title: PBL1035e

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45115.gif

source_name: PBLc1035e Cystinosis control

tag: PBLc1035e Cystinosis control


title: PBLc1032_22mo

status: Public on Dec 26 2012

type: RNA

city: Stanford

first: Minnie

last: Sarwal

state: CA

address: 703 Welch Road

department: Pediatric Nephrology

country: USA

institute: Stanford University

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45123.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: aRNA by SH on 3/27/03 from cell lines

label_protocol: not provided

extract_protocol: not provided

tag: aRNA by SH on 3/27/03 from cell lines

extract_protocol: lihua_extract preparation; RNA Isolation, Microarray Target Preparation and Hybridization: Total RNA extracted from peripheral blood was subject to microarray and Q-PCR experiments. Sample preparation for array hybridization was done following the manufactures recommended protocols, and hybridized on 75 GeneChip Human Genome U133 Plus2.0 arrays (Affymetrix Inc. Santa Clara, CA), 26 Agilent Human genome 44K arrays (Agilent, CA) and 21 cDNA arrays (Stanford, CA). Details of sample collection, RNA isolation, microarray target preparation and hybridization protocols are as followings: For total RNA extracted from whole blood, 2.5 ml of peripheral blood was collected in PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen) and processed using the PAXgene Blood RNA Kit (PreAnalytiX, Qiagen). For RNA extracted from leukocyte, 5 -10 ml whole blood was collected in sodium heparin tubes.  Leukocytes were recovered by initial separation of the white blood cells by centrifugation and  lysis of erythrocytes (ref. Lily method paper). RNA was extracted using RNeasy Midi Kit (Qiagen Inc, Valencia, CA). RNA concentration was measured using NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) and the integrity of RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chips (Agilent Technologies, Santa Clara, CA). RNA was stored in -80 oC until further use for microarray and qPCR. Sample preparation for array hybridization was done using the T7 protocol (T7), which employs one-cycle cRNA synthesis by using T7-Oligo (dT) Primer. A total of 2 microg total RNA was used for the synthesis of cRNA as the final product following manufacturer's Technical manual, Affymetrix). cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc. Santa Clara, CA).; Protocol Type = Extract preparation; Performer: Minnie,,Sarwal

tag: Disease State

tag: LIhua_samples; Patients and Samples

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample; Performer:Minnie,,Sarwal


title: STA_STA14_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82417.gif

scan_protocol: Affymetrix protocol

data_processing: dChip

label: biotin

source_name: PB from kidney transplant recipients

tag: Kidney, Peripheral Blood

tag: disease state


title: STA_STA07_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82449.gif

tag: Kidney, Peripheral Blood leukocyte


title: WRKY45kd#3-BTH(24hr)-1

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and software G2565BA using default parameters

data_processing: The scanned images were analyzed with Feature Extraction software (version 9.1; Agilent Technologies)  using default parameters.

organism: Oryza sativa

source_name: leaves

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies)

growth_protocol: Rice plants were grown on soil from seeds.

extract_protocol: Total RNA was isolated using an RNeasy plant mini kit (Qiagen).

treatment_protocol: seedlings at the four-leaf stage were sprayed with 0.5 mM BTH in 0.5% acetone / 0.05% Tween20 (BTH) or the solvent only (mock)  for 24 h

tag: developmental stage

value: 4th leaves at 4-leaf stage

tag: cultivar

value: Nipponbare

tag: tissue

value: leaf

tag: protocol

value: WRKY45kd#3 knockdown

tag: treatment

value: BTH

tag: time


title: WRKY45kd#3-BTH(24hr)-2


title: Control 3

city: New Delhi

first: Anil

last: Grover

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
Cont3
Control replicate 3
Agilent Feature Extraction file
US83000164_251524111358_S01_GE1_105_Dec08_1_3.txt

hyb_protocol: Hybridization and wash processes were performed according to the manufacturer’s instructions.

scan_protocol: Hybridized microarrays were scanned using agilent microarray scanner (g2505b, agilent technologies, usa) at 5µ resolution.

data_processing: Feature extraction software (version 10.5.1.1 Agilent Technologies, USA) was employed for the image analysis and data extraction process. The normalization was done using GeneSpring GX 10.2 (Agilent Technologies, USA) using the recommended Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile Per Gene: Normalize to Specific Samples (Treated Vs Control). Data analysis was done using GeneSpring GX version 7.3.1 (Agilent Technologies, USA) and Microsoft Excel. In total three biological replicates were processed in a similar manner for the microarray analysis.  Genes showing differential expression (up or down) by 2 fold or more (log2 values) with a p- value less than or equal to 0.05 were considered statistically significant.

organism: Oryza sativa Indica Group

source_name: Control 3

label_protocol: Total RNA (200ng) was labeled with Cy3 using Agilent Low RNA Input fluorescent Linear Amplification Kit (Agilent Technologies). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: Seedlings were grown at 28+2oC and 14 h light/ 10 h dark cycle maintained in growth room (light intensity ~250µmol.m-2.s-2, humidity 40-50%) for 10 d.

extract_protocol: Total RNA was isolated from ~100 mg tissue using Tri- Reagent (Sigma, USA) as per the manufacturer’s instructions, and further purified using RNAesy Mini Elute Kit (Qiagen).

treatment_protocol: For oxidative Stress prior to High Temperature Stress (PO_HS) or Low Temperature Stress (PO_CS) uniformly grown seedlings (10 day old) were transferred to beakers, which contain 10mM H2O2 at 28+2oC for oxidative stress (OS) for 4 h and followed by heat stress (HS) 42+1oC for 30 minutes/ cold stress (HS) 5+1oC for 5 h in the growth chamber with lights on. Similarly for oxidative Stress during High Temperature Stress (DO_HS)/ during Low temperature stress (DO_CS) uniformly grown seedlings (10 day old) were transferred to beakers, which contain 10mM H2O2 maintained at 42+1oC for heat stress (HS) for 30 minutes/5+1oC for cold stress (CS) in the BOD with lights on. All Samples were harvested, frozen in liquid nitrogen and kept at -80°C immediately after stress treatment.

value: Pusa Basmati (PB1)

tag: age

value: 10-days old

value: whole seedling

tag: oxidative stress

value: control

tag: temperature stress


title: NB-#3BTH(24hr)-4


title: PBLc1020_2yr

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45122.gif


title: PBL1038e

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45114.gif

source_name: PBLc1038e Cystinosis control

tag: PBLc1038e Cystinosis control


title: Control 2

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
Cont2
Control replicate 2
Agilent Feature Extraction file
US83000164_251524111358_S01_GE1_105_Dec08_1_2.txt

source_name: Control 2


title: PBLc485_7yr

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45125.gif


title: PBL1022d2_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38755.gif

scan_protocol: GenePix Results 1.3

source_name: aRNA pool 20cell lines from PB lab labeled 030103

source_name: originally submitted as PBL1020d_AR but this is the wrong Pt. ID#


title: PBL1057d

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45116.gif

source_name: PBLc1057d Cystinosis control

tag: PBLc1057d Cystinosis control


title: NB-#3BTH(24hr)-3


title: Control 1

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
Cont1
Control replicate 1
Agilent Feature Extraction file
US83000164_251524111358_S01_GE1_105_Dec08_1_1.txt

source_name: Control 1


title: Oxidative stress during cold stress 3

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_CS3
Oxidative stress during cold stress replicate 3
Agilent Feature Extraction file
US83000164_251524112328_S01_GE1_105_Dec08_1_1.txt

source_name: Oxidative stress during cold stress 3

value: concurrent oxidative stress

value: cold stress


title: PBLc1064

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45119.gif

tag: aRNA by SH on 3/27/03 from cell lines


title: PBLc486_D0

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45126.gif

tag: Disease State


title: NB-#3BTH(24hr)-1


title: NB-#3BTH(24hr)-2


title: WRKY45kd#3-Mock(24hr)-4

value: Mock


title: PBL1053_8mo

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45117.gif

source_name: PBLc1053_8mo Cystinosis control

tag: PBLc1053_8mo Cystinosis control

tag: LIhua_samples; Patients and Samples


title: Oxidative stress during cold stress 1

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_CS1
Oxidative stress during cold stress replicate 1
Agilent Feature Extraction file
US83000164_251524111359_S01_GE1_105_Dec08_1_3.txt

source_name: Oxidative stress during cold stress 1


title: Oxidative stress during cold stress 2

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_CS2
Oxidative stress during cold stress replicate 2
Agilent Feature Extraction file
US83000164_251524111359_S01_GE1_105_Dec08_1_4.txt

source_name: Oxidative stress during cold stress 2


title: WRKY45kd#3-Mock(24hr)-3


title: WRKY45kd#3-Mock(24hr)-2


title: Oxidative stress during heat stress 3

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_HS3
Oxidative stress during heat stress replicate 3
Agilent Feature Extraction file
US83000164_251524112329_S01_GE1_105_Dec08_1_3.txt

source_name: Oxidative stress during heat stress 3

value: heat stress


title: bAgilent PBL93_stable

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59918.gif

scan_protocol: Agilent G2505A

data_processing: Agilent Feature Extraction software

source_name: hum ref CRH

tag: hum ref CRH

source_name: Agilent PBL93_stable

label_protocol: RNA was stored in -80 oC until further use for microarray and qPCR. Sample preparation for array hybridization was done using the T7 protocol (T7), which employs one-cycle cRNA synthesis by using T7-Oligo (dT) Primer. A total of 2 microg total RNA was used for the synthesis of cRNA as the final product following manufacturer's Technical manual, Affymetrix). cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc. Santa Clara, CA).; Protocol Type = Extract preparation;

tag: Agilent PBL93_stable

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample


title: DSBs_rec10d_1

type: genomic

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

description: Rec12-FLAG IP.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Dark spot and control probes were removed. Output ratios were then normalized to the genome median.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: IP DSBs (Rec12 covalently linked to DNA) in rec10Δ

label_protocol: Immunoprecipitated material was PCR amplified to increase signal and incorporate Cy3/Cy5-labeled dUTPs.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize the cells. Nitrogen was added and the temperature shifted to 34°C, marking the start of meiosis (t=0).

