title: Hippocampus deletion carrier, A888_13_H7

source_name: Hippocampus, deletion carrier


title: CD4 T cell HFD d10 replicate 5

status: Public on Nov 18 2015

type: RNA

city: Toulouse

first: Lucile

last: Garidou

address: 1 Avenue J. Poulhes

country: France

institute: INSERM

description: Gene expression after 10 days of high fat diet diet

hyb_protocol: The Cy3-labeled cDNA were hybridized overnight (17hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarray 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray scanner System (Agilent technologies).

data_processing: The Agilent Feature Extraction Software was used to read and process the microarray image files. The software determines features intensities, reject outliers and calculate statistical confidences.

molecule: total RNA

organism: Mus musculus

source_name: CD4 T cell HFD d10

label_protocol: 250 ng of cDNA was used as template for Cy3 labelling which was performed according to Myltenyi undisclosed protocol.

extract_protocol: Leukocytes were collected into SuperAmp lysis bufferTM and Super Amp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure.

treatment_protocol: Leukocytes from the lamina propria ofthe small intestine were isolated. CD4 T cells were sorted by flow cytometry.

tag: tissue

value: small intestine

tag: gender

value: male

tag: cell type

value: lamina propria CD4 lymphocytes


title: Primary hepatocyte

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description: Gene expression

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Primary hepatocyte from C57B6 mice-rep 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: strain

tag: cellular origin

value: liver


title: mHep2-3

description: Gene expression

source_name: mHeps from C57B6-No1-rep 3


title: mHep2-2

description: Gene expression

source_name: mHeps from C57B6-No1-rep 2


title: Striatum wildtype, A888_12_S20

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

hyb_protocol: Affymetrix Mouse Gene 2.1 ST arrays were hybridized, washed and stained according to the protocol described in the Affymetrix GeneChip 3' IVT Express Kit Manual.

scan_protocol: The arrays were scanned using the Affymetrix GeneTitan Instrument, and raw data were extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: The Affymetrix GeneTitan Instrument was used for automated array processing. Raw data was generated and extracted from the scanned images for analysis with the Affymetrix GeneChip Command Console (AGCC) Software and Expression Console Software packages.

label: Biotin

source_name: Striatum, wildtype

label_protocol: For each sample, 100 ng of total RNA was processed according to the Affymetrix GeneChip 3' IVT Express Kit manual (P/N 702646 Revision 6) and hybridized to Affymetrix Mouse Gene 2.1 ST arrays.

extract_protocol: The manufacturer’s protocol for RNA isolation was performed. Upon RNA isolation, RNA clean-up was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany), including the DNase treatment step, according to the manufacturer’s protocol.

tag: strain/background

tag: genotype/variation

value: wildtype

tag: developmental stage

value: adult

value: striatum


title: Striatum duplication carrier, A888_11_S19

source_name: Striatum, duplication carrier

value: carrier of 16p11.2 duplication


title: mHep1-3

description: Gene expression

source_name: mHeps from 129S1-No1-rep 3


title: CD4 T cell HFD d10 replicate 2


title: mHep1-2

description: Gene expression

source_name: mHeps from 129S1-No1-rep 2


title: Striatum wildtype, A888_10_S6


title: mHep3

description: Gene expression

source_name: eHeps from 129S1-No2-rep 1


title: Cerebellum wildtype, A888_02_C10

source_name: Cerebellum, wildtype

value: cerebellum


title: CD4 T cell HFD d10 replicate 1


title: CD4 T cell control replicate 4

description: Gene expression under normal chow diet

source_name: CD4 T cell control


title: CD4 T cell control replicate 2

description: Gene expression under normal chow diet


title: CD4 T cell control replicate 3

description: Gene expression under normal chow diet


title: Cerebellum deletion carrier, A888_01_C26

source_name: Cerebellum, deletion carrier

value: carrier of 16p11.2 deletion


title: mHep2-1

description: Gene expression

source_name: mHeps from C57B6-No1-rep 1


title: CD4 T cell control replicate 5

description: Gene expression under normal chow diet


title: Cerebellum wildtype, A888_04_C48


title: Striatum deletion carrier, A888_09_S11

source_name: Striatum, deletion carrier


title: eHep3

description: Gene expression


title: Cerebellum duplication carrier, A888_03_C47

source_name: Cerebellum, duplication carrier


title: mHep1-1

description: Gene expression

source_name: mHeps from 129S1-No1-rep 1


title: APC HFD day 30 replicate 5

description: gene expression after 30 days of HFD

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17 hour, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: APC HFD day 30

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: Leukocytes were collected into SuperAmp Lysis bufferTM and SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure.

treatment_protocol: Leukocytes from the lamina propria of the small intestine were isolated. Antigen presenting cells (MHCII+CD19-TCR- cells) were sorted by flow cytometry.

value: lamina propria antigen presenting cells


title: APC HFD day 30 replicate 4

description: gene expression after 30 days of HFD


title: APC HFD day 30 replicate 3

description: gene expression after 30 days of HFD


title: CD4 T cell control replicate 1

description: Gene expression under normal chow diet


title: eHep2-1

description: Gene expression

source_name: eHeps from C57B6-No1-rep 1


title: APC HFD day 30 replicate 2

description: gene expression after 30 days of HFD


title: eHep1-3

description: Gene expression

source_name: eHeps from 129S1-No1-rep 3


title: eHep1-2

description: Gene expression

source_name: eHeps from 129S1-No1-rep 2


title: APC HFD day 30 replicate 1

description: gene expression after 30 days of HFD


title: eHep2-2

description: Gene expression

source_name: eHeps from C57B6-No1-rep 2


title: APC HFD day 10 replicate 5

description: gene expression after 10 days of HFD

source_name: APC HFD day 10


title: TAB-GCA, C41

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description:
C41
Gene expression of VSMC isolated from temporal artery of TAB-GCA patient.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

organism: Homo sapiens

source_name: VSMC, TAB-GCA

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target Labelling Assay Kit Affymetrix).

growth_protocol: Cultured in smooth muscle cell growth medium until passage four.

extract_protocol: Trizol extraction of total RNA.

value: vascular smooth muscle cells from temporal artery

tag: disease status

value: GCA lacking histological proof


title: TAB-GCA, C42

description:
C42
Gene expression of VSMC isolated from temporal artery of TAB-GCA patient.


title: APC HFD day 10 replicate 3

description: gene expression after 10 days of HFD


title: APC HFD day 10 replicate 4

description: gene expression after 10 days of HFD


title: GCA-control, C49

description:
C49
Gene expression of VSMC isolated from temporal artery of patient with another diagnosis than GCA.

source_name: VSMC, GCA-control

value: other diagnosis than GCA


title: APC HFD day 10 replicate 2

description: gene expression after 10 days of HFD


title: APC control replicate 3

description: gene expression under normal diet

source_name: APC control


title: APC control replicate 4

description: gene expression under normal diet


title: GCA-control, C26

description:
C26
Gene expression of VSMC isolated from temporal artery of patient with another diagnosis than GCA.


title: TAB-GCA, C32

description:
C32
Gene expression of VSMC isolated from temporal artery of TAB-GCA patient.


title: TAB-GCA, C34

description:
C34
Gene expression of VSMC isolated from temporal artery of TAB-GCA patient.


title: TAB+GCA, H13

description:
H13
Gene expression of VSMC isolated from temporal artery of TAB+GCA patient.

source_name: VSMC, TAB+GCA

value: histology proven GCA


title: GCA-control, C37

description:
C37
Gene expression of VSMC isolated from temporal artery of patient with another diagnosis than GCA.


title: PB12_EB_rep1

status: Public on Nov 17 2015

city: Chilly-Mazarin

first: Dominique

last: Lesuisse

address: 1, avenue Pierre Brossolette

department: Rare and neurologic diseases therapeutic area

institute: Sanofi

hyb_protocol: 1650 ng of Cy3-labeled cRNA was hybridized on Human Gene Expression 4x44K v2 microarrays  (Agilent Technologies)  using Agilent’s Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65°C in a rotating hybridization oven at 10 r.p.m. according to the company’s recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The TIFF-images were processed using Agilent’s Feature Extraction software version 11.0.1.1
Raw data were imported into GeneSpring GX 12.6 software (Agilent Technologies). The intensities were log2 transformed and normalized by using 75th percentile shift. An unpaired T-test with a Benjamini Hochberg FDR multiple testing correction was performed to identify genes differentially expressed between the two tested groups, EB with good versus poor hematopoietic potential (H1, PB7 and PB11 versus PB6 and PB12).  A subset of  differentially regulated genes, was selected on the basis of two criteria corrected ≤ 0.05 and an absolute fold-change ≥ 2  (2957 probes).

source_name: EB from PSC with poor hematopoietic potential

label_protocol: Labeling and hybridization was performed following the manufacturer’s protocol. In brief, 100 ng of total RNA was linearly amplified and labeled with Cy3 using Agilent’s one-color Low Input Quick Amp Labeling Kit according to protocol instructions.

