title: Malignant Breast Cell Line:HCC1599

description:
HCC1599
0=negative; 1=positive

value: malignant breast cell line


title: Malignant Breast Cell Line:HCC1187

status: Public on Mar 01 2013

type: genomic

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

country: USA

institute: leslie cope

description:
HCC1187
0=negative; 1=positive

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan with Illumina scanner settings for the Infinium chip.

data_processing: GenomeStudio V2011.1. Beta=M/(M+U).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Malignant breast cell line, BaA

label_protocol: Standard Illumina Protocol for Infinium Methylation27 BeadChip.

extract_protocol: DNA was extracted with TNES/PK (Tris/NaCl/EDTA/SDS/proteinase K) lysis buffer prior to sodium bisulfite conversion using the Zymo Research EZ DNA Methylation Kit.

tag: cell line

tag: cell type

tag: expression subtype

value: BaA

tag: er

tag: pr


title: Whole peripheral blood_Tempus Tube, Sample 46

type: RNA

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression Module)

data_processing:
The raw log2 transformed 14,343 probes that are expressed in the CHDWB study were normalized by ANOVA fitting technical effects of date of hybridization and RNA quality using JMP Genomics 5.0 (SAS Institute, Cary NC) and mean centered.
log2 transformed 14,343 probes expressed in CHDWB study, DATE and RIN3 effects removed, and mean-centered signal

molecule: total RNA

source_name: Whole peripheral blood

label_protocol: Illumina's BeadArray protocol

extract_protocol: Total RNA was extracted from Whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.

tag: gender

value: FEM

tag: age

tag: percentage of body fat

tag: ethnicity

value: AFR

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: H


title: Whole peripheral blood_Tempus Tube, Sample 49

value: MAL

value: A


title: Whole peripheral blood_Tempus Tube, Sample 45

value: CAU

value: F


title: Whole peripheral blood_Tempus Tube, Sample 42

value: K


title: Whole peripheral blood_Tempus Tube, Sample 44

value: D


title: Whole peripheral blood_Tempus Tube, Sample 48

value: L


title: Malignant Breast Cell Line:HS578T

description:
HS578T
0=negative; 1=positive

source_name: Malignant breast cell line, BaB/CLDNlow

value: BaB/CLDNlow


title: Whole peripheral blood_Tempus Tube, Sample 50

value: C


title: Malignant Breast Cell Line:AU565

description:
AU565
0=negative; 1=positive

source_name: Malignant breast cell line, Lu

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 47

value: J


title: Whole peripheral blood_Tempus Tube, Sample 41

value: I


title: Whole peripheral blood_Tempus Tube, Sample 36


title: Non-Malignant Breast Cell Line:HBL100

description:
HBL100
0=negative; 1=positive

source_name: Non-malignant breast cell line, BaB/CLDNlow

value: non-malignant breast cell line


title: Whole peripheral blood_Tempus Tube, Sample 68


title: Whole peripheral blood_Tempus Tube, Sample 39

value: E


title: Whole peripheral blood_Tempus Tube, Sample 35

value: FEM


title: Whole peripheral blood_Tempus Tube, Sample 40

value: AFR

value: G


title: Whole peripheral blood_Tempus Tube, Sample 43

value: B


title: Whole peripheral blood_Tempus Tube, Sample 38

value: MAL

value: ASN


title: Malignant Breast Cell Line:HCC1395

description:
HCC1395
0=negative; 1=positive

value: malignant breast cell line


title: Malignant Breast Cell Line:HCC202

description:
HCC202
0=negative; 1=positive


title: Malignant Breast Cell Line:HCC38

description:
HCC38
0=negative; 1=positive


title: Malignant Breast Cell Line:UACC893

description:
UACC893
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 34

value: CAU

value: H


title: Malignant Breast Cell Line:HCC2185

description:
HCC2185
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 32

value: D


title: Whole peripheral blood_Tempus Tube, Sample 33

value: F


title: Whole peripheral blood_Tempus Tube, Sample 37

value: A


title: Malignant Breast Cell Line:MDAMB134

description:
MDAMB134
0=negative; 1=positive

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 31


title: Whole peripheral blood_Tempus Tube, Sample 30

value: K


title: Malignant Breast Cell Line:CAMA1

description:
CAMA1
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 24


title: Whole peripheral blood_Tempus Tube, Sample 28


title: Whole peripheral blood_Tempus Tube, Sample 27

value: C


title: Whole peripheral blood_Tempus Tube, Sample 26


title: Whole peripheral blood_Tempus Tube, Sample 23

value: L


title: Whole peripheral blood_Tempus Tube, Sample 25


title: Whole peripheral blood_Tempus Tube, Sample 29

value: I


title: Malignant Breast Cell Line:BT474

description:
BT474
0=negative; 1=positive


title: Malignant Breast Cell Line:600M

description:
600M
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 18


title: Malignant Breast Cell Line:BT20

description:
BT20
0=negative; 1=positive

value: BaA


title: Whole peripheral blood_Tempus Tube, Sample 17


title: Whole peripheral blood_Tempus Tube, Sample 57


title: Head and neck squamous cell carcinoma HN160 Agilent 4x44K

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

description: Stratagene Human Universal RNA Reference

hyb_protocol: Hybridization was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

scan_protocol: Scanned on an Agilent High Resolution Model B scanner that has been upgraded to Model C. Images were quantified using Agilent Feature Extraction software.

data_processing: The normexp background correction and loess normalization procedures were applied to the probe-level data using the limma R package. Normalized log2 ratios (test/reference) were then computed.

label_protocol: Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

treatment_protocol: Not applicable

tag: tissue

value: Tumor

tag: race

value: African American

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Well

tag: tumor site

value: Oral Cavity

tag: Stage

value: III

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

tag: hpv status

tag: reference


title: Head and neck squamous cell carcinoma HN161 Agilent 4x44K

tag: age

value: Caucasian

tag: gender

value: None or Light/Moderate

value: Moderate

value: Larynx

value: Concurrent Chemoradiation

source_name: Stratagene Human Universal RNA Reference


title: Malignant Breast Cell Line:HCC3153

description:
HCC3153
0=negative; 1=positive

tag: cell line

tag: cell type

value: malignant breast cell line

tag: expression subtype

tag: er

tag: pr


title: Malignant Breast Cell Line:HCC1500

description:
HCC1500
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 11

value: FEM

tag: percentage of body fat

tag: ethnicity

value: CAU

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: J


title: Whole peripheral blood_Tempus Tube, Sample 21

value: AFR


title: Whole peripheral blood_Tempus Tube, Sample 16

value: MAL

value: G


title: Malignant Breast Cell Line:HCC1428

description:
HCC1428
0=negative; 1=positive

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 22

value: K


title: Head and neck squamous cell carcinoma HN158 Agilent 4x44K

tag: tissue

value: Tumor

tag: race

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Poor

tag: tumor site

value: Oropharynx

tag: Stage

value: IVb

tag: tumor status

tag: node status

value: HPV+

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 15

tag: gender

tag: age

value: E


title: Malignant Breast Cell Line:MCF7

description:
MCF7
0=negative; 1=positive

tag: cell line

tag: cell type

value: malignant breast cell line

tag: expression subtype

tag: er

tag: pr


title: Whole peripheral blood_Tempus Tube, Sample 13

tag: percentage of body fat

tag: ethnicity

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: A


title: Whole peripheral blood_Tempus Tube, Sample 7

value: CAU

value: B


title: Whole peripheral blood_Tempus Tube, Sample 8

value: FEM

value: AFR

value: D


title: Whole peripheral blood_Tempus Tube, Sample 5

value: I


title: Malignant Breast Cell Line:BT549

description:
BT549
0=negative; 1=positive

value: BaB/CLDNlow


title: Whole peripheral blood_Tempus Tube, Sample 6

value: K


title: Whole peripheral blood_Tempus Tube, Sample 12

value: L


title: Head and neck squamous cell carcinoma HN159 Agilent 4x44K

tag: tissue

value: Tumor

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

tag: tumor site

value: IVa

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status

tag: reference


title: Whole peripheral blood_Tempus Tube, Sample 9

tag: gender

tag: age

value: F


title: Whole peripheral blood_Tempus Tube, Sample 20

value: MAL

tag: percentage of body fat

value: CAU


title: Head and neck squamous cell carcinoma HN154 Agilent 4x44K

value: Moderate

value: Larynx

tag: Stage

value: III

tag: tumor status

tag: node status

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 4

value: FEM

tag: ethnicity

tag: zip code

tag: rna integrity score

tag: batch effect_date

value: G


title: LFYasEMF1/ult1-3_15D_SD

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

description: Gene expression of 15D old seedlings grown under short day condition

hyb_protocol: According to the instruction of Agilent One-Color Microarray-Based Gene Expression Analysis Protocol, version 6.5, the chips were hybridized with equal amounts (1.65 μg) of Alexa 555 labeled aRNA derived from different samples for 17 h at 65 °C and washed according to the manufacturer’s instructions of the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack.