extract_protocol: For DSB analysis, no exogenous crosslinking agent was used and cells were broken with a bead beater. Chromatin was sonicated to ~500-1000 bp and Rec12-FLAG was immunoprecipitated.

tag: strain/background

tag: genotype/variation

value: rec10Δ mutation

tag: time since meiosis started

value: 5 hours

tag: chip antibody

value: monoclonal anti-FLAG M2 mouse antibody

tag: antibody vendor (catalog #)

value: Sigma (F3165)

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in rec10Δ

tag: time since meoisis started


title: Agilent PBL280_stable

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59916.gif

source_name: Agilent PBL280_stable

tag: Agilent PBL280_stable


title: WRKY45kd#3-Mock(24hr)-1

source_name: leaves

tag: developmental stage

value: 4th leaves at 4-leaf stage

tag: cultivar

value: Nipponbare

tag: tissue

tag: protocol

tag: treatment

tag: time


title: DSBs_rec8d_1

description:
Rec12-FLAG IP.
Replicate 1 of 2.

source_name: IP DSBs (Rec12 covalently linked to DNA) in rec8Δ

value: rec8Δ mutation

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in rec8Δ


title: DSBs_rec8d_2

description:
Rec12-FLAG IP.
Replicate 2 of 2.


title: Oxidative stress during heat stress 2

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_HS2
Oxidative stress during heat stress replicate 2
Agilent Feature Extraction file
US83000164_251524112329_S01_GE1_105_Dec08_1_2.txt

source_name: Oxidative stress during heat stress 2

tag: age

tag: oxidative stress

tag: temperature stress


title: Agilent PBL1055_14mo_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63773.gif

tag: hum ref CRH

source_name: Agilent PBL1055_14mo_AR

tag: Agilent PBL1055_14mo_AR

tag: LIhua_samples; Patients and Samples

tag: Disease State


title: Agilent PBL62_3y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63765.gif

source_name: Agilent PBL62_3y_AR

tag: Agilent PBL62_3y_AR


title: Agilent PBL217_20mo_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63766.gif

source_name: Agilent PBL217_20mo_AR

tag: Agilent PBL217_20mo_AR


title: Partially ligated left carotid artery Replicate 6

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description: Biological replicate 6 of 6. Atherosclerotic left carotid artery, partially ligated.

data_processing: Taqman low density arrays were run on the 7900 HT Sequence Detection system.  The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.  Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].  Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA135 and snoRNA202 for Card A and B) according to the Genorm algorithm.

organism: Mus musculus

source_name: Mouse

growth_protocol: 6 weeks on high fat diet (21% crude fat, 0.15% cholesterol and 19.5% casein)

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

treatment_protocol: Partial Ligation: the left external carotid, the internal carotid and the occipital artery were ligated allowing blood flow only via the superior thyroid artery.

tag: strain

value: apoE-/-

value: 6-8 weeks

tag: Sex

value: Female

value: Left carotid artery


title: NB-#3Mock(24hr)-4

tag: developmental stage

value: leaf

value: control


title: DSBs_rec27d_1

description: Rec12-FLAG IP.

source_name: IP DSBs (Rec12 covalently linked to DNA) in rec27Δ

tag: strain/background

tag: genotype/variation

value: rec27Δ mutation

tag: time since meiosis started

tag: chip antibody

tag: antibody vendor (catalog #)

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in rec27Δ

tag: time since meoisis started


title: DSBs_WT_1

description: Rec12-FLAG IP.

source_name: IP DSBs (Rec12 covalently linked to DNA) in WT

value: WT

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in WT


title: NB-#3Mock(24hr)-2

tag: cultivar

tag: tissue

tag: protocol

tag: treatment

value: Mock

tag: time


title: Oxidative stress during heat stress 1

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_HS1
Oxidative stress during heat stress replicate 1
Agilent Feature Extraction file
US83000164_251524112329_S01_GE1_105_Dec08_1_1.txt

source_name: Oxidative stress during heat stress 1

value: Pusa Basmati (PB1)

tag: age

value: 10-days old

value: whole seedling

tag: oxidative stress

value: concurrent oxidative stress

tag: temperature stress

value: heat stress


title: Prior oxidative stress to cold stress 2

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_CS2
Prior oxidative stress to cold stress replicate 2
Agilent Feature Extraction file
US83000164_251524111359_S01_GE1_105_Dec08_1_1.txt

source_name: Prior oxidative stress to cold stress 2

value: prior oxidative stress

value: cold stress


title: Prior oxidative stress to cold stress 3

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_CS3
Prior oxidative stress to cold stress replicate 3
Agilent Feature Extraction file
US83000164_251524111359_S01_GE1_105_Dec08_1_2.txt

source_name: Prior oxidative stress to cold stress 3


title: Agilent PBL1022d_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59786.gif

source_name: hum ref CRH

tag: hum ref CRH

tag: LIhua_samples; Patients and Samples

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample

tag: Disease State


title: Partially ligated left carotid artery Replicate 5

description: Biological replicate 5 of 6. Atherosclerotic left carotid artery, partially ligated.

tag: strain

value: apoE-/-

tag: Sex


title: Agilent PBL1065_9mo_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63771.gif

source_name: Agilent PBL1065_9mo_AR

tag: Agilent PBL1065_9mo_AR


title: Prior oxidative stress to cold stress 1

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_CS1
Prior oxidative stress to cold stress replicate 1
Agilent Feature Extraction file
US83000164_251524111358_S01_GE1_105_Dec08_1_4.txt

source_name: Prior oxidative stress to cold stress 1


title: Agilent PBL1051_1.5y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63770.gif

source_name: Agilent PBL1051_1.5y_AR

tag: Agilent PBL1051_1.5y_AR


title: Agilent PBL269_5.7y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63768.gif

source_name: Agilent PBL269_5.7y_AR

tag: Agilent PBL269_5.7y_AR


title: Agilent PBL269b_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60006.gif

source_name: Agilent PBL269b_AR

tag: Agilent PBL269b_AR


title: NB-#3Mock(24hr)-1

source_name: leaves

tag: developmental stage

value: 4th leaves at 4-leaf stage

tag: cultivar

value: Nipponbare


title: Partially ligated left carotid artery Replicate 4

description: Biological replicate 4 of 6. Atherosclerotic left carotid artery, partially ligated.

value: 6-8 weeks

value: Female

tag: tissue

value: Left carotid artery


title: Agilent PBL295_11.7y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63767.gif

source_name: Agilent PBL295_11.7y_AR

tag: Agilent PBL295_11.7y_AR


title: M1-type bone marrow-derived macrophage, replicate 5

description: Biological replicate 5 of 5. M1-type macrophage cells.

data_processing: Taqman low-density arrays were run on the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software. Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php]. Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA202, snoRNA135, snoRNA429 and MammU6 for Card A and B) according to the Genorm algorithm. Because of the problems of the RT and preamplification primers of miR-10a, -100, -146b and -99a, their data from custom miRNA Taqman miRNA assays were used instead of the corresponding data from the arrays.

label: FAM

source_name: Mouse bone marrow cells, stimulated

label_protocol: Samples were labeled with FAM.

growth_protocol: Mouse bone marrow-derived macrophages were cultured in DMEM-F12/10% FCS/10% L929-conditioned medium at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: mirVana miRNA Isolation Kit (see http://www.ambion.com/catalog/CatNum.php?1560).

treatment_protocol: Macrophages were stimulated with LPS (100ng/ml, 14 hours) and INF-g (10ng/ml, 6 hours).

value: female

tag: cell type

value: bone marrow-derived macrophage cells

tag: treatment

value: stimulated with LPS and INF-g


title: M1-type bone marrow-derived macrophage, replicate 4

description: Biological replicate 4 of 5. M1-type macrophage cells.

tag: age


title: Agilent PB126a_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60008.gif

source_name: Agilent PB126a_AR

tag: Agilent PB126a_AR


title: Control untreated right carotid artery Replicate 6

description: Biological replicate 6 of 6. Non-atherosclerotic right carotid artery (control), untreated.

source_name: Mouse

value: Right carotid artery


title: Agilent PBL89_8.2y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63774.gif

tag: hum ref CRH

source_name: Agilent PBL89_8.2y_AR

tag: Agilent PBL89_8.2y_AR


title: bAgilent PBL308_stable

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59919.gif

source_name: Agilent PBL308_stable

tag: Agilent PBL308_stable

tag: LIhua_samples; Patients and Samples

tag: Disease State


title: M1-type bone marrow-derived macrophage, replicate 3

description: Biological replicate 3 of 5. M1-type macrophage cells.

