title: 13913498 - OE1 vs WT3 1

hyb_protocol: WT3 1 Cy5 / OE1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT3 1

growth_protocol: leaf - Media: MS medium for 7 days. Plants were subsquently transferred on soil Hygrometry: 50%/70% (day/night) Temperature: 22°C Light: 200 µE m-2 s-1

growth_protocol: leaf - Media: MS medium + kanamycin 50 µg/mL for 7 days. Plants were subsquently transferred on soil. Hygrometry: 50%/70% (day/night) Temperature: 22°C Light: 200 µE m-2 s-1

value: columbia mutant (35s::AtTCTP)


title: Tissue 1 (BT1) - 001

status: Public on Mar 17 2011

type: RNA

city: Seoul

first: Tae Hoon

last: Kim

state: Socho-gu

address: 505 Bonpo-dong

department: Pathology

country: South Korea

institute: Medical College of the Catholic University

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 1 (BT1) - 001
GTC2BT-001_rep 1

hyb_protocol: The labelled cDNAs are resuspended in 10ul of hybridization solution (GenoCheck, Korea), and are placed on Roche NimbleGen Human Whole genome 12-plex array (Roche NimbleGen Inc., WI) and covered by a NimbleGen H12 mixer (Roche NimbleGen Inc., WI).

scan_protocol: These arrays are scanned using Axon GenePix 4000B scanner with associated software (Molecular Devices Corp.)

data_processing: Each signal intensity of genes is processed with RMA (Robust Multi-array Average) and quantile normalization using NimbleScan Version 2.4 (Roche NimbleGen Inc.,WI).

molecule: total RNA

organism: Homo sapiens

source_name: BT patient

label_protocol: Each total RNA sample is labelled with Cy3 using SuperScript II (Invitrogen, CA).

extract_protocol: Total RNA is extracted from the Human sample using the TRI reagent (MRC, OH) according to the manunfacturer's instructions.

tag: tissue

value: Skin biopsy

tag: origin

value: Philippines


title: Asthma_pool_A_r1_Nsp

type: genomic

city: Bologna

first: Giampaolo

last: Ricci

state: BO

address: Massarenti 9

department: Pediatric Allergologic Center

country: Italy

institute: University of Bologna

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing: Probe intensity data was taken directly from the CEL file and used to calculate a Relative Allele Signal (RAS) score by the MPAM algorithm implemented in the SNP-MaP script (http://sgdp.iop.kcl.ac.uk/oleo/affy). This method calculates the average of RAS1 (sense) and RAS2 (antisense) values as a quantitative index of allele frequencies in pooled DNA

label: Biotin

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood samples from allergic / asthmatic children using the Nucleospin DNA kit (Macherey & Nagel, Duren, Germany) and individual DNA concentration was determined in triplicate with the Quant-iT Pico-Green dsDNA Assay Kit (Invitrogen, Milan, Italy).

value: peripheral blood

tag: disease state

value: Asthma

tag: pool

value: A

tag: replicate


title: 13913503 - WT3 2 vs OE2

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP)

hyb_protocol: OE2 Cy5 / WT3 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

treatment_protocol: no treatment

tag: strain

tag: dev.stage (boyes et al. plant cell 2001)

source_name: WT3 2

value: columbia


title: RC_pool_F_r1_Sty

description: Hybridized to 250K_Sty

value: Rhinoconjunctivitis

value: F


title: 13912900 - WT3 1 vs OE1

hyb_protocol: OE1 Cy5 / WT3 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: BC009_13_2

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

country: USA

institute: Princeton University

description: English Channel time series N uptake study

hyb_protocol: hybridization at 65 oC using Agilent hybridization solution

scan_protocol: Arrays were scanned on an Agilent High-Resolution C Scanner

data_processing: Data were analyzed using GenePix Pro (Version 6.0)

organism: marine metagenome

source_name: ST-80 4 L seawater from 1 m depth at Station L4 in the English Channel collected 6 July 2004

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: DNA was extracted using the Gentra PureGene cell culture protocol (Qigen); RNA was extracted using the RNAqueous kit (Ambion)

treatment_protocol: Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC  until extraction

value: particulate material from ~4 L of surface seawater

tag: hybd material

value: 200 ng nitrate reductase PCR product from cDNA

molecule: other

organism: synthetic construct

source_name: 20-mer internal standard

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy5 to the dUaa

extract_protocol: not applicable

value: 20-mer internal standard


title: periodontitis 11

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

country: Germany

institute: University Göttingen

hyb_protocol: using the genechip hybridisation, wash and stain kit

scan_protocol: Array washing and staining as described in chp 6 of above manual using the GeneChip Fluidics station 450 (fluidics script FS450-007). Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning.

data_processing: Gene level probe set summarisation (signal value), calculation of QC metrics and CHP file generation were performed using GeneChip® Expression Console software using the Robust Multichip Analysis (RMA) algorithm

label: biotin

source_name: human periodontal ligament from patient with periodontitis P11

label_protocol: GeneChip Whole Transcript (WT) sense target labeling assay manual, version 4 - starting with 300ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays(omitting RiboMinus procedure).

growth_protocol: RNA was extracted directly from the middle third of the human periodontal ligament

extract_protocol: The RNA was extracted using of Trizol, followed by RNeasy to remove traces of phenol and ethanol.

value: periodontal ligament


title: BC009_21_2

source_name: ST-47 4 L seawater from 1 m depth at Station L4 in the English Channel collected 10 May 2004


title: Tissue 2 (BT2) - 002

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 2 (BT2) - 002
GTC2BT-002_rep 1


title: Blood 6 (MB6) - 06

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-06_rep1

source_name: MB patient

value: Blood


title: Blood 4 (MB4) - 04

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-04_rep1


title: BC008_37

source_name: ST-82 4 L seawater from 1 m depth at Station L4 in the English Channel collected 6 July 2004

value: 200 ng nitrase reductase PCR product from DNA


title: BC009_20_2

source_name: ST-14 4 L seawater from 1 m depth at Station L4 in the English Channel collected 1 March 2004


title: BC008_38


title: Blood 3 (MB3) - 03

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-03_rep1


title: 13913499 - WT1 2 vs KO2 2

hyb_protocol: KO2 2 Cy5 / WT1 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: KO2 2

growth_protocol: leaf - Media: IVC medium (5% sucrose, 2.2 g/L MS salts, 400 mg/L glutamine, 0,3% Phytagel, pH 5.9) for 5 days. Germinated seeds were subsequently transferred onto Arabidopsis Medium (1% sucrose, 2.2 g/L MS salts, 0.5 g/L MES, 0,8% agar, pH 5.9) for 7 days. Plants were subsquently transferred on soil. Hygrometry:50%/70% (day/night) Temperature: 22°C Light:150 µE m-2 s-1

value: columbia mutant (tctp-2 -/-)

source_name: WT1 2

growth_protocol: leaf - Media:IVC medium (5% sucrose, 2.2 g/L MS salts, 400 mg/L glutamine, 0,3% Phytagel, pH 5.9) for 5 days. Germinated seeds were subsequently transferred onto $Arabidopsis Medium (1% sucrose, 2.2 g/L MS salts, 0.5 g/L MES, 0,8% agar, pH 5.9) for 7 days. Plants were subsquently transferred on soil. Hygrometry:50%/70% (day/night) Temperature: 22°C Light:150 µE m-2 s-1


title: 13912897 - KO2 1 vs WT1 1

hyb_protocol: WT1 1 Cy5 / KO2 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT1 1

source_name: KO2 1


title: BC009_17_1

source_name: ST-64 4 L seawater from 1 m depth at Station L4 in the English Channel collected 7 June 2004


title: Blood 2 (MB2) - 02

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-02_rep1


title: 13913504 - OE2 vs WT3 2

hyb_protocol: WT3 2 Cy5 / OE2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Blood 5 (MB5) - 05

