title: treatment: CTRL - genotype: Cappelli - rep1

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. (May still include original submitter created erros/discrepancies)

source_name: Leaf (treatment: CTRL - genotype: Cappelli)


title: treatment: CTRL - genotype: Cappelli - rep3

status: Public on Mar 22 2016

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

label: biotin

molecule: total RNA

organism: Triticum turgidum subsp. durum

label_protocol: Affy- Whole transcript target preparation

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: Cappelli

tag: organism part

value: Leaf

tag: cell type

tag: development stage

value: 3 leaf fully expanded ('PO:0001053')

tag: growth media

value: field soil


title: treatment: CTRL - genotype: Ofanto - rep2

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. DS was imposed by withholding water and allowing the pots to reach a SWC equal to 12.5% of FC, other growing conditions were as in control plants. To monitor the SWC the pots weight was measured twice per day. The flag leaves detached at mid-point of the light period were collected for transcriptomic analysis three days after the imposition of stress (May still include original submitter created erros/discrepancies)

source_name: Leaf (treatment: CTRL - genotype: Ofanto)

value: Ofanto


title: treatment: Drought - genotype: Ofanto - rep2

source_name: Leaf (treatment: Drought - genotype: Ofanto)


title: Khanty31

type: genomic

city: Los Angeles

first: Anton

last: Valouev

address: 1450 Biggy Street, NRT 2509K

institute: University of Southern California

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed according to standard techniques using proteinase K treatment and phenol–chloroform extraction.

tag: population

value: Khanty


title: treatment: Drought - genotype: Cappelli - rep3

source_name: Leaf (treatment: Drought - genotype: Cappelli)


title: treatment: CTRL - genotype: Ofanto - rep1


title: treatment: CTRL - genotype: Ofanto - rep3


title: treatment: Heat - genotype: Ofanto - rep1

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. HS was imposed by increasing the temperature for two days at 30°C and 22°C in the 15 hrs light and 9 hrs dark regime, for an initial adaptation phase, then the temperature was increased to 34°C and 26°C light/dark for two days and subsequently to 40°C and 32°C light/dark for an additional day when the flag leaves were collected (May still include original submitter created erros/discrepancies)

source_name: Leaf (treatment: Heat - genotype: Ofanto)


title: Khanty28


title: Khanty35


title: Khanty27


title: Khanty26


title: treatment: CTRL - genotype: Cappelli - rep2


title: treatment: Drought - genotype: Ofanto - rep3


title: Khanty25


title: control vs DEHP 90day rep 3

city: Newort on tay

first: Simon

last: Plummer

address: 23 Wellgate Street

country: United Kingdom

institute: Micromatrices Associates ltd

description: Biological replicate 3 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed using Agilent wash buffers according to the Agilent two colour protocol (Agilent part No G4140-90050).

scan_protocol: Agilent FE 8.5.1.1 software, GE2 scan protocol, Agilent G2565B scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Rosetta resolver was used to generate 'signature' lists of significantly (p<0.01) altered genes using the Resolver error model by generating an error weighted mean of the 5 replicate arrays per treatment .

organism: Rattus norvegicus

source_name: pancreas, DEHP 12000 ppm treated, 90day

label_protocol: 1 ug pancreas (tissue) RNA or isolated acinar cell RNA was labelled with Cyanine 3/Cyanine 5 using the Agilent low input labelling kit plus according to the manufacturers instructions.

extract_protocol: Pancreas (tissue) RNA and isolated acinar cell RNA was extracted with Tri reagent and purified using RNeasy Midi columns (Qiagen).

treatment_protocol: Six to seven week old male CD Sprague Dawley rats (Harlan Uk) were fed RM1 powdered diet containing either Wy at 20 ppm or 50 ppm, DEHP at 12000 ppm or APFO at 300 ppm in the diet for either 1, 7, 28, or 90 days. Control animals received powdered RM1 diet ad libitum for the same duration as the test groups. Animals were sacrificed at 1, 7, 28, or 90 days by exposure to a rising concentration of carbon dioxide. Pancreas was removed and snap frozen or perfused with collagenase  and centrifuged through BSA (4%) to prepare isolated acinar cells. The purity of isolated acinar cells was determined by dual immunohistochemistry of fixed smears of isolated acinar cells, using  -amylase- (acinar cell specific) and cytokeratin 19 (duct cell-specific) antibodies.

tag: strain

value: CD Sprague Dawley

tag: gender

value: male

tag: age

value: six to seven week old

tag: treatment

value: DEHP 12000 ppm

tag: time point

source_name: pancreas, control, 90day

value: vehicle


title: control vs DEHP 28day rep 5

description: Biological replicate 5 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.

source_name: pancreas, DEHP 12000 ppm treated, 28day

source_name: pancreas, control, 28day


title: control vs DEHP 90day rep 1

description: Biological replicate 1 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.


title: control vs DEHP 90day rep 2

description: Biological replicate 2 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.


title: control vs DEHP 90day rep 5


title: control vs DEHP 28day rep 4

description: Biological replicate 4 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.


title: control vs DEHP 90day rep 4


title: control vs DEHP 28day rep 1


title: control vs DEHP 28day rep 3


title: control vs DEHP 28day rep 2


title: control vs DEHP 7day rep 4

source_name: pancreas, DEHP 12000 ppm treated, 7day

source_name: pancreas, control, 7day


title: control vs DEHP 7day rep 2


title: control vs DEHP 7day rep 3


title: control vs DEHP 7day rep 5


title: control vs DEHP 1day rep 4

source_name: pancreas, DEHP 12000 ppm treated, 1day

source_name: pancreas, control, 1day


title: control vs Wy 20 90day rep 1

source_name: pancreas, Wy 20ppm treated, 90day

value: Wy 20ppm


title: control vs Wy 20 90day rep 5


title: control vs DEHP 1day rep 5


title: control vs DEHP 1day rep 2


title: control vs Wy 20 28day rep 5

source_name: pancreas, Wy 20ppm treated, 28day


title: control vs Wy 20 90day rep 3


title: control vs Wy 20 28day rep 4


title: control vs Wy 20 28day rep 3


title: control vs Wy 20 28day rep 2


title: control vs Wy 20 28day rep 1


title: control vs DEHP 7day rep 1


title: control vs DEHP 1day rep 1


title: control vs Wy 20 7day rep 5

source_name: pancreas, Wy 20ppm treated, 7day


title: control vs Wy 20 90day rep 2


title: control vs Wy 20 90day rep 4


title: WT_Veh_1

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: WT hECs + Veh, replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using the lumiN command in the lumi package in R

source_name: Eahy926 cells stably transfected with human ERalpha expression vector

label_protocol: Total RNA samples hybridized to Illumina BeadChips are prepared using the Illumina TotalPrep RNA Amplification kit from Applied Biosystems/Ambion, catalog # AMIL1791 (library preparation & array hybridization was performed by the Yale Center for Genome Analysis).

growth_protocol: EAhy926 cells (a human umbilical vein endothelial cell hybrid, kind gift of C.J. Edgell, University of North Carolina at Chapel Hill), that do not express ERalpha, were transfected with pCMV3-ERalpha plasmid (WT-EC cells) or the same vector into which a triple point mutation of ERalpha amino acids 231, 233 & 234 were mutated to alanine (KRR->AAA)  using PolyFect transfection reagent (Qiagen). After 24 hours the cells were placed in selective media with 5 micrograms/ml puromycin (Sigma) for 2 to 3 weeks. Eight to ten single colonies were selected and maintained in the presence of 2 micrograms/ml puromycin.  ERa expression was confirmed by western blot.

extract_protocol: Total RNA was purified with the RNeasy mini kit (Qiagen)

treatment_protocol: EAhy926 stable cells were grown in 6-well plates to 80% confluence, switched to serum free medium for 24 hours, and then treated with 10 nM E2 or ethanol vehicle for 16 hours.

