title: Hsbb-28-33

description:
P6-8-SLO-2 Print ID:Hsbb-28
Sample name: 85330

source_name: SLO Stimulated CD8+ cells


title: Hsbb-28-04

status: Public on Nov 24 2011

type: RNA

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

country: USA

institute: HiThru Analytics

description:
P5-4-SLO-2 Print ID:Hsbb-28
Sample name: 84925

hyb_protocol: Oligo arrays were hybridized to the cDNA probes in formamide based hybridization buffer (MWG's Coverslips Hybridization Buffer) at 42C overnight and subsequently washed in room temperature baths (2X SSC, 0.2% SDS; followed by 2X SSC, and then 0.2X SSC) for 12 min. each.  Fluorescent Cy3/Cy5 capture reagents were added to each array in MWG's Coverslips Hybridization Buffer.  Arrays were incubated for 3 hrs at 50C and washed as above.

scan_protocol: Axon's GenePix 4000B fluorescent scanner

data_processing: Data was processed using Partek Genomics Suite. Intensities in both channels were thresholded to 100, log2 transformation was done and duplicate probes averaged. Both channels of each array was median normalized. Control probes, as well as probes with mean < 7 or sd<0.7 were filtered out. Samples were again median normalized using the remaining probes.

molecule: total RNA

organism: Homo sapiens

source_name: SLO Stimulated CD4+ cells

label_protocol: Ovation Aminoallyl RNA amplification and Labeling System (NuGen) was used to reverse transcribe 40 ng total RNA (37C 30 min; 75C 15 min). 2 ug of aminoallyl amplified cDNA was labeled with Cy3 dye (antigen samples) and Cy5 dye (unstimulated samples) using Amersham Post Labeling Reactive Dye Packs; Cy3 and Cy5 samples were combined for hybridization

growth_protocol: PBMCs were cultured for 18 hrs in RPMI media supplemented with 10% fetal calf serum

extract_protocol: Cells were harvested and purified for CD3+ T cells and then for CD4+ and CD8+ cells by Dynal magnetic bead separation; total RNA was extracted with Trizol followed by phase separation with chloroform; RNA was purified with RNeasy Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cells were left unstinmulated or stimulated with microfilarial (MfAg) or streptolysin O (SLO) antigens

tag: patient id

tag: patient type

value: Expatriate

tag: cell type

tag: technical replicates

source_name: Unstimulated CD4+ cells


title: Hsbb-27-02

description:
P3-4-Mf-1 Print ID:Hsbb-27
Sample name: 85987

source_name: MfAg Stimulated CD4+ cells

value: Endemic


title: Hsbb-28-15

description:
P6-8-Mf-1 Print ID:Hsbb-28
Sample name: 84937

source_name: MfAg Stimulated CD8+ cells

source_name: Unstimulated CD8+ cells


title: Hsbb-28-14

description:
P6-4-Mf-1 Print ID:Hsbb-28
Sample name: 84936


title: Hsbb-28-32

description:
P6-4-SLO-2 Print ID:Hsbb-28
Sample name: 85329


title: Hsbb-28-05

description:
P5-8-SLO-2 Print ID:Hsbb-28
Sample name: 84926


title: Hsbb-27-05

description:
P3-8-Mf-2 Print ID:Hsbb-27
Sample name: 85990


title: Hsbb-27-04

description:
P3-4-Mf-2 Print ID:Hsbb-27
Sample name: 85989


title: Hsbb-28-02

description:
P5-4-SLO-1 Print ID:Hsbb-28
Sample name: 84923


title: Hsbb-28-16

description:
P6-4-Mf-2 Print ID:Hsbb-28
Sample name: 84938


title: Hsbb-27-26

description:
P5-4-Mf-1 Print ID:Hsbb-27
Sample name: 84208


title: Hsbb-28-30

description:
P6-4-SLO-1 Print ID:Hsbb-28
Sample name: 85327


title: Hsbb-20-38

description:
P4-4-Mf-2 Print ID:Hsbb-20
Sample name: 83754


title: Hsbb-27-27

description:
P5-8-Mf-1 Print ID:Hsbb-27
Sample name: 84209


title: Hsbb-27-08

description:
P4-4-SLO-2 Print ID:Hsbb-27
Sample name: 83758


title: Hsbb-27-29

description:
P5-8-Mf-2 Print ID:Hsbb-27
Sample name: 84211


title: Hsbb-28-17

description:
P6-8-Mf-2 Print ID:Hsbb-28
Sample name: 84939


title: Hsbb-20-39

description:
P4-8-Mf-2 Print ID:Hsbb-20
Sample name: 83755


title: Hsbb-20-37

description:
P4-8-Mf-1 Print ID:Hsbb-20
Sample name: 83753


title: Hsbb-28-03

description:
P5-8-SLO-1 Print ID:Hsbb-28
Sample name: 84924


title: Hsbb-25-36

description:
P3-4-SLO-2 Print ID:Hsbb-25
Sample name: 83507


title: Hsbb-28-31

description:
P6-8-SLO-1 Print ID:Hsbb-28
Sample name: 85328


title: Hsbb-27-12

description:
P4-4-Mf-1 Print ID:Hsbb-27
Sample name: 83760


title: Hsbb-25-34

description:
P3-4-SLO-1 Print ID:Hsbb-25
Sample name: 83505


title: Hsbb-27-09

description:
P4-8-SLO-2 Print ID:Hsbb-27
Sample name: 83759


title: Hsbb-27-28

description:
P5-4-Mf-2 Print ID:Hsbb-27
Sample name: 84210


title: Hsbb-25-37

description:
P3-8-SLO-2 Print ID:Hsbb-25
Sample name: 83508


title: Hsbb-25-35

description:
P3-8-SLO-1 Print ID:Hsbb-25
Sample name: 83506


title: Hsbb-27-07

description:
P4-8-SLO-1 Print ID:Hsbb-27
Sample name: 83757


title: Hsbb-27-06

description:
P4-4-SLO-1 Print ID:Hsbb-27
Sample name: 83756


title: M9ENL1, triplicate 2

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing: The data was processed using Bioconductor (affy package 1.30.0) by reading CEL files with default 'ReadAffy()' function. Data was background corrected with RMA, normalized by quantiles method, PM only correction, and then median polished. To account for batch variation, the log2 values were adjusted using ComBat (version 2) in GenePattern with a parametric Empirical Bayes priors distribution estimation method and without covariate analysis.

label: Biotin

source_name: M9-ENL1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: TEX cells were maintained in IMDM, 15% FBS, 2 mM L-glutamine, 1% Pen/Strep, 20 ng/mL SCF, 2 ng/mL IL3. M9-ENL1 cells were maintained in MEM, 20% FBS, 5% human adult plasma, 2mM L-glutamine, 1% Pen/Strep, 100 ng/mL SCF, 10 ng/mL IL3, 5 ng/mL IL7, 5 ng/mL FLT3-ligand.

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

treatment_protocol: Cells were treated with DMSO

tag: cell line

tag: treatment

value: DMSO

tag: leukemia type

value: pre B-ALL


title: THP1, replicate 2

source_name: THP-1 AML cells

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was harvested using the RNeasy Mini Kit from Qiagen

value: monocytic AML


title: M9ENL1, triplicate 3


title: Hsbb-24-29

description:
P2-8-S-2 Print ID:Hsbb-24
Sample name: 80845


title: M9ENL1, triplicate 1


title: THP1, replicate 1


title: Hsbb-24-26

description:
P2-4-S-1 Print ID:Hsbb-24
Sample name: 80841


title: Hsbb-24-28

description:
P2-8-S-1 Print ID:Hsbb-24
Sample name: 80843


title: Hsbb-24-25

description:
P2-8-Mf-2 Print ID:Hsbb-24
Sample name: 80647


title: Hsbb-24-24

description:
P2-8-Mf-1 Print ID:Hsbb-24
Sample name: 80646


title: HL60, replicate B1

source_name: HL60 AML cells

value: promyelocytic AML


title: Hsbb-24-27

description:
P2-4-S-2 Print ID:Hsbb-24
Sample name: 80842


title: control rep2

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: scramble control siRNA sample

hyb_protocol: Hybridization to the HumanHT-12 v4 Expression BeadChip (Illumina) was performed according to manufacturer's protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression data were transfomed to log2 scale and normalized using quantile normalization without background subtraction

label: biotin

source_name: empty vector replicate 2

label_protocol: Next, 500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: After 72h, RNA was isolated using the RNeasy plus mini kit (QIAGEN) according to manufacturer's protocol. Knockdown of ETV6 was evaluated by RT-PCR and western blot analysis

treatment_protocol: SiRNA mediated knockdown of ETV6 in LOUCY cells was performed by electroporation of 50nM ETV6 specific siRNAs (Applied Biosystems) or 50nM of scramble control siRNAs, using an exponential decay pulse (300 V, 1000 µF; Genepulser MxCell, Bio-Rad)

value: LOUCY

tag: sample type

value: scramble control siRNAs


title: TEX, triplicate 3

source_name: TEX cells

value: TEX

value: AML


title: HL60, replicate A1

growth_protocol: HL-60 cells were cultivated in RPMI medium with 10 % FCS, 1 % penecillin and 1 % streptavidin at 37°C and 5 % CO2


title: ETV6 siRNA rep1

description: ETV6 siRNA sample

source_name: siRNA ETV6 replicate 1

value: siRNA meditated ETV6 knockdown


title: HL60, replicate B2


title: Hsbb-24-22

description:
P2-4-Mf-1 Print ID:Hsbb-24
Sample name: 80644


title: ETV6 siRNA rep2

description: ETV6 siRNA sample

source_name: siRNA ETV6 replicate 2


title: Hsbb-24-13

description:
P1-8-MfAg-2 Print ID:Hsbb-24
Sample name: 80505


title: Hsbb-24-11

description:
P1-4-MfAg-2 Print ID:Hsbb-24
Sample name: 80503


title: Hsbb-24-12

description:
P1-8-MgAg-1 Print ID:Hsbb-24
Sample name: 80504


title: Hsbb-24-23

description:
P2-4-Mf-2 Print ID:Hsbb-24
Sample name: 80645


title: BC binding (hg18)

type: genomic

city: Meguro-ku

first: aya

last: nonaka

state: Tokyo

address: 4-6-1, Komaba

country: Japan

institute: The University of Tokyo

description: beta-catenin ChIP, Biological Reps 1-2, chip A.

hyb_protocol: Approximately 7μg of DNA was hybridized per array using the Affymetrix hybridization kit.

