title: Optic fissure_mouse_E12.5_B

source_name: Mouse embryo, optic fissure tissue, embryonic day 12.5

value: C57BL/6,  Age:Embryonic day 12.5, Tissue:Optic fissure


title: TA side population 2Tsp

status: Public on Oct 09 2008

type: RNA

city: Philadelphia

first: Murat

middle: T

last: Budak

state: PA

country: USA

institute: University of Pennsylvania

description:
SP cell preparations were washed, pelleted and resuspended in 20µl of PBS and stored at –80oC until processing for microarray analysis using manufacturers instructions and previously described methods from our laboratory . Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA). The purity, concentration and integrity of RNA was determined using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).
Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays.  Raw intensities for each probe set were stored in electronic formats by expression summaries calculated using Microarray Suite version 5.0 (MAS5) algorithms.

hyb_protocol: The GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Agilent model G2500A GeneArray scanner used.

data_processing: MAS5 normalized data

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Side population cells of TA

tag: C57BL/10ScSnJ mice were used to have SP cells of TA muscle


title: EOM side population 3Esp

source_name: Side population cells of EOM

label_protocol: RNAs were subjected to linear amplification using the GeneChip® Two cycle target-labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA).

tag: C57BL/10ScSnJ mice were used to have SP cells of EOM muscle


title: EOM side population 2Esp

tag: C57BL/10ScSnJ mice were used to have SP cells of EOM muscle.


title: Optic fissure_mouse_E10.5_B

status: Public on Oct 08 2008

city: Bethesda

first: Jacob

last: Brown

state: MD

address: 10 Center Drive

institute: NEI

description: Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter.

hyb_protocol: Labeled samples from each timepoint were then hybridized to Affymetrix MOE 430 2.0 expression microarrays according to manufacturer’s protocol and scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: Raw expression signals and present/absent calls were made using Affymetrix GCOS 1.4.

label: biotin

source_name: Mouse embryo, optic fissure tissue, embryonic day 10.5

label_protocol: Biotin labeling of transcripts was performed in the final round of in vitro transcription using GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: A Veritas laser capture microdissection instrument (Molecular Devices) was used to collect optic fissure tissue from frozen sections through staged, wild-type C57BL6/J mouse embryos.

extract_protocol: Tissue lysates from three embryos from separate litters and the same embryonic stage were pooled and total RNA was extracted using Absolutely RNA Microprep Kit (Stratagene). Pooled RNA was amplified linearly with two rounds of T7 polymerase-mediated in vitro transcription as per instructions in RiboAmp OA kit (Molecular Devices).

treatment_protocol: Wild type embryos dissected in Rnase free 1X PBS.

tag: Strain

value: C57BL/6,  Age:Embryonic day 10.5, Tissue:Optic fissure


title: EOM side population 0Esp


title: Optic fissure_mouse_E12.5_A

scan_protocol: Labeled samples from each timepoint were then hybridized to Affymetrix MOE 430 2.0 expression microarrays according to manufacturer’s protocol and scanned using GeneChip Scanner 3000 (Affymetrix).


title: Optic fissure_mouse_E11.5_A

source_name: Mouse embryo, optic fissure tissue, embryonic day 11.5

value: C57BL/6,  Age:Embryonic day 11.5, Tissue:Optic fissure


title: High Exploration: Neuro-59

first: mark

last: alter

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

description:
Gene expression data from high exploratory Balb c/J females
female balb c/J mice obtained from Jackson and born on the same day were characterized over multiple days and lighting condition:s in the open field behavioir.  Animals were ranked based on the composite behavior (average mean normalized behavior across multiple days and multiple open-field measures:center ambulation:, percent path center, center time, center entries, and total ambulation:.

hyb_protocol: Following fragmentation:, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430_2.0 expression array.

scan_protocol: Affymetrix Mouuse 430_2.0 Array scanned on Affymetrix’s GeneChip Scanner 3000 7G and reviewed for quality control.

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 150.

source_name: whole hippocampus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen RNA/DNA columns per manufacturers instruction:s.

tag: Balb c/J 12 week old females


title: Low Exploration: Neuro-29

description:
Gene expression data from low exploratory Balb c/J females
female balb c/J mice obtained from Jackson and born on the same day were characterized over multiple days and lighting condition:s in the open field behavioir.  Animals were ranked based on the composite behavior (average mean normalized behavior across multiple days and multiple open-field measures:center ambulation:, percent path center, center time, center entries, and total ambulation:.


title: Low Exploration: Neuro-13


title: Low Exploration: Neuro-42


title: High Exploration: Neuro-58


title: High Exploration: Neuro-56


title: High Exploration: Neuro-41


title: Optic fissure_mouse_E10.5_C


title: High Exploration: Neuro-28


title: Non-handled: NH147

description: Gene expression data from non-handled Balb c/J females

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430_2.0 expression array.

data_processing: The data were analyzed with Robust Multiarray Analysis using Affymetrix Expression Console default analysis settings.

source_name: CA1 region hippocampus

extract_protocol: Samples 1-17: Qiagen RNA/DNA columns per manufacturers instructions.  Samples 18-25:Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: handled animals were separated from mothers for 15 minutes every morning on postnatal days 1-14.  Pups and mothers are placed in clean cages during the separation and returned to the original cage after 15 minutes


title: Low Exploration: Neuro-45


title: Handled: H126

description: Gene expression data from postnally handled Balb c/J females


title: Non-handled: NH146


title: Non-handled: NH170


title: Non-handled: NH166


title: Low Exploration: Neuro-30


title: Non-handled: NH144


title: Handled: H130


title: Non-handled: NH167


title: Non-handled: NH163


title: Non-handled: NH155


title: Non-handled: NH138


title: Non-handled: NH165


title: Handled: H131


title: Handled: H113


title: Non-handled: NH157


title: Non-handled: NH156


title: Non-handled: NH142


title: Non-handled: NH162


title: Optic fissure_mouse_E11.5_C


title: Handled: H118


title: LWD1 and LWD2 in Arabidopsis photoperiod regulation (wt rep 2)

city: Taipei

first: Shu-Hsing

last: Wu

address: 128, Sec 2, Academia Road

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica

description: This experiment was conducted to reveal genes differentially expressed between wild-type Arabidopsis and lwd1lwd2 double mutant at ZT5-9.

hyb_protocol: Eleven microgram labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 hr.  Washing and staining involved Fluidic Station-450 and the ATH1 Genome

scan_protocol: Array was scanned with use of the Affymetrix GeneChip Scanner 7G.

data_processing: The results were quantified and analyzed by use of MicroArray Suite 5.0 software (Affymetrix Inc.).

organism: Arabidopsis thaliana

source_name: wild-type

label_protocol: Ten microgram of total RNA was used for cDNA synthesis, labeled by in vitro transcription, followed by fragmentation according to the manufacturer’s suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

extract_protocol:
Pine tree extraction method
Chang S, Puryear J, Cainey J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11: 113-116

tag: wild-type rep 2


title: Handled: H123


title: Handled: H110


title: Handled: H116


title: Handled: H108


title: Handled: H117


title: LWD1 and LWD2 in Arabidopsis photoperiod regulation (lwd1lwd2 rep 2)

source_name: lwd1lwd2 rep 2

tag: ground tissues of 31-d-old wild-type Arabidopsis grown under 12 h L/12 h D  were harvested at ZT5~9.