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-05_rep1


title: Asthma_pool_A_r1_Sty

description: Hybridized to 250K_Sty


title: periodontitis 4

source_name: human periodontal ligament from patient with periodontitis P4


title: Asthma_pool_B_r1_Sty

description: Hybridized to 250K_Sty

value: B


title: 13913500 - KO2 2 vs WT1 2

hyb_protocol: WT1 2 Cy5 / KO2 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: periodontitis 5

source_name: human periodontal ligament from patient with periodontitis P5


title: Asthma_pool_C_r1_Sty

description: Hybridized to 250K_Sty

value: C


title: BC009_24_1


title: Blood 1 (MB1) - 01

description:
This sample is diagnosed with MB according to classification of Ridley and Jopling
GTC2MB-01_rep1


title: periodontitis 2

source_name: human periodontal ligament from patient with periodontitis P2


title: 13912896 - WT1 1 vs KO2 1

hyb_protocol: KO2 1 Cy5 / WT1 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: periodontitis 6

source_name: human periodontal ligament from patient with periodontitis P6


title: BC009_18_2

source_name: ST-40 4 L seawater from 1 m depth at Station L4 in the English Channel collected 26 April 2004


title: healthy periodont 4

source_name: human periodontal ligament from patient with healthy periodontium G4


title: Blood 5 (BT5) - 005

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-005_rep 1

source_name: BT patient


title: Asthma_pool_D_r1_Sty

description: Hybridized to 250K_Sty

value: D


title: Footpads_M. leprae infected_12 month_rep4

hyb_protocol: Purifed cDNA were denatured, and the samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential ((1) 2XSSC, 0.1%SDS, (2) 1XSSC, (3) 0.2XSSC) and were dried by centrifuge

scan_protocol: Scanned on an Genepix 4000B scanner. Images were quantified using GenePix pro Software (version 5.1).

data_processing: Box plot and Intesity dependent (LOWESS) normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix pro 5.1 was used.

organism: Mus musculus

source_name: M. lepare non-infected footpads

label_protocol:
Direct Labeling (20 µg of total RNA were primed with oligo dT(18) primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of Reverse transcriptase, and dNTP, cyanine dCTP (control - Cy3 and sample-Cy5)
Labeled cDNA were purifed with 3M sodium acetate and absoulte ethanol, checked quality of synthesized labeled-cDNA (Spectrophotometer A260, A650, A550), and the calculated concentration and incorporation rate

extract_protocol: (1) Total RNA extracted using Trizol following manufacturer's instructions, (2) DNA removal using Rneasy RNA extraction column following manufacturer's instructions

treatment_protocol: M. leprae non-infected footpads: PBS (subcutaneous injection), M. leprae-infected footpads: 2´10^6 bacteria (subcutaneous injection)

value: footpads

tag: experimental period

value: 12 months

source_name: M. lepare-infected footpads

tag: period


title: Footpads_M. leprae infected_12 month_rep6


title: healthy periodont 8

source_name: human periodontal ligament from patient with healthy periodontium G8


title: Footpads_M. leprae infected_12 month_rep5


title: Blood 3 (BT3) - 003

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-003_rep 1

value: Philippines


title: healthy periodont 2

source_name: human periodontal ligament from patient with healthy periodontium G2


title: Footpads_M. leprae infected_12 month_rep3


title: Blood 6 (BT6) - 006

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-006_rep 1


title: BC009_19_1

source_name: ST-46 4 L seawater from 1 m depth at Station L4 in the English Channel collected 10 May 2004

source_name: 20-mer internal standard


title: Blood 2 (BT2) - 002

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-002_rep 1


title: healthy periodont 6

source_name: human periodontal ligament from patient with healthy periodontium G6


title: BC009_18_1

source_name: ST-13 4 L seawater from 1 m depth at Station L4 in the English Channel collected 1 March 2004


title: Blood 1 (BT1) - 001

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-001_rep 1


title: healthy periodont 1

source_name: human periodontal ligament from patient with healthy periodontium G1


title: 3 mo day 7 post PNX biorep 15

status: Public on Mar 16 2011

city: North Grafton

first: Julia

middle: A

last: Paxson

state: MA

address: 200 Westboro Road

department: Clinical Sciences

institute: Tufts Cummings School of Veterinary Medicine

description: Replicate 3 - pooled RNA sample from the day 7 post-PNX right lungs of mouse 15a and 15b

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probe sets were background corrected and summarized using the RMA algorithm along with quantile normalization, all of which are available in BioConductor's lumi package. Quality control on the arrays was performed by again using the lumi package to visualize intensity distributions, percentage present calls, and correlations between arrays; none of which turned up any reasons for concern and resulted in the inclusion of all arrays in the analysis. Following quality inspection, probe sets were filtered to include only those detected on all arrays. This step eliminated all probes with signal intensities reported at background level and resulted in the inclusion of roughly 17,500 probe sets for further analysis. Data analysis of the filtered probe set can be described in two steps. First, differential gene expression was calculated between pneumonectomy and control samples for the animals within each age group and at each time point following surgery. This was accomplished using the limma (Linear Modeling for Microarray Data) package in BioConductor, with pneumonectomy and control sample pairings built into the model. Fold-change and p-values for each probe set were calculated using a moderated t-statistic, with the variance estimate being adjusted by incorporating global variation measures for the complete set of probes on the array. The P-value data were then corrected for multiple hypothesis testing using the Benjamini and Hochberg method. This analysis resulted in unique sets of differentially expressed genes for each age group and time point. An absolute fold-change value ≥ 1.5 and adjusted P-value < 0.05 were used as criteria for defining a set of genes for further exploration. Following completion of this analysis, second analysis addressed the question of how differential gene expression differed between the aged and young age groups. To determine differences in differential gene expression between the aged and young animals, individual pair-wise fold-changes were calculated for each of the groups analyzed in step 1, providing threefold-change values per group (one for each paired replicate sample). This allowed for groups of fold-change values for a given time point in the aged group to be directly compared to those in the young group, again using the t-statistic. An absolute fold-change value ≥ 1.5 in at least one of the groups tested (i.e. either 3 month or 9 month groups) and adjusted P-value < 0.05 were used as criteria for defining a set of genes for further exploration. Results of this analysis provided genes showing significant differential expression specific to the aged group compared to the young group with baseline differences subtracted.

source_name: Mouse right lung

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Purelink RNA mini kit (Invitrogen #12183-018A) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Two samples were obtained from each mouse; the left lung was removed at day 0 during the pneumonectomy surgery and processed as a control sample; then, the remaining lung tissue was removed at one of three time points post-pneumonectomy (1 day, 3 days, or 7 days). For each of the three time points, two groups of mice were used: (1) aged and (2) young, with six animals in each group. For the microarray experiment, equal amounts of RNA from 2 animals (control and PNX samples) were pooled, resulting in a total of 3 control and 3 PNX microarray samples at each time point.

value: right lung

tag: Sex

value: female

tag: age

value: 3 months

tag: group

tag: day

value: Young

value: Pnx

tag: sample

tag: biorep

tag: condition


title: 9 mo day 7 post-PNX biorep 17

description: Replicate 2 - pooled RNA sample from the day 7 post-PNX right lungs of mouse 17a and 17b

tag: tissue

value: 9 months

value: Aged


title: 3 mo day 7 post PNX biorep 13

description: Replicate 1 - pooled RNA sample from the day 7 post-PNX right lungs of mouse 13a and 13b


title: 9 mo left lung control biorep 16

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 16a and 16b

source_name: Mouse left lung

value: left lung

value: Control


title: BC008_7

description: English Channel time series N uptake study

source_name: ST-30A 4 L seawater from 1 m depth at Station L4 in the English Channel collected 13 April 2004

tag: origin

value: particulate material from ~4 L of surface seawater

value: 200 ng nitrase reductase PCR product from DNA

value: 20-mer internal standard


title: 9 mo day 7 post-PNX biorep 18

description: Replicate 3 - pooled RNA sample from the day post-PNX right lungs of mouse 18a and 18b


title: 9 mo left lung control biorep 18

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 18a and 18b


title: Blood 4 (BT4) - 004

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling
GTC2BT-004_rep 1

value: Blood


title: Footpads_M. leprae infected_12 month_rep1


title: 3 mo left lung control biorep 15

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 15a and 15b


title: 9 mo day 3 post-PNX biorep 11

description: Replicate 2 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 11a and 11b


title: 3 mo left lung control biorep 14

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 14a and 14b


title: 9 mo day 3 post-PNX biorep 12

description: Replicate 3 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 12a and 12b


title: 9 mo left lung control biorep 12

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 12a and 12b


title: 9 mo left lung control biorep 17

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 17a and 17b


title: Footpads_M. leprae infected_12 month_rep2


title: 3 mo day 3 post PNX biorep 9

description: Replicate 3 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 9a and 9b


title: 9 mo left lung control biorep 10

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 10a and 10b


title: 9 mo day 3 post-PNX biorep 10

description: Replicate 1 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 10a and 10b


title: 3 mo day 3 post PNX biorep 8

description: Replicate 2 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 8a and 8b


title: 3 mo day 3 post PNX biorep 7

description: Replicate 1 - pooled RNA sample from the day 3 post-PNX right lungs of mouse 7a and 7b


title: 3 mo left lung control biorep 9

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 9a and 9b


title: 9 mo left lung control biorep 11

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 11a and 11b


title: 3 mo left lung control biorep 8

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 8a and 8b


title: 3 mo day 7 post PNX biorep 14

description: Replicate 2 - pooled RNA sample from the day 7 post-PNX right lungs of mouse 14a and 14b