value: ethanol vehicle


title: control vs Wy 20 7day rep 4


title: WT_E2_2

description: WT hECs + E2, replicate 2

source_name: Eahy926 cells stably transfected with empty vector

value: 10nM E2


title: control vs DEHP 1day rep 3


title: WT_Veh_2

description: WT hECs + Veh, replicate 2


title: WT_E2_3

description: WT hECs + E2, replicate 3


title: KRR_Veh_3

description: KRR hECs + Veh, replicate 3

source_name: Eahy926 cells stably transfected with a vector expressing full length KRR mutant human Eralpha


title: WT_E2_1

description: WT hECs + E2, replicate 1


title: KRR_Veh_2

description: KRR hECs + Veh, replicate 2


title: control vs Wy 20 7day rep 3


title: control vs Wy 20 7day rep 2


title: control vs Wy 20 7day rep 1


title: KRR_E2_2

description: KRR hECs + E2, replicate 2


title: 9250939026_G

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description: Replicate 1

data_processing: Normal-exponential background correction and quantile normalization were performed using limma in R

source_name: 24hr after gamma radiation

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

growth_protocol: The cells were grown in hESC+ medium containing Knockout DMEM, 17% Knockout Serum Replacer, 5 ng/mL human bFGF, 1× Non-essential Amino Acids, 0.4× Insulin-Transferrin-Selenium (ITS-G), 1× GlutaMax (all from Life Technologies), and 0.1 mM 2-Mercaptoethanol (Sigma-Aldrich).

extract_protocol: RNA was isolated with RNeasy Mini Kit (Qiagen)

tag: cell line

value: H9 cell


title: KRR_E2_3

description: KRR hECs + E2, replicate 3


title: KRR_E2_1

description: KRR hECs + E2, replicate 1


title: control vs Wy 50 90day rep 2

source_name: pancreas, Wy 50ppm treated, 90day

value: Wy 50ppm


title: control vs Wy 50 90day rep 3


title: control vs Wy 50 90day rep 5


title: control vs Wy 20 1day rep 4

source_name: pancreas, Wy 20ppm treated, 1day


title: KRR_Veh_1

description: KRR hECs + Veh, replicate 1


title: 9250939026_H

description: Replicate 2


title: control vs Wy 50 28day rep 3

source_name: pancreas, Wy 50ppm treated, 28day


title: WT_Veh_3

description: WT hECs + Veh, replicate 3


title: 9250939026_B

description: Replicate 2

source_name: before gamma radiation

value: 0 hr


title: control vs Wy 50 7day rep 5

source_name: pancreas, Wy 50ppm treated, 7day


title: control vs Wy 50 90day rep 1

source_name: pancreas, control, 90day


title: control vs Wy 20 1day rep 5


title: control vs Wy 20 1day rep 2


title: control vs Wy 20 1day rep 1


title: control vs Wy 50 28day rep 1

source_name: pancreas, control, 28day


title: control vs Wy 50 28day rep 5


title: control vs Wy 50 90day rep 4


title: control vs Wy 50 28day rep 4


title: 9250939026_A

description: Replicate 1


title: control vs Wy 50 7day rep 4

source_name: pancreas, control, 7day


title: Mansi23

source_name: Blood

value: Mansi


title: Mansi22


title: control vs Wy 50 28day rep 2


title: Mansi21


title: Mansi20


title: control vs Wy 50 7day rep 2


title: control vs Wy 50 7day rep 1


title: Mansi19


title: Khanty23


title: control vs Wy 20 1day rep 3

source_name: pancreas, control, 1day


title: Khanty22


title: Khanty24


title: control vs Wy 50 1day rep 5

source_name: pancreas, Wy 50ppm treated, 1day


title: Mansi18


title: Mansi17


title: control vs Wy 50 7day rep 3


title: Mansi24


title: Khanty21


title: Khanty20


title: Khanty19


title: control vs Wy 50 1day rep 3


title: control vs Wy 50 1day rep 1


title: Khanty18


title: control vs Wy 50 1day rep 4


title: control vs APFO 28day rep 5

source_name: pancreas, APFO treated, 28day

value: APFO 300ppm


title: control vs Wy 50 1day rep 2


title: control vs APFO 90day rep 4

source_name: pancreas, APFO treated, 90day


title: control vs APFO 90day rep 1


title: Khanty16


title: Khanty17


title: Khanty14


title: control vs APFO 28day rep 4


title: control vs APFO 90day rep 5


title: Khanty13


title: Khanty11


title: control vs APFO 90day rep 3


title: control vs APFO 28day rep 1


title: Khanty12


title: control vs APFO 90day rep 2


title: Khanty9


title: Khanty10


title: control vs APFO 28day rep 3


title: Khanty7


title: control vs APFO 7day rep 4

source_name: pancreas, APFO treated, 7day


title: control vs APFO 28day rep 2


title: control vs APFO 7day rep 2


title: Khanty6


title: control vs APFO 7day rep 5


title: control vs APFO 7day rep 3


title: control vs APFO 1day rep 5

source_name: pancreas, APFO treated, 1day


title: control vs APFO 1day rep 4


title: Khanty15


title: Mansi16


title: Khanty8


title: control vs APFO 7day rep 1


title: Mansi15


title: control vs APFO 1day rep 2


title: control vs APFO 1day rep 3


title: control vs APFO 1day rep 1


title: control vs Wy acinar 28day rep 5

description: Biological replicate 5 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.

source_name: pancreas acinar cells, Wy 50 ppm treated, 28day

source_name: pancreas acinar cells, control, 28day


title: Khanty3


title: Mansi14


title: Mock d3, batch3

first: Kevin

last: Bi

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
TR249D_M3
Gene expression data from PBMC of non-coinfected mice, d3 post YFV-17D challenge

hyb_protocol: Samples were hybridized to Affymetrix Mouse 430 2.0 arrays

scan_protocol: Gene chips were scanned using an Affymetrix GeneChip Scanner 3000 7G with Autoloader

data_processing: The data were normalized using the MAS5 method and batch-corrected using the ComBat algorithm through GenePattern

organism: Mus musculus

source_name: PBMC

label_protocol: Samples were amplified using NuGEN Ovation RNA Amplification and labeledlabeled using Nugen Encore Biotin kit

extract_protocol: Blood cell pellets were processed using RiboPure RNA purification kit from whole blood (Thermo Fisher Scientific) according to manufacturers protocols.

tag: tissue

value: blood

tag: condition

value: Mock


title: Mock d21, batch3

description:
TR249D_M21
Gene expression data from PBMC of non-coinfected mice, d21 post YFV-17D challenge


title: Mock d7, batch3

description:
TR249D_M7
Gene expression data from PBMC of non-coinfected mice, d7 post YFV-17D challenge


title: Mock d0, batch3

description:
TR249D_M0
Gene expression data from PBMC of non-coinfected mice, d0 post YFV-17D challenge


title: Coinfected d21, batch3

description:
TR249D_C21
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d21 post YFV-17D challenge

value: Coinfection


title: control vs Wy acinar 28day rep 2

description: Biological replicate 2 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: control vs Wy acinar 28day rep 4

description: Biological replicate 4 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: Coinfected d7, batch3

description:
TR249D_C7
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d7 post YFV-17D challenge


title: control vs Wy acinar 28day rep 1

description: Biological replicate 1 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: Coinfected d3, batch3

description:
TR249D_C3
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d3 post YFV-17D challenge


title: control vs Wy acinar 7day rep 5

source_name: pancreas acinar cells, Wy 50 ppm treated, 7day

source_name: pancreas acinar cells, control, 7day


title: Khanty4

value: Khanty


title: Khanty5


title: Khanty2


title: Khanty1


title: Mansi10


title: Mansi11


title: Mock d21, batch2

description:
TR249C_M21
Gene expression data from PBMC of non-coinfected mice, d21 post YFV-17D challenge


title: Mansi9


title: Mansi12


title: Mock d7, batch2

description:
TR249C_M7
Gene expression data from PBMC of non-coinfected mice, d7 post YFV-17D challenge


title: Mansi8


title: control vs Wy acinar 1day rep 2

description: Biological replicate 2 of 4. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.

source_name: pancreas acinar cells, Wy 50 ppm treated, 1day

value: CD Sprague Dawley

source_name: pancreas acinar cells, control, 1day


title: Mansi6


title: Coinfected d7, batch2

description:
TR249C_C7
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d7 post YFV-17D challenge


title: Mock d3, batch2

description:
TR249C_M3
Gene expression data from PBMC of non-coinfected mice, d3 post YFV-17D challenge


title: control vs Wy acinar 1day rep 3

description: Biological replicate 3 of 4. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.

value: male


title: Coinfected d0, batch3

description:
TR249D_C0
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d0 post YFV-17D challenge


title: control vs Wy acinar 1day rep 1

description: Biological replicate 1 of 4. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.