tag: strain

tag: Sex


title: PBL1033e_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38775.gif

source_name: aRNA pool 20cell lines from PB lab labeled 030503

label_protocol: Sarwal_2007_pnas_amplification; Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method.; Protocol Type = Amplification; Performer: Minnie,,Sarwal

extract_protocol: lihua_extract preparation; <b>RNA Isolation, Microarray Target Preparation and Hybridization:</b> Total RNA extracted from peripheral blood was subject to microarray and Q-PCR experiments. Sample preparation for array hybridization was done following the manufactures recommended protocols, and hybridized on 75 GeneChip Human Genome U133 Plus2.0 arrays (Affymetrix Inc. Santa Clara, CA), 26 Agilent Human genome 44K arrays (Agilent, CA) and 21 cDNA arrays (Stanford, CA). Details of sample collection, RNA isolation, microarray target preparation and hybridization protocols are as followings: For total RNA extracted from whole blood, 2.5 ml of peripheral blood was collected in PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen) and processed using the PAXgene Blood RNA Kit (PreAnalytiX, Qiagen). For RNA extracted from leukocyte, 5 -10 ml whole blood was collected in sodium heparin tubes.  Leukocytes were recovered by initial separation of the white blood cells by centrifugation and  lysis of erythrocytes (ref. Lily method paper). RNA was extracted using RNeasy Midi Kit (Qiagen Inc, Valencia, CA). RNA concentration was measured using NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) and the integrity of RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chips (Agilent Technologies, Santa Clara, CA). RNA was stored in -80 oC until further use for microarray and qPCR. Sample preparation for array hybridization was done using the T7 protocol (T7), which employs one-cycle cRNA synthesis by using T7-Oligo (dT) Primer. A total of 2 microg total RNA was used for the synthesis of cRNA as the final product following manufacturer's Technical manual, Affymetrix). cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc. Santa Clara, CA).; Protocol Type = Extract preparation; Performer: Minnie,,Sarwal

treatment_protocol: Sarwal_2007_pnas_sample_treatment; 1) Immunosuppressive drug-free operationally tolerant test-group (TOL-Test or TT; N=12): all new patients shared the same clinical and pathological criteria as described above.All stopped their immunosuppression for non-adherence reasons.  2) Minimal immunosuppression test-group (MIS, N=10): patients with stable graft function on steroid monotherapy (<10mg/day) for 4.6+/-2.6 years. Calcineurin inhibitors and CellCept? were removed in these patients because of previous PTLD (N=6), cancer (N=2) or uncontrolled infectious disease (N=2). 3) Long-term stable test-group (STA, N=12): patients with stable kidney graft function at > 5 years post-transplantation while under mycophenolate mofetil or azathioprine, and maintenance steroids with (n=5) or without (N=7) an associated calcineurin inhibitor. 4) Acute rejection test-group (AR, N=14): patients experiencing rapid decline (>20% from baseline) in graft function and biopsy proven acute rejection (51). 5) Chronic rejection test-group (CR-Test, N=11). 6) Age-matched healthy volunteers (N, N=8). They all had a normal blood formulae and no infectious or other concomitant pathology for at least 6 months prior to the study. To limit the number of array experiments, this group was used for RT-PCR validation only. Detailed demographic and clinical data for all these patients are shown in Supplemental Table 3.; Protocol Type = Treatment; Performer: Minnie,,Sarwal


title: Prior oxidative stress to heat stress 2

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_HS2
Prior oxidative stress to heat stress replicate 2
Agilent Feature Extraction file
US83000164_251524112328_S01_GE1_105_Dec08_1_3.txt

source_name: Prior oxidative stress to heat stress 2

value: Pusa Basmati (PB1)

value: 10-days old

tag: oxidative stress

tag: temperature stress


title: PBL1002_29mo

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43729.gif

source_name: aRNA by SH on 3/27/03 from cell lines

tag: aRNA by SH on 3/27/03 from cell lines

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample; Performer:Minnie,,Sarwal


title: Prior oxidative stress to heat stress 3

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_HS3
Prior oxidative stress to heat stress replicate 3
Agilent Feature Extraction file
US83000164_251524112328_S01_GE1_105_Dec08_1_4.txt

source_name: Prior oxidative stress to heat stress 3

tag: cultivar

value: whole seedling

value: heat stress


title: Agilent PBL1003_stable

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59917.gif

source_name: hum ref CRH

source_name: Agilent PBL1003_stable

tag: Agilent PBL1003_stable


title: Control untreated right carotid artery Replicate 4

description: Biological replicate 4 of 6. Non-atherosclerotic right carotid artery (control), untreated.

tag: tissue


title: Agilent PBL530_11.7y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63769.gif

source_name: Agilent PBL530_11.7y_AR

tag: Agilent PBL530_11.7y_AR


title: Agilent PBL1033c_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59921.gif

source_name: Agilent PBL1033c_AR

tag: Agilent PBL1033c_AR


title: M1-type bone marrow-derived macrophage, replicate 2

description: Biological replicate 2 of 5. M1-type macrophage cells.

tag: age

tag: cell type

tag: treatment


title: PBL271a_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38794.gif

source_name: aRNA pool 20cell lines from PB lab labeled 031003


title: M1-type bone marrow-derived macrophage, replicate 1

description: Biological replicate 1 of 5. M1-type macrophage cells.


title: Unstimulated bone marrow-derived macrophage, replicate 5

description: Biological replicate 5 of 5. MФ

source_name: Mouse bone marrow cells, unstimulated


title: Unstimulated bone marrow-derived macrophage, replicate 4

description: Biological replicate 4 of 5. MФ


title: Agilent PBL1_4.6y_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63772.gif

tag: hum ref CRH

source_name: Agilent PBL1_4.6y_AR

tag: Agilent PBL1_4.6y_AR


title: Control untreated right carotid artery Replicate 5

description: Biological replicate 5 of 6. Non-atherosclerotic right carotid artery (control), untreated.


title: Partially ligated left carotid artery Replicate 2

description: Biological replicate 2 of 6. Atherosclerotic left carotid artery, partially ligated.

treatment_protocol: Partial Ligation: the left external carotid, the internal carotid and the occipital artery were ligated allowing blood flow only via the superior thyroid artery


title: Partially ligated left carotid artery Replicate 3

description: Biological replicate 3 of 6. Atherosclerotic carotid, partially ligated.


title: Partially ligated left carotid artery Replicate 1

description: Biological replicate 1 of 6. Atherosclerotic left carotid artery, partially ligated.


title: shScr replicate 3

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from mESCs stably expressing a control shRNA

hyb_protocol: The labeled ssDNA was hybridized to Affymetrix Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Chips were processed on an Affymetrix GeneChip Fluidics Station 450 and Scanner 3000

data_processing: Data were analyzed using the oligo (v1.18.1) R/Biocondutor package and normalized using the RMA algorithm

source_name: mouse embryonic stem cells

label_protocol: Sense ssDNA was fragmented and labeled using the GeneChip® WT Terminal Labeling and Controls Kit.

growth_protocol: regular ES media supplemented with 10 ng/mL LIF

extract_protocol: Total RNA extraction (Rneasy mini kit) + DNAse treatment

treatment_protocol: samples were collected in parallel in 4 biological independent replicates

value: embryonic stem cells

tag: shRNA

value: shScrambled

tag: shRNA sequence

value: CCTAAGGTTAAGTCGCCCTCG

tag: passages


title: Control untreated right carotid artery Replicate 3

description: Biological replicate 3 of 6. Non-atherosclerotic right carotid artery (control), untreated.

tag: strain

value: apoE-/-

tag: Sex


title: PBL1033c_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38773.gif

tag: aRNA pool 20cell lines from PB lab labeled 030503

tag: Disease State


title: Unstimulated bone marrow-derived macrophage, replicate 3

description: Biological replicate 3 of 5. MФ


title: PBL1039a_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38786.gif

tag: aRNA pool 20cell lines from PB lab labeled 031003


title: shScr replicate 1


title: shScr replicate 2


title: Unstimulated bone marrow-derived macrophage, replicate 2

description: Biological replicate 2 of 5. MФ


title: Agilent PB89b_AR2

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59785.gif

tag: LIhua_samples; Patients and Samples

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample


title: Control untreated right carotid artery Replicate 2

description: Biological replicate 2 of 6. Non-atherosclerotic right carotid artery (control), untreated.

value: 6-8 weeks

tag: tissue


title: ShKdm2b replicate 4

description: Gene expression data from mESC stably expressing shRNA targeting Kdm2b

value: CGCTGTGGAAATATCTGTCAT


title: Unstimulated bone marrow-derived macrophage, replicate 1

description: Biological replicate 1 of 5. MФ


title: PBL1002_27Mo

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40276.gif

tag: aRNA by SH on 3/27/03 from cell lines

source_name: B14 previously called AR? B14_27mo.

tag: B14 previously called AR? B14_27mo.


title: Control untreated right carotid artery Replicate 1

description: Biological replicate 1 of 6. Non-atherosclerotic right carotid artery (control), untreated.

tag: age

value: Female


title: shScr replicate 4

tag: cell type


title: Pglyrp1-/- mice sensitized with HDM for 5 weeks, expt 1

status: Public on Dec 25 2012

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

description: P1 HDM5-1

data_processing: For each gene, ΔCt was calculated using the same threshold (0.2) for all genes and Ct>35 considered as no expression, followed by normalization to 5 housekeeping genes (Hsp90ab1, Gusb, Hprt1, Gapdh, and Actb) included in each array, followed by calculation of ΔΔCt for each gene from two arrays: ΔΔCt = ΔCt1 – ΔCt2, where ΔCt1 is the HDM-sensitized mice group and ΔCT2 is the unsensitized mice group, using the program provided by Qiagen/SA Biosciences.

label: SYBR Green

source_name: Pglyrp1-/-_HDM for 5 weeks

label_protocol: Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the lungs using custom RT2 Profiler PCR Arrays manufactured by Qiagen/SA Biosciences. The arrays included 40 assay genes, 5 housekeeping genes, and reverse transcription efficiency and DNA contamination controls. All primer sets were from Qiagen/SA Biosciences, except for the Pglyrp1 primers. cDNA was synthesized from 2 µg of RNA using RT2 PCR Array First Strand Kit (Qiagen/SA Biosciences) and the arrays were performed according to the manufacturer instructions using Qiagen/SA Biosciences Master Mix. Each experiment was performed on RNA pooled from 4–5 mice/group and repeated 3 times with new groups of mice.

