title: V. campbellii luxAB deletion mutant, biological rep3

status: Public on Aug 31 2012

type: RNA

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

country: USA

institute: US Naval Research Laboratory

description:
NRL_WB_V campbellii-BAA1116_DluxAB_12_07202011
Gene expression data from V. campbellii with luxAB deletion

hyb_protocol: The cocktail was hybridized onto the Custom design Vharveyi520694 arrays (affymetrix). Hybridization was carried out for 16 h at 49 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000. GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: CEL files were processed using the Bioconductor affy package.

label: biotin

molecule: total RNA

organism: Vibrio campbellii

source_name: ATCC® BAA-1117

label_protocol: Target Preparation and Hybridization to Arrays: 500ng of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures. The labeling reaction is carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol. Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX). Fragmentation from reaction was carried out in a reaction volume of 33 uL containing 1x fragmentation buffer (Ambion), labeled mRNA, and incubated at 70oC for 15 minutes. After incubation, the reaction is stopped by adding 1 uL stop solution.

growth_protocol: Six total cultures (three biological replicates of the wild type (STR) V. campbellii BAA-1116 and three biological replicates of the isogenic luxAB deletion mutant) were seeded with 1.0E+5 mid-log phase bacteria/mL in 25 mL of autoinducer bioassay medium and 125 mL baffled Erlenmeyer flasks. Cultures were incubated at 30°C and 200 rpm for 15 h (empirical observations demonstrated peak bioluminescence in the wild type (STR) cultures at this time point) and then harvested for total RNA extraction.

extract_protocol: Total RNA were extracted using RiboPure Bacteria Kit (Ambion Inc., Austin, TX) according to the manufacturer's instructions. The quality and quantity of RNA samples were determined using RNA 6000 Nano kit with 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) and NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer. The RNA samples were accepted for mRNA enrichment if the A260/A280 ratios were between 1.9-2.1, the ratio of intensities of the 23S and 16S rRNA were 1.5-2.5: 1 and the RNA integrity no. is between 7 and 10. mRNA enrichment were performed with 10 ug total RNA using using the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. The quantity of mRNA samples were determined by NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.

tag: genotype/variation

value: luxAB deletion mutant

tag: growth phase

value: Mid-log phase


title: V. campbellii, biological rep2

description:
NRL_WB_V campbellii-BAA1116_4_07202011
Gene expression data from wild type V. campbellii (STR)

source_name: ATCC® BAA-1116

value: WT


title: V. campbellii, biological rep1

description:
NRL_WB_V campbellii-BAA1116_2_07202011
Gene expression data from wild type V. campbellii (STR)


title: V. campbellii luxAB deletion mutant, biological rep2

description:
NRL_WB_V campbellii-BAA1116_DluxAB_9_07202011
Gene expression data from V. campbellii with luxAB deletion


title: V. campbellii, biological rep3

description:
NRL_WB_V campbellii-BAA1116_5_07202011
Gene expression data from wild type V. campbellii (STR)


title: V. campbellii luxAB deletion mutant, biological rep1

description:
NRL_WB_V campbellii-BAA1116_DluxAB_7_07202011
Gene expression data from V. campbellii with luxAB deletion


title: Cell_Culture_Stimulated_rep3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Mouse Exon 1.0 ST arrays were hybridized with 5 micrograms of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0001)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each experiment separately.

organism: Mus musculus

source_name: primary cortical culture 3 hours after stimulation with a neurotransmitter excitatory cocktail

label_protocol: For the in vivo experiment, RNA extracted from 3 mice from the same groups were combined. For all samples, 100 ng of total RNA was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

growth_protocol: Dissociated cortical primary cultures were prepared from C57BL/6J mouse brains either at birth or at embryonic day 16 to 18 (E16-E18). Briefly, cortical tissues from pups or embryos were dissected in a solution of phosphate buffer containing Hepes, 33mM glucose, and 40mM sucrose. The isolated cortices were digested with a solution containing 50U of Papain for 30min at 37°C. Digestion was stopped by the addition of trypsin inhibitor for 10min. Cells were dissociated mechanically through a fire-polished glass pipette several times in neurobasal medium supplemented with 2% B-27, 0.5mM Glutamax and penicillin/streptomycin. Cells were plated either on 35mm dishes (at 1.5 x 106 cells; density = 1560 cells/mm2) pre-coated with 0.1mg/mL poly-L-lysine or on 60-channel Micro Electrode Arrays (MEAs, from Multichannel Systems, Reutlingen, Germany) pre-coated with 0.1% polyethyleneimine plus 20µg/mL laminin (same cell numbers resulting in a density of 4780 cells/mm2). Cultures were maintained in a humidified CO2 incubator (5% CO2, 37°C) and half of the medium was changed once a week.

extract_protocol: Total RNA from mice cortex was isolated with the RNeasy Lipid Tissue Midi kit (Quiagen). Total RNA from cell cultures and from mice cortex for the time course experiment were extracted using RNA easy mini kit (Quiagen). All RNA samples were DNase-treated and quantified on a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: In vivo experiment was performed on 27 C57BL/6J mice: 9 sleep deprived for 6 hours, 9 home cage controls, and 9 after 24 hours of recovery from a 6 hour sleep deprivation.In vitro experiment was performed on 9 dishes of 3 different cultures: 3 hours after stimulation with an excitatory cocktail, 3 hours after sham stimulation with water, and 24 hours after stimulation.

tag: strain

tag: cell culture

value: primary cortical culture (from C57BL/6J mouse brains either at birth or at embryonic day 16 to 18)

tag: protocol

value: neurotransmitter excitatory cocktail

tag: time

value: 3 hours


title: Naive CD4 T cells 6hr medium only Smad3-/- rep2

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Qc

address: 5415 de L'Assomption

country: Canada

institute: CR-HMR

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium only

hyb_protocol: 6 μg of Cy3 labeled material and 6 μg of Cy5 labeled material were resuspended in a total of 6 μl of water. The labeled material was mixed with 9 μl NimbleGen 2X hyb buffer (Roche Nimblegen Inc, Madison, WI), 3.6 μl NimbleGen Hyb  component and 0.4 μl NimbleGen alignment oligo, for a total volume of 19 μl. The samples were heated at 95 °C for 5 min and transferred to 42 °C for at least 5 min before loading. Samples were hybridized overnight unto NimbleGen Mouse Gene Expression 385K Arrays at 42 oC in a Maui hybridization station with mixing.

scan_protocol: Arrays were scanned at 5 μm resolution on an Axon 4000B scanner using GenePix version 6.1 (Molecular Devices, Sunnyvale CA). Features were extracted using the Pair Reports function of NimbleScan version 2.5.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis) quantile normalization and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).
RMA-normalized gene-level signal intensity. Features (probe sets) having an intensity above the background intensity in less than 3 samples (out of a total of 18 microarrays) were excluded for final analysis.

label_protocol: Five hundred ng of total RNA was reverse transcribed using oligo dT primers and SuperScript II (Invitrogen, Carlsbad, CA) at 42 °C.  Following purification (using Qiagen PCR purification column as per the manufacturer’s protocol), up to 1 μg of purified cDNA in a total volume of 40 μl was mixed with 40 μl of 5' Cy3 labeled random nonamers for the test sample or 5' Cy5 labeled random nonamers for the control sample (Trilink Biotechnology San Diego, CA) and heated at 95 °C for 10 min. After a quick chill in ice/water slurry for 10 min, the samples were mixed with 10 μl of 50X dNTP mix (10 mM dATP, dTTP, dGTP, dCTP each in 1X Tris-EDTA buffer), 8 μl of water and 2 μl of Klenow fragment (3'to 5' exo-) (NEB) and incubated at 37 ºC for at least 2 hours. The labeling reaction was then stopped using 10 μl 0.5M EDTA, purified with 11 μl NaCl and 110 μl isopropanol, washed with 80% Ethanol and resuspended in 40 μl water.

growth_protocol: N/A - Primary naive CD4 T cells were sorted from single cell suspensions obtained form spleen and lymph nodes. Mice used were Smad3-/- or Smad3+/+ littermates from the commercially available 129-Smad3tm1Par/J strain (Jackson Laboratory, Bar Harbor, ME)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was concentrated and cleaned using the Qiagen micro kit. The integrity and concentration of RNA was then assessed using the Agilent  2100 bioanalyser (Agilent Technologies, Santa Clara, CA) at the IRIC core genomic facility (University of Montreal, Canada). A RNA integrity number of 9.5/10 or more was deemed acceptable for reverse transcription.