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

data_processing:
The BAR file was generated by Model based Analysis of Tiling-arrays (MAT) software.
Human genome build hg18.

molecule: genomic DNA

source_name: BC ChIP DNA from SW480

label_protocol: Samples were enzymatically fragmented and labeled using Terminal Transferase (Roche) to add a biotinylated compound to the ends of the fragments.

extract_protocol: Chromatin immunoprecipitation (ChIP) assays were carried out in accordance with a previous report (Schwartz DR et al., 2003 (PMID 12782598)).

tag: chip antibody

value: beta-catenin rabbit polyclonal

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number

source_name: Input DNA from SW480


title: control rep1

description: scramble control siRNA sample

source_name: empty vector replicate 1


title: Pf-5_tannic160_replicate 6

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

description: Technical replicate 2 of biological replicate 3

hyb_protocol: Microarray slides were immersed in pre-hybridization buffer (1 % BSA, 5X SSC, 0.1 % SDS, 0.45 mm-filtered) before hybridization. Slides were washed with sterile water (4x) and isopropanol (3x), spin-dried and covered with lifterslip. cDNA probes were dried using Speedvac and then resuspended in hybridization buffer (50 % formamide, 5X SSC, 0.1 % SDS, 0.45 mm-filtered). Probes were heated at 95 degrees Celcius (15 min) before applying to the slides. Hybridization was performed overnight at 42 degrees Celcius. After hybridization, slides were washed with the following steps: 2x wash buffer 1 (1X SSC, 0.2% SDS) at 42 degrees Celcius, 1x wash buffer 2 (0.1X SSC, 0.1% SDS) and 3x wash buffer 3 (0.1X SSC, 0.1% SDS).

scan_protocol: Images were scanned with Axon 4000B scanner and GenePix 4.0 software

data_processing: The microarray data was analyzed with Spotfinder (TIGR) and normalized using the LOWESS algorithm in the TIGR-MIDAS package with block mode and smoothing parameter value of 0.33

label: Alexa fluor 555 (IB)

organism: Pseudomonas fluorescens

source_name: Pseudomonas fluorescens Pf-5, non-tannic acid treated

label_protocol: Reverse transcription of RNA samples was performed using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) with random hexamer primers. Approximately 7 µg of total RNA was used for cDNA synthesis in each reaction. cDNA samples were labeled with either Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen) according to manufacturer's instruction. Spike-in controls were made from RNA transcribed from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) with the MegaScript Kit (Ambion). Spike-in control were prepared as follow. For Alexa Fluor 555 pool,  0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.06 ng ltp6 RNA, 0.25 ng crp1 RNA, 0.95 ng nac RNA, 0.08 ng xcp2 RNA, 0.17 ng prk RNA and 0.21 ng tim RNA. For Alexa Fluor 647 pool, 0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.02 ng ltp6 RNA, 0.08 ng crp1 RNA, 0.31 ng nac RNA, 0.25 ng xcp2 RNA, 0.50 ng prk RNA and 0.63 ng tim RNA.

growth_protocol: Pseudomonas fluorescens Pf-5 was grown in Mueller-Hinton broth supplemented with 100 µg/ mL streptomycin. The cultures were grown aerobically with shaking at room temperature until reaching OD600 of about 1.3.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and and treated with RNAse-free DNAse (Ambion) as per manufacturer's instruction

treatment_protocol: The treated cultures were supplemented with 160 µg/mL tannic acid (Sigma-Aldrich) whereas the control cultures were not treated with any tannic acid

tag: strain

label: Alexa fluor 555 (IA)

source_name: Pseudomonas fluorescens Pf-5, tannic acid (160 µg/ mL) treated


title: TEX, triplicate 1


title: TEX, triplicate 2


title: HL60, replicate A2


title: Hsbb-22-31_s8-m8-4

description:
M8S8-4 Print ID:Hsbb-22
Sample name: 79799

source_name: SLO Stimulated CD8+ cells


title: Hsbb-22-29_s4-m4-2

description:
M4S4-2 Print ID:Hsbb-22
Sample name: 79797

source_name: SLO Stimulated CD4+ cells

source_name: Unstimulated CD4+ cells


title: Hsbb-22-30_s8-m8-3

description:
M8S8-3 Print ID:Hsbb-22
Sample name: 79798


title: Hsbb-22-28_s4-m4-1

description:
M4S4-1 Print ID:Hsbb-22
Sample name: 79796


title: Pf-5_tannic160_replicate 5

description: Technical replicate 1 of biological replicate 3


title: Hsbb-24-10

description:
P1-4-MfAg-1 Print ID:Hsbb-24
Sample name: 80502

source_name: MfAg Stimulated CD4+ cells


title: Pf-5_tannic20_replicate 3

description: Technical replicate 3 of biological replicate 1

treatment_protocol: The treated cultures were supplemented with 20 µg/mL tannic acid (Sigma-Aldrich) whereas the control cultures were not treated with any tannic acid

source_name: Pseudomonas fluorescens Pf-5, tannic acid (20 µg/ mL) treated


title: Pf-5_tannic160_replicate 2

description: Technical replicate 1 of biological replicate 2


title: Mr vs. Fc, 13373938 A

status: Public on Nov 23 2011

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: Hybridizations conducted using Balanced, Interwoven Loop Design: 2 Dyes Swaps and 4 total technical replicates.

hyb_protocol: Products of the cDNA synthesis reactions were combined according to dye-swap assignments and hybridized onto microarrays.  Two µL of blocking agent, locked nucleic acid (LNA) dT Blocker (Genisphere) was included in each hybridization.  RNA sample probes were hybridized at 55ºC overnight (~16h), then washed for 20 min in 60ºC 2x SSC including 0.2% SDS, 20 min in 2x SSC at room temperature, and 20 min in 0.2x SSC also at room temperature.  Slides were then spin dried and subsequently hybridized to A647- and Cy3-labeled secondary hybridization probes in 100 µL hybridization buffer with 1 µL of Anti-Fade Reagent for 4h at 60ºC.  Microarrays were washed as described above only at 15 minute wash intervals and spin dried.  Slides were stored for no more than 1 week in a darkened desiccation chamber prior to microarray scanning.

scan_protocol: Microarrays were scanned at 5μm using a VersArray Chipreader™ (Bio-Rad, Hercules, CA). To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the High Intensity Scan. Independent statistical analyses were run on high- and low-intensity scan data, and significant targets were summed among analyses. Grids were manually fit to microarray spots for each image file and both positive and negative controls were flagged prior to spot analysis. Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from the analysis.

data_processing: Summary data consisted of LOWESS-normalized Cy3:A647 ratio values calculated using background-normalized median-signal intensities. The statistical analysis was conducted using Bayesian Analysis of Gene Expression Levels (BAGEL) software version 3.62 (Townsend and Hartl, 2002).  Non-overlapping 97.5% confidence intervals (C.I.) among treatments were established a priori as statistically significant differences in expression.  Only targets for which both technical replicates were found to be differentially expressed were considered to be true differentially expressed transcripts.

organism: Colinus virginianus

source_name: male brain, RDX seizure

label_protocol: Probes for microarray hybridizations were prepared from 600 ng total RNA/sample following the Genisphere®, Array 900™ Alexa Fluor 647 and Cy3 secondary hybridization labeling protocol (Genisphere, Hatfield, PA) according to manufacturer’s instructions.

growth_protocol: Juvenile Northern bobwhite quail (age 12 weeks) were obtained from Trace Pheasantry. On arrival to the U.S. Army Center for Health Promotion and Preventive Medicine (CHPPM), birds were kept individually in 24-cage units; each cage was 28 cm wide by 30.5 cm tall by 38 cm deep and volume did not exceed 1.3 ml.

extract_protocol: RNeasy® Mini RNA extraction kits (Qiagen, Valencia, CA) were used for total RNA extractions.  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® RNA. Only samples with a 28s/18s ratio {greater than or equal to} 1.4 and RNA integrity number (RIN) {greater than or equal to} 6 were used for downstream applications.  The majority of RNA samples greatly exceeded these minimum requirements.  Total RNA was utilized for cDNA library construction, microarray analysis and RT-qPCR.

treatment_protocol:
A 14-day RDX high-dose exposure administering RDX at 0, 20, 80, 125, or 180 mg/kg/day. Each treatment group included seven birds (at least three of each sex per treatment). All RDX doses in the 14-day high-dose experiment elicited seizures within 3 days of experiment initiation (Johnson et al., 2007).

The complete toxicology protocol is presented in: Johnson MS, Quinn MJ, Bazar MA, KA Gust, Escalon BL Perkins EJ. (2007) Subacute Toxicity of Oral 2,6-Dinitrotoluene and 1,3,5-trinitro-1,3,5-triazine (RDX) Exposure to the Northern Bobwhite (Colinus virginianus) Environ Toxicol Chem 26(7):1481–1487 (PMID 17665690).

tag: gender

value: male

tag: developmental stage

value: juvenile

tag: tissue

value: brain

tag: treatment duration

value: 14 days

source_name: female brain, control non-seizure

value: female


title: Fc vs. Fr, 13373939 A

source_name: female brain, RDX seizure


title: Fr vs. Mc, 13373940 A

source_name: male brain, control non-seizure


title: Pf-5_tannic20_replicate 4

description: Biological replicate 2


title: Mc vs. Mr, 13373941 A


title: Pf-5_tannic160_replicate 1

description: Biological replicate 1


title: Pf-5_tannic160_replicate 4

description: Technical replicate 3 of biological replicate 2


title: Pf-5_tannic160_replicate 3

description: Technical replicate 2 of biological replicate 2


title: Pf-5_tannic20_replicate 1

description: Technical replicate 1 of biological replicate 1


title: Pf-5_tannic20_replicate 6


title: Fc vs. Fr, 13373932 A


title: Pf-5_tannic20_replicate 5


title: Mc vs. Mr, 13373934 A


title: Mc vs. Mr, 13373930 A


title: Pf-5_tannic20_replicate 2

description: Technical replicate 2 of biological replicate 1


title: Mc vs. Fr, 13373928 A


title: Fr vs. Fc, 13373929 A


title: Mr vs. Fc, 13373923 A


title: Mr vs. Fc, 13373931 A


title: Mr vs. Mc, 13373927 A


title: Mc vs. Mr, 13373920 A


title: Fr vs. Mc, 13373921 A


title: Mr vs. Mc, 13373919 A


title: Fc vs. Mr, 13373926 A


title: Fc vs. Fr, 13373922 A


title: Fr vs. Mc, 13368845 A


title: Fr vs. Mc, 13373933 A


title: 0 vs. 60, 13368866

description: Hybridizations conducted using an Interwoven Loop Design.

scan_protocol: Microarrays were scanned at 5μm using a VersArray Chipreader™ (Bio-Rad, Hercules, CA). To broaden signal detection, each microarray was scanned at high and low laser power to resolve low-intensity spots and reduce signal saturation, respectively (Skibbe et al., 2006). This dataset represents the Low Intensity Scan. Independent statistical analyses were run on high- and low-intensity scan data, and significant targets were summed among analyses. Grids were manually fit to microarray spots for each image file and both positive and negative controls were flagged prior to spot analysis. Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from the analysis.

source_name: male brain, control

treatment_protocol:
A 14-day 2,6-DNT exposure in male Northern bobwhite administering 2,6-DNT at 0, 50, 100, 190, or 350 mg/kg/day with each treatment group including seven birds (at least three of each sex per treatment). The males were examined in this microarray assay.

