title: Transgenic Atlantic salmon 12605187t replicate 1

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

description: Replicate 1 of 4, top half of the array

hyb_protocol: Labelled targets were combined (Cy3 and Cy5) with hybridization solution (Amersham hybridization buffer + deionized formamide) and applied to microarray. Microarrays were sealed in diRisi chambers and hybridized at 42C for 16h. After hybridization, microarray slides were washed sequentially with 1X SSC/ 0.2% SDS, 0.1X SSC/0.2% SDS and 0.1 X SSC at 42C before scanning.

scan_protocol: Scanned on ScanArray 5000XL, Images were quantified with QuantArray (version 3.1)

data_processing: Lowess NORMALIZATION , data background subtracted. VALUE obtained from NORMALIZED background subtracted ratio of EXP/REF, Log 2 transformed

organism: Salmo salar

source_name: mRNA extracted from wild type liver tissue, labelled with Cy3

extract_protocol: mRNA isolated using Invitrogen's FastTrack 2.0 kit.

tag: Wild type Atlantic salmon (control), mRNA extracted from a pooled sample

source_name: mRNA extracted from Transgenic liver tissue, labelled with Cy5

tag: Transgenic Atlantic salmon (experimental),mRNA extracted from a pooled sample


title: HMEC-cy3 and MCF7-cy5

status: Public on Dec 30 2005

type: RNA

city: Duarte

first: Ren-Jing

last: Lin

state: CA

address: 1500 E. Duarte Rd.

department: Molecular Biology

country: USA

institute: Beckman Research Institute

description: MCF7 vs. HMEC

scan_protocol: GenePix pro 4.1

data_processing: After background correction and removal of flagged values, oligonucleotide spots with both F635 and F532 readings lower than the average plus two standard deviations of all ??untargeted?? spots were removed from the raw data.

molecule: total RNA

organism: Homo sapiens

source_name: A pleural effusion of breast adenocarcinoma

label_protocol: Indirect labeling

growth_protocol: MCF7 cultured in DMEM supplemented with 10% FBS, 1% non-essential amino acids and 1% Penicillin/Streptomycin

extract_protocol: Trizol

treatment_protocol: No treatment

source_name: Human mammary epithelial cells

growth_protocol: HMEC cultured in MEGM supplemented with 10% FBS and MEGM BulletKit

tag: HMEC


title: Transgenic Atlantic salmon 12841777b replicate 2

description: Replicate 1 of 4, top half of the array

molecule: polyA RNA

source_name: mRNA extracted from wild type liver tissue, labelled with Cy5

source_name: mRNA extracted from transgeneic liver tissue, labelled with Cy3


title: Transgenic Atlantic salmon 12841777t replicate 2

description: Replicate 1 of 4, top half of the array


title: Transgenic Atlantic salmon 12841776t replicate 2

description: Replicate 1 of 4, top half of the array

source_name: mRNA extracted from transgenic liver tissue, labelled with Cy5


title: HMEC-cy5 and MDA-cy3

description: HMEC vs. MDA

growth_protocol: MDA-MB-231 cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin/Streptomycin


title: EB017.063 Oct 19 16k Coho Salmon GH Transgenic Study

status: Public on Dec 31 2005

city: Milwaukee

first: Matthew

middle: Lawrence

last: Rise

state: WI

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

description: See Channel Characteristics.

data_processing: log2 of (CH2 signal median/CH1 signal median)

organism: Oncorhynchus kisutch

source_name: Cy3 ration fed GH transgenic (R)

tag: GRASP microarray studies were conducted using liver samples. To minimize technical variability within a study, all targets were synthesized in one round, and all hybridizations were conducted simultaneously on slides from a single batch (EB017). Total RNA, prepared from flash-frozen adult liver tissues using TRIzol reagent and methods (Invitrogen), was quantified and quality-checked by spectrophotometer and agarose gel. The microarray experiments used pooled RNA templates

value: pooled C contained equal quantities from 10 individual C fish, pooled R contained equal quantities from 10 individual R fish, and pooled T contained equal quantities from 10 individual T fish. Microarray experimental design involved 3 comparisons (C vs. R, C vs. T, R vs. T), each run in duplicate (1 chip and a dye flip). Microarray hybridizations were performed using the Genisphere Array50 kit and instructions. Briefly, 20 ug total RNA (pooled C, pooled R, or pooled T) were reverse transcribed using oligo d(T) primers with 3' or 5' unique sequence overhangs for the Cy3 or Cy5 labeling reactions, respectively. Microarrays were prepared for hybridization by washing 2 X 5 min in 0.1% SDS, washing 5 X 1 min in MilliQ H2O, immersing 3 min in 95 C MilliQ H2O, and drying by centrifugation (5 min 2000 rpm in 50 ml conical tube). Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 48 C water bath. The coho salmon liver cDNAs were hybridized to the salmonid cDNA microarray in a formamide-based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 16 h at 48 C. Coverslips were floated off in 48 C (2X SSC, 0.1% SDS), and arrays were washed 1 X 10 min in 2X SSC, 0.1% SDS at 48 C, 2 X 5 min in 2X SSC, 0.1% SDS at room temperature (RT), 2 X 5 min in 1X SSC at RT, and 2 X 5 min in 0.1X SSC at RT, and dried by centrifugation as before. The Cy3 and Cy5 3-dimensional fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized to the bound cDNA on the microarray in a formamide-based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) for 3 h at 48 C, and washed and dried as before.

tag: Fluorescent images of hybridized arrays were acquired using ScanArray and extracted using QuantArray (Perkin Elmer). The same laser power (90%) and photomultiplier tube (PMT) settings were used for all slides in each study (Cy3 PMT 78-80, Cy5 PMT 72-76).

source_name: Cy5 control non-transgenic (C)


title: Transgenic Atlantic salmon 12841776b replicate 2

description: Replicate 1 of 4, top half of the array

source_name: mRNA extracted from Transgeneic liver tissue, labelled with Cy5


title: EB017.065 Oct 19 16k Coho Salmon GH Transgenic Study

description: See Channel Characteristics.

source_name: Cy5 full ration transgenic (T)


title: EB017.066 Oct 19 16k Coho Salmon GH Transgenic Study

description: See Channel Characteristics.

source_name: Cy3 labeled full-ration GH transgenic (T)


title: EB017.064 Oct 19 16k Coho Salmon GH Transgenic Study

description: See Channel Characteristics.

source_name: Cy3 control non-transgenic (C)

source_name: Cy5 ration fed GH transgenic (R)


title: NA11995 , IVT: 1, Hyb: 8, SAM: 1269933, Array: H11

status: Public on Dec 01 2005

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: HapMap CEU parent

hyb_protocol: 1ug cRNA as per "Gene expression on Sentrix Arrays direct hybridization system manual" (Illumina Doc. #11161707, Rev. B) 2-21 2-32. Arrays were hybridized for 18 hours and stained with Cy3-Streptavidin.

scan_protocol: Standard Illumina protocol, PMT 671 (factor 1.9573)

data_processing: background-corrected values for each single bead type (raw data) were normalized on a log scale using a quantile normalization method (Bolstad et al. Bioinformatics, 2003. 19(2): p. 185-93)

label: biotin

source_name: lymphoblastoid cell line

label_protocol: One-quarter scale Message Amp II reactions (Ambion) were performed for each RNA extraction using 200 ng of total RNA. Biotin-16-UTP (Perkin Elmer) made up half of the UTP used in the in vitro transcription (IVT) reaction (37?C for 18 hours).

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 – 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80 oC.

extract_protocol: RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen).

tag: HapMap CEU parent, Female


title: NA12057 , IVT: 2, Hyb: 5, SAM: 1274134, Array: B1

description: HapMap CEU parent


title: NA12057 , IVT: 2, Hyb: 4, SAM: 1274134, Array: A1

description: HapMap CEU parent


title: EB017.062 Oct 19 16k Coho Salmon GH Transgenic Study

description: See Channel Characteristics.


title: HMEC-cy3 and MDA-cy5

description: MCF7 vs. HMEC


title: MDA-3D-cy5 and MCF7-3D-cy3

description: MDA-3D vs. MCF7-3D

growth_protocol: MDA-MB-231 cultured in Matrigel provided by BD Clontech

tag: MDA-MB-231 cells cultured in Matrigel

growth_protocol: MCF7 cultured in Matrigel provided by BD Clontech

tag: MCF7 cultrued in Matrigel


title: EB017.061 Oct 19 16k Coho Salmon GH Transgenic Study

description: See Channel Characteristics.

tag: GRASP microarray studies were conducted using liver samples.  To minimize technical variability within a study, all targets were synthesized in one round, and all hybridizations were conducted simultaneously on slides from a single batch (EB017).  Total RNA, prepared from flash-frozen adult liver tissues using TRIzol reagent and methods (Invitrogen), was quantified and quality-checked by spectrophotometer and agarose gel.  The microarray experiments used pooled RNA templates

value: pooled C contained equal quantities from 10 individual C fish, pooled R contained equal quantities from 10 individual R fish, and pooled T contained equal quantities from 10 individual T fish.  Microarray experimental design involved 3 comparisons (C vs. R, C vs. T, R vs. T), each run in duplicate (1 chip and a dye flip).  Microarray hybridizations were performed using the Genisphere Array50™ kit and instructions.  Briefly, 20 ug total RNA (pooled C, pooled R, or pooled T) were reverse transcribed using oligo d(T) primers with 3’ or 5’ unique sequence overhangs for the Cy3 or Cy5 labeling reactions, respectively.  Microarrays were prepared for hybridization by washing 2 X 5 min in 0.1% SDS, washing 5 X 1 min in MilliQ H2O, immersing 3 min in 95˚C MilliQ H2O, and drying by centrifugation (5 min 2000 rpm in 50 ml conical tube).  Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 48˚C water bath.  The coho salmon liver cDNAs were hybridized to the salmonid cDNA microarray in a formamide-based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 16 h at 48˚C.  Coverslips were floated off in 48˚C (2X SSC, 0.1% SDS), and arrays were washed 1 X 10 min in 2X SSC, 0.1% SDS at 48˚C, 2 X 5 min in 2X SSC, 0.1% SDS at room temperature (RT), 2 X 5 min in 1X SSC at RT, and 2 X 5 min in 0.1X SSC at RT, and dried by centrifugation as before.  The Cy3 and Cy5 3-dimensional fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized to the bound cDNA on the microarray in a formamide-based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) for 3 h at 48˚C, and washed and dried as before.

tag: Fluorescent images of hybridized arrays were acquired using ScanArray and extracted using QuantArray (Perkin Elmer).  The same laser power (90%) and photomultiplier tube (PMT) settings were used for all slides in each study (Cy3 PMT 78-80, Cy5 PMT 72-76).

tag: Fluorescent images of hybridized arrays were acquired using QuantArray (Perkin Elmer).  The same laser power (90%) and photomultiplier tube (PMT) settings were used for all slides in each study (Cy3 PMT 78-80, Cy5 PMT 72-76).


title: NA11995 , IVT: 1, Hyb: 7, SAM: 1269933, Array: G11

description: HapMap CEU parent


title: NA07056 , IVT: 1, Hyb: 8, SAM: 1269933, Array: F12

description: HapMap CEU parent


title: NA12005 , IVT: 1, Hyb: 7, SAM: 1269933, Array: G10

description: HapMap CEU parent

tag: HapMap CEU parent, Male


title: Transgenic Atlantic salmon 12605532b replicate 1

description: Replicate 1 of 4, top half of the array

source_name: mRNA extracted from Transgenic liver tissue, labelled with Cy3


title: HMEC-cy5 and MCF7-cy3

description: HMEC vs. MCF7


title: Transgenic Atlantic salmon 12605187b replicate 1

description: Replicate 1 of 4, top half of the array


title: NA12761 , IVT: 2, Hyb: 6, SAM: 1274134, Array: C2

description: HapMap CEU parent


title: NA12813 , IVT: 1, Hyb: 7, SAM: 1269933, Array: E11

description: HapMap CEU parent


title: NA12006 , IVT: 1, Hyb: 8, SAM: 1269933, Array: F10

description: HapMap CEU parent


title: NA12006 , IVT: 1, Hyb: 7, SAM: 1269933, Array: E10

description: HapMap CEU parent


title: NA12813 , IVT: 1, Hyb: 8, SAM: 1269933, Array: F11

description: HapMap CEU parent


title: NA12815 , IVT: 1, Hyb: 8, SAM: 1269933, Array: D11

description: HapMap CEU parent


title: muscle tissue from a fish injected with IHNV DNA Vaccine, replicate 3

status: Public on Dec 09 2005

city: West Lafayette

first: Krista

last: Nichols

state: IN

address: 915 W State Street

department: Biological Sciences

institute: Purdue University

description: muscle tissue from a single clonal HC individual injected with IHNV vaccine compared to a major reference pool of tissues from untreated, unhandled HC individuals (n=3)

hyb_protocol: Pre-processing, hybridization and washing of the slides was performed as recommended by GRASP (http://web.uvic.ca/cbr/grasp), and as described in von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs RA, Nelson CC, Davidson WS, Koop BF.  2005.  Fish and Chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6: 126.