scan_protocol: Chip images were scanned using the Agilent DNA microarray scanner (G2565CA, Agilent Technologies).

data_processing: The images were analyzed by the use of the Feature Extraction software (version 10.7.1.1) following the GE1-107_Sep09 protocol (Agilent Technologies). Signal intensities were Quantile normalized using GeneSpring 11.2 software.

label: Alexa Flour 555

organism: Arabidopsis thaliana

source_name: 15D old LFYasEMF1/ult1-3 seedlings grown under short day

label_protocol: One microgram total RNA of each sample was used as a template to generate amino allyl modified RNA (aRNA), respectively. The amplified aRNA was labeled with Alexa Flour 555 reactive dyes (Invitrogen) and fragmented  according to the manual instruction of the Amino Allyl MessageAmp aRNA Amplification Kit (Ambion) before hybridization to an Arabidopsis Gene Expression Microarray chip version 4.

growth_protocol: Seeds of WT, LFYasEMF1, ult1-3 and LFYasEMF1/ult1-3 were saw on 0.8% 1/2 MS agar plate containing 1.5% sucrose and seedlings were grown under short day condition.

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

treatment_protocol: Seedings of WT, LFYasEMF1, ult1-3 and LFYasEMF1/ult1-3 were harvested at 7 days and 15 days.

tag: genotype/variation

value: grown under short day

tag: tissue

value: whole seedlings

value: 15 days


title: Head and neck squamous cell carcinoma HN155 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Oropharynx


title: Head and neck squamous cell carcinoma HN153 Agilent 4x44K

value: None or Light/Moderate

tag: tumor site

value: Oral Cavity

value: II

tag: treatment

value: Surgery Alone

tag: hpv status

value: HPV-

tag: reference


title: Bmel-erythritol-1

city: Madison

first: Erik

last: Petersen

state: WI

address: 1656 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
This sample is of B. melitensis grown in the presence of 1% erythritol (experimental sample), replicate 1
NC_003317 & NC_003318

hyb_protocol: Hybridization was performed at 42C for 16hr in 300ul of buffer containing 50mM MES, 0.5M NaCl, 10mM EDTA, 0.05% Tween 20, 1nM CPK6 Oligo, 0.2 mg of BSA, and 0.04 mg herring sperm DNA. Chips were washed 3x at room temperature with non-stringent buffer (0.18mM NaCl, 10mM NaH2PO4, 1mM EDTA, pH7.7) and 4x at 42C with stringent wash buffer (100mM MES, 0.1M NaCl, 0.01% Tween 20).  Chips were stained with a streptavidin-Cy3 conjugate (Amersham) for 25 min. at room temperature, then washed with wash buffer (Nimblegen).

scan_protocol: Scanning was performed at a 5um resolution on an Axon 4000b scanner (Axon) and image files were processed using Nimblescan software (Nimblegen)

data_processing:
The raw data (.pair file) was analyzed with Nimblescan software (Nimblegen) and Robust Multi-Array Analysis (RMA) was used to convert the raw data to .calls files.
RMA-normalized values were used to generate gene-specific average intensities.  In cases in which a single copy of a probe was present, that probe value was excluded.  Gene-specific valuse for each chip were used to compare the erythritol values to the glucose values using gamma-gamma and log-normal-normal analysis.

organism: Brucella melitensis bv. 1 str. 16M

source_name: Brucella melitensis strain 16M (ATCC23456) in 1% erythritol

label_protocol: Biotin labeling of cDNA products was accomplished using biotin-6-dd-ATP and terminal transferase (Roche).

growth_protocol:
Brucella melitensis strain 16M (ATCC23456) was grown in brucella broth at 37C for 48hrs to stationary phase.  300ul of culture was added to 30ml of yeast-extract minimal medium (YEMM) containing either 1% glucose or 1% erythritol as the sole carbon source. (Plommet, Zentralbl Bakteriol 275(4):436-50)
B. melitensis 16M cultures were grown in YEMM containing either 1% glucose or 1% erythritol as the sole carbon source to late log phase (OD ~1.0) and prepped for RNA.

extract_protocol: Total RNA was extracted using the Masterpure RNA Extraction Kit (Epicentre) and DNAse treated with the DNAse Turbo Kit (Ambion). Loss of genomic DNA was confirmed by PCR. cDNA was generated using 10ug RNA and Superscript II RT (Invitrogen).

tag: carbon source

value: 1% Erythritol


title: Whole peripheral blood_Tempus Tube, Sample 14

tag: gender

tag: age

tag: percentage of body fat

value: CAU

tag: plate id

value: C


title: Bmel-erythritol-2

description:
This sample is of B. melitensis grown in the presence of 1% erythritol (experimental sample), replicate 2
NC_003317 & NC_003318


title: Whole peripheral blood_Tempus Tube, Sample 2

value: FEM

tag: ethnicity

value: AFR

tag: zip code

tag: rna integrity score


title: Bmel-glucose-2

description:
This sample is of B. melitensis grown in the presence of 1% glucose (control sample), replicate 2
NC_003317 & NC_003318

source_name: Brucella melitensis strain 16M (ATCC23456) in 1% glucose

value: 1% Glucose


title: Head and neck squamous cell carcinoma HN157 Agilent 4x44K

tag: tissue

value: Moderate

tag: Stage

value: IVa

tag: tumor status

tag: node status

value: Concurrent Chemoradiation

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 1

tag: batch effect_date

value: A


title: Whole peripheral blood_Tempus Tube, Sample 19

value: B


title: LFYasEMF1/ult1-3_7D_SD

description: Gene expression of 7D old seedlings grown under short day condition

source_name: 7D old LFYasEMF1/ult1-3 seedlings grown under short day

tag: genotype/variation

value: grown under short day

value: whole seedlings

value: 7 days


title: ult1-3_7D_SD

source_name: 7D old ult1-3 seedlings grown under short day

tag: treatment


title: Whole peripheral blood_Tempus Tube, Sample 3

value: E


title: LFYasEMF1_15D_SD

source_name: 15D old LFYasEMF1 seedlings grown under short day

value: 15 days


title: Head and neck squamous cell carcinoma HN152 Agilent 4x44K

value: Tumor

tag: race

value: African American

value: Female

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Well

tag: tumor site

value: Oral Cavity

value: Surgery and Concurrent Chemoradiation

tag: hpv status


title: Whole peripheral blood_Tempus Tube, Sample 10

tag: gender

value: FEM

tag: age

tag: percentage of body fat

value: AFR

tag: plate id

value: H


title: Bmel-glucose-1

description:
This sample is of B. melitensis grown in the presence of 1% glucose (control sample), replicate 1
NC_003317 & NC_003318

tag: carbon source

value: 1% Glucose


title: Head and neck squamous cell carcinoma HN156 Agilent 4x44K

tag: tissue

value: Male

value: Moderate

value: Hypopharynx

tag: Stage

value: IVb

value: Concurrent Chemoradiation

value: HPV-

tag: reference

value: Stratagene Human Universal RNA Reference


title: ult1-3_15D_SD

source_name: 15D old ult1-3 seedlings grown under short day

value: grown under short day

value: whole seedlings

value: 15 days


title: LFYasEMF1_7D_SD

source_name: 7D old LFYasEMF1 seedlings grown under short day

value: 7 days


title: GIST19

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: GIST

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: Total RNA, including small RNAs, was extracted from the snap frozen tissues by using miRNeasy mini kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions.