The complete toxicology protocol is presented in: Johnson MS, Quinn MJ, Bazar MA, KA Gust, Escalon BL Perkins EJ. (2007) Subacute Toxicity of Oral 2,6-Dinitrotoluene and 1,3,5-trinitro-1,3,5-triazine (RDX) Exposure to the Northern Bobwhite (Colinus virginianus) Environ Toxicol Chem 26(7):1481–1487 (PMID 17665690).

source_name: male brain, 2,6-DNT, 60mg/kg/d

value: 2,6-dinitrotoluene (2,6-DNT)

tag: treatment dosage


title: Mc vs. Fr, 13373916 A


title: 0 vs. 60, 13368870


title: Mr vs. Fc, 13368843 A


title: 60 vs. 0, 13425871


title: 60 vs. 0, 13368867


title: Fc vs. Fr, 13368844 A


title: Fc vs. Mr, 13373918 A


title: 0 vs. 0, 13368868


title: Fr vs. Fc, 13373917 A


title: 60 vs. 0, 13425872


title: 0 vs. 0, 13368869


title: 0 vs. 60, 13368862


title: Brain_SUUR II

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description:
ch1 raw data file: 415603-A4_DamSur_b(2)_100,640_635.pair
ch2 raw data file: 415603-A4_Dam_b(2)_100,530_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)

hyb_protocol: The labeled  DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containin\herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using ArrayStar software (http://www.dnastar.com/). Each array was RMA background corrected and quantile normalized.

organism: Drosophila melanogaster

source_name: Dam-SUUR binding in Br

label_protocol: 1 µg  DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 50 biological samples (embryos, salivary glands or brains) were dissected in PBS and homogenized. 10ul of 100mg/ml Dispase II were added to each sample and kept at 56C for 6h. DNA was extracted using standard phoenol-chloroform-isopropanol protocol. DamID samples preparation was performed as described previously (Greil et al., 2006)

treatment_protocol: dissection in PBS

tag: cell origin

value: 3rd inst female larval brains

tag: protocol

value: Dam-SUUR binding

source_name: Dam alone in Br

value: Dam-alone binding


title: 60 vs. 0, 13425872A

treatment_protocol:
A 14-day 2,6-DNT exposure in male Northern bobwhite administering 2,6-DNT at 0, 50, 100, 190, or 350 mg/kg/day with each treatment group including seven birds (at least three of each sex per treatment). The males were examined in this microarray assay.

The complete toxicology protocol is presented in: Johnson MS, Quinn MJ, Bazar MA, KA Gust, Escalon BL Perkins EJ. (2007) Subacute Toxicity of Oral 2,6-Dinitrotoluene and 1,3,5-trinitro-1,3,5-triazine (RDX) Exposure to the Northern Bobwhite (Colinus virginianus) Environ Toxicol Chem 26(7):1481–1487 (PMID 17665690).
A subchronic 60d 2,6-DNT exposure in Northern bobwhite administering 2,6-DNT at 0, 5, 10, 40, or 60 mg/kg/day with each treatment including 12 replicates per sex.


title: Brain_SUUR I

description:
ch1 raw data file: 415603-A3_DamSur_b_100,640_635.pair
ch2 raw data file: 415603-A3_Dam_b_100,520_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)


title: 0 vs. 0, 13368869A


title: Salivary glands_SUUR II

description:
ch1 raw data file: 415603-A2_DamSur_sg(2)_100,620_635.pair
ch2 raw data file: 415603-A2_Dam_sg(2)100,520_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)

source_name: Dam-SUUR binding in SG

value: 3rd inst female larval salivary glands

source_name: Dam alone in SG


title: 0 vs. 60, 13368870A


title: Embryo_SUUR II

description:
ch1 raw data file: 343365-A4_DS2_100,6100_635.pair
ch2 raw data file: 343365-A4_D2_100,530_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)

source_name: Dam-SUUR binding in Em

treatment_protocol: harvesting from media

value: 12-14h Embryo

source_name: Dam alone in Em


title: Salivary glands_SUUR I

description:
ch1 raw data file: 415603-A1_DamSur_sg_100,620_635.pair
ch2 raw data file: 415603-A1_Dam_sg_560_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)


title: 0 vs. 0, 13368868A


title: Embryo_SUUR I

description:
ch1 raw data file: 343365-A3_DS1_100,620_635.pair
ch2 raw data file: 343365-A3_D1_100,510_532.pair
amplified genomic DNA
log2(SUUR-Dam binding/Dam alone binding)


title: Mc vs. F60, 13425901

description: Hybridizations conducted using Balance Interwoven Loop Design including 2 technical replicates per treatment and 2 dye swaps.

source_name: male, control

treatment_protocol:
A subchronic 60d 2,6-DNT exposure in Northern bobwhite administering 2,6-DNT at 0, 5, 10, 40, or 60 mg/kg/day with each treatment including 12 replicates per sex.

The complete toxicology protocol is presented in: Quinn Jr. MJ, MA Bazar, CA McFarland, EJ Perkins, KA Gust, RM Gogal, MS Johnson (2007) Effects of Subchronic Exposure to 2,6-Dinitrotoluene in the Northern Bobwhite (Colinus virginianus) Environ Toxicol Chem. 26(10):2202-2207 (PMID 17867889).

source_name: female brain, 2,6-DNT, 60mg/kg/d

value: 60 days


title: 60 vs. 0, 13425871A


title: M60 vs. Mc, 13425899

source_name: male, 2,6-DNT, 60mg/kg/d


title: 0 vs. 60, 13368866A


title: F60 vs. Fc, 13425904

source_name: female, 2,6-DNT, 60mg/kg/d

source_name: female brain, control


title: 60 vs. 0, 13368867A


title: KO_gata7

city: Bethesda

first: Natalia

last: Shulzhenko

state: MD

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

description:
gata7green
full-thickness 2 cm of jejunum from the middle of small intestine

hyb_protocol: Corresponding experimental (knock-out) and control samples were co-hybridized using Agilent protocol

scan_protocol: Images were scanned using Agilent scanner

data_processing: After subtraction of local background, signal intensity values were filtered to remove those lower than 10 and median normalized using BRB Array Tools.

organism: Mus musculus

label_protocol: 20 ug of total RNA were directly fluorescently labeled in a reverse transcription reaction using Cy3-dUTP or Cy5-dUTP (GE Healthcare) and Oligo(dT)12-18 Primer and SuperScript II reverse transcriptase

extract_protocol: tissues were homogenized in Trizol or RLT buffer from Qiagen RNAeasy KIT. Total RNA were isolated according to standard protocol

tag: genotype/variation

value: conditional KO (Gata4KOvil)

value: jejunum

tag: pair

value: X

tag: additional id


title: control_gata5

description:
gata5green
full-thickness 2 cm of jejunum from the middle of small intestine

value: control


title: KO_gata5

description:
gata5red
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_gata8

description:
gata8green
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_gata3

description:
gata3green
full-thickness 2 cm of jejunum from the middle of small intestine


title: KO_gata3

description:
gata3red
full-thickness 2 cm of jejunum from the middle of small intestine


title: F60 vs. Fc, 13431681

tag: treatment


title: KO_gata4

description:
gata4green
full-thickness 2 cm of jejunum from the middle of small intestine


title: Fc vs. M60, 13425898

source_name: female, control


title: control_gata2

description:
gata2red
full-thickness 2 cm of jejunum from the middle of small intestine


title: Fc vs. M60, 13425896


title: Δscj1_rep3

city: Singapore

first: Guillaume

last: Thibault

address: 1 Research Link, National University of Singapore

department: Cell Stress and Homeostasis

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Hybridized on Custom Microarray Agilent GE 8x60K array

scan_protocol: Arrays were scanned using High-resolution DNA Microarray Scanner model: G2505C (Agilent Technologies).

data_processing: Data was analyzed using GeneSpring GX software (Agilent Technologies).

organism: Saccharomyces cerevisiae

label_protocol: Labeling System with 100 ng of total RNA as starting material following manufacturer instruction: One-Color Microarray-Based Gene Expression Analysis Protocol version 6.5 (Agilent Technologies).

growth_protocol: Culture were grown to an OD600 of 0.25 at 30C in selective synthetic complete media.

extract_protocol: Total RNA was extracted by the hot acid phenol method as previously described (Spellman et al., 1998). Total RNA was subsequently cleaned up using Rnease Mini Kit (Qiagen).

treatment_protocol: The UPR was induced by the addition of 2 mM DTT or 1 µg/ml Tm for one hour prior to harvest the cells.

tag: strain background

value: W303, mat alpha


title: 0 vs. 60, 13368862A

value: male


title: control_gata4

description:
gata4red
full-thickness 2 cm of jejunum from the middle of small intestine


title: Mc vs. F60, 13431680

value: juvenile


title: Influenza vaccine #2

type: other

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

description:
SAMPLE 5
Human patient with 32 titer

hyb_protocol: Primary was added at 1:500 to peptide array for 1 hour.  Wash buffer is 1x PBS pH 7.2, 0.5% Tween 20, 0.5% BSA and is used for 1 hour for each wash.  Incubation temperature is 37C.  Tecan Hybstation 4800 was used for all incubations.

scan_protocol: Slides were scanned on the Perkin Elmer 4channel microarray scanner at 10um, 70PMT, 100% laser power at 540nm.

data_processing: Numerical data was obtained from Molecular Probes' GenePix Pro 6.  Tiff files were aligned, gpr (GenePix Report) files were saved as-is.

molecule: other

source_name: influenza vaccine recipients

label_protocol: Biotinylated anti-human secondary from Novus was used to detect a 1:500 primary concentration of human IgG.  Secondary concentration was 5nm.  Alexa555-labeled Streptavidin was used at 5nm to detect secondary antibodies.

extract_protocol: Serum was unmodified.

treatment_protocol: Valley Fever patients were seen at University of Arizona Health Care Center between 1999 and 2006. Serym was stored at -80C until tested.  Influenza vaccine recipients were drawn on day 28 post-2006 seasonal influenza vaccine receipt.  Serum was stored at -20C until tested.

value: serum


title: Influenza vaccine #3

description:
SAMPLE 6
Human patient with 32 titer


title: KO_gata1

description:
gata1red
full-thickness 2 cm of jejunum from the middle of small intestine


title: KO_gata2

description:
gata2green
full-thickness 2 cm of jejunum from the middle of small intestine


title: Δscj1_rep2


title: M60 vs. Mc, 13431677

value: brain


title: Δscj1_rep1


title: Cocci #3

description:
SAMPLE 3
Human patient with 32 titer

source_name: Valley Fever (Coccidiodes) patients


title: M60 vs. Mc, 13431679


title: control_IgA9

description:
IgA9red
full-thickness 2 cm of jejunum from the middle of small intestine

hyb_protocol: Corresponding experimental (knock-out) and control samples were co-hybridized using MAUI hybridization system as described by Schaupp et al. 2005; PMID: 15679093

scan_protocol: Images were scanned by GenePix4000B Scanner (Axon Instruments/Molecular Devices).