treatment_protocol: After sorting, cells were rested on ice for 2 hours. The cells were then incubated in serum-free medium (Ex-vivo 15 - Lonza, Basel Switzerland). Depending on experimental conditions, TGF-beta (Peprotech, Rocky Hill, NJ) at a final concentration of 2.5ng/ml was added to the milieu. In the condition were T cell receptor stimulation was done, plate bound anti-CD3e (BD Biosciences San Jose CA) at the dose of 10ug/ml was used to coat the wells along with soluble anti-CD28 (eBiosciences, San Diego, CA) at a final concentration of 1ug/ml. Cells were treated for 6 hours at a concentration of 500,000 cells/ml in 96 u-shaped well plates (volume of 200ul per well).

tag: genotype

tag: genetic background

tag: cell type

value: Naive CD4 T cell

tag: treatment

value: 6hr medium only Smad3-/- rep2


title: Cell_Culture_Recovered_rep3

source_name: primary cortical culture 24 hours after stimulation with a neurotransmitter excitatory cocktail

value: 24 hours


title: Cell_Culture_Recovered_rep2


title: Naive CD4 T cells 6hr medium + TGFb Smad3-/- rep1

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: 6hr medium + TGFb Smad3-/- rep1


title: Cell_Culture_Stimulated_rep2


title: Cell_Culture_Recovered_rep1


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation Smad3-/- rep1

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28


title: Naive CD4 T cells 6hr medium + TGFb wild type rep1

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: Wild type

value: 6hr medium + TGFb wild type rep1


title: Naive CD4 T cells 6hr medium only Smad3-/- rep3

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium only

value: 6hr medium only Smad3-/- rep3


title: Human Colon Tumor Tissue 83

type: genomic

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

country: Japan

institute: Sapporo medical university

hyb_protocol: Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Colon Tumor Tissue 83

label_protocol: Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.

growth_protocol: A total of 84 colorectal tumor specimens were obtained from endoscopic biopsy.

extract_protocol: Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.

tag: gender

value: M

tag: age (y)

tag: braf/kras mutation

tag: tumor location

value: right

tag: tissue

value: colon tumor

tag: pathology

value: HGD/CRC

tag: cimp

value: CIMP-L

source_name: Human Genomic DNA (Promega)

tag: sample type

value: Human Genomic DNA (Promega)


title: Naive CD4 T cells 6hr medium only wild type rep2

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium only

value: 6hr medium only wild type rep2


title: Human Colon Tumor Tissue 84

source_name: Human Colon Tumor Tissue 84

value: left

value: CIMP-N


title: Naive CD4 T cells 6hr medium only Smad3-/- rep1

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium only

value: 6hr medium only Smad3-/- rep1


title: Naive CD4 T cells 6hr medium only wild type rep3

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium only

value: Naive CD4 T cell

value: 6hr medium only wild type rep3


title: Human Colon Tumor Tissue 81

source_name: Human Colon Tumor Tissue 81

value: rectum

value: T-ad potion


title: Cell_Culture_Stimulated_rep1

value: primary cortical culture (from C57BL/6J mouse brains either at birth or at embryonic day 16 to 18)

value: neurotransmitter excitatory cocktail

value: 3 hours


title: Human Colon Tumor Tissue 79

source_name: Human Colon Tumor Tissue 79

value: F

value: Wild type


title: Human Colon Tumor Tissue 80

source_name: Human Colon Tumor Tissue 80

value: M

value: colon tumor

value: HGD/CRC potion(T-ad)


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation wild type rep3

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28


title: Naive CD4 T cells 6hr medium + TGFb Smad3-/- rep2

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: 6hr medium + TGFb Smad3-/- rep2


title: Naive CD4 T cells 6hr medium + TGFb wild type rep3

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: 6hr medium + TGFb wild type rep3


title: Naive CD4 T cells 6hr medium + TGFb wild type rep2

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: 6hr medium + TGFb wild type rep2


title: Cell_Culture_Control_rep3

source_name: primary cortical culture 3 hours after sham stimulation with water

value: control


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation Smad3-/- rep3

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28


title: Human Colon Tumor Tissue 82

source_name: Human Colon Tumor Tissue 82

value: KRAS

value: HGD/CRC

value: CIMP-N

value: Human Genomic DNA (Promega)


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation Smad3-/- rep2

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28

value: Naive CD4 T cell


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation wild type rep1

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28


title: Naive CD4 T cells 6hr medium + TGFb + anti-CD3e/anti-CD28 stimulation wild type rep2

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the second of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml) and stimulated by antiCD3e and CD28


title: Naive CD4 T cells 6hr medium only wild type rep1

description: From naive CD4 T cells obtained from wild type mice (at least two mice per biological replicate). This is the first of three biological replicate involving cells cultured in serum-free medium only

value: 6hr medium only wild type rep1


title: Naive CD4 T cells 6hr medium + TGFb Smad3-/- rep3

description: From naive CD4 T cells obtained from Smad3-deficient mice (at least two mice per biological replicate). This is the third of three biological replicate involving cells cultured in serum-free medium and TGF-beta (2.5ng/ml)

value: 6hr medium + TGFb Smad3-/- rep3


title: Cortex_Sleep_Deprived_pool3

source_name: cortex from sleep deprived mice for 6 hours

value: male

value: cortex

value: sleep deprived


title: Cell_Culture_Control_rep2

value: primary cortical culture (from C57BL/6J mouse brains either at birth or at embryonic day 16 to 18)

value: 3 hours


title: Cortex_Control_pool3

source_name: cortex from undisturbed mice


title: Cortex_Recovered_pool3

source_name: cortex from sleep deprived mice for 6 hours allowed to recover for 18 hours

value: sleep deprived, allowed to recover


title: Cortex_Sleep_Deprived_pool1


title: Cortex_Control_pool1


title: Cortex_Recovered_pool1


title: Cell_Culture_Control_rep1


title: DeltaPT high d4 a

city: Baltimore

first: Nicholas

last: Carbonetti

state: MD

address: 685 W. Baltimore St. HSF I-380

department: Microbiology and Immunology

institute: University of Maryland Baltimore

description: deltaPT-treated, high dose, sacrificed 4 dpi, biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized by median method implemented in R package beadarray.

source_name: Mouse whole lung

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit from Ambion.

extract_protocol: RNA was extracted with RNA STAT-60 reagent  (Tel Test, Inc.), followed by  DNase I treatment  and clean-up with QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.

value: BALB/c

value: female

tag: age

value: 7 wk

value: lung

tag: infection

value: 30 x 10^6 CFU DeltaPT Bordetella pertussis

value: 4 dpi


title: Human Colon Tumor Tissue 75

source_name: Human Colon Tumor Tissue 75

value: M

value: KRAS

value: right

value: colon tumor

value: HGD/CRC potion(T-ad)

value: CIMP-L


title: Human Colon Tumor Tissue 76

source_name: Human Colon Tumor Tissue 76

value: Wild type

value: HGD/CRC

value: CIMP-N

value: Human Genomic DNA (Promega)


title: Cortex_Recovered_pool2

tag: strain

value: male

value: cortex

value: sleep deprived, allowed to recover


title: DeltaPT d4 c

description: deltaPT-treated, sacrificed 4 dpi, biological replicate 3

value: BALB/c

value: female

value: 7 wk

value: 1 x 10^6 CFU DeltaPT Bordetella pertussis


title: DeltaPT high d4 c

description: deltaPT-treated, high dose, sacrificed 4 dpi, biological replicate 3

value: lung

value: 30 x 10^6 CFU DeltaPT Bordetella pertussis

value: 4 dpi


title: Cortex_Control_pool2

tag: protocol

value: control


title: Human Colon Tumor Tissue 78

source_name: Human Colon Tumor Tissue 78

value: F

value: right

value: colon tumor

value: TV-ad potion


title: Human Colon Tumor Tissue 73

source_name: Human Colon Tumor Tissue 73

value: M

value: KRAS

value: HGD/CRC

value: CIMP-N


title: DeltaPT high d4 b

description: deltaPT-treated, high dose, sacrificed 4 dpi, biological replicate 2

tag: time


title: Human Colon Tumor Tissue 74

source_name: Human Colon Tumor Tissue 74

value: left

value: Human Genomic DNA (Promega)


title: PBS d2 a

description: PBS treated, sacrificed 2 dpi, biological replicate 1

value: BALB/c

value: female

value: mock

value: 2 dpi


title: Human Colon Tumor Tissue 77

source_name: Human Colon Tumor Tissue 77

value: HGD/CRC potion(TV-ad)


