title: Nasal Biopsy of subject 28 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 24 hr before sampling


title: Hdh knock-in embryonic stem cells, Q20 line, biological replicate 2

status: Public on May 04 2011

type: RNA

city: Boston

first: Jong-Min

last: Lee

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Research

country: USA

institute: Massachusetts General Hospital

description: Gene expression data from Hdh knock-in embryonic stem cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: gcRMA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

label_protocol: IVT labeling kit from the Affy company

growth_protocol: Standard growth condition for mouse embryonic stem cells

extract_protocol: Trizol extraction and Qiagen Rneasy mini coulmn clean up

tag: strain

tag: group

value: knock-in

tag: genotype (hdh cag repeat length)

tag: differentiation status

value: undifferentiated

tag: cell line


title: Nasal Biopsy of subject 36 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

hyb_protocol: According to Affymetrix. GeneChip Fluidics Station 450 was used for washing.

scan_protocol: GeneChip Scanner 3000 was used for scanning.

data_processing: BRB Array Tools. Data were normalized using RMA. The different tissue groups were normalized separately.

organism: Homo sapiens

label_protocol: One Cycle Target Labelling Protocol.

extract_protocol: RNeasy Mini Kit (Qiagen) for nasal biopsies;  PAXGene RNA Kit and QIAmp RNA Blood Mini Kit (Qiagen) for blood samples.

treatment_protocol: Male non-smokers were exposed to formaldehyde (FA) vapors for 4 h per day over a period of 5 working days under strictly controlled conditions. For each exposure day, different exposure concentrations were used in a random order ranging from 0 up to 0.7 ppm. During exposure, subjects had to perform bicycle exercises (about 80 W) four times for 15 min. Samples were taken before the first and after the last exposure.

tag: tissue

value: nasal biopsy

tag: gender

value: male

tag: smoking status

value: non-smoker

tag: treatment

value: formaldehyde vapors

tag: treatment dosage

value: 0.7 ppm

tag: time before sampling

tag: subject

value: B


title: CeA_LAB_19

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

institute: Max Planck Institute of Psychiatry

description: Biological replicate of LAB 3

hyb_protocol: Each microarray slide had the capacity for six samples, same brain regions were hybridized in the same batch comparing a maximum of six individual mice of each breeding line. Reagents and material were provided by Illumina, the procedure was strictly conducted according to the manufacturer’s protocol. In brief, each sample was mixed with hybridization buffer, loaded onto the designated array field and the slides were put into hybridization chambers and incubated for 17h in incubation chambers provided by Illumina. Arrays were washed in several steps, incubated with Cy3, washed several times again and dried by centrifugation.

scan_protocol: Fluorescence signals were detected on a BeadStation scanner (Illumina) and analyzed by the BeadStudio (Illumina) software. The manufacturer's built-in controls have been analyzed including hybridization controls and sample dependent parameters. Only microarrays fulfilling Illumina's recommendations for quality control have been used for further evaluation.

data_processing: Illumina BeadStudio gene expression results were further analyzed using R-packages, based on ‘beadarray’ system as described by Dunning et al. (2007), which simplifies the comparison between a high number of arrays. First, pair wise box plots were generated to compare mean expression within each line and brain region. Normalization for expression values has been applied to all samples with the ‘QSpline’ function. Each sample has been clustered to ensure that each brain region per line shows similar expression patterns using the ‘hclust’ function. Three samples from different brain regions have been identified as inadequate during the scan process and have therefore been excluded from further analysis. For differential expression analysis, functions of the ‘LIMMA’ package have been applied on log2-transformed values. The resulting matrix has been used for all subsequent analyses. Significantly regulated genes were ranked using an empirical BAYES method implemented in the LIMMA R-package (Lonnstedt and Speed, 2002; Smyth, 2004).

label: biotin, Cy3

source_name: Central amygdala, LAB mouse  19

label_protocol: RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion) with only one round of in vitro transcription, where biotinylated uracyl bases were built in to the newly synthesized aRNA. 5µg per sample were required for loading to the microarray slides. Correct quantification was ensured by measurement of optic density in a NanoPhotometer (Implen, Munich, Germany) and additional analysis on agarose gel. Samples not fulfilling all criteria of homogeneity (inadequate concentrations, too many small but few larger aRNA fragments) were excluded from further analysis.

extract_protocol: From all samples, total RNA was extracted individually (one sample per mouse and brain region) in presterilized 1.5ml Safelock tubes (Eppendorf, Hamburg, Germany) using a TRIzol (Invitrogen, Karlsruhe, Germany) chloroform standard protocol. After tissue homogenization in 300µl of TRIzol by pipetting, 1µl linear acrylamide (5mg/ml, Ambion, Austin, TX) and 60µl of chloroform (Carl Roth, Karlsruhe, Germany) were added and the samples vortexed. Centrifugation for 5min at 18°C and 13,000rpm followed, then RNA was precipitated with 180µl isopropanol (Carl Roth) overnight at -20°C, centrifuged at 4°C and 13,000rpm for 30min and washed twice in 500µl 70% ethanol (Carl Roth) with centrifugation steps at 4°C and 13,000rpm of 10min in between. Following the last centrifugation step, all remaining liquid was removed with a pipet, pellets were dried in an incubator for 15min at 45°C and resolved in 13µl of autoclaved bidistilled water.

treatment_protocol: Brains were collected, dissected in slices of 25µm and mounted to Superfrost microscope slides (Menzel, Braunschweig, Germany) or onto LMD6000 metallic frame slides covered with a membrane of polyethylene terephthalate (Leica Microsystems Deutschland, Bensheim, Germany) in a cryostat (Microm MH50, Microm, Walldorf, Germany) from rostral to caudal.  Only brain slices containing the brain areas of interest were sampled, including the anterior part of the cingulate cortex (Cg), the hypothalamic paraventricular nucleus (PVN), the anterior dentate gyrus (DG), the basolateral (BLA) and the central amygdala (CeA). For the DG, the same coordinates as for the PVN were applied. To cover the whole area of interest an overall depth of 400µm per region was chosen. While sampling the CG, BLA and CeA four brain slices were mounted onto an LMD6000 metallic frame slide (Leica Microsystems), the following four to Superfrost slides (Menzel). This procedure was repeated for the next eight slices. For the region containing the PVN and DG only two slices were mounted to one slide always alternating the LMD6000 frame and the Superfrost microscope slides. Only the LMD6000 slides were used for further processing and stored at -80°C. Right before laser-microdissection, brain slices on the LMD6000 frame slides were stained with cresyl violet applying a modified staining protocol that included 1.5min staining in cresyl violet, followed by washing in 70% and 96% ethanol for 20s each and in isopropanol for 5min. The slides were refrozen and processed at the laser-microdissection microscope (AS LMD, Leica). For the dissection procedure of the required brain areas, a magnification of 100x was chosen with laser power between 80-100% and speed varying between 1 and 4. Cut-out brain areas were captured in the caps of 0.2ml PCR soft tubes (Biozym Scientific, Hessisch Oldendorf, Germany) and cooled on dry ice immediately after completion of one brain region. Pictures of the processed brain slices were acquired by means of the IM1000 software.  Microm, Walldorf, Germany) from rostral to caudal.

tag: age

value: 10 weeks

tag: source tissue

value: brain


title: CeA_HAB_20

description: Biological replicate of HAB 3

source_name: Central amygdala, HAB mouse  20


title: CeA_LAB_06

description: Biological replicate of LAB 2

source_name: Central amygdala, LAB mouse  06


title: Nasal Biopsy of subject 29 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: CeA_LAB_14

description: Biological replicate of LAB 4

source_name: Central amygdala, LAB mouse  14


title: CeA_NAB_08

description: Biological replicate of NAB 4

source_name: Central amygdala, NAB mouse  08


title: CeA_HAB_01

description: Biological replicate of HAB 1

source_name: Central amygdala, HAB mouse  01


title: Nasal Biopsy of subject 28 before inhalation; Group B

source_name: Nasal biopsy before inhalation


title: CeA_NAB_02

description: Biological replicate of NAB 2

source_name: Central amygdala, NAB mouse  02


title: Nasal Biopsy of subject 29 before inhalation; Group B


title: CeA_LAB_03

description: Biological replicate of LAB 1

source_name: Central amygdala, LAB mouse  03


title: Hdh knock-out embryonic stem cells, biological replicate 6

description: Gene expression data from control embryonic stem cells

value: knock-out


title: Hdh knock-out embryonic stem cells, biological replicate 4


title: Cg_HAB_05

description: Biological replicate of HAB 2

source_name: Cingulate cortex, HAB mouse  05


title: Nasal Biopsy of subject 42 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 72 hr before sampling

value: A


title: Cg_LAB_06

description: Biological replicate of LAB 2

source_name: Cingulate cortex, LAB mouse  06


title: Hdh knock-out embryonic stem cells, biological replicate 2


title: Hdh knock-out embryonic stem cells, biological replicate 5


title: Hdh knock-out embryonic stem cells, biological replicate 3


title: Nasal Biopsy of subject 44 before inhalation; Group A


title: Cg_HAB_09

description: Biological replicate of HAB 3

source_name: Cingulate cortex, HAB mouse  09


title: Nasal Biopsy of subject 43 before inhalation; Group A


title: Cg_HAB_11

description: Biological replicate of HAB 4

source_name: Cingulate cortex, HAB mouse  11


title: Cg_LAB_07

description: Biological replicate of LAB 3

source_name: Cingulate cortex, LAB mouse  07


title: Cg_NAB_15

description: Biological replicate of NAB 6

source_name: Cingulate cortex, NAB mouse  15


title: Hdh knock-out embryonic stem cells, biological replicate 1

source_name: mouse embryonic stem cells


title: Nasal Biopsy of subject 43 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: Nasal Biopsy of subject 25 before inhalation; Group B


title: Cg_NAB_12

description: Biological replicate of NAB 4

source_name: Cingulate cortex, NAB mouse  12


title: Hdh knock-in embryonic stem cells, Q20 line, biological replicate 1


title: Cg_LAB_14

description: Biological replicate of LAB 5

source_name: Cingulate cortex, LAB mouse  14


title: Cg_HAB_17

description: Biological replicate of HAB 5

source_name: Cingulate cortex, HAB mouse  17


title: CeA_NAB_18

description: Biological replicate of NAB 1

source_name: Central amygdala, NAB mouse  18


title: Nasal Biopsy of subject 44 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: Cg_LAB_16

