title: HN093_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN093

tag: tissue

value: Tumor

value: Caucasian

value: Male

value: Oropharynx

value: IVa

value: HPV+


title: colon_epithelium_C57mouse_6weeks_rep5

status: Public on Mar 01 2013

type: RNA

city: Palmerston North

first: Anna

last: Moore

address: Tennent Drive

country: New Zealand

institute: AgResearch Ltd

description: Sample 41

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed. All steps were performed according to the manufacturer instructions - protocol G4140-90050_Hyb_Label_two-colour_GE_v5.5.

scan_protocol: Scanned on an Agilent G2565AA scanner and images were quantified using Agilent Feature Extraction Software (version 8.5.1.1 (samples 1-24) or 10.10.1.1 (samples 24-47)).

data_processing:
Cy5 and Cy3 intensity ratios for all microarray spots were normalized using a global loess algorithm using the limma package in R 2.14.1.  No background correction was applied. Spots that did not pass quality control metrics were flagged and removed from the normalisation calculations.
Note that samples 1-24 were analysed as one experiment, and samples 25-47 were analysed as another up to generation of differentially expressed gene lists. These two sets of arrays cannot be directly compared due to the different amplification procedure required for samples 25-48 due to starting material limitations.

molecule: total RNA

organism: Mus musculus

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

label_protocol: For channel 1, all samples, and channel 2, samples 1-24, 500 ng total RNA was amplified according to the Agilent protocol protocol G4140-90050_Hyb_Label_two-colour_GE_v5.5. For channel 2 samples 25-47, 30 ng total RNA was amplified using 2 rounds of amplification by the Arcturus RiboAmp Plus kit and labelled using the Arcturus Turbo Labelling kit.

growth_protocol: Male mice of C57BL/6J background with or without IL10 gene knockout were kept in conventional conditions (not germ-free or specific-pathogen-free) from approximately 5 weeks of age and inoculated with a mixture of Enteroccocus strains and complex intestinal flora harvested from C57BL/6J mice kept in conventional conditions. Mice were fed AIN76A diet and euthanased by CO2 followed by cervical dislocation.

extract_protocol: Total RNA was extracted from frozen colon samples using Trizol according to the manufacturer instructions followed by cleanup with Qiagen RNeasy columns according to manufacturer instructions for all channel 1 samples and samples 1-24 of channel 2. Total RNA was extracted from frozen microdissected colon epithelial cells using the Arcturus Picopure RNA extraction kit for channel 2 samples 25-48.

tag: strain

value: Swiss

source_name: colon epithelium, C57 mouse, 6 weeks

tag: genotype/variation

value: wildtype

tag: sampling age

value: 6 weeks

value: colon epithelium


title: C6 site sediment DNA [C6 Sept 2008]

type: mixed

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

country: USA

institute: Boston University

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 65°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes, and the Cy3/Cy5 was not at least 1% of the total amoA signal from all 31 probes.

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard 20-mer

label_protocol: Hybridization targets were prepared from whole DNA amplified with random primers. Briefly, the cleaned products were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.9 mM d(AGC)TP, 0.4 mM dTTP, and 4.8 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (200 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: Total DNA extracted using BIO 101 following manufacturer's instructions

tag: sample type

value: Universal Internal Standard 20-mer

molecule: genomic DNA

organism: uncultured ammonia-oxidizing archaeon

source_name: C6 site sediment DNA

value: environmental sample


title: LNCaP-shControl-DHT-B

first: Esther

last: Baena

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Childrens Hospital Boston

description: LNCaP cells transfected with shControl were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.

label: biotin

organism: Homo sapiens

source_name: LNCaP cells

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

growth_protocol: Normal growth conditions

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

treatment_protocol: VCaP or LNCao cells were transfected with siRNA or shRNA, and then grown in hormone deprived conditions for 2 days, and then in the presence of EtOH or 10nM DHT.

tag: cell line

value: LNCaP

value: prostate

tag: tumor stage

value: androgen-dependent cancer cell

tag: treatment

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT


title: colon_epithelium_C57 mouse_12weeks_rep4

description: Sample 40

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: colon epithelium, C57 mouse, 12 weeks

value: 12 weeks


title: C6 site sediment DNA [C6 July 2008]


title: C6 site sediment DNA [C6 Jan 2009]


title: HN091_Affymetrix_GenomeWide_SNP6.0

type: genomic

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

description: Hybridized to SNP6

hyb_protocol: Method 2, as outlined in the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide, with the following changes:  A Bio-Rad DNA Engine PCR machine is used in the specified thermal cycler program.  Four samples are loaded onto four arrays, the septa is covered with tough spots, and the arrays are placed into the hybridization oven.  This is continued in four-array blocks until all of the arrays are loaded in the oven.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, then scanned with an Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader.

data_processing: CEL files were processed using the 'aroma R package, and log_2 copy numbers were produced using a reference of pooled normal samples.  Missing values were imputed using the nearest non-missing value.  Segmentation was performed using the DNAcopy R package.  The resulting copy number profiles were median centered and smoothed.

label: Biotin

source_name: Head and neck squamous cell carcinoma HN091

label_protocol: Labeling was performed as per the manufacturer's instructions in the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide.

growth_protocol: Not applicable

extract_protocol: 1. Collect the saved flow-through from RNA extract with Qiagen’s  RNeasy kit, add 100% EtOH –about 1/3 volume of flow through, mix well and freeze at -20C for 1-2 hours.  2. Spin for 15’ at 10,000 RPM in cold room. Discard the supernatant and re-suspend pellet in ATL buffer from Qiagen’s  QiaAMP DNA mini kit, proceed following the manufactory’s protocol.  3. DNA quantity was measured with nano-drop and DNA quality was checked by running agarose gel.

treatment_protocol: Not applicable

value: Tumor

tag: age

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

tag: tumor status

tag: node status

value: Surgery Alone

tag: hpv status

value: HPV-


title: colon_epithelium_C57mouse_6weeks_rep4

description: Sample 39

tag: strain

value: Swiss

tag: tissue

tag: genotype/variation

value: wildtype

value: 6 weeks


title: HN090_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN090

value: Female

value: Heavy

value: Larynx

value: IVa

value: Concurrent Chemoradiation


title: Deepwater Horizon site sediment DNA [DWH May 2011-1]

tag: sample type

value: Universal Internal Standard 20-mer

source_name: Deepwater Horizon site sediment DNA

value: environmental sample


title: Control site sediment DNA [CT May 2011]

source_name: Control site sediment DNA


title: LNCaP-shETV1-EtOH-B

description: LNCaP cells transfected with shETV1 were grown in androgen deprived serum for 2 days and then in the presence of EtOH (vehicle)

tag: cell line

value: LNCaP

value: prostate

tag: tumor stage

value: androgen-dependent cancer cell


title: colon_epithelium_IL10mouse_6weeks_rep4

description: Sample 38

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: colon epithelium, IL10 mouse, 6 weeks

tag: sampling age

value: colon epithelium


title: LNCaP-shETV1-EtOH-C

tag: treatment

value: transfected with shETV1 were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: HN089_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN089

value: Tumor

tag: age

tag: race

value: Caucasian

tag: gender

value: None or Light/Moderate

value: Poor

value: Surgery and Concurrent Chemoradiation

value: HPV-


title: colon_epithelium_IL10mouse_6weeks_rep3

description: Sample 36

value: Swiss

value: 6 weeks


title: LNCaP-shETV1-EtOH-A


title: Control site sediment DNA [CT Aug 2010]


title: colon_epithelium_IL10mouse_12weeks_rep4

description: Sample 37

source_name: colon epithelium, IL10 mouse, 12 weeks

value: 12 weeks


title: LNCaP-shControl-DHT-A

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT


title: HN087_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN087

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

value: Oropharynx

value: IVc

value: Concurrent Chemoradiation


title: colon_epithelium_C57 mouse_12weeks_rep3

description: Sample 35

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: wildtype

value: colon epithelium


title: Control site sediment DNA [CT Jan 2009]

value: Universal Internal Standard 20-mer

value: environmental sample


title: colon_epithelium_C57mouse_6weeks_rep3

description: Sample 34


title: HN088_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN088

value: Tumor

value: Caucasian

value: None or Light/Moderate

tag: tumor site

tag: Stage

value: IVa

tag: tumor status

value: HPV+


title: LNCaP-shControl-EtOH-B

description: LNCaP cells transfected with shControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH (vehicle)

value: LNCaP

value: prostate

value: androgen-dependent cancer cell

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: colon_epithelium_IL10mouse_12weeks_rep2

description: Sample 32

tag: strain

value: Swiss

value: 12 weeks


title: Control site sediment DNA [CT Aug 2009]


title: Control site sediment DNA [CT Sept 2008]