title: WT d4 c

description: WT-treated, sacrificed 4 dpi, biological replicate 3

value: 7 wk

value: lung

value: 1 x 10^6 CFU WT Bordetella pertussis

value: 4 dpi


title: PBS d2 b

description: PBS treated, sacrificed 2 dpi, biological replicate 2


title: Human Colon Tumor Tissue 72

source_name: Human Colon Tumor Tissue 72

value: Wild type

value: rectum

value: colon tumor

value: T-ad potion

value: CIMP-L

source_name: Human Genomic DNA (Promega)


title: DeltaPT high d2 c

description: deltaPT-treated, high dose, sacrificed 2 dpi, biological replicate 3

value: 30 x 10^6 CFU DeltaPT Bordetella pertussis


title: DeltaPT d4 b

description: deltaPT-treated, sacrificed 4 dpi, biological replicate 2

value: 1 x 10^6 CFU DeltaPT Bordetella pertussis


title: DeltaPT d4 a

description: deltaPT-treated, sacrificed 4 dpi, biological replicate 1


title: Human Colon Tumor Tissue 70

source_name: Human Colon Tumor Tissue 70

value: M

value: KRAS

value: left

value: CIMP-N

value: Human Genomic DNA (Promega)


title: WT d4 b

description: WT-treated, sacrificed 4 dpi, biological replicate 2

value: BALB/c

value: female


title: Human Colon Tumor Tissue 71

source_name: Human Colon Tumor Tissue 71

value: HGD/CRC potion(T-ad)


title: Human Colon Tumor Tissue 69

source_name: Human Colon Tumor Tissue 69

value: T-ad


title: RM6608R-Stationary phase-REP3-2

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Escherichia coli O157:H7

source_name: Escherichia coli RM6608W-Stationary phase

label_protocol: 2 µg of genomic DNA were Cy3-dUTP labeled during random primed synthesis with Klenow fragment (NEB) at 37°C for 16 h. 20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy5-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Liquid cultures of E. coli were obtained by inoculation of colonies into LB broth and growth at 37°C with shaking (150 rpm) to stationary phase (16 h).

extract_protocol: E. coli genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit. Total E. coli RNA was extracted from stationary phase cultures with the Promega SV Total RNA Isolation Kit according to the manufacturer’s specifications.

value: Escherichia coli O157:H7 str. RM6608W

source_name: Genomic DNA E. coli strain RM6607

value: Escherichia coli O157:H7 str. RM6607


title: RM6608W-Stationary phase-REP3-1


title: RM6608W-Stationary phase-REP3-2


title: WT d4 a

description: WT-treated, sacrificed 4 dpi, biological replicate 1

value: 7 wk

value: lung

value: 1 x 10^6 CFU WT Bordetella pertussis

value: 4 dpi


title: Human Colon Tumor Tissue 68

source_name: Human Colon Tumor Tissue 68

value: right

value: colon tumor

value: HGD/CRC


title: RM6608W-Stationary phase-REP2-2


title: RM6608R-Stationary phase-REP3-1


title: Cortex_Sleep_Deprived_pool2

source_name: cortex from sleep deprived mice for 6 hours

value: male

value: cortex

value: sleep deprived


title: DeltaPT high d2 a

description: deltaPT-treated, high dose, sacrificed 2 dpi, biological replicate 1

value: 30 x 10^6 CFU DeltaPT Bordetella pertussis

value: 2 dpi


title: WT d2 b

description: WT-treated, sacrificed 2 dpi, biological replicate 2

value: BALB/c

value: female


title: WT d2 c

description: WT-treated, sacrificed 2 dpi, biological replicate 3


title: DeltaPT high d2 b

description: deltaPT-treated, high dose, sacrificed 2 dpi, biological replicate 2


title: DeltaPT d2 a

description: deltaPT-treated, sacrificed 2 dpi, biological replicate 1

value: 1 x 10^6 CFU DeltaPT Bordetella pertussis


title: Human Colon Tumor Tissue 67

source_name: Human Colon Tumor Tissue 67

value: M

value: KRAS

value: rectum

value: T-ad

value: CIMP-N

value: Human Genomic DNA (Promega)


title: Human Colon Tumor Tissue 65

source_name: Human Colon Tumor Tissue 65

value: F

value: SA

value: CIMP-L


title: DeltaPT d2 c

description: deltaPT-treated, sacrificed 2 dpi, biological replicate 3

source_name: Mouse whole lung

value: 7 wk

value: lung


title: RM6608W-Stationary phase-REP2-1

value: Escherichia coli O157:H7 str. RM6608W

value: Escherichia coli O157:H7 str. RM6607


title: DeltaPT d2 b

description: deltaPT-treated, sacrificed 2 dpi, biological replicate 2

value: 2 dpi


title: WT d2 a

description: WT-treated, sacrificed 2 dpi, biological replicate 1

value: BALB/c

value: 1 x 10^6 CFU WT Bordetella pertussis


title: Human Colon Tumor Tissue 63

source_name: Human Colon Tumor Tissue 63

value: right

value: colon tumor

value: HGD/CRC

value: CIMP-H


title: PRB18401

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way

institute: Genentech

description: Universal Mouse Reference RNA, Stratagene, Cat #740100-41

hyb_protocol: Samples were hybridized to the Agilent microarrays at 60°C for 18 hours in a rotisserie oven. Arrays were washed using SSC buffers.

scan_protocol: Arrays were scanned in the Agilent G2505B model Scanner.

data_processing:
Expression signals were calculated using the Agilent feature extraction software (version 8.5 Agilent Technologies, Palo Alto, CA).
Lowess normalized ratios, obtained by taking antilog (base 10) of values reported by agilent software, which are lowess-normalized log10-transformed values. Values that were reported as zero by agilent's software are reported as null here.

source_name: MMTV Wnt-1 and MMTV-Her2 tumors

label_protocol: The methods for preparation of cRNA and hybridization/scanning of the arrays were provided by Agilent Technologies (Palo Alto, CA).  Briefly, 1 ug of total RNA was converted into double-stranded cDNA using a T7 Promoter Primer and MMLV-RT (Agilent, Low RNA Input Fluorescent Linear Amplification Kit, Product #  5184-3523).  After cDNA synthesis, cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated cyanine 3- or cyanine 5- labeled CTP.  The labeled cRNA was purified on an affinity resin column (RNeasy Mini Kits, Qiagen).  The amount of labeled cRNA was determined by measuring absorbance at 260 nm and using the convention that 1 OD at 260 nm corresponds to 40 ug/ml of RNA.  Incorporation of dye was determined by measuring the sample using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) which measured the absorbance of cyanine 3- and cyanine 5- labeled CTP.  Seven hundred fifty nanograms of cyanine 3-labeled Universal Human Reference cRNA (Stratagene, La Jolla, CA, Product # 740000) and 750 ng of cyanine 5-labeled cRNA was fragmented by incubating at 60°C for 30 minutes in fragmentation buffer (Agilent In situ Hybridizatyion kit-plus, Product # 5184-3568).  Fragmentation was terminated by adding hybridization buffer containing LiCl and lithium lauryl sulfate.

growth_protocol: Fresh isolated tumor cells are FACS sorted for GFP- cells

extract_protocol: RNA was purified using Qiagen kit

treatment_protocol: Tumor cells were treated Wnt inhibitor (Fzd8-CRD)

value: Control

source_name: 11 strains pooled together

tag: sample

value: pooled reference


title: Human Colon Tumor Tissue 62

source_name: Human Colon Tumor Tissue 62

value: KRAS

value: Human Genomic DNA (Promega)


title: Human Colon Tumor Tissue 61

source_name: Human Colon Tumor Tissue 61

value: F

value: SA


title: Human Colon Tumor Tissue 64

source_name: Human Colon Tumor Tissue 64

value: rectum

value: CIMP-L


title: PRB18402


title: RM6608R-Stationary phase-REP2-2

source_name: Escherichia coli RM6608R-Stationary phase

value: Escherichia coli O157:H7 str. RM6608R


title: RM6608W-Stationary phase-REP1-1

value: Escherichia coli O157:H7 str. RM6607


title: RM6608R-Stationary phase-REP2-1


title: RM6608W-Stationary phase-REP1-2


title: RM6608R-Stationary phase-REP1-2


title: Human Colon Tumor Tissue 59

source_name: Human Colon Tumor Tissue 59

value: M

value: BRAF

value: SSA

source_name: Human Genomic DNA (Promega)


