title: LT262371RM_COPD


title: LT228241RL_ILD

status: Public on May 30 2013

type: RNA

city: Pittsburgh

first: John

last: Tedrow

state: PA

address: 3471 Fifth Avenue, Suite 1211

department: Internal Medicine

country: USA

institute: University of Pittsburgh

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized to the specified arrays as per manufacturer instructions.  Hybridization was in a rotating oven at the specified temperature

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K arrays or 8x60K arrays as noted

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default perameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The resulting array data was normalized using a cyclic loess approach in pairwise fashion.  Probes were then collapsed to one gene/one probe by highest signal intensity.

molecule: total RNA

organism: Homo sapiens

source_name: Flash frozen whole lung

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

extract_protocol: 30 mg of whole lung was homogenized with Trizol and then total RNA was extracted using the QiaCube system (Qiagen, Valencia CA).  RNA quality was determined by Agilent Bioanalyzer 2100 (Agilent Technologies Inc, Santa Clara, CA) with RIN > 7.0 being acceptable for microarray usage.

tag: disease state

value: Interstitial lung disease

tag: Sex

tag: age

tag: gold stage

value: 3-Severe COPD

tag: smoker?

tag: %predicted fev1 (pre-bd)

tag: %predicted fvc (pre-bd)

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)

tag: %predicted dlco

tag: ild subtype

value: 9-Hypersensitive Pneumonitis (HP)


title: LT243058RU_COPD

value: Chronic Obstructive Lung Disease

tag: pneumocystis colonization

value: Negative

tag: %emphysema (f-950)

value: 4-Very Severe COPD


title: LT257433RU_COPD

value: 0-At Risk


title: LT223474RM_ILD


title: LT213735RU_COPD

value: 2-Moderate COPD


title: LT213352LU_COPD


title: LT214473RL_ILD


title: ExVivotARPCs 2

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description: miRNAs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: tARPCs

label_protocol: 600 ng of total RNA isolated from each cell lines were first dephosphorylated with a calf intestine alkaline phosphatase treatment for 30 minutes at 37°C before labeling. Samples were diluted with DMSO, denatured for 10 minutes at 100°C and labeled using pCp-Cy3 in T4 RNA ligation buffer. According to the Agilent kit guidelines, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

extract_protocol: Total RNA was extracted from a minimum of 10e6 cells/line using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.

tag: tissue

value: tubular adult renal stem/progenitor cells


title: ExVivotARPCs 1

description: miRNAs


title: LT212777RU_COPD


title: LT211379RL_ILD


title: LT216419RL_COPD


title: LT208778RU_COPD


title: LT210463LU_COPD


title: LT199987LU_ILD


title: LT203231RM_COPD


title: LT208505LU_COPD

value: 1-Mild COPD


title: LT206005RL_ILD


title: LT199384RL_COPD


title: DFL12 wild-type vs. ∆ctrA OD600 0.4

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: Hybridization was performerd according to the Agilent two-color microarray protocol

scan_protocol: Microarays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent feature extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Backround correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantile-normalization was used for seperate microarrays.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: wild-type OD600 0.4

label_protocol: total RNA was labelled using the Universal Linker System (Kreatech) according to the manufacturers  protocol

growth_protocol: DFL12 was grown in a defined minimal medium with succinate as sole carbon source. Growth temperature was 30°C, cells were kept in the dark

extract_protocol: Samples were collected by centrifugation, coverd with 1ml Trizol reagent and frozen in liquid nitrogen. RNA was extracted using the Rneasy Mini kit (Qiagen) with on column DNA digestion according to the manufacturers protocol followed by a second DNA digestion step in solution using DnaseI (Quiagen) and RNA purification using the RNeasy mini kit.

tag: strain

value: wild-type

tag: growth phase (od600)

source_name: ∆ctrA OD600 0.4

value: ∆ctrA


title: DFL12 ∆ctrA vs. ∆cckA OD600 0.4

source_name: ∆cckA OD600 0.4

value: ∆cckA


title: DFL12 ∆ctrA vs. ∆cckA 6h stationary

source_name: ∆ctrA 6h stationary

value: stationary

source_name: ∆cckA 6h stationary


title: DFL12 ∆cckA vs. ∆chpT OD600 0.4

source_name: ∆chpT OD600 0.4

value: ∆chpT


title: LT203541RU_COPD


title: 4888TG1_U133plus2

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix genechip scanner protocol

data_processing: data were analyzed in R using the GCRMA R package with defaults

label: Biotin

source_name: Excised tumor

label_protocol: Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols

growth_protocol: Patient-derived xenografts are grown by transplantation into the epithelium-free mammary fat pad of recipient SCID/Bg mice. Transplantation was performed without intervening culture in vitro or experimental manipulation of any kind

extract_protocol: Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.