title: 9 mo day 1 post-PNX biorep 4

description: Replicate 1 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 4a and 4b


title: 3 mo left lung control biorep 7

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 7a and 7b


title: 9 mo day 7 post-PNX biorep 16

description: Replicate 1 - pooled RNA sample from the day 7 post-PNX right lungs of mouse 16a and 16b


title: 3 mo day 1 post PNX biorep 1

description: Replicate 1 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 1a and 1b


title: 3 mo day 1 post PNX biorep 2

description: Replicate 2 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 2a and 2b


title: 9 mo day 1 post-PNX biorep 6

description: Replicate 3 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 6a and 6b


title: 9 mo day 1 post-PNX biorep 5

description: Replicate 2 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 5a and 5b


title: 3 mo day 1 post PNX biorep 3

description: Replicate 3 - pooled RNA sample from the day 1 post-PNX right lungs of mouse 3a and 3b


title: 9 mo left lung control biorep 6

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 6a and 6b


title: 9 mo left lung control biorep 4

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 4a and 4b


title: 9 mo left lung control biorep 5

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 5a and 5b


title: 3 mo left lung control biorep 3

description: Replicate 3 - pooled RNA sample from the left lungs of mouse 3a and 3b


title: 3 mo left lung control biorep 1

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 1a and 1b


title: 3 mo left lung control biorep 2

description: Replicate 2 - pooled RNA sample from the left lungs of mouse 2a and 2b


title: FFPE-17

city: South San Francisco

first: Peng

last: Yue

state: CA

address: 1 DNA Way

institute: Genentech Inc

hyb_protocol: according to the manufacturer’s instruction

data_processing: Expression was normalized and estimated using VSN.

source_name: DLBCL

growth_protocol: Matched frozen and fixed DLBCL cases were commercially procured from Cytomyx (Rockville, MD)

extract_protocol: total cellular RNA were extracted with mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX)

tag: tissue type

value: DLBCL tumor, FFPE


title: FFPE-18

scan_protocol: according to the manufacturer’s instruction


title: FFPE-15

label_protocol: according to the manufacturer’s instruction


title: FFPE-11


title: FFPE-14


title: FFPE-13


title: FFPE-7


title: FFPE-8


title: FFPE-3


title: FFPE-12


title: FFPE-2


title: FFPE-16


title: FFPE-6


title: FFPE-5


title: FFPE-1


title: FFPE-9


title: FFPE-10


title: Frozen-15

value: DLBCL tumor, Frozen


title: Frozen-16


title: Frozen-14


title: Frozen-13


title: Frozen-10


title: FFPE-4


title: Frozen-17


title: Frozen-9


title: Frozen-12


title: Frozen-4


title: Frozen-5


title: Frozen-8


title: Frozen-6


title: DLBCL patient_A0020372

treatment_protocol: Patients were all treated with SGN-40

tag: response

value: SD

tag: spdpct


title: Frozen-18


title: DLBCL patient_A0020396

value: PD


title: DLBCL patient_A0020395


title: DLBCL patient_A0020373


title: Frozen-3


title: DLBCL patient_A0020386


title: Frozen-7


title: DLBCL patient_A0020393


title: DLBCL patient_A0020394


title: Frozen-11


title: Frozen-2


title: Frozen-1


title: DLBCL patient_A0020379


title: DLBCL patient_A0020595


title: DLBCL patient_A0020596


title: DLBCL patient_A0020397


title: DLBCL patient_A0020371


title: DLBCL patient_A0020382


title: DLBCL patient_A0020398


title: DLBCL patient_A0020389

source_name: T-CELL RICH LARGE B-CELL LYMPHOMA


title: DLBCL patient_A0020390


title: DLBCL patient_A0020374

value: PR


title: DLBCL patient_A0020597


title: DLBCL patient_A0020391


title: Male_Smoker_0.1Gy_rep4

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description:
MSm4_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded. Log2 transformed signal intensities were normalized to median array for all samples.

source_name: Peripheral blood, male, smoker, 0.1Gy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Qucik Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: After irradiation, blood samples were diluted 1:1 with RPMI 1640 medium (Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT), as previously described (Grace et al., Int J Radiat Biol 2002; 78:1011-21; PMID 12456288), and were incubated for 6 h  at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: The RNA was prepared using the PerfectPure RNA blood kit (PerfectPure, Gaithersburg, MD) following the manufacturer’s recommendations. This protocol differentially lyses red and white blood cells in whole blood to preferentially deplete globin mRNA. Remaining globin mRNA was further reduced using GLOBINclear (Ambion Inc., Austin, TX) specifically to remove both a- and b-globin. The RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood from smoker and non-smoker volunteers was drawn into 0.105 mol/l sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ). The blood was divided into 3-ml aliquots and exposed at a rate of 0.82 Gy/min to 0, 0.1, 0.5, 2 Gy gamma-rays using a Gammacell-40 137Cs irradiator (AECL, Ottawa, Ontario, Canada).

value: whole blood

tag: gender

value: male

value: 28 years

tag: smoking status

value: smoker

tag: radiation dose

tag: donor


title: Male_Smoker_2Gy_rep5

description:
MSm5_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

source_name: Peripheral blood, male, smoker, 2Gy

value: 59 years


title: Male_Smoker_2Gy_rep4

description:
MSm4_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Smoker_0.5Gy_rep2

description:
MSm2_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.

source_name: Peripheral blood, male, smoker, 0.5Gy

value: 31 years


title: Male_Smoker_2Gy_rep1

description:
MSm1_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 41 years


title: Male_Smoker_2Gy_rep6

description:
MSm6_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 64 years


title: Male_Smoker_0Gy_rep1

description:
MSm1_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

source_name: Peripheral blood, male, smoker, 0Gy


title: DLBCL patient_A0020376

value: CR


title: Male_Smoker_0.5Gy_rep4

description:
MSm4_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: DLBCL patient_A0020387


title: Male_Smoker_0.1Gy_rep6

description:
MSm6_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Smoker_0Gy_rep6

description:
MSm6_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Smoker_0Gy_rep3

description:
MSm3_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: 52 years


title: Male_Smoker_0.5Gy_rep6

description:
MSm6_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Smoker_0.1Gy_rep3

description:
MSm3_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Smoker_0.1Gy_rep5

description:
MSm5_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: DLBCL patient_A0020381


title: Male_Smoker_2Gy_rep3

description:
MSm3_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Smoker_0.1Gy_rep2

description:
MSm2_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Smoker_0.5Gy_rep1

description:
MSm1_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Smoker_0.5Gy_rep5

description:
MSm5_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Smoker_0Gy_rep4

description:
MSm4_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Smoker_2Gy_rep2

description:
MSm2_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Smoker_0Gy_rep5

description:
MSm5_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: DLBCL patient_A0020388


title: Male_Smoker_0.5Gy_rep3

description:
MSm3_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Non-smoker_2Gy_rep6

description:
MNs6_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

source_name: Peripheral blood, male, non-smoker, 2Gy

value: non-smoker


title: Male_Non-smoker_0Gy_rep6

description:
MNs6_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

source_name: Peripheral blood, male, non-smoker, 0Gy


title: Male_Smoker_0.1Gy_rep1

description:
MSm1_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Non-smoker_0.1Gy_rep6

description:
MNs6_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

source_name: Peripheral blood, male, non-smoker, 0.1Gy


title: Male_Non-smoker_2Gy_rep5

description:
MNs5_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 23 years


title: Male_Non-smoker_0.5Gy_rep6

description:
MNs6_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.

source_name: Peripheral blood, male, non-smoker, 0.5Gy


title: Male_Non-smoker_0.5Gy_rep3

description:
MNs3_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Non-smoker_0.1Gy_rep5

description:
MNs5_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Non-smoker_0Gy_rep2

description:
MNs2_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: 38 years


title: Male_Non-smoker_0Gy_rep3

description:
MNs3_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Non-smoker_0Gy_rep4

description:
MNs4_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Non-smoker_0.5Gy_rep4

description:
MNs4_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Non-smoker_0.1Gy_rep3

description:
MNs3_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Non-smoker_2Gy_rep2

description:
MNs2_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Non-smoker_0.5Gy_rep5

description:
MNs5_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Non-smoker_0Gy_rep5

description:
MNs5_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Non-smoker_0.1Gy_rep2

description:
MNs2_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Non-smoker_2Gy_rep4

description:
MNs4_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Non-smoker_0.5Gy_rep2

description:
MNs2_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Male_Non-smoker_2Gy_rep1

description:
MNs1_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 29 years


title: Male_Non-smoker_2Gy_rep3

description:
MNs3_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Male_Non-smoker_0.1Gy_rep4

description:
MNs4_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Non-smoker_0Gy_rep1

description:
MNs1_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Smoker_0.1Gy_rep6

description:
FSm6_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

source_name: Peripheral blood, female, smoker, 0.1Gy

value: female

value: 54 years


title: Female_Smoker_0.5Gy_rep6

description:
FSm6_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.