title: RM6608R-Stationary phase-REP1-1


title: PRB18400


title: PRB21702

value: Fzd


title: RM6607W-Stationary phase-REP3-3

source_name: Escherichia coli RM6607W-Stationary phase

value: Escherichia coli O157:H7 str. RM6607W


title: PRB21701


title: RM6607W-Stationary phase-REP2-3


title: Human Colon Tumor Tissue 60

source_name: Human Colon Tumor Tissue 60

value: right

value: colon tumor


title: Human Colon Tumor Tissue 58

source_name: Human Colon Tumor Tissue 58

value: TV-ad potion

value: CIMP-H


title: PRB18399

value: Control

value: pooled reference


title: PRB21703


title: PRB21699

source_name: MMTV Wnt-1 and MMTV-Her2 tumor


title: Human Colon Tumor Tissue 57

source_name: Human Colon Tumor Tissue 57

value: KRAS

value: HGD/CRC potion(TV-ad)

value: Human Genomic DNA (Promega)


title: PRB21700


title: Human Colon Tumor Tissue 55

source_name: Human Colon Tumor Tissue 55

value: left

value: T-ad

value: CIMP-N


title: Human Colon Tumor Tissue 56

source_name: Human Colon Tumor Tissue 56

value: M

value: Wild type

value: HGD/CRC


title: Human Colon Tumor Tissue 53

source_name: Human Colon Tumor Tissue 53

value: F


title: RM6607W-Stationary phase-REP3-2

value: Escherichia coli O157:H7 str. RM6607W

source_name: Genomic DNA E. coli strain RM6607

value: Escherichia coli O157:H7 str. RM6607


title: Human Colon Tumor Tissue 52

source_name: Human Colon Tumor Tissue 52

value: rectum

value: colon tumor

value: T-ad potion


title: RM6607W-Stationary phase-REP1-3


title: RM6607W-Stationary phase-REP1-2


title: Human Colon Tumor Tissue 50

source_name: Human Colon Tumor Tissue 50


title: Human Colon Tumor Tissue 66

source_name: Human Colon Tumor Tissue 66


title: Human Colon Tumor Tissue 54

source_name: Human Colon Tumor Tissue 54

value: TV-ad


title: RM6607W-Stationary phase-REP2-2


title: Human Colon Tumor Tissue 51

source_name: Human Colon Tumor Tissue 51

value: HGD/CRC potion(T-ad)


title: RM6607W-Stationary phase-REP3-1


title: RM6607W-Stationary phase-REP2-1


title: Human Colon Tumor Tissue 49

source_name: Human Colon Tumor Tissue 49


title: RM6607R-Stationary phase-REP3-3

source_name: Escherichia coli RM6607R-Stationary phase

value: Escherichia coli O157:H7 str. RM6607R


title: RM6607W-Stationary phase-REP1-1


title: Human Colon Tumor Tissue 47

source_name: Human Colon Tumor Tissue 47

value: KRAS

value: right

value: HGD/CRC potion(TV-ad)

value: CIMP-L

source_name: Human Genomic DNA (Promega)


title: Human Colon Tumor Tissue 45

source_name: Human Colon Tumor Tissue 45

value: left

value: CIMP-H

value: Human Genomic DNA (Promega)


title: RM6607R-Stationary phase-REP1-3


title: RM6607R-Stationary phase-REP2-3


title: Human Colon Tumor Tissue 46

source_name: Human Colon Tumor Tissue 46

value: M

value: HGD/CRC


title: Human Colon Tumor Tissue 43

source_name: Human Colon Tumor Tissue 43

value: CIMP-N


title: Human Colon Tumor Tissue 44

source_name: Human Colon Tumor Tissue 44

value: TV-ad potion


title: RM6607R-Stationary phase-REP3-2

value: Escherichia coli O157:H7 str. RM6607


title: Human Colon Tumor Tissue 40

source_name: Human Colon Tumor Tissue 40

value: colon tumor


title: Human Colon Tumor Tissue 48

source_name: Human Colon Tumor Tissue 48

value: F


title: RM6607R-Stationary phase-REP2-2


title: Human Colon Tumor Tissue 41

source_name: Human Colon Tumor Tissue 41

value: Wild type


title: Human Colon Tumor Tissue 42

source_name: Human Colon Tumor Tissue 42

value: rectum


title: RM6607R-Stationary phase-REP1-2

value: Escherichia coli O157:H7 str. RM6607R

source_name: Genomic DNA E. coli strain RM6607


title: Human Colon Tumor Tissue 38

source_name: Human Colon Tumor Tissue 38

value: KRAS


title: RM6607R-Stationary phase-REP3-1


title: Human Colon Tumor Tissue 39

source_name: Human Colon Tumor Tissue 39


title: RM6607R-Stationary phase-REP1-1


title: RM6607R-Stationary phase-REP2-1


title: Human Colon Tumor Tissue 36

source_name: Human Colon Tumor Tissue 36

value: BRAF

value: right


title: Human Colon Tumor Tissue 35

source_name: Human Colon Tumor Tissue 35


title: Godfrey_9926__GenomeWideSNP_6

city: Boston

first: Steven

middle: E

last: Schumacher

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Each sample was genotyped using the Sty I chip of the 500K Human Mapping Array wet (Affymetrix), containing probes to 238,270 SNP loci, according to manufacturer’s instructions. In brief, 250 ng of genomic DNA was digested with the StyI restriction enzyme (New England Biolabs), ligated to an adaptor with T4 ligase (New England Biolabs), and PCR-amplified using a 9700 Thermal Cycler I (Applied Biosystems) and Titanium Taq (Clontech) to achieve fragments ranging from 200-1100 bp. These fragments were pooled, concentrated, processed through a clean-up step, and further fragmented with DNaseI (Affymetrix) before being labeled, denatured, and hybridized to arrays

scan_protocol: Arrays were washed and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using five closest normal method, in which tumor signal intensities are divided by the geometric mean of the five normal samples closest to the tumor in Euclidean log2 ratio space (as described in Weir et al, Nature 2007).  Cancer samples were normalized against the plate normals included in this submission and also normals used in the TCGA ovarian cancer study (TCGA network, Nature, 2011). GEO Sample tables (VALUE) contain the resulting normalized copy-number values.

label: Biotin

source_name: non-malignant

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was obtained from cell line pellets or tumors frozen at the time of surgical dissection and maintained at -80C until use.

tag: cancer type

value: non-malignant

tag: batch


title: Human Colon Tumor Tissue 37

source_name: Human Colon Tumor Tissue 37


title: Human Colon Tumor Tissue 33

source_name: Human Colon Tumor Tissue 33


title: Human Colon Tumor Tissue 31

source_name: Human Colon Tumor Tissue 31

value: HGD/CRC potion(TV-ad)

source_name: Human Genomic DNA (Promega)


title: YS026

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: The Illumina hybridization protocol was used. Hybridization in HYB buffer for 16 hours at 58°C with gentle rocking followed by standard Illumina washes and streptavidin-Cy3 staining.

scan_protocol: Using Illumina Beadarray reader, standard Illumina scanning was performed.

data_processing: The raw intensity data were not normalised and the missing values were imputed by GenomeStudio software (version 1.7.0). For data normalization, quantile normalization was performed on log2 tranformed data, and each array was centered by setting the average value to 0.

source_name: normal

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with mirVana miRNA extraction kit. Quality control was performed with Agilent Bioanalyser.

tag: disease status

value: surrounding normal liver

value: liver


title: Human Colon Tumor Tissue 34

source_name: Human Colon Tumor Tissue 34

tag: gender

value: Human Genomic DNA (Promega)


title: Human Colon Tumor Tissue 32

source_name: Human Colon Tumor Tissue 32

value: M

tag: age (y)

value: TV-ad

value: CIMP-H


title: YS025


title: Godfrey_7601__GenomeWideSNP_6


title: Human Colon Tumor Tissue 29

source_name: Human Colon Tumor Tissue 29

tag: braf/kras mutation

value: HGD/CRC


title: YS024


title: Human Colon Tumor Tissue 30

source_name: Human Colon Tumor Tissue 30

tag: tumor location

value: colon tumor

value: HP

value: CIMP-N


title: Godfrey_7574__GenomeWideSNP_6


title: Human Colon Tumor Tissue 28

source_name: Human Colon Tumor Tissue 28

value: F

value: left

tag: tissue


title: Godfrey_7529__GenomeWideSNP_6


title: Godfrey_7515__GenomeWideSNP_6


title: YS022


title: YS023


title: Godfrey_10875__GenomeWideSNP_6


title: Godfrey_7527__GenomeWideSNP_6


title: YS021

source_name: Hepatocellular carcinoma (HCC)

value: Hepatocellular carcinoma (HCC)


title: Godfrey_10820__GenomeWideSNP_6


title: Human Colon Tumor Tissue 27

source_name: Human Colon Tumor Tissue 27

value: KRAS

tag: pathology

value: TV-ad potion

value: CIMP-L


title: Godfrey_6980_2__GenomeWideSNP_6

value: non-malignant


title: YS020

source_name: cholangiocarcinoma (CC)