value: balbc

tag: array name

tag: tissue type


title: Δlhs1_rep3


title: Δlhs1_rep2


title: Cocci #2

description:
SAMPLE 2
Human patient with 32 titer


title: F60 vs. Fc, 13431674

value: female

value: 2,6-dinitrotoluene (2,6-DNT)


title: Δlhs1_rep1


title: KO_IgA9

description:
IgA9green
full-thickness 2 cm of jejunum from the middle of small intestine

value: IgA KO (lacking IgA)


title: KO_IgA8

description:
IgA8red
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_gata1

description:
gata1green
full-thickness 2 cm of jejunum from the middle of small intestine


title: Fc vs. M60, 13431676


title: HIV-1 5 [miRNA]

city: Pittsburgh

first: Pruthvi S. R.

last: Nagilla

state: PA

address: 416 Parran Hall, 130 DeSoto Street

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

description: Infected PBMC from donor 5

data_processing: Raw Ct values obtained after the 7900 HT RT-PCR run were uploaded onto SA Biosciences online analysis tool to generate fold changes for differential expression of miRNA in Infected group i.e. HIV-1 (N=6) over Uninfected group i.e Control group (N=6).

label: SYBR Green/Rox

source_name: PBMC

label_protocol:
One ug of total RNA enriched for miRNA was reverse transcribed to cDNA using SA Biosciences RT2 miRNA first strand Kit (MA-03). Then the cDNA product along with SA Biosciences RT2 Real-time SYBR Green/Rox PCR master mix (PA-012) was used for detection.
Cycles   Duration & Temperature  1           10 minutes at 95°C  40             15 seconds at 95°C -> 40 seconds at 60°C -> 30 seconds at 72°C

growth_protocol: We purchased normal donor blood from the American Red Cross Blood Bank in Pittsburgh using appropriate IRB approval forms from the University of Pittsburgh. PBMCs were isolated by Ficoll-Hypaque gradient centrifugation. Freshly isolated normal donor PBMCs (5×106/mL) were stimulated with 5 µg/ml PHA-P (Sigma, St. Louis, MO) for three days. Cells were washed, divided into two parts and cultured in RPMI medium (GIBCO, CA) containing 10% FBS (Hyclone, Logan, UT), 1% L-glutamine (Cambrex, MD), 1% penicillin-streptomycin (GIBCO, CA), and IL-2 (200 U/mL, Chiron, Emoryville, CA).

extract_protocol: Total RNA was isolated using the TRIzol method (InVitrogen) as suggested by the manufacturer. Next, to enhance the sensitivity and detection, we enriched the small RNA using a microRNA isolation kit (SABiosciences) with two separating columns as per the manufacturer's instructions.

treatment_protocol: One half of the cells were subsequently infected with 0.1 MOI of virus particles using standard protocols as described and the remaining half of the culture is maintained under similar conditions and used as control. Seven days post infection (pi), cells were collected and frozen for total RNA isolation.

value: Blood

tag: infection


title: HIV-1 4 [miRNA]

description: Infected PBMC from donor 4


title: HIV-1 3 [miRNA]

description: Infected PBMC from donor 3


title: HIV-1 6 [miRNA]

description: Infected PBMC from donor 6


title: Mc vs. F60, 13431673


title: Cocci #1

description:
SAMPLE 1
Human patient with 32 titer


title: KO_IgA7

description:
IgA7red
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_IgA7

description:
IgA7green
full-thickness 2 cm of jejunum from the middle of small intestine


title: F60 vs. Mc, 13431672

description: Hybridizations conducted using Balance Interwoven Loop Design including 2 technical replicates per treatment and 2 dye swaps.

source_name: male brain, control


title: HIV-1 2 [miRNA]

description: Infected PBMC from donor 2


title: Δalg5_rep1


title: Δalg5_rep2


title: Δalg5_rep3


title: Fc vs. F60, 13431671


title: HIV-1 1 [miRNA]

description: Infected PBMC from donor 1


title: Control 6 [miRNA]

description: Uninfected PBMC from donor 6


title: WT_DTT_rep3

source_name: WT treated 1h with 2 mM DTT


title: Control 5 [miRNA]

description: Uninfected PBMC from donor 5


title: M60 vs. Fc, 13431670


title: Control 4 [miRNA]

description: Uninfected PBMC from donor 4


title: control_IgA6r

description:
IgA6r red
full-thickness 2 cm of jejunum from the middle of small intestine


title: KO_IgA5r

description:
IgA5r green
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_IgA5r

description:
IgA5r red
full-thickness 2 cm of jejunum from the middle of small intestine


title: Fc vs. F60, 13431664


title: M60 vs. Fc, 13431663


title: control_IgA4

description:
IgA4red
full-thickness 2 cm of jejunum from the middle of small intestine


title: WT_DTT_rep2


title: Mc vs. M60, 13431667

source_name: male brain, 2,6-DNT, 60mg/kg/d


title: Control 2 [miRNA]

description: Uninfected PBMC from donor 2


title: Control 3 [miRNA]

description: Uninfected PBMC from donor 3


title: F60 vs. Mc, 13431666


title: KO_IgA6r

description:
IgA6r green
full-thickness 2 cm of jejunum from the middle of small intestine


title: WT_DTT_rep1


title: Control 1 [miRNA]

description: Uninfected PBMC from donor 1


title: WT_rep3

source_name: Wild type


title: KO_IgA3r

description:
IgA3Rred
full-thickness 2 cm of jejunum from the middle of small intestine


title: KO_IgA4

description:
IgA4green
full-thickness 2 cm of jejunum from the middle of small intestine


title: control_IgA3r

description:
IgA3Rgreen
full-thickness 2 cm of jejunum from the middle of small intestine


title: WT_rep2


title: control_IgA3

description:
IgA3green
full-thickness 2 cm of jejunum from the middle of small intestine


title: WT_rep1


title: KO_IgA2

description:
IgA2red
full-thickness 2 cm of jejunum from the middle of small intestine


title: M60 vs. Fc, 13431659


title: Fc vs. F60, 13431660


title: Mc vs. M60, 13425906


title: Mc vs. M60, 13431662


title: Mc vs. F60, 13425901a


title: F60 vs. Mc, 13431661


title: F60 vs. Fc, 13425904a


title: M60 vs. Mc, 13425899a


title: control_IgA1

description:
IgA1red
full-thickness 2 cm of jejunum from the middle of small intestine


title: Fc vs. M60, 13425896a


title: F1  Aire WT MEC rep1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 4-6 weeks Isolation: FACS-sorted CD45- Ly51int classIIhi MECs Strain: (B6xNOD)F1

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640. After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: Raw data were preprocessed with the RMA algorithm

source_name: MHC class II high thymic medullary epithelial cells, F1aireWT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

treatment_protocol: MECs were isolated from thymi by standard Collagenase Dispase protocol and sorted into Trizol on Aria instrument

tag: cell type

tag: genotype

value: Aire WT

tag: genetic background


title: F1  Aire KO MEC rep2

description: 4-6 weeks Isolation: FACS-sorted CD45- Ly51int classIIhi MECs Strain: Aire-/-(B6xNOD)F1

source_name: MHC class II high thymic medullary epithelial cells, F1aireKO

value: Aire KO


title: control_IgA2

description:
IgA2green
full-thickness 2 cm of jejunum from the middle of small intestine

tag: gender

tag: strain


title: Goat #10  0 Hours Blood

city: Lodi

first: Marcello

last: Del Corvo

address: via Einstein - Loc. Cascina Codazza

department: Bioinformatics

country: Italy

institute: CNR-Ibba

description: Goat10 _0h_blood

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/µl Salmon Sperm DNA, 0.05% SDS) for 30 minutes at 45 °C. 4 µg of labeled aRNA were fragmented by incubation with 5 µl of Fragmentation Solution (200mM Tris Acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc) for 20 min at 95 °C.  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/µl Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as the following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST wash solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a GenePix 4000B microarray scanner (Axon, Toronto, CA) and the accompanying acquisition software (CombiMatrix Microarray Imager Software). Multiple scanning at different PMT was provided for each hybridization

data_processing: Data were extracted and loaded into R software using the Limma analysis package from Bioconductor and the signal intensities were processed and normalized using standard procedures. Limma performs a linear regression analysis on the hybridizations, using a group-means parameterization approach to compare the different conditions and performs a false discovery rate adjustment with Benjamini-Hochberg correction for multiple testing [Smyth, 2004]. DE genes were selected using an adjusted P-value cut off equal to 0.01

organism: Capra hircus

source_name: White blood cells

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with Cy5-ULS using the RNA Amplification and Labelling Kit from CombiMatrix (ampULSe Cat. no. GEA-022; Kreatech Biotechnology, Amsterdam, The Netherlands) according to manufacturer's instructions

extract_protocol: Total RNA was extracted  with Trizol reagent following the instructions of the supplier (Invitrogen, Milan, Italy). High-quality RNA was obtained through purification with RNeasy MinElute spin column (Qiagen, Milan, Italy) and eluted in RNase-free water. RNA was then quantified using a NanoDrop spectrophotometer (Agilent, Santa Clara, CA) and quality-checked using a Bioanalyser 2100 (Agilent, Santa Clara, CA).

tag: challenge

value: S. aureus

value: White blood cells

tag: time

tag: sample type

value: White blood cells  0h


title: F1  Aire KO MEC rep1

value: MHC class II high thymic medullary epithelial cells


title: Fc vs. M60, 13425898a

tag: developmental stage

tag: tissue

tag: treatment dosage

tag: treatment duration

value: 60 days


title: Goat #9  0 Hours Blood

description: Goat9 _0h_blood


title: Goat #9  30 Hours Blood

description: Goat9 _30h_blood

value: 30h after challenge

value: White blood cells  30h after challenge


title: F1  Aire WT MEC rep3


title: KO_IgA10r

description:
IgA10r red
full-thickness 2 cm of jejunum from the middle of small intestine

tag: genotype/variation

value: jejunum

tag: additional id


title: F1  Aire WT MEC rep2


title: control_IgA10r

description:
IgA10r green
full-thickness 2 cm of jejunum from the middle of small intestine

value: control

tag: array name


title: Goat #8  0 Hours Blood

description: Goat8 _0h_blood


title: F1  Aire KO MEC rep3


title: KO_IgA1

description:
IgA1green
full-thickness 2 cm of jejunum from the middle of small intestine

tag: tissue type


title: Goat #10  30 Hours Blood

description: Goat10 _30h_blood


title: Goat #8  30 Hours Blood

description: Goat8 _30h_blood


title: F60 vs. Fc, 13431681a

description: Hybridizations conducted using Balance Interwoven Loop Design including 2 technical replicates per treatment and 2 dye swaps.