title: Handled: H109


title: Light damage RPE replicate 2

status: Public on Oct 07 2008

city: Baltimore

first: Amir

last: Rattner

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

description:
Light damaged replicate 2
contact Amir Rattner (arattne1@jhmi.edu) for details

hyb_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

data_processing: RMA (bioconductor)

source_name: BALBc mouse RPE RNA, light damaged

label_protocol:
Affymetrix small sample labeling protocol VII
Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/

extract_protocol: Total RNA from RPE was extracted with Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA).

tag: RPE RNA from BALBc mice, light damaged for 1.5 hours under 6,000 lux white fluorescent light and allowed to recover for 24 hours in the dark.


title: LWD1 and LWD2 in Arabidopsis photoperiod regulation (lwd1lwd2 rep 1)

tag: lwd1lwd2 double mutant rep 1


title: Light damage RPE replicate 1

description:
Light damaged replicate 1
contact Amir Rattner (arattne1@jhmi.edu) for details

scan_protocol: Affymetrix protocol Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/


title: Dark adapted RPE control replicate 2

description:
Dark adapted control replicate 2
contact Amir Rattner (arattne1@jhmi.edu) for details

source_name: BALBc mouse RPE RNA, dark adapted

tag: RPE RNA from BALBc mouse, dark adapted


title: LWD1 and LWD2 in Arabidopsis photoperiod regulation (wt rep 1)

source_name: wild-type rep 1

tag: Above ground tissues of 31-d-old wild-type Arabidopsis grown under 12 h L/12 h D  were harvested at ZT5~9.


title: Dark adapted RPE control replicate 3

description:
Dark adapted control replicate 3
contact Amir Rattner (arattne1@jhmi.edu) for details


title: Light damage RPE replicate 3

description:
Light damaged replicate 3
contact Amir Rattner (arattne1@jhmi.edu) for details


title: Dark adapted RPE control replicate 1

description:
Dark adapted control replicate 1
contact Amir Rattner (arattne1@jhmi.edu) for details


title: 1mg/kg/day PFOA, Rep 3, Block 4, liver (low dose)

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

state: NC

department: Reproductive Toxicology

institute: U.S. EPA

description: Fetal liver gene expression data from full term pups exposed to PFOA throughout gestation.

hyb_protocol: Following fragmentation, samples were hybridized overnight at 45C according to the protocols recommended by the manufacturer in an Affymetrix Model 640 GeneChip hybridization oven

scan_protocol: The arrays were washed and stained using an Affymetrix 450 fluidics station as recommended by the manufacturer, and scanned on an Affymetrix Model 3000 scanner.

data_processing: Probe set data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (Irizarry et al., 2003) as provided by RMA Express (version 0.4).

source_name: Fetal liver CD-1 background

label_protocol: Biotin-labeled cRNA was produced from 2 ug total RNA using an Affymetrix “one-way” labeling kit (cat# 900493).

extract_protocol: Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturer’s directions. RNA pellets were then washed in cold 80% ethanol and stored at -80?C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturer’s directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.0.

treatment_protocol: Timed-pregnant CD-1 mice were dosed by oral gavage from gestation day (GD)1 through GD 17 with PFOA (ammonium salt) prepared fresh each day in deionized water.  The presence of a sperm plug was considered GD 0.   On GD18, dams were euthanized by CO2 asphyxiation and three fetuses per litter were collected for preparation of total RNA from a portion of the liver and lung.

tag: Pooled litter samples were collected 24 hrs after the final compound dose.


title: 1mg/kg/day PFOA, Rep 4, Block 1, liver (low dose)


title: 3mg/kg/day PFOA, Rep 5, Block 2, liver (low dose)

source_name: Fetal liver, CD-1 background


title: 3mg/kg/day PFOA, Rep 4, Block 4, liver (low dose)


title: 3mg/kg/day PFOA, Rep 2, Block 1, liver (low dose)


title: 3mg/kg/day PFOA, Rep 3, Block 5, lung (low dose)

description: Fetal lung gene expression data from full term pups exposed to PFOA throughout gestation.

source_name: Fetal lung, CD-1 background


title: 0mg/kg/day PFOA, Rep 5, Block 3, lung (low dose)


title: 3mg/kg/day PFOA, Rep 1, Block 3, lung (low dose)


title: 3mg/kg/day PFOA, Rep 4, Block 4, lung (low dose)


title: 1mg/kg/day PFOA, Rep 3, Block 4, lung (low dose)


title: 1mg/kg/day PFOA, Rep 2, Block 3, lung (low dose)


title: 3mg/kg/day PFOA, Rep 1, Block 3, liver (low dose)


title: 0mg/kg/day PFOA, Rep 5, Block 3, liver (low dose)


title: 1mg/kg/day PFOA, Rep 1, Block 2, liver (low dose)


title: 1mg/kg/day PFOA, Rep 1, Block 2, lung (low dose)


title: 3mg/kg/day PFOA, Rep 2, Block 1, lung (low dose)


title: 3mg/kg/day PFOA, Rep 5, Block 2, lung (low dose)


title: 1mg/kg/day PFOA, Rep 1, Block 5, liver (low dose)


title: 3mg/kg/day PFOA, Rep 3, Block 5, liver (low dose)


title: 0mg/kg/day PFOA, Rep 4, Block 4, liver (low dose)


title: 1mg/kg/day PFOA, Rep 4, Block 1, lung (low dose)

source_name: Fetal lung CD-1 background


title: 1mg/kg/day PFOA, Rep 2, Block 3, liver (low dose)


title: 0mg/kg/day PFOA, Rep 4, Block 4, lung (low dose)


title: colon cells, at 0h

city: Hamburg

first: Annika

last: Sprüssel

address: Orchideenstieg 14

country: Germany

institute: Indivumed GmbH

description: Gene expression data from cells of cell line HT29 from colorectal adenocarcinoma, directly before cell seeding (0h)

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed and normalized with ArrayAssist 4.2.0 (MAS 5.0).

organism: Homo sapiens

source_name: cells after 0h of cultivation, cell line HT29

growth_protocol: reference tissues were snap frozen in liquid nitrogen (resection to freezing interval < 14 min), whereas second pieces of tissue were used to isolate viable primary cells, which were collected for samples directly after isolation (means 0h) and cultured in multi well plates for 24 and 72 hours before sampling for microarray analysis.

extract_protocol: RNA Stat60 extraction (phenol chloroform) of total RNA was performed with protocol described by Chomczymski and Sacchi (1987).

treatment_protocol: Primary cells, tissue slices or cell line HT29 were cultured indicated times bevor sampling for microarray analysis without any treatment.