treatment_protocol: Tumor fragments were excised and frozen at -80C prior to RNA extraction

value: Xenograft

tag: transplant generation

tag: ethicity

value: C

value: M

value: N

value: H

value: P


title: DFL12 wild-type vs. ∆ctrA 6h stationary

source_name: wild-type 6h stationary


title: LT198612RL_COPD

tag: disease state

value: Chronic Obstructive Lung Disease

tag: Sex


title: 4913TG1_U133plus2


title: DFL12 ∆chpT vs. wild-type 6h stationary

source_name: ∆chpT 6h stationary


title: 4664TG1_U133plus2

value: NR

value: Y


title: DFL12 ∆chpT vs. wild-type OD600 0.4


title: 4400TG1_U133plus2

value: A

value: B


title: DFL12 ∆cckA vs. ∆chpT 6h stationary


title: LT198062LL_COPD

tag: age

tag: gold stage

value: 2-Moderate COPD


title: LT198134LU_COPD

value: Positive

value: 4-Very Severe COPD

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: 4849TG1_U133plus2


title: 4013TG1_U133plus2

value: I


title: 4272TG1_U133plus2


title: LT195188RL_ILD

value: Interstitial lung disease

tag: %predicted fvc (pre-bd)

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: 3963TG5_U133plus2

value: Xenograft


title: 3963TG1_U133plus2


title: 3936TG5_U133plus2


title: LT195871RU_COPD

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: 4169TG2_U133plus2


title: 4175TG1_U133plus2


title: 4400TG5_U133plus2


title: LT194473RU_COPD

value: 3-Severe COPD

tag: %predicted dlco


title: LT197511LU_COPD

tag: pneumocystis colonization

value: Negative


title: 3887TG1_U133plus2

value: N


title: 3904TG5_U133plus2

value: H


title: 3887TG5_U133plus2

value: P


title: 3807TG5_U133plus2


title: LT192758RU_COPD

value: Chronic Obstructive Lung Disease

tag: %emphysema (f-950)

value: 1-Mild COPD


title: LT191087RM_ILD

value: 0-At Risk

tag: ild subtype

value: 9-Hypersensitive Pneumonitis (HP)


title: LT220968RU_COPD


title: LT189721RL_ILD


title: LT190004RU_COPD


title: 3904TG1_U133plus2

tag: tissue

value: Y

value: B


title: LT188524RL_ILD


title: 3936TG1_U133plus2


title: 3824TG2_U133plus2


title: 3613TG5_U133plus2


title: 3611TG1_U133plus2

value: A


title: 3611TG5_U133plus2


title: 3613TG1_U133plus2


title: 3204TG1_U133plus2

value: C


title: 3561TG5_U133plus2

value: I


title: 3204TG5_U133plus2


title: 3143TG5_U133plus2


title: 3561TG1_U133plus2


title: 3807TG1_U133plus2


title: LT186521RU_COPD

value: 2-Moderate COPD


title: LT185970RL_COPD


title: 3143TG1_U133plus2


title: 3107TG5_U133plus2


title: 3107TG1_U133plus2


title: 3104TG3_U133plus2


title: 3104TG1_U133plus2


title: LT184241RL_ILD

value: Interstitial lung disease


title: LT182636RU_ILD


title: 2665TG6_U133plus2

value: Xenograft


title: 2665TG1_U133plus2


title: LT180781RL_ILD


title: 2277TG1_U133plus2


title: 2277TG9_U133plus2


title: 2147TG1_U133plus2


title: 2147TG6_U133plus2


title: 2665TG15_U133plus2


title: 2147TG15_U133plus2


title: LT178967RL_COPD


title: 2147TG11_U133plus2


title: LT178929RL_COPD


title: LT178790LL_ILD


title: LT177956LL_COPD


title: LT184772RL_COPD


title: Melanoma tumor sample from patient 62

city: Rixensart

first: Fernando

last: Ulloa Montoya

address: rue de l'Institut, 89

country: Belgium

institute: GlaxoSmithKline Biologicals

hyb_protocol: Affymetrix HG-U133.Plus 2.0 gene chips were hybridized, washed and scanned according to the standard Affymetrix protocols (Affymetrix, Santa Clara CA, USA) using Affymetrix Fluidic station 450

scan_protocol: Affymetrix Genechip scanner 3000

data_processing: The CEL files obtained after scanning were normalized by using a modified gene-chip robust multi-array averaging algorithm (GC‑RMA) package from R Bioconductor (Wu, 2004) to obtain summarized values for each probe set. The normalization reference dataset was composed of 65 samples. ABS_CALL were obtained with a modified version of PANP, a probeset was discarded for analysis if Absent (A) in all the samples in normalization dataset.