value: juvenile

value: brain

tag: treatment


title: Serum samples of internistic controls (INC) 8-2

type: protein

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: pool C of 10 serum samples

hyb_protocol: The array consisted of three glass slides (array 6, 7, and 8) that were pretreated according to the manufacturer's instructions and incubated with 2-fold diluted serum pools for 2 hours. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with Cy3-conjugated streptavidin.

scan_protocol: Fluorescence intensities (Cy3) were recorded with an Axon GenePix 4000B scanner.

data_processing: Raw data was analyzed with the Raybiotech analysis tool, a data analysis program based on Microsoft Excel technology specifically designed for the analysis of these microarrays. Signals were normalized using internal, positive and negative controls included on the array. Signals were normalized using positive and negative control features on the microarray, the fold changes are relative expression to positive control features, i.e. a value of 1 is same expression than positive control, 2 a 2 fold higher, 0.5 a 2-fold lower expression.

molecule: protein

source_name: serum

label_protocol: According to manufacturer's protocols. In brief, 70ul of 1,500 fold diluted Fluorescent dye-conjugated streptavidin ws added to each subarray and incubated in a dark room at room temperature for 1-2 hours.

extract_protocol: serum samples

tag: disease state

value: internistic INC

tag: block in gpr file

value: serum


title: Serum samples of healthy controls (HC) 8-4

description: pool B of 10 serum samples

value: healthy HC


title: Serum samples of internistic controls (INC) 8-1

description: pool C of 10 serum samples


title: Mc vs. F60, 13431680a

value: male

value: female

value: 2,6-dinitrotoluene (2,6-DNT)


title: Goat #7  0 Hours Blood

description: Goat7 _0h_blood

value: S. aureus

tag: cell type


title: M60 vs. Mc, 13431677a

tag: gender


title: Goat #7  30 Hours Blood

description: Goat7 _30h_blood

value: White blood cells


title: Serum samples of healthy controls (HC) 8-2

description: pool A of 10 serum samples


title: Serum samples of healthy controls (HC) 8-1

description: pool A of 10 serum samples


title: Serum samples of healthy controls (HC) 8-3

description: pool B of 10 serum samples


title: Fc vs. M60, 13431676a


title: HepG2-HBx compare to control

city: Philadelphia

first: Ke

last: Yuan

address: 1900 N 12th Broad St

department: Biology

institute: Temple University

description: compare HepG2HBx cells with its control CAT cells

hyb_protocol: standard LCScience protocol

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: Array pro default global normalization

label_protocol: standard LCScience protocol

growth_protocol: 1XMEM with 10%FBS,10%P/S,sodium pyruvate and supplementary amino acid

extract_protocol: Ambion mirVana microRNA extraction kit

treatment_protocol: 100ug/ml G418 for antibiotic selection

tag: overexpression

value: HBx

tag: cell line

source_name: total RNA from HepG2CAT


title: Goat #6  30 Hours Blood

description: Goat6 _30h_blood

tag: challenge

tag: time


title: Goat #5  30 Hours Blood

description: Goat5 _30h_blood

tag: sample type


title: Serum samples of patients with Parkinson’s disease (PD) 8-4

description: pool B of 10 serum samples

value: Parkinson's disease PD


title: M60 vs. Mc, 13431679a

tag: developmental stage

tag: tissue

value: 60 days


title: Intestinal eosinophil 1

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

description: SAMPLE 5

hyb_protocol: Hybridization chamber : a standard Probe Array Cartidge (GeneChip Mouse Gene 1.0 ST Array fymetrix) Hybridization cocktail for a single probe array that contains 2.5 ug of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 2 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 90 uL of the hybridization cocktail. Incubate at 45C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, Scanning software: Genechip Operating Software (Affymetrix)

data_processing: Raw data were analyzed by Genespring GX 11 using RMA

source_name: Intestinal eosinophil

label_protocol: The WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) is used to prepare target cDNA.  Then the WT-Ovation Exon Module v1.0 (NuGEN) is used to create target sense transcript cDNA. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragments and labels the target sense cDNA

extract_protocol: Following the QIAGEN RNeasy kit procedures

tag: strain

value: BALB/c

tag: age

value: 2-3 months

value: FACS sorted eosinophils from GI


title: lung eosinophil 4

description: SAMPLE 4

source_name: lung eosinophil

value: FACS sorted eosinophils from lung


title: Goat #6  0 Hours Blood

description: Goat6 _0h_blood

value: White blood cells  0h


title: Intestinal eosinophil 2

description: SAMPLE 6


title: Goat #4  30 Hours Blood

description: Goat4 _30h_blood

value: 30h after challenge

value: White blood cells  30h after challenge


title: Serum samples of patients with Parkinson’s disease (PD) 8-3

description: pool B of 10 serum samples

value: serum


title: F60 vs. Fc, 13431674a

source_name: female brain, 2,6-DNT, 60mg/kg/d

value: juvenile

value: brain

tag: treatment dosage

tag: treatment duration


title: Intestinal eosinophil 4

description: SAMPLE 8


title: Goat #5  0 Hours Blood

description: Goat5 _0h_blood


title: lung eosinophil 3

description: SAMPLE 3


title: Intestinal eosinophil 3

description: SAMPLE 7


title: lung eosinophil 2

description: SAMPLE 2


title: Serum samples of patients with Parkinson’s disease (PD) 8-2

description: pool A of 10 serum samples


title: Mc vs. F60, 13431673a

value: male

value: female


title: Serum samples of patients with Parkinson’s disease (PD) 8-1

description: pool A of 10 serum samples


title: Goat #4  0 Hours Blood

description: Goat4 _0h_blood

value: S. aureus


title: Serum samples of patients with multisystem atrophy (MSA) 8-2

description: pool A of 10 serum samples

value: multisystem atrophy MSA


title: Newman mutant strain sigB1(Am) replicate 3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus aureus Newman MS64 sigB1(truncated and inactivated sigB) versus Staphylococcus aureus gDNA pool

hyb_protocol: A mixture of RNA from WT or DAPR strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus Newman MS64 sigB1(truncated and inactivated sigB)

label_protocol: Incorporation during reverse transcription

growth_protocol: 5 hours growth in Muller-Hinton

extract_protocol: RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit. Genomic DNA extraction: Genomic DNA from S. aureus strains was extracted using the DNeasy extraction kit (Qiagen, Hilden, Germany) following manufacturer’s protocol with the following modifications: fresh colonies harvested from agar plates were washed with 500µl TE 1X and centrifuged for 10 minutes at 3’000g. Then, suspended in 200µl TE 1X with 10µl lysostaphin (Sigma; 50µg/ml final concentration) and incubated for 5 minutes at 37°C. The DNeasy protocol was then followed except for the elution step where we used 50µl RNase-DNAse-free water (Sigma).

value: Newman

tag: genotype/variation

label: cyanine 5

source_name: gDNA pool

value: Staphylococcus aureus gDNA mixture


title: Newman mutant strain sigB1(Am) replicate 2

value: MS64 sigB1(truncated and inactivated sigB)


title: F60 vs. Mc, 13431672a

tag: treatment

value: 2,6-dinitrotoluene (2,6-DNT)

value: 60 days


title: Mc vs. M60, 13431667a


title: M60 vs. Fc, 13431670a

source_name: female brain, control


title: Newman mutant strain DyabJ-spoVG::erm(B) replicate 3

description: Staphylococcus aureus Newman SM148 DyabJ-spoVG::erm(B) versus Staphylococcus aureus gDNA pool

source_name: S. aureus Newman SM148 DyabJ-spoVG::erm(B)

value: SM148 DyabJ-spoVG::erm(B)


title: Newman mutant strain sigB1(Am) replicate 1


title: F60 vs. Mc, 13431666a


title: Goat #2  30 Hours Blood

description: Goat2 _30h_blood

value: White blood cells


title: Fc vs. F60, 13431671a


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 8-3

description: pool A of 10 serum samples

tag: disease state

value: Parkinson's disease, progressive supranuclear palsy PSP/CBS


title: Goat #2  0 Hours Blood

description: Goat2 _0h_blood

value: White blood cells  0h


title: Fc vs. F60, 13431664a


title: Goat #3  0 Hours Blood

description: Goat3 _0h_blood


title: M60 vs. Fc, 13431663a


title: Newman mutant strain DyabJ-spoVG::erm(B) replicate 1


title: Goat #3  30 Hours Blood

description: Goat3 _30h_blood

value: 30h after challenge

value: White blood cells  30h after challenge


title: Serum samples of patients with multisystem atrophy (MSA) 8-3

description: pool A of 10 serum samples

tag: block in gpr file

value: serum


title: Goat #1  30 Hours Blood

description: Goat1 _30h_blood

tag: cell type


title: lung eosinophil 1

hyb_protocol: Hybridization chamber: a standard Probe Array Cartidge (GeneChip Mouse Gene 1.0 ST Array Affymetrix) Hybridization cocktail for a single probe array that contains 2.5 ug of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 2 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 90 uL of the hybridization cocktail. Incubate at 45C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

value: BALB/c

value: 2-3 months

value: FACS sorted eosinophils from lung


title: Serum samples of patients with multisystem atrophy (MSA) 8-1

description: pool A of 10 serum samples


title: Wild type strain Newman replicate 2

description: Staphylococcus aureus Newman wild type versus Staphylococcus aureus gDNA pool

source_name: S. aureus Newman WT


title: Wild type strain Newman replicate 3


title: Wild type strain Newman replicate 1


title: Newman mutant strain DyabJ-spoVG::erm(B) replicate 2


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 8-1

description: pool A of 10 serum samples


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 8-2

description: pool A of 10 serum samples


title: Mc vs. M60, 13431662a

source_name: male brain, control

tag: gender

value: male

value: juvenile

value: brain


title: Goat #10 24 Hours Milk

description: Goat10 _24h_milk

source_name: Milk somatic cells (MSC)

value: S. aureus

value: Milk somatic cells (MSC)

value: 24h after challenge

value: Milk somatics cells (MSC) 24h after challenge


title: ∆E vs. Control_Dye swap

city: chennai

first: Dinesh

last: Kumar

state: tamilnadu

address: mayor v.r ramanathan road

department: Immunology

country: India

institute: Tuberculosis research centre (ICMR)

description: ∆E vs. Control _Dye swap

hyb_protocol: 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the 22k Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Scanned on an Agilent G2505B scanner and Images were quantified using Agilent Feature Extraction Software (version 8.1.1.1)

data_processing: Normalization of the data was done using Per spot per chip intensity dependant lowess normalization. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. One fold and above differentially regulated genes were filtered from the data. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, pathways that were significantly regulated was done using bio script library in GeneSpring Gx

source_name: uninfected control

label_protocol: Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.