growth_protocol: For Embryoid Bodies (EB) formation, ES and iPS cells, at day 6-7 after cell passage, were treated with collagenase IV. Small clumps were cultured in Iscove’s modified Dulbecco’s medium (IMDM, Invitrogen) supplemented with 1% penicillin/streptomycin, 1 mM L-glutamine, 15% fetal calf serum (FCS, Invitrogen), 450 μM monothioglycerol, 50 μg/mL ascorbic acid (Sigma Aldrich) and 200 μg/L transferrin (Sigma Aldrich), as previously described supplemented with hematopoietic cytokines: 100 ng/mL stem cell factor (SCF) and 100 ng/mL fms-like tyrosine kinase 3 ligand (Flt-3L) and 50 ng/mL thrombopoietin (TPO) (all from Peprotech). ES and IPS derived EB were cultured in ultra low attachment 6-well plates (Costar) for 16 days. Media was changed two or three times depending on EB proliferation. All cultures were incubated at 37°C in 5% CO2

extract_protocol: Total RNA from EB was isolated using miRNeasy Mini Kit. Integrity of the isolated RNA was assessed using the 2100 Bioanalyzer (Agilent Technologies).

tag: tissue origin

value: amniocytes from Down syndrome

tag: psc hematopoietic potential

value: poor

value: Embryonic bobies (EB) derived from Induced pluripotent stem cells (iPS)

tag: time point

value: at day 16 of culture


title: Human immortalized gingival epithelial cell line, OBA-9

city: Tokushima

first: Yasusei

last: Kudo

address: 3-18-15 Kuramoto

department: Institute of Biomedical Sciences

country: Japan

institute: Tokushima University Graduate School

description: Gene expression data from OBA-9 cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat the hybridization cocktails at 99 °C for 5 minutes, then 45 °C for 5 minutes • Transfer 130 μl of cocktail to Human Gene 2.0ST Array (Affymetrix). • Hybridize 17 hours at 45° at 60 rpm.

scan_protocol: GeneChips were washed and stained immediately after completion of hybridization. Fluidics Script Protocol is FS450_0002. GeneChips were scanned using the Scanner 3000 7G (Affymetrix), and CEL files were generated.

data_processing: The scanned images were analyzed with GeneSpring GX 13.0 ( Agilent Technologies).

label: biotin

source_name: OBA-9 cell

label_protocol: cRNA was synthesized from 400 ng of total RNA using the WT Expression Kit (Ambion) according to the manufacturer’s instruction. By second cycle reactions, first strand cDNA was synthesized from 10 ug of cRNA. 5.5 ug of cDNA was fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA). cRNA and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Sigma-Aldrich, St. Louis, MO USA) with 10% fetal bovine serum (FBS, Gibco BRL, Grand Island, NY) and 100 U/ml penicillin-streptomycin (Gibco BRL) under conditions of 5% CO2 in air at 37 ˚C.

extract_protocol: Total RNA from cells was isolated using an RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

tag: cell line

value: Gingival epithelial cell


title: eHep1-1

description: Gene expression

source_name: eHeps from 129S1-No1-rep 1

value: liver


title: PB11_EB_rep2

source_name: EB from PSC with good hematopoietic potential

value: normal amniocytes

value: good


title: PB12_EB_rep2


title: APC control replicate 2

description: gene expression under normal diet

value: small intestine

value: male


title: APC HFD day 10 replicate 1

description: gene expression after 10 days of HFD


title: APC control replicate 5

description: gene expression under normal diet


title: GCA-control, C19

description:
C19
Gene expression of VSMC isolated from temporal artery of patient with another diagnosis than GCA.


title: TAB+GCA, C39

description:
C39
Gene expression of VSMC isolated from temporal artery of TAB+GCA patient.


title: Cerebellum deletion carrier, A888_25_C28

source_name: Cerebellum, deletion carrier

value: adult

value: cerebellum


title: TAB+GCA, C11

description:
C11
Gene expression of VSMC isolated from temporal artery of TAB+GCA patient.


title: H1_EB_rep1

source_name: EB from ES with good hematopoietic potential

value: blastocyst

value: Embryonic bobies (EB) derived from Embryonic stem cells (ES)


title: TAB+GCA, C12

description:
C12
Gene expression of VSMC isolated from temporal artery of TAB+GCA patient.

value: vascular smooth muscle cells from temporal artery


title: PB6_EB_rep2


title: H1_EB_rep2


title: PB6_EB_rep1


title: APC control replicate 1

description: gene expression under normal diet

value: lamina propria antigen presenting cells


title: Human odontogenic epithelial cell line, OdE

description: Gene expression data from OdE cells

source_name: OdE cell

value: OdE

value: Odontogenic epithelial cell


title: obesity_VAT_rep3

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

description: Gene expression in visceral adipose tissue from zebrafish overfed with Artemia for 1 week.

hyb_protocol: 860 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacturer's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction, 100 uL was hybridized to an Agilent-026437 Zebrafish DNA Oligo Microarray for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using limma package in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.

organism: Danio rerio

source_name: visceral adipose tissue, obese, no resveratrol

label_protocol: Fifty nanograms of total RNA from each visceral AT depot were converted into labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

growth_protocol: Zebrafish were raised at 28.5 ± 0.5°C with a 14 h/10 h light/dark cycle.

extract_protocol: The adipose tissue was stored in RNA-later (Applied Biosystems, Foster City, CA, USA). Total RNA was then extracted using an RNeasy Plus Micro Kit (Qiagen, Valencia, CA, USA), qualified by an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and quantified using a spectrophotometer (NanoDrop ND-100, Wilmington, DE, USA).

treatment_protocol: Zebrafish (MieKomachi 001 line created by crossing nacre and rose) in the OF and OF+RSV groups were fed three times per day with freshly hatched Artemia. Zebrafish in the OF+RSV group was fed with gluten containing RSV (corresponding to 20 μg /fish/day) at 20 min before feeding Artemia in morning. Zebrafish in the OF group were fed with gluten without RSV at 20 min before feeding Artemia in morning.

tag: line

value: MieKomachi 001

value: visceral adipose tissue

tag: age

value: 4 mpf

tag: phenotype

value: diet-induced obesity

tag: treatment


title: obesity_RSV_VAT_rep1

source_name: visceral adipose tissue, obese, resveratrol

tag: tissue

value: resveratrol


title: control_VAT_rep1

description: Gene expression in visceral adipose tissue from zebrafish.

source_name: visceral adipose tissue, control

value: control


title: obesity_RSV_VAT_rep3


title: obesity_VAT_rep1


title: control_VAT_rep3


title: obesity_VAT_rep2


title: control_VAT_rep2


title: PB11_EB_rep1

value: normal amniocytes

value: good

value: Embryonic bobies (EB) derived from Induced pluripotent stem cells (iPS)

value: at day 16 of culture


title: spinal cord_SNL 10d_rep1

city: nantong city

first: Bao-chun

last: Jiang

address: seyuan road

institute: nantong university

description: Gene expression after SNL operation in mouse spinal cord

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4858A-028005) for 17 hours at 65°C and 10 rpm in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). The wash buffers contained 0.005% Triton X-102.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100617) to obtain background subtracted and spatially detrended green Processed Signal intensities.Normalized signal intensity (log2 transformed and quantile normalized) calculated from the green processed signal after Feature Extraction using the GeneSpring software version 11.0 (Agilent)

source_name: L5 spinal cord, SNL, 10day

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

growth_protocol: Adult male ICR mice (male, 8 weeks) were maintained on a 12:12 light–dark cycle at a room temperature of 22 ± 1°C with free access to food and water. The experimental procedures were approved by the Animal Care and Use Committee of Nantong University and performed in accordance with the guidelines of the International Association for the Study of Pain.

extract_protocol: RNA was extracted using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: To produce a spinal nerve ligation, animals were anesthetized with isoflurane and the L6 transverse process was removed to expose the L4 and L5 spinal nerves. The L5 spinal nerve was then isolated and tightly ligated with 6-0 silk threads. For sham operations, the L5 spinal nerve was exposed but not ligated.We prepared 2 mice for SNL and 2 mice for sham-operation. At 10 days after operation, the animals were deeply anesthetized with isoflurane and perfused through the ascending aorta with saline. After the perfusion, the L4-L5 spinal cord segments were collected.

value: ICR

value: SNL

value: spinal cord

tag: gender

value: male


title: obesity_RSV_VAT_rep2


title: spinal cord_SNL 10d_rep2


title: spinal cord_Sham10d_rep2

description: Gene expression after Sham operation in mouse spinal cord

source_name: L5 spinal cord, Sham, 10day

value: sham


title: HepG2 cell line Orthotopic L4-3

city: Singapore

first: Yonghui

last: Wu

address: 11 Hospital Drive

country: Singapore

institute: NCCS

description: gene expression data of HepG2 cell line Orthotopic L4-3

hyb_protocol: Extracted RNA was labelled with streptavidin-phycoerythrin conjugate (SAPE) and hybridized to Affymetrix Gene Chip Human Genome U133 Plus 2.0 single arrays.