value: gastrointestinal stromal tumor

tag: site

value: large intestine

tag: size(cm)


title: WT_15D_SD_rep2

source_name: 15D old WT seedlings grown under short day

tag: genotype/variation

value: wild type

tag: treatment


title: GIST18

value: stomach


title: GIST17

value: small intestine


title: GIST16


title: GIST14


title: GIST15


title: WT_7D_SD_rep2

source_name: 7D old WT seedlings grown under short day


title: WT_15D_SD_rep1


title: GIST13


title: GIST12


title: Head and neck squamous cell carcinoma HN148 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

tag: smoking packyears

value: Heavy

value: Larynx

value: IVa

tag: tumor status

tag: node status

value: Surgery and Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN149 Agilent 4x44K

value: Female

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

value: II

value: Surgery Alone

tag: hpv status


title: Head and neck squamous cell carcinoma HN150 Agilent 4x44K

tag: age

value: Native American

tag: gender

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN145 Agilent 4x44K

tag: tissue

value: Male

value: Surgery and Radiation

value: HPV-


title: Head and neck squamous cell carcinoma HN151 Agilent 4x44K

value: Tumor

value: Well

tag: Stage


title: Head and neck squamous cell carcinoma HN146 Agilent 4x44K

value: Caucasian

value: III

tag: reference


title: GIST11

value: gastrointestinal stromal tumor

tag: site

value: stomach


title: GIST10

tag: size(cm)


title: Head and neck squamous cell carcinoma HN147 Agilent 4x44K

value: Heavy


title: GIST9

value: small intestine


title: WT_7D_SD_rep1

tag: genotype/variation

value: wild type

value: grown under short day

value: whole seedlings

value: 7 days


title: Head and neck squamous cell carcinoma HN142 Agilent 4x44K

value: Female

value: Unknown

value: Moderate

value: Oral Cavity

value: IVa

tag: treatment

value: Surgery Alone


title: GIST8


title: Head and neck squamous cell carcinoma HN143 Agilent 4x44K

value: Tumor

tag: race

value: African American

value: Male

value: Oropharynx

value: Concurrent Chemoradiation

value: HPV-

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN140 Agilent 4x44K

value: Caucasian

tag: smoking packyears

value: None or Light/Moderate

value: Well

value: Surgery and Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN141 Agilent 4x44K

value: Poor

value: Other

tag: tumor status

value: Radiation Alone


title: Head and neck squamous cell carcinoma HN139 Agilent 4x44K

value: Moderate

value: Oral Cavity

value: III

tag: node status

value: Surgery and Radiation


title: GIST7

value: gastrointestinal stromal tumor

value: small intestine


title: GIST6

value: stomach


title: wt replica 2

city: Cambridge

first: Xicotencatl

last: Gracida

address: 52 Oxford St.

institute: Harvard University

description: Gene expression in wild type animals fed a standard diet

hyb_protocol: 0.6 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 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl containing of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 8x60K Custom Gene Expression Microarrays (Design ID: 037908) for 17 hours at 65°C and 10 rpm in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according to the manufacturers instructions .

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Agilent G3_GX_1_color) for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%, 20 but file).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 037908_D_F_20111216) to obtain background subtracted and spatially detrended Processed Signal intensities.  Normalization of the data was performed using the software GeneSpring GX. The normalization algorithm was Quantile. No baseline transformation was transformed. Data are log2 transformed.

label: Cyanine-3 (Cy3)

organism: Caenorhabditis elegans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions (Agilent One-Color Microarray-Based Gene Expression Analysis v.6.5 Protocol), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: To synchronize animals, embryos were obtained by chlorine treatment and larvae hatched overnight in M9 solution. Arrested L1 larvae were transferred to respective plates and were grown at 25ºC. nhr-114(RNAi) sterile animals were single picked. Worm pellets were frozen in liquid nitrogen and stored at -80ºC until use.

extract_protocol: RNA was extracted with Trizol as in Sambrook (2001).

treatment_protocol: nhr-114, glp-1 and wt animals were fed standard E. coli OP50 diets. Wild type (wt+TRP) animals were fed E. coli OP5O supplemented with Tryptophan, as decribed in manuscript Gracida and Eckmann 2013.

tag: diet

value: E. coli OP50

tag: genotype

value: wild type

tag: genetic background


title: Head and neck squamous cell carcinoma HN137 Agilent 4x44K

value: Tumor

value: Female

tag: alcohol use

tag: differentiation

tag: tumor site

value: Larynx

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-

value: Stratagene Human Universal RNA Reference


title: wt replica 3


title: GIST4

tag: tissue

value: large intestine


title: GIST5


title: wt+TRP replica 3

description: Gene expression in wild type animals fed a tryptophan supplemented diet

value: E. coli OP50 + Tryptophan (TRP)


title: wt replica 1


title: Head and neck squamous cell carcinoma HN136 Agilent 4x44K

tag: age

value: Caucasian

tag: gender

value: None or Light/Moderate

value: Well

tag: Stage

value: Surgery Alone

tag: reference


title: wt+TRP replica 2


title: GIST3

value: gastrointestinal stromal tumor

tag: site

tag: size(cm)


title: Head and neck squamous cell carcinoma HN134 Agilent 4x44K

tag: race

value: Male

tag: smoking packyears

value: Heavy

value: Moderate

value: Oral Cavity

value: IVa

tag: treatment

value: Surgery and Chemotherapy


title: Head and neck squamous cell carcinoma HN135 Agilent 4x44K

value: Tumor

value: Female

value: Hypopharynx

tag: tumor status

tag: node status

value: Surgery and Concurrent Chemoradiation


title: nhr-114 replica 3

description: Gene expression in nhr-114 sterile animals

tag: diet

value: E. coli OP50

tag: genotype

tag: genetic background


title: Head and neck squamous cell carcinoma HN133 Agilent 4x44K

tag: alcohol use

tag: differentiation

value: Poor

tag: tumor site

value: Larynx

value: Stratagene Human Universal RNA Reference


title: wt+TRP replica 1

value: E. coli OP50 + Tryptophan (TRP)

value: wild type


title: glp-1  replica 3

description: Gene expression in otherwise somatic wild type sterile animals


title: nhr-114 replica-1


title: Paired non-neoplastic tissue [P228N]

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Control

data_processing:
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.
For the normalization it uses the average of four housekeeping genes: EIF2B1, MRPL19, IPO8, and UBB
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.

label: FAM

source_name: Paired non-neoplastic tissue

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

tag: tissue

value: Control


title: Head and neck squamous cell carcinoma HN132 Agilent 4x44K

tag: age

value: Caucasian

tag: gender

value: Male

value: None or Light/Moderate

value: Other

tag: hpv status

value: HPV-


title: glp-1  replica 1


title: Paired non-neoplastic tissue [P191N]

description: Control


title: Head and neck squamous cell carcinoma HN138 Agilent 4x44K

value: Moderate

value: Oral Cavity

tag: Stage

value: II

value: Surgery Alone

tag: reference


title: GIST1

value: gastrointestinal stromal tumor

tag: site

value: small intestine

tag: size(cm)


title: Paired non-neoplastic tissue [P249N]

description: Control


title: Paired non-neoplastic tissue [P260N]

description: Control


title: glp-1  replica 2

value: E. coli OP50


title: GIST2

value: stomach


title: Paired non-neoplastic tissue [P167N]

description: Control


title: Paired non-neoplastic tissue [P185N]

description: Control


title: Paired non-neoplastic tissue [P168N]

description: Control


title: Paired non-neoplastic tissue [P156N]

description: Control


title: Paired non-neoplastic tissue [P169N]

description: Control


title: Paired non-neoplastic tissue [P170N]

description: Control


title: Head and neck squamous cell carcinoma HN131 Agilent 4x44K

value: Tumor

tag: race

tag: smoking packyears

value: Larynx

value: IVa

tag: treatment

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN129 Agilent 4x44K

value: African American

value: Oropharynx

tag: tumor status

tag: node status

value: Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN128 Agilent 4x44K

value: Caucasian

value: Female

value: Heavy


title: Head and neck squamous cell carcinoma HN127 Agilent 4x44K

value: Male

value: Well

value: HPV-


title: Head and neck squamous cell carcinoma HN126 Agilent 4x44K

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

value: III

value: Surgery and Radiation


title: Paired non-neoplastic tissue [P155N]

description: Control

value: Control


title: nhr-114 replica 2

tag: diet

value: E. coli OP50

tag: genotype

tag: genetic background


title: Paired non-neoplastic tissue [P178N]

description: Control


title: Paired non-neoplastic tissue [P143N]

description: Control


title: Paired non-neoplastic tissue [P144N]

description: Control


title: Paired non-neoplastic tissue [P131N]

description: Control


title: Paired non-neoplastic tissue [P123N]

description: Control


title: Paired non-neoplastic tissue [P117N]

description: Control


title: Paired non-neoplastic tissue [P118N]

description: Control


title: Paired non-neoplastic tissue [P133N]

description: Control


title: Paired non-neoplastic tissue [P114N]

description: Control


title: Paired non-neoplastic tissue [P102N]

description: Control


title: Paired non-neoplastic tissue [P109N]

description: Control


title: Paired non-neoplastic tissue [P96N]

description: Control


title: Paired non-neoplastic tissue [P134N]

description: Control


title: Paired non-neoplastic tissue [P95N]

description: Control


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal M998

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Rhesus Macaque Genome Arrays (Affymetrix, Santa Clara, CA).