value: six to seven week old


title: control vs Wy acinar 7day rep 2


title: Coinfected d3, batch2

description:
TR249C_C3
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d3 post YFV-17D challenge


title: control vs Wy acinar 7day rep 1


title: Coinfected d21, batch2

description:
TR249C_C21
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d21 post YFV-17D challenge


title: control vs APFO acinar 28day rep 5

description: Biological replicate 5 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.

source_name: pancreas acinar cells, APFO 300 ppm treated, 28day


title: control vs Wy acinar 1day rep 4

description: Biological replicate 4 of 4. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: control vs Wy acinar 7day rep 4


title: Mansi5


title: Mock d0, batch2

description:
TR249C_M0
Gene expression data from PBMC of non-coinfected mice, d0 post YFV-17D challenge


title: control vs Wy acinar 7day rep 3

description: Biological replicate 3 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: Mock d21, batch1

description:
TR249A_M21
Gene expression data from PBMC of non-coinfected mice, d21 post YFV-17D challenge


title: Mansi4


title: control vs Wy acinar 28day rep 3


title: control vs APFO acinar 28day rep 4

description: Biological replicate 4 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: Mock d7, batch1

description:
TR249A_M7
Gene expression data from PBMC of non-coinfected mice, d7 post YFV-17D challenge


title: Coinfected d0, batch2

description:
TR249C_C0
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d0 post YFV-17D challenge


title: Mansi3


title: Mansi2


title: control vs APFO acinar 28day rep 1

description: Biological replicate 1 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: Mock d0, batch1

description:
TR249A_M0
Gene expression data from PBMC of non-coinfected mice, d0 post YFV-17D challenge


title: control vs APFO acinar 28day rep 2

description: Biological replicate 2 of 5. Pancreas acinar cells taken from rats exposed to Wyeth 14,643 (Wy) 50ppm or APFO 300ppm.


title: control vs APFO acinar 28day rep 3


title: Mansi1


title: control vs APFO acinar 7day rep 5

source_name: pancreas acinar cells, APFO 300 ppm treated, 7day


title: Corn oil-treated Liver Tissue 1

city: Pusan

first: Jeongeun

last: Hyun

address: Pusandaehak-ro 63-beon gil

country: South Korea

institute: Pusan National University

description: MicroRNA expression of corn-oil-treated mouse liver

hyb_protocol: Desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

data_processing: Raw data were extracted using Feature Extraction Software (v11.0.1.1; Agilent) and were firstly filtered by a flag signal detected in all samples. Filtered raw data were processed using the Limma Bioconductor package (http://www.bioconductor.org/) in the R statistical environment (http://www.r-project.org/).

source_name: Liver Tissue of Male C57BL/6 mouse treated with corn-oil for 10 weeks

label_protocol: Desalted labeled RNA were prepared from 100ng total RNA Agilent's miRNA Complete Labeling and Hyb Kit.

growth_protocol: Male C57BL/6 mice were housed with 12 hour light/dark cycle and allowed free access to normal food and water.

extract_protocol: Total RNA including miRNA was isolated with TRIzol Reagent (Ambion, Life Technologies, Carlsbad, CA, USA) from liver tissues treated with CCl4 or corn-oil for 10 weeks, following the manufacturer’s instructions. RNA quantity and quality were determined using a nanodrop (Thermo Scientific, Waltham, MA, USA) and Bioanalyzer (Agilent Inc., Santa Clara, CA, USA).

treatment_protocol: To induce liver fibrosis, seven-week-old mice received 0.6 ml/kg body weight of carbon-tetrachloride (CCl4) dissolved in corn-oil by intraperitoneal (i.p.) injection, twice a week for 10 weeks. As a conrol, mice were injected with equal volume of corn-oil.

value: Male

value: Liver


title: Coinfected d21, batch1

description:
TR249A_C21
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d21 post YFV-17D challenge


title: control vs APFO acinar 7day rep 3

value: vehicle


title: CCl4-treated Liver Tissue 1

description: MicroRNA expression of CCl4-treated mouse liver

source_name: Liver Tissue of Male C57BL/6 mouse treated with CCl4 for 10 weeks


title: CCl4-treated Liver Tissue 3


title: control vs APFO acinar 7day rep 1


title: Corn oil-treated Liver Tissue 2


title: control vs APFO acinar 7day rep 4


title: Corn oil-treated Liver Tissue 3


title: control vs APFO acinar 1day rep 4

source_name: pancreas acinar cells, APFO 300 ppm treated, 1day


title: Coinfected d0, batch1

description:
TR249A_C0
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d0 post YFV-17D challenge


title: Coinfected d7, batch1

description:
TR249A_C7
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d7 post YFV-17D challenge


title: Mansi7

source_name: Blood


title: control vs APFO acinar 7day rep 2


title: control vs APFO acinar 1day rep 5


title: Coinfected d3, batch1

description:
TR249A_C3
Gene expression data from PBMC of mice coinfected with MHV68, MCMV, Flu, and H. polygyrus, d3 post YFV-17D challenge


title: control vs APFO acinar 1day rep 3


title: control vs APFO acinar 1day rep 2


title: SKOV3_CFG_monomer_TGFbeta-3

city: Hangzhou

first: Fangfang

last: Tao

state: Zhejiang

address: 540 Binwen Road，binjiang district

country: China

institute: Zhejiang Chinese Medical University

hyb_protocol: After fragmentation, the amplified transcripts were hybridized to an Affymetrix 901838 GeneChip PrimeView Human Gene Expression Array (Affymetrix Inc.) for 16 h in a GeneChip Hybridization Oven 645

scan_protocol: Arrays were washed and stained by a GeneChip Fluidics Station 450 and scanned by a GeneChip Scanner 3000

data_processing: Raw data were imported into GeneSpring GX 11.0.1 and analyzed

source_name: human ovarian cancer cell line

label_protocol: The amplified RNA was prepared with the GeneChip 3’IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: maintained in DMEM supplemented with 10% fetal bovine serum at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from treated and non-treated cell lines using Trizol reagent (Invitrogen, Carlsbad, San Diego, USA) following the manufacturer’s protocol

treatment_protocol: After serum starvation for 24 h, the ovarian cancer cells were treated with 3 mg/ml CFG only or in combination with 10 ng/ml TGFβ1 for 24 h

value: female


title: CCl4-treated Liver Tissue 2


title: MCF-7 cell culture treated with Dioscin

city: University

first: Asok

middle: K

last: Dasmahapatra

state: MS

address: 313 Faser Hall

department: National Center for Natural Product Research

institute: University of Mississippi

description: two biological replicates

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Global scaling normalization (scatter plot, histogram and volcano plot, principal component analysis) was carried out, and the fold changes (cut-off (log2 |fold change|≧ 1) were calculated based on the relative signal intensities (scanned by Agilent 0.1 XDR protocol)
A filtering step was performed using Rosetta error model (Weng et al., Bioinformatics, 22:1111-1121, 2006) which allowed for determination of the statistical significance of every pair wise gene between different groups. The default multiple testing corrections used was Benjamini and Hochberg [J.R. Stat Soc. B57, 289-300, 1995) false discovery rate with a q value cutoff <0.05. The testing correction is the least stringent of all corrections and provides a good balance between the discovery of statistically significant genes and the limitation of false positive occurrences by removing all gene spots with a q value > 0.05 in all conditions

source_name: Human breast cancer cell line

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAMP II aRNA. Labeled aRNA coupled with NHS-CyDye (Cy5).

growth_protocol: MCF-7 and MDA-MB-231 cells were cultured in phenol red free DMEM-F12 (1:1) medium supplemented with 10% dextran charcoal treated fetal bovine serum, 50 U/mL penicillin and 50 µg/mL streptomycin as Pen-Strep and 2 mM of L-glutamine  at 37 degree C in a humidified atmosphere of 95% air and 5% CO2. The cells (500 x 1000 cells) were allowed to attach in the 25 cubic cm culture flasks in 6 mL volume and after 24h the cultures were treated with DS (2. 30 µM) for three days

extract_protocol: Extraction of total RNA was made by Trizol reagent following the protocol provided by the manufacturer (Life Technology, Grand Island, NY)

treatment_protocol: Cells were treated with vehicle or  2.3 µM of dioscin for three days

value: Estrogen receptor positive, noninvasive human breast cancer cell lines


title: SKOV3_CFG_TGFbeta-3


title: MDA-MB-231 cells treated with vehicle

description: two biological replicates

value: Triple negative invasive human breast cancer cell line


title: SKOV3_CFG_monomer_TGFbeta-2


title: SKOV3_CFG_monomer_TGFbeta-1


title: MDA-MB-231 cells treated with Dioscin

description: two biological replicates


title: SKOV3_CFG_TGFbeta-2


title: control vs APFO acinar 1day rep 1


title: Sample tb9026, placenta, fetal side

status: Public on Mar 21 2016

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description: Methylation data using Illumina 450K BeadChips are available for this sample

hyb_protocol: Genomic DNA was hybridized according to manufacturers instructions.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Data was extracted using GenomeStudio v2011.1 Genotyping Module (v1.9.4). All probes mapping to the X or Y chromosome were removed.

source_name: Normal placenta, fetal side

label_protocol: According to manufacturers instructions.