scan_protocol: These arrays were scanned using GeneChip Scanner 3000 and images are produced and analysed to give an intensity level for each probe. The intensity level corresponds to the level of hybridisation that occurs for each probe.

data_processing: The data were RMA normalized with BRB-ArrayTools and had removed batch effects by Partek software.

source_name: human hepatoma cell line HepG2 cell line Orthotopic L4-3

extract_protocol: Total RNA samples were extracted and purified from tumors using methods described in the RNeasy Mini-Handbook

value: hepatoma cell line HepG2

tag: injection into scid mice

value: Orthotopic


title: HepG2 cell line Orthotopic L4-5

description: gene expression data of HepG2 cell line Orthotopic L4-5

source_name: human hepatoma cell line HepG2 cell line Orthotopic L4-5

label_protocol: Extracted RNA was labelled with streptavidin-phycoerythrin conjugate (SAPE) and hybridized to Affymetrix Gene Chip Human Genome U133 Plus 2.0 single arrays.


title: HepG2 cell line Orthotopic L4-2

description: gene expression data of HepG2 cell line Orthotopic L4-2

source_name: human hepatoma cell line HepG2 cell line Orthotopic L4-2


title: HepG2 cell line Orthotopic L4-4

description: gene expression data of HepG2 cell line Orthotopic L4-4

source_name: human hepatoma cell line HepG2 cell line Orthotopic L4-4


title: HepG2 cell line Subcutaneous S3-2

description: gene expression data of HepG2 cell line Subcutaneous S3-2

source_name: human hepatoma cell line HepG2 cell line Subcutaneous S3-2

value: Subcutaneous (Ectopic)


title: Explant 01-0207 Orthotopic L1-3(B3)

description: gene expression data of Explant 01-0207 Orthotopic L1-3(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Orthotopic L1-3(B3)

value: Hepatocellular carcinoma tissue explant


title: HepG2 cell line Subcutaneous S3-3

description: gene expression data of HepG2 cell line Subcutaneous S3-3

source_name: human hepatoma cell line HepG2 cell line Subcutaneous S3-3


title: iTreg cells MIEG3(control) vs. YY1

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

description: Biological replicate 1

hyb_protocol: The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: M (MIEG3)

label_protocol: For control and test RNAs, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to the manufacturer’s instructions.

growth_protocol: Splenic CD4 T cells were isolated from 6-8-week-old C57BL/6 mice. Naïve CD4 T cells were sorted based on surface marker expression (CD4+, CD62Lhigh, and CD44low). Naïve CD4 T cells were stimulated by plate-bound anti-CD3 (5 microgram/ml) and soluble anti-CD28 (2 microgram/ml) for 24 hours. Activated cells were infected with viruses containing either MIEG3 (control) or YY1-expression vector with polybrene (4 μg ml-1) at 1,500 × g for 90 min at 32°C. Cell were treated with TGF-beta (5 microgram/ml), IL-2 (1 nanogram/ml), XMG1.2 antibody (10 microgram/ml), and 11B11 antibody (10 microgram/ml) for additional 4 days. Cells were harvested for RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: culture duration

value: 5 days

value: spleen

tag: strain

tag: infection

source_name: Y (YY1)

value: YY1-expression vector with polybrene (4 ug ml-1)


title: Explant 01-0207 Orthotopic L1-1(B3)

description: gene expression data of Explant 01-0207 Orthotopic L1-1(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Orthotopic L1-1(B3)


title: Explant 01-0207 Subcutaneous S1-2(B3)

description: gene expression data of Explant 01-0207 Subcutaneous S1-2(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Subcutaneous S1-2(B3)


title: HepG2 cell line Subcutaneous S3-1

description: gene expression data of HepG2 cell line Subcutaneous S3-1

source_name: human hepatoma cell line HepG2 cell line Subcutaneous S3-1


title: Explant 01-0207 Subcutaneous S1-4(B3)

description: gene expression data of Explant 01-0207 Subcutaneous S1-4(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Subcutaneous S1-4(B3)


title: HepG2 cell line Orthotopic L4-1

description: gene expression data of HepG2 cell line Orthotopic L4-1

source_name: human hepatoma cell line HepG2 cell line Orthotopic L4-1


title: GF 6

city: Oita

first: Yasushi

last: Teshima

address: 1-1 Idaigaoka, Yufu

institute: Oita University

description: miRNA expression in the heart of diabeticl rat with glucose fluctuation

hyb_protocol: After Cy3-labeling, RNA was dried up and re-solved with 18 ul RNase-free water.  And then, 4.5 ul of 10x Gene expression blocking agent and 22.5 ul of 2x hybridization buffer HI-RPM were added to the RNA sample, and the mixture hybridized to Agilent rat miRNA Microarrays (Grid ID19159, Rat Rel. 10.1, Agilent Technologies) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 5% and 100%, extended dynamic range scan mode).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent Technologies) using default parameters (protocol miRNA-v1_95_May07 and Grid: 019159_D_20081121) to obtain background subtracted Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: rat hearts

label_protocol: One hundred ng of total RNA was labeled with Cy3 using a miRNA labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA from rat heart was extracted with a miRNeasy Mini kit (QIAGEN) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Diabetes mellitus was induced in Sprague-Dawley rats by a single injection of streptozotocin (STZ; 60 mg/kg) into the tail vein. The plasma glucose concentration in the rats was > 300 mg/dL and they were assigned to groups with diabetes mellitus and with DM and plasma glucose fluctuations induced by 24 hours of starvation and intraperitoneal insulin (0.5 IU/kg) injection.

value: Heart

value: Sprague-Dawley

value: Male

value: glucose fluctuation was induced by a 24-h- fast and an insulin injection (0.5 IU/kg)


title: GF 5


title: Explant 2-1318 Orthotopic L2-3

description: gene expression data of Explant 2-1318 Orthotopic L2-3

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Orthotopic L2-3


title: Explant 2-1318 Subcutaneous S2-3

description: gene expression data of Explant 2-1318 Subcutaneous S2-3

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Subcutaneous S2-3


title: Explant 2-1318 Subcutaneous S2-2

description: gene expression data of Explant 2-1318 Subcutaneous S2-2

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Subcutaneous S2-2


title: Explant 01-0207 Subcutaneous S1-3(B3)

description: gene expression data of Explant 01-0207 Subcutaneous S1-3(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Subcutaneous S1-3(B3)


title: GF 4


title: Explant 2-1318 Orthotopic L2-4

description: gene expression data of Explant 2-1318 Orthotopic L2-4

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Orthotopic L2-4


title: Explant 2-1318 Subcutaneous S2-1

description: gene expression data of Explant 2-1318 Subcutaneous S2-1

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Subcutaneous S2-1


title: spinal cord_Sham10d_rep1

description: Gene expression after Sham operation in mouse spinal cord

source_name: L5 spinal cord, Sham, 10day


title: Explant 01-0207 Subcutaneous S1-1(B3)

description: gene expression data of Explant 01-0207 Subcutaneous S1-1(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Subcutaneous S1-1(B3)


title: Explant 2-1318 Orthotopic L2-1

description: gene expression data of Explant 2-1318 Orthotopic L2-1

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Orthotopic L2-1


title: Explant 2-1318 Orthotopic L2-2

description: gene expression data of Explant 2-1318 Orthotopic L2-2

source_name: Hepatocellular carcinoma tissue Explant 2-1318 Orthotopic L2-2


title: Explant 261004 Orthotopic L1-2

description: gene expression data of Explant 261004 Orthotopic L1-2

source_name: Hepatocellular carcinoma tissue Explant 261004 Orthotopic L1-2


title: Exp B MMP3 100K

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

description: Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX13 using Affymetrix default analysis settings (RMA processing)

source_name: SCp2 cells plated at 100K and treated with MMP-3 for three days

label_protocol: This project used the Affymetrix Mouse 430 2.0 GeneChip 200 ng of total RNA was used as input

growth_protocol: Cells were grown in DMEM+2% FCS

extract_protocol: Phenol/Chloroform

treatment_protocol: Treatment with MMP3

value: mammary gland

value: SCp2 mouse mammary epithelial cells

tag: cell density

tag: agent

tag: experiment

value: B


title: DM 5

description: miRNA expression in the heart of diabeticl rat

value: diabetes mellitus was induced with an intravenous injection of streptozotocin (60 mg/kg)


title: Explant 261004 Orthotopic L1-1

description: gene expression data of Explant 261004 Orthotopic L1-1

source_name: Hepatocellular carcinoma tissue Explant 261004 Orthotopic L1-1


title: Exp B MMP3 250K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 250K and treated with MMP-3 for three days


title: eHep2-3

description: Gene expression

source_name: eHeps from C57B6-No1-rep 3

tag: cellular origin

value: liver


title: Explant 261004 Orthotopic L1-3

description: gene expression data of Explant 261004 Orthotopic L1-3

source_name: Hepatocellular carcinoma tissue Explant 261004 Orthotopic L1-3


title: Veh 5

description: miRNA expression in the heart of control rat

source_name: rat hearts

value: exposed to vehicle


title: Veh 4


title: Exp B MMP3 50K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 50K and treated with MMP-3 for three days


title: DM 4


title: Explant 01-0207 Orthotopic L1-2(B3)

description: gene expression data of Explant 01-0207 Orthotopic L1-2(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Orthotopic L1-2(B3)


title: Veh 3


title: Explant 261004 Subcutaneous S1-4

description: gene expression data of Explant 261004 Subcutaneous S1-4

source_name: Hepatocellular carcinoma tissue Explant 261004 Subcutaneous S1-4


title: liver at 3 week old of H3, biological rep1

city: Shanghai

first: Yanhong

last: HUANG

address: 1665 Kong Jiang Road

institute: Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicne

description: Experimental group 3

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw signal intensities of gene expression data were processed and analyzed by Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) and Gene Spring Software 11.0 (Agilent technologies, Santa Clare, CA, US).