description: Biological replicate of LAB 6

source_name: Cingulate cortex, LAB mouse  16


title: Cg_NAB_08

description: Biological replicate of NAB 3

source_name: Cingulate cortex, NAB mouse  08


title: Cg_LAB_10

description: Biological replicate of LAB 4

source_name: Cingulate cortex, LAB mouse  10


title: Cg_NAB_13

description: Biological replicate of NAB 5

source_name: Cingulate cortex, NAB mouse  13


title: Nasal Biopsy of subject 25 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 24 hr before sampling


title: control embryonic stem cells, biological replicate 5

description: Gene expression data from embryonic stem cells without Hdh

value: control


title: control embryonic stem cells, biological replicate 6


title: Cg_NAB_04

description: Biological replicate of NAB 2

source_name: Cingulate cortex, NAB mouse  04


title: Cg_NAB_02

description: Biological replicate of NAB 1

source_name: Cingulate cortex, NAB mouse  02


title: Nasal Biopsy of subject 10after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 72 hr before sampling


title: control embryonic stem cells, biological replicate 2


title: Cg_LAB_03

description: Biological replicate of LAB 1

source_name: Cingulate cortex, LAB mouse  03


title: control embryonic stem cells, biological replicate 3


title: control embryonic stem cells, biological replicate 4


title: Nasal Biopsy of subject 9 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: Nasal Biopsy of subject 10 before inhalation; Group A

source_name: Nasal biopsy before inhalation


title: Cg_HAB_01

description: Biological replicate of HAB 1

source_name: Cingulate cortex, HAB mouse  01


title: SF50

status: Public on May 03 2011

type: genomic

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

hyb_protocol: A total of 5 μg of labeled DNA was hybridized to Affymetrix T. gondii GeneChips using standard Affymetrix hybridization protocols.

scan_protocol: Standard Affymetrix protocol.

data_processing: Hybridization intensities were processed and normalized with the software package R (http://www.r-project.org/) using the following R library functions: bg.correct = rma, normalize = quantiles.

molecule: genomic DNA

organism: Toxoplasma gondii

source_name: SF50 - I X II progeny

label_protocol: The BioPrime Labeling System (Invitrogen) was used to label 600 ng gDNA per reaction for 2 hr at 37°C.

growth_protocol: Parasites were grown in human foreskin fibroblast (HFF) cell monolayers sustained in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum at 37°C under 5% CO2

extract_protocol: Freshly egressed parasites grown in HFF cells were harvested and genomic DNA (gDNA) was purified using the DNAeasy kit (Qiagen) with addition of a RNase cocktail (Ambion).  gDNA was sheared by nebulization (Invitrogen) for 3 min at ≈ 40 psi, precipitated, washed in 70% ethanol, and re-suspended in water.

treatment_protocol: No treatment, standard growth for tachyzoites.

tag: develpomental stage

value: tachyzoite


title: control embryonic stem cells, biological replicate 1

source_name: mouse embryonic stem cells


title: SF44

source_name: SF44 - I X II progeny


title: SF61

source_name: SF61 - I X II progeny


title: SF60

source_name: SF60 - I X II progeny


title: SF58

source_name: SF58 - I X II progeny


title: SF47

source_name: SF47 - I X II progeny


title: SF56

source_name: SF56 - I X II progeny


title: Nasal Biopsy of subject 9 before inhalation; Group A


title: SF38

source_name: SF38 - I X II progeny


title: SF46

source_name: SF46 - I X II progeny


title: SF40

source_name: SF40 - I X II progeny


title: SF42

source_name: SF42 - I X II progeny


title: SF34

source_name: SF34 - I X II progeny


title: SF41

source_name: SF41 - I X II progeny


title: SF39

source_name: SF39 - I X II progeny


title: SF36

source_name: SF36 - I X II progeny


title: SF37

source_name: SF37 - I X II progeny


title: SF35

source_name: SF35 - I X II progeny


title: SF26

source_name: SF26 - I X II progeny


title: SF28

source_name: SF28 - I X II progeny


title: SF23

source_name: SF23 - I X II progeny


title: SF24

source_name: SF24 - I X II progeny


title: SF20

source_name: SF20 - I X II progeny


title: SF57

source_name: SF57 - I X II progeny


title: SF30

source_name: SF30 - I X II progeny


title: SF22

source_name: SF22 - I X II progeny


title: SF21

source_name: SF21 - I X II progeny


title: SF16

source_name: SF16 - I X II progeny


title: SF15

source_name: SF15 - I X II progeny


title: SF18

source_name: SF18 - I X II progeny


title: SF12

source_name: SF12 - I X II progeny


title: C7C2

source_name: C7C2 - I X II progeny


title: SF14

source_name: SF14 - I X II progeny


title: SF8

source_name: SF8 - I X II progeny


title: SF7

source_name: SF7 - I X II progeny


title: SF3

source_name: SF3 - I X II progeny


title: Me49_Fudr_b

source_name: Me49-Fudr - I X II parent


title: C7B1

source_name: C7B1 - I X II progeny


title: SF9

source_name: SF9 - I X II progeny


title: C7K4

source_name: C7K4 - I X II progeny


title: C7E4

source_name: C7E4 - I X II progeny


title: Me49_Fudr_a


title: 2C10F8

source_name: 2C10F8 - I X II progeny


title: 2C10B5

source_name: 2C10B5 - I X II progeny


title: Nasal Biopsy of subject 42 before inhalation; Group A

source_name: Nasal biopsy before inhalation


title: SF17

source_name: SF17 - I X II progeny


title: 2C10A3

source_name: 2C10A3 - I X II progeny


title: SF19

source_name: SF19 - I X II progeny


title: GT1_SNF_b

source_name: GT1-SNF - I X II parent


title: E1310N-B

city: Gaithersburg

first: Wusheng

last: Yan

address: 8717 Grovemont Circle

institute: NCI

hyb_protocol: Per sample,15μg of biotin-labeled cRNA sample was fragmented and processed for hybridization to Human Genome U133A 2.0 Genechips (Affymetrix Inc., Santa Clara, CA), according to the Expression Kit User Manual (http://www.affymetrix.com/support/technical/manuals.affx)).

scan_protocol: Arrays were washed and stained using the Midi_euk2v3_450 protocol (V4).  Fluorescent intensity emitted by the labeled target was measured using a GeneChip Scanner 7G (Affymetrix Inc.).

data_processing: GCOS

source_name: LCM normal basal layer of human esphageal epithelium

label_protocol: Two rounds of linear amplification were performed by combining reagents supplied in MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, Catalog# AM1791, Austin, TX) and MessageAmp™ II aRNA Amplification Kit (Ambion, Catalog# AM1751), resulting in biotin-labeled antisense cRNA [21].

growth_protocol: Frozen tissue

extract_protocol: RNA was isolated using the PicoPure RNA Isolation kit (Arcturus Engineering, Inc. Mountain View, CA) digested with Dnase.

treatment_protocol: ESCC tumor and match normal

tag: sample type

value: frozen tissue


title: E1255N-D

source_name: LCM normal differentiated layer of human esphageal epithelium


title: E1408T-B

source_name: LCM tumor cluster

value: tumor cluster


title: E0911N-D

value: normal differentiated layer of human esphageal epithelium


title: Bm4temoin_2 with array type maize from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: Main objectives of this study: - role of plant cell wall during AM symbiosis - regulation pattern during AM symbiosis - understanding of the original mycorrhizal phenotype of bm4 - search of candidate-genes to study AM symbiosis

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003) using R-2.6.2 version and AFFYMETRIX Bioconductor packages (Gentleman and Carey, 2002).

label: Biotin

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - Media: milieu M low phosphate -Light : 12h day/night - temperature: 24 °C

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
Bm4temoin_2:59.37ug.

treatment_protocol: no treatment

tag: genotype/variation

value: mutant (bm4)

tag: growth condition


title: GT1_SNF_a

source_name: GT1-SNF  - I X II parent


title: bm4myc_2 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
bm4myc_2:54.83ug.

treatment_protocol: Name:myco - inoculation - mycorrhiza,glomus intraradices:. Factor value : 6000 spores/plant

value: arbuscular mycorrhizal symbiosis


title: E0866N-D


title: E0911N-B

value: normal basal layer of human esphageal epithelium


title: E1255N-B


title: E1264N-D


title: E0866N-B


title: E0848T-B

source_name: LCM tumor cluster peripheral


title: E1264N-B


title: F2tem_1 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
F2tem_1:37.87ug.

value: wild type


title: E1408N-D


title: F2tem_2 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
F2tem_2:34.22ug.


title: F2myc_1 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
F2myc_1:38.07ug.


title: E0848N-D


title: bm4myc_1 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
bm4myc_1:70.09ug.


title: E0848N-B


title: C10B5

source_name: C10B5 - I X II progeny


title: F2myc_2 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
F2myc_2:58ug.


title: E1408N-B


title: Metastatic Prostate Cancer 4

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

description: Metastatic prostate cancer tissue sample hybridized against pool of benign tissue samples

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Metastatic Prostate Cancer

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Human prostate tissue samples were obtained from the University of Michigan SPORE program. Total RNA were isolated from tissues using RNeasy Mini kit (Qiagen, Valencia, CA Inc, Valencia, CA) according to manufacturer’s instructions.

value: Prostate

tag: cell type

value: Cancer

source_name: Pool of Benign Prostate Tissue (CPP)

tag: tissue type

value: Benign


title: Metastatic Prostate Cancer 3


title: Metastatic Prostate Cancer 1


title: Bm4temoin_1 with array type maize from Affymetrix

extract_protocol:
Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.
Bm4temoin_1:39.97ug.


title: E0832N-D


title: E0796N-B


title: E0832N-B


title: Metastatic Prostate Cancer 2


title: E1310N-D


title: Localized Postate Cancer 4

description: Localized prostate cancer tissue sample hybridized against pool of benign tissue samples

source_name: Localized Postate Cancer


title: E0796N-D


title: E0782N-B


title: Localized Postate Cancer 2


title: E0782N-D


title: Localized Postate Cancer 5


title: Localized Postate Cancer 3


title: MAD04-385

city: Charlottesville

first: Alexander

last: Baras

state: Virginia

address: 3024 University Hospital, PO Box 800214

institute: University of Virginia

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: The data was processed through the Affymetrix Power Tools (APT) suite using quantile normalization, perfect-match vs. mismatch correction, and the PLIER algorithm.