label: biotin

source_name: Melanoma tumor biopsy prior to MAGE-A3 immunotherapy

label_protocol: RNA amplification and labelling were performed with the Nugen 3’ ovation biotin kit (NuGEN Technologies, San Carlos, CA, USA)) according to the manufacturers’ instructions

extract_protocol: Total RNA was purified using Tripure (Roche, Mannheim, Germany) followed by DNase treatment in RNeasy Mini kit column (Qiagen, Hilden, Germany).  RNA from melanoma samples with high melanin content was further purified by CsCl centrifugation.

tag: treatment response for gene profiling

value: NE

tag: response

value: not evaluable


title: Melanoma tumor sample from patient 61

value: Melanoma tumor biopsy prior to MAGE-A3 immunotherapy


title: LT176562LL_COPD


title: Melanoma tumor sample from patient 59


title: Melanoma tumor sample from patient 60


title: Melanoma tumor sample from patient 58


title: Melanoma tumor sample from patient 64


title: Melanoma tumor sample from patient 65


title: Melanoma tumor sample from patient 63


title: LT170158LL_ILD


title: Melanoma tumor sample from patient 56

value: NR

value: non-responder


title: UPN_051_Relapse

type: genomic

city: Ulm

first: Jan

last: Kroenke

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

country: Germany

institute: University Hospital of Ulm

hyb_protocol: according to manufactor's instructions  (Genome-Wide Human SNP  6.0 User Guide, Affymetrix)

scan_protocol: Chips were scanned using the Gene Chip Scanner 3000

data_processing:
CEL-files were generated using Affymetrix Command console software.
CHP files were generated using the birdseed-v2 algorithm in Genotyping Console Version 4.2

molecule: genomic DNA

source_name: bone marrow

extract_protocol: DNA was isolated using the AllPrep Mini Kit (Qiagen) from cryopreserved mononuclear cells

tag: gender

value: female

tag: disease status

value: relapsed AML


title: LT175949LL_COPD

tag: disease state

value: Chronic Obstructive Lung Disease

tag: Sex

value: 1-Mild COPD


title: UPN_047_Relapse

label_protocol: according to manufactor's instructions  (Genome-Wide Human SNP  6.0 User Guide, Affymetrix)

value: male


title: Melanoma tumor sample from patient 57


title: Melanoma tumor sample from patient 54

value: R

value: responder


title: UPN_053_Relapse


title: Melanoma tumor sample from patient 55


title: Melanoma tumor sample from patient 51


title: Melanoma tumor sample from patient 53


title: UPN_052_Relapse


title: UPN_044_Relapse


title: Melanoma tumor sample from patient 52


title: LT165736LL_ILD

tag: age


title: Melanoma tumor sample from patient 49


title: UPN_046_Relapse


title: UPN_048_Relapse


title: UPN_042_Relapse


title: LT163771RU_COPD

value: Negative

tag: gold stage

value: 3-Severe COPD

tag: smoker?


title: Melanoma tumor sample from patient 50


title: Melanoma tumor sample from patient 48


title: Melanoma tumor sample from patient 47


title: LT162479RU_COPD

tag: %predicted fev1 (pre-bd)

tag: %predicted fvc (pre-bd)


title: UPN_043_Relapse


title: UPN_039_Relapse


title: UPN_045_Relapse

source_name: blood


title: UPN_036_Relapse


title: Melanoma tumor sample from patient 45


title: LT161434RL_ILD

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: Melanoma tumor sample from patient 43


title: Melanoma tumor sample from patient 44


title: UPN_037_Relapse


title: UPN_040_Relapse


title: Melanoma tumor sample from patient 41


title: LT158647RU_COPD

value: 4-Very Severe COPD


title: UPN_033_Relapse


title: UPN_041_Relapse


title: Melanoma tumor sample from patient 40


title: UPN_035_Relapse


title: UPN_034_Relapse


title: Melanoma tumor sample from patient 42


title: LT157177RU_COPD

value: 2-Moderate COPD


title: Melanoma tumor sample from patient 39


title: LT156276RL_ILD

value: Interstitial lung disease

value: 0-At Risk


title: Melanoma tumor sample from patient 36


title: Melanoma tumor sample from patient 38


title: LT168128RU_COPD

tag: %predicted dlco


title: Melanoma tumor sample from patient 37


title: Melanoma tumor sample from patient 35


title: LT154785RU_COPD

tag: pneumocystis colonization

tag: %emphysema (f-950)


title: LT152653LU_COPD


title: Melanoma tumor sample from patient 33

tag: tissue


title: Melanoma tumor sample from patient 32

tag: treatment response for gene profiling


title: UPN_030_Relapse


title: LT167064RL_ILD

tag: ild subtype

value: 9-Hypersensitive Pneumonitis (HP)