tag: cells after 0h of cultivation

tag: cell line HT29


title: colon cells, at 72h

description: Gene expression data from cells of cell line HT29 from colorectal adenocarcinoma, cultivated 72 hours

source_name: cells after 72h of cultivation, cell line HT29

tag: cells after 72h of cultivation


title: colon7, primary cells at 72h

description: Gene expression data from primary cells of patient number 7 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 7

tag: primary cells after 72h of cultivation

tag: patient 7


title: colon7, primary cells at 0h

description: Gene expression data from primary cells of patient number 7 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 7

tag: primary cells after 0h of cultivation


title: colon cells, at 24h

description: Gene expression data from cells of cell line HT29 from colorectal adenocarcinoma, cultivated 24 hours

source_name: cells after 24h of cultivation, cell line HT29

tag: cells after 24h of cultivation


title: colon7, primary cells at 24h

description: Gene expression data from primary cells of patient number 7 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 7

tag: primary cells after 24h of cultivation


title: 0mg/kg/day PFOA, Rep 2, Block 1 lung (low dose)


title: 0mg/kg/day PFOA, Rep 3, Block 2 lung (low dose)


title: colon6, primary cells at 72h

description: Gene expression data from primary cells of patient number 6 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 6

tag: patient 6


title: 0mg/kg/day PFOA, Rep 3, Block 2, liver (low dose)


title: 0mg/kg/day PFOA, Rep 2, Block 1 liver (low dose)


title: colon5, primary cells at 72h

description: Gene expression data from primary cells of patient number 5 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 5

tag: patient 5


title: 10mg/kg/day PFOA, Rep 4, Block 4, lung (high dose)

label_protocol: Biotin-labeled cRNA was produced from 2 ug total RNA using an Affymetrix ôone-wayö labeling kit (cat# 900493).

extract_protocol: Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturerÆs directions. RNA pellets were then washed in cold 80% ethanol and stored at -80?C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturerÆs directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.0.


title: 0mg/kg/day PFOA, Rep 1, Block 5 lung (low dose)


title: colon6, tissue at reference

description: Gene expression data from reference tissue of patient number 6 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 6

tag: reference tissue after resection


title: colon6, primary cells at 0h

description: Gene expression data from primary cells of patient number 6 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 6


title: colon6, primary cells at 24h

description: Gene expression data from primary cells of patient number 6 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 6


title: colon5, primary cells at 24h

description: Gene expression data from primary cells of patient number 5 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 5


title: 10mg/kg/day PFOA, Rep 4, Block 4, liver (high dose)


title: 10mg/kg/day PFOA, Rep 3, Block 3, lung (high dose)


title: 10mg/kg/day PFOA, Rep 5, Block 5, lung (high dose)


title: colon7, tissue at reference

description: Gene expression data from reference tissue of patient number 7 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 7


title: 0mg/kg/day PFOA, Rep 1, Block 5 liver (low dose)


title: 10mg/kg/day PFOA, Rep 5, Block 5, liver (high dose)


title: 10mg/kg/day PFOA, Rep 2, Block 1, liver (high dose)


title: 10mg/kg/day PFOA, Rep 3, Block 3, liver (high dose)


title: colon4, primary cells at 72h

description: Gene expression data from primary cells of patient number 4 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 4

tag: patient 4


title: colon5, tissue at reference

description: Gene expression data from reference tissue of patient number 5 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 5


title: colon3, primary cells at 24h

description: Gene expression data from primary cells of patient number 3 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 3

tag: patient 3


title: colon4, primary cells at 24h

description: Gene expression data from primary cells of patient number 4 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 4


title: 10mg/kg/day PFOA, Rep 1, Block 2, liver (high dose)

description: Fetal liver gene expression data from full term pups exposed to PFOA throughout gestation.

source_name: Fetal liver, CD-1 background


title: colon4, primary cells at 0h

description: Gene expression data from primary cells of patient number 4 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 4


title: colon4, tissue at reference

description: Gene expression data from reference tissue of patient number 4 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 4


title: colon3, primary cells at 0h

description: Gene expression data from primary cells of patient number 3 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 3


title: colon3, primary cells at 72h

description: Gene expression data from primary cells of patient number 3 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 3


title: 10mg/kg/day PFOA, Rep 2, Block 1, lung (high dose)

description: Fetal lung gene expression data from full term pups exposed to PFOA throughout gestation.

source_name: Fetal lung, CD-1 background


title: 5mg/kg/day PFOA, Rep 5, Block 4, liver (high dose)

source_name: Fetal liver CD-1 background


title: colon2, tissue at reference

description: Gene expression data from reference tissue of patient number 2 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 2

tag: patient 2


title: colon2, primary cells at 0h

description: Gene expression data from primary cells of patient number 2 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 2


title: colon2, primary cells at 72h

description: Gene expression data from primary cells of patient number 2 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 2


title: 5mg/kg/day PFOA, Rep 5, Block 4, lung (high dose)

source_name: Fetal lung CD-1 background


title: colon3, tissue at reference

description: Gene expression data from reference tissue of patient number 3 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 3


title: 5mg/kg/day PFOA, Rep 2, Block 1, lung (high dose)


title: 10mg/kg/day PFOA, Rep 1, Block 2, lung (high dose)


title: 5mg/kg/day PFOA, Rep 3, Block 2, liver (high dose)


title: 5mg/kg/day PFOA, Rep 4, Block 3, lung (high dose)


title: 5mg/kg/day PFOA, Rep 4, Block 3, liver (high dose)


title: 5mg/kg/day PFOA, Rep 1, Block 5, liver (high dose)


title: 5mg/kg/day PFOA, Rep 1, Block 5, lung (high dose)


title: 5mg/kg/day PFOA, Rep 3, Block 2, lung (high dose)


title: 0mg/kg/day PFOA, Rep 4, Block 4, lung (high dose)


title: colon1, tissue at reference

description: Gene expression data from reference tissue of patient number 1 with colorectal cancer, directly after tumor resection

source_name: reference tissue after resection, patient 1

tag: patient 1


title: Multipotent stromal cells (MSCs)_outside of colonies_2

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description: Transcriptome analysis of cells from the outside region of MSC colonies.

hyb_protocol: Biotin-labeled cDNA (1.6-2.2 ug) was hybridized on the HG-U133 Plus 2.0 microarray. After washing, the array was stained with streptavidin-phycoerythrin (Invitrogen), amplified with biotinylated anti-streptavidin (Vector Laboratories) and stained with streptavidin-phycoerythrin.

scan_protocol: The array was scanned on a GeneChip Scanner 3000 (Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix).

data_processing: The data was analyzed with GeneChip Operating Software 1.0 (GCOS, Affymetrix) and dChip program. The arrays in the set were normalized using the invariant set normalization method and model-based expression values were calculated using the signal from perfect match and mismatch probes. Negative values were assigned a value of one.

source_name: Cells from the outside region of bone marrow multipotent stromal cell (MSCs) colonies

label_protocol: Ten nanograms of total RNA was used in the amplification and labeling steps performed with Ovation™ Biotin RNA Amplification and Labeling System (NuGEN Technologies). First strand cDNA was prepared using DNA/RNA chimeric primers and reverse transcriptase. A DNA/RNA heteroduplex double stranded cDNA was then synthesized using DNA polymerase. The synthesized cDNA was used for SPIA™ amplification with SPIA™ DNA/RNA chimeric primer, DNA polymerase and RNase H. The amplified cDNA was purified (Zymo Research DNA Clean and Concentrator™-25 columns, Zymo Research) and enzymatically fragmented. Biotin was attached chemically and the product was purified with DyeEx 2.0 kit (Qiagen).