extract_protocol: RNA was isolated from right lobes of unsensitized or sensitized lungs using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen). In each experiment, for qRT-PCR gene expression array RNA was pooled from 4-5 mice per group.

tag: strain background

value: BALB/c

tag: genotype/variation

tag: sensitized with

value: 10 µl per application of 2.5 mg/ml of purified house dust mite allergen (HDM) for 5 weeks

value: lung, right lobe


title: Pglyrp1-/- mice sensitized with HDM for 5 weeks, expt 2

description: P1 HDM5-2


title: WT mice sensitized with HDM for 5 weeks, expt 1

description: WT HDM5-1

source_name: WT_HDM for 5 weeks

value: wild type


title: Pglyrp1-/- mice sensitized with HDM for 5 weeks, expt 3

description: P1 HDM5-3


title: Pglyrp1-/- mice sensitized with HDM for 3 weeks, expt 3

description: P1 HDM3-3

source_name: Pglyrp1-/-_HDM for 3 weeks

value: 10 µl per application of 2.5 mg/ml of purified house dust mite allergen (HDM) for 3 weeks


title: PBL1033f_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38777.gif


title: ShKdm2b replicate 1

tag: shRNA


title: WT mice sensitized with HDM for 5 weeks, expt 2

description: WT HDM5-2


title: Pglyrp1-/- mice sensitized with HDM for 3 weeks, expt 2

description: P1 HDM3-2


title: Pglyrp1-/- mice sensitized with HDM for 3 weeks, expt 1

description: P1 HDM3-1


title: WT mice sensitized with HDM for 3 weeks, expt 3

description: WT HDM3-3

source_name: WT_HDM for 3 weeks


title: ShKdm2b replicate 3

tag: shRNA sequence


title: pst_lpm/pst_hpm

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

hyb_protocol: Hybridization was conducted as per Agilent 2 color microarray-based gene expression analysis manual (version 5.7) with the modification 4 microg of labeled total RNA was used per hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software

organism: Citrobacter rodentium

source_name: liquid culture

label_protocol: 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions

growth_protocol: overnight cultures of Citrobacter rodentium were inoculated 1:50 into morpholinepropanesulfonic acid (MOPS) minimal medium containing 0.4% (w/v) 94 glucose, 0.01 mM Casamino acids, and 0.01 mM thiamine medium and 1.0 mM for high phosphate medium (HPM) or 0.2 mM for low phosphate medium (LPM) and grown until the OD600 was 0.7

extract_protocol: 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min. Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene). RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen)

treatment_protocol: K2HPO4 was added to a final concentration of 1.0 mM for high phosphate medium (HPM) 0.2 mM for low phosphate medium (LPM)

tag: genotype

value: pstCA

tag: phosphate

value: low

value: high


title: pho_hpm/wt_hpm

tag: strain

value: phoB

value: wt


title: pst_hpm/wt_hpm


title: WT mice sensitized with HDM for 3 weeks, expt 2

description: WT HDM3-2


title: wt_lpm/pst_lpm


title: pho_lpm/pho_hpm


title: WT mice sensitized with HDM for 3 weeks, expt 1

description: WT HDM3-1


title: WT mice sensitized with HDM for 5 weeks, expt 3

description: WT HDM5-3


title: Pglyrp1-/- mice treated with PBS, expt 3

description: P1 PBS-3

tag: treated with

value: PBS (control)


title: Agilent PBL1027_stable

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59784.gif

tag: hum ref CRH

tag: Disease State


title: NB-#3Mock(24hr)-3

source_name: leaves

tag: developmental stage

value: 4th leaves at 4-leaf stage

tag: cultivar

value: Nipponbare

value: leaf

tag: protocol

value: control

tag: treatment

value: Mock

tag: time


title: wt_hpm/wt_lpm


title: Pglyrp1-/- mice treated with PBS, expt 2

description: P1 PBS-2

tag: tissue


title: Pglyrp1-/- mice treated with PBS, expt 1

description: P1 PBS-1

tag: strain background


title: pho_hpm/pst_hpm


title: ShKdm2b replicate 2

tag: cell type

value: embryonic stem cells

value: CGCTGTGGAAATATCTGTCAT

tag: passages


title: wt_lpm/wt_hpm


title: Prior oxidative stress to heat stress 1

description:
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
PO_HS1
Prior oxidative stress to heat stress replicate 1
Agilent Feature Extraction file
US83000164_251524112328_S01_GE1_105_Dec08_1_2.txt

source_name: Prior oxidative stress to heat stress 1

value: Pusa Basmati (PB1)

tag: age

value: 10-days old

value: whole seedling

tag: oxidative stress

value: prior oxidative stress

tag: temperature stress

value: heat stress


title: RNA from PB in Kidney Transplant 6

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82310.gif

source_name: common reference fron cell lines

tag: common reference fron cell lines

source_name: RNA from kidney transplant PB

tag: RNA from kidney transplant PB

tag: LIhua_samples; Patients and Samples

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample


title: PBL269b_AR

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38760.gif

source_name: aRNA pool 20cell lines from PB lab labeled 030103


title: WT mice treated with PBS, expt 2

description: WT PBS-2

value: BALB/c

tag: genotype/variation

value: wild type

tag: treated with

value: lung, right lobe


title: WT mice treated with PBS, expt 1

description: WT PBS-1

value: PBS (control)


title: wt_hpm/pho_hpm

tag: strain

tag: genotype

value: wt

tag: phosphate

value: high

value: phoB


title: pho_lpm/wt_lpm

value: low


title: RNA from PB in Kidney Transplant 3

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82307.gif

source_name: common reference from cell lines

tag: common reference from cell lines

source_name: RNA from PB

tag: RNA from PB

tag: Disease State


title: pho_lpm/pst_lpm

value: pstCA


title: RNA from PB in Kidney Transplant 5

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82309.gif


title: pst_lpm/wt_lpm


title: pho_hpm/pho_lpm


title: WT mice treated with PBS, expt 3

description: WT PBS-3

tag: strain background

tag: tissue


title: RalR/delta2_rep

data_processing:
Data was normalized within arrays using loess normalization in limma. DE presented in the paper was analyzed in R/bioconductor/limma with
design <- cbind(dye=  c( 1,  1,  1,  1,  1,  1,  1,  1),
cr1=  c( 1,  0,  1,  0, -1,  0, -1,  0),
cr2=  c( 0, -1,  0, -1,  0,  1,  0,  1))

organism: Escherichia coli E22

source_name: liquid culture of EcE22_5293 (RalR)

growth_protocol: overnight cultures of Escherichia coli E22 were inoculated 1:100 into Luria Broth and grown until the OD600 was 0.85

source_name: liquid culture of E22delta2


title: delta2/RalR_rep


title: pst_hpm/pst_lpm


title: RalR/delta2


title: delta2/RegR_rep

source_name: liquid culture of RegR

value: RegR


title: delta2/RalR


title: delta2/RegR


title: RegR/delta2_rep


title: KT2440(pCAR1)_8hr

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas putida

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: Each strain was grown in 5 ml of LB at 300 strokes/min for 14-14.5 h (pre-culture) and then washed and transferred into 100-ml of NMM-4 buffer (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 0.1% succinate adjusting its turbidity (600 nm) at 0.05. The resultant culture was incubated on a rotary shaker at 120 rpm and cell growth was monitored in by measuring its turbidity (600 nm).

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: growth time


title: KT2440(pCAR1)_4hr


title: KT2440(pCAR1)_6hr


title: RNA from PB in Kidney Transplant 4

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82308.gif


title: RNA from PB in Kidney Transplant 2

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82306.gif


title: KT2440(pCAR1)_2hr


title: RNA from PB in Kidney Transplant

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82305.gif


title: KT2440_8hr

source_name: cDNA prepared from succinate culture of KT2440


title: KT2440_2hr


title: RegR/delta2


title: wt_lpm/pho_lpm


title: Day0 Replicate 4

city: Hyderabad

first: Tushar

last: Vaidya

address: Uppal Road Habshiguda

institute: Centre for Cellular and Molecular Biology

description: Analysis used IgD+ B Cells stimulated with LPS as control and LPS+ anti-CD40 as test

hyb_protocol: Hybridisation was done as per manufacturer's instructions. Briefly,the Cy3 labelled cDNA was resuspended in hybridisation buffer,mixed thoroughly and added to Cy5 labeled  cDNA,denatured at 95°C for 2 min,chilled on ice and was placed on array slides.

scan_protocol: Images were quantified using Genescan 3.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Midas software was used.

source_name: LPS treated Naïve IgD+ B Cells

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: The murine IgD+B Cells were seeded at a density of 1million cells/ml of  RPMI 1640 supplemented with 10% FCS,2mM L-glutamin,0.2mM 2-ME, and penicillin (100u/ml) and streptomycin(100μg/ml),gentamycin(50μg/ml).Cells were incubated at 37C and 5% CO2 for 48 hours.

extract_protocol: Total RNA was extracted using Qiagen's RNA easy plus mini kit following manufacture's instructions.

treatment_protocol: Naive IgD+B Cells were stimulated in a 6-well Plate with 10μg/ml LPS as test group. Untreated Naive IgD+B Cells served as control group.

value: Balb/C

tag: age

value: 3-4 months old

value: Spleen

tag: cell type

value: Primary B Cells

source_name: Untreated Naïve IgD+B Cells

tag: tag


title: PAO1(pCAR1)_6hr

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas aeruginosa PAO1 chromosome (RefSeq: NC_002516) at 11-bp density.  BPMAP files are provided as supplementary files. PAO1b520519FF-3.bpmap represents  the forward strand of PAO1chromosome, and PAO1b520519FR-3.bpmap represents the reverse strand of PAO1 chromosome.