value: cholangiocarcinoma (CC)


title: Human Colon Tumor Tissue 25

source_name: Human Colon Tumor Tissue 25

value: BRAF

value: right

value: SSA potion

tag: cimp


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B12_433552

value: SULKY


title: Human Colon Tumor Tissue 24

source_name: Human Colon Tumor Tissue 24

value: HGD/CRC potion(SSA)

value: CIMP-H

tag: sample type

value: Human Genomic DNA (Promega)


title: Godfrey_6967_2__GenomeWideSNP_6


title: YS019

value: liver


title: Human Colon Tumor Tissue 23

source_name: Human Colon Tumor Tissue 23

value: colon tumor


title: Human Colon Tumor Tissue 26

source_name: Human Colon Tumor Tissue 26

value: F

value: HGD/CRC


title: YS017

value: Hepatocellular carcinoma (HCC)


title: YS018


title: Godfrey_10768__GenomeWideSNP_6

source_name: non-malignant


title: Godfrey_10767__GenomeWideSNP_6


title: Godfrey_10809__GenomeWideSNP_6


title: Human Colon Tumor Tissue 22

source_name: Human Colon Tumor Tissue 22

value: KRAS

value: HGD/CRC potion(TV-ad)

value: CIMP-N


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B10_433602

value: non-malignant


title: YS016


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B08_433606


title: Godfrey_6906_2__GenomeWideSNP_6


title: YS015


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B09_433604


title: Godfrey_10535__GenomeWideSNP_6


title: Human Colon Tumor Tissue 20

source_name: Human Colon Tumor Tissue 20

value: M

value: rectum

value: SA


title: Human Colon Tumor Tissue 21

source_name: Human Colon Tumor Tissue 21

value: BRAF

source_name: Human Genomic DNA (Promega)


title: YS013

source_name: Hepatocellular carcinoma (HCC)_fibrous stroma

tag: carcinoma type

value: scirrhous


title: Human Colon Tumor Tissue 19

source_name: Human Colon Tumor Tissue 19

value: Wild type

value: right


title: Human Colon Tumor Tissue 17

source_name: Human Colon Tumor Tissue 17

value: Human Genomic DNA (Promega)


title: Human Colon Tumor Tissue 18

source_name: Human Colon Tumor Tissue 18

value: TV-ad potion


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B07_433608

value: SULKY


title: YS012

value: liver


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B06_433610


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A09_433596


title: YS010


title: YS009


title: YS014


title: YS011


title: Human Colon Tumor Tissue 15

source_name: Human Colon Tumor Tissue 15

value: colon tumor


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G08_160210

value: GHATS


title: Human Colon Tumor Tissue 16

source_name: Human Colon Tumor Tissue 16

value: KRAS

value: CIMP-H


title: Human Colon Tumor Tissue 14

source_name: Human Colon Tumor Tissue 14

value: CIMP-N


title: YS007

value: Hepatocellular carcinoma (HCC)


title: Human Colon Tumor Tissue 12

source_name: Human Colon Tumor Tissue 12

value: F

value: SSA potion


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A10_433594

value: non-malignant


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A08_433598


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A07_433618


title: Human Colon Tumor Tissue 13

source_name: Human Colon Tumor Tissue 13

value: M

value: HGD/CRC potion(TV-ad)


title: Human Colon Tumor Tissue 11

source_name: Human Colon Tumor Tissue 11

value: BRAF

value: HGD/CRC potion(SSA)


title: YS005

source_name: cholangiocarcinoma (CC)

value: cholangiocarcinoma (CC)


title: YS004


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G06_160178


title: YS006

value: scirrhous


title: Human Colon Tumor Tissue 10

source_name: Human Colon Tumor Tissue 10

value: Wild type

value: rectum

value: T-ad potion

value: Human Genomic DNA (Promega)


title: YS008

value: liver


title: Human Colon Tumor Tissue 9

source_name: Human Colon Tumor Tissue 9

value: colon tumor

value: HGD/CRC potion(T-ad)


title: Big_Wekiva_1_3 (Quantile)

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization. Data were also normalized using LOESS for the manuscript.

organism: Micropterus salmoides

source_name: whole brain female

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

value: whole brain

tag: location

value: Big Wekiva, Santa Fe


title: YS003


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B11_433600

source_name: non-malignant

value: SULKY


title: Welaka_4 (Quantile)

value: St. John's Rivers Florida


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G02_160114

value: non-malignant

value: GHATS


title: Human Colon Tumor Tissue 8

source_name: Human Colon Tumor Tissue 8

value: M

value: KRAS

value: right

value: CIMP-H


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G04_160146


title: YS001

value: cholangiocarcinoma (CC)


title: YS002


title: Human Colon Tumor Tissue 7

source_name: Human Colon Tumor Tissue 7

source_name: Human Genomic DNA (Promega)


title: Welaka_2 (Quantile)


title: Welaka_1 (Quantile)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_E12_160270


title: Human Colon Tumor Tissue 5

source_name: Human Colon Tumor Tissue 5

value: Wild type

value: left

value: HGD/CRC potion(TV-ad)

value: CIMP-N


title: ga1-3 rga-t2_stratified_rep1

city: Singapore

first: Petra

last: Stamm

address: Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National Univerisity of Singapore

hyb_protocol: 1650n of the Cy-3 labeled cRNAs were fragmented  with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out at 65°C for 16 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer 1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37°C for 1 min. The slides were then washed with Acetonitrile for 30 seconds.

scan_protocol: Immediately after washing, the microarray slide was scanned using Agilent Scanner (Agilent Technologies, Part Number G2565CA) using one color scan setting for 4x44k array slides, with a scan resolution of 5µm.

data_processing: Data extraction from Images was done using Feature Extraction software of Agilent Version 10.5, and analyzed using GeneSpring GX Version 10 software from Agilent.  Normalization of the data was done in GeneSpring GX using the percentile shift and normalization to specific samples.

organism: Arabidopsis thaliana

source_name: ga1-3 rga-t2 seeds_stratified_5days

label_protocol: Cyanine-3 (Cy-3) labelling was performed using Quick-Amp Labeling Kit, One Color (Agilent Technologies, Part Number: 5190-0442), according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen, Cat No: 74106). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Seed RNA was extracted as described in  Vicient and Delseny (1999), with slight modifications. For each isolation 50mg (dry weight) seeds were used. Crude RNA was purified by extractions with chloroform, phenol, phenol:chloroform:isoamyl alcohol (25:24:1) and chloroform:isoamyl alcohol (24:1), once each. After precipitation, RNA was dissolved in 30 to 50µl water.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After-ripened seeds (after 2 to 4 months dry storage) were stratified in water at 4°C for five days prior to RNA extraction.

tag: genotype/variation

value: ga1-3 rga-t2

value: whole seeds

tag: germination

value: non-germinating


title: Welaka_3 (Quantile)

value: whole brain


title: ga1-3 rga-t2_stratified_rep2


title: St__Mary_s_3_9 (Quantile)

value: St. Mary's River, Florida


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F04_160144


title: Human Colon Tumor Tissue 4

source_name: Human Colon Tumor Tissue 4

value: colon tumor

value: HGD/CRC potion(T-ad)

value: Human Genomic DNA (Promega)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F08_160208

value: non-malignant

value: GHATS


title: Human Colon Tumor Tissue 6

source_name: Human Colon Tumor Tissue 6

value: M

value: TV-ad potion


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F12_160272


title: ga1-3 rga-t2 rgl2-1_stratified_rep2

source_name: ga1-3 rga-t2 rgl2-1 seeds_stratified_5days

value: ga1-3 rga-t2 rgl2-1

value: germinating


title: Human Colon Tumor Tissue 3

source_name: Human Colon Tumor Tissue 3

value: Wild type

value: right

value: T-ad potion


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F06_160176


title: ga1-3 rga-t2 rgl2-1_stratified_rep1


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F11_416454

value: COXES


title: St__Mary_s_3_7 (Quantile)


title: MesoJan4 [January]

description: fish in late stages of maturation

data_processing: Normalized signal intensity provided here is LOESS normalization. The software was JMP Genomics (4.0).