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

value: Placenta, fetal side

tag: disease state

value: Normal


title: Sample tb8232, placenta, fetal side


title: Sample tb8624, placenta, fetal side


title: Sample tb9008, placenta, fetal side


title: Sample tb9101, placenta, fetal side


title: Sample tb9023, placenta, fetal side


title: SKOV3_CFG_TGFbeta-1


title: Mock d3, batch1

description:
TR249A_M3
Gene expression data from PBMC of non-coinfected mice, d3 post YFV-17D challenge


title: Sample tb9033, placenta, fetal side


title: Sample tb8234, placenta, fetal side


title: Sample tb8993, placenta, fetal side


title: Sample tb8926, placenta, fetal side


title: Sample tb8231, placenta, fetal side


title: Sample tb8229, placenta, fetal side


title: MCF-7 cell culture treated with vehicle

description: two biological replicates


title: Sample tb8678, placenta, fetal side


title: SKOV3_TGFbeta-3


title: SKOV3_TGFbeta-2


title: Sample tb8225, placenta, fetal side


title: Sample tb8227, placenta, fetal side


title: Sample tb8169, placenta, fetal side


title: Sample tb8134, placenta, fetal side


title: Mansi13

value: Mansi


title: Sample tb8228, placenta, fetal side


title: Sample tb8634, placenta, fetal side


title: Sample tb8069, placenta, fetal side


title: Sample tb9000, placenta, fetal side


title: Sample tb7888, placenta, fetal side


title: SKOV3_TGFbeta-1


title: Sample tb7819, placenta, fetal side


title: Sample tb7734, placenta, fetal side


title: Sample tb7872, placenta, fetal side


title: Sample tb7723, placenta, fetal side


title: Sample tb7811, placenta, fetal side


title: Sample tb7881, placenta, fetal side


title: Sample tb7670, placenta, fetal side


title: Sample tb7729, placenta, fetal side


title: Sample tb7647, placenta, fetal side


title: Sample tb7877, placenta, fetal side


title: Sample tb7641, placenta, fetal side


title: Sample tb7697, placenta, fetal side


title: Brain t845, temporal cortex

description: Methylation data using Illumina 450K BeadChips from whole brain, neurons and glia are available for this brain

source_name: Alzheimer's disease temporal cortex

value: Temporal cortex

value: Alzheimer's disease


title: Brain t778, temporal cortex


title: Sample tb7636, placenta, fetal side


title: Brain t551, temporal cortex

source_name: Normal temporal cortex


title: Brain t4699, temporal cortex


title: Brain t4931, temporal cortex


title: Brain t779, temporal cortex


title: Brain t4539, temporal cortex


title: Sample tb7908, placenta, fetal side


title: Brain t4534, temporal cortex


title: Brain t4455, temporal cortex


title: Brain t4479, temporal cortex


title: Brain t4518, temporal cortex


title: Brain t4415, temporal cortex


title: Brain t4444, temporal cortex


title: Sample tb7666, placenta, fetal side


title: Brain t4307, temporal cortex


title: Brain t4303, temporal cortex


title: Brain t4135, temporal cortex


title: Brain t4215, temporal cortex


title: Brain t4308, temporal cortex


title: Brain t4388, temporal cortex


title: Brain t4233, temporal cortex


title: Brain t4118, temporal cortex


title: Brain t4053, temporal cortex


title: Brain t4032, temporal cortex


title: Brain t4006, temporal cortex


title: Brain t4451, temporal cortex


title: Brain t4454, temporal cortex


title: Brain t3966, temporal cortex


title: Brain t4099, temporal cortex


title: Brain t3925, temporal cortex


title: Brain t3923, temporal cortex


title: Brain t3914, temporal cortex


title: Brain t3901, temporal cortex


title: Brain t3998, temporal cortex


title: Brain t3893, temporal cortex


title: Brain t3867, temporal cortex


title: SMC3 shRNA2 Rep2

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

hyb_protocol: Per affymetrix manual

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner LR15  After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner Description LR15

data_processing: .gct and .res files were created by RMA normalization using GenePattern (https://www.broad.harvard.edu/cancer/software/genepattern/). These files (specifically the .gct) was used for downstream analysis by GSEA

label: Biotin

label_protocol: The cDNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual

growth_protocol: CJ9 (129svj derived ESCs) were grown under standard conditions prior to infection

extract_protocol: Cells were lysed with Trizol and total RNA collected. Total RNA was further purified by the Qiagen RNA isolation system per manufacturer's protocol.

treatment_protocol: Adherent cells were infected with lentivirus for 48 hrs in the presence of polybrene 10 mcg/mL. Media was then changed to ES cell media with LIF and puromycin (4 mcg/mL). Cells were then cultured for 48hrs post infection.

value: ESC

tag: genotype/variation

value: Smc3 shRNA2


title: Brain t3799, temporal cortex


title: SMC3 shRNA2 Rep 1


title: SMC3 shRNA1 Rep 2

value: Smc3 shRNA1


title: SMC3 shRNA1 Rep 1


title: Wapal shRNA2 Rep 2

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner LR15

source_name: Wapal shRNA2

value: Wapal shRNA2


title: Wapal shRNA2 Rep 1


title: Brain t336, temporal cortex


title: Empty Vector Rep 2

source_name: Negative Control

value: Empty Vector


title: Wapal shRNA1 Rep 1

source_name: Wapal shRNA1

value: Wapal shRNA1


title: Brain t317, temporal cortex


title: Wapal shRNA1 Rep 2


title: tb8232_placenta

description: Normal placenta, fetal side

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

data_processing: Data was extracted using GenomeStudio v2011.1. Background correction, normalization to Illumina internal control probes, and quantile normalization were performed. All probes mapping to the X or Y chromosome were removed, along with probes that queried CpGs overlapping the positions of known common DNA variants as reported in dbSNP build 138 (allele frequency>1 percent). As recommended by Illumina, fractional methylation (AVG_Beta) values with a detection p-value>0.05 were excluded from the analysis and replaced by missing values. In each tissue, probes with more than 20 percent missing values were excluded.

label: Cy5 and Cy3

source_name: Sample tb8232, normal placenta, fetal side

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol. Genomic DNA (500 ng) was then bisulfite-converted using the EpiTect Bisulfite Kit (Qiagen)