title: HN084_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN084

tag: tissue

value: Male

value: Moderate

value: Hypopharynx

tag: node status

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-


title: HN085_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN085

value: Poor

value: Oral Cavity

value: III


title: colon_epithelium_IL10mouse_12weeks_rep3

description: Sample 33

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

tag: genotype/variation

value: colon epithelium


title: LNCaP-shControl-EtOH-A

tag: cell line

tag: tumor stage


title: Control site sediment DNA [CT July 2008]

tag: sample type

value: Universal Internal Standard 20-mer

value: environmental sample


title: VCaP-siERG-DHT-A

description: VCaP cells transfected with siERG were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT

source_name: VCaP cells

value: VCaP

tag: treatment


title: HN075_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN075

value: Tumor

tag: age

tag: race

value: Caucasian

value: None or Light/Moderate

value: Oropharynx

value: Surgery and Radiation

value: HPV+


title: VCaP-siERG-DHT-B

value: prostate

value: androgen-dependent cancer cell

value: transfected with siERG were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT


title: HN086_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN086

value: African American

tag: gender

value: Male

tag: smoking packyears

value: Heavy

value: Well

value: I

value: Surgery Alone

value: HPV-


title: VCaP-siERG-DHT-C

value: VCaP


title: colon_epithelium_C57 mouse_12weeks_rep2

description: Sample 30

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: wildtype

tag: sampling age

value: 12 weeks

value: colon epithelium


title: 250ng 16S rRNA gene amplicon of faecal sample 205

type: other

city: Clermont-Ferrand

first: Nicolas

last: Parisot

address: 28 place Henri Dunant

country: France

institute: EA 4678 CIDAM

description:
16S rRNA gene amplified from gDNA extracted from faecal samples of elderly patients.
Sample name: Faecal 205

hyb_protocol: For microarray hybridization, 250ng of each labelled faecal sample were used. Hybridization was performed following the Agilent OligoaCGH hybridization protocol (Agilent Technologies, Palo Alto, CA) at 65°C for 24h.

scan_protocol: slides were scanned at a 3-µm resolution using a Surescan microarray scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Pixel intensities were extracted using the “Feature Extraction” software (Agilent Technologies, Palo Alto, CA). No normalization step was performed and the retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.

organism: uncultured bacterium

source_name: faecal sample 205, elderly patient

label_protocol: For each sample (faecal samples and the mock community), the purified 16S rRNA gene PCR products (1 µg) were labelled with either Cy3 or Cy5 using the Genomic DNA ULS labelling Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

growth_protocol: Faecal samples were collected by the Department of Microbiology and Alimentary Pharmabiotic Centre (Cork, Ireland) from three elderly patients (176, 204 and 205).

extract_protocol: Total DNA was extracted from three human faecal samples using Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). Total genomic DNA was extracted from pure bacterial cultures using DNeasy Blood and Tissue Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w/v) agarose gel and were purified using the MinElute PCR Purification Kit (Qiagen Ltd., UK) following manufacturer’s instructions and stored at -20°C.

treatment_protocol: No treatment were studied in this experience

value: faecal sample


title: VCaP-siControl-DHT-C

description: VCaP cells transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT

value: prostate


title: colon_epithelium_C57mouse_6weeks_rep2

description: Sample 31

source_name: colon epithelium, C57 mouse, 6 weeks

value: 6 weeks


title: 250ng 16S rRNA gene amplicon of faecal sample 204

description:
16S rRNA gene amplified from gDNA extracted from faecal samples of elderly patients.
Sample name: Faecal 204

source_name: faecal sample 204, elderly patient


title: LNCaP-shControl-EtOH-C

source_name: LNCaP cells

value: LNCaP

value: androgen-dependent cancer cell

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: colon_epithelium_IL10mouse_6weeks_rep2

description: Sample 29


title: HN076_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN076

value: Tumor

value: Caucasian

value: Female

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Poor

tag: tumor site

value: Hypopharynx

value: IVa

value: Concurrent Chemoradiation


title: Control site sediment DNA [CT May 2010]

source_name: Universal Internal Standard 20-mer

value: Universal Internal Standard 20-mer

source_name: Control site sediment DNA

value: environmental sample


title: 250ng 16S rRNA gene amplicon of faecal sample 176

description:
16S rRNA gene amplified from gDNA extracted from faecal samples of elderly patients.
Sample name: Faecal 176

hyb_protocol: For microarray hybridization, 100 ng of labelled artificial bacterial DNA mix and 250ng of each labelled faecal sample were used. Hybridization was performed following the Agilent OligoaCGH hybridization protocol (Agilent Technologies, Palo Alto, CA) at 65°C for 24h.

source_name: faecal sample 176, elderly patient

growth_protocol: Faecal samples were collected by the Department of Microbiology and Alimentary Pharmabiotic Centre (Cork, Ireland) from three elderly patients (176, 204 and 205). The mock community was performed after culture of each individual bacterial strain in their reference medium at their optimal temperature for several days.

extract_protocol: Total DNA was extracted from three human faecal samples using  Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). Total genomic DNA was extracted from pure bacterial cultures using DNeasy Blood and Tissue Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w/v) agarose gel and were purified using the MinElute PCR Purification Kit (Qiagen Ltd., UK) following manufacturer’s instructions and stored at -20°C.


title: 100ng 16S rRNA gene amplicon of a mock community

description:
16S rRNA gene amplified from gDNA extracted from bacterial strains.
Sample name: Mock community

organism:
Escherichia coli
Bacteroides fragilis
[Clostridium] leptum
Lactobacillus acidophilus
Blautia producta

source_name: Mock community

value: mock community [artificial bacterial DNA mix]


title: HN074_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN074

value: African American

value: Male

tag: Stage

tag: tumor status

value: Surgery Alone

value: HPV-


title: colon_epithelium_C57mouse_6weeks_rep1

description: Sample 28

tag: strain

value: Swiss

tag: tissue

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: wildtype

value: 6 weeks

value: colon epithelium


title: VCaP-siControl-DHT-B

value: VCaP

value: prostate

value: androgen-dependent cancer cell

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT


title: colon_epithelium_IL10mouse_12weeks_rep1

description: Sample 27

source_name: colon epithelium, IL10 mouse, 12 weeks

tag: genotype/variation

value: 12 weeks


title: VCaP-siERG-EtOH-C

description: VCaP cells transfected with siERG were grown in androgen deprived serum for 2 days and then in the presence of EtOH (vehicle)

tag: cell line


title: HN072_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN072

value: Tumor

value: Caucasian

value: None or Light/Moderate

value: Well

value: Oral Cavity

value: IVa

tag: node status

tag: hpv status


title: VCaP-siControl-DHT-A

tag: tumor stage

tag: treatment


title: HN067_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN067

tag: age

tag: race

value: Male

value: Poor

value: III

value: Surgery and Concurrent Chemoradiation

value: HPV-


title: colon_epithelium_IL10mouse_6weeks_rep1

description: Sample 26

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

value: Swiss

source_name: colon epithelium, IL10 mouse, 6 weeks

value: 6 weeks

value: colon epithelium


title: VCaP-siERG-EtOH-B

source_name: VCaP cells

value: VCaP

value: prostate

value: androgen-dependent cancer cell

value: transfected with siERG were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: colon_epithelium_C57 mouse_12weeks_rep1_1

description: Sample 25

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: colon epithelium, C57 mouse, 12 weeks

value: wildtype

value: 12 weeks


title: VCaP-siERG-EtOH-A


title: VCaP-siControl-EtOH-C

description: VCaP cells transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH (vehicle)


title: colon_C57 mouse_12weeks_rep6

description: Sample 23

source_name: colon, C57 mouse, 12 weeks

value: colon


title: HN064_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN064

value: Tumor

value: Caucasian

tag: gender

value: Female

tag: smoking packyears

value: None or Light/Moderate

value: Moderate

value: Oropharynx

value: IVa

value: Concurrent Chemoradiation

value: HPV+


title: colon_IL10mouse_6weeks_rep6

description: Sample 24

value: Swiss

source_name: colon, IL10 mouse, 6 weeks

tag: sampling age

value: 6 weeks


title: HN070_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN070

value: African American

value: Male

tag: alcohol use

value: Heavy

tag: differentiation

value: II

value: Unknown

value: HPV-


title: VCaP-siControl-EtOH-B

value: VCaP

value: prostate

value: androgen-dependent cancer cell

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: RWPE-1-ERG-C

description: control cells expressing BirA and ERG

source_name: RWPE-1 cells

treatment_protocol: RWPE-1 cells were transduced with MSCV retroviruses, and selected to obtain stable clones.