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using PAO1b520519FR-3.bpmap for the forward strand and PAO1b520519FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of PAO1 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas aeruginosa

source_name: cDNA prepared from succinate culture of PAO1(pCAR1)


title: KT2440_6hr


title: PAO1(pCAR1)_8hr


title: Day0 Replicate 3

source_name: untreated Naïve IgD+B Cells

source_name: LPS treated Naïve IgD+B Cells


title: 72 hour after anti-CD40 stimulation Replicate3

description:
Analysis used IgD+ B Cells stimulated with LPS as control and LPS+ anti-CD40 as test
In the raw data files, column headers that include *_1 and *_2 refer to channel 1 and channel 2, respectively.

hyb_protocol: Hybridisation was done as per manufacturer's instructions. Briefly,the Control cDNA was resuspended in hybridisation buffer,mixed thoroughly and added to Test cDNA,denatured at 95°C for 2 min,chilled on ice and was placed on array slides.

source_name: LPS+anti-CD40 Treated Naïve IgD+ B Cells

growth_protocol: The murine IgD+ B Cells were seeded at a density of 1million cells/ml of  RPMI 1640 supplemented with 10% FCS,2mM L-glutamin,0.2mM 2-ME, and penicillin (100u/ml) and streptomycin(100μg/ml),gentamycin(50μg/ml).Cells were incubated at 37°C and 5% CO2 for 72 hours.

treatment_protocol: Cells were stimulated in a 6-well Plate with 10μg/ml LPS in controls and 10μg/ml LPS and anti-CD40(clone IC10) in test wells

value: 3-4 months old mice

tag: cell line

value: Primary B Cells (Naïve IgD+ B Cells)

tag: agent

value: LPS + anti-CD40

tag: time

value: 72 hours

value: LPS


title: PAO1_8hr

source_name: cDNA prepared from succinate culture of PAO1

tag: genotype/variation

value: wild type


title: PAO1(pCAR1)_4hr


title: T cell from T-iPSC_reT-2.1

first: Toshinobu

last: Nishimura

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine

institute: The Institute of Medical Science, The University of Tokyo

description:
TNK_003
Gene expression 2 weeks after TCR stimulation.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in 1x Agilent Fragmentation Buffer and 2x Agilent Gene Expression Blocking Agent following the manufacturer's instructions. On completion of the fragmentation reaction, 2x Agilent Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F or G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 minute at 37°C with Agilent Gene Expression Wash buffer 2, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned and images were acquired by the DNA Microarray Scanner (G2565CA, Agilent Technologies) on the green dye channel. The quality was assessed with the Feature Extraction software (Agilent Technologies).

data_processing: Raw data were processed with Feature Extraction software 10.5 (Agilent Technologies) to obtain signal intensities. On-chip quantile normalization (threshold set at 1.0 of raw signals) was applied to assure comparability across samples using GeneSpring software 12.0 (Agilent Technologies). Genes with a present flag value in all samples were used for analyses.

source_name: iPSC-derived T cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Low Input Quick-Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) according to the manufacturer's instructions.

growth_protocol: ESCs/iPSCs were cultured in human iPS medium (DMEM/F12 FAM supplemented with 20% KSR, 2 mM L-glutamine, 1% non-essential amino acids, 10 μM 2-mercaptoethanol, and 5 ng/ml bFGF). T cells were stimulated by PHA-L and cultured for 2 weeks in RH10 medium (RPMI-1640 supplemented with 10% human AB Serum, 2 mM L-glutamine, 100 U/ml penicillin, and 100 ng/ml streptomycin) in the presence of 10 ng/ml IL-7 and 10 ng/ml IL-15.

extract_protocol: RNA was prepared using the RNeasy Micro kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SSEA-4+ cells (ESCs/iPSCs); TCRαβ+, CD3+, CD45+ cells (T cells); and TCRαβ-, CD3-, CD16+, CD56+ cells (NK cells) were isolated by FACS AriaII (BD Bioscience, San Jose, CA).

value: iPSC-derived T cells

tag: disease status


title: KT2440_4hr

tag: strain


title: PAO1(pCAR1)_2hr


title: Day0 Replicate 1


title: PAO1_6hr


title: PAO1_4hr


title: 72 hour after anti-CD40 stimulation Replicate 1


title: BM DMSO-treated 8 hours, rep3

city: East Melbourne

first: Lynette

last: Chee

address: A'Beckett Street

department: Research

institute: Peter MacCallum Cancer Centre

description: Gene expression data from #D220 BM cells after 8 hours of DMSO treatment.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA was hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data was analysed using R and Bioconductor. RMA normalisation was applied using the Affy package and as one of the chips had an abnormal intensity distribution, two analyses were performed: one with all the chips included and another with the affected chip downweighted to 0.33.

source_name: #D220 BM cells, DMSO treatment, 8 hours

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: Harvested BM cells were plated in 3% methylcellulose-based media with IMDM (Gibco), 20% FBS (Multiser, Trace Biosciences), Antibiotic-Antimycotic 1% (Gibco), L-glutamine 2mM/ml, rhEPO 3U/ml (Janssen-Cilag), rmSCF 100ng/ml (Peprotech), rmIL-3 10ng/ml (Peprotech) and rmIL-6 1000U/ml (Peprotech). Following 2 weeks in culture, cells were harvested, pooled and replated in suspension cultures containing IMDM and cytokines as described.

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen) as per the manufacturer's instructions.

treatment_protocol: DMSO (1:10000), ATRA 10E-6M or NRX195183 10E-6M were added to the respective suspension cultures. Cells were harvested following 8 hours and 24 hours of treatment for RNA extraction and purification.

tag: genotype

value: bone marrow

tag: treatment

value: DMSO

tag: treatment duration

value: 8 hours

tag: mouse identifier


title: PB NK cell

description:
TNK_004
Gene expression of cells soon after the extraction from peripheral blood.

source_name: NK cells from peripheral blood

value: peripheral blood

value: NK cells

value: healthy


title: Day0 Replicate 2

value: Balb/C


title: PAO1_2hr


title: Pf0-1(pCAR1)_8hr_IncP-7 array

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444.1) at 9-bp density.  BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 130 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of GeneChip Fluidics station 450 (Affymetrix).

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FR-3.bpmap for the forward strand and pCAR1_8b520435FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of pCAR1. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas fluorescens

source_name: cDNA prepared from succinate culture of Pf0-1(pCAR1)


title: T cell from T-iPSC_reT-1

description:
TNK_002
Gene expression 2 weeks after TCR stimulation.


title: CTL clone_H25-#4

description:
TNK_001
Gene expression 2 weeks after TCR stimulation.

source_name: T cells

value: T cells


title: Pf0-1(pCAR1)_6hr_IncP-7 array


title: BM DMSO-treated 24 hours, rep3

description: Gene expression data from #D220 BM cells after 24 hours of DMSO treatment.

source_name: #D220 BM cells, DMSO treatment, 24 hours

value: 24 hours


title: 72 hour after anti-CD40 stimulation Replicate 2

value: Spleen


title: BM ATRA-treated 24 hours, rep3

description: Gene expression data from #D220 BM cells after 24 hours of ATRA treatment.

source_name: #D220 BM cells, ATRA treatment, 24 hours

value: ATRA


title: BM ATRA-treated 8 hours, rep3

description: Gene expression data from #D220 BM cells after 8 hours of ATRA treatment.

source_name: #D220 BM cells, ATRA treatment, 8 hours


title: Pf0-1(pCAR1)_2hr_IncP-7 array


title: Pf0-1(pCAR1)_4hr_IncP-7 array


title: wt_hpm/pst_hpm

source_name: liquid culture

value: wt

tag: phosphate

value: high

value: pstCA


title: BM NRX195183-treated 8 hours, rep3

description: Gene expression data from #D220 BM cells after 8 hours of NRX195813 treatment.

source_name: #D220 BM cells, NRX195183 treatment, 8 hours


title: PAO1(pCAR1)_6hr_IncP-7 array


title: 48 hour after anti-CD40 stimulation Replicate 2

description:
Analysis used IgD+ B Cells stimulated with LPS as control and LPS+ anti-CD40 as test.
In the raw data files, column headers that include *_1 and *_2 refer to channel 1 and channel 2, respectively.

hyb_protocol: Hybridisation was done as per manufacturer's instructions. Briefly,the  Control cDNA was resuspended in hybridisation buffer,mixed thoroughly and added to Test cDNA,denatured at 95°C for 2 min,chilled on ice and was placed on array slides.

source_name: LPS treated Naïve IgD+ B Cells

growth_protocol: The murine IgD+ B Cells were seeded at a density of 1million cells/ml of  RPMI 1640 supplemented with 10% FCS,2mM L-glutamin,0.2mM 2-ME, and penicillin (100u/ml) and streptomycin(100μg/ml),gentamycin(50μg/ml).Cells were incubated at 37°C and 5% CO2 for 48 hours.

value: 3-4 months

value: Primary B Cells (Naïve IgD+ B Cells)

value: LPS

value: 48 hours

value: LPS + anti-CD40


title: PAO1(pCAR1)_8hr_IncP-7 array


title: PAO1(pCAR1)_4hr_IncP-7 array


title: PAO1(pCAR1)_2hr_IncP-7 array


title: 48 hour after anti-CD40 stimulation Replicate 4

source_name: LPS + anti-CD40 treated Naïve IgD+ B Cells

source_name: LPS Treated Naïve IgD+ B Cells


title: KT2440(pCAR1)_2hr_IncP-7 array

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)


title: KT2440(pCAR1)_4hr_IncP-7 array


title: KT2440(pCAR1)_8hr_IncP-7 array


title: KT2440(pCAR1)_6hr_IncP-7 array


title: 48 hour after anti-CD40 stimulation Replicate3


title: BM ATRA-treated 8 hours, rep2

description: Gene expression data from #D218 BM cells after 8 hours of ATRA treatment.

source_name: #D218 BM cells, ATRA treatment, 8 hours

value: bone marrow

value: 8 hours


title: 24 hours after anti-CD40 stimulation, replicate 3

description:
Analysis used IgD+ B cells stimulated with LPS as a control, and IgD+ B cells stimulated with LPS + anti-CD40 as the test.