source_name: Peripheral blood, female, smoker, 0.5Gy


title: Female_Smoker_2Gy_rep5

description:
FSm5_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

source_name: Peripheral blood, female, smoker, 2Gy


title: Male_Non-smoker_0.1Gy_rep1

description:
MNs1_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Smoker_0Gy_rep4

description:
FSm4_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

source_name: Peripheral blood, female, smoker, 0Gy

value: 55 years


title: Female_Smoker_0Gy_rep6

description:
FSm6_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: whole blood


title: Female_Smoker_0.1Gy_rep5

description:
FSm5_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Smoker_0Gy_rep5

description:
FSm5_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Smoker_0.5Gy_rep5

description:
FSm5_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Smoker_0.1Gy_rep4

description:
FSm4_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Male_Smoker_0Gy_rep2

description:
MSm2_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: male


title: Female_Smoker_2Gy_rep4

description:
FSm4_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Smoker_0.5Gy_rep4

description:
FSm4_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Smoker_2Gy_rep3

description:
FSm3_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 27 years


title: Female_Smoker_0.1Gy_rep3

description:
FSm3_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

value: smoker


title: Female_Smoker_0.1Gy_rep1

description:
FSm1_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

value: 32 years


title: Female_Smoker_0Gy_rep3

description:
FSm3_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Smoker_0.5Gy_rep2

description:
FSm2_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.

value: 35 years


title: Female_Smoker_0Gy_rep1

description:
FSm1_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Male_Non-smoker_0.5Gy_rep1

description:
MNs1_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Smoker_0.5Gy_rep1

description:
FSm1_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Smoker_0.1Gy_rep2

description:
FSm2_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Non-smoker_0Gy_rep6

description:
FNs6_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

source_name: Peripheral blood, female, non-smoker, 0Gy

value: 21 years


title: Female_Non-smoker_2Gy_rep6

description:
FNs6_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

source_name: Peripheral blood, female, non-smoker, 2Gy


title: Female_Smoker_2Gy_rep1

description:
FSm1_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Smoker_2Gy_rep2

description:
FSm2_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Non-smoker_0.5Gy_rep6

description:
FNs6_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.

source_name: Peripheral blood, female, non-smoker, 0.5Gy


title: Female_Non-smoker_2Gy_rep5

description:
FNs5_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 40 years


title: Female_Non-smoker_0.1Gy_rep6

description:
FNs6_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.

source_name: Peripheral blood, female, non-smoker, 0.1Gy


title: Female_Non-smoker_0.5Gy_rep5

description:
FNs5_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Smoker_0Gy_rep2

description:
FSm2_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Non-smoker_0Gy_rep5

description:
FNs5_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Non-smoker_0Gy_rep4

description:
FNs4_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: 39 years


title: Female_Non-smoker_0.5Gy_rep4

description:
FNs4_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Non-smoker_0.1Gy_rep5

description:
FNs5_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Non-smoker_2Gy_rep3

description:
FNs3_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.

value: 24 years


title: Female_Non-smoker_0Gy_rep3

description:
FNs3_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: non-smoker


title: Female_Non-smoker_0.1Gy_rep4

description:
FNs4_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Non-smoker_2Gy_rep4

description:
FNs4_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Non-smoker_0.5Gy_rep3

description:
FNs3_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Non-smoker_0.1Gy_rep3

description:
FNs3_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: genomic DNA  called "refrerence 103" Affymetrix

city: BRON

first: Joël

last: LACHUER

address: 16 avenue du Doyen Lépine

institute: INSERM

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0
CHP files were processed using Birdseed (v2.0) analysis algorithm with Affymetrix Genotyping Console software

extract_protocol: Genomic DNA were isolated from tissues with QIAamp DNA micro kit (Qiagen, Hilden, Germany), quantified with an UV spectrophotometer (NanoDrop, Wilmington, DE, USA) and quality verified on agarose gel.


title: Female_Non-smoker_0.5Gy_rep2

description:
FNs2_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Non-smoker_0.1Gy_rep1

description:
FNs1_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Non-smoker_0.5Gy_rep1

description:
FNs1_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: Female_Non-smoker_0.1Gy_rep2

description:
FNs2_0.1Gy
Gene expression after 6hr in 0.1Gy-irradiated human blood.


title: Female_Non-smoker_2Gy_rep2

description:
FNs2_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Non-smoker_2Gy_rep1

description:
FNs1_2Gy
Gene expression after 6hr in 2Gy-irradiated human blood.


title: Female_Non-smoker_0Gy_rep2

description:
FNs2_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.


title: Female_Smoker_0.5Gy_rep3

description:
FSm3_0.5Gy
Gene expression after 6hr in 0.5Gy-irradiated human blood.


title: non-invasive prolactin pituitary tumours 13

value: pituitary tumour

tag: tumor stage


title: Treatment_ day 11 CL_18 h post PGF2α treatment _biological rep2

city: BANGALORE

first: KUNAL

last: SHAH

state: KARNATAKA

address: C.V.RAMAN AVENUE, MALLESHWARAM

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science, Bangalore

description: Probe level measurements using robust multichip average (RMA) algorithm.

scan_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001) using Affymetrix Genearray scanner 3000 series

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).

organism: Bubalus bubalis

label_protocol: The isolated RNA was labeled and hybridized to Affymetrix GeneChip Bovine Genome Arrays following standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)

extract_protocol: Following retrieval of CL from the ovary, flash frozen in liquid nitrogen and stored at -70 °C for the purpose of RNA isolation. Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) according to manufacturer’s instructions.

treatment_protocol: In the experiments with buffalo cows, animals with history of normal estrous cyclicity were treated with Cloprostenol (a PGF2α analogue; 500µg i.m.) on day 11 of the estrous cycle to induce luteolysis and CL tissues were collected at 0 (control; n=4 amimals/time point), 3 (n=2 animals/time point), 6 and 18 (n=3 animals/time point) h post PGF2α administration.

value: Corpus luteum

tag: treatment

tag: tissue collection time

value: 18 h post PGF2α administration

tag: day of estrous cycle

value: Day 11


title: Treatment_ day 11 CL_18 h post PGF2α treatment _biological rep1

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)


title: non-invasive prolactin pituitary tumours 9


title: Treatment_ day 11 CL_3 h post PGF2α treatment _biological rep1

value: 3 h post PGF2α administration


title: Treatment_ day 11 CL_3 h post PGF2α treatment _biological rep3


title: Female_Non-smoker_0Gy_rep1

description:
FNs1_0Gy
Gene expression after 6hr in 0Gy-irradiated human blood.

value: female

tag: age


title: Treatment_ day 11 CL_6 h post PGF2α treatment _biological rep2

value: 6 h post PGF2α administration


title: Control_ day 11 CL_0 h _biological rep4

source_name: Control_ day 11 CL_0 h

value: 0 h (control)


title: Treatment_ day 11 CL_6 h post PGF2α treatment _biological rep1


title: invasive prolactin pituitary tumours 8

source_name: invasive prolactin pituitary tumours

value: invasive prolactin pituitary tumours


title: Treatment_ day 11 CL_6 h post PGF2α treatment _biological rep3


title: Treatment_ day 11 CL_18 h post PGF2α treatment _biological rep3


title: non-invasive prolactin pituitary tumours 11


title: Control_ day 11 CL_0 h _biological rep3


title: Control_ day 11 CL_0 h _biological rep1


title: Control_ day 11 CL_0 h _biological rep2


title: P. falciparum T30

city: Cambridge

first: Kate

middle: Mariel

last: Broadbent

address: FAS Center for Systems Biology Northwest Building, room 469 52 Oxford Street

department: Systems Biology

institute: Harvard University

description: P falciparum transcriptome mapping on DNA tiling arrays

hyb_protocol: Arrays were hybridized in a NimbleGen Hybridization System with constant mixing at 42C for 16 hours, per NimbleGen protocol.

scan_protocol: Arrays were washed per NimbleGen protocol and scanned using an Axon 4000B scanner and Genepix software.

data_processing: Probe signal intensities (obtained using NimbleScan software provided by Nimblegen) were quantile normalized, log2 transformed, and median centered.

molecule: polyA RNA

organism: Plasmodium falciparum 3D7

source_name: P falciparum RNA, 30 hpi

label_protocol: The resulting aRNA was labeled with Superscript II reverse transcriptase (Invitrogen), using random hexamers, and either Cy3- or Cy5-dUTPs (Amersham) for 2 hours at 42C following a 10 minute primer annealing step at 65C.