source_name: ovary

value: female

tag: collection site

value: Apopka mesocosms

tag: collection month

value: January


title: Human Colon Tumor Tissue 2

source_name: Human Colon Tumor Tissue 2

value: F

value: left

value: HGD/CRC potion(TV-ad)

value: CIMP-N


title: MesoJan3 [January]

description: fish in late stages of maturation


title: Big_Wekiva_1_8 (Quantile)

value: whole brain

value: Big Wekiva, Santa Fe


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F12_416482

tag: cancer type

value: non-malignant


title: St__Mary_s_3_2 (Quantile)

value: St. Mary's River, Florida


title: Human Colon Tumor Tissue 1

source_name: Human Colon Tumor Tissue 1

value: colon tumor

value: TV-ad potion

value: Human Genomic DNA (Promega)


title: St__Mary_s_3_8 (Quantile)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F10_160240

tag: batch

value: GHATS


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F02_160112


title: Big_Wekiva_1_3 (Loess)

data_processing: Normalized signal intensity provided here is LOESS Normalization. Data were also normalized using Quantile for the manuscript.


title: Welaka_4 (Loess)

value: St. John's Rivers Florida


title: DeLeon3 [January]

description: fish in late stages of maturation

value: DeLeon Springs


title: DeLeon4 [January]

description: fish in late stages of maturation

value: female


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_E10_160238


title: Big_Wekiva_1_16 (Quantile)


title: Big_Wekiva_1_17 (Quantile)


title: Welaka_3 (Loess)


title: DeLeon2 [January]

description: fish in late stages of maturation


title: MesoJan2 [January]

description: fish in late stages of maturation

value: Apopka mesocosms


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F09_416458

value: COXES


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E07_416610


title: Welaka_2 (Loess)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F08_416460


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F07_416462


title: eOM4 [January]

description: fish in late stages of maturation

value: St John River

value: January


title: St__Mary_s_3_9 (Loess)


title: MesoJan1 [January]

description: fish in late stages of maturation


title: DeLeon1 [January]

description: fish in late stages of maturation


title: Welaka_1 (Loess)


title: St__Mary_s_3_8 (Loess)


title: eOM2 [January]

description: fish in late stages of maturation


title: eOM3 [January]

description: fish in late stages of maturation


title: St__Mary_s_3_2 (Loess)


title: eOM1 [January]

description: fish in late stages of maturation


title: Mesocosm_418_14 [April]

value: April


title: Mesocosm_418_27 [April]


title: Big_Wekiva_1_8 (Loess)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E04_416608


title: Mesocosm_418_4 [April]


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E05_416606


title: eOM4 [April]


title: Big_Wekiva_1_17 (Loess)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E02_416604


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F10_416456


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E06_416612


title: St__Mary_s_3_7 (Loess)


title: Mesocosm_418_2 [April]


title: MeHg3 (Quantile)

data_processing: Normalized signal intensity provided here is Quantile Normalization. Data were also normalized using Loess for the manuscript.

source_name: female hypothalamus

value: hypothalamus

tag: treatment

value: Hg injection 2.5 µg/g body weight


title: Big_Wekiva_1_16 (Loess)

value: whole brain

value: Big Wekiva, Santa Fe


title: eOM3 [April]

tag: gender


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E01_416598

value: non-malignant


title: Control_6 (Quantile)


title: eOM1 [April]


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D07_416618


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D04_416616


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D10_416628


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D12_416600


title: MeHg2 (Quantile)


title: MeHg1 (Quantile)


title: eOM2 [April]


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D05_416614


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H02_160116


title: MeHg3 (Loess)


title: Control_6 (Loess)


title: MeHg2 (Loess)


title: Control_2 (Quantile)


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B02_433586

source_name: gastric

value: gastric

value: SULKY


title: Control_1 (Quantile)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_D09_416622


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G12_160274


title: MeHg1 (Loess)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F06_416464


title: Control_5 (Quantile)


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B04_433614


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A12_433590


title: microdissected HRS cells, replicate 29 [treatment outcome reanalysis]

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

institute: BC Cancer Agency

description: Gene expression data from microdissected HRS cells

hyb_protocol: Following fragmentation, cRNA were hybridized O/N at 45C on Affymetrix GeneChip HG 2.0 Plus Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The simpleaffy (v2.20.0) from Bioconductor (v2.4) was used to generate RMA expression and perform QC.

source_name: Lymph node

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (2-cycle amplification)

extract_protocol: Qiagen Allprep extraction columns

value: Lymph node

tag: disease status

value: Hodgkin lymphoma

tag: hd number

tag: age (years)

tag: Sex

value: M

tag: histology subtype

value: NS

value: DIAGNOSTIC

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

value: ADV

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: Control_2 (Loess)

tag: tissue

tag: treatment


title: Control_1 (Loess)


title: Control_5 (Loess)


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B01_433588

tag: cancer type

tag: batch


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B05_433612


title: microdissected HRS cells, replicate 26 [treatment outcome reanalysis]

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)


title: microdissected HRS cells, replicate 27 [treatment outcome reanalysis]

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

value: LIM

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: microdissected HRS cells, replicate 28 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 25 [treatment outcome reanalysis]

tag: histology subtype

value: MC

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E03_416602

tag: cancer type

tag: batch

value: COXES


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A11_433592


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A03_433626


title: CRC 27

source_name: Human Colon Tumor Tissue

label_protocol: Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and reference DNA was labeled with Cy3.

growth_protocol: A total of 86 colorectal tumor specimens were obtained from endoscopic biopsy.

treatment_protocol: No treatment was carried out.

tag: tissue type

value: Human Colon Tumor

tag: pathology

value: CRC

tag: age

tag: gender

source_name: Human Genomic DNA from Normal Colon

value: Normal colon


title: CRC 30

source_name: cell line

value: cell line


title: CRC 28


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A04_433620


title: CRC 29


title: microdissected HRS cells, replicate 23 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: microdissected HRS cells, replicate 24 [treatment outcome reanalysis]

tag: Sex

tag: histology subtype

tag: sample type

value: RELAPSE

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 22 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_B03_433584

tag: cancer type

tag: batch


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H04_319184

value: ROOKY


title: microdissected HRS cells, replicate 21 [treatment outcome reanalysis]

tag: Sex

tag: histology subtype

tag: sample type

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H05_319186

value: gastric


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A05_433622

value: SULKY


title: microdissected HRS cells, replicate 20 [treatment outcome reanalysis]

tag: tissue

value: Lymph node

tag: disease status

value: F

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: SULKY_p_CCGD_CLLGasRenALT_plt7_GenomeWideSNP_6_A02_433624

tag: cancer type

tag: batch


title: microdissected HRS cells, replicate 19 [treatment outcome reanalysis]

value: Hodgkin lymphoma

tag: hd number

tag: age (years)

tag: Sex

value: M

tag: histology subtype

tag: sample type

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: mass size (cm)


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H01_319178


title: CRC 25

tag: tissue type

tag: pathology

tag: age

tag: gender


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H06_319188


title: CRC 24


title: microdissected HRS cells, replicate 17 [treatment outcome reanalysis]

tag: tissue

tag: disease status

value: NS

value: DIAGNOSTIC

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)

tag: disease specific survival (years)


title: CRC 26

tag: tissue type


title: CRC 23

tag: pathology


title: microdissected HRS cells, replicate 16 [treatment outcome reanalysis]

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

value: LIM

tag: mass size (cm)

tag: progression-free survival (years)


title: CRC 19

tag: age

tag: gender


title: CRC 22


title: microdissected HRS cells, replicate 18 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H03_319182

tag: cancer type

tag: batch


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_H02_319180


title: CRC 20

tag: tissue type

tag: pathology


title: microdissected HRS cells, replicate 13 [treatment outcome reanalysis]

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 14 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

value: ADV

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival


title: microdissected HRS cells, replicate 15 [treatment outcome reanalysis]

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G12_319176

tag: cancer type

tag: batch


title: CRC 17

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 12 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G11_319174

tag: cancer type

tag: batch


title: CRC 16

tag: tissue type

tag: pathology

tag: age


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G07_319166


title: CRC 21

tag: gender


title: CRC 15


title: CRC 18


title: microdissected HRS cells, replicate 9 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival


title: microdissected HRS cells, replicate 10 [treatment outcome reanalysis]

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F08_509678

tag: cancer type

tag: batch

value: PLOPS


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G09_319170


title: CRC 14

tag: tissue type

value: Human Colon Tumor

tag: pathology

tag: age

tag: gender


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F12_509582


title: CRC 12

value: CRC


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G10_319172


title: CRC 13

value: Normal colon


title: microdissected HRS cells, replicate 8 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival


title: microdissected HRS cells, replicate 11 [treatment outcome reanalysis]

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 7 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type


title: CRC 11

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 6 [treatment outcome reanalysis]

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F09_509710

tag: cancer type

tag: batch


title: CRC 10

tag: tissue type


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F11_509720


title: microdissected HRS cells, replicate 5 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: mass size (cm)

tag: hasenclever score

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 4 [treatment outcome reanalysis]