growth_protocol: Human MSCs were isolated from 1– 4-ml bone marrow aspirates taken from the iliac crest of normal adult donors. Nucleated cells were isolated with a density gradient and resuspended in complete culture medium (CCM) consisting of alpha-minimal essential medium, 17% fetal bovine serum (FBS), 100 units/ml penicillin, 100 ug/ml streptomycin, and 2 mM L-glutamine. All of the nucleated cells were plated in 20 ml of medium in a 175-cm2 culture dish and incubated at 37°C with 5% CO2. After 24 hours, nonadherent cells were discarded, and adherent cells were thoroughly washed twice with phosphate-buffered saline (PBS). The cells were incubated 4 –11 days until approximately 70% confluent, harvested with 0.25% trypsin and 1 mM EDTA for 5 minutes at 37°C, and replated at 50 cells/cm2 in an intercommunicating system of cultureflasks. The cells were incubated 7–10 days until approximately 70% confluent, harvested with trypsin/EDTA, suspended at 1 million cells/ml in 5% dimethyl sulfoxide and 30% FBS, and frozen in 1-ml aliquots at -80°C overnight and then placed in liquid nitrogen (passage 1 cells). A frozen vial of MSCs was then thawed and cells were plated in a 145-cm2 culture dish in CCM. After 24-hour incubation at 37°C and 5% CO2, the medium was removed, cells were washed with PBS, and adherent viable cells were harvested with trypsin/EDTA. Recovered passage 1 MSCs were then plated at 2 cells/cm2 on laser capture microdissection and pressure catapulting (LMPC) slides that were placed into 57-cm2 plastic dishes. Cells were cultured for 10-12 days in CCM until dense colonies that were at least 4 mm in diameter were observed. Slides were washed with PBS, fixed with ice-cold 100% ethanol, and dried. Colonies with distinct outer (OUT) and inner (IN) regions were outlined and laser microdissected. Dissected OUT or IN cells from two colonies were catapulted separately into one cap, filled with 20 ul of extraction buffer.

extract_protocol: Dissected OUT or IN cells from two colonies were catapulted separately into one cap, filled with 20 ul of extraction buffer (PicoPure RNA Isolation Kit, Molecular Devices). Cells were spun down at 800g for 2 minutes, mixed by pipetting, and incubated at 42°C for 30 minutes before cooling to 4°C. Total RNA was extracted with PicoPure RNA Isolation Kit with DNase treatment (RNase-Free DNase Set, Qiagen).

tag: MSCs isolated from the iliac crest of normal adult donors.


title: 0mg/kg/day PFOA, Rep 4, Block 4, liver (high dose)

tag: Pooled litter samples were collected 24 hrs after the final compound dose.


title: 0mg/kg/day PFOA, Rep 5, Block 5, liver (high dose)


title: 0mg/kg/day PFOA, Rep 5, Block 5, lung (high dose)


title: 5mg/kg/day PFOA, Rep 2, Block 1, liver (high dose)


title: Multipotent stromal cells (MSCs)_outside of colonies_3


title: colon2, primary cells at 24h

description: Gene expression data from primary cells of patient number 2 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 2


title: Multipotent stromal cells (MSCs)_inside of colonies_3

description: Transcriptome analysis of cells from the inside region of MSC colonies.

source_name: Cells from the inside region of bone marrow multipotent stromal cell (MSCs) colonies


title: colon1, primary cells at 24h

description: Gene expression data from primary cells of patient number 1 with colorectal cancer, cultivated 24 hours after cell isolation

source_name: primary cells after 24h of cultivation, patient 1


title: colon1, primary cells at 0h

description: Gene expression data from primary cells of patient number 1 with colorectal cancer, directly after cell isolation (0h)

source_name: primary cells after 0h of cultivation, patient 1


title: Multipotent stromal cells (MSCs)_inside of colonies_2


title: Multipotent stromal cells (MSCs)_outside of colonies_1


title: colon1, primary cells at 72h

description: Gene expression data from primary cells of patient number 1 with colorectal cancer, cultivated 72 hours after cell isolation

source_name: primary cells after 72h of cultivation, patient 1


title: Multipotent stromal cells (MSCs)_inside of colonies_1


title: 0mg/kg/day PFOA, Rep 1, Block 2 liver (high dose)

description: Fetal liver gene expression data from full term pups exposed to PFOA throughout gestation.

source_name: Fetal liver, CD-1 background


title: 0mg/kg/day PFOA, Rep 3, Block 3, liver (high dose)


title: 0mg/kg/day PFOA, Rep 2, Block 1 liver (high dose)


title: 0mg/kg/day PFOA, Rep 1, Block 2 lung (high dose)


title: C57BL/6 whole lung-resiquimod treated and ovalbumin challenged-biological rep.1

status: Public on Oct 04 2008

city: Montreal

first: Pierre

last: Camateros

state: Quebec

address: 1650 Cedar Ave

department: Experimental Medicine

country: Canada

institute: McGill University

description: gene expression data from the lungs of an acute mouse model of allergic asthma, and following resiquimod treatment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C with a rotation of 60rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: Background correction and normalization were performed with the RMA method (default settings, version 1.12.2) as implemented in the affy package in the R environment.

source_name: whole lung, C57BL/6 mouse, resiquimod treated and ovalbumin challenged

label_protocol: Following double stranded cDNA synthesis, labeled cRNA was produced with the ENZO BioArray High Yield RT Labeling Kit according to the manufacturer's instructions

growth_protocol: Mice were maintained in the Montreal General Hospital conventional rodent facility. Standard wood chip bedding and rodent chow were used. Food and water provided ad libitum. One to five animals per cage.

extract_protocol: Whole lungs were homogenized in 4mL of TRIzol reagent and RNA was isolated per manufacturer's instructions

treatment_protocol: Mice were sensitized once a week for three consecutive weeks by intraperitoneal injections of 100 μg of ovalbumin adsorbed to 37.5 μL Imject Alum (Pierce, Rockford, IL) in a total volume of 0.2 ml of sterile PBS. Seven days following the final sensitization mice were challenged on 3 consecutive days by aerosol exposure to either a 1% ovalbumin solution (OVA-OVA and OVA-S28 group) or PBS alone (OVA-PBS group) for 30 min. One group of mice was injected intraperitoneally with 100 μg of S-28463 (resiquimod, R-848) on 3 consecutive days starting 1 day before the first ovalbumin challenge (OVA-S28 group).

tag: Strain

value: C57BL/6 Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, resiquimod treated, ovalbumin challenged


title: A/J whole lung-ovalbumin challenged-biological rep.1

source_name: whole lung, A/J mouse, ovalbumin challenged

value: A/J Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, ovalbumin challenged


title: C57BL/6 whole lung-ovalbumin challenged-biological rep.1

source_name: whole lung, C57BL/6 mouse, ovalbumin challenged

value: C57BL/6 Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, ovalbumin challenged


title: A/J whole lung-ovalbumin challenged-biological rep.3


title: C57BL/6 whole lung-resiquimod treated and ovalbumin challenged-biological rep.3


title: C57BL/6 whole lung-PBS challenged-biological rep.2

source_name: whole lung, C57BL/6 mouse, PBS challenged

value: C57BL/6 Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, PBS challenged


title: 0mg/kg/day PFOA, Rep 3, Block 3 lung (high dose)

source_name: Fetal lung, CD-1 background


title: C57BL/6 whole lung-PBS challenged-biological rep.1


title: A/J whole lung-resiquimod treated and ovalbumin challenged-biological rep.2

source_name: whole lung, A/J mouse, resiquimod treated and ovalbumin challenged

value: A/J Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, resiquimod treated, ovalbumin challenged


title: A/J whole lung-PBS challenged-biological rep.2

source_name: whole lung, A/J mouse, PBS challenged

value: A/J Gender:Male Age:16 weeks Tissue:whole lung Treatment:Ovalbumin sensitized, PBS challenged


title: A/J whole lung-ovalbumin challenged-biological rep.2


title: 0mg/kg/day PFOA, Rep 2, Block 1 lung (high dose)


title: head, PatDp(dist2)