tag: diagnosis


title: tb9026_placenta

description: Normal placenta, fetal side

source_name: Sample tb9026, normal placenta, fetal side


title: tb8234_placenta

description: Normal placenta, fetal side

source_name: Sample tb8234, normal placenta, fetal side


title: tb8993_placenta

description: Normal placenta, fetal side

source_name: Sample tb8993, normal placenta, fetal side


title: tb8227_placenta

description: Normal placenta, fetal side

source_name: Sample tb8227, normal placenta, fetal side


title: tb8926_placenta

description: Normal placenta, fetal side

source_name: Sample tb8926, normal placenta, fetal side


title: tb9023_placenta

description: Normal placenta, fetal side

source_name: Sample tb9023, normal placenta, fetal side


title: tb8231_placenta

description: Normal placenta, fetal side

source_name: Sample tb8231, normal placenta, fetal side


title: Brain t319, temporal cortex


title: tb8225_placenta

description: Normal placenta, fetal side

source_name: Sample tb8225, normal placenta, fetal side


title: tb8169_placenta

description: Normal placenta, fetal side

source_name: Sample tb8169, normal placenta, fetal side


title: tb9000_placenta

description: Normal placenta, fetal side

source_name: Sample tb9000, normal placenta, fetal side


title: tb8134_placenta

description: Normal placenta, fetal side

source_name: Sample tb8134, normal placenta, fetal side


title: tb8678_placenta

description: Normal placenta, fetal side

source_name: Sample tb8678, normal placenta, fetal side


title: Brain t271, temporal cortex

source_name: Alzheimer's disease temporal cortex


title: tb8634_placenta

description: Normal placenta, fetal side

source_name: Sample tb8634, normal placenta, fetal side


title: tb8228_placenta

description: Normal placenta, fetal side

source_name: Sample tb8228, normal placenta, fetal side


title: tb8624_placenta

description: Normal placenta, fetal side

source_name: Sample tb8624, normal placenta, fetal side


title: tb8229_placenta

description: Normal placenta, fetal side

source_name: Sample tb8229, normal placenta, fetal side


title: tb9008_placenta

description: Normal placenta, fetal side

source_name: Sample tb9008, normal placenta, fetal side


title: tb7888_placenta

description: Normal placenta, fetal side

source_name: Sample tb7888, normal placenta, fetal side


title: tb8069_placenta

description: Normal placenta, fetal side

source_name: Sample tb8069, normal placenta, fetal side


title: tb9101_placenta

description: Normal placenta, fetal side

source_name: Sample tb9101, normal placenta, fetal side


title: Brain t256, temporal cortex

source_name: Normal temporal cortex


title: tb7872_placenta

description: Normal placenta, fetal side

source_name: Sample tb7872, normal placenta, fetal side


title: tb9033_placenta

description: Normal placenta, fetal side

source_name: Sample tb9033, normal placenta, fetal side


title: 100Hz_NR_24h_PAG5 rat

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

description:
Channel 1: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 24 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42?  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of pro cessed Red signal/processed Green signal

source_name: the tissue of periaqueductal gray of 100Hz electroacupuncture low responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and non-sensitivity on  electroacupuncture analgesia was labeled with Cy3.

extract_protocol: Total RNA was prepared from PAG using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

value: Sprague-Dawley

value: PAG

value: 100Hz electroacupuncture

tag: responder type

value: low responder(NR)

tag: time

source_name: the tissue of PAG of control rats

extract_protocol: Total RNA was prepared from PAG of control rats using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

value: control


title: Brain t250, temporal cortex


title: tb7877_placenta

description: Normal placenta, fetal side

source_name: Sample tb7877, normal placenta, fetal side


title: Brain t242, temporal cortex


title: Brain t267, temporal cortex


title: tb7908_placenta

description: Normal placenta, fetal side

source_name: Sample tb7908, normal placenta, fetal side


title: 100Hz_NR_24h_PAG4 rat


title: Brain t239, temporal cortex


title: tb7881_placenta

description: Normal placenta, fetal side

source_name: Sample tb7881, normal placenta, fetal side


title: Brain t1488, temporal cortex

source_name: Alzheimer's disease temporal cortex


title: tb7819_placenta

description: Normal placenta, fetal side

source_name: Sample tb7819, normal placenta, fetal side


title: 100Hz_NR_24h_PAG2 rat


title: 100Hz_NR_24h_PAG3 rat


title: Brain t145, temporal cortex


title: 100Hz_HR_24h_PAG5 rat

description:
Channel 1: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 24 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 100Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.

value: high responder(HR)


title: Sample tb8187, T cells, peripheral blood

source_name: Normal T cells, peripheral blood

value: T cells, peripheral blood


title: 100Hz_HR_24h_PAG3 rat


title: 100Hz_NR_24h_PAG1 rat


title: tb7734_placenta

description: Normal placenta, fetal side

source_name: Sample tb7734, normal placenta, fetal side

value: Placenta, fetal side

value: Normal


title: tb7729_placenta

description: Normal placenta, fetal side

source_name: Sample tb7729, normal placenta, fetal side


title: Sample tb8060, T cells, peripheral blood


title: 100Hz_HR_24h_PAG4 rat


title: 100Hz_HR_24h_PAG2 rat


title: 100Hz_HR_24h_PAG1 rat


title: tb7723_placenta

description: Normal placenta, fetal side

source_name: Sample tb7723, normal placenta, fetal side


title: tb7670_placenta

description: Normal placenta, fetal side

source_name: Sample tb7670, normal placenta, fetal side


title: 2Hz_NR_24h_PAG5 rat

description:
Channel 1: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 24 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 2Hz electroacupuncture low responder(NR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and non-sensitivity on  electroacupuncture analgesia was labeled with Cy3.

value: 2Hz electroacupuncture


title: Empty Vector Rep 1

source_name: Negative Control

tag: cell type


title: tb7666_placenta

description: Normal placenta, fetal side

source_name: Sample tb7666, normal placenta, fetal side


title: Sample tb7978, T cells, peripheral blood


title: 2Hz_NR_24h_PAG3 rat


title: t4534_glia

description: Glia from normal temporal cortex

source_name: Brain t4534, glia from normal temporal cortex

value: Glia, temporal cortex


title: Sample tb7913, T cells, peripheral blood


title: t4444_glia

description: Glia from normal temporal cortex

source_name: Brain t4444, glia from normal temporal cortex


title: t4539_glia

description: Glia from Alzheimer's disease temporal cortex

source_name: Brain t4539, glia from Alzheimer's disease temporal cortex

value: Alzheimer's disease


title: Sample tb8067, T cells, peripheral blood


title: t4308_glia

source_name: Brain t4308, glia from Alzheimer's disease temporal cortex


title: 2Hz_NR_24h_PAG2 rat

source_name: the tissue of PAG of control rats


title: Sample tb7827, T cells, peripheral blood


title: Sample tb7984, T cells, peripheral blood


title: t4518_glia

description: Glia from normal temporal cortex

source_name: Brain t4518, glia from normal temporal cortex


title: tb7641_placenta

description: Normal placenta, fetal side

source_name: Sample tb7641, normal placenta, fetal side


title: tb7697_placenta

description: Normal placenta, fetal side

source_name: Sample tb7697, normal placenta, fetal side


title: t4931_glia

description: Glia from normal temporal cortex

source_name: Brain t4931, glia from normal temporal cortex


title: Sample tb7806, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: 2Hz_NR_24h_PAG4 rat


title: t4303_glia

description: Glia from normal temporal cortex

source_name: Brain t4303, glia from normal temporal cortex


title: t4454_glia

source_name: Brain t4454, glia from Alzheimer's disease temporal cortex


title: Sample tb7776, T cells, peripheral blood


title: t4415_glia

description: Glia from normal temporal cortex

source_name: Brain t4415, glia from normal temporal cortex


title: t4118_glia

source_name: Brain t4118, glia from Alzheimer's disease temporal cortex


title: tb7647_placenta

description: Normal placenta, fetal side

source_name: Sample tb7647, normal placenta, fetal side


title: 2Hz_HR_24h_PAG4 rat

description:
Channel 1: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 24 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 2Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 24 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.


title: tb7636_placenta

description: Normal placenta, fetal side

source_name: Sample tb7636, normal placenta, fetal side


title: tb7811_placenta

description: Normal placenta, fetal side

source_name: Sample tb7811, normal placenta, fetal side


title: t4135_glia

source_name: Brain t4135, glia from Alzheimer's disease temporal cortex


title: t4307_glia

description: Glia from normal temporal cortex

source_name: Brain t4307, glia from normal temporal cortex


title: 2Hz_HR_24h_PAG3 rat


title: t3966_glia

description: Glia from normal temporal cortex

source_name: Brain t3966, glia from normal temporal cortex


title: Sample tb7725, T cells, peripheral blood


title: 2Hz_HR_24h_PAG2 rat

source_name: the tissue of PAG of control rats


title: Sample tb7764, T cells, peripheral blood


title: t4053_glia

source_name: Brain t4053, glia from Alzheimer's disease temporal cortex


title: Sample tb7613, T cells, peripheral blood


title: t4032_glia

source_name: Brain t4032, glia from Alzheimer's disease temporal cortex


title: t239_glia

source_name: Brain t239, glia from Alzheimer's disease temporal cortex


title: t317_glia

source_name: Brain t317, glia from Alzheimer's disease temporal cortex


title: t4099_glia

source_name: Brain t4099, glia from Alzheimer's disease temporal cortex


title: Sample tb7703, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: Sample tb7585, T cells, peripheral blood


title: Sample tb7769, T cells, peripheral blood


title: t3867_glia

description: Glia from normal temporal cortex

source_name: Brain t3867, glia from normal temporal cortex


title: 2Hz_HR_24h_PAG5 rat


title: Sample tb7429, T cells, peripheral blood


title: 2Hz_HR_24h_PAG1 rat


title: 100Hz_NR_1h_PAG4 rat

description:
Channel 1: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 100Hz electroacupuncture low responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and non-sensitivity on  electroacupuncture analgesia was labeled with Cy3.