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

data_processing: Background adjustment, normalization and median polish summarization of .CEL files was performed using the robust multi-chip average (RMA) algorithm. Quality of hybridized chips was assessed after normalization by the distribution of their NUSE and RLE plots using the RACE tool. Downstream analyses were performed using Partek Genomics Suite software v6.5 (Partek Inc. St. Louis, MO) with the exception of Bayesian analysis, which were performed in RACE.

label: biotin

organism: Macaca mulatta

source_name: Animal  M998, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge

label_protocol: RNA was amplified and labeled using the NuGen Ovation Pico system according to kit instructions.

growth_protocol: All the animals used in this study were colony-bread rhesus macaques (Macaca mulatta) obtained from Covance Research Products (Alice, Texas). The animals were housed and maintained in accordance with the standards of the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC). All macaques were negative for Simian Retrovirus, Simian T-Cell Leukemia virus type 1 and Herpes virus B.

extract_protocol: 0.5-1 cm cubes of snap frozen rectal mucosal biopsies were placed into 350 μl of RLT buffer (QIAGEN, Valencia, CA) and total RNA was purified using RNEasy Mini kits (QIAGEN) according to manufacturer’s specifications with optional on-column DNAse digestion.

treatment_protocol: Twenty macaques were immunized at 0 and 8 weeks with intramuscular injection of 2ml of a DNA-SIVgpe mix containing 206S-sivgag (1mg), 209S-MCP3-p39 (1mg), 99S-sivENV (2mg), 103S-LAMP-POL (2mg) and 147S-LAMP-NTV (2mg) (14). All the animals were boosted with ALVAC-SIVgpe at week 21, 40 and 57/61 (Fig. 1A). Each vaccination with ALVAC-SIVgpe boost consisted of 108 PFU in a volume of 150 µl of PBS delivered intra-dermally and dispersed over three chest sites on each animal; at week 40 and 57/61 all the animals received simultaneously the homologous gp120 protein, adjuvanted in Alum, intramuscularly in opposite thigh of the ALVAC-SIVgpe inoculum. Twenty macaques were used as control and received Alum only at week 40 and 57/61. All the animals were intrarectally exposed after 4 weeks from infection. A SIVmac251 stock (16) propagated in human cells was utilized at 2 doses of 6100- or 470 TCID50.

tag: array facility id

tag: animal id

tag: vaccination

value: UNVACCINATED CONTROL

tag: challenge dose (tcid50)

value: Rectal mucosal biopsy


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal P015

source_name: Animal  P015, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge

tag: tissue


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P143

source_name: Animal  P143, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: Paired non-neoplastic tissue [P85N]

description: Control


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal P074

source_name: Animal  P074, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge


title: Paired non-neoplastic tissue [P57N]

description: Control


title: Paired non-neoplastic tissue [P84N]

description: Control


title: Paired non-neoplastic tissue [P43N]

description: Control


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P071

source_name: Animal  P071, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal P134

source_name: Animal  P134, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal P136

source_name: Animal  P136, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge


title: Paired non-neoplastic tissue [P135N]

description: Control


title: Paired non-neoplastic tissue [P13N]

description: Control


title: Paired non-neoplastic tissue [P24N]

description: Control


title: Paired non-neoplastic tissue [P15N]

description: Control


title: Paired non-neoplastic tissue [P32N]

description: Control


title: Paired non-neoplastic tissue [P8N]

description: Control


title: Paired non-neoplastic tissue [P9N]

description: Control


title: Paired non-neoplastic tissue [P7N]

description: Control


title: Paired non-neoplastic tissue [P5N]

description: Control


title: Paired non-neoplastic tissue [P4N]

description: Control


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal M881

source_name: Animal  M881, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge


title: Paired non-neoplastic tissue [P3N]

description: Control


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal P007

source_name: Animal  P007, Rectal mucosal biopsy,  ALVAC+,  high dose challenge

value: ALVAC+


title: Breast tumor [P260T]

description: Tumor

source_name: Breast tumor

value: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal P012

source_name: Animal  P012, Rectal mucosal biopsy,  ALVAC+,  high dose challenge

tag: array facility id

tag: animal id

tag: vaccination


title: Rectal mucosal biopsy_NAIVE_high dose challenge_Animal P066

source_name: Animal  P066, Rectal mucosal biopsy,  UNVACCINATED,  high dose challenge

tag: challenge dose (tcid50)

tag: tissue


title: Breast tumor [P253T]

description: Tumor

tag: sampleID

tag: age

tag: menopause


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal M904

source_name: Animal  M904, Rectal mucosal biopsy,  ALVAC+,  high dose challenge


title: Breast tumor [P249T]

description: Tumor

tag: histology

tag: grade

tag: size

value: unknown


title: Breast tumor [P242T]

description: Tumor

tag: Stage

tag: pt

tag: pn


title: Breast tumor [P228T]

description: Tumor

tag: er

tag: pr

tag: neo-anthracycline


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal M896

source_name: Animal  M896, Rectal mucosal biopsy,  ALVAC+,  high dose challenge

tag: array facility id


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal M891

source_name: Animal  M891, Rectal mucosal biopsy,  ALVAC+,  high dose challenge

tag: animal id


title: Breast tumor [P223T]

description: Tumor

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P088

source_name: Animal  P088, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge

tag: vaccination

tag: challenge dose (tcid50)

tag: tissue


title: Breast tumor [P191T]

description: Tumor

tag: sampleID

tag: age

tag: menopause


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal M887

source_name: Animal  M887, Rectal mucosal biopsy,  ALVAC+,  high dose challenge


title: Rectal mucosal biopsy_ALVAC+_high dose challenge_Animal P002

source_name: Animal  P002, Rectal mucosal biopsy,  ALVAC+,  high dose challenge


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P059

source_name: Animal  P059, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: Breast tumor [P186T]

description: Tumor

tag: histology

tag: grade

tag: size


title: Breast tumor [P185T]

description: Tumor

tag: Stage

tag: pt

tag: pn


title: SFRS2_MEF_rep3_tetOFF

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
GPL13185_mjay.pgf
GPL13185_mjay.clf

organism: Mus musculus

source_name: MEF cells from tet-repressible SFRS2-HA mice, treated with doxycycline

label_protocol: cDNA synthesis and amplification was performed using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix).  Targets were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

growth_protocol: 4 biological replicate sets of SFRS1 or SFRS2 tet-repressible MEFs were grown for 5 days in DMEM -/+ 10ug/ml docycline.

extract_protocol: Total RNA was isolated with the RNAeasy kid (Qiagen), then treated with Ribominus (Invitrogen).

tag: transgene

value: tet-repressible SFRS2-HA

tag: cell type

value: MEF

tag: treatment

value: tet off

tag: genetic background


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P130

source_name: Animal  P130, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge

tag: array facility id

tag: animal id


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P095

source_name: Animal  P095, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge

tag: vaccination

tag: challenge dose (tcid50)


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P121

source_name: Animal  P121, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge

tag: tissue


title: SFRS2_MEF_rep1_tetOFF

treatment_protocol: 4 biological replicate sets of SFRS1 or SFRS2 tet-repressible MEFs were grown for 5 days in DMEM -/+ 10ug/ml docycline.