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Comparison of gene expression levels between MatDp(dist2) and PatDp(dist2) mice. Identification of highly differentially expressed transcripts. See T11H series record.

hyb_protocol: 15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol.

scan_protocol: The Affymetrix Scanner 3000 system was used. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

source_name: newborn head, PatDp(dist2) (=MatDp(dist9)), distal T11H

label_protocol: Isolated total RNA was quantified on an Agilent Bioanalyser and 5 to 7µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Total RNA was isolated from tissues using the Qiagen RNeasy mini (Cat. No. 74104) kit

treatment_protocol: Tissues were snap frozen in liquid nitrogen, permanently stored at -80C, and put on dry ice during transport.

value: offspring of T(2:9)11H translocation mice (see MRC at Harwell, Mammalian Genetics Unit) having a paternally-derived uniparental duplication of Chr 2 distal of the T11H breakpoint and, consequently, a maternally-derived uniparental duplication of Chr 9 distal of the T11H breakpoint

tag: Age

value: newborn

tag: Tissue

value: whole head


title: A/J whole lung-PBS challenged-biological rep.1


title: A/J whole lung-resiquimod treated and ovalbumin challenged-biological rep.3


title: A/J whole lung-resiquimod treated and ovalbumin challenged-biological rep.1


title: C57BL/6 whole lung-ovalbumin challenged-biological rep.3


title: head, MatDp(dist2)

source_name: newborn head, MatDp(dist2) (=PatDp(dist9)), distal T11H

value: offspring of T(2:9)11H translocation mice (see MRC at Harwell, Mammalian Genetics Unit) having a maternally-derived uniparental duplication of Chr 2 distal of the T11H breakpoint and, consequently, a paternally-derived uniparental duplication of Chr 9 distal of the T11H breakpoint


title: C57BL/6 whole lung-ovalbumin challenged-biological rep.2


title: C57BL/6 whole lung-resiquimod treated and ovalbumin challenged-biological rep.2


title: A/J whole lung-PBS challenged-biological rep.3


title: Circadian time 65 Liver_CT65

status: Public on Oct 03 2008

first: Michael

last: Hughes

address: 421 Curie Bvd, Brb 835

institute: UPenn

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.

source_name: Liver

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Mice were house in light-tight chambers and entrained to a 12 hours light, 12 hours dark environment before being released into constant darkness.

extract_protocol: Mice were euthanized in the dark and liver samples were quickly excised.

tag: adult, male C57Bl/6J


title: Circadian time 63 Liver_CT63


title: Circadian time 61 Liver_CT61


title: C57BL/6 whole lung-PBS challenged-biological rep.3


title: Circadian time 62 Liver_CT62


title: Circadian time 60 Liver_CT60


title: Circadian time 55 Liver_CT55


title: Circadian time 58 Liver_CT58


title: Circadian time 64 Liver_CT64


title: Circadian time 57 Liver_CT57


title: Circadian time 56 Liver_CT56


title: Circadian time 59 Liver_CT59


title: Circadian time 54 Liver_CT54


title: Circadian time 53 Liver_CT53


title: Circadian time 52 Liver_CT52


title: Circadian time 51 Liver_CT51


title: Circadian time 49 Liver_CT49


title: Circadian time 45 Liver_CT45


title: Circadian time 42 Liver_CT42


title: Circadian time 43 Liver_CT43


title: Circadian time 40 Liver_CT40


title: Circadian time 50 Liver_CT50


title: Circadian time 46 Liver_CT46


title: Circadian time 44 Liver_CT44


title: Circadian time 48 Liver_CT48


title: Circadian time 41 Liver_CT41


title: Circadian time 39 Liver_CT39


title: Circadian time 34 Liver_CT34


title: Circadian time 38 Liver_CT38


title: Circadian time 37 Liver_CT37


title: Circadian time 36 Liver_CT36


title: Circadian time 35 Liver_CT35


title: Circadian time 31 Liver_CT31


title: Circadian time 29 Liver_CT29


title: Circadian time 33 Liver_CT33


title: Circadian time 32 Liver_CT32


title: Circadian time 28 Liver_CT28


title: Breast - 486191

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 10
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Mammogram: Yes
Retreatment T: 2
Retreatment N: 2a
Retreatment M: X
Retreatment Stage: Unknown
Retreatment Grade: 3
Retreatment Multiple Tumors: No
Retreatment ER: Negative
Retreatment PR: Negative
Retreatment HER/2 Neu: Negative
Primary Site: Breast
Histology: Invasive Ductal Carcinoma

source_name: Breast


title: Circadian time 24 Liver_CT24


title: Stomach - 486178

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Melanoma of Skin
Histology: Metastatic Malignant melanoma,NOS

source_name: Stomach


title: Rectosigmoid - 486168

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Colon - 486175

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 80-89
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Kidney - 486176

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-59
Gender: Female
Ethnic Background: American Indian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 43
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Rectosigmoid Colon - 486190

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Rectosigmoid Colon


title: Circadian time 25 Liver_CT25


title: Circadian time 27 Liver_CT27


title: Circadian time 30 Liver_CT30


title: Circadian time 26 Liver_CT26


title: Colon - 486173

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 30-39
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 36
Presenting Symptoms: Abdominal Pain
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Circadian time 22 Liver_CT22


title: Lung - 472804

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Bronchioloalveolar carcinoma

source_name: Lung


title: Pancreas - 486167

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 36
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Pancreas
Histology: Ductal adenocarcinoma

source_name: Pancreas


title: Cervix - 472800

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 30-39
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B1
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Mucinous Adenocarcinoma, Endocervical Type

source_name: Cervix


title: Circadian time 23 Liver_CT23


title: Vulva - 472787

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Vulva
Histology: Keratinizing squamous cell carcinoma

source_name: Vulva


title: Uterus - 472798

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: Kidney - 472789

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-59
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Endometrium - 468499

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3a
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Papillary Serous Adenocarcinoma

source_name: Endometrium


title: Breast - 486165

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 29
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2A
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical ER: Positive
Clinical PR: Positive
Clinical HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Circadian time 20 Liver_CT20


title: Circadian time 19 Liver_CT19


title: Colon - 468495

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Pathological T: 4
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: D
Primary Site: Colon
Histology: Mucinous Adenocarcinoma


title: Circadian time 18 Liver_CT18


title: 61 hours NIH3T3_Forskolin_61

source_name: NIH3T3 fibroblasts

growth_protocol: NIH3T3 cells (ATCC) were grown to confluence in DMEM supplimented with 10% FCS and P/S/G on 35mm dishes.

extract_protocol: Cells were washed briefly with 1X PBS.  1 mL Trizol (Invitrogen) was used to homogenize cells, and samples were frozen at -80 until total RNA was purified.

treatment_protocol: Cells were synchronized with forskolin 20 hours before samples were collected.