In the raw data files, column headers that include *_1 and *_2 refer to channel 1 and 2, respectively.

hyb_protocol: Hybridization was done as per manufacturer's instructions. Briefly, the Control cDNA was resuspended in hybridization buffer, mixed thoroughly and added to the Test cDNA, denatured at 95°C for 2 min, chilled on ice and placed on array slides.

source_name: LPS-treated naïve IgD+ B cells, 24hrs

label_protocol: Labeled with Cy3 and Cy5 during cDNA synthesis from total RNA using the Superscript III Kit (Invitrogen) as per manufacturer's instructions. Samples were purified using the QIAGEN PCR purification kit before hybridization.

growth_protocol: The murine IgD+ B cells were seeded at a density of 1 million cells/ml of RPMI 1640 supplemented with 10% FCS, 2mM L-glutamin, 0.2mM 2-ME, and penicillin (100u/ml) and streptomycin (100μg/ml), gentamycin (50μg/ml). Cells were incubated at 37°C and 5% CO2 for 24 hours.

extract_protocol: Total RNA was extracted using Qiagen's RNeasy Plus mini kit following the manufacturer's instructions.

treatment_protocol: Cells were stimulated in a 6-well plate with 10μg/ml LPS in control wells, and 10μg/ml LPS and anti-CD40 (clone IC10) in test wells.

value: spleen

value: primary IgD+ B cells

tag: time after treatment

source_name: LPS- and anti-CD40-treated naïve IgD+ B cells, 24hrs

value: LPS and anti-CD40


title: 24 hours after anti-CD40 stimulation, replicate 4

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Midas software was used. The VALUEs in the Sample data table represent log2 (Cy3/Cy5) ratios.

value: Balb/C

tag: tissue


title: 48 hour after anti-CD40 stimulation Replicate 1

source_name: LPS+anti-CD40 Treated Naïve IgD+ B Cells


title: BM NRX195183-treated 24 hours, rep2

description: Gene expression data from #D218 BM cells after 24 hours of NRX195813 treatment.

source_name: #D218 BM cells, NRX195183 treatment, 24 hours

value: 24 hours


title: BM DMSO-treated 8 hours, rep1

description: Gene expression data from #D203 BM cells after 8 hours of DMSO treatment.

source_name: #D203 BM cells, DMSO treatment, 8 hours

value: DMSO


title: BM NRX195183-treated 8 hours, rep2

description: Gene expression data from #D218 BM cells after 8 hours of NRX195813 treatment.

source_name: #D218 BM cells, NRX195183 treatment, 8 hours


title: THP-1 cells-frozen-rep2

city: Yokohama

first: Alistair

middle: R

last: Forrest

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN OMICS science centre

institute: RIKEN

description:
frozen-2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: THP-1 monoblastic leukemia cell line

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

extract_protocol: Total RNA was extracted from cell pellets using QIAGEN miRNeasy mini kit


title: BM DMSO-treated 24 hours, rep2

description: Gene expression data from #D218 BM cells after 24 hours of DMSO treatment.

source_name: #D218 BM cells, DMSO treatment, 24 hours


title: 24 hours after anti-CD40 stimulation, replicate 2


title: Pf0-1(pCAR1)_8hr

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas fluorescens Pf0-1 chromosome (RefSeq: NC_007492) at 11-bp density.  BPMAP files are provided as supplementary files. PFO1b520543F-3-REV.bpmap represents  the forward strand of Pf0-1 chromosome, and PFO1b520543F-3-FWD.bpmap represents the reverse strand of Pf0-1 chromosome.

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using PFO1b520543F-3-REV.bpmap for the forward strand and PFO1b520543F-3-FWD.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of Pf0-1 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

source_name: cDNA prepared from succinate culture of Pf0-1(pCAR1)

tag: growth time


title: BM NRX195183-treated 24 hours, rep3

description: Gene expression data from #D220 BM cells after 24 hours of NRX195813 treatment.

source_name: #D220 BM cells, NRX195183 treatment, 24 hours


title: THP-1 cells-frozen-rep1

description:
frozen-1
replicate 1


title: BM ATRA-treated 8 hours, rep1

description: Gene expression data from #D203 BM cells after 8 hours of ATRA treatment.

source_name: #D203 BM cells, ATRA treatment, 8 hours

value: ATRA


title: THP-1 cells-frozen-rep3

description:
frozen-3
replicate 3


title: THP-1 cells-replated-rep3

description:
replated-3
replicate 3


title: THP-1 cells-replated-rep1

description:
replated-1
replicate 1


title: THP-1 cells-fresh-rep3

description:
fresh-3
replicate 3


title: THP-1 cells-replated-rep2

description:
replated-2
replicate 2


title: BM NRX195183-treated 8 hours, rep1

description: Gene expression data from #D203 BM cells after 8 hours of NRX195813 treatment.

source_name: #D203 BM cells, NRX195183 treatment, 8 hours


title: Control4

city: Galway

first: Paul

middle: Kibet

last: Korir

state: Co Galway

address: University Road

department: School of Mathematics, Statistics and Applied Mathematics

country: Ireland

institute: National University of Ireland, Galway

hyb_protocol: The labelled samples were hybridised to Affymetrix GeneChip Human Exon Array 1.0 ST chips according to the prescribed protocol.

scan_protocol: Following hybridization, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Raw exon array intensities were summarised into probesets and metaprobesets at the core and full probeset/metaprobeset level using Affymetrix Power Tools (APT) by the robust multi-chip averaging (RMA) algorithm. APT was also used to determine probesets and metaprobesets that were detectable above the background (DABG). We excluded from further analysis all probesets that were detectable above background in fewer than half of the samples. We also used the annotation files provided by Affymetrix to exclude all probesets with probes likely to cross-hybridise. A similar procedure was applied to metaprobesets: only those having at least half of the associated probesets expressed above background in all samples were retained. Probeset RMA values were gene-normalised by subtracting the corresponding metaprobeset RMA values (because they lie on a logarithmic scale). The resulting list of normalised probesets were reduced to a one-to-one map between probesets and exons. Exons that had more than one probeset had one selected at random. Similarly, probesets that overlapped multiple exons had one exon selected at random.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: whole blood, control4

label_protocol: The RNA was then processed with the Whole Transcript (WT) Sense Target Labelling assay.

extract_protocol: Three blood samples per subject were collected into PAXgene tubes (PreAnalytiX), according to the manufacturer's instructions, and incubated at room temperature. RNA extractions were performed 16 hours (A sample), 20 hours (B sample) and 39 hours (C sample) after collection. Total RNA was extracted using the PAXgene Blood RNA kit, following the manufacturer's recommended protocol. The RNA samples were not heat denatured following elution, but immediately stored at -80 degrees Celsius. The A and B RNA isolations of each sample were pooled, and the Affymetrix GeneChip Blood RNA Concentration Kit was used to concentrate the RNA. Quality control checks to determine RNA concentration and integrity were performed for each sample, using the NanoDrop (Thermo Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively. It was determined that one of the cases showed poor integrity of A/B and C RNA samples leading to its exclusion together with its sibling-pair. Ribosomal RNA reduction was performed on the eight remaining samples using the RiboMinus Transcriptome Isolation Kit (Human/Mouse) (Invitrogen), in accordance with a modified Affymetrix protocol.

value: whole blood

value: absent

tag: rp symptomatic

value: no

tag: sibling pair


title: Pf0-1(pCAR1)_6hr


title: BM DMSO-treated 24 hours, rep1

description: Gene expression data from #D203 BM cells after 24 hours of DMSO treatment.

source_name: #D203 BM cells, DMSO treatment, 24 hours


title: BM ATRA-treated 24 hours, rep2

description: Gene expression data from #D218 BM cells after 24 hours of ATRA treatment.

source_name: #D218 BM cells, ATRA treatment, 24 hours


title: Pf0-1(pCAR1)_4hr


title: Pf0-1(pCAR1)_2hr


title: Case4

source_name: whole blood, case4

value: present

value: yes


title: Case3

source_name: whole blood, case3


title: BM ATRA-treated 24 hours, rep1

description: Gene expression data from #D203 BM cells after 24 hours of ATRA treatment.

source_name: #D203 BM cells, ATRA treatment, 24 hours


title: Pf0-1_5hr

source_name: cDNA prepared from succinate culture of Pf0-1

value: wild type


title: Pf0-1_7hr


title: BM NRX195183-treated 24 hours, rep1

description: Gene expression data from #D203 BM cells after 24 hours of NRX195813 treatment.