scan_protocol: All arrays were scanned on an Agilent Microarray Scanner using Agilent's Feature Extraction Software (v. 7.5.1).  Default parameters were used for scanning for Cy3 aqnd Cy5 signals, and resolution was set at 10 um.

data_processing: Parameters used for the processing of raw data may be found in the supplementary information.  Briefly, global background for each slide in each channel was subtracted from raw feature signals.  Background-subtracted signal intensities in each channel were normalized for dye-bias using the LOWESS (locally weighted linear regression) method.  In the case of very low or negative background-subtracted signal intensities, surrogates were used to replace these values for final ProcessedSignal intensities in each channel, used for the calculation of LogRatios.  Surrogates used for each negative or low signal value were calculated as one standard deviation of the local background used for that feature in the particular channel.  Finally, the feature extraction software calculated the log base 10 ratio of rProcessedSignal/gProcessed signal.  This LogRatio (VALUE) was used for all subsequent data analysis.

organism: Oncorhynchus mykiss

source_name: muscle tissue from site of IHNV DNA vaccine injection from a single HC individual, replicate 3

label_protocol: Total muscle RNA (1.5 µg) from the I.M. site of injection was subjected to one round of amplification with the Message Amp aRNA kit (Ambion) following the manufacturer’s protocol. The quality of the total RNA and the synthesized aRNA for all the samples was confirmed using the Agilent Bioanalyzer 2100 (Agilent Technologies). Labelling and hybridization of the microarray was performed by the University of Washington Center for Expression Arrays (http://ra.microslu.washington.edu/index.html). The treatment aRNA was directly labelled with Cy3 using the Center for Expression Array protocols, as described in Purcell et al.

extract_protocol: Tissues were placed in individual tubes containing beads (Matrix D; Bio 101 Systems) and RNeasy Buffer RLT (Qiagen). Samples were homogenized using FastPrep instrument (Bio101 Systems). RNA was extracted using the RNeasy Mini Kit (Qiagen) with in-column DNase treatment following manufacturer’s instructions. A modified protocol provided by the manufacturer for fibrous tissues which incorporates a proteinase K digestion of the tissue was used to extract the muscle RNA.

treatment_protocol: Vaccine-injected individuals were treated by injecting 10 µg of pIHNw-G vaccine construct diluted in 50 µl 1X PBS just below the dorsal fin.  Muscle tissue, at the site of injection, was collected from individuals 7 days post-injection.

tag: Strain

value: Hot Creek (HC) rainbow trout clonal line; Tissue: muscle from site of injection, just below the dorsal fin; Number of individuals:1; Sex:male; Age:~1 yr

source_name: pooled reference sample from 3 HC individuals

label_protocol: The pool of RNA that constituted the major reference control was also subjected to a single round of aRNA synthesis, as described for treatment samples, but a total of 2 µg was used to initiate amplification.  Labelling of aRNA was conducted in the same manner as for treatment samples, with Cy5.

extract_protocol: Individual tissues (anterior kidney, spleen, liver, epaxial muscle) were extracted separately as described for treatment muscle.  Equal quantities of RNA from each tissue were mixed for the pooled sample.

treatment_protocol: Reference individuals were unhandled prior to the collection of tissues for RNA.  Anterior kidney, spleen, liver, and epaxial muscle tissue were collected from 3 HC individuals for a pooled reference sample against which all treatments were compared.

value: Hot Creek (HC) rainbow trout clonal line; Tissue: anterior kidney, spleen, liver, and muscle; Number of individuals:3; Sex:male; Age:1 yr, 7 mo


title: NA12761 , IVT: 2, Hyb: 5, SAM: 1274134, Array: B2

description: HapMap CEU parent


title: Transgenic Atlantic salmon 12605532t replicate 1

description: Replicate 1 of 4, top half of the array


title: NA12815 , IVT: 1, Hyb: 7, SAM: 1269933, Array: C11

description: HapMap CEU parent


title: muscle tissue from a fish injected with vector, replicate 1

description: muscle tissue from a single vector-injected clonal HC individual compared to a major reference pool of tissues from untreated, unhandled HC individuals (n=3)

source_name: muscle tissue from site of vector injection from a single HC individual, replicate 1

treatment_protocol: Vector-injected individuals were treated by injecting 10 µg of pCDNA 3.1 plasmid vector DNA diluted in 50 µl of 1X PBS just below the dorsal fin.  Muscle tissue, at the site of injection, was collected from individuals 7 days post-injection.


title: muscle tissue from a fish injected with vector, replicate 3

source_name: muscle tissue from site of vector injection from a single HC individual, replicate 3


title: muscle tissue from a fish injected with IHNV DNA Vaccine, replicate 1

source_name: muscle tissue from site of IHNV DNA vaccine injection from a single HC individual, replicate 1


title: NA11829 , IVT: 1, Hyb: 8, SAM: 1269933, Array: D10

description: HapMap CEU parent


title: muscle tissue from a fish injected with IHNV DNA Vaccine, replicate 2

source_name: muscle tissue from site of IHNV DNA vaccine injection from a single HC individual, replicate 2


title: muscle tissue from a fish injected with IHNV DNA Vaccine, replicate 4

source_name: muscle tissue from site of IHNV DNA vaccine injection from a single HC individual, replicate 4


title: NA12761 , IVT: 2, Hyb: 4, SAM: 1274134, Array: A2

description: HapMap CEU parent


title: NA12057 , IVT: 2, Hyb: 6, SAM: 1274134, Array: C1

description: HapMap CEU parent


title: NA07056 , IVT: 1, Hyb: 7, SAM: 1269933, Array: E12

description: HapMap CEU parent


title: muscle tissue from a control fish, injected with PBS, replicate 2

description: muscle tissue from a single PBS-injected clonal HC individual compared to a major reference pool of tissues from untreated, unhandled HC individuals (n=3)

source_name: muscle tissue from site of injection of PBS from a single HC individual, control, replicate 2

treatment_protocol: Control individuals were treated by injecting 50 uL of 1X PBS into the muscle just below the dorsal fin.  Muscle tissue, at the site of injection, was collected from individuals 7 days post-injection.


title: muscle tissue from a fish injected with vector, replicate 2

source_name: muscle tissue from site of vector injection from a single HC individual, replicate 2


title: NA07357 , IVT: 2, Hyb: 6, SAM: 1269933, Array: H9

description: HapMap CEU parent


title: muscle tissue from a control fish, injected with PBS, replicate 1

scan_protocol: All arrays were scanned on an Agilent Microarray Scanner using Agilent's Feature Extraction Software (v. 7.5.1).

source_name: muscle tissue from site of injection of PBS from a single HC individual, control, replicate 1

label_protocol: Total muscle RNA (1.5 ug) from the I.M. site of injection was subjected to one round of amplification with the Message Amp aRNA kit (Ambion) following the manufacturer's protocol. The quality of the total RNA and the synthesized aRNA for all the samples was confirmed using the Agilent Bioanalyzer 2100 (Agilent Technologies). Labelling and hybridization of the microarray was performed by the University of Washington Center for Expression Arrays (http://ra.microslu.washington.edu/index.html). The treatment aRNA was directly labelled with Cy3 using the Center for Expression Array protocols, as described in Purcell et al.

extract_protocol: Tissues were placed in individual tubes containing beads (Matrix D; Bio 101 Systems) and RNeasy Buffer RLT (Qiagen). Samples were homogenized using FastPrep instrument (Bio101 Systems). RNA was extracted using the RNeasy Mini Kit (Qiagen) with in-column DNase treatment following manufacturer�s instructions. A modified protocol provided by the manufacturer for fibrous tissues which incorporates a proteinase K digestion of the tissue was used to extract the muscle RNA.

value: Hot Creek (HC) rainbow trout clonal line

tag: Tissue

value: muscle from site of injection, just below the dorsal fin

tag: Number of individuals

tag: Sex

value: male

tag: Age

value: ~1 yr

label_protocol: The pool of RNA that constituted the major reference control was also subjected to a single round of aRNA synthesis, as described for treatment samples, but a total of 2 ug was used to initiate amplification.  Labelling of aRNA was conducted in the same manner as for treatment samples, with Cy5.

value: anterior kidney, spleen, liver, and muscle

value: 1 yr, 7 mo


title: muscle tissue from a control fish, injected with PBS, replicate 3

source_name: muscle tissue from site of injection of PBS from a single HC individual, control, replicate 3


title: NA12751 , IVT: 2, Hyb: 6, SAM: 1269933, Array: H3

description: HapMap CEU parent


title: NA06993 , IVT: 2, Hyb: 6, SAM: 1269933, Array: G9

description: HapMap CEU parent


title: NA12874 , IVT: 1, Hyb: 7, SAM: 1269933, Array: C12

description: HapMap CEU parent


title: NA11829 , IVT: 1, Hyb: 7, SAM: 1269933, Array: C10

description: HapMap CEU parent


title: NA12874 , IVT: 1, Hyb: 8, SAM: 1269933, Array: D12

description: HapMap CEU parent


title: NA12005 , IVT: 1, Hyb: 8, SAM: 1269933, Array: H10

description: HapMap CEU parent


title: NA06993 , IVT: 2, Hyb: 4, SAM: 1269933, Array: G7

description: HapMap CEU parent


title: NA12155 , IVT: 1, Hyb: 8, SAM: 1269933, Array: B12

description: HapMap CEU parent


title: NA12155 , IVT: 1, Hyb: 7, SAM: 1269933, Array: A12

description: HapMap CEU parent


title: NA12750 , IVT: 1, Hyb: 2, SAM: 1269933, Array: G2

description: HapMap CEU parent


title: NA12750 , IVT: 1, Hyb: 1, SAM: 1269933, Array: G1

description: HapMap CEU parent


title: NA12717 , IVT: 1, Hyb: 8, SAM: 1269933, Array: B11

description: HapMap CEU parent


title: NA12717 , IVT: 1, Hyb: 7, SAM: 1269933, Array: A11

description: HapMap CEU parent


title: NA11832 , IVT: 1, Hyb: 8, SAM: 1269933, Array: B10

description: HapMap CEU parent


title: NA06994 , IVT: 2, Hyb: 5, SAM: 1269933, Array: F8

description: HapMap CEU parent

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 û 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80 oC.