tag: expression

value: BirA and ERG

value: Non-tumorigenic


title: HN066_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN066

value: Tumor

value: Caucasian

value: Female

value: None or Light/Moderate

value: Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

tag: tumor status

value: Surgery Alone


title: colon_C57mouse_6weeks_rep6

description: Sample 22

tag: strain

value: Swiss

tag: tissue

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: colon, C57 mouse, 6 weeks

tag: genotype/variation

value: wildtype

value: 6 weeks

value: colon


title: colon_IL10mouse_12weeks_rep6

description: Sample 21

source_name: colon, IL10 mouse, 12 weeks

value: 12 weeks


title: HN068_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN068

value: Male

value: IVa

tag: node status

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: HPV-


title: HN065_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN065

value: Tumor

value: Heavy

value: Well

tag: treatment

value: Concurrent Chemoradiation


title: RWPE-1-ERG-B

description: control cells expressing BirA and ERG

value: prostate

tag: cell line

value: BirA and ERG

tag: tumor stage

value: Non-tumorigenic


title: HN062_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN062

tag: age

tag: race

value: Caucasian

tag: gender

value: Female

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

value: III

value: Surgery and Radiation


title: colon_IL10mouse_12weeks_rep5

description: Sample 20

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

tag: sampling age

value: 12 weeks

value: colon


title: HN069_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN069

value: Tumor

value: African American

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Poor

value: Larynx

value: II


title: colon_C57mouse_6weeks_rep5

description: Sample 19

value: wildtype

value: 6 weeks


title: VCaP-siControl-EtOH-A

value: VCaP

value: prostate

value: androgen-dependent cancer cell

value: transfected with siControl were grown in androgen deprived serum for 2 days and then in the presence of EtOH


title: RWPE-1-ERG-A

description: control cells expressing BirA and ERG

tag: expression

value: BirA and ERG

value: Non-tumorigenic


title: RWPE-1-ETV1-D

description: control cells expressing BirA and ETV1

value: BirA and ETV1


title: HN063_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN063

value: Caucasian

value: None or Light/Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

value: III

tag: tumor status

value: Concurrent Chemoradiation

value: HPV-


title: HN060_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN060

tag: tissue

value: Tumor

value: Male

value: Moderate


title: colon_C57 mouse_12weeks_rep5

description: Sample 18

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

tag: strain

value: Swiss

tag: genotype/variation

value: wildtype

value: 12 weeks

value: colon


title: colon_IL10mouse_6weeks_rep5

description: Sample 17

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: 6 weeks


title: RWPE-1-ETV1-C

description: control cells expressing BirA and ETV1

value: prostate

value: Non-tumorigenic


title: HN057_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN057

value: African American

value: Heavy

value: Oropharynx

value: IVa

tag: node status

tag: treatment

tag: hpv status


title: colon_IL10mouse_12weeks_rep4

description: Sample 15


title: RWPE-1 -control-C

description: control cells expressing BirA

tag: cell line

value: BirA

tag: tumor stage


title: RWPE-1-control-B

description: control cells expressing BirA


title: colon_C57mouse_6weeks_rep4

description: Sample 16


title: colon_IL10mouse_6weeks_rep4

description: Sample 14


title: HN061_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN061

tag: age

tag: race

tag: gender

value: Well

value: III

value: Concurrent Chemoradiation

value: HPV-


title: colon_C57 mouse_12weeks_rep4

description: Sample 13

value: Swiss

source_name: colon, C57 mouse, 12 weeks

tag: sampling age


title: RWPE-1-ETV1-B

description: control cells expressing BirA and ETV1

value: BirA and ETV1


title: RWPE-1- control-A

description: control cells expressing BirA


title: colon_C57 mouse_12weeks_rep3

description: Sample 12

value: wildtype

value: 12 weeks


title: HN059_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN059

value: Tumor

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

value: I

value: Surgery Alone


title: HN056_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN056

value: Heavy

tag: tumor site

value: Larynx

tag: Stage

value: IVa

value: Surgery and Concurrent Chemoradiation


title: GBM 5

city: Nanjing

first: Huibo

last: Wang

state: Jiangsu

address: 300# Guangzhou Rd.

department: Department of Neurosurgery

country: China

institute: First Affiliated Hospital of Nanjing Medical University

description: miRNA expression of primary glioma cells isolated from GBM tissues

hyb_protocol: Cy3-labeled RNA was hybridized to microarrays overnight at 65°C in a hybridization mixture. Slides were washed in SSC at increasing stringency (from 2× to 0.4×).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to  Hi 100% and Lo 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 021827_D_F_20091031) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GBM

label_protocol: Total RNA was 3' end labeled using T4 RNA ligase to couple Cy3-labeled RNA linkers.

growth_protocol: Paired primary glioma cells and astrocytes was cultured according to the methods described in a previous study (Soroceanu et al., 2001)

extract_protocol: Total RNA from cultured cells was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions.

tag: tissue

value: brain


title: GBM 4


title: HN048_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN048

value: Well

value: Oral Cavity

tag: tumor status

value: HPV-


title: GBM 6


title: colon_IL10mouse_6weeks_rep2

description: Sample 8

tag: strain

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: colon, IL10 mouse, 6 weeks

tag: genotype/variation

value: 6 weeks

value: colon


title: GBM 3


title: GBM 2


title: colon_C57mouse_6weeks_rep3

description: Sample 9

source_name: colon, C57 mouse, 6 weeks

value: wildtype


title: HN049_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN049

value: Tumor

value: African American

value: Male

value: Oropharynx

tag: node status

tag: treatment


title: colon_IL10mouse_6weeks_rep3

description: Sample 11


title: RWPE-1-ETV1-A

description: control cells expressing BirA and ETV1

source_name: RWPE-1 cells

value: prostate

tag: cell line

tag: expression

value: BirA and ETV1

value: Non-tumorigenic


title: colon_IL10mouse_12weeks_rep2

description: Sample 7

source_name: colon, IL10 mouse, 12 weeks

value: 12 weeks


title: GBM 1

value: brain


title: HN047_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN047

tag: age

value: Heavy

value: Moderate

value: IVa

value: Concurrent Chemoradiation

tag: hpv status


title: HN045_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN045

tag: race

value: Caucasian

tag: gender

value: None or Light/Moderate

value: Larynx

value: III

value: HPV-


title: HN046_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN046

value: Tumor

value: Female

tag: smoking packyears

value: Well

value: Oral Cavity


title: colon_C57 mouse_12weeks_rep2

description: Sample 6

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: wildtype

tag: sampling age

value: colon


title: colon_IL10mouse_12weeks_rep3

description: Sample 10

value: 12 weeks


title: non-tumor tissue 5

description: miRNA expression of astrocytes isolated from peripheral non-tumor glial brain tissues

value: brain


title: HN055_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN055

value: African American

value: Male

tag: alcohol use

value: Heavy

tag: differentiation

value: Moderate

value: IVa

value: HPV+


title: non-tumor tissue 6

source_name: peripheral non-tumor glial brain tissues


title: non-tumor tissue 4


title: HN044_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN044

value: Caucasian

tag: tumor site

tag: Stage

value: Surgery and Concurrent Chemoradiation

value: HPV-


title: colon_C57 mouse_12weeks_rep1

description: Sample 4

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

tag: tissue


title: colon_C57mouse_6weeks_rep2

description: Sample 5

tag: strain

value: 6 weeks


title: HN042_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN042

value: Tumor

value: None or Light/Moderate

value: Hypopharynx

tag: tumor status

value: Surgery Alone


title: colon_C57mouse_6weeks_rep1

description: Sample 3

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

tag: genotype/variation

value: wildtype

value: colon


title: non-tumor tissue 1

value: brain


title: colon_IL10mouse_12weeks_rep1

description: Sample 1

value: 12 weeks


title: colon_IL10mouse_6weeks_rep1

description: Sample 2


title: HN041_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN041

value: African American

value: Male

value: Heavy

value: Moderate

value: Oral Cavity

tag: node status

tag: treatment


title: HN040_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN040

value: Caucasian

value: IVa

value: Surgery and Concurrent Chemoradiation

value: HPV-


title: HN043_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN043

value: Tumor

value: Female

value: None or Light/Moderate

value: Poor

value: Hypopharynx

value: Concurrent Chemoradiation


title: non-tumor tissue 2

value: brain


title: HN038_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN038

value: Oropharynx


title: Con

city: Harbin

first: Shan

address: 2 Yikuang Street, Nangang District

institute: Harbin Institute of Technology

description: Gene expression after transfected with pcDNA3.1 vector

hyb_protocol: 1.65 μl of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 37°C prewarmed Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Then export data to txt type file.

source_name: NIH3T3 with pcDNA3.1 vector

label_protocol: One microgram RNA was labeled with Cyanine-3 (Cy3) using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit purification (QIAGEN). Yield and specific activity were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NIH3T3 cells were grown under 5% CO2 at 37ºC in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 100 units/ml penicillin/streptomycin.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen) and purified by RNeasy Mini Kit (Qiagen). The purity and quantity of RNA was determined by measuring the A260/A280 ratio on a NanoDrop ND-1000.

treatment_protocol: MARVELD1 was transfected into NIH3T3 cells and stable cell lines were screened by G418.

tag: transfection

value: pcDNA3.1 vector

tag: cell line


title: HN039_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN039

tag: age

value: Male

tag: hpv status


title: H.zea_48 hpi_replicate 1

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description:
Gene expression of H. zea cell line at 48 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983).