growth_protocol: THP-1 cells were differentiated using  5nM PMA into adherent macrophage- like cells by overnight exposure . Cells were rested 3 days following chemical differentiation to ensure that they reverted to a resting phenotype before infection

extract_protocol: Total RNA extracted  using Qiagen’s RNeasy minikit following manufacturer's instructions

treatment_protocol: differentiated cells were infected with  H37Rv ( wild-type) , ∆E ( deletion mutant of PknE) ,C∆E ( complemented ∆E)

value: THP-1 macrophage

source_name: ∆E


title: Goat #1  0 Hours Blood

description: Goat1 _0h_blood

value: White blood cells


title: F60 vs. Mc, 13431661a

value: female

value: 2,6-dinitrotoluene (2,6-DNT)

value: 60 days


title: C∆E vs. Control_Dye swap

description: C∆E vs. Control _Dye swap

source_name: C∆E


title: Goat #9 0 Hours Milk

description: Goat9 _0h_milk

value: Milk somatics cells (MSC) 0h


title: Goat #10 0 Hours Milk

description: Goat10 _0h_milk


title: SJTALL165

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: RNA extracted from tumor cells obtained at diagnosis

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: RNA extracted from diagnostic leukemic blasts of early T-cell precursor acute lymphoblastic leukemia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases

extract_protocol: Trizol

value: tumor cells


title: SJTALL164


title: Goat #8 30 Hours Milk

description: Goat8 _30h_milk

value: 30h after challenge

value: Milk somatics cells (MSC) 30h after challenge


title: ∆E vs. Control

description: ∆E vs. Control


title: Goat #9 24 Hours Milk

description: Goat9 _24h_milk


title: Goat #8 24 Hours Milk

description: Goat8 _24h_milk


title: SJTALL163


title: Fc vs. F60, 13431660a


title: C∆E vs. Control

description: C∆E vs. Control


title: H37Rv vs. Control_Dye swap

description: H37Rv vs. Control_Dye swap


title: Goat #8 0 Hours Milk

description: Goat8 _0h_milk


title: Mc vs. M60, 13425906a

source_name: male brain, 2,6-DNT, 60mg/kg/d


title: H37Rv vs. Control

description: H37Rv vs. Control


title: SJTALL162


title: M60 vs. Fc, 13431659a


title: Goat #7 0 Hours Milk

description: Goat7 _0h_milk


title: Goat #7 24 Hours Milk

description: Goat7 _24h_milk


title: Goat #6 0 Hours Milk

description: Goat6 _0h_milk


title: Goat #5 0 Hours Milk

description: Goat5 _0h_milk


title: Goat #5 30 Hours Milk

description: Goat5 _30h_milk


title: Goat #6 24 Hours Milk

description: Goat6 _24h_milk


title: SJTALL161


title: Goat #5 24 Hours Milk

description: Goat5 _24h_milk


title: Goat #4 24 Hours Milk


title: Goat #4 30 Hours Milk

description: Goat4 _30h_milk


title: Goat #4 0 Hours Milk

description: Goat4 _0h_milk


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00376

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Rat 230 2.0 GenechipÆ arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification One-Cycle Target labeling kit according to manufacturerís protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÆ Operating Software.

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).

organism: Rattus norvegicus

source_name: Kidney tissue, treated with Rapamycin_10 mg/kg_28 dose

extract_protocol: Male SD rats approximately 5-7 weeks old were maintained on certified rodent chow and dosed i.p. with olive oil, CsA (2.5 or 25 mg/kg/day), FK506 (0.6 or 6 mg/kg/day), or Rapa (1 or 10 mg/kg/day) for 1, 7, 14 or 28 consecutive days. Blood was collected at the terminal necropsy (24 hours after 1, 7, 14 or 28 days of treatment) for clinical chemistry analysis. Each kidney was cut in half (one cross section and the other longitudinal). One half of the left kidney and one half of the right kidney were used for histopathological evaluation and the remaining portions of the kidney were processed for gene expression analysis. Total RNA was isolated from rat kidney using QIAGEN RNeasy kits (QIAGEN Inc., Valencia, CA) following manufacture’s instruction.

value: Sprague-Dawley rats

value: Male

value: 5-7 weeks old before treatment

tag: organ

value: Kidney


title: Goat #3 30 Hours Milk

description: Goat3 _30h_milk

value: S. aureus


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00374

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÆ Operating Software.

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3í Amplification One-Cycle Target labeling kit according to manufacturerís protocol.


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00370


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00378


title: Goat #2 30 Hours Milk

description: Goat2 _30h_milk

value: Milk somatic cells (MSC)


title: Goat #3 0 Hours Milk

description: Goat3 _0h_milk


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00372


title: Kidney_Rapamycin_10 mg/kg_28 dose_Rat 05-00368


title: Goat #3 24 Hours Milk

description: Goat3 _24h_milk

value: 24h after challenge


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00334

source_name: Kidney tissue, treated with Rapamycin_1 mg/kg_28 dose


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00342


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00336


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00332


title: Goat #2 0 Hours Milk

description: Goat2 _0h_milk


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00340


title: Goat #2 24 Hours Milk

description: Goat2 _24h_milk

value: Milk somatics cells (MSC) 24h after challenge


title: Kidney_6 mg/kg_FK-506_28 dose_Rat 05-00300

source_name: Kidney tissue, treated with 6 mg/kg_FK-506_28 dose


title: Kidney_6 mg/kg_FK-506_28 dose_Rat 05-00298


title: Kidney_Rapamycin_1 mg/kg_28 dose_Rat 05-00338


title: WT_Ras3

city: Barcelona

first: Angel

last: Nebreda

state: Barcelona

address: C/ Baldiri Reixac 10

country: Spain

institute: Institute for Research in Biomedicine (IRB Barcelona)

description: spontaneously immortalized MEFs by 3T3 protocol and stably transduced with H-RasG12V

hyb_protocol: Hybridizations were performed by using 5 mg samples of cRNA and 100 ng of internal reference that were labelled with Cy-5 and Cy-3 dyes, respectively (GE Healthcare)

scan_protocol: Slides were scanned by using a GenePix 4000b semiconfocal scanner (Molecular Devices)

data_processing: Microarray data was analyzed with the CodeLink Expression Analysis software and dataset normalization was performed via cyclic loess. Differentially expressed genes were obtained by applying linear models with R limma package.

label_protocol: Complementary RNAs (cDNAs) were labelled with Cy5 and Cy3, pooled, hybridized and processed with the Amersham Codelink 20K mouse platform (GeneCore Laboratory, EMBL, Heidelberg)

growth_protocol: Medium: DMEM + 10% foetal bovine serum + 1% L-glutamine + 1% penicillin + 1% streptomycin. 80% cultures were trypsinized (0.25% trypsin + 1mM EDTA), seeded to 30%-40% confluence, cultured for 72 h and harvested when at 70%-90% confluence. Medium yellowing, cell clustering and multi-layered growth were avoided.

extract_protocol: mRNA was extracted from three biological replicates of exponentially proliferating WT and p38α-/- MEFs expressing H-RasG12V using the Qiagen RNeasy kit according to manufacturer’s instructions.

treatment_protocol: 70%-90% confluent cultures grown for 72 h were washed on ice twice with cold PBS and scrapped off with sterile rubber policemen.

value: mixed background 129/svev × C57Bl/6

value: wild type

value: mouse embryo fibroblast

tag: pool id.


title: Kidney_6 mg/kg_FK-506_28 dose_Rat 05-00296


title: Goat #1 30 Hours Milk

description: Goat1 _30h_milk

tag: challenge


title: WT_Ras2


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00268

source_name: Kidney tissue, treated with FK-506_0.6 mg/kg_28 dose


title: Kidney_6 mg/kg_FK-506_28 dose_Rat 05-00304


title: WT_Ras1


title: Goat #1  24 Hours Milk

description: Goat1 _24h_milk

tag: time


title: Goat #1  0 Hours Milk

description: Goat1 _0h_milk

tag: sample type


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00266


title: KO_Ras3

value: p38α- deficient (p38α-/-)


title: Kidney_6 mg/kg_FK-506_28 dose_Rat 05-00306


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00264


title: Kidney_Cyclosporine A_25 mg/kg_28 dose_Rat 05-00232

source_name: Kidney tissue, treated with Cyclosporine A_25 mg/kg_28 dose


title: Kidney_Cyclosporine A_25 mg/kg_28 dose_Rat 05-00234


title: KO_Ras2


title: KO_Ras1


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00270


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00260


title: Kidney_Cyclosporine A_25 mg/kg_28 dose_Rat 05-00226


title: Arabidopsis root section, longitudinal zone 1, low sulfur, replicate 1

city: Durham

first: Anjali

middle: S

last: Iyer-Pascuzzi

institute: Duke University

description: Gene expression data from root developmental stage zone 1

hyb_protocol: hybs with fragmented cRNA were preformed by Expression Analysis (Durham, NC)

scan_protocol: scans were preformed by Expression Analysis (Durham, NC)

data_processing: CHP files contain MAS 5.0 probe set summarizations using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 250.

organism: Arabidopsis thaliana

source_name: root tissue

label_protocol: Biotinylated cRNA were prepared according to the standard two-cycle Affymetrix protocol

growth_protocol: Seedlings were grown for 5 days on 1X MS media before transfer to sulfur deficient media 3 hours prior to dissection

extract_protocol: Total RNA was extracted with Qiagen Rneasy Plant mini kit according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on 1X MS media. After 5 days seedlings were transferred to sulfur deficient media for 3 hours. Sulfur deficient media is composed of 20.6 mM NH4NO3, 18.8 mM KNO3, 1.25 mM KPO4H2, 5 μM KI, 2.99 mM CaCl2, 0.1 mM H3BO3, 1 μM Na2MoO42H2O, 0.1 μM CoCl26H2O, 0.1 mM Na2EDTA2H20, 1.5 mM MgCl2, 0.1 μM CuCl2, 0.1mM FeCl2, 0.1 mM MnCl2, 0.03 mM ZnCl2, 0.05% MES, 1% sucrose, 1% agar.

