiotic)_ replica 6

description:
raw data file: Muscle Array_12.DAT
Slide 12_LPS chicken_prebiotic group_ replica 6 (Cy3) vs saline chicken_antibiotic group_ replica 6 (Cy5)


title: whole blood mRNA from patients presenting with MI (MM_MI_5_4)

value: MI


title: whole blood mRNA from patients presenting with MI (MM_MI_3_4)

value: blood


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 5

description:
raw data file: Muscle Array_11.DAT
Slide 11_saline chicken_antibiotic group_ replica 5 (Cy3) vs LPS chicken_prebiotic group_ replica 5 (Cy5)

source_name: Total RNA from skeletal muscles of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).

value: MOS birds


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 6

description:
raw data file: Muscle Array_10.DAT
Slide 10_LPS chicken_antibiotic group_ replica 6 (Cy3) vs saline chicken_prebiotic group_ replica 6 (Cy5)

source_name: Total RNA from skeletal muscles of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).


title: Genomic DNA from trisomy 21 fetal skin 3

description:
FT9_t21_skin
Trisomy 21 skin sample.

value: skin

value: fetal


title: Genomic DNA from trisomy 21 fetal skin 1

description:
FT1_t21_skin
Trisomy 21 skin sample.

value: female

value: trisomy 21


title: Genomic DNA from trisomy 21 fetal lung 5

description:
mT21-5_t21_lung
Trisomy 21 lung sample.

source_name: Fetal lung, trisomy 21

value: lung


title: Genomic DNA from trisomy 21 fetal skin 2

description:
FT8_t21_skin
Trisomy 21 skin sample.

value: male


title: CLL_non-del11q_rep9_case132

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

description: 50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 48 deg C with rotation at 60 rpm.  Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix GeneChip data were analyzed as described (Ouillette et al., Cancer Res. 2008;68:1012-21).  Raw probe-level data were converted to expression measures using the Robust Multi-array Average (RMA) method, which is implemented in the Affymetrix package of  Bioconductor (Izarry et al., Biostatistics. 2003;4:249-64; R version 2.7.0, Bioconductor Affymetrix package version 1.17.5). Briefly, the raw perfect match (PM) probes are first quartile normalized to reduce array-to-array variation. The normalized probe data are then converted to an expression measure (log scale) for each gene on each chip. For differential expression analysis relating to 11q deletion status, we used two-sample Z-tests to compare the mean log-scale expression level between del11q and non-del11q samples.  Genes with a False Discovery Rate (33) below 0.1 were selected, then fold-changes, FDR values, and Z-scores were used to identify genes having a strong association with 11q deletion status.
Robust multi-array average (RMA)-computed expression values (Izarry et al., Biostatistics, 4:249-64, 2003).  Note that the expression values are log2-transformed data.

source_name: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.

label_protocol: 50ng total RNA was amplified using the Ovation RNA Amplification system (NuGen, Inc.), labeled with the FL-Ovation cDNA Biotin module (NuGen, Inc.) and hybridized to the Human 133 2.0 plus GeneChip (Affymetrix) following the manufacturer's recommended protocols.

growth_protocol: Material used was cryopreserved primary human peripheral blood cells, prepared as below.

extract_protocol: CLL peripheral blood mononuclear cells were stained with propidium iodide and CD19*PE, then sorted  using a high-speed FACS Aria (Becton Dickinson) sorter to purity. RNA was extracted using the Trizol reagent. RNA was further purified using the RNAeasy kit (Qiagen).

tag: cell type

tag: del11q status

tag: treatment status prior to enrollment [ut = untreated; t = treated]

value: UT

tag: net insr expression by facs

tag: delta ctm insr-gapd

tag: zap70%+ mean

tag: igvh (98%) [um = unmutated; m = mutated]

value: UM

tag: FISH (>25% of nuclei)

value: normal

tag: FISH-all

tag: snp 6.0 total subchromosomal and chromosomal lesions


title: Genomic DNA from trisomy 21 fetal lung 2

description:
FT8_t21_lung
Trisomy 21 lung sample.

tag: gender

tag: tissue


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 3

description:
raw data file: Muscle Array_5.DAT
Slide 5_saline chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_prebiotic group_ replica 3 (Cy5)

tag: age


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 2

description:
raw data file: Muscle Array_6.DAT
Slide 6_LPS chicken_prebiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 2 (Cy5)