title: NA07357 , IVT: 2, Hyb: 5, SAM: 1269933, Array: H8

description: HapMap CEU parent


title: NA11832 , IVT: 1, Hyb: 7, SAM: 1269933, Array: A10

description: HapMap CEU parent


title: NA06994 , IVT: 2, Hyb: 6, SAM: 1269933, Array: F9

description: HapMap CEU parent


title: NA12156 , IVT: 1, Hyb: 1, SAM: 1269933, Array: H4

description: HapMap CEU parent


title: NA06994 , IVT: 2, Hyb: 4, SAM: 1269933, Array: F7

description: HapMap CEU parent


title: NA12156 , IVT: 1, Hyb: 2, SAM: 1269933, Array: H5

description: HapMap CEU parent


title: NA07357 , IVT: 2, Hyb: 4, SAM: 1269933, Array: H7

description: HapMap CEU parent


title: NA12156 , IVT: 1, Hyb: 3, SAM: 1269933, Array: H6

description: HapMap CEU parent


title: NA06993 , IVT: 2, Hyb: 5, SAM: 1269933, Array: G8

description: HapMap CEU parent


title: NA12239 , IVT: 2, Hyb: 6, SAM: 1269933, Array: E9

description: HapMap CEU parent


title: NA12751 , IVT: 2, Hyb: 5, SAM: 1269933, Array: H2

description: HapMap CEU parent


title: NA12751 , IVT: 2, Hyb: 4, SAM: 1269933, Array: H1

description: HapMap CEU parent


title: NA12239 , IVT: 2, Hyb: 4, SAM: 1269933, Array: E7

description: HapMap CEU parent


title: NA12236 , IVT: 1, Hyb: 3, SAM: 1269933, Array: G6

description: HapMap CEU parent


title: NA12236 , IVT: 1, Hyb: 1, SAM: 1269933, Array: G4

description: HapMap CEU parent


title: NA12236 , IVT: 1, Hyb: 2, SAM: 1269933, Array: G5

description: HapMap CEU parent


title: NA07034 , IVT: 2, Hyb: 4, SAM: 1269933, Array: E4

description: HapMap CEU parent


title: NA12750 , IVT: 1, Hyb: 3, SAM: 1269933, Array: G3

description: HapMap CEU parent


title: NA12044 , IVT: 2, Hyb: 5 SAM: 1269933, Array: F5

description: HapMap CEU parent


title: NA12044 , IVT: 2, Hyb: 4, SAM: 1269933, Array: F4

description: HapMap CEU parent


title: NA12716 , IVT: 2, Hyb: 6, SAM: 1269933, Array: F3

description: HapMap CEU parent


title: NA12044 , IVT: 2, Hyb: 6, SAM: 1269933, Array: F6

description: HapMap CEU parent


title: NA12716 , IVT: 2, Hyb: 4, SAM: 1269933, Array: F1

description: HapMap CEU parent


title: NA12716 , IVT: 2, Hyb: 5, SAM: 1269933, Array: F2

description: HapMap CEU parent


title: NA12145 , IVT: 1, Hyb: 2, SAM: 1269933, Array: D8

description: HapMap CEU parent


title: NA06994 , IVT: 1, Hyb: 3, SAM: 1269933, Array: D6

description: HapMap CEU parent


title: NA07034 , IVT: 2, Hyb: 5, SAM: 1269933, Array: E5

description: HapMap CEU parent


title: NA07034 , IVT: 2, Hyb: 6, SAM: 1269933, Array: E6

description: HapMap CEU parent


title: NA12239 , IVT: 2, Hyb: 5, SAM: 1269933, Array: E8

description: HapMap CEU parent


title: NA06994 , IVT: 1, Hyb: 2, SAM: 1269933, Array: D5

description: HapMap CEU parent


title: NA12264 , IVT: 2, Hyb: 5, SAM: 1269933, Array: E2

description: HapMap CEU parent


title: NA12249 , IVT: 2, Hyb: 4, SAM: 1269933, Array: D1

description: HapMap CEU parent


title: NA12249 , IVT: 2, Hyb: 6, SAM: 1269933, Array: D3

description: HapMap CEU parent


title: NA12264 , IVT: 2, Hyb: 6, SAM: 1269933, Array: E3

description: HapMap CEU parent


title: NA12145 , IVT: 1, Hyb: 3, SAM: 1269933, Array: D9

description: HapMap CEU parent


title: NA12264 , IVT: 2, Hyb: 4, SAM: 1269933, Array: E1

description: HapMap CEU parent


title: NA12248 , IVT: 2, Hyb: 6, SAM: 1269933, Array: C3

description: HapMap CEU parent


title: NA12145 , IVT: 1, Hyb: 1, SAM: 1269933, Array: D7

description: HapMap CEU parent


title: NA06994 , IVT: 1, Hyb: 1, SAM: 1269933, Array: D4

description: HapMap CEU parent


title: NA12872 , IVT: 2, Hyb: 5, SAM: 1269933, Array: C8

description: HapMap CEU parent


title: NA12872 , IVT: 2, Hyb: 6, SAM: 1269933, Array: C9

description: HapMap CEU parent


title: NA12249 , IVT: 2, Hyb: 5, SAM: 1269933, Array: D2

description: HapMap CEU parent


title: NA12750 , IVT: 2, Hyb: 6, SAM: 1269933, Array: B79

description: HapMap CEU parent


title: NA12815 , IVT: 2, Hyb: 6, SAM: 1269933, Array: B6

description: HapMap CEU parent


title: NA12815 , IVT: 2, Hyb: 5, SAM: 1269933, Array: B5

description: HapMap CEU parent


title: NA12145 , IVT: 2, Hyb: 5, SAM: 1269933, Array: C5

description: HapMap CEU parent


title: NA12145 , IVT: 2, Hyb: 4, SAM: 1269933, Array: C4

description: HapMap CEU parent


title: NA12248 , IVT: 2, Hyb: 4, SAM: 1269933, Array: C1

description: HapMap CEU parent


title: NA12248 , IVT: 2, Hyb: 5, SAM: 1269933, Array: C2

description: HapMap CEU parent


title: NA12872 , IVT: 2, Hyb: 4, SAM: 1269933, Array: C7

description: HapMap CEU parent


title: NA12145 , IVT: 2, Hyb: 6, SAM: 1269933, Array: C6

description: HapMap CEU parent


title: NA11829 , IVT: 2, Hyb: 5, SAM: 1269933, Array: A8

description: HapMap CEU parent


title: NA11829 , IVT: 2, Hyb: 6, SAM: 1269933, Array: A9

description: HapMap CEU parent


title: NA12750 , IVT: 2, Hyb: 5, SAM: 1269933, Array: B8

description: HapMap CEU parent


title: NA12234 , IVT: 2, Hyb: 6, SAM: 1269933, Array: B3

description: HapMap CEU parent


title: NA11882 , IVT: 1, Hyb: 1, SAM: 1269941, Array: H10

description: HapMap CEU parent


title: NA12750 , IVT: 2, Hyb: 4, SAM: 1269933, Array: B7

description: HapMap CEU parent


title: NA12815 , IVT: 2, Hyb: 4, SAM: 1269933, Array: B4

description: HapMap CEU parent


title: NA12144 , IVT: 1, Hyb: 2, SAM: 1269941, Array: H8

description: HapMap CEU parent


title: NA12234 , IVT: 2, Hyb: 5, SAM: 1269933, Array: B2

description: HapMap CEU parent


title: NA11882 , IVT: 1, Hyb: 2, SAM: 1269941, Array: H11

description: HapMap CEU parent


title: NA12234 , IVT: 2, Hyb: 4, SAM: 1269933, Array: B1

description: HapMap CEU parent


title: NA11882 , IVT: 1, Hyb: 3, SAM: 1269941, Array: H12

description: HapMap CEU parent


title: NA12144 , IVT: 1, Hyb: 3, SAM: 1269941, Array: H9

description: HapMap CEU parent


title: NA11829 , IVT: 2, Hyb: 4, SAM: 1269933, Array: A7

description: HapMap CEU parent


title: NA12892 , IVT: 1, Hyb: 3, SAM: 1269941, Array: G9

description: HapMap CEU parent


title: NA12763 , IVT: 1, Hyb: 3, SAM: 1269941, Array: G6

description: HapMap CEU parent


title: NA12812 , IVT: 1, Hyb: 1, SAM: 1269941, Array: H4

description: HapMap CEU parent


title: NA12892 , IVT: 1, Hyb: 2, SAM: 1269941, Array: G8

description: HapMap CEU parent


title: NA12043 , IVT: 1, Hyb: 3, SAM: 1269941, Array: G12

description: HapMap CEU parent


title: NA12043 , IVT: 1, Hyb: 2, SAM: 1269941, Array: G11

description: HapMap CEU parent


title: NA12763 , IVT: 1, Hyb: 2, SAM: 1269941, Array: G5

description: HapMap CEU parent


title: NA12812 , IVT: 1, Hyb: 2, SAM: 1269941, Array: H5

description: HapMap CEU parent


title: NA12234 , IVT: 1, Hyb: 2, SAM: 1269941, Array: H2

description: HapMap CEU parent


title: NA12144 , IVT: 1, Hyb: 1, SAM: 1269941, Array: H7

description: HapMap CEU parent


title: NA12763 , IVT: 1, Hyb: 1, SAM: 1269941, Array: G4

description: HapMap CEU parent


title: NA12043 , IVT: 1, Hyb: 1, SAM: 1269941, Array: G10

description: HapMap CEU parent


title: NA12057 , IVT: 1, Hyb: 2, SAM: 1269941, Array: G2

description: HapMap CEU parent


title: NA12234 , IVT: 1, Hyb: 3, SAM: 1269941, Array: H3

description: HapMap CEU parent


title: NA12057 , IVT: 1, Hyb: 3, SAM: 1269941, Array: G3

description: HapMap CEU parent


title: NA12892 , IVT: 1, Hyb: 1, SAM: 1269941, Array: G7

description: HapMap CEU parent


title: NA07345 , IVT: 1, Hyb: 2, SAM: 1269941, Array: F11

description: HapMap CEU parent


title: NA12812 , IVT: 1, Hyb: 3, SAM: 1269941, Array: H6

description: HapMap CEU parent


title: NA12234 , IVT: 1, Hyb: 1, SAM: 1269941, Array: H1

description: HapMap CEU parent


title: NA12891 , IVT: 1, Hyb: 3, SAM: 1269941, Array: F9

description: HapMap CEU parent


title: NA12057 , IVT: 1, Hyb: 1, SAM: 1269941, Array: G1

description: HapMap CEU parent


title: NA07345 , IVT: 1, Hyb: 1, SAM: 1269941, Array: F10

description: HapMap CEU parent


title: NA07345 , IVT: 1, Hyb: 3, SAM: 1269941, Array: F12

description: HapMap CEU parent


title: NA12891 , IVT: 1, Hyb: 2, SAM: 1269941, Array: F8

description: HapMap CEU parent


title: NA12762 , IVT: 1, Hyb: 2, SAM: 1269941, Array: F5

description: HapMap CEU parent


title: NA12056 , IVT: 1, Hyb: 2, SAM: 1269941, Array: F2

description: HapMap CEU parent


title: NA12762 , IVT: 1, Hyb: 1, SAM: 1269941, Array: F4

description: HapMap CEU parent


title: NA12762 , IVT: 1, Hyb: 3, SAM: 1269941, Array: F6

description: HapMap CEU parent


title: NA12891 , IVT: 1, Hyb: 1, SAM: 1269941, Array: F7

description: HapMap CEU parent


title: NA12056 , IVT: 1, Hyb: 3, SAM: 1269941, Array: F3

description: HapMap CEU parent


title: NA12056 , IVT: 1, Hyb: 1, SAM: 1269941, Array: F1

description: HapMap CEU parent


title: NA06993 , IVT: 1, Hyb: 2, SAM: 1269941, Array: E11

description: HapMap CEU parent


title: NA12875 , IVT: 1, Hyb: 2, SAM: 1269941, Array: E8

description: HapMap CEU parent


title: NA12760 , IVT: 1, Hyb: 1, SAM: 1269941, Array: E4

description: HapMap CEU parent


title: NA07055 , IVT: 1, Hyb: 3, SAM: 1269941, Array: D12

description: HapMap CEU parent


title: NA06993 , IVT: 1, Hyb: 1, SAM: 1269941, Array: E10

description: HapMap CEU parent


title: NA12760 , IVT: 1, Hyb: 3, SAM: 1269941, Array: E6

description: HapMap CEU parent


title: NA12760 , IVT: 1, Hyb: 2, SAM: 1269941, Array: E5

description: HapMap CEU parent


title: NA12875 , IVT: 1, Hyb: 1, SAM: 1269941, Array: E7

description: HapMap CEU parent


title: NA12875 , IVT: 1, Hyb: 3, SAM: 1269941, Array: E9

description: HapMap CEU parent


title: NA07055 , IVT: 1, Hyb: 2, SAM: 1269941, Array: D11

description: HapMap CEU parent


title: NA12006 , IVT: 1, Hyb: 1, SAM: 1269941, Array: E1

description: HapMap CEU parent


title: NA12873 , IVT: 1, Hyb: 3, SAM: 1269941, Array: D9

description: HapMap CEU parent


title: NA12006 , IVT: 1, Hyb: 3, SAM: 1269941, Array: E3

description: HapMap CEU parent


title: NA07055 , IVT: 1, Hyb: 1, SAM: 1269941, Array: D10

description: HapMap CEU parent


title: NA12873 , IVT: 1, Hyb: 1, SAM: 1269941, Array: D7

description: HapMap CEU parent


title: NA12717 , IVT: 2, Hyb: 6, SAM: 1269941, Array: D6

description: HapMap CEU parent


title: NA12717 , IVT: 2, Hyb: 4, SAM: 1269941, Array: D4

description: HapMap CEU parent


title: NA12006 , IVT: 1, Hyb: 2, SAM: 1269941, Array: E2

description: HapMap CEU parent


title: NA12717 , IVT: 2, Hyb: 5, SAM: 1269941, Array: D5

description: HapMap CEU parent


title: NA12873 , IVT: 1, Hyb: 2, SAM: 1269941, Array: D8

description: HapMap CEU parent


title: NA12005 , IVT: 2, Hyb: 6, SAM: 1269941, Array: D3

description: HapMap CEU parent


title: NA07056 , IVT: 1, Hyb: 3, SAM: 1269941, Array: C12

description: HapMap CEU parent


title: NA12872 , IVT: 1, Hyb: 2, SAM: 1269941, Array: C8

description: HapMap CEU parent


title: NA12005 , IVT: 2, Hyb: 5, SAM: 1269941, Array: D2

description: HapMap CEU parent


title: NA12264 , IVT: 1, Hyb: 3, SAM: 1269941, Array: C6

description: HapMap CEU parent


title: NA12264 , IVT: 1, Hyb: 1, SAM: 1269941, Array: C4

description: HapMap CEU parent


title: NA12264 , IVT: 1, Hyb: 2, SAM: 1269941, Array: C5

description: HapMap CEU parent


title: NA07056 , IVT: 1, Hyb: 2, SAM: 1269941, Array: C11

description: HapMap CEU parent


title: NA12004 , IVT: 1, Hyb: 2, SAM: 1269941, Array: C2

description: HapMap CEU parent


title: NA07056 , IVT: 1, Hyb: 1, SAM: 1269941, Array: C10

description: HapMap CEU parent


title: NA12872 , IVT: 1, Hyb: 1, SAM: 1269941, Array: C7

description: HapMap CEU parent


title: NA07022 , IVT: 1, Hyb: 1, SAM: 1269941, Array: B10

description: HapMap CEU parent