growth_protocol: standard Trager-Jensen method

extract_protocol: Trizol extraction of total RNA + RNeasy column (Qiagen). 1 μg of total RNA was subjected to poly-A selective amplification using Message Amp II (Ambion), substituting biased dNTP/NTP mixes (2A/T/U:1C/G).

tag: strain

tag: time

value: 30 hours post invasion of RBC


title: GQ-ODN pretreatment, THS, IL6 resuscitation, biological rep2

city: Houston

first: Stephen

middle: Andrew

last: Thacker

state: TX

address: One Baylor Plaza  BCM 286, Room N1319

department: Medicine, Section of Infectious Disease

institute: Baylor College of Medicine

description:
n
Gene expression data from rat liver homogenate following GQ-ODN pre-treatment followed by trauma plus hemorrhagic shock with resuscitation with IL6
hnl_DT_3993_RA_15079.CHP
hnl_DT_3993_RA_15079.CEL

hyb_protocol: A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Rat 230A GeneChip® array.  The array was hybridized for 16 hours at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain.

scan_protocol: Signal amplification was done using biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images are analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1.2.

data_processing: We used Affymetrics GCOS, dChip and Array Analyzer (Insightful Corporation) software packages for quality assessment and statistical analysis and annotation; default analysis settings and global scaling as normalization method. Expression estimation and group comparisons were done with Array Analyzer. Low-level analyses included background correction, quartile normalization and expression estimation using GCRMA.  NOTE: MAS5.0 signal presented in data table.

organism: Rattus norvegicus

source_name: Rat liver homogenate following GQ-ODN pre-treatment followed by trauma plus hemorrhagic shock with resuscitation with IL6

label_protocol: Samples were labeled using the One-Cycle Affymetrix linear amplification protocol for eukaryotic expression arrays.  All sample protocols for this project were started with 5ug total RNA. The total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was then quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.

growth_protocol: Rats cared for in the Baylor Animal Core and allowed to feed and drink ad libitum

extract_protocol: Total RNA was isolated from 4-5 micron cryotome sections of liver using TRIzol® Reagent (Invitrogen, Carlsbad, California) single step RNA isolation protocol followed by purification with RNeasy® Mini Kit (QIAGEN, Hilden, Germany) as instructed by the manufacturer.

treatment_protocol: Rats were subjected to the sham or T/HS protocols. Blood was withdrawn into a heparinized syringe episodically to maintain the target MAP at 35 mmHg until blood pressure compensation failed. Blood was then returned as needed to maintain the target MAP. The amount of shed blood returned (SBR) defined 5 different levels of shock severity reflected in the duration of hypotension: the rats here received 50% SBR (SBR50; duration of hypotension, 273 ± 24.9 minutes). At the end of the hypotensive period, rats were resuscitated and humanely sacrificed 60 minutes after the start of resuscitation in order to capture the first wave of transcriptional change. Where indicated, rats received 10 μg/kg of recombinant human IL-6 in 0.1 ml PBS at the initiation of the resuscitation or PBS alone. Sham rats were anesthetized and cannulated for 250 minutes but were not subjected to hemorrhage or resuscitation.  A subset of rats were randomized to receive by tail vein injection a G-rich, quartet-forming oligodeoxynucleotide (GQ-ODN) T40214 (2.5 mg ODN/kg) complexed in polyethyleneimine, 24 hours prior to subjecting them to the SBR50 protocol with IL-6 treatment. The half-life of T40214 in tissues is ≥ 48 hr.

value: Sprague-Dawley

value: homogenized liver

tag: genotype/variation

value: wild type

value: 8 weeks (adult)

tag: protocol

value: GQ-ODN pre-treatment followed by T/HS with resuscitation with IL6


title: agressive-invasive prolactin pituitary tumours 6

tag: tissue


title: non-invasive prolactin pituitary tumours 10


title: normal pituitary

source_name: normal pituitary

value: normal pituitary


title: Pf_3D7

city: Rockville

first: Hongying

last: Jiang

state: MD

address: 12735 Twinbrook Parkway

institute: NIAID/NIH

hyb_protocol: Affymetrix's EukGE-WS2v5, i.e. all samples were hybridized for 16 hours at 45°C at 60rpm.

scan_protocol: Chips were scanned at 570 nm emission wavelength using Affymetrix scanner 3000.

data_processing:
The scanned image CEL files were processed using the RMA method, averaged for each sample, compared with the reference genome 3D7, and lastly assigned either 7G8 or GB4 alleles based on similarities to the two parent lines. Only P. falciparum-specific probes were used for this study.

The RMA-normalized data for this sample is included in the supplementary .txt file that is linked to this Sample record. The parental allele-assigned genotype calls are included in the supplementary files that are linked to the Series GSE25656 record.

organism: Plasmodium falciparum

source_name: 3D7 genomic DNA

label_protocol: Ten microgram of genomic DNA was fragmented and end-labeled using Affymetrix's GeneChip Mapping 250K Nsp Assay Kit without the PCR amplification step.

growth_protocol: P. falciparum parasites were maintained in RPMI 1640 medium containing 5% human O+ erythrocytes (5% hematocrit), 0.5% Albumax (GIBCO, Life Technologies, Grand Island, NY, USA), 24 mM sodium bicarbonate, and 10 µg/ml gentamicin at 37C under an atmosphere 5% CO2, 5% O2, and 90% N2.

extract_protocol: Genomic DNA was extracted from parasites in in vitro culture using the phenol:chloroform method.

tag: isolate

tag: sample type

value: reference


title: agressive-invasive prolactin pituitary tumours 2

value: pituitary tumour


title: P. falciparum T24

source_name: P falciparum RNA, 24 hpi

value: 24 hours post invasion of RBC


title: GQ-ODN pretreatment, THS, IL6 resuscitation, biological rep3

description:
o
Gene expression data from rat liver homogenate following GQ-ODN pre-treatment followed by trauma plus hemorrhagic shock with resuscitation with IL6
hnl_DT_3993_RA_15080.CHP
hnl_DT_3993_RA_15080.CEL


title: Pf_XF12

source_name: XF12 genomic DNA

value: 7G8 × GB4

value: progeny


title: THS, PBS resuscitation, biological rep3

description:
J
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with PBS during resuscitation
hnl_DT_3993_RA_15075.CHP
hnl_DT_3993_RA_15075.CEL

source_name: Rat liver homogenate following trauma plus hemorrhagic shock with resuscitation with PBS

value: T/HS with resuscitation with PBS


title: THS, IL6 resuscitation, biological rep2

description:
l
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with IL6 during resuscitation
hnl_DT_3993_RA_15077.CHP
hnl_DT_3993_RA_15077.CEL

source_name: Rat liver homogenate following trauma plus hemorrhagic shock with resuscitation with IL6

value: T/HS with resuscitation with IL6


title: P. falciparum T18

source_name: P falciparum RNA, 18 hpi

value: 18 hours post invasion of RBC


title: P. falciparum T36

source_name: P falciparum RNA, 36 hpi

value: 36 hours post invasion of RBC


title: GQ-ODN pretreatment, THS, IL6 resuscitation, biological rep1

description:
m
Gene expression data from rat liver homogenate following GQ-ODN pre-treatment followed by trauma plus hemorrhagic shock with resuscitation with IL6
hnl_DT_3993_RA_15078.CHP
hnl_DT_3993_RA_15078.CEL


title: non-invasive prolactin pituitary tumours 12


title: THS, PBS resuscitation, biological rep1

description:
F
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with PBS during resuscitation
hnl_DT_3993_RA_15071.CHP
hnl_DT_3993_RA_15071.CEL


title: Pf_XG10

source_name: XG10 genomic DNA


title: agressive-invasive prolactin pituitary tumours 4


title: Pf_XE8

source_name: XE8 genomic DNA


title: Sham, biological rep4

description:
Sham4
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure
hnl_DT_3993_RA_14646.CHP
hnl_DT_3993_RA_14646.CEL

source_name: Rat liver homogenate following sham shock procedure

value: sham shock


title: Pf_XE7

source_name: XE7 genomic DNA


title: agressive-invasive prolactin pituitary tumours 3


title: THS, IL6 resuscitation, biological rep1

description:
I
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with IL6 during resuscitation
hnl_DT_3993_RA_15074.CHP
hnl_DT_3993_RA_15074.CEL


title: agressive-invasive prolactin pituitary tumours 1


title: Pf_WF12

source_name: WF12 genomic DNA


title: Pf_XD8

source_name: XD8 genomic DNA


title: Pf_XB3

source_name: XB3 genomic DNA


title: invasive prolactin pituitary tumours 7

source_name: invasive prolactin pituitary tumours

value: invasive prolactin pituitary tumours


title: THS, IL6 resuscitation, biological rep4

description:
p
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with IL6 during resuscitation
hnl_DT_3993_RA_15081.CHP
hnl_DT_3993_RA_15081.CEL

value: Sprague-Dawley


title: THS, PBS resuscitation, biological rep4

description:
K
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with PBS during resuscitation
hnl_DT_3993_RA_15076.CHP
hnl_DT_3993_RA_15076.CEL

value: homogenized liver


title: THS, IL6 resuscitation, biological rep3

description:
E
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with IL6 during resuscitation
hnl_DT_3993_RA_15070.CHP
hnl_DT_3993_RA_15070.CEL

value: wild type


title: SEY6210 strain, biological rep2

city: Heidelberg

first: Sabine

last: Strahl

address: Im Neuenheimer Feld 360

department: Heidelberg Institute for Plant Sciences

institute: University of Heidelberg

description: Gene expression data from SEY6211

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning on a GeneChip Scanner 3000 controlled by the GCOS software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Saccharomyces cerevisiae

source_name: SEY6210 yeast strain

label_protocol: Biotinylated cRNA were prepared with the One-cycle cDNA sinthesis kit, according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Growing on YPD medim supplemented with adenine to an OD600=1

extract_protocol: Phenol extraction according to Schmitt et al. (1990. NAR 18: 3091-92).