tag: synchronized with forskolin


title: Circadian time 21 Liver_CT21


title: 60 hours NIH3T3_Forskolin_60


title: Breast - 468479

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Invasive Ductal Carcinoma


title: stomach - 465760

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 8
Have you ever had esophagitis/reflux?: Yes
Pathological T: 2b
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Osseous
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Stomach
Histology: Adenocarcinoma, intestinal type

source_name: stomach


title: Bone - 468494

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 20-29
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Retreatment T: 2
Retreatment N: 0
Retreatment M: X
Pathological Stage: Unknown
Retreatment Stage: Unknown
Retreatment Grade: 3
Pathological Multiple Tumors: No
Retreatment Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Bone
Histology: Osteosarcoma

source_name: Bone


title: 64 hours NIH3T3_Forskolin_64


title: 63 hours NIH3T3_Forskolin_63


title: 62 hours NIH3T3_Forskolin_62


title: 65 hours NIH3T3_Forskolin_65


title: 67 hours NIH3T3_Forskolin_67


title: 66 hours NIH3T3_Forskolin_66


title: Circadian time 47 Liver_CT47


title: Vulva - 468484

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Vulva
Histology: Keratinizing squamous cell carcinoma


title: Uterus - 472782

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Rectum - 465701

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-49
Gender: Female
Ethnic Background: American Indian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological Dukes Stage: D
Primary Site: Rectum
Histology: Signet Ring Cell Carcinoma

source_name: Rectum


title: Kidney - 465699

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: 58 hours NIH3T3_Forskolin_58


title: Rectosigmoid colon - 468475

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-49
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: is
Pathological N: 0
Pathological M: 0
Pathological Stage: 0
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Rectosigmoid
Histology: Adenocarcinoma In Situ in a Villous Adenoma

source_name: Rectosigmoid colon


title: Femoral Lymph Node - 465731

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Night sweats
Have you ever had mononucleousis?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Retreatment Stage: 3
Retreatment Symptoms: B
Primary Site: Lymph Nodes (Nodal Lymphoma)
Histology: Mantle cell lymphoma

source_name: Femoral Lymph Node


title: 57 hours NIH3T3_Forskolin_57


title: Brain - 465700

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 20-29
Gender: Male
Ethnic Background: Caucasian
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Clinical Question: Stage
Clinical Value: No AJCC Staging Scheme for this Site/Histology
Clinical Question: Grade
Clinical Value: WHO Grade II
Primary Site: Brain
Clinical Question: Histology
Clinical Value: Astrocytoma

source_name: Brain


title: liver - 465685

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Screening studies performed?: Yes
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: 3
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Retreatment Dukes Stage: D
Primary Site: Rectosigmoid
Histology: Metastatic Adenocarcinoma

source_name: liver


title: Kidney - 465657

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: 55 hours NIH3T3_Forskolin_55


title: Ascending Colon - 465682

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 15
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Ascending Colon


title: 56 hours NIH3T3_Forskolin_56


title: Kidney - 465654

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Kidney - 465640

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: 54 hours NIH3T3_Forskolin_54


title: 59 hours NIH3T3_Forskolin_59


title: 52 hours NIH3T3_Forskolin_52


title: Small Intestine - 458417

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: X
Clinical N: X
Clinical M: X
Clinical Grade: X
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Small Intestine
Histology: Carcinoid Tumor

source_name: Small Intestine


title: Ascending Colon - 465656

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Kidney - 465652

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 3b
Pathological N: 1
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: 49 hours NIH3T3_Forskolin_49


title: Colon - 438154

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical Question: Stage
Clinical Value: No AJCC Staging Scheme for this Site/Histology
Clinical Question: Grade
Clinical Value: 3
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Clinical Question: Symptoms
Clinical Value: Nausea & Vomiting
Primary Site: Unknown Primary
Clinical Question: Histology
Clinical Value: Metastatic Adenocarcinoma

source_name: Colon


title: 44 hours NIH3T3_Forskolin_44


title: 50 hours NIH3T3_Forskolin_50


title: 45 hours NIH3T3_Forskolin_45


title: Breast - 438183

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Mammogram: No
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 3
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Invasive Ductal Carcinoma

source_name: Breast


title: 48 hours NIH3T3_Forskolin_48


title: 46 hours NIH3T3_Forskolin_46


title: Colon - 438173

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: 53 hours NIH3T3_Forskolin_53


title: Prostate - 426428

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Clinical T: 2c
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Kidney - 458411

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 438178

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma


title: Cervix - 440434

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Have you ever been diagnosed as having HPV on your PAP smear?: No
Retreatment T: 1b1
Retreatment N: 0
Retreatment M: 0
Retreatment Stage: 1B1
Retreatment Grade: 1
Retreatment Multiple Tumours: No
Retreatment Staged During or Following Multimodality Therapy: Yes
Primary Site: Cervix Uteri
Histology: Mucinous Adenocarcinoma, Endocervical Type

source_name: Cervix


title: Prostate - 458403

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
PSA: Elevated
Clinical T: 2a
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: 51 hours NIH3T3_Forskolin_51


title: 47 hours NIH3T3_Forskolin_47


title: 42 hours NIH3T3_Forskolin_42


title: Prostate - 426426

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 50
Presenting Symptoms: Hesitancy
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Clinical T: 2a
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Uterus - 426427

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 40
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Adenocarcinoma

source_name: Uterus


title: 43 hours NIH3T3_Forskolin_43


title: Chest Wall - 426425

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 3
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Brain
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Metastatic Squamous cell carcinoma

source_name: Chest Wall


title: 41 hours NIH3T3_Forskolin_41

source_name: NIH3T3 fibroblasts


title: Prostate - 426423

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
PSA: Normal
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Clinical T: 2b
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: 38 hours NIH3T3_Forskolin_38


title: 40 hours NIH3T3_Forskolin_40


title: 39 hours NIH3T3_Forskolin_39


title: Ovary - 426416

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 9
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma

source_name: Ovary


title: 35 hours NIH3T3_Forskolin_35


title: 36 hours NIH3T3_Forskolin_36


title: Liver - 426424

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Clinical Question: T
Clinical Value: 1
Clinical Question: N
Clinical Value: 0
Clinical Question: M
Clinical Value: 0
Clinical Question: Stage
Clinical Value: 1
Clinical Question: Grade
Clinical Value: 2
Clinical Question: Multiple Tumors
Clinical Value: No
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Primary Site: Liver
Clinical Question: Histology
Clinical Value: Hepatocellular Carcinoma

source_name: Liver


title: Rectosigmoid - 426421

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 31
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Axillary Lymph Node - 421749

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Days from Patient Diagnosis to Excision: 20
Mammogram: Yes
Mammogram calcifications?: No
Pathological T: 1b
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Axillary Lymph Node


title: Cecum - 423078

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Cecum


title: 34 hours NIH3T3_Forskolin_34


title: Vulva - 409632

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 4b
Clinical N: 2c
Clinical M: X
Clinical Stage: 3B
Clinical Multiple Tumors: Yes
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Melanoma of Skin
Histology: Nodular melanoma

source_name: Vulva


title: 37 hours NIH3T3_Forskolin_37


title: 32 hours NIH3T3_Forskolin_32


title: 29 hours NIH3T3_Forskolin_29


title: Liver - 366611

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Pathological T: X
Pathological N: 2
Pathological M: 0
Pathological Stage: 3A
Primary Site: Breast
Histology: Metastatic Adenocarcinoma


title: 27 hours NIH3T3_Forskolin_27


title: 28 hours NIH3T3_Forskolin_28


title: Breast - 383900

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 43
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Invasive Ductal Carcinoma


title: Breast - 192994

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 18
Mammogram: Yes
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Invasive Ductal Carcinoma