title: t250_glia

source_name: Brain t250, glia from Alzheimer's disease temporal cortex


title: 100Hz_NR_1h_PAG3 rat


title: Sample tb7386, T cells, peripheral blood


title: 100Hz_NR_1h_PAG5 rat


title: Sample tb7286, T cells, peripheral blood


title: 2Hz_NR_24h_PAG1 rat

source_name: the tissue of periaqueductal gray of 2Hz electroacupuncture low responder(NR) rats


title: Sample tb7274, T cells, peripheral blood


title: 100Hz_NR_1h_PAG1 rat


title: t4444_neuron

description: Neurons from normal temporal cortex

source_name: Brain t4444, neurons from normal temporal cortex

value: Neurons, temporal cortex


title: t4931_neuron

description: Neurons from normal temporal cortex

source_name: Brain t4931, neurons from normal temporal cortex


title: 100Hz_NR_1h_PAG2 rat


title: t4539_neuron

description: Neurons from Alzheimer's disease temporal cortex

source_name: Brain t4539, neurons from Alzheimer's disease temporal cortex


title: t145_glia

description: Glia from normal temporal cortex

source_name: Brain t145, glia from normal temporal cortex


title: t271_glia

source_name: Brain t271, glia from Alzheimer's disease temporal cortex


title: 100Hz_HR_1h_PAG5 rat

description:
Channel 1: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 100Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.


title: t4518_neuron

description: Neurons from normal temporal cortex

source_name: Brain t4518, neurons from normal temporal cortex


title: 100Hz_HR_1h_PAG4 rat

source_name: the tissue of PAG of control rats


title: Sample tb7252, T cells, peripheral blood


title: Sample tb7261, T cells, peripheral blood


title: t4454_neuron

source_name: Brain t4454, neurons from Alzheimer's disease temporal cortex


title: t4415_neuron

description: Neurons from normal temporal cortex

source_name: Brain t4415, neurons from normal temporal cortex


title: 100Hz_HR_1h_PAG3 rat


title: 100Hz_HR_1h_PAG2 rat


title: Sample tb6893, T cells, peripheral blood


title: 100Hz_HR_1h_PAG1 rat


title: t271_neuron

source_name: Brain t271, neurons from Alzheimer's disease temporal cortex


title: Sample tb6889, T cells, peripheral blood


title: 2Hz_NR_1h_PAG4 rat

description:
Channel 1: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and non-sensitivity on  electroacupuncture analgesia was labeled with Cy3.


title: t4303_neuron

description: Neurons from normal temporal cortex

source_name: Brain t4303, neurons from normal temporal cortex


title: Sample tb7216, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: t4118_neuron

source_name: Brain t4118, neurons from Alzheimer's disease temporal cortex


title: t317_neuron

source_name: Brain t317, neurons from Alzheimer's disease temporal cortex


title: t4135_neuron

source_name: Brain t4135, neurons from Alzheimer's disease temporal cortex


title: Sample tb6884, T cells, peripheral blood


title: 2Hz_NR_1h_PAG3 rat

source_name: the tissue of periaqueductal gray of 2Hz electroacupuncture low responder(NR) rats


title: t3966_neuron

description: Neurons from normal temporal cortex

source_name: Brain t3966, neurons from normal temporal cortex


title: t4099_neuron

source_name: Brain t4099, neurons from Alzheimer's disease temporal cortex


title: t239_neuron

source_name: Brain t239, neurons from Alzheimer's disease temporal cortex


title: t336_neuron

description: Neurons from normal temporal cortex

source_name: Brain t336, neurons from normal temporal cortex


title: t4032_neuron

source_name: Brain t4032, neurons from Alzheimer's disease temporal cortex


title: t551_brain

description: Whole brain from normal  temporal cortex

source_name: Brain t551, whole brain from normal  temporal cortex

value: whole brain, temporal cortex


title: t4053_neuron

source_name: Brain t4053, neurons from Alzheimer's disease temporal cortex


title: Sample tb6883, T cells, peripheral blood


title: t845_brain

description: Whole brain from Alzheimer's disease  temporal cortex

source_name: Brain t845, whole brain from Alzheimer's disease  temporal cortex


title: 2Hz_NR_1h_PAG2 rat

source_name: the tissue of PAG of control rats


title: Sample tb6881, T cells, peripheral blood


title: t3867_neuron

description: Neurons from normal temporal cortex

source_name: Brain t3867, neurons from normal temporal cortex


title: t778_brain

source_name: Brain t778, whole brain from Alzheimer's disease  temporal cortex


title: t779_brain

source_name: Brain t779, whole brain from normal  temporal cortex


title: 2Hz_NR_1h_PAG1 rat


title: Sample tb6875, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: t4931_brain

source_name: Brain t4931, whole brain from normal  temporal cortex


title: t4534_brain

source_name: Brain t4534, whole brain from normal  temporal cortex


title: t4699_brain

source_name: Brain t4699, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6870, T cells, peripheral blood


title: t4455_brain

source_name: Brain t4455, whole brain from normal  temporal cortex


title: 2Hz_HR_1h_PAG4 rat

description:
Channel 1: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's PAG was then collected for transcript profiling analysis.
Channel 2: strain: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of PAG were collected for transcript profilinf analysis
Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

source_name: the tissue of periaqueductal gray of 2Hz electroacupuncture high responder(HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each PAG which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.


title: 2Hz_HR_1h_PAG5 rat


title: t4415_brain

source_name: Brain t4415, whole brain from normal  temporal cortex


title: 2Hz_HR_1h_PAG3 rat


title: t4454_brain

source_name: Brain t4454, whole brain from Alzheimer's disease  temporal cortex


title: t4479_brain

source_name: Brain t4479, whole brain from Alzheimer's disease  temporal cortex


title: 2Hz_HR_1h_PAG2 rat


title: t4451_brain

source_name: Brain t4451, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6869, T cells, peripheral blood


title: t4539_brain

source_name: Brain t4539, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6868, T cells, peripheral blood


title: t4308_brain

source_name: Brain t4308, whole brain from Alzheimer's disease  temporal cortex


title: 2Hz_HR_1h_PAG1 rat


title: Sample tb6867, T cells, peripheral blood


title: Sample tb6865, T cells, peripheral blood


title: Sample tb6874, T cells, peripheral blood


title: t4388_brain

source_name: Brain t4388, whole brain from normal  temporal cortex


title: Sample tb6864, T cells, peripheral blood


title: t4307_brain

description: Whole brain from Aging  temporal cortex

source_name: Brain t4307, whole brain from Aging  temporal cortex

value: Aging


title: t4215_brain

source_name: Brain t4215, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6861, T cells, peripheral blood


title: Sample tb6862, T cells, peripheral blood


title: Sample tb6860, T cells, peripheral blood


title: Sample tb6859, T cells, peripheral blood


title: t4135_brain

source_name: Brain t4135, whole brain from Alzheimer's disease  temporal cortex


title: t4303_brain

source_name: Brain t4303, whole brain from normal  temporal cortex


title: t4233_brain

source_name: Brain t4233, whole brain from normal  temporal cortex


title: t4006_brain

source_name: Brain t4006, whole brain from normal  temporal cortex


title: Sample tb6810, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: t4118_brain

source_name: Brain t4118, whole brain from Alzheimer's disease  temporal cortex


title: t3925_brain

source_name: Brain t3925, whole brain from normal  temporal cortex


title: t4099_brain

source_name: Brain t4099, whole brain from Alzheimer's disease  temporal cortex


title: t3998_brain

source_name: Brain t3998, whole brain from normal  temporal cortex


title: t3966_brain

source_name: Brain t3966, whole brain from normal  temporal cortex


title: t3923_brain

source_name: Brain t3923, whole brain from normal  temporal cortex


title: t3914_brain

source_name: Brain t3914, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6802, T cells, peripheral blood