title: Sham, biological rep2

description:
Sham2
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure
hnl_DT_3993_RA_14644.CHP
hnl_DT_3993_RA_14644.CEL

value: 8 weeks (adult)


title: Pf_WE2

source_name: WE2 genomic DNA


title: Pf_WC4

source_name: WC4 genomic DNA


title: MEY12A (CCW12 mutant), biological rep2

description: Gene expression data from CCW12 yeast mutant

source_name: CCW12 yeast mutant based on SEY6219 strain

value: CCW12 mutant


title: Sham, biological rep1

description:
Sham1
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure
hnl_DT_3993_RA_14643.CHP
hnl_DT_3993_RA_14643.CEL


title: SEY6210 strain, biological rep1

description: Gene expression data from SEY6210 yeast strain


title: MEY12A (CCW12 mutant), biological rep1


title: Pf_TF1

source_name: TF1 genomic DNA


title: Pf_QF5

source_name: QF5 genomic DNA


title: Pf_NIC

source_name: NIC genomic DNA


title: HL-1 cardiomyocyte hypox2

city: Gothenburg

first: Jeanna

middle: C

last: Perman

address: Bruna Stråket 16

country: Sweden

institute: Wallenberg Laboratory for cardiovascular research

description: HL-1 cardiomyocyte hypox2

hyb_protocol: Following fragmentation,15 ug of biotinylated cRNA were hybridized for 16 hr at 45C MOE430A microarrays according to the standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol (G2500A GeneArray scanner)  Standrd Affymetrix protocol, (

data_processing: MAS 5, signal algorithm, global scaling (target intensity 100)

source_name: HL-1 cardiomyocyte

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

growth_protocol: HL-1 cells were grown according to standard protocol, as described in Claycomb WC et. al. Proc Natl Acad Sci U S A 95: 2979-2984, 1998.

extract_protocol: QIAGEN Rneasy Mini Kit, extraction according to protocol

treatment_protocol: Confluent cells were incubated in hypoxia (1% O2) or normoxia (21% O2) for 8 hours before harvest.

tag: cell line

tag: culture

value: Hypoxia (1% O2)


title: HL-1 cardiomyocyte normox2

description: HL-1 cardiomyocyte normox2

value: Normoxia (21% O2)


title: HL-1 cardiomyocyte normox1

description: HL-1 cardiomyocyte normox1


title: HL-1 cardiomyocyte normox3

description: HL-1 cardiomyocyte normox3


title: HL-1 cardiomyocyte hypox1

description: HL-1 cardiomyocyte hypox1


title: Pf_LC12

source_name: LC12 genomic DNA


title: agressive-invasive prolactin pituitary tumours 5

value: pituitary tumour


title: HL-1 cardiomyocyte hypox3

description: HL-1 cardiomyocyte hypox3


title: Pf_LA10

source_name: LA10 genomic DNA


title: Pf_KC5

source_name: KC5 genomic DNA


title: Pf_KH7

source_name: KH7 genomic DNA


title: Pf_NF10

source_name: NF10 genomic DNA


title: Pf_KC2

source_name: KC2 genomic DNA


title: Pf_KB8

source_name: KB8 genomic DNA


title: Sham, biological rep3

description:
Sham3
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure
hnl_DT_3993_RA_14645.CHP
hnl_DT_3993_RA_14645.CEL

source_name: Rat liver homogenate following sham shock procedure


title: Lung EC, experimental, rep2

city: Boston

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

description: Gene expression data from lung endothelial cells isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Cel files were processed with dChip (http://biosun1.harvard.edu/complab/dchip/).

source_name: Lung endothelial cells isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

label_protocol: 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

extract_protocol: RNA was isolated using Trizol (Invitrogen) and the RNeasy mini kit (Qiagen).

tag: cell type

value: Lung endothelial cells

tag: genotype

value: MxCre+ Fk1 L/L Fk2 L/L Afx L/L

tag: genetic background

value: FVBn


title: Liver sinusoidal EC, experimental, rep2

description: Gene expression data from liver sinusoidal endothelial cells isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

source_name: Liver sinusoidal endothelial cells isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

value: Liver Sinusoidal Endothelial Cells


title: Liver sinusoidal EC, control, rep3

description: Gene expression data from liver sinusoidal endothelial cells isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse

source_name: Liver sinusoidal endothelial cells isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse

value: MxCre- Fk1 L/L Fk2 L/L Afx L/L


title: Pf_JF6

source_name: JF6 genomic DNA

value: 7G8 × GB4

value: progeny


title: Pf_JH6

source_name: JH6 genomic DNA


title: Liver sinusoidal EC, control, rep1


title: Thymus, experimental, rep2

description: Gene expression data from thymus isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

source_name: Thymus isolated from MxCre+ Fk1 L/L Fk2 L/L Afx L/L mouse

value: Thymus


title: Liver sinusoidal EC, control, rep2


title: Thymus, experimental, rep1


title: Liver sinusoidal EC, experimental, rep3


title: Lung EC, control, rep2

description: Gene expression data from lung endothelial cells isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse

source_name: Lung endothelial cells isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse


title: Thymus, control, rep1

description: Gene expression data from thymus isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse

source_name: Thymus isolated from MxCre- Fk1 L/L Fk2 L/L Afx L/L mouse


title: Liver sinusoidal EC, experimental, rep1


title: Thymus, control, rep2


title: Pf_JC9

source_name: JC9 genomic DNA


title: Pf_JC3

source_name: JC3 genomic DNA


title: Lung EC, control, rep1


title: Lung EC, experimental, rep1


title: Pf_JON

source_name: JON genomic DNA


title: Pf_KA6

source_name: KA6 genomic DNA


title: Pf_JE11

source_name: JE11 genomic DNA


title: Pf_JB12

source_name: JB12 genomic DNA


title: Pf_DEV

source_name: DEV genomic DNA


title: Mtb-Infected  + CC3052 12w rep2

city: Newark

first: Selvakumar

last: Subbian

address: 225 Warren Street

department: Medicine

institute: Public Health Research Institute at UMDNJ

description:
CC-treated-12w-2
ch1: Mtb HN878-infected; 12 wks post infection-2
ch2: Mtb HN878-infected+CC3052; 12 wks post infection-2
Biological replicate

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing: Data from the scanned images were extracted using the software from Agilent.  The normalised data was processed through PARTEK Genomics Suite for further analysis

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

growth_protocol: New Zealand White rabbits were infected with Mtb HN878 at 3.2log10 (on day 0). At 4 weeks post infection, one group of infected rabbits were treated with a phosphodiesterase-4 (PDE4) inhibitor, CC-3052.  Lung tissue from Uninfected, Untreated and CC-3052 treated rabbits were isolated at Day0, 4,8 and 12 weeks post infection and used for total RNA isolation.