tag: ecotype

value: Columbia

tag: longitudinal zone


title: Arabidopsis root section, longitudinal zone 4, low sulfur, replicate 2

description: Gene expression data from root developmental stage zone 4


title: Arabidopsis root section, longitudinal zone 4, low sulfur, replicate 1


title: Arabidopsis root section, longitudinal zone 2, low sulfur, replicate 2

description: Gene expression data from root developmental stage zone 2


title: Arabidopsis root section, longitudinal zone 2, low sulfur, replicate 1


title: Arabidopsis root section, longitudinal zone 3, low sulfur, replicate 2

description: Gene expression data from root developmental stage zone 3


title: Kidney_Cyclosporine A_2.5 mg/kg_28 dose_Rat 05-00192

source_name: Kidney tissue, treated with Cyclosporine A_2.5 mg/kg_28 dose

tag: strain


title: Kidney_Cyclosporine A_25 mg/kg_28 dose_Rat 05-00224

tag: age


title: Kidney_olive oil_28 dose_Rat 05-00158

source_name: Kidney tissue, treated with olive oil_28 dose


title: Kidney_FK-506_0.6 mg/kg_28 dose_Rat 05-00262


title: Arabidopsis root section, longitudinal zone 1, low sulfur, replicate 2


title: Kidney_Cyclosporine A_2.5 mg/kg_28 dose_Rat 05-00198


title: Kidney_Cyclosporine A_2.5 mg/kg_28 dose_Rat 05-00194


title: SJTALL022

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)


title: Arabidopsis root section, longitudinal zone 3, low sulfur, replicate 1


title: Kidney_Cyclosporine A_2.5 mg/kg_28 dose_Rat 05-00196


title: Kidney_olive oil_28 dose_Rat 05-00380


title: Kidney_olive oil_28 dose_Rat 05-00154


title: Kidney_olive oil_28 dose_Rat 05-00156


title: Kidney_Cyclosporine A_2.5 mg/kg_28 dose_Rat 05-00188


title: Kidney_Rapamycin_10 mg/kg_14 dose_Rat 05-00360

source_name: Kidney tissue, treated with Rapamycin_10 mg/kg_14 dose


title: Kidney_Rapamycin_10 mg/kg_14 dose_Rat 05-00362


title: Serum samples of internistic controls (INC) 7-2

description: pool C of 10 serum samples

source_name: serum

value: internistic INC

value: serum


title: Kidney_olive oil_28 dose_Rat 05-00152


title: SJTALL015

value: tumor cells


title: Kidney_Rapamycin_10 mg/kg_14 dose_Rat 05-00364


title: Serum samples of internistic controls (INC) 7-1

description: pool C of 10 serum samples


title: Serum samples of healthy controls (HC) 7-4

description: pool B of 10 serum samples

value: healthy HC


title: Kidney_Rapamycin_1 mg/kg_14 dose_Rat 05-00328

source_name: Kidney tissue, treated with Rapamycin_1 mg/kg_14 dose

value: Sprague-Dawley rats


title: SJTALL005


title: SJTALL009


title: SJTALL002


title: SJTALL006


title: SJTALL021


title: SJTALL011


title: Kidney_6 mg/kg_FK-506_14 dose_Rat 05-00292

source_name: Kidney tissue, treated with 6 mg/kg_FK-506_14 dose

value: Male


title: Kidney_Rapamycin_1 mg/kg_14 dose_Rat 05-00330

value: 5-7 weeks old before treatment


title: Kidney_Rapamycin_10 mg/kg_14 dose_Rat 05-00382

value: Kidney


title: SJTALL010


title: SJTALL001


title: Kidney_6 mg/kg_FK-506_14 dose_Rat 05-00290


title: Kidney_6 mg/kg_FK-506_14 dose_Rat 05-00294


title: Serum samples of healthy controls (HC) 7-3

description: pool B of 10 serum samples


title: Serum samples of healthy controls (HC) 7-1

description: pool A of 10 serum samples


title: Serum samples of patients with Parkinson’s disease (PD) 7-1

description: pool A of 10 serum samples

value: Parkinson's disease PD


title: Kidney_Rapamycin_1 mg/kg_14 dose_Rat 05-00324


title: Serum samples of patients with Parkinson’s disease (PD) 7-2

description: pool A of 10 serum samples


title: Influenza vaccine #1

description:
SAMPLE 4
Human patient with 32 titer

source_name: influenza vaccine recipients

tag: tissue


title: Serum samples of patients with Parkinson’s disease (PD) 7-4

description: pool B of 10 serum samples


title: Serum samples of patients with multisystem atrophy (MSA) 7-2

description: pool A of 10 serum samples

value: multisystem atrophy MSA


title: Serum samples of patients with multisystem atrophy (MSA) 7-3

description: pool A of 10 serum samples


title: Kidney_Rapamycin_1 mg/kg_14 dose_Rat 05-00326


title: Serum samples of healthy controls (HC) 7-2

description: pool A of 10 serum samples


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 7-3

description: pool A of 10 serum samples

value: Parkinson's disease, progressive supranuclear palsy PSP/CBS


title: Serum samples of patients with Parkinson’s disease (PD) 7-3

description: pool B of 10 serum samples


title: Serum samples of patients with multisystem atrophy (MSA) 7-1

description: pool A of 10 serum samples


title: Kidney_FK-506_0.6 mg/kg_14 dose_Rat 05-00256

source_name: Kidney tissue, treated with FK-506_0.6 mg/kg_14 dose


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 7-1

description: pool A of 10 serum samples


title: Kidney_Cyclosporine A_2.5 mg/kg_14 dose_Rat 05-00182

source_name: Kidney tissue, treated with Cyclosporine A_2.5 mg/kg_14 dose


title: Kidney_Cyclosporine A_25 mg/kg_14 dose_Rat 05-00216

source_name: Kidney tissue, treated with Cyclosporine A_25 mg/kg_14 dose


title: SNK-6

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

institute: Cancer Science Institute Singapore

description: miRNA expression profiling

hyb_protocol: The labeled samples were hybridized to Agilent human microRNA microarray V2 slide for 20hrs at 55°C, 20RPM as per manufacturer's instruction.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2565CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NKTCL cell line

label_protocol: For each sample, 100ng of total RNA was dephosphorylated, denatured and labeled with Cy3 according to Agilent miRNA system protocol v2.0 (Agilent Technologies, Santa Clara, CA)

extract_protocol: Ambion Recoverall Kit

tag: cell line


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 7-2

description: pool A of 10 serum samples


title: Kidney_FK-506_0.6 mg/kg_14 dose_Rat 05-00258


title: Kidney_Cyclosporine A_25 mg/kg_14 dose_Rat 05-00222


title: Kidney_FK-506_0.6 mg/kg_14 dose_Rat 05-00252


title: KHYG

description: miRNA expression profiling

value: KHYG


title: HANK-1

description: miRNA expression profiling


title: NK-92

description: miRNA expression profiling


title: NKYS

description: miRNA expression profiling

value: NKYS


title: Kidney_olive oil_14 dose_Rat 05-00148

source_name: Kidney tissue, treated with olive oil_14 dose


title: normal LN 2

description: miRNA expression profiling

source_name: NKTCL FFPE archival samples

value: normal LN


title: normal LN

description: miRNA expression profiling


title: Kidney_Cyclosporine A_25 mg/kg_14 dose_Rat 05-00218


title: Kidney_FK-506_0.6 mg/kg_14 dose_Rat 05-00254


title: Kidney_Cyclosporine A_2.5 mg/kg_14 dose_Rat 05-00184


title: Kidney_Cyclosporine A_25 mg/kg_14 dose_Rat 05-00220


title: SNT-8

description: miRNA expression profiling


title: Kidney_olive oil_14 dose_Rat 05-00150


title: Kidney_olive oil_14 dose_Rat 05-00144


title: normal colon 2

description: miRNA expression profiling

value: normal colon


title: normal nasal 2

description: miRNA expression profiling

value: normal nasal


title: Kidney_Rapamycin_10 mg/kg_7 dose_Rat 05-00354

source_name: Kidney tissue, treated with Rapamycin_10 mg/kg_7 dose


title: Kidney_Cyclosporine A_2.5 mg/kg_14 dose_Rat 05-00180


title: normal nasal

description: miRNA expression profiling


title: normal skin

description: miRNA expression profiling

value: normal skin


title: normal colon

description: miRNA expression profiling


title: normal skin 2

description: miRNA expression profiling


title: Normal_s 5

description: miRNA expression profiling

source_name: Normal NK cell

value: NK cell from whole blood (stimulated with cytokines)


title: Kidney_olive oil_14 dose_Rat 05-00146


title: Kidney_Rapamycin_10 mg/kg_7 dose_Rat 05-00352


title: Normal_s 4

description: miRNA expression profiling


title: Kidney_Rapamycin_10 mg/kg_7 dose_Rat 05-00356


title: Normal_s 3

description: miRNA expression profiling


title: Kidney_Cyclosporine A_2.5 mg/kg_14 dose_Rat 05-00186


title: Kidney_Rapamycin_1 mg/kg_7 dose_Rat 05-00320

source_name: Kidney tissue, treated with Rapamycin_1 mg/kg_7 dose


title: Kidney_Rapamycin_1 mg/kg_7 dose_Rat 05-00318


title: Normal_s 6

description: miRNA expression profiling


title: Kidney_Rapamycin_1 mg/kg_7 dose_Rat 05-00322


title: Kidney_6 mg/kg_FK-506_7 dose_Rat 05-00286

source_name: Kidney tissue, treated with 6 mg/kg_FK-506_7 dose


title: Kidney_6 mg/kg_FK-506_7 dose_Rat 05-00280


title: Normal_s 2

description: miRNA expression profiling


title: Normal_s 1

description: miRNA expression profiling


title: Kidney_Rapamycin_1 mg/kg_7 dose_Rat 05-00316


title: NKTL 36

description: miRNA expression profiling

value: skin


title: NKTL 35

description: miRNA expression profiling

value: nasal


title: Kidney_6 mg/kg_FK-506_7 dose_Rat 05-00282


title: Kidney_6 mg/kg_FK-506_7 dose_Rat 05-00284


title: NKTL 37

description: miRNA expression profiling


title: Kidney_FK-506_0.6 mg/kg_7 dose_Rat 05-00248

source_name: Kidney tissue, treated with FK-506_0.6 mg/kg_7 dose


title: NKTL 12

description: miRNA expression profiling


title: Kidney_FK-506_0.6 mg/kg_7 dose_Rat 05-00246


title: NKTL 38

description: miRNA expression profiling


title: Kidney_Cyclosporine A_25 mg/kg_7 dose_Rat 05-00208

source_name: Kidney tissue, treated with Cyclosporine A_25 mg/kg_7 dose


title: Kidney_Cyclosporine A_25 mg/kg_7 dose_Rat 05-00214


title: Ler vs hy5 3

city: Madrid

first: Rafael

last: Catalá

state: Madrid

address: Ramiro de Maeztu nº9

department: Biologia Medioambiental

institute: CIB-CSIC

description: Biological replicate 3 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7).