source_name: adenoid cystic carcinoma

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol: All xenografts reported here were implanted in mice within 36 hours of tissue being removed from the human subjects. Nude mice (nu/nu) were anesthetized with intraperitoneal injection of Ketamine/Xylazine 60-80/5-10 mg/kg. Cutaneous incisions were made in the midscapular and bilateral flank regions, with a subcutaneous pocket created by blunt dissection. One to four fragments of minced tumor (1-2 mm in diameter) were placed in each pocket, with subsequent closure of the incision with surgical staples. Tumors were allowed to grow to a maximum diameter of 1 to 1.5 cm, and were then surgically harvested. Aliquots of the xenograft tumor were minced and passaged into new mice as described above.

extract_protocol: Frozen tissue samples of ACC xenografts and corresponding human cancers were embedded in O.C.T. compound (Sakura Finetek) and subjected to cryostat sectioning. The stained frozen sections were used to direct the dissection of tumor that corresponded to > 80% tumor cellularity. These dissected subsamples were disrupted using a tissue homogenizer (Pro-200, ProScientific) in lysis buffer supplied in the RNeasy kit (Qiagen) with subsequent RNA isolation using columns and materials supplied by the manufacturer.

tag: specimen id

value: adenoid cystic carcinoma

tag: tissue source

value: Xenograft


title: M167

tag: tissue


title: ACCX6

tag: xenograft source


title: Normal Prostate 1

description: Benign tissue sample hybridized against pool of benign tissue samples

source_name: Normal Prostate


title: Localized Postate Cancer 1


title: Normal Prostate 2


title: ACCX9


title: ACCX5M1


title: E0404N-D


title: ACCX4


title: ACCX2


title: Benign Prostate 2

source_name: Benign Prostate


title: E0404N-B


title: Benign Prostate 1


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 6

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equal amounts  of labeled cDNA from 35000HP or 35000HPcpxA were thoroughly mixed and used to hybridize microarray slides in Amersham microarray hybridization buffer.  Hybridization was carried out at 50C for 16 hr in the dark.

scan_protocol: After hybridization, the slides were washe in saline-sodium phosphate EDTA buffer and scanned with GenePix  4100A scanner and analyzed with GenePix Pro 5.0 software (Axon instruments)

data_processing: Data was subjected to two types of normalization, a ratio-based normalization so that the mean or median intensities are the same across the array, and a non-linear locally weighed scatterplot smoothing (LOWESS) normalization, which corrects intensity dependent variation in dye basis, before being combined into a single data set for further analysis.  Differential expression was defined as a minimum of two fold over or under expression of 35000HPcpxA relative to 35000HP.  The data were further scrutinized so as to only include expression profiles that were observed in at least 4 of the 6 experiments and had a p<0.05 after one t-test analysis.

organism: [Haemophilus] ducreyi

source_name: Haemophilus ducreyi 35000HPcpxRpLS88

label_protocol: Twenty micrograms of total RNA for cells grown in Columbia broth for 8 hr were used to generate cDNA using the Amino Allyl cDNA Labeling kit ragents (Ambion).  After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization.  The cDNAs were purified using the Qiaquick gel extraction columns (Qiagen).  After purification, Cy5 dye (GE Healthcare) was added following manufacturer's instructions.  The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal devices (Millipore) and labeling efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: Haemophilus ducreyi strain was resucitated from frozen stock on Chocolate agar plates, and incubated ON at 33C in a humidified atmosphere containing 95% air and 5% CO2.  Columbia broth supplemented with 2.5% FCS is inoculated from the plate and cultures are grown in a 33C gyratory water bath at 100 rpm for 8 hrs

extract_protocol: Total RNA from 2-4 ml of culture was extracted using the Ribopure Bacteria kit (Ambion) following manufacturer's instructions.  After isolation, RNA was treated twice with DNaseI (NEB) for 1 hr at 37C, and purified using RNeasy system (Qiagen).  Samples were checked for residual DNA by PCR and re-treated if necessary. Quality assessment was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Strains were grown under normal conditions.

tag: strain

value: cpxRpLS88 (vector control)

source_name: Haemophilus ducreyi 35000HPcpxRpML125

label_protocol: Twenty micrograms of total RNA for cells grown in Columbia broth for 8 hr were used to generate cDNA using the Amino Allyl cDNA Labeling kit ragents (Ambion).  After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization.  The cDNAs were purified using the Qiaquick gel extraction columns (Qiagen).  After purification, Cy3 dye (GE Healthcare) was added following manufacturer's instructions.  The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal devices (Millipore) and labeling efficiency was determined using a Nanodrop spectrophotometer.

value: cpxRpML125 (over-expresses CpxR in a CpxR deletion background)


title: E0362N-D


title: E0362T-B


title: E0362N-B


title: ACCX11


title: Biceps femoris muscle_AQM_Treatment_3

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

description:
RLPA-Day5_N_CS_S-3PC.CEL
RLPA-Day5_N_CS_S-3PC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

data_processing: The data were normalized using RMA.

organism: Sus scrofa

source_name: biceps femoris muscle, treated with non-depolarizing neuromuscular blocking agents(NMBA),Corticosteroids(CS) and sepsis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

treatment_protocol: Five female domestic piglets (Sus scrofa, average body weight 26.9 kg) were used in this study. Five subjects were included for masseter muscle and same four subjects were included for the biceps femoris muscle. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period. A neuromuscular blocking agent (NMBA) was administered as a continuous infusion of pancuronium bromide 0.1mg/kg/h (Pavolun; Organon, Boxtel, The Netherlands) for 5days while a corticosteroid (CS) was given as bolus doses of betamethasone 0.1 mg/kg (Betapred; GSK, Slona, Sweden) twice daily for 5days.Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.

tag: breed

value: Eurasian wild boar

tag: gender

value: female

tag: disease state

value: acute quadriplegic myopathy (AQM)

tag: treatment

value: non-depolarizing neuromuscular blocking agents (NMBA),Corticosteroids(CS) and sepsis

tag: time

value: 5 days

value: biceps femoris muscle


title: ACCX12


title: ACCX16


title: Biceps femoris muscle_AQM_Treatment_4

description:
RLPA-Day5_N_CS_S-4PC.CEL
RLPA-Day5_N_CS_S-4PC


title: ACCX5


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 5


title: Biceps femoris muscle_AQM_Treatment_1

description:
RLPA-Day5_N_CS_S-1PC.CEL
RLPA-Day5_N_CS_S-1PC


title: ACC7M1

value: Human


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 4


title: SR150

city: Seattle

first: Jie Hong

last: Hu

state: WA

address: 1959 NE Pacific St, HSB K-127

department: Medicine

institute: University of Washington

hyb_protocol: cRNA was hybridized to Sentrix Mouse Ref-8 Expression BeadChips (Illumina). After hybridization, the chips were washed and then stained with streptavidin-Cy3.

scan_protocol: Illumina chips were scanned for fluorescence intensity at the Center for Array Technology at the University of Washington, with two images generated per sample.

data_processing: Images were processed to extract bead-level intensities and summarized in terms of un-normalized and normalized probe-level intensities using the Illumina BeadStudio software.  Normalization was carried out using the cubic spline algorithm.

label_protocol: cDNA was transcribed to biotin-labeled cRNA by in vitro transcription using T7 Enzyme Mix and biotin-NTP. cRNA was purified with a cRNA filter cartridge, quantified with a Nanodrop spectrophotomoter, and quality-checked by Agilent Bioanalyzer.

growth_protocol: Six SR-uPA+/0 and 6 nontransgenic mice (all Apoe–/–) were fed the Western diet from 5 – 15 wk of age, then injected intraperitoneally with thioglycollate.  Peritoneal macrophages were harvested in ice-cold PBS 5 d later, centrifuged (300 × g for 5 min), resuspended in DMEM without phenol red (GIBCO) and plated onto tissue culture dishes.

extract_protocol: Attached cells were harvested using Trizol Reagent (Invitrogen).  Total RNA was extracted and purified using Total RNA PureLink Micro-to-Midi Total RNA Purification System (Invitrogen) and quantified using a Nanodrop spectrophotometer (Thermo Scientific).  RNA integrity was analyzed using Agilent 2010 Bioanalyzer, the RNA integrity number for all samples was 8.9 – 9.7 with the majority > 9.5. cRNA was amplified and labeled using Illumina® TotalPrep RNA Amplification Kit (Illumina). Briefly, single-stranded cDNA was synthesized from total RNA using T7 Oligo(dT) Primer and ArrayScript. The single-stranded cDNA was then converted to double-   stranded cDNA using DNA polymerase and RNase H. The double-stranded cDNA was purified with a cDNA filter cartridge.

treatment_protocol: After 2 h, nonadherent cells were removed.

value: Apoe-/- SR-uPA+/0

tag: age

value: 15 weeks

tag: diet

value: Western diet (for 10 weeks)

value: peritoneal macrophage


title: SR133

value: injected intraperitoneally with thioglycollate


title: SR144

value: Apoe-/- nontransgenic


title: ACCX1

value: adenoid cystic carcinoma


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 3


title: SRmix2

description: Pooled from all nontransgenic samples, replicate 2


title: ACC7


title: Biceps femoris muscle_AQM_Treatment_2

description:
RLPA-Day5_N_CS_S-2PC.CEL
RLPA-Day5_N_CS_S-2PC


title: Biceps femoris muscle_AQM_Control_4

description:
RLPA-Day1_N_CS_S-4PC.CEL
RLPA-Day1_Control-4PC

value: 1 day


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 1

value: cpxRpLS88 (vector control)


title: ACC6


title: SR142


title: Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88 sample 2

value: cpxRpML125 (over-expresses CpxR in a CpxR deletion background)


title: Biceps femoris muscle_AQM_Control_1

description:
RLPA-Day1_N_CS_S-1PC.CEL
RLPA-Day1_Control-1PC

value: Eurasian wild boar


title: ACC48


title: ACC43


title: Biceps femoris muscle_AQM_Control_3

description:
RLPA-Day1_N_CS_S-3PC.CEL
RLPA-Day1_Control-3PC

value: female


title: Biceps femoris muscle_AQM_Control_2

description:
RLPA-Day1_N_CS_S-2PC.CEL
RLPA-Day1_Control-2PC

value: acute quadriplegic myopathy (AQM)


title: SR124


title: SR131


title: SRmix3

description: Pooled from all SR-uPA+/0 samples, replicate 1


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 5

source_name: Haemophilus ducreyi 35000HP

treatment_protocol: Cells are grown under normal conditions

value: wild type

source_name: Haemophilus ducreyi 35000HPcpxA

value: cpxA deletion mutant


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 6


title: adrenal_medulla_TAC_3

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

hyb_protocol: 10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

scan_protocol: The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

source_name: adrenal medulla after TAC

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification Two-Cycle Target Labeling and Control Reagents, 900494) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification Two-Cycle Target Labeling and Control Reagents, 900494). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

extract_protocol: Total RNA from both adrenal medulla of one animal was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany).