title: SFRS2_MEF_rep4

source_name: MEF cells from tet-repressible SFRS2-HA mice

value: tet on


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P144

source_name: Animal  P144, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P017

source_name: Animal  P017, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P089

source_name: Animal  P089, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: SFRS2_MEF_rep2_tetOFF


title: Rectal mucosal biopsy_NAIVE_low dose challenge_Animal P113

source_name: Animal  P113, Rectal mucosal biopsy,  UNVACCINATED,  low dose challenge


title: SFRS2_MEF_rep1


title: Breast tumor [P213T]

description: Tumor

source_name: Breast tumor

tag: sampleID

tag: age

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Breast tumor [P178T]

description: Tumor

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: pt

tag: pn


title: Paired non-neoplastic tissue [P162N]

description: Control

source_name: Paired non-neoplastic tissue


title: SFRS1_MEF_rep3_tetOFF

source_name: MEF cells from tet-repressible SFRS1-HA mice, treated with doxycycline

tag: transgene

value: tet-repressible SFRS1-HA

tag: cell type

tag: treatment

tag: genetic background


title: SFRS2_MEF_rep4_tetOFF


title: Breast tumor [P170T]

description: Tumor

tag: tissue

tag: sampleID

tag: age


title: Breast tumor [P169T]

description: Tumor

tag: er

tag: pr

tag: neo-anthracycline


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal M890

source_name: Animal  M890, Rectal mucosal biopsy,  ALVAC+,  low dose challenge

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: SFRS1_MEF_rep1_tetOFF


title: SFRS2_MEF_rep2


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P014

source_name: Animal  P014, Rectal mucosal biopsy,  ALVAC+,  low dose challenge


title: Breast tumor [P168T]

description: Tumor

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: neo-taxane

tag: response


title: Breast tumor [P167T]

description: Tumor

tag: tissue

tag: pt

tag: pn


title: SFRS2_MEF_rep3

tag: transgene

tag: cell type

tag: treatment

tag: genetic background


title: SFRS1_MEF_rep4

source_name: MEF cells from tet-repressible SFRS1-HA mice


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P013

source_name: Animal  P013, Rectal mucosal biopsy,  ALVAC+,  low dose challenge

tag: array facility id

tag: animal id


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P016

source_name: Animal  P016, Rectal mucosal biopsy,  ALVAC+,  low dose challenge

tag: vaccination

tag: challenge dose (tcid50)


title: TAM#1 2nd mouse from m3-8 (8-3)

city: Tokyo

first: Aiko

last: Sato-Otsubo

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m3-8 (8-3)
TAM#1 m3-8 2nd(8-3)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

label: Biotin

label_protocol: standard Affymetrix protocol

growth_protocol: Patient derived TAM cells were transplanted into NOG mice. Recipient BM cells were collected 12–18 weeks after transplantation and sorted by hCD45 antigen.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of TAM blasts obtained from human peripheral blood or murine bone marrow (hCD45 sorted) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease state

value: transient abnormal myelopoiesis

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P001

source_name: Animal  P001, Rectal mucosal biopsy,  ALVAC+,  low dose challenge


title: SFRS1_MEF_rep4_tetOFF


title: Breast tumor [P162T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: er

tag: pr

tag: neo-anthracycline


title: SFRS1_MEF_rep2

tag: transgene

tag: cell type

tag: treatment


title: TAM#2 1st mouse from m3-6

description:
Hybridized to 250K_Nsp
TAM#2 1st mouse from m3-6
TAM#2 m3-6 1st


title: Breast tumor [P161T]

description: Tumor

tag: tissue

tag: Stage

tag: pt

tag: pn

tag: neo-taxane

tag: response


title: TAM#1 2nd mouse from m3-8 (8-2)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m3-8 (8-2)
TAM#1 m3-8 2nd(8-2)

tag: disease state

tag: subject


title: TAM#2 patient sample in complete remission phase rep2

description:
Hybridized to 250K_Nsp
TAM#2 patient sample in complete remission phase
TAM#2 CR

value: transient abnormal myelopoiesis in complete remission

value: TAM blasts from human peripheral blood (hCD45 sorted)


title: Breast tumor [P157T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology


title: SFRS1_MEF_rep3

tag: genetic background


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P009

source_name: Animal  P009, Rectal mucosal biopsy,  ALVAC+,  low dose challenge

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P019

source_name: Animal  P019, Rectal mucosal biopsy,  ALVAC+,  low dose challenge

tag: tissue


title: Breast tumor [P164T]

description: Tumor

tag: grade

tag: size

tag: Stage

tag: er

tag: pr

tag: neo-anthracycline


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal P008

source_name: Animal  P008, Rectal mucosal biopsy,  ALVAC+,  low dose challenge


title: Rectal mucosal biopsy_ALVAC+_low dose challenge_Animal M898

source_name: Animal  M898, Rectal mucosal biopsy,  ALVAC+,  low dose challenge


title: TAM#1 1st mouse from m3-11

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m3-11
TAM#1 m3-11 1st

tag: disease state

tag: cell type

tag: subject


title: SFRS1_MEF_rep1

tag: transgene

tag: treatment


title: Breast tumor [P155T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: pt

tag: pn

tag: neo-taxane

tag: response


title: TAM#1 2nd mouse from m3-4 (4-1)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m3-4 (4-1)
TAM#1 m3-4 2nd(4-1)


title: Breast tumor [P144T]

description: Tumor

tag: tissue

tag: grade

tag: size

tag: Stage


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P074

source_name: Animal P074, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)

growth_protocol: All the animals used in this study were colony-bred rhesus macaques (Macaca mulatta) obtained from Covance Research Products (Alice, Texas). The animals were housed and maintained in accordance with the standards of the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC). All macaques were negative for Simian Retrovirus, Simian T-Cell Leukemia virus type 1 and Herpes virus B.

tag: array facility id

tag: animal id

tag: vaccination

value: CONTROL

tag: challenge dose (tcid50)


title: TAM#1 1st mouse from m3-8

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m3-8
TAM#1 m3-8 1st

tag: disease state

tag: cell type

tag: subject


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P084

source_name: Animal P084, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)


title: TAM#1 1st mouse from m3-7

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m3-7
TAM#1 m3-7 1st


title: Breast tumor [P143T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: er

tag: pr

tag: neo-anthracycline


title: TAM#1 2nd mouse from m3-4 (4-2)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m3-4 (4-2)
TAM#1 m3-4 2nd(4-2)


title: TAM#1 1st mouse from m3-5

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m3-5
TAM#1 m3-5 1st


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P134

source_name: Animal P134, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)

tag: tissue


title: TAM#1 1st mouse from m3-4

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m3-4
TAM#1 m3-4 1st


title: Breast tumor [P141T]

description: Tumor

tag: histology

tag: grade

tag: pt

tag: pn

tag: neo-taxane

tag: response


title: SFRS1_MEF_rep2_tetOFF

tag: transgene

tag: treatment

tag: genetic background


title: TAM#1 patient sample in complete remission phase rep3

description:
Hybridized to 250K_Nsp
TAM#1 patient sample in complete remission phase
TAM#1 CR

tag: disease state

tag: cell type

tag: subject


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P136

source_name: Animal P136, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: Breast tumor [P135T]

description: Tumor

source_name: Breast tumor

tag: tissue

tag: sampleID

tag: age

tag: menopause

tag: size

tag: Stage

tag: er

tag: pr

tag: neo-anthracycline


title: Breast tumor [P156T]

description: Tumor

tag: histology

tag: grade

tag: pt

tag: pn

tag: neo-taxane

tag: response


title: Breast tumor [P134T]

description: Tumor


title: TAM#1 1st mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m1-1
TAM#1 m1-1 1st

tag: disease state

tag: cell type

tag: subject


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P061

source_name: Animal P061, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)

tag: tissue


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P066

source_name: Animal P066, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)


title: TAM#1 2nd mouse from m2-5 (5-5-4)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-5-4)
TAM#1 m2-5 2nd(5-5-4)


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal M904

source_name: Animal M904, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

value: +ALVAC


title: Breast tumor [P133T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: size

tag: Stage

tag: er


title: TAM#1 patient sample in complete remission phase rep2


title: TAM#1 2nd mouse from m2-5 (5-5-3)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-5-3)
TAM#1 m2-5 2nd(5-5-3)


title: TAM#1 2nd mouse from m2-5 (5-4-1)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-4-1)
TAM#1 m2-5 2nd(5-4-1)


title: TAM#1 2nd mouse from m2-5 (5-4-3)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-4-3)
TAM#1 m2-5 2nd(5-4-3)


title: Rectal mucosal biopsy_CONTROL_HIGH DOSE CHALLENGE (TCID50=6100)_Animal M881

source_name: Animal M881, Rectal mucosal biopsy,  CONTROL  , HIGH DOSE CHALLENGE (TCID50=6100)


title: Breast tumor [P132T]

description: Tumor

tag: histology

tag: grade

tag: pt

tag: pn

tag: pr

tag: neo-anthracycline


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal M887

source_name: Animal M887, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

tag: array facility id


title: TAM#1 2nd mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m1-1
TAM#1 m1-1 2nd

tag: disease state

tag: cell type

tag: subject


title: Breast tumor [P123T]

description: Tumor

tag: tissue

tag: neo-taxane

tag: response


title: Breast tumor [P131T]

description: Tumor

tag: sampleID

tag: age

tag: menopause


title: TAM#1 patient sample in complete remission phase


title: TAM#9 1st mouse from m2-5

description:
Hybridized to 250K_Nsp
TAM#9 1st mouse from m2-5
TAM#9 m2-5 1st


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal M896

source_name: Animal M896, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: HN159_Affymetrix_GenomeWide_SNP6.0

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.

source_name: Head and neck squamous cell carcinoma HN159

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

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.