title: t4032_brain

source_name: Brain t4032, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6801, T cells, peripheral blood


title: t3799_brain

source_name: Brain t3799, whole brain from normal  temporal cortex


title: t271_brain

source_name: Brain t271, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6788, T cells, peripheral blood


title: t4053_brain

source_name: Brain t4053, whole brain from Alzheimer's disease  temporal cortex


title: t317_brain

source_name: Brain t317, whole brain from Alzheimer's disease  temporal cortex


title: t3867_brain

source_name: Brain t3867, whole brain from normal  temporal cortex


title: t3901_brain

source_name: Brain t3901, whole brain from Alzheimer's disease  temporal cortex


title: tb8067_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb8067, normal T cells, peripheral blood


title: Sample tb6708, T cells, peripheral blood


title: t336_brain

source_name: Brain t336, whole brain from normal  temporal cortex


title: Sample tb6808, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: t256_brain

source_name: Brain t256, whole brain from normal  temporal cortex


title: t3893_brain

source_name: Brain t3893, whole brain from Alzheimer's disease  temporal cortex


title: t319_brain

source_name: Brain t319, whole brain from normal  temporal cortex


title: t242_brain

source_name: Brain t242, whole brain from normal  temporal cortex


title: tb8187_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb8187, normal T cells, peripheral blood


title: t267_brain

source_name: Brain t267, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6666, T cells, peripheral blood


title: t1488_brain

source_name: Brain t1488, whole brain from Alzheimer's disease  temporal cortex


title: t250_brain

source_name: Brain t250, whole brain from Alzheimer's disease  temporal cortex


title: t239_brain

source_name: Brain t239, whole brain from Alzheimer's disease  temporal cortex


title: Sample tb6665, T cells, peripheral blood


title: Sample tb6663, T cells, peripheral blood


title: Sample tb6664, T cells, peripheral blood


title: Sample tb6650, T cells, peripheral blood


title: Sample tb6599, T cells, peripheral blood


title: Sample tb6598, T cells, peripheral blood


title: tb7806_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7806, normal T cells, peripheral blood


title: Sample tb6667, T cells, peripheral blood


title: tb7776_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7776, normal T cells, peripheral blood


title: tb7978_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7978, normal T cells, peripheral blood


title: tb7769_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7769, normal T cells, peripheral blood


title: tb7827_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7827, normal T cells, peripheral blood


title: tb7913_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7913, normal T cells, peripheral blood


title: SKOV3-miR21 precursor-replica 3

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description:
Gene expression data from SKOV3 cell line transfected with miR21 precursor
SKOV3_miR21#3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: SKOV3_miR21 precursor

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: All cell lines were cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNAs were isolated using TRI reagent (Molecular Research Center) according to the manufacturer's instructions.

treatment_protocol: prior to treatment, cells were trypsinized, counted and seeded in 60mm cell culture dishes. 24 hours after cell seeding, according to the treatment group, SKOV3 cells were transfected with either 5 nM miR21 precursor or negative control precursor miRNA for 24 h

value: High grade serous ovarian cancer cells

tag: transfected with

value: 5 nM miR21 precursor for 24hr


title: Sample tb6351, T cells, peripheral blood

source_name: Normal T cells, peripheral blood


title: tb7386_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7386, normal T cells, peripheral blood


title: tb7585_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7585, normal T cells, peripheral blood


title: tb8060_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb8060, normal T cells, peripheral blood


title: tb7725_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7725, normal T cells, peripheral blood


title: tb7613_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7613, normal T cells, peripheral blood


title: SKOV3-miR21 precursor-replica 1

description:
Gene expression data from SKOV3 cell line transfected with miR21 precursor
SKOV3_miR21#1


title: tb7764_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7764, normal T cells, peripheral blood


title: SKOV3-miR21 precursor-replica 2

description:
Gene expression data from SKOV3 cell line transfected with miR21 precursor
SKOV3_miR21#2


title: SKOV3-Control presursor miRNA-replica 3

description:
Gene expression data from SKOV3 cell line transfected with control precursor miRNA
SKOV3_control#3

source_name: SKOV3_Control presursor miRNA

value: negative control precursor miRNA for 24hr


title: tb7286_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7286, normal T cells, peripheral blood


title: tb7429_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7429, normal T cells, peripheral blood


title: SKOV3-Control presursor miRNA-replica 2

description:
Gene expression data from SKOV3 cell line transfected with control precursor miRNA
SKOV3_control#2


title: tb7984_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7984, normal T cells, peripheral blood


title: SKOV3-Control presursor miRNA-replica 1

description:
Gene expression data from SKOV3 cell line transfected with control precursor miRNA
SKOV3_control#1


title: tb7274_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7274, normal T cells, peripheral blood


title: tb6875_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6875, normal T cells, peripheral blood


title: tb7252_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7252, normal T cells, peripheral blood


title: tb7216_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7216, normal T cells, peripheral blood


title: tb6893_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6893, normal T cells, peripheral blood


title: tb7703_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7703, normal T cells, peripheral blood


title: Umbilical Aorta Smooth Muscle Cells, biological rep2

city: Durham

first: Nicolas

last: Christoforou

state: NC

address: 136 Hudson Hall, Box 90281

department: Biomedical Engineering

institute: Duke University

description: UASMC 2

hyb_protocol: Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific / Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Human Genome U133A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.

data_processing:
Data analysis was performed as previously described. Briefly using the Partek Genomics Suite raw data (CEL files) was imported and normalized using the RMA algorithm. Subsequently ANOVA statistical analysis was performed on the entire data set searching for significant differences between any one of the three groups (iSMC 2 weeks, iSMC 4 weeks, UASMC) and the negative control (EPC). Subsequently significantly upregulated or downregulated genes were identified based on the fact that p-value<0.05 and Fold Change< or >1.5. Hierarchical clustering analysis and principal component analysis were performed within the software suite itself. Identification of molecular pathways associated with significantly upregulated or downregulated genes was performed using the WEB-based GEne SeT AnaLysis Toolkit (WebGestalt)50. Derivation of the molecular pathway associated with smooth muscle contraction and based on the set of upregulated genes in the iSMC cell population was done using the GeneMANIA prediction server51.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Umbilical Aorta Smooth Muscle Cells

treatment_protocol: EPC were seeded at a density of 20,000 cells/cm^2 and were subsequently induced to transdifferentiate via MYOCD overexpression 24 hours post initial seeding as previously described. Control cell groups (wild-type EPC or UASMC) were similarly prepared (20,000 cells/cm^2). 2 weeks post initiation of EPC transdifferentiation, cells were enzymatically dissociated and 1x10^6 cells from each sample were used for flow cytometry. Total RNA was collected from the remaining of dissociated cells (RNeasy Mini, Qiagen) for iSMC, EPC, UASMC (n=3). This was repeated for iSMC at the 4-week time-point (n=3). One week post initiation of transdifferentiation the culture medium used to maintain the derived iSMC was switched to SmBM (supplemented with SmGM-2, Lonza) and kept the same for the remainder of the experiment. Doxycycline was added to the iSMC culture medium only for the initial 2 weeks.

tag: tissu/cell source

value: Umbilical Aorta Whole Blood

tag: cell subtype

value: primary human smooth muscle cells isolated from the umbilical artery (UASMC)


title: tb6874_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6874, normal T cells, peripheral blood


title: Umbilical Aorta Smooth Muscle Cells, biological rep3

description: UASMC 3

scan_protocol: Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific / Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Human Genome U133A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.

extract_protocol: Total RNA was collected from the remaining of dissociated cells (RNeasy Mini, Qiagen) for iSMC, EPC, UASMC (n=3).


title: tb6889_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6889, normal T cells, peripheral blood


title: Umbilical Aorta Smooth Muscle Cells, biological rep1

description: UASMC 1

label_protocol: Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific / Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Human Genome U133A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.