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival


title: CRC 9

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 3 [treatment outcome reanalysis]

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)


title: CRC 8


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F07_509622

tag: cancer type

tag: batch


title: CRC 7

tag: tissue type


title: microdissected HRS cells, replicate 2 [treatment outcome reanalysis]

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 29

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival


title: microdissected HRS cells, replicate 1 [treatment outcome reanalysis]

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: overall survival (years)


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_E08_509674

tag: cancer type

tag: batch


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_E09_509724


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F01_509680


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_E07_509732


title: CRC 3

tag: tissue type

tag: pathology

tag: age

tag: gender


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F02_509612


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F04_509560


title: CRC 4


title: CRC 5


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F03_509672


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G07_160194

value: GHATS


title: microdissected HRS cells, replicate 27

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival

tag: disease specific survival (years)

tag: progression-free survival (years)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G03_160130

tag: cancer type

tag: batch


title: microdissected HRS cells, replicate 25

value: MC

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)


title: CRC 2

tag: tissue type

tag: pathology

tag: age

tag: gender


title: CRC 1


title: microdissected HRS cells, replicate 24

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

value: RELAPSE

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 26

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)


title: HGD 14

tag: tissue type

tag: pathology

value: HGD

tag: age

tag: gender


title: microdissected HRS cells, replicate 23

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival


title: HGD 13


title: HGD 12


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F11_160256

tag: cancer type

value: gastric

tag: batch


title: microdissected HRS cells, replicate 21

value: Lymph node

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: HGD 11

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 20

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

value: F

tag: histology subtype

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival

tag: code disease-specific survival


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F09_160224

tag: cancer type

tag: batch


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F07_160192


title: HGD 10

tag: tissue type


title: microdissected HRS cells, replicate 19

value: Hodgkin lymphoma

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: microdissected HRS cells, replicate 18

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: code overall survival


title: HGD 8

tag: tissue type

tag: pathology

tag: age

tag: gender

value: M


title: microdissected HRS cells, replicate 22

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: microdissected HRS cells, replicate 17

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

value: NS

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C11_350760

tag: cancer type

tag: batch

value: DITSY


title: HGD 7

tag: tissue type

tag: pathology

tag: age

tag: gender


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F05_160160


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C09_350756


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C12_350762


title: microdissected HRS cells, replicate 28

tag: tissue

value: DIAGNOSTIC

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_E09_160222

tag: cancer type

tag: batch


title: microdissected HRS cells, replicate 16

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: ann arbor stage

tag: stage group (limited/ advanced)

value: LIM

tag: disease specific survival (years)

tag: progression-free survival (years)


title: HGD 5

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 15

tag: tissue

tag: who performance status

tag: ldh (g/l)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

value: ADV

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_E11_160254

tag: cancer type

tag: batch


title: HGD 4

tag: tissue type

value: Human Colon Tumor

tag: pathology

tag: age


title: HGD 3

tag: gender


title: microdissected HRS cells, replicate 13

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C05_350748

tag: cancer type

tag: batch


title: microdissected HRS cells, replicate 12

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: HGD 2

tag: tissue type

tag: pathology

tag: age

tag: gender


title: microdissected HRS cells, replicate 11

tag: tissue

tag: disease status

tag: hd number

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C02_350742

tag: cancer type

tag: batch


title: HGD 1

tag: tissue type

tag: pathology

tag: age


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C06_350750


title: HGD 9

tag: gender


title: CRC 6

value: CRC


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C03_350744


title: microdissected HRS cells, replicate 10

tag: tissue

tag: disease status

tag: hd number

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: Precursor 28

tag: tissue type

value: TV-ad

value: Normal colon


title: Precursor 27

tag: pathology


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C01_350740

tag: cancer type

tag: batch


title: ROOKY_p_CCGD_July08_GenomeWideSNP_6_G06_319164

value: ROOKY


title: microdissected HRS cells, replicate 8

tag: tissue

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

value: RELAPSE

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B12_350738


title: Precursor 26

tag: age

tag: gender


title: microdissected HRS cells, replicate 9

tag: disease status

tag: hd number

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: microdissected HRS cells, replicate 7

tag: tissue

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: stage group (limited/ advanced)


title: Precursor 25

tag: tissue type

tag: pathology

tag: age

tag: gender


title: HGD 6

value: HGD


title: microdissected HRS cells, replicate 14

tag: disease status

tag: hd number

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: mass size (cm)

tag: hasenclever score

tag: code overall survival

tag: disease specific survival (years)

tag: progression-free survival (years)


title: Precursor 24


title: microdissected HRS cells, replicate 5

tag: tissue

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: code disease-specific survival

tag: code progression-free survival

tag: overall survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C04_350746

tag: cancer type

value: gastric

tag: batch


title: microdissected HRS cells, replicate 6

value: Lymph node

tag: disease status

tag: hd number

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_C08_350754


title: PLOPS_p_ICP_SNP_Plate3_GenomeWideSNP_6_F05_509712

value: PLOPS


title: Precursor 21

tag: tissue type

tag: pathology

tag: age

tag: gender

value: F


title: Precursor 22


title: Precursor 20

value: M


title: microdissected HRS cells, replicate 2

tag: tissue

value: Hodgkin lymphoma

tag: age (years)

tag: Sex

tag: histology subtype

value: NS

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

tag: code overall survival

tag: code disease-specific survival

tag: code progression-free survival

tag: disease specific survival (years)

tag: progression-free survival (years)


title: Precursor 23

tag: tissue type


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B07_350728

tag: cancer type

tag: batch

value: DITSY


title: microdissected HRS cells, replicate 1

tag: disease status

tag: hd number

value: DIAGNOSTIC

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: stage group (limited/ advanced)

tag: mass size (cm)

tag: hasenclever score

tag: overall survival (years)


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B08_350730


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B09_350732


title: microdissected HRS cells, replicate 4

tag: tissue

tag: age (years)

tag: Sex

tag: histology subtype

tag: sample type

tag: who performance status

tag: ldh (g/l)

tag: ann arbor stage

value: ADV

tag: code overall survival

tag: code disease-specific survival


title: Precursor 19

tag: tissue type

value: Human Colon Tumor

tag: pathology

tag: age

tag: gender


title: Precursor 18

value: T-ad


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B10_350734

tag: cancer type

tag: batch


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G05_160162

value: GHATS


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G01_160098


title: Precursor 17

value: Normal colon


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F04_416468

value: COXES


title: Microdissected germinal center, replicate 4 (RMA reanalysis)

description: Gene expression data from microdissected germinal centers (reactive lymph node tissue)

tag: disease status

value: Reactive lymph node

tag: reanalysis of


title: microdissected HRS cells, replicate 3

tag: tissue

tag: hd number

tag: age (years)

tag: albumin (g/l)

tag: white blood count (10^9/l)

tag: hemoglobin (g/l)

tag: lymphocyte count  (10^9/l)

tag: stage group (limited/ advanced)

value: LIM

tag: mass size (cm)

tag: hasenclever score

tag: code progression-free survival

tag: overall survival (years)

tag: disease specific survival (years)

tag: progression-free survival (years)


title: Microdissected germinal center, replicate 3 (RMA reanalysis)


title: Precursor 16

tag: tissue type

tag: pathology

tag: age

tag: gender


title: Precursor 15


title: Microdissected germinal center, replicate 2 (RMA reanalysis)

tag: tissue

tag: disease status

tag: reanalysis of


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F05_416466

tag: cancer type

value: gastric

tag: batch


title: Hodgkin lymphoma cell line HDLM-2 (RMA reanalysis)

description: Gene expression data from Hodgkin lymphoma cell line

growth_protocol: Cell lines: Standard conditions (www.dsmz.de)

tag: cell type

value: Hodgkin lymphoma cell line HDLM-2


title: Precursor 13


title: Microdissected germinal center, replicate 5 (RMA reanalysis)

value: Lymph node


title: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_B11_350736


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F03_160128


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F03_416438


title: Precursor 11

value: SSA


title: Precursor 14

value: F


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E11_416446


title: Precursor 12

value: M


title: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_F01_160096


title: Hodgkin lymphoma cell line L-540 (RMA reanalysis)

value: Hodgkin lymphoma cell line L-540

value: Hodgkin lymphoma


title: Hodgkin lymphoma cell line L-428 (RMA reanalysis)

value: Hodgkin lymphoma cell line L-428


title: Microdissected germinal center, replicate 1 (RMA reanalysis)


title: Precursor 10


title: Precursor 9


title: Hodgkin lymphoma cell line L-1236 (RMA reanalysis)

value: Hodgkin lymphoma cell line L-1236


title: Hodgkin lymphoma cell line KM-H2 (RMA reanalysis)

value: Hodgkin lymphoma cell line KM-H2


title: CD77+ centroblasts, specimen 5

source_name: Tonsil 5

value: CD77+ centroblasts

value: Tonsil


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F02_416440


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E12_416444


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E08_416452


title: Precursor 8

value: Human Colon Tumor

value: Normal colon


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_F01_416442

value: COXES


title: Precursor 5

value: SA


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B12_416582

value: gastric


title: Precursor 7


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_C01_416584


title: CD77+ centroblasts, specimen 4

source_name: Tonsil 4


title: CD77+ centroblasts, specimen 3

source_name: Tonsil 3


title: CD77+ centroblasts, specimen 1

source_name: Tonsil 1


title: Precursor 4

value: HP


title: CD77+ centroblasts, specimen 2

source_name: Tonsil 2


title: Precursor 6


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B11_416542


title: HCT116/GFP_wt_spheroids

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from HCT116 wt/GFP cells grown as spheroids.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed. and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Colon cancer cell line HCT116 wt/GFP