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

tag: tumor site

value: Oropharynx

tag: Stage

value: IVa

tag: tumor status

tag: node status

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal M899

source_name: Animal M899, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

tag: array facility id

tag: tissue

value: Rectal mucosal biopsy


title: Breast tumor [P120T]

description: Tumor

value: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P012

source_name: Animal P012, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: Breast tumor [P122T]

description: Tumor

tag: tissue

tag: Stage


title: HN153_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN153

tag: age

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

value: II

tag: tumor status

tag: node status

tag: treatment

value: Surgery Alone

tag: hpv status

value: HPV-


title: TAM#9 1st mouse from m2-3

description:
Hybridized to 250K_Nsp
TAM#9 1st mouse from m2-3
TAM#9 m2-3 1st

tag: disease state

value: transient abnormal myelopoiesis

tag: cell type

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


title: HN158_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN158

value: Female

value: Poor

value: IVb

value: HPV+


title: TAM#9 1st mouse from m2-1

description:
Hybridized to 250K_Nsp
TAM#9 1st mouse from m2-1
TAM#9 m2-1 1st


title: Breast tumor [P118T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Breast tumor [P117T]

description: Tumor

tag: tissue

tag: age

tag: Stage


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_HIGH DOSE CHALLENGE (TCID50=6100)_Animal P002

source_name: Animal P002, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, HIGH DOSE CHALLENGE (TCID50=6100)

tag: array facility id

tag: animal id

tag: vaccination

value: +ALVAC

tag: challenge dose (tcid50)


title: HN147_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN147

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

tag: tumor site

tag: tumor status

tag: node status

tag: treatment

tag: hpv status


title: TAM#9 patient diagnostic sample

description:
Hybridized to 250K_Nsp
TAM#9 patient diagnostic sample
TAM#9 diagnostic

tag: disease state

tag: cell type

value: TAM blasts from human peripheral blood (hCD45 sorted)

tag: subject


title: HN145_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN145

tag: tissue

value: Tumor

tag: age

tag: Stage

value: Surgery and Radiation


title: HN146_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN146

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

value: III

value: Surgery and Concurrent Chemoradiation


title: Breast tumor [P114T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P071

source_name: Animal P071, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

value: CONTROL

tag: challenge dose (tcid50)

value: Rectal mucosal biopsy


title: HN132_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN132

tag: tissue

tag: age

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

value: Other

tag: Stage

value: IVa

tag: tumor status

tag: node status

tag: treatment

tag: hpv status

value: HPV-


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P113

source_name: Animal P113, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id


title: Breast tumor [P109T]

description: Tumor

source_name: Breast tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P095

source_name: Animal P095, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)

tag: tissue


title: HN143_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN143

tag: age

tag: race

value: African American

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

value: Oropharynx

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status


title: TAM#1 1st mouse from m2-5

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m2-5
TAM#1 m2-5 1st

tag: disease state

value: transient abnormal myelopoiesis

tag: cell type

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


description:
Hybridized to 250K_Nsp
TAM#9 patient sample in complete remission phase
TAM#9 CR

value: transient abnormal myelopoiesis in complete remission

value: TAM blasts from human peripheral blood (hCD45 sorted)


title: TAM#1 2nd mouse from m2-5 (5-5)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-5)
TAM#1 m2-5 2nd(5-5)


title: Breast tumor [P102T]

description: Tumor

value: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: TAM#1 2nd mouse from m2-5 (5-4)

description:
Hybridized to 250K_Nsp
TAM#1 2nd mouse from m2-5 (5-4)
TAM#1 m2-5 2nd(5-4)


title: HN151_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN151

tag: tissue

tag: age

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

tag: tumor site

value: Larynx

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Surgery Alone


title: HN130_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN130

value: Heavy

value: Moderate

value: Oral Cavity

value: Surgery and Concurrent Chemoradiation

tag: hpv status


title: HN131_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN131

value: IVa

value: HPV-


title: HN142_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN142

value: Female

value: Unknown


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P121

source_name: Animal P121, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

value: CONTROL

tag: challenge dose (tcid50)

value: Rectal mucosal biopsy


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P130

source_name: Animal P130, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: tissue


title: Breast tumor [P101T]

description: Tumor

value: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: HN141_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN141

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Poor

tag: tumor site

value: Other

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Radiation Alone

tag: hpv status


title: Breast tumor [P97T]

description: Tumor

tag: tissue

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P088

source_name: Animal P088, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: TAM#1 6th mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 6th mouse from m1-1
TAM#1 m1-1 6th

tag: disease state

value: transient abnormal myelopoiesis

tag: cell type

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


title: Breast tumor [P95T]

description: Tumor

tag: Stage

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P144

source_name: Animal P144, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: tissue


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P143

source_name: Animal P143, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P017

source_name: Animal P017, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)


title: TAM#2 1st mouse from m2-1

description:
Hybridized to 250K_Nsp
TAM#2 1st mouse from m2-1
TAM#2 m2-1 1st


title: TAM#1 7th mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 7th mouse from m1-1
TAM#1 m1-1 7th


title: Breast tumor [P91T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size


title: HN129_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN129

tag: race

value: African American

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

tag: tumor site

value: Oropharynx

tag: tumor status

tag: node status

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status


title: Rectal mucosal biopsy_CONTROL_LOW DOSE CHALLENGE (TCID50=470)_Animal P059

source_name: Animal P059, Rectal mucosal biopsy,  CONTROL  , LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)

tag: tissue


title: Breast tumor [P96T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

value: unknown

tag: Stage

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Breast tumor [P85T]

description: Tumor

tag: size


title: HN127_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN127

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Well

tag: tumor site

value: Larynx

tag: tumor status

tag: node status

tag: treatment

tag: hpv status

value: HPV-


title: HN128_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN128

tag: tissue

value: Tumor

tag: age

value: Female

value: Moderate

tag: Stage

value: IVa


title: Breast tumor [P84T]

description: Tumor

source_name: Breast tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline


title: TAM#2 patient sample in complete remission phase rep1

description:
Hybridized to 250K_Nsp
TAM#2 patient sample in complete remission phase
TAM#2 CR

tag: disease state

value: transient abnormal myelopoiesis in complete remission

tag: cell type

value: TAM blasts from human peripheral blood (hCD45 sorted)

tag: subject


title: HN124_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN124

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

value: Hypopharynx

value: II

tag: tumor status

tag: node status

tag: treatment

value: Radiation Alone


title: HN126_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN126

tag: tissue

tag: age

value: Caucasian

value: None or Light/Moderate

value: Oral Cavity

tag: Stage

value: III

value: Surgery and Radiation

tag: hpv status


title: TAM#2 patient diagnostic sample

description:
Hybridized to 250K_Nsp
TAM#2 patient diagnostic sample
TAM#2 diagnostic

value: transient abnormal myelopoiesis


title: pombe 10 RPL3202, biological rep3

city: Nanjing

first: Lei

last: Sun

address: 1 Wenyuan Rd

country: China

institute: Nanjing Normal University

description: Gene expression profile of S. pombe SP-Q01 harboring vector pESP3 with RPL3202 overexpression cultured in EMM2 medium to OD600 of 10

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

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

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

organism: Schizosaccharomyces pombe

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual  Affymetrix).

growth_protocol: The yeast strains were cultured in EMM2 medium at 30C, and cells were harvested when the OD600 was 0.5 and 10 respectively.

treatment_protocol: Cells were cellected and frozen in liquid nitrogen quickly for extraction of total RNA.