title: Induced Smooth Muscle Cells Week 4, biological rep3

description: iSMCw4 3

source_name: Induced Smooth Muscle Cells_Week 4

value: Endothelial Progenitor Cells

value: Induced Smooth Muscle Cells

value: 2 wks of continuous MYOCD expression followed by 2 wks of culture under standard conditions (iSMC-4w)


title: tb7261_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb7261, normal T cells, peripheral blood

value: T cells, peripheral blood


title: tb6881_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6881, normal T cells, peripheral blood


title: tb6883_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6883, normal T cells, peripheral blood


title: Induced Smooth Muscle Cells Week 4, biological rep2

description: iSMCw4 2


title: tb6870_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6870, normal T cells, peripheral blood


title: Induced Smooth Muscle Cells Week 4, biological rep1

description: iSMCw4 1


title: Induced Smooth Muscle Cells Week 2, biological rep3

description: iSMCw2 3

source_name: Induced Smooth Muscle Cells_Week 2

value: following 2 wks of continuous MYOCD expression (iSMC-2w)


title: tb6869_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6869, normal T cells, peripheral blood

value: Normal


title: tb6860_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6860, normal T cells, peripheral blood


title: tb6859_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6859, normal T cells, peripheral blood


title: tb6867_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6867, normal T cells, peripheral blood


title: tb6862_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6862, normal T cells, peripheral blood


title: Induced Smooth Muscle Cells Week 2, biological rep1

description: iSMCw2 1


title: tb6868_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6868, normal T cells, peripheral blood


title: tb6864_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6864, normal T cells, peripheral blood


title: Endothelial Progenitor Cells, biological rep1

description: EPC 1

source_name: Endothelial Progenitor Cells

value: Whole Blood


title: Endothelial Progenitor Cells, biological rep2

description: EPC 2


title: MEC1, ATO, biological rep3

city: MADRID

first: M Ángeles

last: García-Pardo

state: MADRID

address: RAMIRO DE MAEZTU, 9

country: Spain

institute: CENTRO DE INVESTIGACIONES BIOLÓGICAS, CSIC

description: Gene expression data from MEC-1 cells cultured with ATO for 24h

hyb_protocol: Following fragmentation, cRNAs were hybridized to an Affymetrix GeneChip® Human Gene 1.0 ST Array on a GeneChip Hybridation Oven 640. GeneChips were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: Hybridized Affymetrix arrays were scanned using an Affymetrix Gene Array Scanner 3000 7G.

data_processing: The Robust Multi-array Analysis (RMA) was used for background correction, intra- and inter-microarray normalization, and  calculation of the absolute expression signal for each gene.

source_name: MEC-1 cells cultured with 5 µM ATO for 24 h

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: 5 x 106 MEC-1 cells were cultured in IMDM/0.1% FBS at a final density of 2 x 106 cells/ml

extract_protocol: Total RNA was extracted and purified using the Qiagen AllPrep® DNA/RNA/Protein Mini kit following the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: MEC-1 cells were incubated with or without 5 μM ATO for 24 hours at 37ºC, 5% CO2.

value: chronic lymphocytic leukemia cell line MEC-1


title: tb6802_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6802, normal T cells, peripheral blood


title: Endothelial Progenitor Cells, biological rep3

description: EPC 3


title: tb6861_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6861, normal T cells, peripheral blood


title: tb6801_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6801, normal T cells, peripheral blood


title: MEC1, ATO, biological rep2


title: Induced Smooth Muscle Cells Week 2, biological rep2

description: iSMCw2 2


title: tb6808_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6808, normal T cells, peripheral blood


title: tb6810_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6810, normal T cells, peripheral blood


title: MDAMB231-inhibitor PD325901-biological rep 3

first: Miles

last: Miller

address: 185 Cambridge St

institute: Massachusetts General Hospital

description:
P3
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 3uM PD325901

hyb_protocol: cRNA was hybridized using manufacturer's guidelines on Affymetrix Human Genome PrimeView Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450. Performed at Massachusetts Institute of Technology BioMicroCenter Core Service

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G. Performed at Massachusetts Institute of Technology BioMicroCenter Core Service

data_processing: Data were preprocessed using the R/Bioconductor package “affy” and the RMA normalization routine using expresso.

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's protocol using the NuGEN Applause system using the Massachusetts Institute of Technology BioMicroCenter Core Service

growth_protocol: MDA-MB231 cells were plated overnight in 10cm tissue culture plates at 70% confluency, in DMEM + 10% FBS.  Treatments were performed with fresh media change the following day.

extract_protocol: Total RNA was extracted following manufacturer's guidelines using Qiagen Rneasy Mini Kit.  RNA QC was performed using Agilent Bioanalyzer.

treatment_protocol: From 10mM DMSO stock diluted into fresh DMEM+10% FBS, cells were treated with either 10uM BB94 (batimastat metalloproteinase inhibitor) or 3uM PD325901 (MEK inhibitor) or DMSO vehicle control for 24h.

value: human breast cancer cell line

tag: treated with


title: MDAMB231-inhibitor PD325901-biological rep 2

description:
P2
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 3uM PD325901


title: FTC236 Notch1_48hr_0ugDox_rep3

city: Madison

first: Brian

middle: P

last: Johnson

address: 1400 University Ave

department: Oncology

institute: UW-Madison

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 3um 16bit

data_processing: Agilent Feature extraction version 10.7.3.1 for background subtraction - Background and Multiplicitive detrending. Data analyzed in R using Limma.  Threshold: 1.0   Logbase: 2   Technology: Agilent.SingleColor.28005  Normalization: Quantile

source_name: FTC236-Notch1 cell line, 48hr, 0ug/ml Dox, replicate 3

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent One Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: FTC236-Notch1 cells were maintained in DMEM/Ham’s F-12 (1:1; Invitrogen) medium supplemented with 10% FBS, 0.01 U/mL of thyroid-stimulating hormone (TSH) and 10 µg/mL of insulin (Sigma-Aldrich) and were under dual antibiotic selection (G418 and hygromycin)

extract_protocol: Processed with an Qiagen Rneasy Mini kit

treatment_protocol: FTC236-Notch1 cells were treated with doxycycline at 1 µg/mL or without doxycycline.

tag: type of cancer

value: follicular cancer

tag: target gene turned on

value: No

value: thyroid


title: FTC236 Notch1_48hr_0ugDox_rep2

source_name: FTC236-Notch1 cell line, 48hr, 0ug/ml Dox, replicate 2


title: tb6667_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6667, normal T cells, peripheral blood


title: tb6788_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6788, normal T cells, peripheral blood


title: MDAMB231-inhibitor PD325901-biological rep 1

description:
P1
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 3uM PD325901


title: tb6666_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6666, normal T cells, peripheral blood


title: MDAMB231-inhibitor BB94-biological rep 1

description:
BB1
Gene expression data from 90% confluent cell culture, 24hr after application of fresh full serum media + 10uM BB94

value: 10uM BB94


title: MEC1, Control, biological rep2

description: Gene expression data from MEC-1 cells cultured without ATO for 24h

source_name: MEC-1 cells cultured without ATO for 24 h


title: tb6708_Tcells

description: Normal T cells, peripheral blood

source_name: Sample tb6708, normal T cells, peripheral blood


title: MEC1, Control, biological rep1


title: FTC236 Notch1_48hr_1ugDox_rep1

source_name: FTC236-Notch1 cell line, 48hr, 1ug/ml Dox, replicate 1

value: Yes


title: MMP-9, biological replicate5

description: Gene expression data from MEC-1 cells overexpressing MMP-9

data_processing: The Robust Multi-array Analysis (RMA) was used for background correction, intra- and inter-microarray normalization, and calculation of the absolute expression signal for each gene. Significance Analysis of Microarray (SAM) was applied to calculate significant differential expression and find the gene probe sets differentially expressed in MMP-9 cells respect to Mock cells. The method uses permutations to provide robust statistical inference of the most significant genes and, by using a false discovery rate (FDR), adjust the raw p-values to take multiple testing into account. An FDR cut-off of = 0.1 was used for all the differential expression calculations.

source_name: MEC-1 cells overexpressing MMP-9

growth_protocol: 3 x 106 MEC-1 cells were cultured in IMDM/0.1% FBS at a final density of 2 x 106 cells/ml

extract_protocol: Total RNA was extracted and purified using the AllPrep® DNA/RNA/Protein Mini kit (Qiagen) following the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MEC-1 cells were genetically modified using a GFP lentiviral vector with (MMP-9 cells) or without (Mock cells) a proMMP-9 DNA construct.

value: Chronic lymphocytic leukemia cell line MEC-1