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 5

description:
raw data file: Muscle Array_9.DAT
Slide 9_saline chicken_prebiotic group_ replica 5 (Cy3) vs LPS chicken_antibiotic group_ replica 5 (Cy5)

source_name: Total RNA from skeletal muscles of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 3

description:
raw data file: Muscle Array_3.DAT
Slide 3_LPS chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 3 (Cy5)


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 4

description:
raw data file: Muscle Array_8.DAT
Slide 8_saline chicken_antibiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 4 (Cy5)


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 2

description:
raw data file: Muscle Array_4.DAT
Slide 4_LPS chicken_antibiotic group_ replica 4 (Cy3) vs LPS chicken_prebiotic group_ replica 2 (Cy5)


title: Genomic DNA from trisomy 21 fetal lung 3

description:
FT9_t21_lung
Trisomy 21 lung sample.

tag: developmental stage

tag: disease state


title: Genomic DNA from trisomy 21 fetal lung 4

description:
FT12_t21_lung
Trisomy 21 lung sample.


title: Muscle_saline injected chicken fed VIRG (antibiotic)_ replica 2

description:
raw data file: Muscle Array_2.DAT
Slide 2_LPS chicken_antibiotic group_ replica 2 (Cy3) vs saline chicken_antibiotic group_ replica 2 (Cy5)

tag: status


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 1

description:
raw data file: Muscle Array_1.DAT
Slide 1_saline chicken_antibiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 1 (Cy5)

tag: breed


title: CLL_non-del11q_rep5_case57

tag: cell type

value: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient

value: trisomy 12


title: CLL_non-del11q_rep6_case59

tag: del11q status

value: absent

value: M


title: Genomic DNA from trisomy 21 fetal lung 1

description:
FT1_t21_lung
Trisomy 21 lung sample.


title: CLL_non-del11q_rep7_case66

tag: treatment status prior to enrollment [ut = untreated; t = treated]


title: Genomic DNA from trisomy 21 fetal kidney 5

description:
mT21-5_t21_kidney
Trisomy 21 kidney sample.

source_name: Fetal kidney, trisomy 21

value: kidney


title: CLL_non-del11q_rep8_case77

value: T

tag: net insr expression by facs


title: CLL_non-del11q_rep4_case55

tag: delta ctm insr-gapd


title: Genomic DNA from trisomy 21 fetal kidney 4

description:
FT12_t21_kidney
Trisomy 21 kidney sample.


title: Genomic DNA from trisomy 21 fetal kidney 2

description:
FT8_t21_kidney
Trisomy 21 kidney sample.


title: Genomic DNA from trisomy 21 fetal kidney 3

description:
FT9_t21_kidney
Trisomy 21 kidney sample.


title: CLL_non-del11q_rep3_case27

tag: zap70%+ mean


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 6

source_name: Total RNA from skeletal muscles of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).

value: skeletal breast muscle

value: cobb 500 broiler chicken

value: 14 days


title: Muscle_saline injected chicken fed VIRG (antibiotic)_ replica 5

source_name: Total RNA from skeletal muscles of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).

value: VIRG birds


title: Muscle_saline injected chicken fed VIRG (antibiotic)_ replica 4


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 5

source_name: Total RNA from skeletal muscles of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).

value: MOS birds


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 3

description:
raw data file: Muscle Array_7.DAT
Slide 7_saline chicken_prebiotic group_ replica 3 (Cy3) vs saline chicken_antibiotic group_ replica 3 (Cy5)


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 4


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 6

source_name: Total RNA from skeletal muscles of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 2


title: Muscle_LPS injected chicken fed MOS (prebiotic)_ replica 1


title: Genomic DNA from trisomy 21 fetal kidney 1

description:
FT1_t21_kidney
Trisomy 21 kidney sample.

value: female

value: fetal

value: trisomy 21


title: Muscle_LPS injected chicken fed VIRG (antibiotic)_ replica 4

value: male


title: dorsal root ganglion_axotomised_7day_rep2

description: Biological 2 of 3

value: Male

tag: strain

value: Adult


title: Liver_LPS injected chicken fed MOS (prebiotic)_ replica 5

description:
raw data file: Liver Array_11.DAT
Slide 11_saline chicken_antibiotic group_ replica 5 (Cy3) vs LPS chicken_prebiotic group_ replica 5 (Cy5)

source_name: Total RNA from liver of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).

value: liver


title: Liver_LPS injected chicken fed VIRG (antibiotic)_ replica 5

description:
raw data file: Liver Array_9.DAT
Slide 9_saline chicken_prebiotic group_ replica 5 (Cy3) vs LPS chicken_antibiotic group_ replica 5 (Cy5)

source_name: Total RNA from liver of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).