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression. Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

growth_protocol: HCT116 wt/GFP grown as spheroids

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

tag: cell line

value: HCT116 wt/GFP cells

tag: growth condition

value: grown as speroids.


title: Precursor 3


title: Precursor 2

value: F


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_C02_416586


title: Precursor 1


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E10_416448


title: Normal 16

source_name: Human Colon Tissue

value: Human Colon

value: M


title: HCT116_wt_monolayer

description: Gene expression data from HCT116 wt cells grown as monolayer.

source_name: Colon cancer cell line HCT116 wt

growth_protocol: HCT116 wt cells grown as monolayer.

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

value: HCT116 wt cells

value: grown as monolayer.


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B07_416534


title: HCT116_wt/GFP_monolayer

description: Gene expression data from HCT116 wt/GFP cells grown as monolayer.

growth_protocol: HCT116 wt/GFP cells grown as monolayer.


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_E09_416450


title: Normal 15


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B06_416536


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B08_416548


title: HCT116_wt_spheroids

description: Gene expression data from HCT116 wt cells grown as spheroids.

growth_protocol: HCT116 wt grown as spheroids


title: Normal 14


title: Adjacent_normal_liver_03

city: Kwei-Shan Tao-Yuan

first: Yi

last: Huang

address: 259 Wen-Hwa 1st Road

country: Taiwan

institute: Chang Guang University

description:
T_03
Gene expression data from adjacent normal liver of patient #3

hyb_protocol: Please see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site

data_processing: The raw Affymetrix HG-U133 Plus2 data were MAS5 normalized using the R package, Bioconductor.

source_name: Ajacent normal liver from patient #3

extract_protocol: Total RNA was extracted from biopsied samples using TRIzol following the manufacturer’s protocol (Invitrogen, Carlsbad, CA).

value: Ajacent normal liver


title: Normal 13


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B10_416544


title: Adjacent_normal_liver_02

description:
T_02
Gene expression data from adjacent normal liver of patient #2

scan_protocol: Please see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site

source_name: Ajacent normal liver from patient #2


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B09_416546


title: Normal 10


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B03_416558


title: Adjacent_normal_liver_01

description:
T_01
Gene expression data from adjacent normal liver of patient #1

source_name: Ajacent normal live from patient #1

label_protocol: Please see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site


title: HCC_tissue_01

description:
NT_01
Gene expression data from HCC tissues of patient #1

source_name: HCC tissues from patient #1

value: hepatocellular carcinoma (HCC)


title: Normal 11


title: Normal 12


title: HCC_tissue_03

description:
NT_03
Gene expression data from HCC tissues of patient #3

source_name: HCC tissues from patient #3


title: HCC_tissue_02

description:
NT_02
Gene expression data from HCC tissues of patient #2

source_name: HCC tissues from patient #2


title: Normal 8


title: Adult rhesus skin fibroblasts, biological repB

city: Beaverton

first: Shoukhrat

last: Mitalipov

address: 505 N.W. 185th Avenue

institute: Oregon National Primate Research Center

description: Gene expression profile of Fibroblasts B is  adult rhesus skin fibroblasts in biogical replicate B.

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten mg of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files). Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

organism: Macaca mulatta

source_name: Adult rhesus skin fibroblast (8 years old)

label_protocol: Microarray assays were performed in the Affymetrix Microarray Core of the OHSU Gene Microarray Shared Resource. Messenger RNA is amplified and labeled from 2mg of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

growth_protocol: All monkey pluripotent stem cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mEF feeder cells in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) (Invitrogen) supplemented with 15% defined fetal bovine serum (FBS) (Hyclone), 0.1mM b-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), 2mM L-glutamine (Invitrogen) and a pH of 7.2 (altered with 4N NaOH). Pluripotent colonies were manually passaged every 4-5 days.  Somatic fibroblasts were also grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mEF feeder cells in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and a pH of 7.2 (altered with 4N NaOH).  Stem cells with an undifferentiated morphology were manually removed from culture and Fibroblasts were trypsinized for total RNA purification.

extract_protocol: Total RNA was extracted using Trizol® reagent (Invitrogen) followed by additional purification on RNeasy spin columns (Qiagen) following manufacturer recommendations.

treatment_protocol: All stem and somatic cell lines were generated by us at the Oregon National Primate Research Center. ORMES23, CRES, and RiPS were established from rhesus monkey IVF blastocyst, cloned (SCNT) blastocyst and adult rhesus skin fibroblast rhesus monkey by retroviral transduction with vectors carrying 4 factors (OCT4, SOX2, Klf4 and cMYC), respectively. RNA were isolated from only nice undifferentiated colonies. Somatic fibroblasts were derived from a skin biopsy from an eight year old adult female rhesus monkey.

value: female

value: skin fibroblasts


title: Normal 7

source_name: Human Genomic DNA from Normal Colon


title: Adult rhesus skin fibroblasts, biological repC

description: Gene expression profile of Fibroblasts C is  adult rhesus skin fibroblasts in biogical replicate C.


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B01_416562

source_name: gastric


title: Normal 6


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B02_416560


title: Rhesus induced Pluripotent Stem cells 3 (RiPS3), biological repC

description: Gene expression profile of RiPS3 C is  rhesus adult iPS in biological replicate C.

tag: developmental stage

value: somatic cells, skin fibroblasts

value: iPS


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_B04_416540

value: COXES


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_A07_416528


title: Normal 5

value: Normal colon


title: Normal 4


title: Normal 9


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_A12_416564

value: gastric


title: Rhesus induced Pluripotent Stem cells 2 (RiPS2), biological repC

description: Gene expression profile of RiPS2 C is  rhesus adult iPS in biological replicate C.

source_name: Adult rhesus skin fibroblast (10 years old)


title: Rhesus induced Pluripotent Stem cells 3 (RiPS3), biological repA

description: Gene expression profile of RiPS3 A is  rhesus adult iPS in biological replicate A.


title: Normal 3


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_A09_416554


title: BLADE_p_ICPp4_TCGAb23_SNP_N_GenomeWideSNP_6_C06_529988

value: BLADE


title: Normal 2


title: Adult rhesus skin fibroblasts, biological repA

description: Gene expression profile of Fibroblasts A is  adult rhesus skin fibroblasts in biogical replicate A.


title: BLADE_p_ICPp4_TCGAb23_SNP_N_GenomeWideSNP_6_C05_530012


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_A10_416552


title: Rhesus induced Pluripotent Stem cells 2 (RiPS2), biological repB

description: Gene expression profile of RiPS2 B is  rhesus adult iPS in biological replicate B.


title: BLADE_p_ICPp4_TCGAb23_SNP_N_GenomeWideSNP_6_B09_530046


title: BLADE_p_ICPp4_TCGAb23_SNP_N_GenomeWideSNP_6_C03_530154


title: COXES_p_CCGD_GasCLL_plt6_SNP6_GenomeWideSNP_6_A08_416556


title: Rhesus induced Pluripotent Stem cells 1 (RiPS1), biological repC

description: Gene expression profile of RiPS1 C is  rhesus fetal iPS in biological replicate C.

source_name: Fetal rhesus skin fibroblast.

value: male


title: Rhesus induced Pluripotent Stem cells 3 (RiPS3), biological repB

description: Gene expression profile of RiPS3 B is  rhesus adult iPS in biological replicate B.

source_name: Adult rhesus skin fibroblast (8years old)


title: BLADE_p_ICPp4_TCGAb23_SNP_N_GenomeWideSNP_6_A07_530066