source_name: Rat  liver at weaning from dams fed high fat diet

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The liver tissues from rat were stored at -80℃.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Selected liver tissues from the rat were transferred to a basket,  placed on ice in the Trizol solution(Cat#15596-018，Life technologies, Carlsbad, CA, US).

value: 3 week old offspring

value: liver of offspring

tag: maternal diet

value: high fat diet


title: Explant 261004 Subcutaneous S1-2

description: gene expression data of Explant 261004 Subcutaneous S1-2

source_name: Hepatocellular carcinoma tissue Explant 261004 Subcutaneous S1-2

value: Hepatocellular carcinoma tissue explant

value: Subcutaneous (Ectopic)


title: liver at 3 week old of H2, biological rep1

description: Experimental group 2


title: GF 2

description: miRNA expression in the heart of diabeticl rat with glucose fluctuation


title: Exp B MMP3 25K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 25K and treated with MMP-3 for three days


title: Exp B control 100K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 100K and treated as controls for three days

value: control


title: Explant 261004 Subcutaneous S1-3

description: gene expression data of Explant 261004 Subcutaneous S1-3

source_name: Hepatocellular carcinoma tissue Explant 261004 Subcutaneous S1-3


title: Exp B control 250K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 250K and treated as controls for three days


title: Explant 261004 Subcutaneous S1-1

description: gene expression data of Explant 261004 Subcutaneous S1-1

source_name: Hepatocellular carcinoma tissue Explant 261004 Subcutaneous S1-1


title: GF 1


title: liver at 3 week old of C2, biological rep1

description: Control group 2

source_name: Rat  liver at weaning from dams fed standard chow diet


title: PB7_EB_rep1

source_name: EB from PSC with good hematopoietic potential

tag: tissue origin

value: normal amniocytes

tag: psc hematopoietic potential

value: good

tag: cell type

value: Embryonic bobies (EB) derived from Induced pluripotent stem cells (iPS)

tag: time point

value: at day 16 of culture


title: Exp B control 50K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 50K and treated as controls for three days

tag: cell line


title: liver at 3 week old of C3 ,biological rep1

description: Control group 3

value: Sprague-Dawley

tag: age


title: DM 3

tag: tissue

value: Heart

value: Male

tag: treatment


title: DM 2

tag: gender


title: MCF10A 800K

description:
SAMPLE 6
Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C. GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

data_processing: The data were analyzed with Genespring GX13 using Affymetrix default analysis settings (RMA processing) and genes were normalized to MCF10A 50K (Sample 1)

source_name: MCF10A cells plated at 800K and grown for 24h

label_protocol: This project used the Affymetrix.GeneChip.HG-U133_Plus_2 200 ng of total RNA was used as input

growth_protocol: MCF10A cells were grown in DMEM/F12 (Gibco), supplemented with 5% horse serum (Gibco), 20 ng/ml EGF (Peprotech), 0.5 μg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma) and 100 μg/ml gentamicin (Gibco)

treatment_protocol: Culture at differing densities

value: mammary gland

value: MCF10A human breast epithelial cells


title: Exp B control 25K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 25K and treated as controls for three days

value: SCp2 mouse mammary epithelial cells

value: B


title: MCF10A 600K

description:
SAMPLE 5
Gene expression data from cell culture

source_name: MCF10A cells plated at 600K and grown for 24h


title: liver at 3 week old of H1, biological rep1

description: Experimental group 1

value: 3 week old offspring


title: IMQ_RSV_rep1

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® MoGene 1.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring GX 12.6. RMA16 algorithm was used for normalization
RMA16 Quantile normalized gene level expression values. For variance stabilization 16 was added before log2 transformation. Please note that control probesets were not included in the GeneSpring analysis (resulting 28856 data rows).

source_name: Imiquimod-induced psoriasis treated with Resveratrol

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion)

extract_protocol: TRIzol extraction

value: BALBc/AnNTac

tag: genotype/variation

value: wild type

value: Skin Biopsy

tag: skinfold back thickness

tag: tissue subtype


title: Exp A MMP3 100K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 100K and treated with MMP-3 for three days

tag: cell density

value: A


title: liver at 3 week old of C1, biological rep1

description: Control group 1

tag: strain

value: liver of offspring

value: control


title: DM 1

source_name: rat hearts

value: diabetes mellitus was induced with an intravenous injection of streptozotocin (60 mg/kg)


title: IMQ_RSV_rep2

value: Imiquimod-induced psoriasis treated with Resveratrol


title: IMQ_rep2

source_name: Imiquimod-induced psoriasis-like skin inflammation


title: Exp A MMP3 250K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 250K and treated with MMP-3 for three days

tag: agent

tag: experiment


title: Exp A MMP3 50K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 50K and treated with MMP-3 for three days


title: MCF10A 200K

description:
SAMPLE 3
Gene expression data from cell culture

source_name: MCF10A cells plated at 200K and grown for 24h


title: MCF10A 100K

description:
SAMPLE 2
Gene expression data from cell culture

source_name: MCF10A cells plated at 100K and grown for 24h


title: MCF10A 400K

description:
SAMPLE 4
Gene expression data from cell culture

source_name: MCF10A cells plated at 400K and grown for 24h


title: Veh 2

value: exposed to vehicle


title: Veh 1

value: Sprague-Dawley


title: MCF10A 50K

description:
SAMPLE 1
Gene expression data from cell culture

source_name: MCF10A cells plated at 50K and grown for 24h


title: Exp A control 100K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 100K and treated as controls for three days


title: Control_rep3

source_name: Control


title: IMQ_rep1

value: Imiquimod-induced psoriasis-like skin inflammation


title: PA3Lysates_phage-80min_rep3

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

description: Gene expression after phage infection of 80min

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.Hybridization Kit (Cat#5188-5242, Agilent technologies,  Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent  technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT100%，10%.

organism: Bruynoghevirus PaP3

source_name: PA3 lysates, 80min, replicate 3

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa  Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed  the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: PA3 with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol: Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Bacterial culture were infected with phage PaP3 at MOI of 10 for 0min, 5min, 10min, 20min, 30min and 80min.The uninfected samples (0 min) served as reference.

tag: bacteriophage

tag: time


title: Exp A control 250K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 250K and treated as controls for three days


title: Exp A control 50K

description: Gene expression data from cell culture

source_name: SCp2 cells plated at 50K and treated as controls for three days


title: PA3Lysates_phage-80min_rep2

source_name: PA3 lysates, 80min, replicate 2


title: P. palmivora 1

status: Public on Nov 16 2015

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

hyb_protocol: Hybridizations were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

scan_protocol: Scannings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

data_processing: Microarray analysis was performed using a whole-genome Roche NimbleGen custom oligo expression array as previously described (Maximova et al., 2014). Probe labeling, hybridization, and detection were performed at the Penn State Genomics Core Facility, and the statistical analysis of the microarray data were performed as previously described. (Maximova et al., 2014). Briefly, the Bioconductor package (Gentleman et al., 2004) was used in R to perform quality control checks and calculate normalized expression values using the RMA procedure. Normalized expression values were plotted to ensure all replicates for a given treatment had similar expression patterns. The LIMMA package (Smyth, 2005) was then used to calculate fold induction on a per-probe basis and to calculate a Bayesian moderated test statistic for each comparison (pathogen-treatments relative to water-treatment). A Benjamini-Hochberg multiple testing correction (Benjamini & Hochberg, 1995, Benjamini & Yekutieli, 2001) was then applied. Probes with Benjamini-Hochberg p < 0.05 were considered significant. In identifying individual PR genes with statistically significant differential regulation, any gene with multiple probes below the significance threshold had fold change measured on each probe averaged.