source_name: #D203 BM cells, NRX195183 treatment, 24 hours


title: Pf0-1_3hr


title: THP-1 cells-fresh-rep1

description:
fresh-1
replicate 1


title: Case1

source_name: whole blood, case1


title: 24 hours after anti-CD40 stimulation, replicate 1

source_name: LPS-treated naïve IgD+ B cells, 24hrs

tag: age

value: 3-4 months

tag: cell type

value: LPS

source_name: LPS- and anti-CD40-treated naïve IgD+ B cells, 24hrs


title: BM DMSO-treated 8 hours, rep2

description: Gene expression data from #D218 BM cells after 8 hours of DMSO treatment.

source_name: #D218 BM cells, DMSO treatment, 8 hours

value: bone marrow


title: Control3

source_name: whole blood, control3


title: THP-1 cells-fresh-rep2

description:
fresh-2
replicate 2

source_name: THP-1 monoblastic leukemia cell line


title: Control1

source_name: whole blood, control1


title: Control2

source_name: whole blood, control2


title: 30 min post infection - donor 2 CRAM_OHU28K-358_11-22-05

city: New Haven

first: Diane

last: McMahon-Pratt

state: Ct

address: 60 College St

department: Epidemiology of Microbial Diseases

institute: Yale School of Public Health

description: 30 min post infection - donor 2

hyb_protocol: Labelled cDNA was hybridized to a 70-mer OHU28K Human oligo array, after addition of 1ug of Human Cot-1 DNA to the hybridization mixture in a 22x71 mm AdvaCard. Hybridization was done overnight at 55ºC, followed by washings with 2XSSC/0.2%SDS.

scan_protocol: Arrays were scanned  with Axon GenePix 4000A laser confocal scanner at 532 and 635 nm.

data_processing: Image files were analyzed with GenePix Pro Software and GeneSpring GX 7.2 software was used for gene expression data analysis. Lowess normalization was performed to eliminate dye-related artifacts.

source_name: L.(V.)panamensis infected human macrophage

label_protocol: cDNA was ligated to the appropriate Cy5/Cy3 3DNA capture sequence

extract_protocol: RNA samples were extracted  with Trizol from adherent macrophages, and RNA recovery was done with Rneasy Micro Kit (Qiagen).

value: monocyte differentiated macrophage

tag: infection

tag: individual

value: donor 2

value: 30 min post infection

source_name: human macrophage

value: control


title: 4 hrs post infection - donor 1 CRAM_OHU28K-355_11-22-05

description: 4 hrs post infection - donor 1

value: donor 1

tag: time

value: 4 hrs post infection


title: Case2

source_name: whole blood, case2


title: 4 hrs post infection - donor 2 CRAM_OHU28K-354_11-22-05

description: 4 hrs post infection - donor 2


title: 24 hrs post infection - donor 2 CRAM_OHU28K-363_11-29-05

description: 24 hrs post infection - donor 2

value: 24 hrs post infection


title: PN11_Klf5CN_Cornea_Rep1

city: Pittsburgh

first: Shivalingappa

middle: Kottur

last: Swamynathan

state: PA

address: 203 Lothrop Street Room 1025

department: Ophthalmology

institute: University of Pittsburgh

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 150 using the software default (2% trimmed mean). Prior to scaling, mean microarray expression levels were 449 ± 38 (mean ± SD, n=13 with one outlier of 255), and target sequences were detected (called Present) for 57.8% ± 2.5% (mean ± SD, n=14) of panels on the chip. After scaling, three redundant panels for the housekeeping gene GAPDH reported coefficients of variation of 12.3%, 10.9% and 13.1% respectively (n = 13 for each panel since each had one outlier value).

label: Biotin

source_name: Cornea

label_protocol: Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)

extract_protocol: Four age-matched PN56 WT and Klf5CN mice, and 3 age-matched PN11 WT and Klf5CN mice each were used for comparison of corneal gene expression by microarrays. Two dissected corneas from each mouse were pooled for isolation of total RNA using the RNeasy Mini kit (Qiagen, Germantown, MD). The quality and integrity of the isolated total RNA was confirmed using an Agilent Bioanalyzer.

tag: background strain

value: mixed

tag: genotype/variation

value: Klf5-conditional null

tag: developmental stage

value: postnatal day-11


title: PN11_WT_Cornea_Rep3

value: WT


title: Pf0-1_1hr

tag: strain


title: 4 hrs post infection - donor 2 CRAM_OHU28K-359_11-22-05

description: 4 hrs post infection - donor 2


title: PN11_Klf5CN_Cornea_Rep2


title: PN56_Klf5CN_Cornea_Rep4

value: postnatal day-56


title: BN saline-treated

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

country: Canada

institute: Toronto General Hospital

hyb_protocol: Affymetrix protocol

scan_protocol: MicroArray Suite (Version 5, Affymetrix)

data_processing: MAS5.0 signal intensities were scaled across the GeneChips to 150 fluorescence units

organism: Rattus norvegicus

source_name: Kidney, BN, saline

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated using Trizol according to the manufacturer’s instructions

value: Brown Norway

tag: gender

value: male

value: 9 weeks

tag: treatment

value: saline treated prenatally

value: kidney


title: BN nicotine-treated

source_name: Kidney, BN, nicotine

value: nicotine treated prenatally


title: PN11_Klf5CN_Cornea_Rep3


title: PN11_WT_Cornea_Rep1


title: 30 min post infection - donor A CRAM_OHU28K-348_11-19-05

description: 30 min post infection - donor A

value: monocyte differentiated macrophage

value: donor A


title: PN11_WT_Cornea_Rep2


title: 4 hrs post infection - donor 1 CRAM_OHU28K-353_11-21-05

description: 4 hrs post infection - donor 1

value: control


title: SHR saline-treated

source_name: Kidney, SHR, saline

value: spontaneously hypertensive

value: saline treated prenatally (control)


title: SHR nicotine-treated

source_name: Kidney, SHR, nicotine


title: 30 min post infection - donor A CRAM_OHU28K-347_11-19-05

description: 30 min post infection - donor A

value: 30 min post infection


title: ESC_KhES3

description:
ESiPS48_004
Gene expression of cells in usual ES-culture conditions.

source_name: ESCs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng of total RNA using the Quick-Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) according to the manufacturer's instructions.

tag: cell line

value: ESCs

tag: disease status

value: healthy


title: T-iPSC_TkT3V1-7

description:
ESiPS48_003
Gene expression of cells in usual ES-culture conditions.

source_name: T-iPSCs

value: T-iPSCs


title: PN56_Klf5CN_Cornea_Rep2

value: mixed

value: Klf5-conditional null


title: PN56_Klf5CN_Cornea_Rep1

value: postnatal day-56


title: PN56_WT_Cornea_Rep3

value: WT


title: PB CD4 T cell

description:
ESiPS48_001
Gene expression 2 weeks after TCR stimulation.

source_name: CD4+ T cells from peripheral blood

tag: tissue

value: peripheral blood

value: CD4+ T cells


title: PN56_WT_Cornea_Rep4


title: PB CD8 T cell

description:
ESiPS48_002
Gene expression 2 weeks after TCR stimulation.

source_name: CD8+ T cells from peripheral blood

value: CD8+ T cells


title: PN56_WT_Cornea_Rep2


title: 4 hrs post infection - donor 5 CRAM_OHU28K-344_11-18-05

description: 4 hrs post infection - donor 5

value: donor 5

value: 4 hrs post infection


title: PN56_Klf5CN_Cornea_Rep3


title: PN56_WT_Cornea_Rep1


title: LTH mock rep3

city: Beijing

first: Tong

last: Wei

address: No. 5 Yiheyuan Road

country: China

institute: Peking University

hyb_protocol: Fragmented cRNA were hybridized according to the standard Affymetrix protocol (Eukaryotic Target Preparation, Affymetrix) on the GeneChip Rice Genome Arrays.

scan_protocol: According to the GeneChip standard protocol (Eukaryotic Target Preparation, Affymetrix) using GeneArray® Scanner 3000.

data_processing: The data were analysed in R 2.15.0 using the RMA algorithm from affy package with default settings.

organism: Oryza sativa Japonica Group

source_name: LTH, mock-inoculated, 24 h

label_protocol: Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol (Eukaryotic Target Preparation, Affymetrix) .

growth_protocol: Rice plants grown in a greenhouse between April and May in Kunming, Yunnan Province, China.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Four-week-old rice seedlings were fungal- or mock-inoculated. And the fully-expanded third and fourth leaves of 20 rice seedlings were harvested after incubation under 100% humidity at 26 ℃.

value: leaf

tag: variety

value: LTH

value: mock


title: 24 hrs post infection - donor 5 CRAM_OHU28K-346_11-19-05

description: 24 hrs post infection - donor 5

value: monocyte differentiated macrophage

value: 24 hrs post infection

value: control


title: 24 hrs post infection - donor 5 CRAM_OHU28K-345_11-19-05

description: 24 hrs post infection - donor 5


title: LTH mock rep2


title: ILKS343D2

description: RNA was extracted from left the heart

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: MAS 5.0, signals were scaled to 150

source_name: Heart sample4

label_protocol: Affymetrix standard protocol

extract_protocol: Extract Protocol Extract Protocol Extraction protocol Total RNA (TRNA) was isolated from the heart samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

tag: genotype

value: ILKS343D Tg

value: Heart

value: 8-9 weeks

value: Female


title: 30 min post infection - donor 5 CRAM_OHU28K-342_11-18-05

description: 30 min post infection - donor 5

value: 30 min post infection


title: 4 hrs post infection - donor 5 CRAM_OHU28K-340_11-17-05

description: 4 hrs post infection - donor 5


title: ILKS343D3

description: RNA was extracted from the heart

source_name: Heart sample5


title: ILKR211A3

description: TRNA was extracted from heart

source_name: Heart sample 12

extract_protocol: Total RNA (TRNA) was isolated from heart samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

value: ILKR211A Tg


title: ILKR211A1

description: TRNA was extracted from heart

source_name: Heart sample7


title: WT Littermate1

description: RNA was extracted from left the heart

source_name: Heart sample8

value: WT


title: ILKR211A2

description: TRNA was extracted from heart

source_name: Heart sample9


title: WT Littermate3

description: TRNA was extracted from heart

source_name: Heart sample 11


title: 30 min post infection - donor 5 CRAM_OHU28K-343_11-18-05

description: 30 min post infection - donor 5

source_name: L.(V.)panamensis infected human macrophage

source_name: human macrophage


title: WT Littermate2

description: TRNA was extracted from heart

source_name: Heart sample 10


title: 24 hrs post infection - donor 2 CRAM_OHU28K-339_11-17-05

description: 24 hrs post infection - donor 2

value: donor 2


title: LTH treat rep3

source_name: LTH, fungal-inoculated, 24 h

value: M. oryzae


title: LTH mock rep1


title: Mycobacterium bovis BCG_Triclosan_60min_replicate2

city: Ft. Meade

first: Prashanthi

last: Mulinti

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description:
Triclosan treatment
M_bovis_TCS_60min_2.CEL