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: CC-3052, a PDE4 inhibitor was used to treat one group of Mtb infected rabbits. The compound was used at 25mg/kg body weight, dissolved in distilled water and administered through gavage five days a weeks.  Treatment was started at 4 weeks post infection and continued up to 12 weeks post infection.

tag: infection

value: Mtb HN878-infected

value: 12 wks post infection

tag: agent


title: Mtb-Infected  + CC3052 12w rep1

description:
CC-treated-12w-1
ch1: Mtb HN878-infected; 12 wks post infection-1
ch2: Mtb HN878-infected+CC3052; 12 wks post infection-1
Biological replicate


title: Mtb-Infected  + CC3052 8w rep4

description:
CC-treated-8w-4
ch1: Mtb HN878-infected; 8 wks post infection-4
ch2: Mtb HN878-infected+CC3052; 8 wks post infection-4
Biological replicate

value: 8 wks post infection


title: Pf_AUD

source_name: AUD genomic DNA


title: Pf_AL2t175

source_name: AL2 genomic DNA


title: Mtb-Infected - 12w rep2

description:
Mtb infected-12w-2
ch1: Uninfected; 12 wks post infection-2
ch2: Mtb HN878-infected, 12 wks post infection-2
Biological replicate

value: Uninfected


title: Mtb-Infected  + CC3052 8w rep3

description:
CC-treated-8w-3
ch1: Mtb HN878-infected; 8 wks post infection-3
ch2: Mtb HN878-infected+CC3052; 8 wks post infection-3
Biological replicate


title: Pf_GB4

source_name: GB4 genomic DNA

value: parental line


title: Pf_JB8

source_name: JB8 genomic DNA


title: Pf_7G8

source_name: 7G8 genomic DNA


title: Pf_DAN

source_name: DAN genomic DNA


title: Mtb-Infected  + CC3052 8w rep2

description:
CC-treated-8w-2
ch1: Mtb HN878-infected; 8 wks post infection-2
ch2: Mtb HN878-infected+CC3052; 8 wks post infection-2
Biological replicate


title: Mtb-Infected - 12w rep1

description:
Mtb infected-12w-1
ch1: Uninfected; 12 wks post infection-1
ch2: Mtb HN878-infected, 12 wks post infection-1
Biological replicate


title: Mtb-Infected - 8w rep4

description:
Mtb infected-8w-4
ch1: Uninfected; 8 wks post infection-4
ch2: Mtb HN878-infected; 8 wks post infection-4
Biological replicate


title: RIII_striatum_totalRNA

status: Public on Mar 15 2011

city: Los Angeles

first: Christopher

last: Park

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

description: RI mouse strain from HMDP

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Data were processed using the Illumina BeadStudio software and rank-invariant normalized

source_name: whole striatum

label_protocol: Illumina TotalPrep RNA, biotin-16-UTP

extract_protocol: total RNA extracted from flash frozen tissue using Trizol (Invitrogen) and prepared using the Qiagen Rneasy kit per manufacturers instructions, Agilent Bioanalyser used for quality control

tag: gender

value: male

value: RIII

value: whole striatum


title: THS, PBS resuscitation, biological rep2

description:
G
Gene expression data from rat liver after sham trauam plus hemorrhagic shock procedure with PBS during resuscitation
hnl_DT_3993_RA_15072.CHP
hnl_DT_3993_RA_15072.CEL

source_name: Rat liver homogenate following trauma plus hemorrhagic shock with resuscitation with PBS

value: Sprague-Dawley

value: homogenized liver

value: wild type

value: 8 weeks (adult)

value: T/HS with resuscitation with PBS


title: NZW_striatum_totalRNA

description: RI mouse strain from HMDP

value: NZW


title: NON_striatum_totalRNA

description: RI mouse strain from HMDP

value: NON


title: Mtb-Infected - 8w rep3

description:
Mtb infected-8w-3
ch1: Uninfected; 8 wks post infection-3
ch2: Mtb HN878-infected; 8 wks post infection-3
Biological replicate


title: SM_striatum_totalRNA

description: RI mouse strain from HMDP

value: SM


title: NZB_striatum_totalRNA

description: RI mouse strain from HMDP

value: NZB


title: PL_striatum_totalRNA

description: RI mouse strain from HMDP

value: PL


title: Mtb-Infected  + CC3052 8w rep1

description:
CC-treated-8w-1
ch1: Mtb HN878-infected; 8 wks post infection-1
ch2: Mtb HN878-infected+CC3052; 8 wks post infection-1
Biological replicate

value: Mtb HN878-infected


title: NOD_striatum_totalRNA

description: RI mouse strain from HMDP

value: NOD


title: Mtb-Infected - 8w rep1

description:
Mtb infected-8w-1
ch1: Uninfected; 8 wks post infection-1
ch2: Mtb HN878-infected; 8 wks post infection-1
Biological replicate

value: Uninfected

value: 8 wks post infection


title: KK_striatum_totalRNA

description: RI mouse strain from HMDP

value: male

value: KK


title: LPJ_striatum_totalRNA

description: RI mouse strain from HMDP

value: LPJ

value: whole striatum


title: LG_striatum_totalRNA

description: RI mouse strain from HMDP

value: LG


title: DBA_striatum_totalRNA

description: RI mouse strain from HMDP

value: DBA


title: CE_striatum_totalRNA

description: RI mouse strain from HMDP

value: CE


title: C57L_striatum_totalRNA

description: RI mouse strain from HMDP


title: C58_striatum_totalRNA

description: RI mouse strain from HMDP


title: FVB_striatum_totalRNA

description: RI mouse strain from HMDP

value: FVB


title: SWR_striatum_totalRNA

description: RI mouse strain from HMDP

value: SWR


title: Mtb-Infected - 8w rep2

description:
Mtb infected-8w-2
ch1: Uninfected; 8 wks post infection-2
ch2: Mtb HN878-infected; 8 wks post infection-2
Biological replicate


title: CAST_striatum_totalRNA

description: RI mouse strain from HMDP

value: CAST


title: CBA_striatum_totalRNA

description: RI mouse strain from HMDP

value: CBA


title: MA_striatum_totalRNA

description: RI mouse strain from HMDP

value: MA


title: I_striatum_totalRNA

description: RI mouse strain from HMDP

value: I


title: BXH8_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH7_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH22_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH10_striatum_totalRNA

description: RI mouse strain from HMDP


title: C3H_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH20_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH9_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH6_striatum_totalRNA

description: RI mouse strain from HMDP


title: BalbcJ_striatum_totalRNA

description: RI mouse strain from HMDP

value: BalbcJ


title: BXD5/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH4_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD9/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH14_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXH19_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD6/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD8/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD32/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD40/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD27/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD38/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD28/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD42/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD36/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD33/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD34/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD29/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD24b/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD24a/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD21/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD2/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD19/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD20/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD15/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD39/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD1/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD12/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD18/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD11/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD13/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA8/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD31/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA4/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA7/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD14/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA26/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXD16/TyJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA24/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA2/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA25/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA16/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA14/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA11/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA13/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB23/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: B6Cc3_rep2_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB15/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB6/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA12/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB10/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB8/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BUB_striatum_totalRNA

description: RI mouse strain from HMDP

value: BUB


title: X129X1_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB13/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: B6Cc3_rep1_striatum_totalRNA

description: RI mouse strain from HMDP


title: BTBR_striatum_totalRNA

description: RI mouse strain from HMDP

value: BTBR


title: AXB1/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: B6_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB4/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB19a/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: BXA1/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB19/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB5/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB24/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AXB19b/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP


title: AJ_striatum_totalRNA

description: RI mouse strain from HMDP

value: AJ


title: Late EPC MIR3 notreated 2

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: labeled miRNA was hybridized onto Agilent's Human miRNA Microarrays V3, Release 12.0 (P/N G4471A, AMADID 021827) annotated against the Sanger miRBASE 12.0 database of miRNAs. according to the manufacturer's instructions.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner

data_processing: The scanned images were analyzed with GenePix Pro 6.0 analysis software using default parameters to obtain background subtracted signal intensities. The features flagged Not Found by GenePix as well as with a SNR (Signal to Noise Ratio) less than 3 were removed from the data. The data was normalized with quantile method using R Limma package.