organism: Theobroma cacao

source_name: UF12 cacao seedlings

label_protocol: Labelings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

growth_protocol: Seeds from open pollinated T. cacao mother trees, accession UF12, were collected from a plantation in Charagre, Bocas del Toro province, Panama. The seeds were surface sterilized by immersing them in 0.5% sodium hypochlorite for three minutes and rinsed with sterile water before being placed for germination in plastic trays with soil (2:1 mixture of clay rich soil from Barro Colorado Island, Panama and rinsed river sand) and incubated in Percival growth chambers. One-month-old seedlings were transplanted to individual pots (600 ml volume) containing the same soil mixture and kept in the growth chambers. Germination of seeds and seedling growth was done in growth chambers (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30ºC and 26ºC respectively (Mejía et al., 2014).

extract_protocol: Target leaves were cut with a scissor from the plant, immediately weighted and placed in RNAlater solution in borosilicate vials following manufacturer’s instructions (Applied Biosystems/Ambion, Austin, TX). Vials with samples were shipped to PSU on dry ice where RNA extractions were performed as previously described (Verica et al., 2004). Total RNA sample concentration and purity was assessed using a NanoDrop spectrophotometer and RNA quality was determined using an Agilent Bioanalzyer.

treatment_protocol: Two month old seedlings , with approximately six leaves each, were spray-inoculated with conidia of Colletotrichum theobromicola or zoospores of Phytophthora palmivora. Conidia of C. theobromicola were produced using the same methods as in (Mejía et al., 2014) for production of other species of Colletotrichum and zoospores were produced as in (Mejía et al., 2008).  Whole seedlings were sprayed either with pathogen inoculum or sterile distilled water (controls) and then placed back into the growing chamber, but only stage C leaves (Mejia et al., 2012) at the time of inoculation were considered as target for the experiment. Pathogens C. theobromicola and P. palmivora were re-isolated from lesions developed in inoculated leaves three days post-inoculation and this was considered as a measure of successful inoculation. Leaves sprayed with water remained healthy, did not develop lesions, and no pathogens were re-isolated from them. Leaf samples from a total of four individual seedlings were harvested from the pathogen treatments and from the water sprayed control seedlings. Each sample (biological replicate) consisted of a single individual leaf.

tag: genotype

value: Two months old

tag: developmental stage

value: seedlings from open pollinated UF12 mother tree

tag: stress

value: Spray inoculated with Phytophthora palmivora zoospores

value: leaf

tag: leaf stage

value: C

tag: propagation

value: Seed


title: Control_rep2

value: BALBc/AnNTac

tag: tissue


title: Control_rep1

value: wild type


title: C. theobromicola 2

tag: age

value: Spray inoculated with Colletotrichum theobromicola conidia


title: P. palmivora 2


title: C. theobromicola 4


title: P. palmivora 5


title: H2O 4

value: Mock inoculated (spray) with sterile water


title: C. theobromicola 5


title: P. palmivora 3


title: C. theobromicola 3


title: mPSC-CM d30 rep3

city: Baltimore

first: Hideki

last: Uosaki

state: MD

address: 720 Rutland Ave, Ross 954

department: Division of Cardiology

institute: Johns Hopkins University

hyb_protocol: 16 hr at 45C with constant rotation (60 rpm) following manufacturer's recommended procedure

scan_protocol: Affymetrix GeneChip scanner 3000 7G with manufacturer's recommended setting.

data_processing: Microarray data was processed using bioconductor R. To normalize data, fRMA was used.

source_name: PSC-CMs_30 days after differentiation with selection

label_protocol: Affymetrix 3' IVT express kit following manufacturer's recommended procedure

growth_protocol: mouse ESCs carrying Ncx1 promoter driven PAC were differentiated to cardiomyocytes using cytokines (Activin A, BMP4, VEGF, bFGF, FGF10). From day 7, cells were treated with puromycin to eliminate non-cardiomyocytes.

extract_protocol: Total RNA was isolated following the manufacturers instruction

treatment_protocol: Cells were cultured for 10-30 days and lysed using TRIzole.

tag: cell line

value: synp line generated from R1 ES cells (Yamanaka, Plos One, 2008)

tag: strain background (for r1 es)

tag: cell type

value: mouse embryonic stem cell derived cardiomyocytes (PSC-CMs)

tag: time point


title: P. palmivora 4


title: H2O 5


title: H2O 3


title: mPSC-CM d30 rep2

value: 30 days after differentiation with selection


title: Explant 01-0207 Orthotopic L1-4(B3)

description: gene expression data of Explant 01-0207 Orthotopic L1-4(B3)

source_name: Hepatocellular carcinoma tissue Explant 01-0207 Orthotopic L1-4(B3)

value: Hepatocellular carcinoma tissue explant

tag: injection into scid mice

value: Orthotopic


title: H2O 1


title: H2O 2


title: mPSC-CM d30 rep1


title: mPSC-CM d20 rep3

source_name: PSC-CMs_20 days after differentiation with selection


title: mPSC-CM d10 rep1

source_name: PSC-CMs_10 days after differentiation with selection


title: MDA-MB-231, miR-142-3p transfected, replicate 1

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

country: Germany

institute: University of Muenster

description: Affymetrix GeneChip Human Gene 1.0 ST

hyb_protocol: The prepared targets were hybridized overnight to Affymetrix GeneChip Human Gene 1.0 ST arrays. Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Partek Genomics Suite was used for data anlyses (RMA normalisation).

source_name: MDA-MB-231 cells, miR-142-3p transfected

label_protocol: The samples were amplified from 100 ng of total RNA in accordance with the Ambion WT Expression assay kit (LifeTechnologies GmbH, Darmstadt, Germany) and fragmented and end-labeled in accordance with the Affymetrix GeneChip WT Terminal Labeling protocol (Affymetrix UK Ltd., High Wycombe, UK).

growth_protocol: MDA-MB-231 cells were maintained in DMEM (Gibco) containing 10% fetal calf serum, 1% glutamine and 1% penicillin-streptomycin in a humidified athmosphere of 8.5%CO2 at 37°C. Cells were plated in 6-well plates 1 day before miRNA transfection to reach 70% confluence after 24h.

extract_protocol: Total RNA was isolated using the innuPREP RNA Mini Kit [analytikjena] according to the manufacturers instructions.Reverse transcription of mRNA was performed using the First strand cDNA Synthesis kit and random hexamer primers (Fermentas, St Leon Rot, Germany).

treatment_protocol: Transfection was performed using Dharmafect reagent (Dharmacon) in OPTI-MEM media (Gibco) and 10 nM microRNA precursor miR-142-3p or pre-miR-precursor #1 (Applied Biosystems) according to the manufacturer's instructions. After 24 h of transfection, OPTI-MEM was replaced by regular culture medium. RNA was extracted from the cells 72h after transfection.

tag: treatment

value: miR-142-3p transfected


title: mPSC-CM d20 rep1

value: 20 days after differentiation with selection


title: MDA-MB-231, miR-142-3p transfected, replicate 2

description: Affymetrix GeneChip Human Gene 1.0 ST


title: mPSC-CM d10 rep3

value: 10 days after differentiation with selection


title: C. theobromicola 1

value: Two months old

value: seedlings from open pollinated UF12 mother tree


title: MDA-MB-231, control miRNA transfected, replicate 3

description: Affymetrix GeneChip Human Gene 1.0 ST

source_name: MDA-MB-231 cells, control miRNA transfected

value: control miRNA transfected


title: MDA-MB-231, miR-142-3p transfected, replicate 3

description: Affymetrix GeneChip Human Gene 1.0 ST


title: mPSC-CM d20 rep2


title: mPSC-CM d10 rep2


title: MDA-MB-231, control miRNA transfected, replicate 2

description: Affymetrix GeneChip Human Gene 1.0 ST


title: U373  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C14

city: Brussels

first: Olivier

last: Feron

address: 53 Avenue E. Mounier, bte B1.53.09

department: Pole of Pharmacology and Therapeutics (FATH)  Institute of Experimental and Clinical Research (IREC)

country: Belgium

institute: Université catholique de Louvain

description: U373  24*(0.5h 21%O2 + 0.5h 1% O2)

hyb_protocol: Standard Affymetrix protocol (performed by IGBMC Microarray and Sequencing Platform, Strasbourg - France)

data_processing: The data were analyzed with R/Bioconductor using RMA as normalization method.

source_name: RNA from cell line in Cycling Hypoxia

growth_protocol: Cells were routinely grown in accordance with ATCC-recommended culture conditions.

extract_protocol: Total RNA was extracted from cell lines by using Trireagent (Ambion) and purified with MinElute kit (Qiagen). The quantity of RNA was assessed spectrophotometrically at 260 nm. 260/280 and 260/230 ratios (260/280 and 260/230 ratios of pure RNA were superior or equal to 2). The quality of RNA was determined by visualization of the 18S and 28S RNA bands under UV light after BET stained agarose gel electrophoresis.