treatment_protocol: Adrenal glands were frozen in liquid nitrogen. 12 µm cryosections were dehydrated in xylene. Adrenal medullary tissue was isolated by microdissection with a Leica AM6000 inverted microscope (Leica Microsystems, Wetzlar, Germany). A MicroChisel (Eppendorf, Hamburg, Germany) was used for microdissection. Tissue was aspirated in xylene. Next, xylene was evaporated (Concentrator 5303, Eppendorff, Hamburg, Germany)

value: male


title: SRmix4

description: Pooled from all SR-uPA+/0 samples, replicate 2


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 4


title: ACC42

value: Human


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 2


title: SR120


title: Liver-H3K9me3array1

city: San Francisco

first: Stavros

last: Lomvardas

state: CA

institute: Univesity of California San Francisco

description: Chip-chip with H3K9me3 antibody from liver (chromosomes 1-4)

hyb_protocol: Hybridization of labeled DNA was performed at NimbleGen, Iceland according to their standard protocols.

scan_protocol: Scanning of arrays was performed at NimbleGen, Iceland according to their standard protocols.

data_processing: Normalization and peak detection was done by using the MA2C algorithm (Song et al, Genome Biology 2007). To identify large regions of enrichment, we used a sliding window of 10Kb, minimun number of probes 20 and maximum gap of 1Kb. MA2C analyzes all replicates together, so 1 processed data file is provided for each group of replicates. Processed data files are wiggle files that can be directly uploaded to UCSC browser for viewing. An FDR<5% was selected as a threshold.

source_name: H3K9me3 ChIP DNA from mouse liver

label_protocol: Labeling of ChIP DNA and input was performed at NimbleGen, Iceland according to their standard protocols.

extract_protocol: Native chromatin was prepared from mouse OE and liver (nuclei were extracted and digested with Mnase to a trinucleosomal population). DNA was used in ChIPs following standard protocols.

value: liver

tag: chip antibody

tag: vendor

value: Abcam

tag: cat#

tag: lot#

source_name: Input DNA from liver

value: none, input DNA


title: Liver-H4K20me3array1

description: Chip-chip with H4K20me3 antibody from liver (chromosomes 1-4)

source_name: H4K20me3 ChIP DNA from mouse liver


title: Liver-H4K20me3array2

description: Chip-chip with H4K20me3 antibody from liver (chromosomes 4-9)


title: ACC12


title: adrenal_medulla_sham_3

source_name: adrenal medulla after sham


title: ACC27


title: Liver-H3K9me3array2

description: Chip-chip with H3K9me3 antibody from liver (chromosomes 4-9)


title: adrenal_medulla_TAC_2


title: OE1-H4K20me3array1

description: Chip-chip with H4K20me3 antibody from OE (chromosomes 1-4)

source_name: H4K20me3 ChIP DNA from mouse OE

value: olfactory epithelium

source_name: Input DNA from OE


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 1

tag: genotype/variation


title: adrenal_medulla_sham_1


title: adrenal_medulla_sham_2


title: Haemophilus ducreyi 35000HPcpxA relative to 35000HP sample 3


title: untreated plants of salt-sensitive vs salt-tolerant cotton cultivar

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description:
Comparative analysis of miRNA expression profiles between the untreated plants of salt-sensitive and -tolerant cotton cultivar.

Data derived from reverse-labeled hybridizations. Raw files use the following naming convention:

A: salt-tolerant, untreated
B: salt-sensitive, untreated

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Gossypium hirsutum

source_name: untreated salt-sensitive cotton seedling

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Seeds of  the salt-tolerant and -sensitive cotton were sterilized and germinated in vermiculite at 28°C. At the two-leaf stage, healthy seedlings were grown in pots containing aerated nutrient solution.  The experiment was conducted under a growth chamber at 30/20°C (day/night) with a photosynthetically active radiation of 450 µmol m–2 s–1, a relative humidity of 55–65% and a photoperiod of 14/10 h (light/dark).

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and the low-molecular-weight RNA (LMW-RNA) be isolated using the PEG solution precipitation method.

treatment_protocol: At the three-leaf stage, six seedlings were exposed to salinity by adding NaCl to the growth medium in 50 mM increments every 12 hours, until the final concentrations of 300 mM were reached and treated 24h.

value: seedling

source_name: untreated salt-tolerant cotton seedling


title: untreated vs salt-stressed plants of salt-sensitive cotton cultivar

description:
Comparative analysis of miRNA expression profiles between the untreated and salt-stressed plants of salt-sensitive cotton cultivar.

Data derived from reverse-labeled hybridizations. Raw files use the following naming convention:

B: salt-sensitive, untreated
B+:salt-sensitive, treated

source_name: salt-stressed salt-sensitive cotton seedling


title: OE1-H4K20me3array2

description: Chip-chip with H4K20me3 antibody from OE (chromosomes 4-9)


title: salt-stressed plants of salt-sensitive vs salt-tolerant cotton cultivar

description:
Comparative analysis of miRNA expression profiles between the salt-stressed plants of salt-sensitive and -tolerant cotton cultivar.

Data derived from reverse-labeled hybridizations. Raw files use the following naming convention:

B+:salt-sensitive, treated
A+:salt-tolerant, treated

source_name: salt-stressed salt-tolerant cotton seedling


title: OE1-H3K9me3array1

description: Chip-chip with H3K9me3 antibody from OE (chromosomes 1-4)

source_name: H3K9me3 ChIP DNA from mouse OE


title: OE1-H3K9me3array2

description: Chip-chip with H3K9me3 antibody from OE (chromosomes 4-9)


title: OE1-H4K20me3array3

description: Chip-chip with H4K20me3 antibody from OE (chromosomes 9-14)


title: SR123

value: Apoe-/- SR-uPA+/0

value: 15 weeks

value: Western diet (for 10 weeks)

value: injected intraperitoneally with thioglycollate

tag: cell type

value: peritoneal macrophage


title: SR122


title: ACC10

source_name: adenoid cystic carcinoma

tag: specimen id

value: adenoid cystic carcinoma

tag: tissue source


title: ACC11

tag: tissue


title: SR119

value: Apoe-/- nontransgenic

value: female


title: SR111


title: adrenal_medulla_TAC_1

tag: strain


title: OE1-H3K9me3array3

description: Chip-chip with H3K9me3 antibody from OE (chromosomes 9-14)


title: SR109


title: OE1-H4K20me3array4

description: Chip-chip with H4K20me3 antibody from OE (chromosomes 14-19, X, Y)


title: OE1-H3K9me3array4

description: Chip-chip with H3K9me3 antibody from OE (chromosomes 14-19, X, Y)


title: SRmix1

description: Pooled from all nontransgenic samples, replicate 1


title: untreated vs salt-stressed plants of salt-tolerant cotton cultivar

description:
Comparative analysis of miRNA expression profiles between the untreated and salt-stressed plants of salt-tolerant cotton cultivar.

Data derived from reverse-labeled hybridizations. Raw files use the following naming convention:

A: salt-tolerant, untreated
A+:salt-tolerant, treated


title: ESC N2B27 48 hr Rep 1

city: Cambridge

first: Matt

last: Thomson

address: 52 Oxford Street 368

department: MCB

institute: Harvard University

hyb_protocol: Biotinylated cRNA was hybridized onto Illumina Mouse-Ref8 BeadChip microarrays, according to the manufacturer’s protocol.

scan_protocol: Microarrays were analyzed by an Illumina BeadArray Reader

data_processing: raw data were normalized in BeadStudio

source_name: mES cells Sox1-GFP, 48 hr in N2B27

label_protocol: Biotinylated and amplified cRNA was prepared by the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion).

growth_protocol: Mouse embryonic stem cells were maintained and passaged on gelatin coated plates without feeder cells in N2B27 media containing LIF and BMP without serum as described previously (Ying and Smith, 2003; Ying et al., 2008). ES cell media was supplemented with the FGF receptor inhibitor PD173074 (Sigma, StemGent) at 100 nM to suppress background differentiation. Similar results were obtained using the MEK inhibitor PD0325901 (Sigma, StemGent) at 1 µM. Cells were routinely propagated by trypsinization and re-plating every two to three days, with a split ratio of 1 in 10. N2B27 was prepared with B27 without vitamin A.

extract_protocol: RNA was extracted using Trizol, phenol:chloroform extraction, and isopropanol precipitation.

treatment_protocol: ESC: N2B27 media containing LIF and BMP without serum as described previously (Ying and Smith, 2003; Ying et al., 2008). ES cell media was supplemented with the FGF receptor inhibitor PD173074 (Sigma, StemGent) at 100 nM. 48 hr: ES cells were trypsinized, washed, and replated into N2B27 only media for 48 hours.

tag: cell line

value: 46C mES cells Sox1-GFP

tag: differentiation state

value: Competent to differentiation signals


title: ESC N2B27 48 hr Rep 2


title: mouse_brown_adipose_cells

status: Public on May 02 2011

first: Bingbing

last: Yuan

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing: Affymetrix array data were loaded into the R statistical environment with the affy package from BioConductor. Each probe was mapped to an Entrez Gene with R library mouse4302mmentrezgcdf, and genes were normalized with RMA.

source_name: mouse primary brown preadipocytes, induction for 4 days

label_protocol: manufacturer's protocol

extract_protocol: Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent Bioanalyzer.

treatment_protocol: Primary brown preadipocytes were isolated from young mice 2 weeks according topublished methods  (Cannon and Nedergaard, 2001; Tseng et al., 2002).  When cultured primary brown preadipocytes were at 70-80% confluence, Locked Nucleic Acids (LNAs) miRNA inhibitors (100nM) were transfected by DharmaFect 2 (6ul/ml) according to the manufacturer’s instruction. 24 hrs after transfection, cells were recovered in full culture media and grown to confluence for differentiation for 4 days.