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix AX AGP 4000B. Data were extracted from images using GenePix Pro version 6.0 with local background estimation.

data_processing: Normalization was performed between arrays using the Spike-in control method. Correction for multiple hypothesis testing in the linear model was performed using Benjamini-Hochberg method. The emperical bayes method within limma was used for significant events detection, with false discovery rate lower than 5%. The normalized data is not included in the gProcessedSignal column in the raw Agilent feature extraction files.They are in the processed data matrix.

organism: Helicoverpa zea

source_name: H.zea cells infected by HearSNPV virus at 48 hour post infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Low Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA) and assessed by Agilent 2100 bioanalyzer

growth_protocol: H.zea cells were typically cultivated in 250 ml Erlenmeyer flasks containing 50-100 ml of VPM3 medium at 28 degree C, and grown on an orbital shaker operating at 120 rpm. Cells were routinely passaged twice a week, with a seeding cell density of 2-4x1E5 cells/ml.

extract_protocol: Samples containing 5x1E5 H. zea (HzAM1) cells (Mcintosh and Ignoffo, 1983), grown in shaker-flask suspension cultures using serum free insect medium (VPM3), were collected for total RNA extraction and DNA removal using the Qiagen RNAeasy extraction and on-column DNAse kit (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 5x1E9 caterpillar purified OB are digested with an alkaline solution for 30 minutes, neutralized by the addition of VPM3,  filter sterilized and inoculated to a total culture volume of 100 ml containing H.zea cells at 5x105 cells/ml. Passage 1, (P1), BV harvested at 4 d.p.i. was used for P2 virus production at 17 pfu/cell.

tag: insect cell line

value: Helicoverpa zea cell line (HzAM1)

tag: virus

value: Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV)

tag: hours post infection (hpi)


title: H.zea_48 hpi_replicate 2


title: ERKO, epithelium, EE2 biological rep 2

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to EE2 (10 ng/kg) from E8 to E19

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were scaled using Affymetrix GCOS (target intensity = 500).

label_protocol: Total RNA specimens (~10 ng) were amplified using Ovation Pico WTA System (NuGen), and the cDNA products were biotin labeled using Encore Biotin Module (NuGen).

extract_protocol: Ductal epithelial and peri-ductal stromal components of E19 fetal mammary glands were laser-captured from hematoxylin-stained frozen sections and subjected to total RNA extraction using Arcturus PicoPure RNA Isolation Kit.

treatment_protocol: Pregnant mice were exposed to BPA (250 ng/kg), EE2 (10 ng/kg), or vehicle from E8 until E19.

tag: background strain

tag: genotype

value: ER-alpha knockout null

tag: Sex

value: female

tag: exposure

value: fourth inguinal mammary gland


title: non-tumor tissue 3

tag: tissue


title: ERKO, epithelium, BPA, biological rep 3

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to BPA (250 ng/kg) from E8 to E19


title: MD1

description: Gene expression after transfected with pcDNA3.1-MARVELD1 plasmid

source_name: NIH3T3 with MARVELD1


title: H.zea_24 hpi_replicate 1

description:
Gene expression of H. zea cell line at 24 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.

source_name: H.zea cells infected by HearSNPV virus at 24 hour post infection


title: HN036_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN036

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

value: IVa


title: HN034_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN034

value: Tumor

tag: age

value: None or Light/Moderate

value: Larynx

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

value: HPV+


title: HN035_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN035

value: Well

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-


title: H.zea_12 hpi_replicate 1

description:
Gene expression of H. zea cell line at 12 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983).

source_name: H.zea cells infected by HearSNPV virus at 12 hour post infection

tag: insect cell line

value: Helicoverpa zea cell line (HzAM1)

tag: virus

value: Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV)

tag: hours post infection (hpi)


title: Sample 3 Posterior  +/+

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

state: IL

institute: universty of Chicago

description:
S3PosPls
slide barcode: 251486826533
US80900103_251486826533_S01_GE1_105_Dec08_1_2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C US80900103) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain median background subtracted mean signal of the spot.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Posterior_wild type

label_protocol: Cy3 labeled cRNA was created using the agilent quick-amp RNA labeling kit with RNA spike-in, followed by purification using a QIAGEN RNeasy kit.  0.5 ug was used for each sample, and the labeling was validated using a nanodrop spectrometer.

growth_protocol: To get the Shh -/- mice, shh +/- female mice on mixed background were superovulated using 5 units each pregnant mare serum gonadotropin (PMS-G) and human chorionic gonadotropin (HCG) administered 48 hours apart.  They were mated to Shh +/- male mice after HCG administration.  Embryos were isolated  at E9.5.

extract_protocol: RNA was extracted from pooled, homogenized SHF tissues using the QIAGEN RNeasy kit following the manufacturer's recommendations.  The protocol includes an on-column DNase treatment.  RNA was quantified using a Nanodrop ND-1000 spectrometer and quality was checked using an agilent bioanalyzer.

treatment_protocol: Posterior and anterior second heart field (SHF) tissues were isolated from each embryo and stored in RNAlater RNA stabilization reagent (QIAGEN) at 4 °C.  Non-cardiac tissues were saved for genotyping.  After genotyping, Shh -/-  and Shh +/+ embryos were pooled, homogenized and RNA extracted.

tag: genotype/variation

value: C56B/6 and CD-1 mixed

tag: strain background

value: wild type

value: E9.5 embryos

tag: microdissection

value: posterior second heart field


title: ERKO, epithelium, BPA, biological rep 1

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to BPA (250 ng/kg) from E8 to E19

tag: background strain

tag: genotype

value: ER-alpha knockout null

tag: Sex

value: female

tag: exposure

tag: tissue

value: fourth inguinal mammary gland


title: HN026_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN026

value: Tumor

tag: race

value: African American

tag: gender

value: Female

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Poor

tag: tumor site

tag: Stage

value: I

value: Surgery Alone


title: H.zea_12 hpi_replicate 2

tag: insect cell line

tag: virus


title: H.zea_0 hpi_replicate 2

description:
Gene expression of H. zea cell line at 0 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.

source_name: H.zea cells infected by HearSNPV virus at 0 hour post infection

tag: hours post infection (hpi)


title: Sample 4 Posterior  +/+

description:
S4PosPls
slide barcode: 251486826534
US80900103_251486826534_S01_GE1_105_Dec08_1_2

tag: genotype/variation

tag: strain background

tag: age


title: ERKO, epithelium, control, biological rep 3

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to vehicle

tag: background strain

tag: genotype

value: vehicle


title: ERKO, epithelium, EE2 biological rep 1

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to EE2 (10 ng/kg) from E8 to E19

tag: Sex

tag: exposure


title: Sample 4 Posterior  -/-

description:
S4PosMns
slide barcode: 251486826534
US80900103_251486826534_S01_GE1_105_Dec08_1_1

source_name: Posterior_Shh mutant

value: Shh mutant

tag: tissue

tag: microdissection


title: ERKO, epithelium, BPA, biological rep 2


title: HN024_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN024

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

value: Oral Cavity

value: IVa

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

tag: hpv status

value: HPV-


title: HN028_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN028

value: Unknown

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

tag: tumor site

value: Larynx

tag: Stage

value: Concurrent Chemoradiation


title: HN023_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN023

value: Tumor

tag: age

value: Surgery and Concurrent Chemoradiation


title: HN027_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN027

value: Female

value: Well

value: Oropharynx


title: Noninfected_Cell_control_18_hour

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: miRNA expression in lung epithelial cells after 18 hours of incubation.

hyb_protocol: Labeled RNA was purified and hybridized to Agilent miRNA arrays with eight identical arrays per slide, with each array containing probes interrogating 866 human miRNAs.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent Technologies) using the standard settings for 8x15k array slides.

data_processing: Fluorescence intensity was calculated using Feature Extraction software (Vsn. 10.5.1.1, Agilent) and analysis performed using Genespring GX (Agilent) and Excel (Microsoft, WA). GeneSpring defaults with the percentile shift to the 50th percentile; hence raw signal to 1.0, normalisation by percentile shift to the 50th percentile, and no baseline transformation.

source_name: 18 hour cell control

label_protocol: MiRNAs were labeled using the Agilent miRNA labeling reagent and hybridized to Agilent human miRNA arrays according to the manufacturer’s protocol. Briefly, total RNA (100 ng) was dephosphorylated and ligated with 3', 5'-cytidine bisphosphate (pCp-Cy3).