treatment_protocol: Cells were submitted to cycling hypoxia, i.e. 24 cycles of 30 min incubation under normoxia and 30 min incubation under hypoxic (1% O2) conditions to reproduce the frequency of hypoxic fluctuations. This protocol was further validated by the detection of HIF-1a during each hypoxic periods and its degradation during the normoxic conditions. We also considered a condition of 24h continuous exposure of tumor cells to 1% O2 (Continuous Hypoxia), and a condition of 24h continuous exposure of tumor cells to 21% O2 (Normoxia)

value: Brain

value: Cycling Hypoxia


title: HCT116 p53 -/-  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C7

scan_protocol: Standard Affymetrix protocol (performed by IGBMC Microarray and Sequencing Platform, Strasbourg - France)

value: Colon


title: MDA-MB-231, control miRNA transfected, replicate 1

description: Affymetrix GeneChip Human Gene 1.0 ST


title: PC3  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C13

description: PC3  24*(0.5h 21%O2 + 0.5h 1% O2)

label_protocol: Standard Affymetrix protocol (performed by IGBMC Microarray and Sequencing Platform, Strasbourg - France)

value: Prostate


title: A498  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C19

description: A498  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Kidney


title: HT29  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C8

description: HT29  24*(0.5h 21%O2 + 0.5h 1% O2)


title: siHa  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C12

description: siHa  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Ovary

value: siHa


title: HCT-15  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C11

description: HCT-15  24*(0.5h 21%O2 + 0.5h 1% O2)


title: HT1080  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C20

description: HT1080  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Epithelium


title: Hep3B  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C16

description: Hep3B  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Liver


title: LoVo  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C10

description: LoVo  24*(0.5h 21%O2 + 0.5h 1% O2)

value: LoVo


title: PLC/PRF/5  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C17

description: PLC/PRF/5  24*(0.5h 21%O2 + 0.5h 1% O2)


title: HepG2  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C15

description: HepG2  24*(0.5h 21%O2 + 0.5h 1% O2)


title: Colo-205  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C9

description: Colo-205  24*(0.5h 21%O2 + 0.5h 1% O2)


title: Widr  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C5

description: Widr  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Widr


title: U373 24h at 1% O2 OFN_H14

description: U373 24h at 1% O2

source_name: RNA from cell line in Continuous Hypoxia

value: Continuous Hypoxia


title: Hep3B 24h at 1% O2 OFN_H16

description: Hep3B 24h at 1% O2


title: HT1080 24h at 1% O2 OFN_H20

description: HT1080 24h at 1% O2


title: MDA-MB-231  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C2

description: MDA-MB-231  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Breast


title: A549  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C4

description: A549  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Lung


title: PLC/PRF/5 24h at 1% O2 OFN_H17

description: PLC/PRF/5 24h at 1% O2


title: MCF-7 24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C1

description: MCF-7 24*(0.5h 21%O2 + 0.5h 1% O2)


title: A498 24h at 1% O2 OFN_H19

description: A498 24h at 1% O2


title: HCT116  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C6

description: HCT116  24*(0.5h 21%O2 + 0.5h 1% O2)


title: PC3 24h at 1% O2 OFN_H13

description: PC3 24h at 1% O2


title: HepG2 24h at 1% O2 OFN_H15

description: HepG2 24h at 1% O2


title: T-47D  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C3

description: T-47D  24*(0.5h 21%O2 + 0.5h 1% O2)


title: SK-HEP-1 24h at 1% O2 OFN_H18

description: SK-HEP-1 24h at 1% O2


title: siHa 24h at 1% O2 OFN_H12

description: siHa 24h at 1% O2


title: gangliaw2_wildtype_rep6

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

description: wt w2_6

hyb_protocol: Hybridisation according to manufacturer's protocol (Agilent)

scan_protocol: Scanned with Agilent scanner with standard settings.

data_processing: Data was normalized and processed using AgilentToGCT and LimmaGP modules in GenePattern

source_name: week 2 ganglia_wildtype

label_protocol: Cy3 labelling according to manufacturer's protocol (Agilent)

growth_protocol: primary tissues were extracted from mice by surgical removal

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen)

value: 2 weeks

tag: genotype/variation

value: wild type

value: superior cervical ganglia and coeliac ganglia


title: gangliaw2_wildtype_rep1

description: wt w2_1


title: HCT-15 24h at 1% O2 OFN_H11

description: HCT-15 24h at 1% O2


title: gangliaw2_thmycn_rep5

description: mycn w2_5

source_name: week 2 ganglia_TH-MYCN+/+

value: TH-MYCN+/+


title: gangliaw2_wildtype_rep7

description: wt w2_7


title: gangliaw2_thmycn_rep3

description: mycn w2_3


title: gangliaw2_wildtype_rep2

description: wt w2_2


title: LoVo 24h at 1% O2 OFN_H10

description: LoVo 24h at 1% O2


title: gangliaw2_thmycn_rep1

description: mycn w2_1


title: gangliaw2_wildtype_rep4

description: wt w2_4


title: Widr 24h at 1% O2 OFN_H5

description: Widr 24h at 1% O2


title: HCT116 p53 -/- 24h at 1% O2 OFN_H7

description: HCT116 p53 -/- 24h at 1% O2


title: Colo-205 24h at 1% O2 OFN_H9

description: Colo-205 24h at 1% O2


title: HCT116 24h at 1% O2 OFN_H6

description: HCT116 24h at 1% O2


title: cellline_MYCN2

hyb_protocol: Performed at the Ramaciotti Centre for Genomic as UNSW. 3ug fragmeneted and lebelled ss-CDNA hybridized to the array for 45C for 16 hours rotating at 60 rpm

scan_protocol: Performed at the Ramaciotti Centre for Genomic as UNSW. Affymetrix GeneChip Command Console software using the GCS 3000 7G scanner

data_processing: Genepattern NormaliseAffymetrixST module (v2.2) using RMA

source_name: BE(2)C cells

label_protocol: Performed at the Ramaciotti Centre for Genomic as UNSW. 100ng RNA labelled according to Affymetrix WT PLUS kit

growth_protocol: BE(2)C cells subcultured every 3 days. Grown in DMEM 10%FCS

extract_protocol: Total RNA was extracted using the Purelink RNA kit (Life Technologies)

treatment_protocol: MYCN2 (#SI03113670, Qiagen) or control siRNAs (ONTARGETplus siRNA, #D-001810-0X, Dharmacon) transfected using Lipofectamine 2000 reagent according to manfacturers instuctions (Life Technologies). RNA isolated 36-hours post-transfection

value: BE(2)C cells

value: MYCN siRNA


title: gangliaw2_wildtype_rep5

description: wt w2_5


title: gangliaw2_thmycn_rep4

description: mycn w2_4


title: cellline_control reanalysis

value: control


title: A549 24h at 1% O2 OFN_H4

description: A549 24h at 1% O2


title: cellline_MYCN1

treatment_protocol: MYCN1 (#SI03087518, Qiagen) or control siRNAs (ONTARGETplus siRNA, #D-001810-0X, Dharmacon) transfected using Lipofectamine 2000 reagent according to manfacturers instuctions (Life Technologies). RNA isolated 36-hours post-transfection


title: gangliaw2_wildtype_rep3

description: wt w2_3


title: HT29 24h at 1% O2 OFN_H8

description: HT29 24h at 1% O2

value: Colon


title: gangliaw2_thmycn_rep6

description: mycn w2_6


title: MDA-MB-231 24h at 1% O2 OFN_H2

description: MDA-MB-231 24h at 1% O2


title: T-47D 24h at 1% O2 OFN_H3

description: T-47D 24h at 1% O2


title: gangliaw2_thmycn_rep2

description: mycn w2_2


title: cellline_control


title: MCF-7 24h at 1% O2 OFN_H1

description: MCF-7 24h at 1% O2


title: HT1080  24h at 21% O2 OFN_N20

description: HT1080  24h at 21% O2

source_name: RNA from cell line in Normoxia

value: Normoxia


title: cellline_control_rep1

treatment_protocol: SSRP1 (#J01178306, Dharmacon) or control siRNAs (ONTARGETplus siRNA, #D-001810-0X, Dharmacon) transfected using Lipofectamine 2000 reagent according to manfacturers instuctions (Life Technologies). RNA isolated 72-hours post-transfection


title: SK-HEP-1  24h at 21% O2 OFN_N18

description: SK-HEP-1  24h at 21% O2


title: cellline_SSRP1_rep1

value: SSRP1 siRNA


title: Hep3B  24h at 21% O2 OFN_N16

description: Hep3B  24h at 21% O2


title: SK-HEP-1  24*(0.5h 21%O2 + 0.5h 1% O2) OFN_C18

description: SK-HEP-1  24*(0.5h 21%O2 + 0.5h 1% O2)

value: Cycling Hypoxia


title: PLC/PRF/5  24h at 21% O2 OFN_N17

description: PLC/PRF/5  24h at 21% O2

value: Liver


title: PC3  24h at 21% O2 OFN_N13

description: PC3  24h at 21% O2

value: Prostate


title: A498  24h at 21% O2 OFN_N19

description: A498  24h at 21% O2

value: Kidney


title: LoVo  24h at 21% O2 OFN_N10

description: LoVo  24h at 21% O2

value: LoVo


title: Widr  24h at 21% O2 OFN_N5

description: Widr  24h at 21% O2

value: Widr


title: A549  24h at 21% O2 OFN_N4

description: A549  24h at 21% O2

value: Lung


title: MDA-MB-231  24h at 21% O2 OFN_N2

description: MDA-MB-231  24h at 21% O2

value: Breast


title: U373  24h at 21% O2 OFN_N14

description: U373  24h at 21% O2

value: Brain


title: HCT116  24h at 21% O2 OFN_N6

description: HCT116  24h at 21% O2


title: delat-gbdR delta-souR in pyruvate replica 2

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Following fragmentation, 2.4 ug of cRNA were hybridized on the Pseudomonas aeruginosa PAO1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were first generated using the Expression Console  program (Affymetrix). Probe-level intensities were background-corrected, normalized, and summarized, and Robust Multichip Average (RMA) statistics were calculated for each probe set and sample as is implemented in Transcriptome Analysis Console v2.0 (Affymetrix).