value: control

tag: background

tag: gender

value: male

value: 2 week


title: Oaf1p-myc-Chip low glucose-rep3

first: Jennifer

middle: Joy

last: Smith

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: Chip-CHIP of Oaf1p-myc from cells grown in 0.1% glucose

hyb_protocol: IP and WCE samples were pooled and co-hybridized to tiled arrays (platform GPL5683) at 42 degC by Roche NimbleGen by the method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf).

scan_protocol: Performed by Roche NimbleGen by method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf).

data_processing: Preliminary data processing was performed by Roche NimbleGen by method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf).  NimbleScan software (version 2.4) was used to extract the data, calculate scaled log2-ratios of IP versus WCE, call peaks from ratio data, and map peaks to the transcription start site of genes (using the S. cerevisiae annotation file from NimbleGen (created on 2007-02-02)).

organism: Saccharomyces cerevisiae

source_name: Oaf1-myc ChIP DNA from BY4742 in low glucose

label_protocol: IP and WCE samples were labeled in separate reactions with Cy5 and Cy3, respectively by Roche NimbleGen by the method described in the chip user guide at http://www.nimblegen.com/products/lit  (version chip_userguide_2008_10_27.pdf).

growth_protocol: Cells were grown in YPD overnight and subcultured in SCIM medium (1.7 g YNB without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g CSM/L, 5 g ammonium sulfate/L) containing 0.1% glucose for 16 h to a density of 8x10E6 cells/mL, and then transferred to  fresh SCIM containing 0.1% glucose and grown for an additional 1.75 h.

extract_protocol: This was done by previously a published method (Ren et al., Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22; 290(5500):2306-9).  Proteins were crosslinked to their cognate DNA binding sites by incubating cultures with 3.7% formaldehyde for 20 min at RT and then for 16 h at 4 deg C.  Cells were disrupted and chromatin sheared into fragments by glass bead lysis followed by sonication. myc-tagged factors were collected by  ChIP with magnetic beads. Crosslinking was reversed in fractions of the ChIP and WCE, proteins and RNA were degraded by protease digestion and treatment with RNase A.  DNA ends were blunted and  linkers were ligated to the DNA ends.  DNA was amplified by LM-PCR.

tag: genotype

value: BY4742 OAF1-myc13::kanMX4

value: mouse monoclonal anti-cMyc (9E11)

source_name: Whole cell extract DNA from BY4742 in low glucose


title: ESC N2B27 48 hr Rep 3

tag: treatment


title: Oaf1p-myc-Chip low glucose-rep2


title: Arabidopsis 35:SUB1A, Biol. Rep 2

city: Tuxtepec, OAX

first: Julian

middle: M

last: Pena-Castro

state: South America

address: Circuito Central 200

department: Biotechnology

country: Mexico

institute: Universidad del Papaloapan

description: Gene expression data from 7d old whole seedling.

hyb_protocol: Hybridization to ATH1 GeneChips was performed following the manufacturer’s method (Affymetrix) at the Genomics Core Facility, University of California, Riverside.

scan_protocol: Arrays were scanned using the ScanArray Express (Perkin-Elmer).

data_processing: Data was analyzed from CEL files using Robin (RMA model) (Lohse et al., 2010 [PMID 20388663]).

organism: Arabidopsis thaliana

source_name: Arabidopsis 35:SUB1A

label_protocol: Intact RNA (100 ng) was labeled using the GeneChip 3' IVT Express kit.

growth_protocol: Arabidopsis seeds were sterilized and stratified in water for 3 d at 4 ºC, germinated on 1X Murashige Skoog (MS) agar medium (0.43% [w/v] MS salts, pH 5.75) additionally containing 1% (w/v) sucrose in vertically oriented plates in a growth chamber (23 ºC, 16 h light/ 8 h dark, 125 uE m-2 s-1), and after 7 d of growth they were collected at midday, frozen in liquid nitrogen, and stored at -80C until further processing.

extract_protocol: Total RNA extraction was performed using TRIzol reagent (Invitrogen), followed by further purification on RNeasy columns (Qiagen). RNA integrity was assessed by electrophoresis with a 2100 Bioanalyzer (Agilent).

treatment_protocol: No treatment was applied.

tag: ecotype

value: whole seedling

tag: age

tag: expression


title: Skeletal muscle pooled RNA 2

city: Lund

first: Emely

last: Möller

address: Lund University Hospital

department: Clinical Genetics

institute: Lund University

description: Global gene expression data

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix).

source_name: soft tissue

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen´s RNeasy kit according to the manufacturers´ instructions.

tag: sample type

value: pooled RNA

value: Skeletal muscle


title: ESC Rep 2

source_name: mES cells Sox1-GFP

value: untreated

value: Pluripotent


title: mouse_brown_adipose_cells treated with mir193b inhibitor

treatment_protocol: Primary brown preadipocytes were isolated from young mice 2 weeks according to published methods  (Cannon and Nedergaard, 2001; Tseng et al., 2002).  When cultured primary brown preadipocytes were at 70-80% confluence, Locked Nucleic Acids (LNAs) miRNA inhibitors (100nM) were transfected by DharmaFect 2 (6ul/ml) according to the manufacturer’s instruction. 24 hrs after transfection, cells were recovered in full culture media and grown to confluence for differentiation for 4 days.

value: mir193b inhibitor


title: Oaf1p-myc-Chip low glucose-rep1

tag: chip antibody


title: Oaf1p-myc Chip-5h oleate-rep1

description: Chip-CHIP of Oaf1p-myc from cells grown in oleate (5h)

source_name: Oaf1-myc ChIP DNA from BY4742 in oleate

growth_protocol: Cells were grown in YPD overnight and subcultured in SCIM medium (1.7 g YNB without amino acids and ammonium sulfate/L,  0.5% yeast extract, 0.5% peptone, 0.79 g CSM/L, 5 g ammonium sulfate/L) containing 0.1% glucose for 16 h to a density of 8x10E6 cells/mL, and then transferred to SCIM containing 0.15% oleate and 0.5% Tween 40, and grown for an additional 5 h.

source_name: Whole cell extract DNA from BY4742 in oleate


title: ESC Rep 1


title: LNCaP vs. PrEC

description: Library created from methylation-sensitive enzyme restriction is hybridized on Agilent CpG array.

hyb_protocol: Detailed instructions for hybridzation and washing can be obtained from the following web link http://www.genomics.agilent.com/files/Manual/G4481-90010_MammalianProtocol_10.11.pdf

scan_protocol: Scanned on an Agilent G2565AA scanner.    Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: LNCaP

label_protocol: Two micrograms of the purified products from each PrEC and LNCaP MethylPlex DNA were labeled following the mammalian ChIP-on-chip protocol (Agilent Technologies, Santa Clara, CA) starting at the sample labeling stage which employs a random primed, Klenow-based extension protocol.  The samples were hybridized to an Agilent Human CpG 244K array (Cat# G4492A, Agilent Technologies, Santa Clara, CA), where LNCaP sample was coupled with Cy5 and PrEC to Cy3.  A dye-flip experiment was also performed.  Detailed instructions can be obtained from the following link http://www.genomics.agilent.com/files/Manual/G4481-90010_MammalianProtocol_10.11.pdf

growth_protocol: The PrEC and LNCaP cells were grown in PrEGM media (Lonza Inc. Mapleton IL) and RPMI 1640 containing 10% FBS (Life Technologies, Carlsbad, CA, Carlsbad, CA), respectively.

extract_protocol: Genomic DNA was isolated from cultured cells and tissue using DNeasy Blood and tissue kit (Qiagen, Valencia, CA Inc, Valencia, CA) according to manufacturer’s instructions.

value: LNCaP

tag: type

value: Prostate Cancer

source_name: PrEC

value: Prostate Normal


title: Skeletal muscle pooled RNA 1

description: Global gene expression data


title: Arabidopsis WT, Biol. Rep 2

source_name: Arabidopsis WT Col-0

value: wild type


title: Oaf1p-myc-Chip 5h oleate-rep3


title: Oaf1p-myc Chip-5h oleate-rep2


title: Arabidopsis 35:SUB1C, Biol. Rep 2

source_name: Arabidopsis 35:SUB1C


title: Arabidopsis 35:SUB1C, Biol. Rep 1


title: Arabidopsis WT, Biol. Rep 1


title: PrEC vs. LNCaP

value: PrEC

tag: cell type


title: Arabidopsis 35:SUB1A, Biol. Rep 1


title: mouse_brown_adipose_cells treated with mir193a inhibitor

value: mir193a inhibitor


title: mouse_brown_adipose_cells treated with mir365 inhibitor

value: mir365 inhibitor


title: OsSAP11 expressing transgenic line 22, biological rep. 3

status: Public on May 01 2011

city: New Delhi

first: Akhilesh

middle: Kumar

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus,  Benito Juarez Road  India

description: Gene expression data of 21 days old Arabidopsis seedlings in OsSAP11 expressing transgenic line 22

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Array Assist software (Strandgenomics, Bangalore, India)

source_name: OsSAP11 expressing transgenic line 22

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA

growth_protocol: Seedlings were raised on 1/2 MS medium without antibiotic selection for 21 days.