title: NA07022 , IVT: 1, Hyb: 3, SAM: 1269941, Array: B12

description: HapMap CEU parent


title: NA12004 , IVT: 1, Hyb: 3, SAM: 1269941, Array: C3

description: HapMap CEU parent


title: NA12004 , IVT: 1, Hyb: 1, SAM: 1269941, Array: C1

description: HapMap CEU parent


title: NA07022 , IVT: 1, Hyb: 2, SAM: 1269941, Array: B11

description: HapMap CEU parent


title: NA12814 , IVT: 1, Hyb: 3, SAM: 1269941, Array: B9

description: HapMap CEU parent


title: NA12249 , IVT: 1, Hyb: 3, SAM: 1269941, Array: B6

description: HapMap CEU parent


title: NA12814 , IVT: 1, Hyb: 1, SAM: 1269941, Array: B7

description: HapMap CEU parent


title: NA12814 , IVT: 1, Hyb: 2, SAM: 1269941, Array: B8

description: HapMap CEU parent


title: NA12249 , IVT: 1, Hyb: 2, SAM: 1269941, Array: B5

description: HapMap CEU parent


title: NA12872 , IVT: 1, Hyb: 3, SAM: 1269941, Array: C9

description: HapMap CEU parent


title: NA12249 , IVT: 1, Hyb: 1, SAM: 1269941, Array: B4

description: HapMap CEU parent


title: NA12003 , IVT: 1, Hyb: 3, SAM: 1269941, Array: B3

description: HapMap CEU parent


title: NA12003 , IVT: 1, Hyb: 2, SAM: 1269941, Array: B2

description: HapMap CEU parent


title: NA12003 , IVT: 1, Hyb: 1, SAM: 1269941, Array: B1

description: HapMap CEU parent


title: NA12146 , IVT: 1, Hyb: 3, SAM: 1269941, Array: A12

description: HapMap CEU parent


title: NA12813 , IVT: 1, Hyb: 2, SAM: 1269941, Array: A8

description: HapMap CEU parent


title: NA12813 , IVT: 1, Hyb: 3, SAM: 1269941, Array: A9

description: HapMap CEU parent


title: NA12813 , IVT: 1, Hyb: 1, SAM: 1269941, Array: A7

description: HapMap CEU parent


title: NA12146 , IVT: 1, Hyb: 2, SAM: 1269941, Array: A11

description: HapMap CEU parent


title: NA12248 , IVT: 1, Hyb: 1, SAM: 1269941, Array: A4

description: HapMap CEU parent


title: NA12248 , IVT: 1, Hyb: 2, SAM: 1269941, Array: A5

description: HapMap CEU parent


title: NA11840 , IVT: 1, Hyb: 2, SAM: 1269941, Array: A2

description: HapMap CEU parent


title: NA12248 , IVT: 1, Hyb: 3, SAM: 1269941, Array: A6

description: HapMap CEU parent


title: NA12146 , IVT: 1, Hyb: 1, SAM: 1269941, Array: A10

description: HapMap CEU parent


title: NA11840 , IVT: 1, Hyb: 1, SAM: 1269941, Array: A1

description: HapMap CEU parent


title: NA12761 , IVT: 1, Hyb: 1, SAM: 1216882, Array: H10

description: HapMap CEU parent


title: NA12761 , IVT: 1, Hyb: 2, SAM: 1216882, Array: H11

description: HapMap CEU parent


title: NA12761 , IVT: 1, Hyb: 3, SAM: 1216882, Array: H12

description: HapMap CEU parent


title: NA12236 , IVT: 2, Hyb: 6, SAM: 1216882, Array: H9

description: HapMap CEU parent


title: NA11840 , IVT: 1, Hyb: 3, SAM: 1269941, Array: A3

description: HapMap CEU parent


title: NA11881 , IVT: 1, Hyb: 2, SAM: 1216882, Array: G8

description: HapMap CEU parent


title: NA12156 , IVT: 2, Hyb: 5, SAM: 1216882, Array: F11

description: HapMap CEU parent


title: NA11881 , IVT: 1, Hyb: 1, SAM: 1216882, Array: G7

description: HapMap CEU parent


title: NA12236 , IVT: 2, Hyb: 45 SAM: 1216882, Array: H8

description: HapMap CEU parent


title: NA12156 , IVT: 2, Hyb: 6, SAM: 1216882, Array: F12

description: HapMap CEU parent


title: NA12156 , IVT: 2, Hyb: 4, SAM: 1216882, Array: F10

description: HapMap CEU parent


title: NA11881 , IVT: 1, Hyb: 3, SAM: 1216882, Array: G9

description: HapMap CEU parent


title: NA12236 , IVT: 2, Hyb: 4, SAM: 1216882, Array: H7

description: HapMap CEU parent


title: NA12874 , IVT: 2, Hyb: 6, SAM: 1216882, Array: E12

description: HapMap CEU parent


title: NA07357 , IVT: 1, Hyb: 1, SAM: 1216882, Array: F7

description: HapMap CEU parent


title: NA07357 , IVT: 1, Hyb: 3, SAM: 1216882, Array: F9

description: HapMap CEU parent


title: NA12874 , IVT: 2, Hyb: 4, SAM: 1216882, Array: E10

description: HapMap CEU parent


title: NA07357 , IVT: 1, Hyb: 2, SAM: 1216882, Array: F8

description: HapMap CEU parent


title: NA12874 , IVT: 2, Hyb: 5, SAM: 1216882, Array: E11

description: HapMap CEU parent


title: NA06993 , IVT: 1, Hyb: 3, SAM: 1269941, Array: E12

description: HapMap CEU parent


title: NA11881 , IVT: 2, Hyb: 5, SAM: 1216882, Array: D11

description: HapMap CEU parent


title: NA06985 , IVT: 1, Hyb: 1, SAM: 1216882, Array: E7

description: HapMap CEU parent


title: NA11881 , IVT: 2, Hyb: 6, SAM: 1216882, Array: D12

description: HapMap CEU parent


title: NA07000 , IVT: 1, Hyb: 3, SAM: 1216882, Array: D9

description: HapMap CEU parent


title: NA07000 , IVT: 1, Hyb: 1, SAM: 1216882, Array: D7

description: HapMap CEU parent


title: NA11881 , IVT: 2, Hyb: 4, SAM: 1216882, Array: D10

description: HapMap CEU parent


title: NA06985 , IVT: 1, Hyb: 3, SAM: 1216882, Array: E9

description: HapMap CEU parent


title: NA07000 , IVT: 1, Hyb: 2, SAM: 1216882, Array: D8

description: HapMap CEU parent


title: NA06985 , IVT: 1, Hyb: 2, SAM: 1216882, Array: E8

description: HapMap CEU parent


title: NA06985 , IVT: 2, Hyb: 5, SAM: 1216882, Array: C11

description: HapMap CEU parent


title: NA12239 , IVT: 1, Hyb: 3, SAM: 1216882, Array: C9

description: HapMap CEU parent


title: NA12239 , IVT: 1, Hyb: 2, SAM: 1216882, Array: C8

description: HapMap CEU parent


title: NA12239 , IVT: 1, Hyb: 1, SAM: 1216882, Array: C7

description: HapMap CEU parent


title: NA06985 , IVT: 2, Hyb: 4, SAM: 1216882, Array: C10

description: HapMap CEU parent


title: NA07000 , IVT: 2, Hyb: 5, SAM: 1216882, Array: B11

description: HapMap CEU parent


title: NA07000 , IVT: 2, Hyb: 4, SAM: 1216882, Array: B10

description: HapMap CEU parent


title: NA07000 , IVT: 2, Hyb: 6, SAM: 1216882, Array: B12

description: HapMap CEU parent


title: NA06985 , IVT: 2, Hyb: 6, SAM: 1216882, Array: C12

description: HapMap CEU parent


title: NA11994 , IVT: 2, Hyb: 6, SAM: 1216784, Array: H12

description: HapMap CEU parent


title: NA12874 , IVT: 1, Hyb: 3, SAM: 1216882, Array: B9

description: HapMap CEU parent


title: NA11994 , IVT: 2, Hyb: 5, SAM: 1216784, Array: H11

description: HapMap CEU parent


title: NA11882 , IVT: 2, Hyb: 4, SAM: 1216882, Array: A10

description: HapMap CEU parent


title: NA12874 , IVT: 1, Hyb: 1, SAM: 1216882, Array: B7

description: HapMap CEU parent


title: NA12874 , IVT: 1, Hyb: 2, SAM: 1216882, Array: B8

description: HapMap CEU parent


title: NA11829 , IVT: 1, Hyb: 3, SAM: 1216882, Array: A9

description: HapMap CEU parent


title: NA11882 , IVT: 2, Hyb: 5, SAM: 1216882, Array: A11

description: HapMap CEU parent


title: NA11882 , IVT: 2, Hyb: 6, SAM: 1216882, Array: A12

description: HapMap CEU parent


title: NA11829 , IVT: 1, Hyb: 2, SAM: 1216882, Array: A8

description: HapMap CEU parent


title: NA11994 , IVT: 2, Hyb: 4, SAM: 1216784, Array: H10

description: HapMap CEU parent


title: NA12716 , IVT: 1, Hyb: 2, SAM: 1216784, Array: H8

description: HapMap CEU parent


title: NA12716 , IVT: 1, Hyb: 3, SAM: 1216784, Array: H9

description: HapMap CEU parent


title: NA12716 , IVT: 1, Hyb: 1, SAM: 1216784, Array: H7

description: HapMap CEU parent


title: NA11829 , IVT: 1, Hyb: 1, SAM: 1216882, Array: A7

description: HapMap CEU parent


title: NA11993 , IVT: 2, Hyb: 4, SAM: 1216784, Array: H4

description: HapMap CEU parent


title: NA11993 , IVT: 2, Hyb: 6, SAM: 1216784, Array: H6

description: HapMap CEU parent


title: NA11993 , IVT: 2, Hyb: 5, SAM: 1216784, Array: H5

description: HapMap CEU parent


title: NA12892 , IVT: 2, Hyb: 4, SAM: 1216784, Array: H1

description: HapMap CEU parent


title: NA12044 , IVT: 1, Hyb: 3, SAM: 1216784, Array: G12

description: HapMap CEU parent


title: NA12044 , IVT: 1, Hyb: 1, SAM: 1216784, Array: G10

description: HapMap CEU parent


title: NA12044 , IVT: 1, Hyb: 2, SAM: 1216784, Array: G11

description: HapMap CEU parent


title: NA12892 , IVT: 2, Hyb: 6, SAM: 1216784, Array: H3

description: HapMap CEU parent


title: NA11839 , IVT: 2, Hyb: 6, SAM: 1216784, Array: G9

description: HapMap CEU parent


title: NA12875 , IVT: 2, Hyb: 5, SAM: 1216784, Array: G2

description: HapMap CEU parent


title: NA11839 , IVT: 2, Hyb: 5, SAM: 1216784, Array: G8

description: HapMap CEU parent


title: NA11839 , IVT: 2, Hyb: 4, SAM: 1216784, Array: G7

description: HapMap CEU parent


title: NA12892 , IVT: 2, Hyb: 5, SAM: 1216784, Array: H2

description: HapMap CEU parent


title: NA12875 , IVT: 2, Hyb: 4, SAM: 1216784, Array: G1

description: HapMap CEU parent


title: NA12875 , IVT: 2, Hyb: 6, SAM: 1216784, Array: G3

description: HapMap CEU parent


title: NA11832 , IVT: 1, Hyb: 3, SAM: 1216784, Array: F9

description: HapMap CEU parent


title: NA07055 , IVT: 2, Hyb: 5, SAM: 1216784, Array: F11

description: HapMap CEU parent


title: NA11832 , IVT: 1, Hyb: 1, SAM: 1216784, Array: F7

description: HapMap CEU parent


title: NA07055 , IVT: 2, Hyb: 6, SAM: 1216784, Array: F12

description: HapMap CEU parent


title: NA12873 , IVT: 2, Hyb: 5, SAM: 1216784, Array: F2

description: HapMap CEU parent


title: NA12043 , IVT: 2, Hyb: 5, SAM: 1216784, Array: F5

description: HapMap CEU parent


title: NA11832 , IVT: 1, Hyb: 2, SAM: 1216784, Array: F8

description: HapMap CEU parent


title: NA07034 , IVT: 1, Hyb: 2, SAM: 1216784, Array: E11

description: HapMap CEU parent


title: NA12873 , IVT: 2, Hyb: 4, SAM: 1216784, Array: F1

description: HapMap CEU parent


title: NA12043 , IVT: 2, Hyb: 4, SAM: 1216784, Array: F4

description: HapMap CEU parent


title: NA07055 , IVT: 2, Hyb: 4, SAM: 1216784, Array: F10

description: HapMap CEU parent


title: NA11831 , IVT: 2, Hyb: 6, SAM: 1216784, Array: E9

description: HapMap CEU parent


title: NA07034 , IVT: 1, Hyb: 3, SAM: 1216784, Array: E12

description: HapMap CEU parent


title: NA07034 , IVT: 1, Hyb: 1, SAM: 1216784, Array: E10

description: HapMap CEU parent


title: NA12043 , IVT: 2, Hyb: 6, SAM: 1216784, Array: F6

description: HapMap CEU parent


title: NA11831 , IVT: 2, Hyb: 4, SAM: 1216784, Array: E7

description: HapMap CEU parent


title: NA12873 , IVT: 2, Hyb: 6, SAM: 1216784, Array: F3

description: HapMap CEU parent


title: NA07345 , IVT: 2, Hyb: 4, SAM: 1216784, Array: E4

description: HapMap CEU parent


title: NA12814 , IVT: 2, Hyb: 4, SAM: 1216784, Array: E1

description: HapMap CEU parent


title: NA12814 , IVT: 2, Hyb: 5, SAM: 1216784, Array: E2

description: HapMap CEU parent


title: NA07345 , IVT: 2, Hyb: 6, SAM: 1216784, Array: E6

description: HapMap CEU parent


title: NA11831 , IVT: 2, Hyb: 5, SAM: 1216784, Array: E8

description: HapMap CEU parent


title: NA12891 , IVT: 2, Hyb: 5, SAM: 1216784, Array: D11

description: HapMap CEU parent


title: NA12891 , IVT: 2, Hyb: 4, SAM: 1216784, Array: D10

description: HapMap CEU parent


title: NA11830 , IVT: 2, Hyb: 5, SAM: 1216784, Array: D8

description: HapMap CEU parent


title: NA11830 , IVT: 2, Hyb: 4, SAM: 1216784, Array: D7

description: HapMap CEU parent


title: NA12891 , IVT: 2, Hyb: 6, SAM: 1216784, Array: D12

description: HapMap CEU parent


title: NA11830 , IVT: 2, Hyb: 6, SAM: 1216784, Array: D9

description: HapMap CEU parent


title: NA12814 , IVT: 2, Hyb: 6, SAM: 1216784, Array: E3

description: HapMap CEU parent


title: NA07345 , IVT: 2, Hyb: 5, SAM: 1216784, Array: E5

description: HapMap CEU parent


title: NA12812 , IVT: 2, Hyb: 6, SAM: 1216784, Array: C12

description: HapMap CEU parent


title: NA12812 , IVT: 2, Hyb: 5, SAM: 1216784, Array: C11

description: HapMap CEU parent


title: NA12155 , IVT: 1, Hyb: 3, SAM: 1216784, Array: C9

description: HapMap CEU parent

data_processing: background-corrected values for each single bead type (raw data) were normalized on a log scale  using a quantile normalization method (Bolstad et al. Bioinformatics, 2003. 19(2): p. 185-93)