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa delta-gbdR delta-souR in pyruvate replica 2

label_protocol: Biotinylated cDNA was prepared from 50 ng of whole RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions.

growth_protocol: Cells were pregrown for 24 h in MOPS with 25 mM pyruvate and 5 mM glucose and then resuspended in MOPS pyruvate or MOPS pyruvate + 1 mM sarcosine.

extract_protocol: RNA was extracted from RNA Protect-treated pellets using the Qiagen RNeasy kit using lysozyme-aided lysis. RNA from the first round of columns was treated with DNase I and another round of RNeasy conducted including the on-column DNase step.

treatment_protocol: Cell suspension was treated with two volumes of RNA Protect Bacterial Reagent (Qiagen) and processed to a wet pellet as per manufacturer's instructions

value: PA14 delta-gbdR delta-souR

value: pyruvate control


title: HCT116 p53 -/-  24h at 21% O2 OFN_N7

description: HCT116 p53 -/-  24h at 21% O2


source_name: Pseudomonas aeruginosa delta-gbdR delta-souR in pyruvate, replica 1


title: HepG2  24h at 21% O2 OFN_N15

description: HepG2  24h at 21% O2


title: HT29  24h at 21% O2 OFN_N8

description: HT29  24h at 21% O2


title: delat-gbdR delta-souR in sarcosine, replica 2

source_name: Pseudomonas aeruginosa delta-gbdR delta-souR in sarcosine, replica 2

value: sarcosine


source_name: Pseudomonas aeruginosa delta-gbdR delta-souR in sarcosine, replica 1


title: Colo-205  24h at 21% O2 OFN_N9

description: Colo-205  24h at 21% O2


title: MCF-7 24h at 21% O2 OFN_N1

description: MCF-7 24h at 21% O2


title: HCT-15  24h at 21% O2 OFN_N11

description: HCT-15  24h at 21% O2


title: cellline_control_rep2

value: BE(2)C cells


title: delta-gbdR in pyruvate, replica 2

source_name: Pseudomonas aeruginosa delta-gbdR in pyruvate, replica 2

value: PA14 delta-gbdR


title: delta-gbdR in sarcosine, replica 2

source_name: Pseudomonas aeruginosa delta-gbdR in sarcosine, replica 2


title: delta-gbdR in sarcosine, replica 1

source_name: Pseudomonas aeruginosa delta-gbdR in sarcosine, replica 1


title: delta-gbdR in pyruvate, replica 1

source_name: Pseudomonas aeruginosa delta-gbdR in pyruvate, replica 1


title: treatment: MJ+CD - time: 24 hrs - rep2

status: Public on Nov 15 2015

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=24 hrs rep 2 (May still include original submitter created erros/discrepancies)

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: RMA normalization was performed for Affymetrix Platforms: Using APT (apt-1.12.0: apt-probeset-summarize.cpp,v 1.178).

organism: Vitis vinifera

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: MJ+CD - time: 24 hrs)

label_protocol: CNB Grapegen Affymetrix labeling

extract_protocol: Trizol Plus RNA Purification (Invitrogen)

value: methyl jasmonate  + cyclodextrin

value: cell culture from calli

tag: cultivar

value: Monastrell


title: treatment: MJ+CD - time: 24 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=24 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: treatment: CD - time: 24 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=24 hrs rep 3 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: CD - time: 24 hrs)

value: cyclodextrin


title: treatment: CD - time: 24 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=24 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: Homo-sapiens_EOC-pools_A2vsB2

type: genomic

city: Jena

first: Norman

last: Häfner

address: Bachstrasse 18

department: Gynecology

institute: Jena University Hospital

description: MIRA enriched methylated DNA

hyb_protocol: The complete workflow of microarray processing followed strictly teh Agilent protocol Analysis of methylated DNA immunopreciptiation. Hybridization was done with Agilent Oligo aCGH hybridization kit. After combining specific AlexaFluor3 and 5-labelled DNAs, cot1-DNA, blocking solution, deionized formamid and hybridization buffer samples were denatured 3min at 95°C and incubated for 30min at 37°C. Solutions were then immediately transferred to the microarrays and hybridized for 40h, 67°C at 20rpm in a Agilent hybridization oven. Arrays were washed using Agilent wash procedure B (including the stabilization and drying solution).

scan_protocol: Scanned on an Agilent G2565CA scanner using Agilent G3_CGH settings at 3µm resolution. Images were quantified using Agilent Feature Extraction Software (version 10.5) and the protocol CGH_105_Jan09.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. Log2 ratios of spotted probe duplicates were averaged using Microsoft Excel 2007.

label: Alexa Fluor 3

molecule: genomic DNA

label_protocol: Labelling was done with Invitrogene BioPrime Labelling Kit according to manufacturer protocol. Reaction mixture was denatured for 5min 95°C; after 5min on ice Exo- Klenow fragment was added and samples were incubated 2h at 37°C. After purification (BioPrime Kit) the labelling efficiency was determined by NanoDrop measurements.

extract_protocol:
Genomic DNA extracted by ProteinaseK digestion, phenol-chloroform isolation and ethanol precipitation; pools generated from 1.2µg of each sample
[enrichment protocol] gDNA sonicated to fragments of 150-400bp and enrichment of methylated DNA from 2µg of pool DNA by MethylCollectorUltra Kit (ActiveMotif). Enrichment was validated by qPCR for unmethylated and imprinted (methylated) control regions.

tag: tumor

value: epithelial ovarian cancer, serous histology, FIGO IIIC

tag: gender

value: female

tag: median time to event

value: relapse free until last follow up:2210 days

tag: adjuvant chemotherapy

value: 6 cycles carboplatin+taxane

label: Alexa Fluor 5

value: PFS:447 days


title: Homo-sapiens_EOC-pools_B1vsA2

description: MIRA enriched methylated DNA

value: PFS:928 days


title: Homo-sapiens_EOC-pools_B2vsA1

description: MIRA enriched methylated DNA

value: relapse free until last follow up:1431 days


title: Homo-sapiens_EOC-pools_A1vsB1

description: MIRA enriched methylated DNA


title: treatment: MJ+CD - time: 0 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=0 hrs rep 1 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: MJ+CD - time: 0 hrs)

tag: time

value: 0 h


title: treatment: MJ+CD - time: 0 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=0 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: CD - time: 0 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=0 hrs rep 3 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: CD - time: 0 hrs)


title: treatment: CD - time: 0 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=0 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: MJ+CD - time: 0 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=0 hrs rep 3 (May still include original submitter created erros/discrepancies)


title: treatment: CD - time: 0 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=0 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: treatment: MJ - time: 24 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=24 hrs rep 3 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: MJ - time: 24 hrs)

value: methyl jasmonate


title: treatment: CD - time: 24 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=CD|time=24 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: MJ - time: 24 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=24 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: treatment: MJ - time: 0 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=0 hrs rep 3 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: MJ - time: 0 hrs)


title: treatment: MJ - time: 24 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=24 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: Control - time: 24 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=Control|time=24 hrs rep 3 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: Control - time: 24 hrs)

value: control


title: treatment: MJ - time: 0 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=0 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: treatment: MJ+CD - time: 24 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ+CD|time=24 hrs rep 3 (May still include original submitter created erros/discrepancies)


title: treatment: MJ - time: 0 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=MJ|time=0 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: Control - time: 24 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=Control|time=24 hrs rep 2 (May still include original submitter created erros/discrepancies)


title: treatment: Control - time: 24 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=Control|time=24 hrs rep 1 (May still include original submitter created erros/discrepancies)


title: treatment: Control - time: 0 hrs - rep2

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=Control|time=0 hrs rep 2 (May still include original submitter created erros/discrepancies)

source_name: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell (treatment: Control - time: 0 hrs)


title: treatment: Control - time: 0 hrs - rep3

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
treatment=Control|time=0 hrs rep 3 (May still include original submitter created erros/discrepancies)


title: 161 Area4 09 02 12

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

country: Canada

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal. Values in table are log2 ratios (test/reference) with reference = follicles less than 3mm.