growth_protocol: The bronchial epithelial cells - NCI-H292, derived from human lung mucoepidermoid carcinoma cells (ATCC, CRL-1848, Rockville, MD, USA), were grown as monolayers in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology, Rockville, Md., USA) at 37°C in a 5% CO2 incubator.  Mandin-Darby canine kidney (MDCK) cells were used for growing stocks of influenza virus isolates. MDCK cells were grown and maintained in Eagles Minimal Essential Media (MEM) containing 2% FBS, 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology).

extract_protocol: Total RNA was extracted from normal and infected NCI-H292 cells using Trizol reagent (Invitrogen) following the manufacturer’s protocol at time points 3, 6, 18, 24 hours post-infection. RNA pellets were resuspended in RNase-free water. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: NCI-H292 cells were grown to confluence in sterile T75 tissue culture flasks for the inoculation of virus isolate at a multiplicity of infection (m.o.i.) of one. After 1 hour of absorption, the virus was removed and 2 ml of fresh RPMI-1640 media with 2% FBS, 100 U/ml penicillin, 100 μg/mL streptomycin and 1μg/ml L-1-tosylamido-2-phenylethyl chloromethyl ketone (TPCK)-treated trypsin (all from Gibco, Life Technology) was added, and incubated at 37oC in 5% CO2 humidified air.

tag: cell line


title: HN025_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN025

value: African American

value: Heavy


title: H5N1_infected_18_hour

description: miRNA expression in lung epithelial cells after 18 hours of H5N1 infection.

source_name: 18 hour H5N1 infected cells


title: ERKO, epithelium, EE2 biological rep 3

tag: background strain

tag: genotype

value: ER-alpha knockout null

tag: Sex

value: female

value: fourth inguinal mammary gland


title: Noninfected_Cell_control_24_hour

description: miRNA expression in lung epithelial cells after 24 hours of incubation.

source_name: 24 hour cell control


title: HN015_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN015

tag: tissue

value: Oral Cavity

value: IVa

value: Surgery and Radiation


title: H5N1_infected_24_hour

description: miRNA expression in lung epithelial cells after 24 hours of H5N1 infection.

source_name: 24 hour H5N1 infected cells


title: HN017_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN017

tag: race

value: Caucasian

value: Male

value: None or Light/Moderate

value: III


title: HN014_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN014

value: Tumor

tag: gender

value: Larynx

value: Concurrent Chemoradiation

value: HPV-


title: Noninfected_Cell_control_6_hour

description: miRNA expression in lung epithelial cells after 6 hours of incubation.

source_name: 6 hour cell control


title: HN018_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN018

value: Female

tag: smoking packyears

value: Moderate


title: H5N1_infected_6_hour

description: miRNA expression in lung epithelial cells after 6 hours of H5N1 infection.

source_name: 6 hour H5N1 infected cells


title: H.zea_24 hpi_replicate 2

description:
Gene expression of H. zea cell line at 24 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.

source_name: H.zea cells infected by HearSNPV virus at 24 hour post infection

tag: insect cell line

value: Helicoverpa zea cell line (HzAM1)

tag: virus

tag: hours post infection (hpi)


title: Sample 1 Posterior  +/+

description:
S1PosPls
slide barcode: 251486826811
US80900103_251486826811_S01_GE1_105_Dec08_1_2

source_name: Posterior_wild type

tag: genotype/variation

value: C56B/6 and CD-1 mixed

tag: strain background

value: wild type

value: E9.5 embryos

tag: microdissection

value: posterior second heart field


title: Sample 1 Posterior  -/-

description:
S1PosMns
slide barcode: 251486826811
US80900103_251486826811_S01_GE1_105_Dec08_1_1

source_name: Posterior_Shh mutant

value: Shh mutant


title: wild type, epithelium, EE2 biological rep 2

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to EE2 (10 ng/kg) from E8 to E19

value: female

tag: exposure

value: fourth inguinal mammary gland


title: ERKO, epithelium, control, biological rep 1

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured epithelium exposed to vehicle

value: ER-alpha knockout null

value: vehicle


title: H.zea_0 hpi_replicate 1

description:
Gene expression of H. zea cell line at 0hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.

source_name: H.zea cells infected by HearSNPV virus at 0 hour post infection


title: Sample 2 Posterior  -/-

description:
S2PosMns
slide barcode: 251486826532
US80900103_251486826532_S01_GE1_105_Dec08_1_1
Possibally leaked on tecan during hybridization.


title: ERKO, epithelium, control, biological rep 2


title: wild type, epithelium, EE2 biological rep 1

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to EE2 (10 ng/kg) from E8 to E19


title: H5N1_infected_3_hour

description: miRNA expression in lung epithelial cells after 3 hours of H5N1 infection.

source_name: 3 hour H5N1 infected cells


title: Sample 3 Posterior  -/-

description:
S3PosMns
slide barcode: 251486826533
US80900103_251486826533_S01_GE1_105_Dec08_1_1


title: wild type, epithelium, BPA, biological rep 3

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to BPA (250 ng/kg) from E8 to E19


title: HN037_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN037

value: African American

value: Male

tag: alcohol use

value: Heavy

tag: differentiation

tag: tumor site

value: Oral Cavity

tag: Stage

value: IVa

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

tag: hpv status


title: Noninfected_Cell_control_3_hour

description: miRNA expression in lung epithelial cells after 3 hours of incubation.

source_name: 3 hour cell control

tag: cell line


title: HN013_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN013

tag: tissue

value: Tumor

tag: age

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

value: Moderate

value: Other

value: Surgery and Concurrent Chemoradiation

value: HPV+


title: Human I versus MG1655 technical replicate 2

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

hyb_protocol: Hybridization was performed using protocols developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications: Slides were blocked (using 5X SSC, 0.1% SDS, 1% Roche Blocking Reagent) prior to hybridization as described (http://www.genomics.princeton.edu/dunham/MDhomemadeDNA.pdf) (Roche Applied Science, Mannheim, Germany).

scan_protocol: Hybridized arrays were scanned using an Axon 4000B scanner and software package GenePix  5.0 (Molecular Devices, Sunnyvale, CA).

data_processing: Images were analyzed using a combination of GenePix Pro 6.0, the freely available TIGR TM4 software suite (www.tm4.org ) and Microsoft Excel.  Spots with an intensity: background ratio > 1.5 and overall intensity > 350 in the reference channel and an intensity:background ratio of > 1.0 in the experimental channel were considered acceptable for downstream processing.  Local background was subtracted for each spot, the corresponding log2 ratios were normalized using total intensity normalization, and replicate spots were averaged using TIGR MIDAS.  Genes that had missing data (i.e. unacceptable spots) for more than one-third of the samples were excluded from the downstream analysis leaving 3993 ORFs in the final data set.  Each sample was hybridized twice and the results averaged in Microsoft Excel after processing with MIDAS.  A strict cutoff of log2 ratio > 0.9 or < 0.9 was applied for the determination of gene amplifications and gene absences, respectively.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655

label_protocol: Samples were labeled according to the protocol developed by the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with minor modifications as follows.  First, 5 μg of genomic DNA was sonicated to an average fragment length of 2-5 kb using a Branson Digital Sonifier at 11% amplitude for 1.1 sec.  Second, a final concentration of 0.5 mM, 1:1 aa-dUTP:dTTP labeling mixture was used in the Klenow reaction.

extract_protocol: Genomic DNA was extracted using an SDS lysis/phenol/chloroform method described by (Syn CK, Swarup S (2000) A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Anal Biochem 278: 86-90) with slight modifications as follows:  subsequent to DNA precipitation, spun pellets were treated with 50μg mL-1 DNAse-free RNAse A and incubated at 37°C for 30 min.  Samples were then re-extracted once with phenol:chloroform (3:1), once with phenol:chloroform (1:1), twice with chloroform, reprecipitated and then resuspended in TE, pH 8.0.

tag: strain

value: E. coli K12 MG1655

organism: Escherichia coli

source_name: Human sewage isolate H1

value: Human sewage isolate H1


title: Human III versus MG1655 technical replicate 1

source_name: Human sewage isolate H3

value: Human sewage isolate H3


title: Human II versus MG1655 technical replicate 1

source_name: Human sewage isolate H2

value: Human sewage isolate H2


title: Human II versus MG1655 technical replicate 2


title: Human III versus MG1655 technical replicate 2


title: Yan6x_mock

first: Ilaria

last: Rebay

address: 929 E. 57th St. GCIS W340M

department: Ben May Department

institute: University of Chicago

description: biological replicates 1-3

hyb_protocol: Hybridization were performed as described in the Affymetrix ChIP Assay Protocol.