title: NA12155 , IVT: 1, Hyb: 2, SAM: 1216784, Array: C8

description: HapMap CEU parent


title: NA07056 , IVT: 2, Hyb: 6, SAM: 1216784, Array: D6

description: HapMap CEU parent


title: NA12813 , IVT: 2, Hyb: 5, SAM: 1216784, Array: D2

description: HapMap CEU parent


title: NA07056 , IVT: 2, Hyb: 4, SAM: 1216784, Array: D4

description: HapMap CEU parent


title: NA07022 , IVT: 2, Hyb: 6, SAM: 1216784, Array: C6

description: HapMap CEU parent


title: NA12813 , IVT: 2, Hyb: 6, SAM: 1216784, Array: D3

description: HapMap CEU parent


title: NA07056 , IVT: 2, Hyb: 5, SAM: 1216784, Array: D5

description: HapMap CEU parent


title: NA07022 , IVT: 2, Hyb: 5, SAM: 1216784, Array: C5

description: HapMap CEU parent


title: NA12813 , IVT: 2, Hyb: 4, SAM: 1216784, Array: D1

description: HapMap CEU parent


title: NA12763 , IVT: 2, Hyb: 5, SAM: 1216784, Array: C2

description: HapMap CEU parent


title: NA07022 , IVT: 2, Hyb: 4, SAM: 1216784, Array: C4

description: HapMap CEU parent


title: NA12763 , IVT: 2, Hyb: 4, SAM: 1216784, Array: C1

description: HapMap CEU parent


title: NA12812 , IVT: 2, Hyb: 4, SAM: 1216784, Array: C10

description: HapMap CEU parent


title: NA12760 , IVT: 2, Hyb: 6, SAM: 1216784, Array: B12

description: HapMap CEU parent


title: NA12760 , IVT: 2, Hyb: 5, SAM: 1216784, Array: B11

description: HapMap CEU parent


title: NA12154 , IVT: 2, Hyb: 6, SAM: 1216784, Array: B9

description: HapMap CEU parent


title: NA12760 , IVT: 2, Hyb: 4, SAM: 1216784, Array: B10

description: HapMap CEU parent


title: NA12155 , IVT: 1, Hyb: 1, SAM: 1216784, Array: C7

description: HapMap CEU parent


title: NA12763 , IVT: 2, Hyb: 6, SAM: 1216784, Array: C3

description: HapMap CEU parent


title: NA12146 , IVT: 2, Hyb: 5, SAM: 1216784, Array: B5

description: HapMap CEU parent


title: NA12146 , IVT: 2, Hyb: 4, SAM: 1216784, Array: B4

description: HapMap CEU parent


title: NA12146 , IVT: 2, Hyb: 6, SAM: 1216784, Array: B6

description: HapMap CEU parent


title: NA12762 , IVT: 2, Hyb: 6, SAM: 1216784, Array: B3

description: HapMap CEU parent


title: NA12762 , IVT: 2, Hyb: 5, SAM: 1216784, Array: B2

description: HapMap CEU parent


title: NA12751 , IVT: 1, Hyb: 3, SAM: 1216784, Array: A12

description: HapMap CEU parent


title: NA12154 , IVT: 2, Hyb: 4, SAM: 1216784, Array: B7

description: HapMap CEU parent


title: NA12751 , IVT: 1, Hyb: 1, SAM: 1216784, Array: A10

description: HapMap CEU parent


title: NA12762 , IVT: 2, Hyb: 4, SAM: 1216784, Array: B1

description: HapMap CEU parent


title: NA11995 , IVT: 2, Hyb: 5, SAM: 1216784, Array: A8

description: HapMap CEU parent


title: NA11995 , IVT: 2, Hyb: 6, SAM: 1216784, Array: A9

description: HapMap CEU parent


title: NA12144 , IVT: 2, Hyb: 5, SAM: 1216784, Array: A5

description: HapMap CEU parent


title: NA12717 , IVT: 1, Hyb: 3, SAM: 1216784, Array: A3

description: HapMap CEU parent


title: NA12144 , IVT: 2, Hyb: 6, SAM: 1216784, Array: A6

description: HapMap CEU parent


title: NA12717 , IVT: 1, Hyb: 2, SAM: 1216784, Array: A2

description: HapMap CEU parent


title: NA12717 , IVT: 1, Hyb: 1, SAM: 1216784, Array: A1

description: HapMap CEU parent


title: NA11995 , IVT: 2, Hyb: 4, SAM: 1216784, Array: A7

description: HapMap CEU parent


title: NA12154 , IVT: 2, Hyb: 5, SAM: 1216784, Array: B8

description: HapMap CEU parent


title: NA11831 , IVT: 1, Hyb: 3, SAM: 1221008, Array: H3

description: HapMap CEU parent


title: NA12751 , IVT: 1, Hyb: 2, SAM: 1216784, Array: A11

description: HapMap CEU parent


title: NA12056 , IVT: 2, Hyb: 6, SAM: 1221008, Array: H6

description: HapMap CEU parent


title: NA12144 , IVT: 2, Hyb: 4, SAM: 1216784, Array: A4

description: HapMap CEU parent


title: NA12056 , IVT: 2, Hyb: 4, SAM: 1221008, Array: H4

description: HapMap CEU parent


title: NA11831 , IVT: 1, Hyb: 2, SAM: 1221008, Array: H2

description: HapMap CEU parent


title: NA12056 , IVT: 2, Hyb: 5, SAM: 1221008, Array: H5

description: HapMap CEU parent


title: NA12006 , IVT: 2, Hyb: 4, SAM: 1221008, Array: G4

description: HapMap CEU parent


title: NA11830 , IVT: 1, Hyb: 3, SAM: 1221008, Array: G3

description: HapMap CEU parent


title: NA11830 , IVT: 1, Hyb: 1, SAM: 1221008, Array: G1

description: HapMap CEU parent


title: NA11830 , IVT: 1, Hyb: 2, SAM: 1221008, Array: G2

description: HapMap CEU parent


title: NA12005, IVT: 1, Hyb: 3, SAM: 1221008, Array: F6

description: HapMap CEU parent


title: NA12006 , IVT: 2, Hyb: 5, SAM: 1221008, Array: G5

description: HapMap CEU parent


title: NA11831 , IVT: 1, Hyb: 1, SAM: 1221008, Array: H1

description: HapMap CEU parent


title: NA12005, IVT: 1, Hyb: 2, SAM: 1221008, Array: F5

description: HapMap CEU parent


title: NA12005, IVT: 1, Hyb: 1, SAM: 1221008, Array: F4

description: HapMap CEU parent


title: NA12004, IVT: 2, Hyb: 5, SAM: 1221008, Array: E5

description: HapMap CEU parent


title: NA12155, IVT: 2, Hyb: 6, SAM: 1221008, Array: F3

description: HapMap CEU parent


title: NA12155, IVT: 2, Hyb: 4, SAM: 1221008, Array: F1

description: HapMap CEU parent


title: NA12004, IVT: 2, Hyb: 6, SAM: 1221008, Array: E6

description: HapMap CEU parent


title: NA12155, IVT: 2, Hyb: 5, SAM: 1221008, Array: F2

description: HapMap CEU parent


title: NA12154, IVT: 1, Hyb: 2, SAM: 1221008, Array: E2

description: HapMap CEU parent


title: NA12004, IVT: 2, Hyb: 4, SAM: 1221008, Array: E4

description: HapMap CEU parent


title: NA12006 , IVT: 2, Hyb: 6, SAM: 1221008, Array: G6

description: HapMap CEU parent


title: NA12154, IVT: 1, Hyb: 1, SAM: 1221008, Array: E1

description: HapMap CEU parent


title: NA12154, IVT: 1, Hyb: 3, SAM: 1221008, Array: E3

description: HapMap CEU parent


title: NA12003, IVT: 2, Hyb: 5, SAM: 1221008, Array: D5

description: HapMap CEU parent


title: NA12003, IVT: 2, Hyb: 6, SAM: 1221008, Array: D6

description: HapMap CEU parent


title: NA11995, IVT: 1, Hyb: 1, SAM: 1221008, Array: D1

description: HapMap CEU parent


title: NA11995, IVT: 1, Hyb: 2, SAM: 1221008, Array: D2

description: HapMap CEU parent


title: NA12003, IVT: 2, Hyb: 4, SAM: 1221008, Array: D4

description: HapMap CEU parent


title: NA11995, IVT: 1, Hyb: 3, SAM: 1221008, Array: D3

description: HapMap CEU parent


title: NA11994, IVT: 1, Hyb: 2, SAM: 1221008, Array: C2

description: HapMap CEU parent


title: NA11840, IVT: 2, Hyb: 5, SAM: 1221008, Array: C5

description: HapMap CEU parent


title: NA11840, IVT: 2, Hyb: 6, SAM: 1221008, Array: C6

description: HapMap CEU parent


title: NA11839, IVT: 1, Hyb: 3, SAM: 1221008, Array: B6

description: HapMap CEU parent


title: NA11994, IVT: 1, Hyb: 1, SAM: 1221008, Array: C1

description: HapMap CEU parent


title: NA11994, IVT: 1, Hyb: 3, SAM: 1221008, Array: C3

description: HapMap CEU parent


title: NA11839, IVT: 1, Hyb: 2, SAM: 1221008, Array: B5

description: HapMap CEU parent


title: NA11840, IVT: 2, Hyb: 4, SAM: 1221008, Array: C4

description: HapMap CEU parent


title: NA11993, IVT: 1, Hyb: 3, SAM: 1221008, Array: B3

description: HapMap CEU parent


title: NA11993, IVT: 1, Hyb: 2, SAM: 1221008, Array: B2

description: HapMap CEU parent


title: NA11992, IVT:1, Hyb:3, SAM:1221008, Array: A3

description: HapMap CEU parent


title: NA11832, IVT: 2, Hyb: 6, SAM: 1221008, Array: A6

description: HapMap CEU parent


title: NA11993, IVT: 1, Hyb: 1, SAM: 1221008, Array: B1

description: HapMap CEU parent


title: NA11832, IVT: 2, Hyb: 4, SAM: 1221008, Array: A4

description: HapMap CEU parent


title: NA11992, IVT:2, Hyb:6, SAM:1216874, Array: G6

description: HapMap CEU parent


title: NA11832, IVT: 2, Hyb: 5, SAM: 1221008, Array: A5

description: HapMap CEU parent


title: NA11839, IVT: 1, Hyb: 1, SAM: 1221008, Array: B4

description: HapMap CEU parent


title: NA11992, IVT:2, Hyb:4, SAM:1216874, Array: G4

description: HapMap CEU parent


title: NA11992, IVT:1, Hyb:2, SAM:1221008, Array: A2

description: HapMap CEU parent


title: NA11992, IVT:2, Hyb:5, SAM:1216874, Array: G5

description: HapMap CEU parent


title: NA11992, IVT:1, Hyb:1, SAM:1221008, Array: A1

description: HapMap CEU parent,


title: OSCE-18N

city: Newark

first: Gokce

last: Toruner

state: NJ

address: 225 Warren Street W410Q

department: Center for Human and Molecular Genetics

institute: UMDNJ-NJ Medical School

description: Series of 4 Normals

data_processing: The initial analysis of generated affymetrix data was performed with their MAS 5.0 software.The chip data were scaled to 500,then exported as text files to be loaded into the Genespring 6.0 program (Silicon Genetics,Redwood City,CA).The prescaled data were normalized by using the normalization steps”per chip to 50th percentile” and “per gene to median” as recommended by the manufacturer.

label: Biotin

source_name: Oral Squamous Cell Epithelium Tissue

tag: Oral Squamous cell Epithelium Tissue-Normal

tag: Patient Code:OSCC-18

tag: Primary Site:Floor of Mouth


title: OSCE-12T

description: Series of 16 Tumors

tag: Oral Squamous cell Epithelium Tissue-Tumor

tag: Patient Code:OSCC-12

tag: Primary Site:Maxilla


title: OSCE-16T

description: Series of 16 Tumors

tag: Patient Code:OSCC-16

tag: Primary Site:Mandible


title: OSCE-14T

description: Series of 16 Tumors

source_name: Oral Squamous cell Epithelium Tissue

tag: Patient Code:OSCC-14


title: OSCE-15T

description: Series of 16 Tumors

tag: Patient Code:OSCC-15


title: OSCE-17T

description: Series of 16 Tumors

tag: Patient Code:OSCC-17

tag: Primary Site:Tongue


title: OSCE-11T

description: Series of 16 Tumors

tag: Patient Code:OSCC-11


title: OSCE-18T

description: Series of 16 Tumors


title: OSCE-8T

description: Series of 16 Tumors

tag: Patient Code:OSCC-8


title: OSCE-7T

description: Series of 16 Tumors

tag: Patient Code:OSCC-7

tag: Primary Site:Floor of mouth

tag: TNM:


title: OSCE-5T

description: Series of 16 Tumors

tag: Patient Code:OSCC-5


title: OSCE-14N

description: Series of 4 Normals

tag: Oral Squamous cell Epithelium Tissue-Normal


title: Synechocystis cells treated 90 min with 50 µM cadmium sulfate, replicate 2

city: Gif sur yvette CEDEX

first: Franck

last: Chauvat