title: 33 hours NIH3T3_Forskolin_33


title: Ascending Colon - 345986

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Rectosigmoid - 416798

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-50
Gender: Male
Ethnic Background: Other
Ethnic Background: Hawaiian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectosigmoid
Histology: Adenocarcinoma


title: Pancreas - 351871

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Exocrine Pancreas
Histology: Ductal adenocarcinoma

source_name: Pancreas


title: 31 hours NIH3T3_Forskolin_31


title: 26 hours NIH3T3_Forskolin_26


title: 25 hours NIH3T3_Forskolin_25


title: 30 hours NIH3T3_Forskolin_30


title: Kidney - 192991

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: 24 hours NIH3T3_Forskolin_24


title: 21 hours NIH3T3_Forskolin_21


title: Breast - 192999

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 38
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Hormonal therapy (# of Years)?: 31-35
Pathological T: 4b
Pathological N: 2
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Clinical PR: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: 23 hours NIH3T3_Forskolin_23


title: 22 hours NIH3T3_Forskolin_22


title: 20 hours NIH3T3_Forskolin_20


title: Donor 1 Vpr+

status: Public on Oct 02 2008

city: Boston

first: Alicja

last: Dabrowska

state: MA

address: 300 Longwood Ave.

department: Infectious Diseases

institute: Children's Hospital Boston

description: Gene expression data from donor 1 infected with HIV-1 Env-Nef-/VSVG

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing are provided in the Expression Analysis Technical Manual by Affymetrix Inc. (Santa Clara, CA), and available at http://www.affymetrix.com/Auth/support/downloads/manuals/expression_print_manual.zip

scan_protocol: GeneChipTM arrays were scanned using the HP GeneArray Scanner (Affymetrix). The .cell files were generated using the Microarray Suite v5 software from Affymetrix (http://www.affymetrix.com/Auth/support/downloads/manuals/mas_manual.zip

data_processing: 54,676 probe sets on the Human U133A-2 arrays were analyzed. The data was generated using GCOS, which is an updated version of MAS. The data was scaled and the median intensity was 150.  Probe sets, whose signal intensity was identified as being absent by Microarray Suite v5 (Affymetrix) on all arrays, were not included in further analysis. Expression ratios were calculated for each probe set relative to the intensity in the eGFP control.  Changes in gene expression were considered significant if each of the following criteria was met: (i) expression changed at least 1.6-fold in two of the three donors compared to eGFP control, and (ii) increased gene expression included at least one “Present” call (Affymetrix algorithm), or both eGFP control samples were “Present” when gene expression decreased.

label: fluorescence

source_name: Human CD4+ T-cells infected with HIV-1 Env-Nef-/VSVG

label_protocol: Standard affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

growth_protocol: Total RNA, 0.1 mg was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix).  Hybridization was carried out overnight with 1.5 mg of labeled cRNA product, and arrays were scanned on Affymetrix scanners

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

treatment_protocol: Human CD4+ T-cells were infected with eGFP/VSVG, HIV-1 Env-Nef-, or HIV-1 Env-Nef-Vpr- and sorted 48 hr after infection using GFP as a marker of infectivity.  Ten hours after sorting, total RNA was extracted and prepared for hybridization


title: Donor 2 eGFP

description: Gene expression data from donor 2 infected with eGFP/VSVG

source_name: Human CD4+ T-cells infected with eGFP/VSVG

tag: CD4+ T-cells infected with eGFP/VSVG


title: Donor 3 Vpr+

description: Gene expression data from donor 3 infected with HIV-1 Env-Nef-/VSVG

tag: CD4+ T-cells infected with HIV-1 Env-Nef-/VSVG


title: Donor 1 Vpr-

description: Gene expression data from donor 1 infected with HIV-1 Env-Nef-Vpr-/VSVG

source_name: Human CD4+ T-cells infected with HIV-1 Env-Nef-Vpr-/VSVG


title: Donor 2 Vpr-

description: Gene expression data from donor 2 infected with HIV-1 Env-Nef-Vpr-/VSVG

tag: CD4+ T-cells infected with HIV-1 Env-Nef-Vpr-/VSVG


title: Donor 1 eGFP

description: Gene expression data from donor 1 infected with eGFP/VSVG


title: Donor 2 Vpr+

description: Gene expression data from donor 2 infected with HIV-1 Env-Nef-/VSVG


title: Donor 3 Vpr-

description: Gene expression data from donor 3 infected with HIV-1 Env-Nef-Vpr-/VSVG


title: Donor 3 eGFP

description: Gene expression data from donor 3 infected with eGFP/VSVG


title: CAL2

city: New York

first: Babacar

last: Cisse

state: NY

address: West 168th St HHSC 609

department: Microbiology

institute: Columbia Uinversity

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS Algorithm: 5.0 ExpressionStat

label_protocol: The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP/Biotin-11-CTP in the second round. Labeled aRNA was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.

extract_protocol: Cultured CAL-1 and MOLT-4 cells were washed, pelleted and homogenized in Trizol. Total RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen), and equal amounts of each RNA sample were used for reverse transcription and two-round linear aRNA amplification.

tag: Human pDC cell line


title: Ecotype At_35SAvr2 RNA sample1

city: Wageningen

first: Bart

last: Thomma

state: Gelderland

address: Binnenhaven 5

department: Plant Sciences

country: Netherlands

institute: Wageningen University

description: Each replicate consists of either 10 Avr2-expressing or 10 Col-0 Arabidopsis plants.

hyb_protocol: Standard affymetrix

scan_protocol: Standard affymetrix

data_processing: MAS5.0 algorithm

source_name: Foliar tissue from expression of C. fulvum avirulence gene (Avr2)

label_protocol: Affymetrix 1 cycle target

extract_protocol: Trizol+Machery nagel Kit

tag: Green Plant


title: Het-pDC2

data_processing: MAS algorithm: 5.0 ExpressionStat

source_name: Heterozygous mouse pDCs

extract_protocol: Splenocytes from E2-2+/- mice and wild-type littermates were pooled, stained with antibody conjugates, and PDC (CD11b- CD11clow B220+ Bst2+) were flow-sorted directly into Trizol Reagent (Invitrogen).. Total RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen), and equal amounts of each RNA sample were used for reverse transcription and two-round linear aRNA amplification.

tag: Heterozygous mouse pDCs


title: Ecotype Col0 RNA sample2

source_name: Foliar tissue from wild type Arabidopsis


title: MOLT1

tag: Human immature T cell line


title: Ecotype At_35SAvr2 RNA sample2

tag: Green plant


title: Het-pDC1


title: Brain_p53-Pten-null_rep1

status: Public on Oct 01 2008

first: Hongwu

last: Zheng

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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

data_processing: Arrays were normalized using Invariant Set Normalization, and modeled using the Li and Wong model

extract_protocol: Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.


title: Brain_p53-null_rep2


title: CAL1


title: MOLT2


title: Ecotype At_35SAvr2 RNA sample3

source_name: Foliar tissue  from expression of C. fulvum avirulence gene (Avr2)


title: WT-pDC2

source_name: Wild type mouse pDCs

tag: Wild type mouse pDCs


title: Brain_p53-Pten-null_rep3


title: Brain_p53-Pten-null_rep2


title: WT-pDC1


title: Kidney_Aqp11-/-_P7_3-2

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

description: Standard Affymetrix protocol

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol.  The arrays were washed, stained using Fluidics Station (Affymetrix), and then scanned with the GeneChip Scanner (Affymetrix).  Data collection was performed using GeneChip Operating Software (Affymetrix).