organism: Bos taurus

source_name: oocyte from follicles less 3mm

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Oocytes were collected from slaughterhouse-derived ovaries according to the follicles sizes (<3mm; 3-5mm; 5-8mm and >8mm)

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 11 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cumulus-oocyte complexes (COC’s) were collected byaspiration with a 18G needle attach to a syringe. The COC’s were then washed three times to remove follicular fluid and were mechanically denuded by vortexing to remove all the cumulus cells. Oocytes were then washed, collected in small volumes of PBS, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: oocyte

source_name: oocyte from follicles 3-5mm


title: treatment: Control - time: 0 hrs - rep1

description:
germplasm name: Cell culture from Vitis vinifera L. Monastrell cell calli
organism part: in vitro cultured  cell, tissue and organ, PO:0000005 cultured cell, PO:0009002 plant cell, PO:0000005 cultured cell ('PO:0000004')
development stage: Cell culture from calli
growth media: Supplemented Gamborg B5
Untreated Vitis vinifera L. Monastrell cell culture at 0h time point. (May still include original submitter created erros/discrepancies)


title: 160 Area3 09 02 12


title: 156 Area4 09 02 12

source_name: oocyte from follicles more 8mm


title: 161 Area3 09 02 12


title: 160 Area1 09 02 12

source_name: oocyte from follicles 5-8mm


title: 161 Area2 09 02 12


title: 159 Area1 08 02 12


title: 160 Area2 09 02 12


title: 161 Area1 09 02 12


title: 159 Area4 09 02 12


title: 155 Area3 09 02 12


title: 159 Area3 09 02 12


title: HRSRNAPilot-120

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All available data are provided, with no additional filtering.

source_name: Whole blood (PAXgene RNA)

label_protocol: Standard Illumina target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (PAXgene RNA collection tubes) using a QIACube instrument.

tag: age (yrs)

tag: female

tag: black

tag: hispanic

tag: bmi

tag: diabcvdcastr

tag: smoke

tag: alcohol

tag: loneliness

tag: optimism

tag: pessimism

tag: anxiety

tag: cesd

tag: lifesatisfaction

tag: pa


title: 156 Area3 09 02 12

tag: cell type


title: 160 Area4 09 02 12


title: HRSRNAPilot-118


title: 156 Area2 09 02 12


title: 155 Area2 09 02 12


title: 159 Area2 08 02 12


title: HRSRNAPilot-119


title: HRSRNAPilot-121


title: 155 Area4 09 02 12


title: cellline_SSRP1_rep2

source_name: BE(2)C cells

tag: cell line

value: BE(2)C cells

tag: treatment

value: SSRP1 siRNA


title: HRSRNAPilot-117

tag: age (yrs)

tag: female


title: HRSRNAPilot-113

tag: black

tag: hispanic

value: missing


title: HRSRNAPilot-116

tag: bmi

tag: diabcvdcastr


title: HRSRNAPilot-114

tag: smoke

tag: alcohol


title: HRSRNAPilot-115

tag: loneliness

tag: optimism


title: HRSRNAPilot-111

tag: pessimism

tag: anxiety


title: HRSRNAPilot-112

tag: cesd

tag: lifesatisfaction


title: HRSRNAPilot-110

tag: pa


title: HRSRNAPilot-105


title: HRSRNAPilot-109


title: HRSRNAPilot-104


title: HRSRNAPilot-102


title: HRSRNAPilot-106


title: HRSRNAPilot-101


title: HRSRNAPilot-97


title: HRSRNAPilot-99


title: HRSRNAPilot-96


title: HRSRNAPilot-100


title: HRSRNAPilot-108


title: HRSRNAPilot-94


title: HRSRNAPilot-95


title: HRSRNAPilot-98


title: siHa  24h at 21% O2 OFN_N12

description: siHa  24h at 21% O2

source_name: RNA from cell line in Normoxia

tag: tissue

value: Ovary

tag: cell line

value: siHa

value: Normoxia


title: HRSRNAPilot-103

tag: age (yrs)


title: HRSRNAPilot-93

tag: female


title: HRSRNAPilot-92

tag: black


title: HRSRNAPilot-83

tag: hispanic


title: T-47D  24h at 21% O2 OFN_N3

description: T-47D  24h at 21% O2

value: Breast

tag: treatment


title: HRSRNAPilot-87

tag: bmi

tag: diabcvdcastr


title: HRSRNAPilot-82

tag: smoke

tag: alcohol


title: HRSRNAPilot-88

tag: loneliness

tag: optimism


title: HRSRNAPilot-91

tag: pessimism

tag: anxiety


title: HRSRNAPilot-79

tag: cesd

tag: lifesatisfaction


title: HRSRNAPilot-78

tag: pa


title: HRSRNAPilot-86


title: HRSRNAPilot-90


title: HRSRNAPilot-84


title: HRSRNAPilot-85


title: HRSRNAPilot-107


title: HRSRNAPilot-77


title: HRSRNAPilot-89


title: HRSRNAPilot-80


title: HRSRNAPilot-75


title: HRSRNAPilot-72


title: HRSRNAPilot-76


title: HRSRNAPilot-81


title: HRSRNAPilot-71


title: HRSRNAPilot-67


title: HRSRNAPilot-68


title: HRSRNAPilot-73


title: HRSRNAPilot-70


title: HRSRNAPilot-66


title: HRSRNAPilot-61


title: HRSRNAPilot-63


title: HRSRNAPilot-58


title: HRSRNAPilot-60


title: HRSRNAPilot-55


title: HRSRNAPilot-64


title: HRSRNAPilot-54


title: HRSRNAPilot-74


title: HRSRNAPilot-51


title: HRSRNAPilot-52


title: HRSRNAPilot-65


title: HRSRNAPilot-69


title: HRSRNAPilot-56


title: HRSRNAPilot-49


title: HRSRNAPilot-47


title: HRSRNAPilot-53


title: HRSRNAPilot-62


title: HRSRNAPilot-48


title: HRSRNAPilot-46


title: HRSRNAPilot-44


title: HRSRNAPilot-57


title: HRSRNAPilot-59


title: HRSRNAPilot-43


title: HRSRNAPilot-42


title: HRSRNAPilot-40


title: HRSRNAPilot-41


title: HRSRNAPilot-50


title: PAO1 genomic DNA

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

address: Vail Building Rm 208

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: DNA was denatured and hybridized to Affymetrix Pseudomonas GeneChips according to the manufacturer’s instructions with the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) in the laboratory of Steven Lory (Harvard Medical School).

data_processing: The data were analyzed in R using RMA provided in the Bioconductor affy package.

source_name: PAO1 genomic DNA

label_protocol: DNA fragments were terminally labeled with biotin-ddUTP (Enzo Bio-Array terminal labeling kit, Affymetrix)

growth_protocol: P. aeruginosa were grown overnight at 37 degress C in LB prior to DNA isolation.

extract_protocol: Total DNA was isolated using a phenol-chloroform extraction method, then fragmented using DNase 1.

treatment_protocol: No treatment.

tag: strain


title: PA14 genomic DNA

source_name: PA14 genomic DNA


title: HRSRNAPilot-45

tag: age (yrs)


title: anr mutant biological rep3

description: Pseudomonas aeruginosa grown as biofilms on ∆F508 cystic fibrosis bronchial epithelial cells (CFBEs)

hyb_protocol: cDNAs were hybridized to Affymetrix Pseudomonas GeneChips according to the manufacturer’s instructions with the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) in the Dartmouth Genomics Shared Resource laboratory.

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and processed using robust multi-array average.

label_protocol: cDNAs were terminally labeled with biotin-ddUTP (Enzo Bio-Array terminal labeling kit, Affymetrix)

growth_protocol: P. aeruginosa were grown overnight at 37 degress C in LB prior to exposure to CFBE airway epithelial cells.

extract_protocol: Total RNA from CFBE cells and associated P. aeruginosa biofilms was isolated using the Qiagen RNA Easy extraction protocol. The MICROBExpress Bacterial mRNA Enrichment Kit (Life technologies) was used to deplete eukaryotic RNA from the samples.

treatment_protocol: P. aeruginosa were washed and resuspended at an OD600=0.5 in minimal essential media (MEM). Suspensions were applied to confluent CFBE cell monolayer grown in 24-well plastic dishes and incubated at 37 °C, 5% CO2 for 1 h. After 1 h planktonic cells were aspirated and fresh media was added. After an additional 90 min, planktonic cells were aspirated again, and the CFBE monolayer was washed x2 with PBS prior to recovery of cells for RNA extraction.

tag: genotype/variation

value: ∆anr mutant


title: anr mutant biological rep2


title: anr mutant biological rep1


title: WT PAO1 biological rep1

value: WT


title: WT PAO1 biological rep2


title: HRSRNAPilot-38

tag: female

tag: black