title: Muscle_saline injected chicken fed VIRG (antibiotic)_ replica 1


title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 6

description:
raw data file: Liver Array_10.DAT
Slide 10_LPS chicken_antibiotic group_ replica 6 (Cy3) vs saline chicken_prebiotic group_ replica 6 (Cy5)

source_name: Total RNA from liver of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).


title: Muscle_saline injected chicken fed MOS (prebiotic)_ replica 1

description:
raw data file: Muscle Array_5.DAT
Slide 5_saline chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_prebiotic group_ replica 3 (Cy5)


title: Genomic DNA from trisomy 21 fetal brain 4

description:
mT21-5_t21_brain
Trisomy 21 brain sample.

source_name: Fetal brain, trisomy 21

value: brain


title: CLL_non-del11q_rep2_case19

description: 50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)

value: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient

tag: igvh (98%) [um = unmutated; m = mutated]

value: UM

tag: FISH (>25% of nuclei)

value: normal


title: CLL_del11q rep10_case173

source_name: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.

value: del11q present

value: T

value: M

tag: FISH-all

tag: snp 6.0 total subchromosomal and chromosomal lesions


title: Liver_saline injected chicken fed VIRG (antibiotic)_ replica 3

description:
raw data file: Liver Array_7.DAT
Slide 7_saline chicken_prebiotic group_ replica 3 (Cy3) vs saline chicken_antibiotic group_ replica 3 (Cy5)

source_name: Total RNA from liver of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).

tag: tissue

value: cobb 500 broiler chicken

tag: gender

value: 14 days


title: Liver_LPS injected chicken fed MOS (prebiotic)_ replica 3

description:
raw data file: Liver Array_5.DAT
Slide 5_saline chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_prebiotic group_ replica 3 (Cy5)

value: MOS birds

tag: age


title: Genomic DNA from trisomy 21 fetal brain 2

description:
FT9_t21_brain
Trisomy 21 brain sample.

tag: developmental stage

tag: disease state


title: Liver_LPS injected chicken fed MOS (prebiotic)_ replica 2

description:
raw data file: Liver Array_4.DAT
Slide 4_LPS chicken_antibiotic group_ replica 4 (Cy3) vs LPS chicken_prebiotic group_ replica 2 (Cy5)

tag: status

tag: breed


title: Genomic DNA from trisomy 21 fetal brain 1

description:
FT8_t21_brain
Trisomy 21 brain sample.


title: CLL_non-del11q_rep1_case17

tag: cell type

tag: del11q status

value: absent


title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 2

description:
raw data file: Liver Array_6.DAT
Slide 6_LPS chicken_prebiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 2 (Cy5)


title: CLL_del11q rep8_case155

tag: treatment status prior to enrollment [ut = untreated; t = treated]

value: UT

tag: net insr expression by facs


title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 4

description:
raw data file: Liver Array_8.DAT
Slide 8_saline chicken_antibiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 4 (Cy5)


title: CLL_del11q rep9_case171

tag: delta ctm insr-gapd

tag: zap70%+ mean


title: Genomic DNA from trisomy 21 fetal brain 3

description:
FT12_t21_brain
Trisomy 21 brain sample.

value: female

value: fetal

value: trisomy 21


title: CLL_del11q rep7_case103

tag: igvh (98%) [um = unmutated; m = mutated]


title: CLL_del11q rep5_case81

tag: FISH (>25% of nuclei)


title: Liver_LPS injected chicken fed VIRG (antibiotic)_ replica 3

description:
raw data file: Liver Array_3.DAT
Slide 3_LPS chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 3 (Cy5)

value: VIRG birds

value: male


title: CLL_del11q rep6_case101

tag: FISH-all


title: Liver_saline injected chicken fed VIRG (antibiotic)_ replica 5

source_name: Total RNA from liver of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).

value: liver


title: Liver_LPS injected chicken fed VIRG (antibiotic)_ replica 1

description:
raw data file: Liver Array_1.DAT
Slide 1_saline chicken_antibiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 1 (Cy5)


title: Liver_LPS injected chicken fed VIRG (antibiotic)_ replica 6

source_name: Total RNA from liver of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).


title: Genomic DNA from normal fetal skin 6

description:
mT4-5_N_skin
Normal skin sample.

source_name: Fetal skin, normal

value: skin


title: Genomic DNA from normal fetal skin 5

description:
FT13_N_skin
Normal skin sample.