department: DSV/DBJC

country: France

institute: CEA Saclay

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

data_processing: After background correction and removal of flagged values, expression ratios were normalised using LOWESS method (Genespring software) to obtain values given in the data table.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis cells treated 90 min with 0 µM cadmium sulfate

label_protocol: The cDNA from treated and untreated cells RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 4 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 30 µl of buffer containing 21% formamide, 0.2% DSD, 1x denhardt's, 7x SSPE, and 10 µg each of mouse Cot1 DNA, yeast tRNA and polydeoxyadenylic acid (to limit non-specific hybridization) for hybridization to the microarray.

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 90 min. Following growth, all cell samples were rapidly harvested and disrupted.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 µg) was annealed with 2 µg of random hexanucleotide primers and 0.5 ng of Human TFR mRNA (Takara) used as external control. Then, the reverse-transcription into cDNA was done with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.1 mM dTTP, 0.4 mM amino-allyl dUTP. After hydrolysis of RNA with 3 U of RNAse H (Amersham Pharmacia), cDNA was purified with a Microcon-30 concentrator.


title: Synechocystis cells treated 60 min with 50 µM cadmium sulfate, replicate 2

source_name: Synechocystis cells treated 60 min with 0 µM cadmium sulfate

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 60 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: OSCE-9N

description: Series of 4 Normals

tag: Patient Code:OSCC-9


title: Synechocystis cells treated 60 min with 50 µM cadmium sulfate, replicate 1

tag: Synechocystis cells treated 60 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 360 min with 50 µM cadmium sulfate, replicate 1

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 360 min. Following growth, all cell samples were rapidly harvested and disrupted.

source_name: Synechocystis cells treated 360 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 960 min with 50 µM cadmium sulfate, replicate 2

source_name: Synechocystis cells treated 960 min with 0 µM cadmium sulfate

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 960 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: OSCE-9T

description: Series of 16 Tumors

tag: Oral Squamous cell Epithelium Tissue-Tumor


title: OSCE-4T

description: Series of 16 Tumors

tag: Patient Code:OSCC-4

tag: Primary Site:Floor of the mouth


title: OSCE-13T

description: Series of 16 Tumors

tag: Patient Code:OSCC-13

tag: Primary Site:Floor of Mouth


title: Synechocystis cells treated 90 min with 50 µM cadmium sulfate, replicate 1

tag: Synechocystis cells treated 90 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 360 min with 50 µM cadmium sulfate, replicate 2

tag: Synechocystis cells treated 360 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 960 min with 50 µM cadmium sulfate, replicate 1

tag: Synechocystis cells treated 960 min with 0 µM cadmium sulfate


title: OSCE-6T

description: Series of 16 Tumors

tag: Patient Code:OSCC-6

tag: Primary Site:Vestibule


title: OSCE-10T

description: Series of 16 Tumors

tag: Patient Code:OSCC-10

tag: Primary Site:Tongue


title: Synechocystis cells treated 75 min with 50 µM cadmium sulfate, replicate 1

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 75 min. Following growth, all cell samples were rapidly harvested and disrupted.

source_name: Synechocystis cells treated 75 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 75 min with 50 µM cadmium sulfate, replicate 2

tag: Synechocystis cells treated 75 min with 0 µM cadmium sulfate


title: OSCE-2N

description: Series of 4 Normals

tag: Patient Code:OSCC-2


title: OSCE-2T

description: SERIES OF 16 TUMORS

data_processing: The initial analysis of generated Affymetrix data was performed with their MAS 5.0 software.The chip data were scaled to 500,then exported as text files to be loaded into the Genespring 6.0 program(Silicon Genetics,Redwood City,CA).The prescaled data were normalized by using the normalization steps

label: BIOTIN

tag: Oral Squamous cell epithelium tissue

tag: Patient code:OSCC-2


title: Synechocystis cells treated 30 min with 50 µM cadmium sulfate, replicate 1

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 30 min. Following growth, all cell samples were rapidly harvested and disrupted.

source_name: Synechocystis cells treated 30 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 30 min with 50 µM cadmium sulfate, replicate 2

tag: Synechocystis cells treated 30 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 15 min with 50 µM cadmium sulfate, replicate 1

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 15 min. Following growth, all cell samples were rapidly harvested and disrupted.

tag: As a control RNA, Synechocystis cells treated 15 min with 0 µM cadmium sulfate was used


title: Synechocystis cells treated 300 min with 50 µM cadmium sulfate, replicate 2

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without Cadmium sulfate, 50 µM. Then the plates were incubated ˆ 30¡C under standard light for 300 min. Following growth, all cell samples were rapidly harvested and disrupted.

tag: As a control RNA, Synechocystis cells treated 300 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 300 min with 50 µM cadmium sulfate, replicate 1

source_name: Synechocystis cells treated 300 min with 0 µM cadmium sulfate


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 3)..

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

description: As a control Yeast stationary phase and Exponental mix 1:1

data_processing: After background correction based on negative controls and removal of flaged valuse, data was normalized to Arabidopsis thaliana controls.

organism: Saccharomyces cerevisiae

source_name: Yeast stationary phase culture

tag: Yeast Stationary phase culture, time  0 min


title: Synechocystis cells treated 180 min with 50 µM cadmium sulfate, replicate 1

description: Synechocystis cells treated 15 min with 50 µM cadmium sulfate

source_name: Synechocystis cells treated 180 min with 0 µM cadmium sulfate


title: Synechocystis cells treated 15 min with 50 µM cadmium sulfate, replicate 2

source_name: Synechocystis cells treated 15 min with 0 µM cadmium sulfate


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 2)..

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Synechocystis cells treated 180 min with 50 µM cadmium sulfate, replicate 2

tag: Synechocystis cells treated 180 min with 0 µM cadmium sulfate


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 1)..

source_name: Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture,  (Replicate) time  450 min

tag: Yeast Stationary phase culture, time  450 min


title: Yeast Stationary phase culture, (Replicate) time  35 min.

tag: Yeast Stationary phase culture, time  35 min


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 6)..


title: Yeast Stationary phase culture, (Replicate) time  34 min.

tag: Yeast Stationary phase culture, time  34 min


title: Yeast Stationary phase culture,  (Replicate) time  330 min

tag: Yeast Stationary phase culture, time  330 min


title: Yeast Stationary phase culture, (Replicate) time  32 min.

tag: Yeast Stationary phase culture, time  32 min


title: Yeast Stationary phase culture,  (Replicate) time  300 min

tag: Yeast Stationary phase culture, time  300 min


title: Yeast Stationary phase culture,  (Replicate) time  360 min

tag: Yeast Stationary phase culture, time  360 min


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 4)..


title: Yeast Stationary phase culture, (Replicate) time  60 min.

tag: Yeast Stationary phase culture, time  60 min


title: Yeast Stationary phase culture,  (Replicate) time  420 min

tag: Yeast Stationary phase culture, time  420 min


title: Yeast Stationary phase culture,  (Replicate) time  390 min

tag: Yeast Stationary phase culture, time  390 min


title: Yeast Stationary phase culture, (Replicate) time  33 min.

tag: Yeast Stationary phase culture, time  33 min


title: Yeast Stationary phase culture, (Replicate) time  0 min (Replicate 5)..


title: Yeast Stationary phase culture,  (Replicate) time  240 min

tag: Yeast Stationary phase culture, time  240 min


title: Yeast Stationary phase culture, (Replicate) time  30 min.

tag: Yeast Stationary phase culture, time  30 min


title: Yeast Stationary phase culture,  (Replicate) time  480 min

tag: Yeast Stationary phase culture, time  480 min


title: Yeast Stationary phase culture, (Replicate) time  29 min.

tag: Yeast Stationary phase culture, time  29 min


title: Yeast Stationary phase culture,  (Replicate) time  210 min

tag: Yeast Stationary phase culture, time  210 min

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture, (Replicate) time  28 min.

tag: Yeast Stationary phase culture, time  28 min


title: Yeast Stationary phase culture,  (Replicate) time  270 min

tag: Yeast Stationary phase culture, time  270 min


title: Yeast Stationary phase culture, (Replicate) time  31 min.

tag: Yeast Stationary phase culture, time  31 min


title: Yeast Stationary phase culture, (Replicate) time  27 min.

tag: Yeast Stationary phase culture, time  27 min


title: Yeast Stationary phase culture, (Replicate) time  24 min.

tag: Yeast Stationary phase culture, time  24 min


title: Yeast Stationary phase culture,  (Replicate) time  150 min

tag: Yeast Stationary phase culture, time  150 min


title: Yeast Stationary phase culture,  (Replicate) time  180 min

tag: Yeast Stationary phase culture, time  180 min


title: Yeast Stationary phase culture,  (Replicate) time  60 min

tag: Yeast Stationary phase culture, time  60 min


title: Yeast Stationary phase culture, (Replicate) time  25 min.

tag: Yeast Stationary phase culture, time  25 min


title: Yeast Stationary phase culture,  (Replicate) time  30 min


title: Yeast Stationary phase culture, (Replicate) time  20 min.