tag: strain

tag: growth phase


title: HN125_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN125

value: African American

value: Male

value: Oropharynx

value: IVb

value: Concurrent Chemoradiation


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P008

source_name: Animal P008, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

value: +ALVAC

tag: challenge dose (tcid50)

value: Rectal mucosal biopsy


title: TAM#1 1st mouse from m2-2

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m2-2
TAM#1 m2-2 1st

tag: disease state

tag: cell type

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P001

source_name: Animal P001, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)


title: Breast tumor [P69T]

description: Tumor

value: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: pombe 10 RPL3202, biological rep2

source_name: S. pombe SP-Q01 harboring vector pESP3 with RPL3202 overexpression cultured in EMM2 medium to OD600 of 10

tag: strain

tag: growth phase


title: Breast tumor [P71T]

description: Tumor

tag: tissue

tag: age

tag: Stage


title: Breast tumor [P67T]

description: Tumor

tag: sampleID


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal M890

source_name: Animal M890, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal M898

source_name: Animal M898, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)


title: TAM#1 1st mouse from m2-4

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m2-4
TAM#1 m2-4 1st

tag: disease state

tag: cell type

tag: subject


title: Breast tumor [P57T]

description: Tumor

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr


title: TAM#1 1st mouse from m2-1

description:
Hybridized to 250K_Nsp
TAM#1 1st mouse from m2-1
TAM#1 m2-1 1st


title: HN116_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN116

tag: tissue

tag: age

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Well

tag: tumor site

tag: Stage

value: IVa

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: HPV-


title: pombe 10 RPL3202, biological rep1

tag: strain

tag: growth phase


title: TAM#1 4th mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 4th mouse from m1-1
TAM#1 m1-1 4th

tag: disease state

tag: cell type

tag: subject


title: HN114_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN114

tag: tissue

tag: age

value: None or Light/Moderate

value: Moderate

value: Hypopharynx


title: HN115_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN115

tag: race

tag: gender

value: Oral Cavity


title: Breast tumor [P55T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

value: unknown

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Breast tumor [P52T]

description: Tumor

tag: Stage


title: TAM#1 3rd mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 3rd mouse from m1-1
TAM#1 m1-1 3rd

tag: disease state

value: transient abnormal myelopoiesis

tag: cell type

tag: subject


title: pombe 10 RPL3201, biological rep3

description: Gene expression profile of S. pombe SP-Q01 harboring vector pESP3 with RPL3201 overexpression cultured in EMM2 medium to OD600 of 10

tag: strain

tag: growth phase


title: pombe 10 RPL3201, biological rep2

source_name: S. pombe SP-Q01 harboring vector pESP3 with RPL3201 overexpression cultured in EMM2 medium to OD600 of 10


title: TAM#1 5th mouse from m1-1

description:
Hybridized to 250K_Nsp
TAM#1 5th mouse from m1-1
TAM#1 m1-1 5th


title: pombe 10 RPL3201, biological rep1


title: HN112_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN112

tag: tissue

tag: age

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

value: Larynx

tag: tumor status

tag: node status

tag: treatment

tag: hpv status


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P009

source_name: Animal P009, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: animal id

tag: vaccination

value: +ALVAC

tag: challenge dose (tcid50)


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P014

source_name: Animal P014, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

value: Rectal mucosal biopsy


title: Breast tumor [P47T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P016

source_name: Animal P016, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

tag: array facility id

tag: tissue


title: Breast tumor [P45T]

description: Tumor

source_name: Breast tumor

tag: age


title: pombe 0.5 RPL3202, biological rep3

description: Gene expression profile of S. pombe SP-Q01 harboring vector pESP3 with RPL3202 overexpression cultured in EMM2 medium to OD600 of 0.5

tag: strain

tag: growth phase


title: Rectal mucosal biopsy_+ALVAC vaccine/gp120 boost_LOW DOSE CHALLENGE (TCID50=470)_Animal P019

source_name: Animal P019, Rectal mucosal biopsy,  +ALVAC vaccine/gp120 boost, LOW DOSE CHALLENGE (TCID50=470)

tag: animal id

tag: vaccination

tag: challenge dose (tcid50)


title: s3 CD44+CD24- DU145

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: s3 CD44+CD24- DU145

hyb_protocol: Standard Affymetrix hybridzation for Human 1.0 ST genechips

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000.

data_processing: Data were analysized with bioconductor 2.7 oneChannelGUI package 1.16.5

source_name: DU145 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: The DU 145 human prostate carcinoma cell line was obtained from  the American Type Culture Collection (Manassas, VA). Cells were routinely  cultured in RPMI 1640 medium supplemented with 5% FBS and  antibiotics at 37 C in a humidified atmosphere of 5% CO2.

extract_protocol: CSC CD44+CD24- population were sorted. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

tag: cell line


title: HN111_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN111

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

tag: tumor site

tag: Stage

tag: tumor status

tag: node status

tag: treatment

tag: hpv status


title: s4 CD44+CD24- DU145

description: s4 CD44+CD24- DU145


title: pombe 0.5 RPL3202, biological rep1

source_name: S. pombe SP-Q01 harboring vector pESP3 with RPL3202 overexpression cultured in EMM2 medium to OD600 of 0.5

tag: strain

tag: growth phase


title: pombe 0.5 RPL3202, biological rep2


title: Breast tumor [P40T]

description: Tumor

tag: tissue

value: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response


title: TAM#1 patient diagnostic sample

description:
Hybridized to 250K_Nsp
TAM#1 patient diagnostic sample
TAM#1 diagnostic

tag: disease state

tag: cell type

value: TAM blasts from human peripheral blood (hCD45 sorted)

tag: subject


title: Breast tumor [P32T]

description: Tumor

tag: tissue

tag: Stage


title: pombe 0.5 RPL3201, biological rep3

description: Gene expression profile of S. pombe SP-Q01 harboring vector pESP3 with RPL3201 overexpression cultured in EMM2 medium to OD600 of 0.5

tag: strain

tag: growth phase


title: Breast tumor [P43T]

description: Tumor

tag: sampleID

tag: age

tag: menopause

tag: histology


title: s2 CD44+CD24- DU145

description: s2 CD44+CD24- DU145

tag: cell line


title: Breast tumor [P31T]

description: Tumor

tag: grade

tag: size

tag: pt

tag: pn

tag: er


title: s1 CD44+CD24- DU145

description: s1 CD44+CD24- DU145


title: TAM#1 patient sample in complete remission phase rep1

description:
Hybridized to 250K_Nsp
TAM#1 patient sample in complete remission phase
TAM#1 CR

tag: disease state

value: transient abnormal myelopoiesis in complete remission


title: pombe 0.5 RPL3201, biological rep1

source_name: S. pombe SP-Q01 harboring vector pESP3 with RPL3201 overexpression cultured in EMM2 medium to OD600 of 0.5


title: pombe 10 WT, biological rep3

description: Gene expression profile of S. pombe SP-Q01 harboring empty vector pESP3 cultured in EMM2 medium to OD600 of 10


title: b2 DU145 bulk

description: b2 DU145 bulk

tag: cell type

value: parental DU145


title: pombe 0.5 RPL3201, biological rep2


title: Breast tumor [P24T]

description: Tumor

tag: pr

tag: neo-anthracycline

tag: neo-taxane

tag: response

tag: note

value: unknown NACT


title: b1 DU145 bulk

description: b1 DU145 bulk


title: b3 DU145 bulk

description: b3 DU145 bulk


title: TAM#2 1st mouse from m2-2

description:
Hybridized to 250K_Nsp
TAM#2 1st mouse from m2-2
TAM#2 m2-2 1st

value: TAM blasts from murine bone marrow (hCD45 sorted)

tag: subject


title: HN107_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN107

tag: tissue

tag: age

tag: race

tag: gender

value: Female

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

tag: tumor site

tag: Stage

value: II

tag: tumor status

tag: node status

tag: treatment

value: Surgery Alone

tag: hpv status

value: HPV-


title: Breast tumor [P13T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane


title: Breast tumor [P15T]

description: Tumor

tag: tissue

tag: age

tag: response


title: pombe 10 WT, biological rep1

source_name: S. pombe SP-Q01 harboring empty vector pESP3 cultured in EMM2 medium to OD600 of 10

tag: strain

tag: growth phase


title: HN105_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN105

tag: race

value: African American

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

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: HN104_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN104

value: Tumor

value: Caucasian

value: Oropharynx

value: Concurrent Chemoradiation


title: Breast tumor [P8T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane


title: HN109_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN109

tag: tissue

tag: age

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

value: Surgery and Concurrent Chemoradiation

value: HPV+


title: pombe 10 WT, biological rep2

tag: strain

tag: growth phase


title: Breast tumor [P9T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: response


title: Oculomotor neurons 2

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Oculomotor 1207
Gene expression data from oculomotor neurons from human post-mortem control case.