scan_protocol: Arrays were scanned at the University of Chicago microarray facility and image processed using GCOS

data_processing:
Data was quantile normalized and analyzed with bandwidth of 200 using Affymetrix Tiling Analysis Software (TAS). Log2(IP/Input) fold changes (signal) and p-values are reported in BAR files.
signal.bar and pvalue.bar are TAS and contain log2(IP/Input) fold changes and p-value, respectively for each probe. Bed files report top 3% of TAS p-values with minrun = 100 and maxgap = 300 created using Integrated Genome Browser (IGB, Affymetrix)

organism: Drosophila melanogaster

source_name: Mock treated chromatin from stage 11 YanYFP;YanYFP embryos

label_protocol: Fragmentation and labeling were performed as described in the Affymetrix ChIP Assay Protocol.

extract_protocol: Stage 5-7 or Stage 11 w1118 embryos were collected and aged to 1-3 hrs and 5h20-7h20 respectively. St 11 or yan;YanV105R embryos were hand sorted against GFP-marked balancers (~800 per replicate). Embryos were dechorionated in 50% bleach, incubated for 15 minutes at room temperature in 10ml of Cross-linking Solution (50mM HEPES, pH 7.6, 1mM EDTA, 0.5mM EGTA, 100mM NaCl, 1.8% formaldehyde) and 30ml of n-Heptane, washed twice in Stop Solution (PBS, 0.1% Triton X-100, 125mM Glycine), twice in PBS/T (PBS, 0.1% Triton X-100), and twice in Wash Solution (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton X-100). After homogenization in ChIP Lysis Buffer (50mM HEPES, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1 Sodium Deoxycholate, protease inhibitor tablet [Roche]), the lysates were subjected to 9 cycles of sonication at 15% amplitude for 15 seconds/cycle (Sonic Dismembrator Model 500, Fisher Scientific). Clarified lysates were halved and were either incubated with guinea pig anti-Yan or mock-treated. After overnight incubation at 4°C, 30μl of 50% GammaBind Sepharose (GE Healthcare) slurry was added and incubated for 4 hours at 4° C. The beads were washed 3 times in ChIP Lysis Buffer, once in High Salt ChIP Lysis Buffer (500mM NaCl in ChIP Lysis Buffer), and once in TE (10mM Tris, pH=8.0, 1mM EDTA) for 5 minutes each, resuspended in 150μl of TE/SDS (TE, 1% SDS), incubated at 65°C for 15 minutes with vortexing at 3 minute intervals to elute the DNA, and the supernatants incubated at 65°C overnight to reverse the cross-linking. For input, 5μl of lysates before immunoprecipitation were added to 145μl of TE/SDS and reverse-cross-linked. ChIP DNA was purified using the QIAquick PCR Purification Kit (Qiagen). For microarray hybridization, native ChIP DNA was amplified using the linker-mediated PCR (LM-PCR) method (Lee et al., 2006). Briefly, ChIP DNA was treated with Klenow DNA Polymerase (NEB) and then ligated with a linker produced by annealing the two oligos: 5’-/5Phos/AGAAGCTTGAATTCGAGCAGTCAG-3’ and 5’-CTGCTCGAATTCAAGCTTCT-3’. After adding the linker, DNA was amplified using the 20-mer primer as shown above and purified using the QIAquick PCR Purification Kit (Qiagen). The dNTP mixture used in the amplification reaction contained a 3:7 ratio of dUTP:dTTP so that the products could be fragmented by Uracil DNA Glycosylase and APE1 (Affymetrix).

value: Stage 11

value: embryo

tag: antibody


title: H1N1_infected_18_hour

description: miRNA expression in lung epithelial cells after 18 hours of H1N1 infection.

source_name: 18 hour H1N1 infected cells


title: H1N1_infected_24_hour

description: miRNA expression in lung epithelial cells after 24 hours of H1N1 infection.

source_name: 24 hour H1N1 infected cells


title: H1N1_infected_6_hour

description: miRNA expression in lung epithelial cells after 6 hours of H1N1 infection.

source_name: 6 hour H1N1 infected cells


title: H1N1_infected_3_hour

description: miRNA expression in lung epithelial cells after 3 hours of H1N1 infection.

source_name: 3 hour H1N1 infected cells


title: Human I versus MG1655 technical replicate 1


title: wild type, epithelium, BPA, biological rep 1

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to BPA (250 ng/kg) from E8 to E19

tag: background strain

tag: genotype

value: wild type

tag: Sex

value: female

tag: exposure

value: fourth inguinal mammary gland


title: YanV105R_mock

description: biological replicates 1-3

source_name: Mock treated chromatin from stage 11 yanE833/yanER443;YanV105R-GFPattP2 embryos


title: wild type, epithelium, BPA, biological rep 2


title: Deer II versus MG1655 technical replicate 2

source_name: Deer feces isolate D3

value: Deer feces isolate D3


title: Deer III versus MG1655 technical replicate 1

source_name: Deer feces isolate W6A

value: Deer feces isolate W6A


title: Deer III versus MG1655 technical replicate 2


title: HN012_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN012

value: Tumor

value: Male

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

tag: tumor site

value: Oral Cavity

tag: Stage

value: IVa

value: Concurrent Chemoradiation

value: HPV-


title: wild type, epithelium, control, biological rep 1

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to vehicle

value: vehicle


title: Deer II versus MG1655 technical replicate 1

value: E. coli K12 MG1655


title: HN010_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN010

value: African American

value: Moderate

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

tag: hpv status


title: Yan_stage5_7_mock

description: biological replicates 1-3

source_name: Mock treated chromatin from stage 5-7 w118 embryos

tag: age

value: Stage 5-7

tag: tissue

value: embryo


title: HN009_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN009

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

value: III


title: Yan_stage11_mock

description: biological replicates 1-3

source_name: Mock treated chromatin from stage 11 w118 embryos

value: Stage 11

tag: antibody


title: ERKO, stroma, EE2 biological rep 3

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to EE2 (10 ng/kg) from E8 to E19

tag: background strain

tag: genotype

value: ER-alpha knockout null

value: female

value: fourth inguinal mammary gland


title: wild type, epithelium, control, biological rep 3

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to vehicle

value: wild type

tag: Sex

tag: exposure


title: wild type, epithelium, control, biological rep 2


title: Yan6x_stage11

description: biological replicates 1-3

source_name: gp anti-Yan ChIP from stage 11 (5h20-7h20) YanYFPattP16;YanYFPattP2 (total 6 copies of yan locus) embryos

value: gp anti-Yan


title: Deer I versus MG1655 technical replicate 2

source_name: E. coli K12 MG1655

tag: strain

source_name: Deer feces isolate D1

value: Deer feces isolate D1


title: HN011_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN011

value: Tumor

value: Male

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

tag: tumor site

value: Larynx

value: Surgery Alone

value: HPV-


title: Cattle III versus MG1655 technical replicate 2

value: E. coli K12 MG1655

source_name: Cattle feces isolate C6D

value: Cattle feces isolate C6D


title: ERKO, stroma, EE2 biological rep 2

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to EE2 (10 ng/kg) from E8 to E19


title: Yan_stage11

description: biological replicates 1-3

source_name: gp anti-Yan ChIP from stage 11 (5h20-7h20) w118 embryos

value: embryo


title: ERKO, stroma, EE2 biological rep 1


title: Yan_stages5_7

description: biological replicates 1-3

source_name: gp anti-Yan ChIP from stage 5-7 (1-3hr) w118 embryos

value: Stage 5-7


title: YanV105R_stage11

description: biological replicates 1-3

source_name: gp anti-Yan ChIP from ~800 stage 11 (4h20-7h20) yanE833/yanER443;YanV105R-GFPattP2 embryos

value: Stage 11


title: wild type, epithelium, EE2 biological rep 3

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured epithelium exposed to EE2 (10 ng/kg) from E8 to E19


title: Cattle III versus MG1655 technical replicate 1


title: ERKO, stroma, BPA, biological rep 3

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to BPA (250 ng/kg) from E8 to E19

value: ER-alpha knockout null


title: ERKO, stroma, control, biological rep 3

description: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to vehicle

value: female

value: vehicle


title: Deer I versus MG1655 technical replicate 1


title: ERKO, stroma, control, biological rep 2

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to vehicle

value: fourth inguinal mammary gland


title: ERKO, stroma, BPA, biological rep 1

source_name: C57BL/6 ERalpha-null fetal mouse mammary gland (E19) laser-captured stroma exposed to BPA (250 ng/kg) from E8 to E19


title: Cattle II versus MG1655 technical replicate 1

source_name: Cattle feces isolate C4A

value: Cattle feces isolate C4A


title: Cattle I versus MG1655 technical replicate 2

source_name: Cattle feces isolate C1A

value: Cattle feces isolate C1A


title: Cattle I versus MG1655 technical replicate 1


title: Bear III versus MG1655 technical replicate 2

source_name: Bear feces isolate B5

value: Bear feces isolate B5


title: wild type, stroma, EE2 biological rep 3

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to EE2 (10 ng/kg) from E8 to E19

value: wild type


title: ERKO, stroma, BPA, biological rep 2


title: Cattle II versus MG1655 technical replicate 2


title: Bear III versus MG1655 technical replicate 1


title: wild type, stroma, EE2 biological rep 1

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to EE2 (10 ng/kg) from E8 to E19


title: ERKO, stroma, control, biological rep 1


title: Bear II versus MG1655 technical replicate 2

source_name: Bear feces isolate B3

value: Bear feces isolate B3


title: Bear II versus MG1655 technical replicate 1


title: Bear I versus MG1655 technical replicate 2

source_name: Bear feces isolate B1

value: Bear feces isolate B1


title: wild type, stroma, BPA, biological rep 2

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to BPA (250 ng/kg) from E8 to E19


title: wild type, stroma, EE2 biological rep 2


title: Wall Lizard whole testis from Regressed phase, Replicate C2

city: New Delhi

first: Subeer

middle: S

last: Majumdar

state: Delhi

address: Aruna Asaf Ali Marg, JNU Complex

country: India

institute: National Institute of Immunology

description: Gene expression in the whole testis of wall lizard in Regressed Phase of reproductive cycle