tag: Yeast Stationary phase culture, time  20 min


title: Yeast Stationary phase culture, (Replicate) time  26 min.

tag: Yeast Stationary phase culture, time  26 min


title: Yeast Stationary phase culture, (Replicate) time  22 min.

tag: Yeast Stationary phase culture, time  22 min


title: Yeast Stationary phase culture,  (Replicate) time  120 min

tag: Yeast Stationary phase culture, time  120 min


title: Yeast Stationary phase culture,  (Replicate) time  90 min

tag: Yeast Stationary phase culture, time  90 min


title: Yeast Stationary phase culture, (Replicate) time  19 min.

tag: Yeast Stationary phase culture, time  19 min


title: Yeast Stationary phase culture, (Replicate) time  21 min.

tag: Yeast Stationary phase culture, time  21 min


title: Yeast Stationary phase culture, (Replicate) time  23 min.

tag: Yeast Stationary phase culture, time  23 min

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture, time  330 min


title: Yeast Stationary phase culture, time  450 min


title: Yeast Stationary phase culture, time  360 min


title: Yeast Stationary phase culture, time  390 min


title: Yeast Stationary phase culture, time  480 min


title: Yeast Stationary phase culture, time  420 min


title: Yeast Stationary phase culture, (Replicate) time  18 min.

tag: Yeast Stationary phase culture, time  18 min


title: Yeast Stationary phase culture, (Replicate) time  16 min.

tag: Yeast Stationary phase culture, time  16 min


title: Yeast Stationary phase culture, (Replicate) time  17 min.

tag: Yeast Stationary phase culture, time  17 min


title: Yeast Stationary phase culture, time  300 min


title: Yeast Stationary phase culture, time  210 min


title: Yeast Stationary phase culture, time  240 min


title: Yeast Stationary phase culture, time  180 min


title: Yeast Stationary phase culture, (Replicate) time  15 min.

tag: Yeast Stationary phase culture, time  15 min


title: Yeast Stationary phase culture, time  150 min


title: Yeast Stationary phase culture, time  270 min


title: Yeast Stationary phase culture, (Replicate) time  9 min.

tag: Yeast Stationary phase culture, time  9 min


title: Yeast Stationary phase culture, (Replicate) time  13 min.

tag: Yeast Stationary phase culture, time  13 min


title: Yeast Stationary phase culture, time  90 min


title: Yeast Stationary phase culture, (Replicate) time  10 min.

tag: Yeast Stationary phase culture, time  10 min


title: Yeast Stationary phase culture, (Replicate) time  11 min.

tag: Yeast Stationary phase culture, time  11 min


title: Yeast Stationary phase culture, (Replicate) time  6 min.

tag: Yeast Stationary phase culture, time  6 min


title: Yeast Stationary phase culture, (Replicate) time  12 min.

tag: Yeast Stationary phase culture, time  12 min


title: Yeast Stationary phase culture, time  120 min


title: Yeast Stationary phase culture, (Replicate) time  8 min.

tag: Yeast Stationary phase culture, time  8 min


title: Yeast Stationary phase culture, (Replicate) time  7 hrs

tag: Yeast Stationary phase culture, time  7 hrs


title: Yeast Stationary phase culture, (Replicate) time  5 min.

tag: Yeast Stationary phase culture, time  5 min


title: Yeast Stationary phase culture, time  30 min


title: Yeast Stationary phase culture, (Replicate) time  7.5 hrs

tag: Yeast Stationary phase culture, time  7.5 hrs


title: Yeast Stationary phase culture, (Replicate) time  14 min.

tag: Yeast Stationary phase culture, time  14 min


title: Yeast Stationary phase culture, (Replicate) time  7 min.

tag: Yeast Stationary phase culture, time  7 min


title: Yeast Stationary phase culture, (Replicate) time  5.5 hrs

tag: Yeast Stationary phase culture, time  5.5 hrs

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture, time  60 min


title: Yeast Stationary phase culture, (Replicate) time  6.5 hrs

tag: Yeast Stationary phase culture, time  6.5 hrs


title: Yeast Stationary phase culture, (Replicate) time  2 min.

tag: Yeast Stationary phase culture, time  2 min


title: Yeast Stationary phase culture, (Replicate) time  4 min.

tag: Yeast Stationary phase culture, time  4 min


title: Yeast Stationary phase culture, (Replicate) time  3 min.

tag: Yeast Stationary phase culture, time  3 min


title: Yeast Stationary phase culture, (Replicate) time  1 min.

tag: Yeast Stationary phase culture, time  1 min


title: Yeast Stationary phase culture, (Replicate) time  6 hrs

tag: Yeast Stationary phase culture, time  6 hrs


title: Yeast Stationary phase culture, time  60 min-.


title: Yeast Stationary phase culture, (Replicate) time  4.5 hrs

tag: Yeast Stationary phase culture, time  4.5 hrs


title: Yeast Stationary phase culture, time  33 min.


title: Yeast Stationary phase culture, (Replicate) time  3.5 hrs

tag: Yeast Stationary phase culture, time  3.5 hrs


title: Yeast Stationary phase culture, time  34 min.


title: Yeast Stationary phase culture, (Replicate) time  4 hrs

tag: Yeast Stationary phase culture, time  4 hrs


title: Yeast Stationary phase culture, (Replicate) time  2.5 hrs

tag: Yeast Stationary phase culture, time  2.5 hrs


title: Yeast Stationary phase culture, time  29 min.


title: Yeast Stationary phase culture, (Replicate) time  5 hrs

tag: Yeast Stationary phase culture, time  5 hrs


title: Yeast Stationary phase culture, (Replicate) time  2 hrs

tag: Yeast Stationary phase culture, time  2 hrs


title: Yeast Stationary phase culture, (Replicate) time  3 hrs

tag: Yeast Stationary phase culture, time  3 hrs


title: Yeast Stationary phase culture, time  35 min.


title: Yeast Stationary phase culture, time  25 min.


title: Yeast Stationary phase culture, time  32 min.


title: Yeast Stationary phase culture, (Replicate) time  1 hrs

tag: Yeast Stationary phase culture, time  1 hrs


title: Yeast Stationary phase culture, time  28 min.


title: Yeast Stationary phase culture, time  30 min-.


title: Yeast Stationary phase culture, (Replicate) time  0.5 hrs

tag: Yeast Stationary phase culture, time  0.5 hrs


title: Yeast Stationary phase culture, time  31 min.


title: Yeast Stationary phase culture, time  8 hrs


title: Yeast Stationary phase culture, time  26 min.


title: Yeast Stationary phase culture, (Replicate) time  1.5 hrs

tag: Yeast Stationary phase culture, time  1.5 hrs


title: Yeast Stationary phase culture, time  7.5 hrs

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture, time  24 min.


title: Yeast Stationary phase culture, (Replicate) time  8 hrs

tag: Yeast Stationary phase culture, time  8 hrs


title: Yeast Stationary phase culture, time  6.5 hrs


title: Yeast Stationary phase culture, time  5.5 hrs


title: Yeast Stationary phase culture, time  6 hrs


title: Yeast Stationary phase culture, time  23 min.


title: Yeast Stationary phase culture, time  7 hrs


title: Yeast Stationary phase culture, time  21 min.


title: Yeast Stationary phase culture, time  5 hrs


title: Yeast Stationary phase culture, time  27 min.


title: Yeast Stationary phase culture, time  20 min.


title: Yeast Stationary phase culture, time  4.5 hrs


title: Yeast Stationary phase culture, time  19 min.


title: Yeast Stationary phase culture, time  18 min.


title: Yeast Stationary phase culture, time  22 min.


title: Yeast Stationary phase culture, time  3.5 hrs


title: Yeast Stationary phase culture, time  17 min.


title: Yeast Stationary phase culture, time  4 hrs


title: Yeast Stationary phase culture, time  16 min.


title: Yeast Stationary phase culture, time  15 min.


title: Yeast Stationary phase culture, time  14 min.


title: Yeast Stationary phase culture, time  13 min.


title: Yeast Stationary phase culture, time  11 min.


title: Yeast Stationary phase culture, time  10 min.


title: Yeast Stationary phase culture, time  0 hrs (Replicate 6)


title: Yeast Stationary phase culture, time  2 hrs


title: Yeast Stationary phase culture, time  1 hrs


title: Yeast Stationary phase culture, time  12 min.


title: Yeast Stationary phase culture, time  0.5 hrs


title: Yeast Stationary phase culture, time  3 hrs


title: Yeast Stationary phase culture, time  1.5 hrs


title: Yeast Stationary phase culture, time  0 hrs (Replicate 5)


title: Yeast Stationary phase culture, time  9 min.


title: Yeast Stationary phase culture, time  8 min.


title: Yeast Stationary phase culture, time  7 min.


title: Yeast Stationary phase culture, time  0 hrs (Replicate 3)


title: Yeast Stationary phase culture, time  6 min.


title: Yeast Stationary phase culture, time  0 hrs (Replicate 4)


title: Yeast Stationary phase culture, time  4 min.


title: Yeast Stationary phase culture, time  0 hrs (Replicate 1)


title: Yeast Stationary phase culture, time  5 min..


title: Yeast Stationary phase culture, time  2 min.


title: Yeast Stationary phase culture, time  1 min.


title: Yeast Stationary phase culture, time  3 min.


title: Stationary Phase trypsin treated time 2 mins


title: Stationary Phase trypsin Non-treated time 2 mins


title: Stationary Phase trypsin treated time 2 mins (Replicate)


title: Stationary Phase trypsin treated (Replicate)


title: Yeast Stationary phase culture, time  0 hrs (Replicate 2)


title: Stationary Phase Qiagen Protease treated (Replicate)


title: Stationary Phase trypsin Non-treated time 2 mins (Replicate)


title: Stationary Phase trypsin treated

source_name: Stationary Phase trypsin treated

tag: Stationary Phase trypsin treated


title: Stationary Phase proteinase K Non-treated (Replicate)


title: Stationary Phase Qiagen Protease treated


title: Stationary Phase trypsin Non-treated

source_name: Stationary Phase trypsin Non-treated

tag: Stationary Phase trypsin Non-treated


title: Stationary Phase proteinase K treated (Replicate)


title: Exponential trypsin treated

source_name: Exponential trypsin treated

tag: Exponential trypsin treated


title: Stationary Phase trypsin Non-treated (Replicate)


title: Stationary Phase proteinase K treated

source_name: Stationary Phase proteinase K treated

tag: Stationary Phase proteinase K treated


title: Stationary Phase Qiagen Protease Non-treated


title: Exponential proteinase K treated (Replicate)


title: Stationary Phase Qiagen Protease Non-treated (Replicate)


title: Exponential trypsin Non-treated (Replicate)


title: Yeast Stationary phase culture S288c, (Replicate) time  0 min

source_name: Yeast stationary phase culture S288c

tag: Yeast Stationary phase culture S288c, time  0 min


title: Exponential trypsin Non-treated

source_name: Exponential trypsin Non-treated

tag: Exponential trypsin Non-treated


title: Exponential trypsin treated (Replicate)

source_name: Exponential trypsin treated (Replicate)

tag: Exponential trypsin treated (Replicate)


title: Yeast Stationary phase culture S288c, time  30 min


title: Stationary Phase proteinase K Non-treated


title: Yeast Stationary phase culture, time  2.5 hrs


title: Exponential Qiagen Protease treated (Replicate)


title: Exponential proteinase K Non-treated

source_name: Exponential proteinase K Non-treated

tag: Exponential proteinase K Non-treated


title: Exponential Qiagen Protease Non-treated (Replicate)


title: Yeast Stationary phase culture S288c, time  2 min


title: Exponential proteinase K Non-treated (Replicate)


title: Exponential Qiagen Protease treated

source_name: Exponential Qiagen Protease treated

tag: Exponential Qiagen Protease treated


title: Exponential Qiagen Protease Non-treated

source_name: Exponential Qiagen Protease Non-treated

tag: Exponential Qiagen Protease Non-treated


title: Exponential proteinase K treated

source_name: Exponential proteinase K treated

tag: Exponential proteinase K treated


title: Yeast Stationary phase culture RNA Polymerase II Parental, time  30 min

source_name: Yeast stationary phase culture RNA Polymerase II Parental


title: Yeast Stationary phase culture S288c, time  0 min


title: Yeast Stationary phase culture RNA Polymerase II Mutant, time  30 min

source_name: Yeast stationary phase culture RNA Polymerase II Mutant


title: Yeast Stationary phase culture RNA Polymerase II Mutant, (Replicate) time  0 min

tag: Yeast Stationary phase culture RNA Polymerase II Mutant, time 0 min


title: Yeast Stationary phase culture RNA Polymerase II Mutant, time  2  min


title: Yeast Stationary phase culture RNA Polymerase II Parental, time  2 min


title: Yeast Stationary phase culture, Proteinase K treated during RNA Isolation 0 min (Replicate 2)

source_name: Yeast stationary phase culture Proteinase K treated during RNA Isolation


title: Yeast Stationary phase culture RNA Polymerase II Parental, (Replicate) time  0 min

tag: Yeast Stationary phase culture RNA Polymerase II Parental, time  0 min


title: Yeast Stationary phase culture RNA Polymerase II Parental, time  0 min


title: Yeast Stationary phase culture, Our RNA Isolation 0 min (Replicate 2)

source_name: Yeast stationary phase culture Our RNA Isolation


title: Yeast Stationary phase culture, Hot Phenol RNA Isolation 0 min (Replicate 2)

source_name: Yeast stationary phase culture Hot Phenol RNA Isolation


title: Yeast Stationary phase culture RNA Polymerase II Mutant, time  0 min

source_name: Yeast stationary phase and Exponental mix 1:1


title: Yeast Stationary phase culture, Proteinase K treated during RNA Isolation 0 min (Replicate 1)


title: Yeast Stationary phase culture, Hot Phenol RNA Isolation 0 min (Replicate 1)


title: Donor Cells 9, labeled with dye Cy5

status: Public on Nov 30 2005

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

description:
cDNA from Donor Cell aRNA and the reference standard.
Keywords = NT Donor Cells
Keywords = cow
Keywords = Donor Cells
Keywords = microarray

scan_protocol: Fluoresecent images for both dye channels were obtained using a GenePix 4000B (Axon Instruments, Inc., CA) dual-laser confocal scanner and images were processed using GenePix Pro 4.0 (Axon Instruments, Inc., CA).