data_processing: GeneChip Scanner 3000, GCOS v1.3, raw data

source_name: Aquaporin-11-/-_mouse P7 kidney #3-2

label_protocol: Three micrograms of total RNA obtained from each kidney was individually reverse-transcribed, amplified, and labeled using GeneChip One-Cycle Target Labeling and Control Reagent package (Affymetrix) according to the manufacturer’s protocol.

extract_protocol: Mice were sacrificed by cervical dislocation.  Kidneys were rapidly excised on ice, washed in ice-cold phosphate-buffered saline (PBS), immersed in RNAlater (Ambion) and stored at –20°C.  Total RNA was isolated using TRIzol Reagent (Invitrogen) and cleaned up using an RNeasy minikit with DNase treatment (Qiagen).  The RNA quality and quantity were examined by agarose-gel electrophoresis and a spectrophotometer (GE Healthcare).

tag: Gender

value: female

value: 7 days

value: kidney


title: Kidney_Aqp11+/+_P7_4-1

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #4-1

value: male


title: Ecotype Col0 RNA sample1


title: Kidney_Aqp11+/+_P7_3-1

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #3-1


title: Kidney_Aqp11+/+_P7_4-2

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #4-2


title: Brain_p53-null_rep1


title: Kidney_Aqp11-/-_P7_2-3

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #2-3


title: Kidney_Aqp11-/-_P7_5-2

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #5-2


title: Kidney_Aqp11+/+_P7_5-1

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #5-1


title: Kidney_Aqp11-/-_P7_3-3

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #3-3


title: Kidney_Aqp11+/+_P7_2-1

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #2-1


title: Kidney_Aqp11+/+_P7_2-2

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #2-2


title: Kidney_Aqp11+/+_P7_1-1

description: Standard Affymetrix protocol

source_name: Aquaporin-11+/+_mouse P7 kidney #1-1


title: Kidney_Aqp11-/-_P7_4-3

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #4-3


title: Kidney_Aqp11-/-_P7_3-4

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #3-4


title: Kidney_Aqp11-/-_P7_2-4

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #2-4


title: Kidney_Aqp11-/-_P7_1-2

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #1-2


title: Kidney_Aqp11-/-_P7_4-4

description: Standard Affymetrix protocol

source_name: Aquaporin-11-/-_mouse P7 kidney #4-4


title: CB1

city: Essen

first: Ralf

last: Küppers

address: Virchowstr. 173

department: Institute for Cell Biology (Tumor Research)

institute: University of Duisburg-Essen, Medical School

description: Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)

source_name: centroblasts donor 1

label_protocol: The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).

extract_protocol: The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.

treatment_protocol: Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.

tag: centroblasts, isolated from tonsils by fluorescence-activated cell sorting


title: HL-1 cells with rapid electric stimulation for 24 hr at 300 bpm (exp 2)

city: Nashville

first: yajun

last: yi

state: TN

address: 2215 Garland Ave

institute: vanderbilt univ

hyb_protocol: Affymetrix protocol, Vanderbilt Microarray Shared Resource completed this step accordingly

data_processing: Vanderbilt Microarray Shared Resource completed this step accordingly. CEL files were normalized by RMA method

source_name: HL-1 cells with rapid electric stimulation for 24 hr at 300 bpm, experiment 2

label_protocol: biotinylated cRNA, as well as subsequent steps in completion of the hybridization following the Affymetrix One-Cycle Target Labeling protocol

growth_protocol: HL-1 cells were cultured in supplemented Claycomb Medium (Sigma-Aldrich) as previously described.  Culture dishes were pre-plated with a sterilized, gelatin/fibronectin-coated coverslip, then seeded with HL-1 cells, typically reaching at least 90% confluency at 96 hr.

extract_protocol: RNA samples were extracted from control and stimulated cells using the RNAeasy Mini Kit (Animal Cell Protocol, Qiagen).  To ensure rigorous quality control, all samples were analyzed by the Vanderbilt Microarray Shared Resource for concentration, purity, and integrity (degradation) using spectrophotometry (NanoDrop ND-1000 UV-Vis Spectrophotometer) and a microfluidic assay (Agilent 2100 Bioanalyzer, Agilent Technologies).

treatment_protocol: HL-1 cells were cultured in supplemented Claycomb Media (Sigma-Aldrich) to confluence then electrically stimulated for 24 hr at 300 bpm (approximately 1.5-2 times greater than control).


title: HL-1 cells with rapid electric stimulation for 24 hr at 300 bpm (exp 1)

scan_protocol: Affymetrix protocol, Vanderbilt Microarray Shared Resource completed this step accordingly

source_name: HL-1 cells with rapid electric stimulation for 24 hr at 300 bpm, experiment 1

growth_protocol: HL-1 cells were cultured in supplemented Claycomb Medium (Sigma-Aldrich) as previously described.  Cultured dishes were pre-plated with a sterilized, gelatin/fibronectin-coated coverslip, then seeded with HL-1 cells, typically reaching at least 90% confluency at 96 hr.

treatment_protocol: HL-1 cells were cultured in supplemented Claycomb Medium (Sigma-Aldrich) to confluence then electrically stimulated for 24 hr at 300 bpm (approximately 1.5-2 times greater than control).


title: CB5

source_name: centroblasts donor 5


title: PC4

source_name: plasma cells donor 4

treatment_protocol: Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.

tag: plasma cells, isolated from tonsils by fluorescence-activated cell sorting


title: PC3

source_name: plasma cells donor 3


title: CB2

source_name: centroblasts donor 2


title: PC5

source_name: plasma cells donor 5


title: PC2

source_name: plasma cells donor 2


title: HL-1 cells contracting spontaneously in culture (without stimulation)

treatment_protocol: HL-1 cells were cultured in supplemented Claycomb Medium (Sigma-Aldrich) to confluence.  For experimental sample 2, HL-1 cells were evaluated without rapid electric stimulation.Spontaneous activation rate of these control cells was documented as previously described (Yang Z, et al., J Mol Cell Cardiol. 2005;38:299-308.), with confirmation using qualitative fluorescence microscopy to monitor intracellular Ca2+ release after cells were loaded with the calcium sensitive dye Xrod-1 (5uM, Invitrogen).

tag: Confluent HL-1 cells contracting spontaneously in culture (without electrical stimulation)


title: CB4

source_name: centroblasts donor 4


title: PC1

source_name: plasma cells donor 1


title: HL-1 cells contracting spontaneously in culture (without electrical stimulation)

treatment_protocol: HL-1 cells were cultured in supplemented Claycomb Medium (Sigma-Aldrich) to confluence.  Spontaneous activation rate of these control cells was documented as previously described (Yang Z, et al., J Mol Cell Cardiol. 2005;38:299-308.), with confirmation using qualitative fluorescence microscopy to monitor intracellular Ca2+ release after cells were loaded with the calcium sensitive dye Xrod-1 (5uM, Invitrogen)..


title: M4

source_name: memory B cells donor 4

treatment_protocol: cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.

tag: memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting


title: M3

source_name: memory B cells donor 3


title: M5

source_name: memory B cells donor 5


title: CC3

source_name: centrocytes donor 3

treatment_protocol: Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.

tag: centrocytes, isolated from tonsils by fluorescence-activated cell sorting


title: CC2

source_name: centrocytes donor 2