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

treatment_protocol: Untreated seedlings were used for tissue

value: col 1

tag: genotype/variation

value: OsSAP11 expressing transgenic

value: seedlings

value: three-week-old


title: OsRLCK253 expressing transgenic line 25, biological rep. 3

description: Gene expression data of 21 days old Arabidopsis seedlings in OsRLCK253 expressing transgenic line 25

source_name: OsRLCK253 expressing transgenic line 25

value: OsRLCK253 expressing transgenic


title: Wild-type, biological rep. 3

description: Gene expression data of 21 days old Arabidopsis seedlings in wild-type plants

source_name: Wild-type

value: Wild-type


title: Wild-type, biological rep. 2


title: OsRLCK253 expressing transgenic line 25, biological rep. 1


title: OsSAP11 expressing transgenic line 22, biological rep. 2


title: OsRLCK253 expressing transgenic line 25, biological rep. 2


title: Wild-type, biological rep. 1


title: WP.AB.2007.pm.water-limited.rep3

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

description:
Okanese- ‘Walker’ x (P. laurifolia x P. nigra)
Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073

data_processing: GC-RMA in BioConductor

organism: Populus sp. cv. 'Okanese'

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay

growth_protocol: Saplings were grown without water-limitation for a minimum of nine weeks.

extract_protocol: Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-11

treatment_protocol: Population height was used as a physical measure of developmental stage, and the water-withholding experiment was undertaken when each hybrid population was, on average, between 60 and 70 cm high. One half of each population was grown without further input of water, while the other half was watered as earlier.

tag: cultivar

value: Okanese (WP)

value: Fully expanded, mature leaf, including petiole

tag: year of sample collection

tag: time of day

value: Leaves collected in the hour in the middle of the photoperiod (pm)

value: water-limited

tag: tissue provider

value: Alberta- Pacific Forest Industries Inc., AL-PAC, Grasslands, AB

tag: geographic origin

value: Alberta (AB)


title: WP.SK.2007.pm.water-limited.rep3

tag: tissue

value: Agriculture and Agri-Food Canada, Prairie Farm Rehabilitation Administration (AAFC-PFRA), Shelterbelt Centre, Indian Head, SK

value: Saskatchewan (SK)


title: WP.SK.2007.pm.well-watered.rep1

value: well-watered


title: WP.AB.2007.pm.well-watered.rep2


title: WP.SK.2007.pm.water-limited.rep1


title: WP.SK.2007.am.well-watered.rep2

value: Leaves collected in the hour before lights were turned on (am)


title: WP.AB.2007.am.water-limited.rep2


title: WP.SK.2007.pm.well-watered.rep2


title: OsSAP11 expreesing transgenic line 22, biological rep. 1


title: WP.AB.2007.pm.water-limited.rep1


title: WP.SK.2007.am.water-limited.rep1


title: WP.AB.2007.am.water-limited.rep3


title: WP.SK.2007.am.well-watered.rep1


title: WP.SK.2007.am.well-watered.rep3


title: WK.SK.2007.pm.water-limited.rep2

description:
Walker- P. deltoides var. occidentalis x (P. laurifolia x P. nigra)
Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

organism: Populus sp. cv. 'Walker'

value: Walker (WK)


title: WK.SK.2007.pm.water-limited.rep3


title: WP.AB.2007.pm.water-limited.rep2


title: WP.AB.2007.am.well-watered.rep2


title: WK.SK.2007.pm.well-watered.rep2


title: WP.SK.2007.am.water-limited.rep2


title: WP.AB.2007.am.water-limited.rep1


title: WP.SK.2007.am.water-limited.rep3


title: WP.AB.2007.am.well-watered.rep3


title: WP.AB.2007.pm.well-watered.rep3


title: WK.SK.2007.pm.water-limited.rep1


title: WP.AB.2007.pm.well-watered.rep1


title: WK.SK.2007.pm.well-watered.rep3


title: WP.SK.2007.pm.water-limited.rep2


title: WK.SK.2007.pm.well-watered.rep1


title: WK.SK.2007.am.water-limited.rep1


title: WK.SK.2007.am.water-limited.rep2


title: WK.SK.2007.am.well-watered.rep1


title: WK.AB.2007.pm.water-limited.rep2


title: WK.SK.2007.am.water-limited.rep3


title: WK.SK.2007.am.well-watered.rep3


title: WK.AB.2007.pm.water-limited.rep3


title: WK.AB.2007.pm.well-watered.rep2


title: WK.AB.2007.am.water-limited.rep3


title: WK.SK.2007.am.well-watered.rep2


title: WK.AB.2007.am.well-watered.rep1


title: DN.SK.2007.pm.water-limited.rep3

description:
DN34- Populus x canadensis Moench ‘Eugenei’ (P. deltoides x P. nigra)
Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

organism: Populus x canadensis

value: DN34 (DN)


title: DN.SK.2007.pm.well-watered.rep2


title: WK.AB.2007.am.well-watered.rep2


title: DN.SK.2007.pm.water-limited.rep2


title: WK.AB.2007.pm.water-limited.rep1


title: WK.AB.2007.am.well-watered.rep3


title: DN.SK.2007.pm.water-limited.rep1


title: WK.AB.2007.am.water-limited.rep2


title: DN.SK.2007.pm.well-watered.rep1


title: WK.AB.2007.am.water-limited.rep1


title: WK.AB.2007.pm.well-watered.rep1


title: DN.SK.2007.am.water-limited.rep3


title: DN.SK.2007.am.water-limited.rep2


title: WK.AB.2007.pm.well-watered.rep3


title: DN.SK.2007.am.water-limited.rep1


title: DN.SK.2007.pm.well-watered.rep3


title: WP.SK.2007.pm.well-watered.rep3


title: DN.SK.2007.am.well-watered.rep2


title: DN.SK.2007.am.well-watered.rep3


title: DN.MB.2007.pm.water-limited.rep3

value: L.A. Quality Products Ltd., Portage la Prairie, MB

value: Manitoba (MB)


title: arabinogalactan_1

middle: Charles

last: Martens

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on custom GeneChip GPL7006. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Bacteroides thetaiotaomicron

source_name: In vitro bacterial culture, arabinogalactan

label_protocol: Biotin-UDP end labeling.

growth_protocol: Bacteria were grown in vitro to mid-exponential phase on the defined carbon source indicated.

extract_protocol: Qiagen RNAEasy extraction, Ambicon DNAEasy treatment; Final Qiagen RNAEasy cleanup.

treatment_protocol: Bacterial cells were treated with RNAProtect reagent (Qiagen) and frozen at -80C until RNA extraction.

tag: strain

value: wild-type

value: arabinogalactan

tag: isolation source

value: in vitro culture


title: rhamnogalacturonanII_2

source_name: In vitro bacterial culture, rhamnogalacturonanII

tag: genotype

tag: treatment

value: rhamnogalacturonanII


title: rhamnogalacturonanI_2

source_name: In vitro bacterial culture, rhamnogalacturonanI

value: rhamnogalacturonanI


title: pullulan_2

source_name: In vitro bacterial culture, pullulan

value: pullulan


title: DN.MB.2007.pm.water-limited.rep2

value: Fully expanded, mature leaf, including petiole

value: Leaves collected in the hour in the middle of the photoperiod (pm)

value: water-limited


title: DN.SK.2007.am.well-watered.rep1

value: Agriculture and Agri-Food Canada, Prairie Farm Rehabilitation Administration (AAFC-PFRA), Shelterbelt Centre, Indian Head, SK


title: arabinogalactan_2


title: DN.MB.2007.pm.water-limited.rep1


title: rhamnogalacturonanI_1


title: homogalacturonan_2

source_name: In vitro bacterial culture, homogalacturonan

value: homogalacturonan


title: rhamnogalacturonanII_1


title: homogalacturonan_1


title: DN.MB.2007.pm.well-watered.rep2

value: well-watered


title: DN.MB.2007.am.water-limited.rep3

value: Leaves collected in the hour before lights were turned on (am)


title: DN.MB.2007.pm.well-watered.rep3


title: alpha-arabinan_2

source_name: In vitro bacterial culture, alpha-arabinan

value: alpha-arabinan


title: DN.MB.2007.pm.well-watered.rep1

value: DN34 (DN)


title: WP.AB.2007.am.well-watered.rep1

value: Okanese (WP)

value: Alberta- Pacific Forest Industries Inc., AL-PAC, Grasslands, AB

value: Saskatchewan (SK)


title: DN.MB.2007.am.water-limited.rep1

value: L.A. Quality Products Ltd., Portage la Prairie, MB

value: Manitoba (MB)


title: DN.MB.2007.am.water-limited.rep2


title: pectic galactan_1

source_name: In vitro bacterial culture, pectin galactan

value: wild-type

value: pectic galactan

value: in vitro culture


title: DN.MB.2007.am.well-watered.rep2

value: Fully expanded, mature leaf, including petiole


title: DN.MB.2007.am.well-watered.rep3


title: pectic galactan_2


title: alpha-arabinan_1


title: Healthy_blood_CD14+CD16+_monocytes_donor4_rep2

city: Singapore

first: Kok Loon

last: Wong

address: 8A Biomedical Grove, Biopolis

country: Singapore

institute: A*STAR

description: Healthy donor 4 Nonclassical (CD14+CD16+) monocyte subset replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A quantile normalization variant was applied to the duplicates profiles, followed by the scaling method applied across all profiles to equalize medians readings. The data processing software is an in-house developed Matlab code. This method is elaborated in this published report "Wong WC, Loh M, Eisenhaber F. On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct. 2008 Jun 3;3:23." (PMID: 18522715).

source_name: Isolated from peripheral blood mononuclear cells using fluorescence activated cell sorting

label_protocol: Using Illumina® TotalPrep RNA Amplification Kit according to the manufacturer's protocol.

extract_protocol: RNA was isolated using Trizol extraction followed by Qiagen RNeasy mini kit according to the manufacturer's protocol. RNA quality was confirmed using the Agilent 2100 Bioanalyser.

treatment_protocol: Classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) monocyte subsets purified using fluorescence activated cell sorting based on relative CD14 and CD16 expression

tag: donor

tag: rep

value: monocyte

tag: monocyte subset

value: Nonclassical


title: Leaves_DEX_24h_3

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

description: Leaves were cut into pieces with 1 cm width and then soaked in 10µM DEX solution for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 3 of 3.

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

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

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

organism: Populus tremula x Populus tremuloides

source_name: Leaves of transgenic Poplar carrying 35S:AtVND7-VP16-GR treated with 10µM DEX for 24 hours.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Poplar transgenic plants were grown aseptically on medium containing Murashige and Skoog (MS) salt mixture under SD (8 hours light/16 hours dark) conditions at 23°C.

extract_protocol: Extraction of total RNA was performed by Plant RNA Isolation Reagent (Invitrogen), and then total RNA was purified by RNeasy Mini Kit (QIAGEN), according to the manufacturer's instructions.

treatment_protocol: Leaves were cut into pieces with 1 cm width and then soaked in the water containing 0.033% EtOH as ccontrol, or 10 µ DEX solution for 24 hours. EtOH was a solvent for DEX stock solution.

value: Leaves

value: DEX


title: Leaves_DEX_24h_2

description: Leaves were cut into pieces with 1 cm width and then soaked in 10µM DEX solution for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 2 of 3.

value: transgenic Poplar carrying 35S:AtVND7-VP16-GR


title: Healthy_blood_CD14++CD16-_monocyte_donor4_rep2

description: Healthy donor 4 Clasical (CD14++CD16-) monocyte subset replicate 2

value: Classical


title: Leaves_DEX_24h_1

description: Leaves were cut into pieces with 1 cm width and then soaked in 10µM DEX solution for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 1 of 3.