data_processing: microarray image was acquired and analyzed using GenePix Pro 4.0.

organism: Bos taurus

source_name: Donor Cells 9, type: Donor Cells,labeled with Cy5

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labeled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent three rounds of linear amplification (Baugh et. al. 2001), the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: total RNA isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

extract_protocol: RNA isolation was accomplished using Trizol. The RNA underwent two rounds of linear amplification (Baugh et. al. 2001) , the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: reference total RNA isolated by Trizol from EBTr, MDBK, and BL30 cell lines and brain tissue.


title: Yeast Stationary phase culture, Our RNA Isolation 0 min (Replicate 1)

tag: As a control Yeast stationary phase and Exponental mix 1:1


title: Donor Cells 9, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Donor Cells 9, type: Donor Cells,labeled with Cy3


title: Donor Cells 8, labeled with dye Cy3

source_name: Donor Cells 8, type: Donor Cells,labeled with Cy3


title: Donor Cells 8, labeled with dye Cy5

source_name: Donor Cells 8, type: Donor Cells,labeled with Cy5


title: Embryo 3_1,derived from NT, labeled with dye Cy5

description:
cDNA from embryo aRNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = NT
Keywords = microarray

source_name: Embryo 3_1, type: NT,labeled with Cy5

tag: Single blastocyst total RNA isolated by Trizol


title: Embryo 3_3,derived from NT, labeled with dye Cy5

source_name: Embryo 3_3, type: NT,labeled with Cy5


title: Embryo 3_2,derived from NT, labeled with dye Cy3

source_name: Embryo 3_2, type: NT,labeled with Cy3


title: Embryo 3_3,derived from NT, labeled with dye Cy3

source_name: Embryo 3_3, type: NT,labeled with Cy3


title: Embryo 3_4,derived from NT, labeled with dye Cy3

source_name: Embryo 3_4, type: NT,labeled with Cy3


title: Embryo 3_2,derived from NT, labeled with dye Cy5

source_name: Embryo 3_2, type: NT,labeled with Cy5


title: Embryo 3_5,derived from NT, labeled with dye Cy3

source_name: Embryo 3_5, type: NT,labeled with Cy3


title: Embryo 2_11,derived from NT, labeled with dye Cy3

source_name: Embryo 2_11, type: NT,labeled with Cy3


title: Embryo 2_4,derived from NT, labeled with dye Cy3

source_name: Embryo 2_4, type: NT,labeled with Cy3


title: Embryo 2_7,derived from NT, labeled with dye Cy5

source_name: Embryo 2_7, type: NT,labeled with Cy5


title: Embryo 2_7,derived from NT, labeled with dye Cy3

source_name: Embryo 2_7, type: NT,labeled with Cy3


title: Embryo 2_8,derived from NT, labeled with dye Cy3

source_name: Embryo 2_8, type: NT,labeled with Cy3


title: Embryo 3_6,derived from NT, labeled with dye Cy3

source_name: Embryo 3_6, type: NT,labeled with Cy3


title: Embryo 3_9,derived from NT, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Embryo 3_9, type: NT,labeled with Cy3


title: Embryo 2_8,derived from NT, labeled with dye Cy5

source_name: Embryo 2_8, type: NT,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 2_11,derived from NT, labeled with dye Cy5

source_name: Embryo 2_11, type: NT,labeled with Cy5


title: Embryo 2_9,derived from NT, labeled with dye Cy5

source_name: Embryo 2_9, type: NT,labeled with Cy5


title: Embryo 3_4,derived from NT, labeled with dye Cy5

source_name: Embryo 3_4, type: NT,labeled with Cy5


title: Embryo 3_1,derived from NT, labeled with dye Cy3

source_name: Embryo 3_1, type: NT,labeled with Cy3


title: Embryo 2_9,derived from NT, labeled with dye Cy3

source_name: Embryo 2_9, type: NT,labeled with Cy3


title: Embryo 2_3,derived from NT, labeled with dye Cy5

source_name: Embryo 2_3, type: NT,labeled with Cy5


title: Embryo 2_4,derived from NT, labeled with dye Cy5

source_name: Embryo 2_4, type: NT,labeled with Cy5


title: Embryo 3_6,derived from NT, labeled with dye Cy5

source_name: Embryo 3_6, type: NT,labeled with Cy5


title: Embryo 3_5,derived from NT, labeled with dye Cy5

source_name: Embryo 3_5, type: NT,labeled with Cy5


title: Embryo 3_9,derived from NT, labeled with dye Cy5

source_name: Embryo 3_9, type: NT,labeled with Cy5


title: Embryo 16,derived from IVF, labeled with dye Cy5

description:
cDNA from embryo aRNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = IVF
Keywords = microarray

source_name: Embryo 16, type: IVF,labeled with Cy5


title: Embryo 18,derived from IVF, labeled with dye Cy5

source_name: Embryo 18, type: IVF,labeled with Cy5


title: Embryo 13,derived from IVF, labeled with dye Cy5

source_name: Embryo 13, type: IVF,labeled with Cy5


title: Embryo 2_2,derived from NT, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Embryo 2_2, type: NT,labeled with Cy3


title: Embryo 2_1,derived from NT, labeled with dye Cy3

source_name: Embryo 2_1, type: NT,labeled with Cy3


title: Embryo 2_3,derived from NT, labeled with dye Cy3

source_name: Embryo 2_3, type: NT,labeled with Cy3


title: Embryo 10,derived from IVF, labeled with dye Cy5

source_name: Embryo 10, type: IVF,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 2_1,derived from NT, labeled with dye Cy5

source_name: Embryo 2_1, type: NT,labeled with Cy5


title: Embryo 9,derived from IVF, labeled with dye Cy5

source_name: Embryo 9, type: IVF,labeled with Cy5


title: Embryo 4,derived from IVF, labeled with dye Cy5

source_name: Embryo 4, type: IVF,labeled with Cy5


title: Embryo 18,derived from IVF, labeled with dye Cy3

source_name: Embryo 18, type: IVF,labeled with Cy3


title: Embryo 7,derived from IVF, labeled with dye Cy5

source_name: Embryo 7, type: IVF,labeled with Cy5


title: Embryo 7,derived from IVF, labeled with dye Cy3

source_name: Embryo 7, type: IVF,labeled with Cy3


title: Embryo 19,derived from IVF, labeled with dye Cy3

source_name: Embryo 19, type: IVF,labeled with Cy3


title: Embryo 16,derived from IVF, labeled with dye Cy3

source_name: Embryo 16, type: IVF,labeled with Cy3


title: Embryo 11,derived from IVF, labeled with dye Cy5

source_name: Embryo 11, type: IVF,labeled with Cy5


title: Embryo 10,derived from IVF, labeled with dye Cy3

source_name: Embryo 10, type: IVF,labeled with Cy3


title: Embryo 6,derived from IVF, labeled with dye Cy5

source_name: Embryo 6, type: IVF,labeled with Cy5


title: Embryo 9,derived from IVF, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Embryo 9, type: IVF,labeled with Cy3


title: Embryo 4,derived from IVF, labeled with dye Cy3

source_name: Embryo 4, type: IVF,labeled with Cy3


title: Embryo 12,derived from IVF, labeled with dye Cy5

source_name: Embryo 12, type: IVF,labeled with Cy5


title: Embryo 2_2,derived from NT, labeled with dye Cy5

source_name: Embryo 2_2, type: NT,labeled with Cy5


title: Embryo 13,derived from IVF, labeled with dye Cy3

source_name: Embryo 13, type: IVF,labeled with Cy3


title: Embryo 12,derived from IVF, labeled with dye Cy3

source_name: Embryo 12, type: IVF,labeled with Cy3


title: Embryo 11,derived from IVF, labeled with dye Cy3

source_name: Embryo 11, type: IVF,labeled with Cy3


title: Embryo 6,derived from IVF, labeled with dye Cy3

source_name: Embryo 6, type: IVF,labeled with Cy3


title: Embryo 5,derived from IVF, labeled with dye Cy3

source_name: Embryo 5, type: IVF,labeled with Cy3


title: Embryo 5,derived from IVF, labeled with dye Cy5

source_name: Embryo 5, type: IVF,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 3,derived from IVF, labeled with dye Cy5

source_name: Embryo 3, type: IVF,labeled with Cy5


title: Embryo 19,derived from IVF, labeled with dye Cy5

source_name: Embryo 19, type: IVF,labeled with Cy5


title: Embryo H1,derived from AI, labeled with dye Cy3

description:
cDNA from embryo aRNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = AI
Keywords = microarray

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were purified separately with a QIAquick PCR purification column. Each labelled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.

source_name: Embryo H1, type: AI,labeled with Cy3


title: Embryo 1,derived from IVF, labeled with dye Cy3

source_name: Embryo 1, type: IVF,labeled with Cy3


title: Embryo H3,derived from AI, labeled with dye Cy3

source_name: Embryo H3, type: AI,labeled with Cy3


title: Embryo H5,derived from AI, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Embryo H5, type: AI,labeled with Cy3


title: Embryo 1,derived from IVF, labeled with dye Cy5

source_name: Embryo 1, type: IVF,labeled with Cy5


title: Embryo 3,derived from IVF, labeled with dye Cy3

source_name: Embryo 3, type: IVF,labeled with Cy3


title: Embryo 2,derived from IVF, labeled with dye Cy5

source_name: Embryo 2, type: IVF,labeled with Cy5


title: Embryo H1,derived from AI, labeled with dye Cy5

source_name: Embryo H1, type: AI,labeled with Cy5

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.


title: Embryo 16,derived from AI, labeled with dye Cy5

source_name: Embryo 16, type: AI,labeled with Cy5


title: Embryo 2,derived from IVF, labeled with dye Cy3

source_name: Embryo 2, type: IVF,labeled with Cy3


title: Kidney Replicate K, Round 0, labeled with dye Cy5

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 0
Keywords = microarray

source_name: Kidney K, type: Round 0,labeled with Cy5

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent 1, 2 or 3 rounds of linear amplification (Baugh et. al. 2001), round 0 is equal to unamplified total RNA. The aRNA/total RNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.


title: Kidney Replicate K, Round 2, labeled with dye Cy5

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 2
Keywords = microarray

source_name: Kidney K, type: Round 2,labeled with Cy5


title: Embryo 15,derived from AI, labeled with dye Cy3

source_name: Embryo 15, type: AI,labeled with Cy3


title: Embryo 14,derived from AI, labeled with dye Cy5

source_name: Embryo 14, type: AI,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Kidney Replicate K, Round 2 labeled with dye Cy3

source_name: Kidney K, type: Round 2,labeled with Cy3

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent 1, 2 or 3 rounds of linear amplification (Baugh et. al. 2001) round 0 is equal to unamplfied total RNA. The aRNA/total RNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.


title: Embryo 14,derived from AI, labeled with dye Cy3

source_name: Embryo 14, type: AI,labeled with Cy3


title: Embryo 17,derived from AI, labeled with dye Cy5

source_name: Embryo 17, type: AI,labeled with Cy5


title: Embryo H5,derived from AI, labeled with dye Cy5

source_name: Embryo H5, type: AI,labeled with Cy5