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with an offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

label_protocol: 5 mg of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ml of the probe in the Nanodrop.

growth_protocol: Plants were sown in pots containing a mixture of organic substrate and vermiculite (3:1 v/v). Plants were transferred to 16h light/8 h dark at 22ºC under white fluorescent light during three weeks and one aditional day at 4ºC.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. Then, RNA was purified using the RNeasy MiniKit from QIAGEN following manufacturer's instructions.

tag: time at 4ºc

value: 1 day

source_name: Ler


title: Kidney_Cyclosporine A_25 mg/kg_7 dose_Rat 05-00212

value: Sprague-Dawley rats


title: Whole root - Std pH 12H_rep1

description: Expression profile of whole root exposed to pH 5.7 for 12H

source_name: whole roots transferred to std pH, 12H

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from 1 ug total RNA

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for the indicated time

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for the indicated time. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

tag: developmental stage

value: whole root

value: Columbia

tag: treatment

value: pH 5.7 for 12 hr


title: Kidney_Cyclosporine A_2.5 mg/kg_7 dose_Rat 05-00178

source_name: Kidney tissue, treated with Cyclosporine A_2.5 mg/kg_7 dose

value: Male

value: 5-7 weeks old before treatment

value: Kidney


title: Kidney_FK-506_0.6 mg/kg_7 dose_Rat 05-00250


title: NKTL 34

description: miRNA expression profiling


title: Kidney_FK-506_0.6 mg/kg_7 dose_Rat 05-00244


title: Ler vs hy5 1

description: Biological replicate 1 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.


title: NKTL 13

description: miRNA expression profiling


title: Kidney_Cyclosporine A_25 mg/kg_7 dose_Rat 05-00210


title: NKTL 29

description: miRNA expression profiling

value: mesenteric


title: NKTL 10

description: miRNA expression profiling


title: Kidney_Cyclosporine A_2.5 mg/kg_7 dose_Rat 05-00174


title: HIV-1 6 [mRNA]

description: Infected PBMC from donor 6

hyb_protocol: hybridized onto array bead chips overnight on rocker

scan_protocol: scanned on ‘iScan system’ according to the manufacturer's protocols

data_processing: Initial raw data analysis and cubic spline normalization was done using BeadStudio Gene expression module (Illumina, Inc.).

source_name: PBMC

label_protocol: Total RNA samples were labeled using ‘TotalPrep RNA’ labeling kit (Ambion)

extract_protocol: Total RNA was isolated using the TRIzol method (InVitrogen) as suggested by the manufacturer.

value: Blood

tag: infection


title: NKTL 4

description: miRNA expression profiling


title: Ler vs hy5 2

description: Biological replicate 2 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.


title: NKTL 11

description: miRNA expression profiling


title: NKTL 20

description: miRNA expression profiling


title: Control 6 [mRNA]

description: Uninfected PBMC from donor 6


title: Kidney_Cyclosporine A_2.5 mg/kg_7 dose_Rat 05-00172


title: NKTL 2

description: miRNA expression profiling


title: Kidney_olive oil_7 dose_Rat 05-00140

source_name: Kidney tissue, treated with olive oil_7 dose


title: NKTL 33

description: miRNA expression profiling

value: ileum/jejunum/orbit


title: Kidney_olive oil_7 dose_Rat 05-00138


title: Kidney_Cyclosporine A_2.5 mg/kg_7 dose_Rat 05-00176


title: Kidney_olive oil_7 dose_Rat 05-00142


title: Kidney_olive oil_7 dose_Rat 05-00136


title: HIV-1 5 [mRNA]

description: Infected PBMC from donor 5


title: Kidney_Rapamycin_10 mg/kg_7 dose_Rat 05-00358


title: Kidney_Rapamycin_10 mg/kg_1 dose_Rat 05-00348

source_name: Kidney tissue, treated with Rapamycin_10 mg/kg_1 dose


title: Control 4 [mRNA]

description: Uninfected PBMC from donor 4


title: Kidney_Rapamycin_10 mg/kg_1 dose_Rat 05-00346


title: NKTL 28

description: miRNA expression profiling


title: NKTL 14

description: miRNA expression profiling


title: NKTL 27

description: miRNA expression profiling


title: HIV-1 4 [mRNA]

description: Infected PBMC from donor 4


title: NKTL 17

description: miRNA expression profiling

value: nasal LN NKTCL


title: NKTL 21

description: miRNA expression profiling


title: NKTL 5

description: miRNA expression profiling


title: Control 5 [mRNA]

description: Uninfected PBMC from donor 5


title: NKTL 19

description: miRNA expression profiling


title: HIV-1 3 [mRNA]

description: Infected PBMC from donor 3


title: Control 2 [mRNA]

description: Uninfected PBMC from donor 2


title: Kidney_Rapamycin_10 mg/kg_1 dose_Rat 05-00350


title: Control 3 [mRNA]

description: Uninfected PBMC from donor 3


title: HepG2-URG11 compare to control

description: compare HepG2URG11 cells with its control CAT cells

tag: overexpression

source_name: total RNA from HepG2CAT

value: control


title: Arabidopsis root section, longitudinal zone 4, pH 4.6, replicate 1

source_name: root tissue

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for 24 hours prior to dissection

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for 24 hours prior to dissection. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

value: 6 day old roots


title: Kidney_Rapamycin_1 mg/kg_1 dose_Rat 05-00312

source_name: Kidney tissue, treated with Rapamycin_1 mg/kg_1 dose

tag: gender


title: Kidney_Rapamycin_1 mg/kg_1 dose_Rat 05-00314

tag: organ


title: Kidney_Rapamycin_10 mg/kg_1 dose_Rat 05-00344


title: NKTL 7

description: miRNA expression profiling


title: Kidney_Rapamycin_1 mg/kg_1 dose_Rat 05-00308


title: NKTL 3

description: miRNA expression profiling


title: HIV-1 1 [mRNA]

description: Infected PBMC from donor 1


title: Kidney_Rapamycin_1 mg/kg_1 dose_Rat 05-00310


title: HIV-1 2 [mRNA]

description: Infected PBMC from donor 2


title: NKTL 22

description: miRNA expression profiling


title: Control 1 [mRNA]

description: Uninfected PBMC from donor 1


title: Kidney_6 mg/kg_FK-506_1 dose_Rat 05-00278

source_name: Kidney tissue, treated with 6 mg/kg_FK-506_1 dose


title: NKTL 24

description: miRNA expression profiling

source_name: NKTCL FFPE archival samples

value: skin/soft tissue


title: NKTL 23

description: miRNA expression profiling

value: skin


title: Kidney_FK-506_0.6 mg/kg_1 dose_Rat 05-00242

source_name: Kidney tissue, treated with FK-506_0.6 mg/kg_1 dose


title: NKTL 6

description: miRNA expression profiling

value: nasal


title: NKTL 16

description: miRNA expression profiling


title: NKTL 32

description: miRNA expression profiling

value: soft tissue


title: Kidney_FK-506_0.6 mg/kg_1 dose_Rat 05-00238

value: Sprague-Dawley rats


title: NKTL 25

description: miRNA expression profiling

value: colon


title: TAX577474

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) Signal to noise ratio <5 in either Int1 or Int2 channel. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.

value: breast tumor

tag: molecular subtype

value: LumB

tag: genomic subtype

tag: family status

value: sporadic

tag: er

value: er pos

tag: pr

value: pr pos

tag: size (mm)

tag: lymph node status

value: node neg

tag: histologic grade

tag: s-phase fraction

source_name: promega male reference

value: promega male reference


title: Normal 5

description: miRNA expression profiling

source_name: Normal NK cell

tag: tissue

value: NK cell from whole blood


title: Normal 6

description: miRNA expression profiling


title: Kidney_6 mg/kg_FK-506_1 dose_Rat 05-00274

tag: strain

value: Male

tag: age

value: 5-7 weeks old before treatment

value: Kidney


title: TAX577766

value: familial

value: node pos

tag: sample type


title: TAX577772

label: Cy3, Cy5

label: Cy5, Cy3


title: Kidney_6 mg/kg_FK-506_1 dose_Rat 05-00276


title: Kidney_FK-506_0.6 mg/kg_1 dose_Rat 05-00240


title: Arabidopsis root section, longitudinal zone 1, pH 4.6, replicate 1

tag: longitudinal zone

tag: ecotype

value: Columbia

value: 6 day old roots


title: Kidney_FK-506_0.6 mg/kg_1 dose_Rat 05-00236

value: Sprague-Dawley rats

tag: gender


title: TAX577771


title: TAX577767

value: pr neg


title: Kidney_Cyclosporine A_25 mg/kg_1 dose_Rat 05-00202

source_name: Kidney tissue, treated with Cyclosporine A_25 mg/kg_1 dose

tag: organ


title: Kidney_6 mg/kg_FK-506_1 dose_Rat 05-00272


title: Kidney_Cyclosporine A_25 mg/kg_1 dose_Rat 05-00204


title: TAX577768

value: breast tumor

tag: molecular subtype


title: Kidney_Cyclosporine A_25 mg/kg_1 dose_Rat 05-00200


title: Normal 1

description: miRNA expression profiling


title: Normal 2

description: miRNA expression profiling


title: Normal 4

description: miRNA expression profiling


title: Kidney_Cyclosporine A_25 mg/kg_1 dose_Rat 05-00206


title: Kidney_Cyclosporine A_2.5 mg/kg_1 dose_Rat 05-00170

source_name: Kidney tissue, treated with Cyclosporine A_2.5 mg/kg_1 dose


title: TAX577763

tag: genomic subtype


title: TAX577760

tag: family status

value: er neg


title: TAX577769

value: sporadic

tag: er


title: Kidney_Cyclosporine A_2.5 mg/kg_1 dose_Rat 05-00168


title: TAX577765

value: er pos

tag: pr


title: TAX577770

value: pr pos

tag: size (mm)


title: TAX577761

tag: lymph node status


title: TAX577762

value: LumA

tag: histologic grade


title: Kidney_Cyclosporine A_2.5 mg/kg_1 dose_Rat 05-00164


title: Normal 3

description: miRNA expression profiling


title: TAX577764

tag: s-phase fraction

value: promega male reference


title: Kidney_olive oil_1 dose_Rat 05-00132

source_name: Kidney tissue, treated with olive oil_1 dose


title: Kidney_Cyclosporine A_2.5 mg/kg_1 dose_Rat 05-00166


title: Kidney_olive oil_1 dose_Rat 05-00128


title: 137T

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: as described for Illumina GoldenGate assay

scan_protocol: Illumina BeadXpress scanner

data_processing: Data was processed with BeadStudio version 3.2 (Illumina).

source_name: Esophagus

extract_protocol: Genomic DNA was extracted by proteinase-K/SDS digestion. A total of 500 ng of genomic DNA were treated with sodium bisulfite using the EZ DNA Methylation-Gold Kit (Zymo Research). Before bead array analysis, the quality of DNA modification was verified by pyrosequencing.

tag: tissue

value: ESCC tissue


title: 137S

label_protocol: as described for Illumina GoldenGate assay

value: surrounding tissue


title: 106S


title: 105S


title: TAX577759


title: TAX577756

label: Cy3, Cy3

label: Cy5, Cy5


title: 95T


title: 106T


title: TAX577757


title: 97S


title: Kidney_olive oil_1 dose_Rat 05-00134

tag: strain

value: Male

value: 5-7 weeks old before treatment


title: 97T


title: 95S


title: TAX577755

value: Basal

tag: age


title: TAX577751

tag: sample type


title: TAX577758

value: node neg


title: TAX577754

value: familial


title: TAX577750


title: 91S


title: 91T


title: TAX577752


title: Kidney_olive oil_1 dose_Rat 05-00130

value: Kidney


title: TAX577749

value: LumB


title: 89T


title: TAX577753


title: 81T


title: 89S


title: TAX577748


title: 81S