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent-Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 026986). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software Version 10.5 and 75th Percentile Shift Normalization of the data was done in GeneSpring GX V 11

organism: Hemidactylus flaviviridis

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

growth_protocol: Testes were decapsulated, zap frozen in liquid nitrogen immediately after castration, crushed to powdere form, dissolved in RNALater and stored at -80°C until used for RNA extraction

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit as per the manufacturer’s protocol

treatment_protocol: No treatment was given to testicular tissues

tag: reproductive phase

value: Regressed

value: Whole Testis


title: wild type, stroma, BPA, biological rep 1

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to BPA (250 ng/kg) from E8 to E19


title: Wall Lizard whole testis from Recrudescent phase, Replicate B1

description: Gene expression in the whole testis of wall lizard in Recrudescent Phase of reproductive cycle

value: Recrudescent


title: wild type, stroma, control, biological rep 3

description: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to vehicle


title: Wall Lizard whole testis from Active phase, Replicate A1

description: Gene expression in the whole testis of wall lizard in Active Phase of reproductive cycle

value: Active


title: Bear I versus MG1655 technical replicate 1

source_name: E. coli K12 MG1655

value: E. coli K12 MG1655


title: Wall Lizard whole testis from Recrudescent phase, Replicate B2


title: wild type, stroma, control, biological rep 2

source_name: C57BL/6 wild type fetal mouse mammary gland (E19) laser-captured stroma exposed to vehicle


title: wild type, stroma, BPA, biological rep 3


title: Wall Lizard whole testis from Active phase, Replicate A2


title: C. elegans N2, gonad-ablated versus un-ablated intact animals; Biological Replicate 3

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 3 of 3.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004).

organism: Caenorhabditis elegans

source_name: C. elegans young adults, gonad-ablated

label_protocol: Equal amounts of total RNA (typically 500ng) for 3 biological replicates from each condition was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: C. elegans L1 stage were picked into 2.8 ul PBS on a agar pad containing 1mM NaN3. Ablations would take place within 1 hour of hatching at 20C. After ablation nematodes were stored at 20C and successful ablation was verified 48 hours later. Nematodes unablated were grown in parallel and acted as controls. For microarrays 20 C. elegans (either Z(2,3) ablated or Z(1,4) ablated or unablated) were picked onto 5 separate NGM plates spotted with E. coli OP50 and incubated at 25C for 4 hours. Nematodes were then picked into 500 ul of Trizol and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

value: N2 Bristol

tag: ablation

value: gonad precursors Z1, Z4

source_name: C. elegans young adults, un-ablated controls


title: Wall Lizard whole testis from Regressed phase, Replicate C1


title: 45DAF rep5

city: Saskatoon

first: Adrian

last: Cutler

address: 110 Gymnasium Place

country: Canada

institute: National Research Council of Canada

description: Biological replicate 5 of 6, 45DAF seeds

hyb_protocol: 5 µg fragmented Cy5-aRNAs were mixed with hybridization buffer (6xSSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionized formamide, 0.1 mg/mL sheared salmon sperm DNA and 0.04% SDS) and hybridized to the Combimatrix Brassica 90K arrays at 45°C overnight in the dark. After hybridization, stringent washes were performed according to the manufacturer’s instructions, and the slides were immediately coated with an imaging solution (CombiMatrix) prior to scanning.

scan_protocol: Scanning on a GenePix 4000B scanner (Axon Instruments, CA, USA) using  PMT from 400-500, 5µm resolution and 100% laser power.

data_processing: The image analysis was performed using GenePix Pro version 6.0 software (Axon Instruments, CA, USA). After automatic alignment, feature indicators were manually moved, resized and fine-tuned. The local background corrected spot fluorescence intensities for the Cy5 channel were saved as GPR files.    The GPR files were loaded in GeneSpring GX 11.0 (Agilent Technologies Inc. and Strand Life Sciences Pvt. Ltd) with percentile shift normalization and baseline to median of all samples.  Signal intensity cut-off was set to 200. One way ANOVA analysis was carried out with the asymptotic p-value computation method.  Multiple testing correction method is Benjamini-Hochberg FDR. Corrected p-value (Benjamini-Hochberg FDR) cut-off set to 0.05 and fold change is more than 2.

organism: Brassica napus

source_name: Developing seeds, 45 days after flowering

label_protocol: RNA amplification was carried out using the MessageAmp aRNA kit (Ambion, Catalog# 1750) according to the supplied protocol. During the second round of in vitro transcription, aminoallyl-UTP was incorporated into the newly synthesized aRNA.Dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: Plants of Brassica napus L. cv.DH12075 were grown in 6-in pots containing soil mixture with a slow-release fertilizer 14-14-14 in a growth cabinet with a 16h/8h day/night photoperiod, light intensity of 250μmol m−2 s−1, and day/night temperatures of 22°C/18°C. Individual flowers were tagged with colored tapes on the day of flower opening.

extract_protocol: Total RNA was extracted using RNA aqueous kit (Ambion)

treatment_protocol: Seeds of 10, 15, 20, 25, 30, 35, 40 and 45  days after flowering (DAF) were dissected from siliques and immediately put in RNAlater (Ambion) and kept in 4 degree for a few days and stored in -20 degree

value: Developing seeds

tag: days after flowering


title: C. elegans N2, gonad-ablated versus un-ablated intact animals; Biological Replicate 1

description: Biological replicate 1 of 3.


title: C. elegans N2, germline-ablated versus un-ablated intact animals; Biological Replicate 3 (Dye-swap)

description: Biological replicate 3 of 3. Dye-swap.

source_name: C. elegans young adults, germline-ablated

growth_protocol: C. elegans L1 stage were picked into 2.8 ul PBS on a agar pad containing 1mM NaN3. Ablations would take place within 1 hour of hatching at 20°C. After ablation nematodes were stored at 20°C and successful ablation was verified 48 hours later. Nematodes unablated were grown in parallel and acted as controls. For microarrays 20 C. elegans (either Z(2,3) ablated or Z(1,4) ablated or unablated) were picked onto 5 separate NGM plates spotted with E. coli OP50 and incubated at 25°C for 4 hours. Nematodes were then picked into 500 ul of Trizol and stored at -80C till RNA extraction.

value: germline precursors Z2, Z3


title: liver Tg iNKT activated cells rep 2

city: Milan

first: Giulia

last: Casorati

state: Milan

address: Via Olgettina 58

department: Division of Immunology, Transplantation and Infectious Diseases

country: Italy

institute: San Raffaele Scientific Institute

description: Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice and activated in vitro for 6 hs

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).

scan_protocol: Chips were scanned using on a GeneArray Scanner (Affymetrix).

data_processing: The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.

source_name: sorted iNKT cells from liver of Tg mice after 6 hs of in vitro activation

label_protocol: aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)

growth_protocol: Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%

extract_protocol: Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.

treatment_protocol: Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb

tag: tissue

value: liver

tag: age

value: 8 weeks old mice

tag: treatment

value: activated in vitro for 6 hours


title: liver Tg iNKT activated cells rep 1


title: liver Tg iNKT activated cells rep 3


title: 45DAF rep4

description: Biological replicate 4 of 6, 45DAF seeds


title: 45DAF rep6

description: Biological replicate 6 of 6, 45DAF seeds


title: liver WT iNKT activated cells rep 3

description: Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice and activated in vitro for 6 hs

source_name: sorted iNKT cells from liver of WT mice after 6 hs of in vitro activation


title: C. elegans N2, gonad-ablated versus un-ablated intact animals; Biological Replicate 2 (Dye-swap)

description: Biological replicate 2 of 3. Dye-swap.


title: 45DAF rep3

description: Biological replicate 3 of 6, 45DAF seeds


title: C. elegans N2, germline-ablated versus un-ablated intact animals; Biological Replicate 2 (Dye-swap)

description: Biological replicate 2 of 3. Dye-swap.