source_name: Late EPC MIR3 DMSO 6h

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

extract_protocol: mirVana Ambion

value: EPC Late primary cells


title: Late EPC MIR3 notreated 1


title: AXB12/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP

value: male


title: AKR_striatum_totalRNA

description: RI mouse strain from HMDP

value: AKR


title: Late EPC MIR2 notreated 4

source_name: Late EPC MIR2 DMSO 6h


title: Late EPC MIR3 notreated 3


title: AXB2/PgnJ_striatum_totalRNA

description: RI mouse strain from HMDP

value: whole striatum


title: Late EPC MIR2 notreated 3


title: Late EPC MIR2 adenosine treated 4

source_name: Late EPC MIR2 adenosine 6h


title: Late EPC MIR2 notreated 2


title: Late EPC MIR2 notreated 1


title: Late EPC MIR2 adenosine treated 3


title: Late EPC MIR3 adenosine treated 2

source_name: Late EPC MIR3 adenosine 6h


title: Late EPC MIR3 adenosine treated 3


title: Late EPC MIR3 adenosine treated 1


title: SWR_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus

extract_protocol: total RNA extracted using Trizol (Invitrogen) and prepared using the Qiagen Rneasy kit per manufacturers instructions, Agilent Bioanalyser used for quality control

value: whole hippocampus


title: Late EPC MIR1 notreated 2

source_name: Late EPC MIR1 DMSO 6h


title: PL_hippo_totalRNA

description: RI mouse strain from HMDP

value: PL


title: NOD_hippo_totalRNA

description: RI mouse strain from HMDP

value: NOD


title: SM_hippo_totalRNA

description: RI mouse strain from HMDP

value: SM


title: RIII_hippo_totalRNA

description: RI mouse strain from HMDP

value: RIII


title: NZW_hippo_totalRNA

description: RI mouse strain from HMDP

value: NZW


title: NON_hippo_totalRNA

description: RI mouse strain from HMDP

value: NON


title: MA_hippo_totalRNA

description: RI mouse strain from HMDP

value: MA


title: LG_hippo_totalRNA

description: RI mouse strain from HMDP

value: LG


title: SEA_hippo_totalRNA

description: RI mouse strain from HMDP

value: SEA


title: KK_hippo_totalRNA

description: RI mouse strain from HMDP

value: KK


title: Late EPC MIR2 adenosine treated 2


title: Donor 4 - RV16+CSE

city: Calgary

first: David

last: Proud

state: AB

address: 3330 Hospital DRive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

description:
Gene Expression in response to RV16 in the presence of CSE
Sample 4D
EA09124_102527_H133+_4D.CHP
EA09124_102527_H133+_4D.CEL

hyb_protocol: Following framentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymetrix  U133 plus 2.0 human GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using Expression Console Software using Affymetrix default analysis settings.

source_name: Human bronchial epithelial cells - 24 h RV16+CSE

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip 3'IVT Express kit according to manufacturer's instructions.

growth_protocol: Cells were grown on 6 well plates in Bronchial Epithelial Growth Medium (Lonza).  Hydrocortisone was withdrawn from the medium for the last 24 h before stimulation. Stimulation and incubation were also performed in hydrocortisone-free medium.

extract_protocol: Trizol extractionof total RNA was performed according to manufacturer's instruction and DNase treated.

treatment_protocol: Cells were exposed to medium alone, purified human rhinovirus type 16 (MOI = 1), cigarette smoke extract derived from research grade cigarettes, or rhinvorius + cigarette smoke extract for 24h.

tag: donor

value: bronchi

value: epithelial cell

tag: growth

value: primary cultures

tag: stress


title: Late EPC MIR2 adenosine treated 1

value: EPC Late primary cells


title: Late EPC MIR1 notreated 4


title: Donor 4 - CSE

description:
Gene expression in response to CSE exposure
Sample 4C
EA09124_102526_H133+_4C.CHP
EA09124_102526_H133+_4C.CEL

source_name: Human bronchial epithelial cells - 24 h CSE

value: CSE


title: Late EPC MIR1 notreated 3


title: NZB_hippo_totalRNA

description: RI mouse strain from HMDP

value: male

tag: strain

value: NZB


title: DBA_hippo_totalRNA

description: RI mouse strain from HMDP

value: DBA

value: whole hippocampus


title: Late EPC MIR1 notreated 1


title: Donor 4 - medium

description:
Gene expression in response to medium
Sample 4A
EA09124_102524_H133+_4A.CHP
EA09124_102524_H133+_4A.CEL

source_name: Human bronchial epithelial cells - 24h medium

value: medium


title: Donor 4 - RV16

description:
Gene expression in response to RV16 infection
Sample 4B
EA09124_102525_H133+_4B.CHP
EA09124_102525_H133+_4B.CEL

source_name: Human bronchial epithelial cells - 24 h RV16


title: I_hippo_totalRNA

description: RI mouse strain from HMDP

value: I


title: FVB_hippo_totalRNA

description: RI mouse strain from HMDP

value: FVB


title: LPJ_hippo_totalRNA

description: RI mouse strain from HMDP

value: LPJ


title: Donor 3 - CSE

description:
Gene expression in response to CSE exposure
Sample 3C
EA09124_102522_H133+_3C.CHP
EA09124_102522_H133+_3C.CEL


title: CE_hippo_totalRNA

description: RI mouse strain from HMDP

value: CE


title: Donor 3 - medium

description:
Gene expression in response to medium
Sample 3A
EA09124_102520_H133+_3A.CHP
EA09124_102520_H133+_3A.CEL


title: Donor 2 - RV16+CSE

description:
Gene Expression in response to RV16 in the presence of CSE
Sample 2D
EA09124_102519_H133+_2D.CHP
EA09124_102519_H133+_2D.CEL


title: Late EPC MIR1 adenosine treated 3

source_name: Late EPC MIR1 adenosine 6h


title: Late EPC MIR1 adenosine treated 4


title: Donor 2 - RV16

description:
Gene expression in response to RV16 infection
Sample 2B
EA09124_102517_H133+_2B.CHP
EA09124_102517_H133+_2B.CEL


title: Donor 3 - RV16+CSE

description:
Gene Expression in response to RV16 in the presence of CSE
Sample 3D
EA09124_102523_H133+_3D.CHP
EA09124_102523_H133+_3D.CEL


title: Donor 2 - CSE

description:
Gene expression in response to CSE exposure
Sample 2C
EA09124_102518_H133+_2C.CHP
EA09124_102518_H133+_2C.CEL


title: Late EPC MIR1 adenosine treated 2


title: Donor 3 - RV16

description:
Gene expression in response to RV16 infection
Sample 3B
EA09124_102521_H133+_3B.CHP
EA09124_102521_H133+_3B.CEL


title: Donor 2 - medium

description:
Gene expression in response to medium
Sample 2A
EA09124_102516_H133+_2A.CHP
EA09124_102516_H133+_2A.CEL


title: Donor 1 - RV16+CSE

description:
Gene Expression in response to RV16 in the presence of CSE
Sample 1D
EA09124_102515_H133+_1D.CHP
EA09124_102515_H133+_1D.CEL


title: CBA_hippo_totalRNA

description: RI mouse strain from HMDP

value: CBA


title: C58_hippo_totalRNA

description: RI mouse strain from HMDP


title: CAST_hippo_totalRNA

description: RI mouse strain from HMDP

value: CAST


title: C57L_hippo_totalRNA

description: RI mouse strain from HMDP


title: Donor 1 - RV16

description:
Gene expression in response to RV16 infection
Sample 1B
EA09124_102513_H133+_1B.CHP
EA09124_102513_H133+_1B.CEL


title: Donor 1 - CSE

description:
Gene expression in response to CSE exposure
Sample 1C
EA09124_102514_H133+_1C.CHP
EA09124_102514_H133+_1C.CEL


title: Late EPC MIR1 adenosine treated 1


title: Early EPC 60 notreated 3

source_name: Early EPC 60 DMSO 6h

value: EPC Early primary cells


title: THP1 cells, treated with TNF-alpha 10ng/mL for 2hr, replicate 3 of 3

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

description: Gene expression data for THP1 cells treated with TNF-alpha.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GC-RMA normalization

label_protocol: Affymetrix protocol

growth_protocol: HeLa and THP-1 cells were obtained from ATCC and cultured under recommended conditions.

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

treatment_protocol: RNA were harvest before or after TNF-alpha treatment (10ng/mL) for 2hr


title: Early EPC 60 notreated 2


title: Donor 1 - medium

description:
Gene expression in response to medium
Sample 1A
EA09124_102512_H133+_1A.CHP
EA09124_102512_H133+_1A.CEL

value: bronchi


title: C3H_hippo_totalRNA

description: RI mouse strain from HMDP


title: THP1 cells, replicate 3 of 3

description: Gene expression data for untreated THP1 cells.

source_name: THP1 cells


title: THP1 cells, treated with TNF-alpha 10ng/mL for 2hr, replicate 1 of 3


title: THP1 cells, treated with TNF-alpha 10ng/mL for 2hr, replicate 2 of 3


title: THP1 cells, replicate 2 of 3

data_processing: GC-RMA normalization using GCRMA package (version 2.14.1) in R


title: THP1 cells, replicate 1 of 3


title: BXH9_hippo_totalRNA

description: RI mouse strain from HMDP


title: BalbcJ_hippo_totalRNA

description: RI mouse strain from HMDP

value: BalbcJ


title: Early EPC 60 adenosine treated 4

source_name: Early EPC 60 adenosine 6h


title: Early EPC 60 notreated 1


title: HeLa cells, replicate 2 of 2

description: Gene expression data for untreated HeLa cells.

source_name: HeLa cells

value: HeLa


title: HeLa cells, replicate 1 of 2


title: HeLa cells, treated with TNF-alpha 10ng/mL for 2hr, replicate 2 of 2

description: Gene expression data for HeLa cells treated with TNF-alpha.


title: BXH8_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 60 adenosine treated 2