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 Plus 2.0 Array (Affymetrix) in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post-hybridisation stringency washing was done using the Affymetrix Fluidics Station again following the protocol outlined in the Affymetrix instructions.

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image was processed using the GCOS software package to prepare the .CEL files.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Oculomotor neurons, control case 1207

label_protocol: Biotinylation of antisense RNA was carried out according to the Affymetrix protocol.

growth_protocol: 10 um lumbar spinal cord or midbrain frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.

extract_protocol:
From each case, and each tissue type, 500-1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience).
The PicoPure RNA Extraction Kit was used for RNA extraction according to the manufacturer's instructions.

tag: post-mortem control case

tag: cell type

value: oculomotor neurons

tag: disease state

value: normal control


title: HN110_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN110

tag: tissue

tag: age

tag: race

tag: gender

value: Heavy

value: Poor

value: Other

value: I

tag: tumor status

tag: node status

tag: treatment

tag: hpv status


title: Oculomotor neurons 4

description:
Oculomotor 9807
Gene expression data from oculomotor neurons from human post-mortem control case.

source_name: Oculomotor neurons, control case 9807


title: Breast tumor [P7T]

description: Tumor

tag: sampleID

tag: menopause

tag: pt

tag: pn

tag: er

tag: pr

value: unknown

tag: neo-anthracycline

tag: neo-taxane


title: HN108_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN108

value: Female

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

tag: tumor site

tag: Stage

value: HPV-


title: Breast tumor [P5T]

description: Tumor

tag: tissue

tag: age

tag: histology

tag: grade

tag: size

tag: response


title: Oculomotor neurons 1

description:
Oculomotor 0507
Gene expression data from oculomotor neurons from human post-mortem control case.

source_name: Oculomotor neurons, control case 0507

tag: post-mortem control case

tag: cell type

tag: disease state


title: pombe 0.5 WT, biological rep2

description: Gene expression profile of S. pombe SP-Q01 harboring empty vector pESP3 cultured in EMM2 medium to OD600 of 0.5

tag: strain

tag: growth phase


title: colon_epithelium_C57 mouse_12weeks_rep5

city: Palmerston North

first: Anna

last: Moore

address: Tennent Drive

country: New Zealand

institute: AgResearch Ltd

description: Sample 48

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.

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.

value: Swiss

source_name: colon epithelium, C57 mouse, 12 weeks

tag: genotype/variation

value: wildtype

tag: sampling age

value: 12 weeks

value: colon epithelium


title: Lumbar spinal motor neurons 4

description:
Lumbar 9807
Gene expression data from lumbar spinal motor neurons from human post-mortem control case.

source_name: Lumbar spinal motor neurons, control case 9807

value: lumbar spinal motor neurons


title: Lumbar spinal motor neurons 3

description:
Lumbar 8507
Gene expression data from lumbar spinal motor neurons from human post-mortem control case.

source_name: Lumbar spinal motor neurons, control case 8507


title: HN103_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN103

value: Tumor

tag: race

value: Caucasian

tag: gender

tag: smoking packyears

tag: alcohol use

value: Well

value: Oral Cavity

tag: tumor status

tag: node status

tag: treatment

value: Surgery Alone

tag: hpv status


title: Breast tumor [P4T]

description: Tumor

source_name: Breast tumor

tag: tissue

tag: sampleID

tag: age

tag: menopause

tag: histology

tag: grade

tag: size

tag: Stage

tag: pt

tag: pn

tag: er

tag: pr

tag: neo-anthracycline

tag: neo-taxane


title: HN106_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN106

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

tag: tumor site

value: IVa

tag: tumor status

tag: node status


title: HN100_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN100

tag: tissue

tag: age

value: Heavy

value: Larynx

value: I

tag: treatment

tag: hpv status


title: HN102_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN102

value: Male

value: None or Light/Moderate

tag: Stage


title: Breast tumor [P3T]

description: Tumor

tag: sampleID

tag: menopause

tag: histology

tag: grade

tag: size

tag: pt

tag: pn

tag: er

tag: response


title: colon_epithelium_IL10mouse_6weeks_rep6

description: Sample 47

tag: strain

value: Swiss

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

source_name: colon epithelium, IL10 mouse, 6 weeks

tag: genotype/variation

tag: sampling age

value: 6 weeks


title: pombe 0.5 WT, biological rep3

source_name: S. pombe SP-Q01 harboring empty vector pESP3 cultured in EMM2 medium to OD600 of 0.5

tag: growth phase


title: HN097_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN097

tag: tissue

tag: age

tag: race

tag: gender

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

tag: tumor status

tag: node status

value: Concurrent Chemoradiation

value: HPV-


title: colon_epithelium_IL10mouse_12weeks_rep6

description: Sample 46

source_name: colon epithelium, IL10 mouse, 12 weeks

value: 12 weeks

value: colon epithelium


title: pombe 0.5 WT, biological rep1


title: Oculomotor neurons 3

description:
Oculomotor 8507
Gene expression data from oculomotor neurons from human post-mortem control case.

source_name: Oculomotor neurons, control case 8507

tag: post-mortem control case

tag: cell type

value: oculomotor neurons

tag: disease state

value: normal control


title: Lumbar spinal motor neurons 1

description:
Lumbar 0507
Gene expression data from lumbar spinal motor neurons from human post-mortem control case.

source_name: Lumbar spinal motor neurons, control case 0507

value: lumbar spinal motor neurons


title: HN098_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN098

value: Tumor

value: Caucasian

value: Moderate

tag: Stage

value: III

tag: treatment

tag: hpv status


title: Deepwater Horizon site sediment DNA [DWH May 2011-2]

type: mixed

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

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

organism: uncultured ammonia-oxidizing archaeon

source_name: Deepwater Horizon site sediment DNA

value: environmental sample


title: HN095_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN095

tag: tissue

value: Male

value: None or Light/Moderate

value: Poor

value: Oropharynx

value: IVa

value: Surgery Alone

value: HPV+


title: Lumbar spinal motor neurons 2

description:
Lumbar 1207
Gene expression data from lumbar spinal motor neurons from human post-mortem control case.

source_name: Lumbar spinal motor neurons, control case 1207


title: colon_epithelium_C57mouse_6weeks_rep6

description: Sample 45

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

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: LNCaP-shETV1-DHT-C

first: Esther

last: Baena

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Childrens Hospital Boston

description: LNCaP cells transfected with shETV1 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.

source_name: LNCaP cells

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

growth_protocol: Normal growth conditions

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


title: C6 site sediment DNA [C6 Aug 2010]

source_name: C6 site sediment DNA


title: C6 site sediment DNA [C6 May 2010]


title: LNCaP-shETV1-DHT-B

value: transfected with shETV1 were grown in androgen deprived serum for 2 days and then in the presence of 10nM DHT


title: colon_epithelium_IL10mouse_12weeks_rep5

description: Sample 43

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

value: 12 weeks


title: LNCaP-shETV1-DHT-A


title: colon_epithelium_IL10mouse_6weeks_rep5

description: Sample 44


title: LNCaP-shControl-DHT-C

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

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_rep1_2

description:
Sample 42
The sample used on the array called sample 25 was also used on this array as sample 42 due to the intended sample not meeting QC standards. This sample was used as a technical replicate and not included in downstream analysis.

source_name: colon epithelium, C57 mouse, 12 weeks


title: HN094_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN094

value: Tumor

tag: age

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Moderate

value: Surgery and Concurrent Chemoradiation


title: HN096_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN096

value: None or Light/Moderate

tag: tumor site

value: Oral Cavity

value: I

tag: tumor status

tag: node status

value: Surgery Alone

value: HPV-


title: HN092_Affymetrix_GenomeWide_SNP6.0

description: Hybridized to SNP6

source_name: Head and neck squamous cell carcinoma HN092

value: African American

value: Female

value: Well

value: Hypopharynx

tag: Stage

value: IVb

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status


title: C6 site sediment DNA [C6 May 2011]

tag: sample type

value: Universal Internal Standard 20-mer

value: environmental sample