title: Healthy_blood_CD14++CD16+_monocytes_donor3_rep2

description: Healthy donor 3 Intermediate (CD14++CD16+) monocyte subset replicate 2

value: Intermediate


title: Healthy_blood_CD14+CD16+_monocytes_donor3_rep2

description: Healthy donor 3 Nonclassical (CD14+CD16+) monocyte subset replicate 2


title: Leaves_mock_24h_3

description: Leaves were cut into pieces with 1 cm width and then soaked in the water containing 0.033% EtOH for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 3 of 3.

source_name: Leaves of transgenic Poplar carrying 35S:AtVND7-VP16-GR treated with Water containing 0.033% EtOH for 24 hours.

value: mock


title: DN.MB.2007.am.well-watered.rep1

value: DN34 (DN)

value: Leaves collected in the hour before lights were turned on (am)

value: well-watered


title: Healthy_blood_CD14+CD16+_monocytes_donor1_rep2

description: Healthy donor 1 Nonclassical (CD14+CD16+) monocyte subset replicate 2


title: Healthy_blood_CD14++CD16+_monocytes_donor4_rep2

description: Healthy donor 4 Intermediate (CD14++CD16+) monocyte subset replicate 2


title: Healthy_blood_CD14+CD16+_monocytes_donor2_rep2

description: Healthy donor 2 Nonclassical (CD14+CD16+) monocyte subset replicate 2


title: Healthy_blood_CD14++CD16+_monocytes_donor2_rep2

description: Healthy donor 2 Intermediate (CD14++CD16+) monocyte subset replicate 2


title: Healthy_blood_CD14++CD16-_monocyte_donor2_rep2

description: Healthy donor 2 Clasical (CD14++CD16-) monocyte subset replicate 2


title: Healthy_blood_CD14++CD16-_monocyte_donor3_rep2

description: Healthy donor 3 Clasical (CD14++CD16-) monocyte subset replicate 2


title: Leaves_mock_24h_2

description: Leaves were cut into pieces with 1 cm width and then soaked in the water containing 0.033% EtOH for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 2 of 3.


title: Combination treated_8

city: Houston

first: Scott

middle: E

last: Evans

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3.  Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group.

label_protocol: cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.

growth_protocol: C57BL/6J mice were 5-8 weeks old

extract_protocol: total RNA extracted using Qiagen Rneasy per manufacturers instructions.  cRNA amplification using Ambion total prep kit per manufacturers instructions.

treatment_protocol: C57BL/6J mice were placed, unrestrained, in a aerosolization chamber and inhalationally exposed to 20 minute treatment with an 8 ml volume of PBS (sham), Pam2CSK4 10 ug/ml, ODN 2395 20 ug/ml, or the combination.

tag: age

value: 5-8 weeks


title: Leaves_mock_24h_1

description: Leaves were cut into pieces with 1 cm width and then soaked in the water containing 0.033% EtOH for 24 hours. EtOH was a solvent for DEX stock solution.  Replicate 1 of 3.


title: Healthy_blood_CD14++CD16-_monocyte_donor1_rep2

description: Healthy donor 1 Clasical (CD14++CD16-) monocyte subset replicate 2


title: ODN2395 treated_8


title: Sham treated_7


title: Healthy_blood_CD14++CD16-_monocyte_donor4_rep1

description: Healthy donor 4 Clasical (CD14++CD16-) monocyte subset replicate 1


title: Combination treated_7


title: Healthy_blood_CD14+CD16+_monocytes_donor4_rep1

description: Healthy donor 4 Nonclassical (CD14+CD16+) monocyte subset replicate 1


title: ODN2395 treated_7


title: Healthy_blood_CD14++CD16+_monocytes_donor1_rep2

description: Healthy donor 1 Intermediate (CD14++CD16+) monocyte subset replicate 2


title: Sham treated_8


title: Pam2CSK4 treated_7


title: Pam2CSK4 treated_8


title: Sham treated_6


title: Combination treated_6


title: Healthy_blood_CD14++CD16+_monocytes_donor4_rep1

description: Healthy donor 4 Intermediate (CD14++CD16+) monocyte subset replicate 1


title: Pam2CSK4 treated_6


title: ODN2395 treated_6


title: Healthy_blood_CD14++CD16-_monocyte_donor3_rep1

description: Healthy donor 3 Clasical (CD14++CD16-) monocyte subset replicate 1


title: Healthy_blood_CD14++CD16-_monocyte_donor2_rep1

description: Healthy donor 2 Clasical (CD14++CD16-) monocyte subset replicate 1


title: Healthy_blood_CD14++CD16+_monocytes_donor3_rep1

description: Healthy donor 3 Intermediate (CD14++CD16+) monocyte subset replicate 1


title: Healthy_blood_CD14++CD16+_monocytes_donor2_rep1

description: Healthy donor 2 Intermediate (CD14++CD16+) monocyte subset replicate 1


title: Healthy_blood_CD14+CD16+_monocytes_donor1_rep1

description: Healthy donor 1 Nonclassical (CD14+CD16+) monocyte subset replicate 1


title: Combination treated_5


title: Sham treated_5


title: Healthy_blood_CD14+CD16+_monocytes_donor3_rep1

description: Healthy donor 3 Nonclassical (CD14+CD16+) monocyte subset replicate 1


title: Pam2CSK4 treated_5


title: Healthy_blood_CD14+CD16+_monocytes_donor2_rep1

description: Healthy donor 2 Nonclassical (CD14+CD16+) monocyte subset replicate 1


title: Pam2CSK4 treated_4


title: ODN2395 treated_4


title: Healthy_blood_CD14++CD16+_monocytes_donor1_rep1

description: Healthy donor 1 Intermediate (CD14++CD16+) monocyte subset replicate 1


title: ODN2395 treated_5


title: Sham treated_4


title: Pam2CSK4 treated_3


title: ODN2395 treated_3


title: Combination treated_4


title: mesoangioblasts treated with 1 µM S1P at 24h (replicate 2)

city: Firenze

first: Alberto

last: Magi

address: Viale Morgagni 50

department: Biochemical Sciences

country: Italy

institute: University of Florence

description: Biological replicate 4 of 4

hyb_protocol: Hybridization and washing of the array were performed following the protocols provided by Agilent according to the Two color microarray-based gene expression analysis manufacturer's protocol (Agilent).

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: Labeling reaction was performed following the protocols provided by Agilent according to the Two color microarray-based gene expression analysis manufacturer's protocol (Agilent).

growth_protocol: Human mesoangioblasts, isolated from adult muscle biopsies, were routinely grown in Mega Cell Sigma supplemented with 5% heat-inactivated FCS, 5 ng/ml bFGF, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 1 μg/ml ciprofloxacin (Applichem, GmbH, Darmstadt) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted following manufacturer's instructions.

treatment_protocol: For smooth muscle differentiation experiments, cells were seeded in p35 plates and when 90% confluent were shifted to DMEM without serum containing 1 mg/ml BSA and incubated in the presence or absence of 5 ng/ml TGFβ1 or 1 µM S1P (2 mM stock solution in dimethylsulfoxide). In some experiments cells were treated with 10 μM SKI-2, 60 min before agonist challenge.

tag: developmental stage

value: adult

value: muscle biopsy

value: mesoangioblasts

source_name: mesoangioblasts Control at 24h


title: Sham treated_3


title: neurons_MSC_rep2

city: Athens

first: Vivian

last: Tseveleki

address: 127 Vasilissis Sophias Avenue

department: Molecular Genetics

country: Greece

institute: Hellenic Pasteur Institute

hyb_protocol: Hybridizations for each experimental condition were repeated twice using independent samples.

scan_protocol: Membranes were exposed for 4-5 days on a Storm Phosphorimager screen (Molecular Dynamics, Amersham) and read using the Storm Phosphorimager. Hybridization signals were quantified using Image Quant 5.2.

data_processing: Specific spot intensities were normalized against the average of all spot intensities on each individual array (global normalization) to allow comparisons between independent array experiments.

source_name: primary cortical neurons

label_protocol: Total RNA (20μg) was reverse transcribed to [32P]dATP-labeled cDNA. The resulting cDNA probes were hybridized to the Atlas Mouse 1.2 Array II (Clontech #634545) according to the manufacturer’s instructions.

growth_protocol: MSC were isolated from the bone marrow of C57BL/6 or TgN(act-EGFP)OsbC14-Y01-FM131 (FM131) mice using plastic adherence capacity as previously described {Friedenstein 1995 68 /id}. Briefly, bone marrow cells were dissociated and cultured at 5x105/cm2 in minimum essential medium alpha (α-MEM, Gibco/BRL) supplemented with 10% FCS (Gibco/BRL), L-Glutamine 2mM (Sigma-Aldrich), antibiotics and 2ng/ml recombinant FGF2 with frequent medium changes until they reached confluency. Cells were harvested with 0.05% v/v trypsin/1mM EDTA (Gibco/BRL) and re-plated at 2x104/cm2. MSC were used for experiments after the 6th passage when the purity of MSC (Sca1+CD44+CD11b-) as assessed by FACS analysis was 98%. FACS analysis was performed using antibodies to the surface markers Sca1 (clone E13-161.7), CD44 (clone IM7) and CD11b (clone M1/70) (BD Biosciences) and a FACSCalibur with CellQuest software (BD Biosciences). MSC conditioned medium (MSC cm) was prepared by incubation of MSC for 24 h (2x104/cm2) in high-glucose DMEM. Dissociated neocortical cell cultures were prepared from E15 mice as previously described (Taoufik et al 2007). Briefly, cells were plated onto poly-D-lysine/laminin (Sigma-Aldrich)-coated dishes at 400,000 cells/cm2. Cells were maintained in DMEM supplemented with 4.5 g/L glucose (Sigma-Aldrich, # D5671), 5% foetal bovine serum (Invitrogen), 5% horse serum (Invitrogen) and 2mM glutamine (Invitrogen) (high-glucose DMEM). On day 3 in vitro (DIV3), 10 μM arabinose-C (Sigma-Aldrich) was added to the medium to inhibit the proliferation of non-neuronal cells. Experiments were performed on DIV5, 6 and 7, in cultures containing <5% astrocytes, as determined by GFAP immunocytochemistry.

extract_protocol: Total RNA was isolated from DIV7 primary cortical neurons that had been cultured in high-glucose DMEM in the presence or absence of NMDA, or neurons that had been cultured in MSC-CM in the presence or absence of NMDA, using TRIzol (Invitrogen) according to manufacturers instructions.