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Operating Software (GCOS) version 1.2

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Mycobacterium bovis BCG_Triclosan

label_protocol: Standard Affymetrix procedures. Approximately 10 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated M. bovis cultures at 37°C with shaking at 1.33 G using sterilized Middlebrook 7H9 broth for 5days, (ii) Mycobacteria were harvested, washed and resuspended in sterilized Lurria-Bertani (LB) broth with 0.1% (v/v) Tween 80. The cultures were incubated for a further 24 hours with shaking at 37°C. To test the efficacy of an antimicrobial against mycobacteria, several concentrations of triclosan were added to the cells.

extract_protocol: Total RNA was isolated after 10 and 60 min incubation with and without (control) triclosan using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX)[16]. The mycobacterial cells treated with triclosan and untreated cells as controls were harvested and resuspended in PBS buffer. The mini-bead beater-16 (Bio spec products Inc, Bartlesville, OK) was used to break down the cells for 1 minute (5 times) with intermittent holding on ice for 2 minutes after each beating period.

value: Pasteur 1173P2 Wild type

tag: agent

value: Triclosan


title: LTH treat rep2

value: leaf


title: Mycobacterium bovis BCG_Triclosan_60min_replicate3

description:
Triclosan treatment
M_bovis_TCS_60min_3.CEL


title: 24 hrs post infection - donor 2 CRAM_OHU28K-338_11-17-05

description: 24 hrs post infection - donor 2


title: WT littermat3

description: TRNA was extracted from heart

source_name: Heart sample6

tag: age


title: 4 hrs post infection - donor 2 CRAM_OHU28K-337_11-17-05

description: 4 hrs post infection - donor 2

tag: cell type

value: 4 hrs post infection


title: 30 min post infection - donor 2 CRAM_OHU28K-327_11-16-05

description: 30 min post infection - donor 2

tag: infection


title: WT littermate2

description: TRNA was extracted from heart

source_name: Heart sample3


title: Mycobacterium bovis BCG_Triclosan_10min_replicate3

description:
Triclosan treatment
M_bovis_TCS_10min_3.CEL


title: LTH treat rep1

value: LTH


title: Mycobacterium bovis BCG_Triclosan_60min_replicate1

description:
Triclosan treatment
M_bovis_TCS_60min_1.CEL


title: 24 hrs post infection - donor 1 CRAM_OHU28K-325_11-16-05

description: 24 hrs post infection - donor 1

value: monocyte differentiated macrophage

tag: individual

value: donor 1


title: ILKS343D

description: TRNA was extracted from heart

source_name: Heart sample2


title: IR22 mock rep3

source_name: IR22, mock-inoculated, 24 h

value: mock


title: Mycobacterium bovis BCG_Triclosan_10min_replicate2

description:
Triclosan treatment
M_bovis_TCS_10min_2.CEL

tag: time


title: WT littermate1

description: TRNA was extracted from heart left ventricle

source_name: Heart sample1

value: Male


title: 30 min post infection - donor 2 CRAM_OHU28K-326_11-16-05

description: 30 min post infection - donor 2

value: control


title: IR22 mock rep2


title: Lira_Rep3

description: RNA was extracted from left ventricle of heart

data_processing: affymetrix-algorithm-name = ExpressionStat. affymetrix-algorithm-version = 5.0. program-name = Expression Console. Signals were scaled to 150.

extract_protocol: Extract Protocol Extraction protocol Total RNA (TRNA) was isolated from blood samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

treatment_protocol: High Fat diet

value: Lira


title: Lira_Rep1

source_name: Heart sample4


title: Lira_Rep2

source_name: Heart sample5


title: IR22 treat rep3

source_name: IR22, fungal-inoculated, 24 h


title: CT_Rep2

value: placebo


title: 30 min post infection - donor 1 CRAM_OHU28K-323_11-15-05

description: 30 min post infection - donor 1

value: 30 min post infection


title: 24 hrs post infection - donor 1 CRAM_OHU28K-324_11-15-05

description: 24 hrs post infection - donor 1

value: 24 hrs post infection


title: CT_Rep3


title: Mycobacterium bovis BCG_no treatment_0min_replicate1

description:
No treatment
M_bovis_TCS_0min_1.CEL

value: No treatment


title: Mycobacterium bovis BCG_no treatment_0min_replicate2

description:
No treatment
M_bovis_TCS_0min_2.CEL


title: IR22 mock rep1


title: 30 min post infection - donor 1 CRAM_OHU28K-322_11-15-05

description: 30 min post infection - donor 1


title: Mycobacterium bovis BCG_Triclosan_10min_replicate1

description:
Triclosan treatment
M_bovis_TCS_10min_1.CEL


title: IR22 treat rep1


title: IR18 mock rep3

source_name: IR18, mock-inoculated, 24 h


title: Mycobacterium bovis BCG_no treatment_0min_replicate3

description:
No treatment
M_bovis_TCS_0min_3.CEL


title: IR22 treat rep2


title: IR18 mock rep2


title: Resveratrol treatment exp 3T3-L1 cells, T3

description: All the chips were controlled for presence of any defect before scanning.

scan_protocol: Affymetrix GCOS standard protocol

data_processing: GeneChip Operating Software was used for data processing

source_name: treated Murine 3T3-L1 cells

label_protocol: Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children. Affymetrix standard protocol

extract_protocol: Trizol standard protocol Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

tag: Murine 3T3-L1 progenitor adipocytes cell cultures,T3 (treated with resveratrol)


title: IR18 mock rep1


title: CT_Rep1


title: 24 hrs post infection - donor C CRAM_OHU28K-237_2-18-05

description: 24 hrs post infection - donor C

value: donor C


title: IR18 treat rep3

source_name: IR18, fungal-inoculated, 24 h

value: M. oryzae


title: 4 hrs post infection - donor C CRAM_OHU28K-236_2-18-05

description: 4 hrs post infection - donor C


title: IR18 treat rep2


title: IR18 treat rep1


title: Resveratrol treatment exp 3T3-L1 cells, T2

tag: Murine 3T3-L1 progenitor adipocytes cell cultures, T2 (treated with resveratrol)


title: 4 hrs post infection - donor B CRAM_OHU28K-233low-OI_2-10-05

description: 4 hrs post infection - donor B

value: donor B


title: 30 min post infection - donor B CRAM_OHU28K-232_2-10-05

description: 30 min post infection - donor B


title: Rat aorta Low WSS rep 1

status: Public on Dec 24 2012

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

country: Denmark

institute: National Genome Center

description: Rat aorta from region with Low WSS

hyb_protocol: RNA samples were hybridized at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.

scan_protocol: RNA samples were scanned at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.

data_processing: Raw data from cel-files was pre-processed using the RMA-algorithm. Gene annotation was downloaded from the Affymetrix web page (version RaGene-1_1-st-v1.na31.rn4). Probe sets without annotation and probe sets with mean expression level below 4 were omitted from analysis, resulting in the analysis of 13968 genes.

source_name: Rat aorta Low WSS

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

growth_protocol: Male Wistar rats under constant environmental temperature (21°C) and 12h:12h light/dark cycle, witg free access to standard rodent chow and water.

extract_protocol: With guidance from the CFD simulations, portions of the entire artery from high and low WSS regions, respectively, were cut out under RNase free conditions and directly put in pre-chilled Lysing Matrix D tubes (MP Biomedicals, Illkirch, France) containing Trizol (Invitrogen, Paisley, Scotland, UK). In order to yield significant amounts of RNA, tissue pieces from the specific high and low WSS regions from five animals were pooled for each sample (a total of 28 pools; 14 paired samples of high and low WSS regions). Samples were homogenized with FastPrep. Total RNA was isolated using RNeasy Mini kit (Qiagen, Maryland, USA), including DNase treatment for elimination of potential DNA contamination. RNA integrity was analyzed by the use of an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Paolo Alto, CA, USA) and quantified using NanoDrop (NanoDrop products, Wilmington, DE, USA).

treatment_protocol: No special treatment of rats - different regions of aorta were compared

value: Wistar

tag: stress

value: Low wall shear stress WSS

tag: replicate

value: aorta from region with Low WSS


title: Resveratrol treatment exp 3T3-L1 cells, CT3

source_name: untreated Murine 3T3-L1 cells

tag: Murine 3T3-L1 progenitor adipocytes cell cultures, Control 3 (untreated with resveratrol)


title: Resveratrol treatment exp 3T3-L1 cells, CT2

tag: Murine 3T3-L1 progenitor adipocytes cell cultures, Control 2 (untreated with resveratrol)