title: 45DAF rep2

description: Biological replicate 2 of 6, 45DAF seeds


title: C. elegans N2, germline-ablated versus un-ablated intact animals; Biological Replicate 1

description: Biological replicate 1 of 3.


title: liver Tg iNKT cells rep 3

description: Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice

source_name: sorted iNKT cells from liver of Tg mice

value: no activation


title: liver WT iNKT activated cells rep 2


title: 45DAF rep1

description: Biological replicate 1 of 6, 45DAF seeds


title: wild type, stroma, control, biological rep 1

value: wild type

value: female

value: vehicle

value: fourth inguinal mammary gland


title: liver Tg iNKT cells rep 2


title: 40DAF rep5

description: Biological replicate 5 of 6, 40DAF seeds

source_name: Developing seeds, 40 days after flowering


title: BMK-CabpBVR2_Rep2

city: East Lansing

first: Sookyung

last: Oh

state: MI

address: 612 Wilson Road, Rm. 322

department: Plant Research Laboratories

institute: Michigan State Univ.

hyb_protocol: We submitted ~12 µg of labeled aRNA to the Research Technology Support Facility at Michigan State University for hybridization with a GeneChip® Arabidopsis ATH1 Genome Arrays (Affymetrix, Inc., CA) and acquisition of scanned probe arrays.

data_processing: Microarray data were analyzed using the statistical algorithms within the Affymetrix Microarray Suite (MAS) 5.0 software.

organism: Arabidopsis thaliana

source_name: 7day old FR grown Arabidopsis seedling

label_protocol: Amplified RNA (aRNA) was synthesized using a MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, TX) according to the manufacturer’s instructions with the following modifications. For in vitro transcription reaction, samples were incubated for 8 h at 40 °C. Binding of aRNA to magnetic beads following addition of 100% ethanol was carried out for 5 min with gentle shaking. To capture the magnetic beads-aRNA complex, we placed U bottom plates on a magnetic stand for ~6 min. aRNA was eluted off of the magnetic beads through vigorous shaking for ~7 min. The quality of biotin-labeled aRNA was determined on an Agilent 2100 Bioanalyzer.

extract_protocol: Seven-day-old vegetative whole seedlings (300 – 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber. Total RNA was isolated using an RNeasy® Plant Minikit (Qiagen, CA) according to the manufacturer’s instructions.

treatment_protocol: Seeds of No-0 WT, 35S::pBVR3 and CAB3::pBVR2 on MS plates were exposed to Red (R) light of 75 µmol m-2 s-1 for 5 min and imbibing seeds were cold-stratified at 4 °C in darkness for 3 d. Seedlings were grown under continuous far-red illumination for 7 d. Seven-day-old vegetative whole seedlings (300 – 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber

tag: genetic modification


title: liver WT iNKT cells rep 3

description: Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice

source_name: sorted iNKT cells from liver of WT mice


title: liver Tg iNKT cells rep 1


title: 40DAF rep6

description: Biological replicate 6 of 6, 40DAF seeds


title: BMK-35SpBVR3_Rep3

scan_protocol: We submitted ~12 µg of labeled aRNA to the Research Technology Support Facility at Michigan State University for hybridization with a GeneChip® Arabidopsis ATH1 Genome Arrays (Affymetrix, Inc., CA) and acquisition of scanned probe arrays.

growth_protocol: Seedlings were grown under continuous far-red illumination for 7 d.


title: BMK-CabpBVR2_Rep3


title: liver WT iNKT cells rep 1


title: 40DAF rep1

description: Biological replicate 1 of 6, 40DAF seeds


title: 35DAF rep6

description: Biological replicate 6 of 6, 35DAF seeds

source_name: Developing seeds, 35 days after flowering


title: BMK-CabpBVR2_Rep1


title: 35DAF rep4

description: Biological replicate 4 of 6, 35DAF seeds


title: liver WT iNKT activated cells rep 1


title: BMK-35SpBVR3_Rep2


title: T-ETV1_Luminal cells-D

description: Prostate cells FACS-sorted, GFP+ luminal cells (Lin-Sca1-CD49f+) population

hyb_protocol: Standard Affymetrix protocol.

source_name: Primary prostate cells

label_protocol: Biotinulated cRNA were prepared according to the NuGEN protocol for Affumetrix arrays.

extract_protocol: Trizol extraction of total RNA was performed following the manufacturer's protocol, followed by NuGEN V2cDNA amplification

treatment_protocol: Prostate single cells were isolated from the prostate, and stained for FACS sorting. Sorted cells were resuspended in Trizol for RNA extraction.

tag: cell type

value: prostate luminal cells

tag: genotype/variation


title: liver WT iNKT cells rep 2


title: 40DAF rep4

description: Biological replicate 4 of 6, 40DAF seeds


title: BMK-35SpBVR3_Rep1


title: 35DAF rep3

description: Biological replicate 3 of 6, 35DAF seeds


title: 40DAF rep2

description: Biological replicate 2 of 6, 40DAF seeds


title: 35DAF rep5

description: Biological replicate 5 of 6, 35DAF seeds


title: 40DAF rep3

description: Biological replicate 3 of 6, 40DAF seeds


title: 35DAF rep2

description: Biological replicate 2 of 6, 35DAF seeds


title: BMK-WT_Rep1

value: No-0 wild-type (WT)


title: wildtype Ago2 IP

first: Yan

last: Zeng

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities. Ch1 signals of different RNA samples.  Raw data only.  There was no need for normalization because the MT sample had near background miRNA signals, as expected.

source_name: 293T human cell line

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: 293T cells were grown under standard conditions

extract_protocol: 293T cells were lysed, and lysate incubated with FLAG beads (Sigma).  After washing the beads, RNA was isolated by Trizol (Invitrogen)

treatment_protocol: 293T cells were transfected with plasmids using Lipofectamine 2000 (Invitrogen)

tag: flag ip

value: wildtype Ago2 IP


title: mutant Ago2 IP

value: mutant Ago2 IP


title: T-ETV1_Luminal cells-C

first: Esther

institute: Childrens Hospital Boston

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.


title: BMK-WT_Rep3


title: WT-Luminal cells-C

description: Prostate cells FACS-sorted, luminal cells (Lin-Sca1-CD49f+) population


title: 30DAF rep5

description: Biological replicate 5 of 6, 30DAF seeds

source_name: Developing seeds, 30 days after flowering


title: T-ETV1_Luminal cells-A


title: 30DAF rep3

description: Biological replicate 3 of 6, 30DAF seeds


title: 30DAF rep4

description: Biological replicate 4 of 6, 30DAF seeds


title: Fast_Adult_Muscle_rep3

city: Rennes

first: Pierre-Yves

last: Rescan

address: Campus de Beaulieu

department: Phase

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Scanning with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit).

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots were flagged using the Agilent GeneSpring GX software (v.10.0.2) and data were subsequently normalized using the quantile method.

organism: Oncorhynchus mykiss

label_protocol: GE microarray was performed using One-Color Microarray-Based Gene Expression Analysis kit (Agilent v6.5) according to the manufacturer procedure. Briefly, for each sample, 100 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

extract_protocol: Total RNA of laser captured material was isolated using the PicoPureRNA isolation kit (Arcturus) and had an RNA integrity number of 7.5 (Agilent). Total RNA of muscle was isolated using Trizol reagent

treatment_protocol: Ten-micron- thick transverse frozen sections were cut using a cryostat  mounted onto uncoated glass slides, fixed at −20 °C in 70% ethanol for 1 min, washed briefly in 70% ethanol and sequentially dehydrated in 100% ethanol and xylene. The sections were then microdissected using a Veritas Laser Capture Microdissection system (LCM) (Arcturus). The infrared laser was used with the following parameters: spot diameter, 20 μm; pulse duration, 3500 ms; power, 90 mW. All areas were selected and collected within 30 min of the preparation of the slide. Laser-captured material from 20-30 sections was pooled for each RNA extraction.).

value: Muscle

tag: Stage

value: Fast Adult Muscle 500g

tag: sampling

value: Transverse slice of fast Muscle beneath dorsal fin


title: 30DAF rep2

description: Biological replicate 2 of 6, 30DAF seeds

value: Developing seeds


title: Fast_Adult_Muscle_rep1


title: Laser_Capture_Peripheral Domain_rep4

source_name: Laser_Capture_Peripheral Domain_rep4

value: embryonic myotome

value: 19 days post fertilization

value: Laser Capture microdissection peripheral domain


title: Laser_Capture_Deep Domain_rep2

source_name: Laser_Capture_Deep Domain_rep2

value: Laser Capture microdissection deep domain


title: BMK-WT_Rep2


title: 25DAF rep6

description: Biological replicate 6 of 6, 25DAF seeds

source_name: Developing seeds, 25 days after flowering