treatment_protocol: NMDA excitotoxic death was induced by exposure of neurons to 30 μM NMDA for 24h. N-methyl-d-aspartate (NMDA) (Sigma-Aldrich; M3262) was diluted in water at 340 μM. A final concentration of 30μM NMDA was added to cultured neurons to induce excitotoxic death; (~25% as measured by Hoechst staining and 35% as estimated by LDH assays). Neuron injury was assessed by measurement of LDH release assay (Koh & Choi 1987), WST-1 assay (Roche) and evaluation of nuclear morphology with Hoechst 33342 staining (Cheng et al 1994). Cortical neurons plated in 24 well dishes were fixed with 4% paraformaldehyde and acetone, stained with the Hoechst dye and visualized under a fluorescence microscope as previously described (Farinelli and Greene, 1996; Stefanis et al., 1998). Apoptotic nuclei were identified as nuclei with chromatin margination along the nuclear membrane or with chromatin condensation, with formation of discrete homogeneous chromatin clumps. The percentage of apoptotic nuclei was counted for each condition at 40× magnification in four separate fields of cells and is reported as the mean ± SEM. Measurement of lactate dehydrogenase (LDH) released from damaged neurons into the culture medium was performed as described previously (Koh & Choi 1987) and culture media of untreated neurons was used for normalization. The WST-1 assay was used according to the manufacturer’s protocol to measure the viability of neuronal cells in bFGF neutralization experiments. Once in the interior of metabolic active cells, WST-1 is reduced by mitochondrial succinate-tetrazolium reductase to produce the colorimetrically differentiated formazan product (K. Cesnulevicios et al., 2006). MSC pre-treatment of DIV5 neurons was performed by culture of neurons (400,000 cells/cm2) with conditioned medium from MSC (20.000 cells/cm2 in high-glucose DMEM) (MSC cm) for 24 h. High-glucose DMEM or conditioned medium from NIH/3T3 fibroblasts (12.5 x 104/ml) (3T3 cm) was used as control.

value: neuronal

tag: experimental treatment

value: 24 h treatment with MSC cm


title: pullulan_1

city: Ann Arbor

first: Eric

value: wild-type

value: pullulan

value: in vitro culture


title: mesoangioblasts treated with 1 µM S1P at 6h (replicate 2)

description: Biological replicate 3 of 4

tag: cell type

source_name: mesoangioblasts Control at 6h


title: Pam2CSK4 treated_2


title: Combination treated_2


title: neurons_rep2

value: untreated


title: neurons_MSC_rep1


title: Healthy_blood_CD14++CD16-_monocyte_donor1_rep1

description: Healthy donor 1 Clasical (CD14++CD16-) monocyte subset replicate 1

value: monocyte


title: mesoangioblasts treated with 1 µM S1P at 6h

description: Biological replicate 1 of 4


title: neurons_rep1


title: Combination treated_3


title: ODN2395 treated_2


title: Sham treated_2


title: Pam2CSK4 treated_1


title: Combination treated_1


title: Sham treated_1


title: mesoangioblasts treated with 1 µM S1P at 24h

description: Biological replicate 2 of 4


title: MB_2_Muscle

city: Daejeon

first: JeongSook

last: Lee

address: 335 Gwahangno

department: Biological science

country: South Korea

institute: KAIST

description: replicate 2

data_processing: The data were quantile normalised using rank invariant normalisation with BeadStudio

source_name: β-lapachone treatment, muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with BIO-RAD Experion.

value: Muscle


title: MB_1_Muscle

description: replicate 1


title: CR_3_Muscle

description: replicate 3

source_name: calorie restriction, muscle


title: CR_2_Muscle

description: replicate 2


title: MB_3_Muscle

description: replicate 3


title: CR_1_Muscle

description: replicate 1


title: MB_1_Brain

description: replicate 1

source_name: β-lapachone treatment, brain

value: Brain


title: Control_2_Muscle

description: replicate 2

source_name: untreated control, muscle


title: Control_1_Muscle

description: replicate 1


title: Control_2_Brain

description: replicate 2

source_name: untreated control, brain


title: MCF7 silenced Estrogen receptor, biological rep2

city: Kuwait

first: fahd

last: Al-Mulla

address: Faculty of medicine

department: Pathology

country: Kuwait

institute: Kuwait University

description: Gene expression data from MCF7 breast cancer cell line with silenced Estrogen receptor

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Partek Genomics Suite V 6.5 for RMA background correction, quantile normalisation with GC content adjustment

source_name: MCF7 silenced Estrogen receptor alpha (PII)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF7 derived from the ATCC (American Type Culture Collection, (VA, USA) were maintained at 37˚C in a humidified atmosphere of 5% CO2 in DMEM supplemented with 10% foetal bovine serum (FBS), 600 μg/ml L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin and 6 ml/500 ml 100 x non-essential amino acids (Invitrogen, CA, USA).

treatment_protocol: Endocrine independent cell line pII was established by transfection of MCF7 with ER directed shRNA plasmid. Another transfected cell line designated E2 was established that had retained sensitivity to estrogen and tamoxifen (presumably as a result of failure to produce siRNA) was used as an additional control.

tag: knockdown

value: estrogen receptor alpha KD

tag: cell line


title: ODN2395 treated_1


title: MCF7 silenced Estrogen receptor, biological rep3


title: CR_2_Brain

description: replicate 2

source_name: calorie restriction, brain


title: MCF7 silenced Estrogen receptor, biological rep1


title: MB_2_Brain

description: replicate 2


title: heart_TAC4w_rep1

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

institute: The Catholic University of Korea

description:
4week pressure overload
BTIA_EXON_4WTAC1_053008.CEL

hyb_protocol: RNA samples were hybridizaed with Affymetrix expression arrays offering whole-transcript coverage. After hybridization, non-specific binding was washed off according to the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.

data_processing: In the Expression Console software, hybridization intensity data were normalized using the Robust Multichip Average (RMA) method.

source_name: mouse wildtype ventricle

label_protocol: Biotinylated cRNA were prepared from total RNA as described by Affymetrix.

treatment_protocol: The wile-type mice were subject to sham- or TAC-operation.

value: heart ventricle

tag: gender

value: male

tag: stress

value: transverse aortic constriction

tag: time

value: 4 week


title: CR_1_Brain

description: replicate 1

tag: tissue


title: heart_TAC1w_rep2

description:
1week pressure overload
BTIA_EXON_TAC2_053008.CEL

tag: strain

value: 1 week


title: MCF7, biological rep3

description: Gene expression data from MCF7 breast cancer cell line expressing Estrogen receptor

source_name: MCF7 expressing Estrogen receptor alpha

value: control


title: Control_1_Brain

description: replicate 1


title: heart_TAC4w_rep2

description:
4week pressure overload
BTIA_EXON_4WTAC2_053008.CEL


title: heart_TAC1w_rep1

description:
1week pressure overload
BTIA_EXON_TAC1_053008.CEL


title: MCF7, biological rep2


title: MCF7, biological rep1


title: heart_SHAM_rep2

description:
no pressure overload
BTIA_EXON_SHAM2_053008.CEL

value: sham


title: heart_SHAM_rep1

description:
no pressure overload
BTIA_EXON_SHAM1_053008.CEL


title: Monocyte cell line, serum only 3

city: Copenhagen

first: Morten

last: Hansen

address: Blegdamsvej 3B

department: Department of Cellular and Melocular Medicine

country: Denmark

institute: Faculty of Health Sciences

description: Gene expression data from serum stimulation of a human monocyte cell line

hyb_protocol: The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin (BSA) and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied. The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn (SAPE).

scan_protocol: Scanned with a GeneArray scanner at the excitation wavelength of 488 nm.

data_processing: Scaled and normalized using robust multi-array analysis (RMA) in the statistical software R.

source_name: Monocyte cell line (CRL-9853)

label_protocol: In accordance with the Affymetrix protocol and the one cycle eukaryotic target labelling assay, double-stranded cDNA was synthesized from total RNA and an IVT reaction was subsequently performed to produce biotin-labelled cRNA from the cDNA.

growth_protocol: The monocytes were started up growing in Optimen + 10% FCS + antibiotics. At time 0 hours the monocytes were divided into 13 bottles with 3 x 10E6 cells in each bottle. 15 ml of Optimen medium + 10% FCS + antibiotics was added to each bottle. After 80 hours the medium was changed to 15 ml of Optimen medium + antibiotics (no FSC).

extract_protocol: RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol

treatment_protocol: After 96 hours the bottles were marked into 3 groups and annotated control, serum + inhibitor and serum only. 15 ul of DMSO was added to control and serum only bottles. 15 ul of 10mM U0196 (inhibitor) dissolved in DMSO were added to serum + inhibitor bottles. 2 hours later, after 98 hours, 1.6 ml of fetal calf serum  were added to serum + inhibitor and serum only. After 120 hours each bottle were split equally into 2 centrifuge tubes and spun down.

tag: condition

value: Added serum only


title: Monocyte cell line, serum only 2


title: Monocyte cell line, serum and inhibitor 5

value: Added serum and Erk-1/2 inhibitor U0126


title: Monocyte cell line, serum and inhibitor 2


title: Monocyte cell line, serum only 1


title: Monocyte cell line, serum and inhibitor 3


title: Monocyte cell line, serum and inhibitor 4


title: Monocyte cell line, control 5

value: serum starved


title: Monocyte cell line, serum and inhibitor 1


title: Monocyte cell line, control 3


title: Monocyte cell line, control 1


title: #2691 HUH7.5

city: Dallas

first: Bray

last: Denard

address: 5323 Harry Hines Blvd. L5.226

institute: University of Texas Southwestern Medical Center

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software, version 1.0.0.046 using Affymetrix default analysis settings (MAS 5.0 algorithm) and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

growth_protocol: Cells were maintianed in DMEM (High Glucose) supplemented with 10% Fetal Calf Serum and 1% Pennicillin/Streptomycin.

extract_protocol: Total RNA was extracted with Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

value: Hepatocyte

tag: permissiveness to hcv

value: Permissive


title: Monocyte cell line, control 4


title: HRP1


title: #2691 HUH7

value: Non-Permissive


title: pTracer-CREB3L1Δ381-519 GFP(+)

source_name: HCV Replicon containing Huh7-K2040 cells, transfected with pTracer-CREB3L1

treatment_protocol: We transfected HCV Replicon containing Huh7-K2040 cells with pTracer-CREB3L1 or pTracer.  After overnight incubation, we isolated cells  by trypsinization and utilized FACS to isolate GFP(+) cells.

tag: infected cells

value: HCV-Replicon infected hepatocytes

tag: trasnfection protocol