title: Melanoma tumor sample from patient 31

tag: response

value: Melanoma tumor biopsy prior to MAGE-A3 immunotherapy


title: Melanoma tumor sample from patient 30


title: Melanoma tumor sample from patient 29


title: LT152615RL_ILD


title: Melanoma tumor sample from patient 28

value: NR


title: Melanoma tumor sample from patient 27


title: LT151949RL_ILD

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: Melanoma tumor sample from patient 25

value: non-responder


title: LT156041LU_COPD


title: UPN_029_Relapse

tag: gender

tag: disease status

value: relapsed AML


title: Melanoma tumor sample from patient 23


title: Melanoma tumor sample from patient 24


title: LT151920RL_COPD

tag: disease state

value: Chronic Obstructive Lung Disease

tag: Sex


title: LT151255LL_ILD

tag: age

tag: gold stage


title: Melanoma tumor sample from patient 22


title: Melanoma tumor sample from patient 34


title: Melanoma tumor sample from patient 26


title: UPN_028_Relapse

value: female


title: UPN_031_Relapse

value: male


title: Melanoma tumor sample from patient 46


title: LT140471RU_COPD

value: 1-Mild COPD

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: Melanoma tumor sample from patient 20

value: R

value: responder


title: Melanoma tumor sample from patient 17


title: Melanoma tumor sample from patient 19


title: UPN_024_Relapse


title: UPN_023_Relapse


title: Melanoma tumor sample from patient 18


title: LT148377LU_COPD

value: Negative

value: 3-Severe COPD

tag: %predicted fvc (pre-bd)


title: Melanoma tumor sample from patient 16


title: UPN_021_Relapse


title: UPN_027_Relapse


title: UPN_020_Relapse


title: UPN_022_Relapse


title: UPN_049_Relapse


title: LT139601RU_ILD


title: LT140046RU_COPD


title: LT139051LU_COPD

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: Melanoma tumor sample from patient 15


title: Melanoma tumor sample from patient 14


title: UPN_050_Relapse


title: Melanoma tumor sample from patient 12


title: Melanoma tumor sample from patient 13


title: Melanoma tumor sample from patient 11


title: Melanoma tumor sample from patient 10


title: LT138418LU_COPD

tag: pneumocystis colonization

value: 2-Moderate COPD

tag: %predicted dlco


title: Melanoma tumor sample from patient 21

tag: tissue


title: UPN_025_Relapse


title: LT137832LU_COPD

tag: %emphysema (f-950)


title: Melanoma tumor sample from patient 8

tag: treatment response for gene profiling


title: UPN_038_Relapse


title: UPN_019_Relapse


title: Melanoma tumor sample from patient 6

tag: response


title: LT148511LU_ILD

value: Interstitial lung disease

tag: ild subtype


title: LT136415RU_COPD

value: 4-Very Severe COPD


title: Melanoma tumor sample from patient 7


title: Melanoma tumor sample from patient 9


title: Melanoma tumor sample from patient 4


title: Melanoma tumor sample from patient 2


title: Melanoma tumor sample from patient 3


title: LT134829RL_ILD

value: 0-At Risk


title: LT134719RU_COPD


title: Melanoma tumor sample from patient 1

value: Melanoma tumor biopsy prior to MAGE-A3 immunotherapy


title: UPN_018_Relapse

tag: gender

tag: disease status


title: Melanoma tumor sample from patient 5


title: LT134279LL_ILD

tag: disease state

tag: Sex


title: T-ALL patient #257

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

hyb_protocol: Hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000

data_processing: Probeset intensities were extracted in R.

source_name: leukemia

label_protocol: Copy-DNA and ccRNA syntheses from total RNA, hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

extract_protocol: Genomic DNA and total cellular RNA were isolated using Trizol (Invitrogen) according to the manufacturers’ protocol, with minor modifications. An additional phenol-chloroform extraction was performed and the RNA was precipitated with isopropanol along with 1 mL (20 mg/mL) glycogen (Roche, Almere, The Netherlands). After precipitation, RNA pellets were dissolved in 20 mL RNAse-free TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8.0). The RNA concentration was quantified spectrophotometrically. Integrity of total RNA was checked using the Agilent 2100 Bio-analyzer (Agilent, Santa-Clara, USA).

treatment_protocol: Leukemic cells were isolated and enriched from these samples. Within 24 hours after sampling, mononuclear cells were isolated by density gradient centrifugation using Lymphoprep (density 1.077 g/mL; Nycomed Pharma, Oslo, Norway), and centrifuged at 480g for 15 minutes at room temperature. The collected mononuclear cells were washed twice and kept in culture medium consisting of RPMI 1640 medium (Dutch modification without L-glutamine; Gibco BRL, Life Technologies, Breda, The Netherlands), 20% fetal calf serum (FCS; Integro, Zaandam, The Netherlands), 2 mM L-glutamine (Gibco BRL, Life Technologies) 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL sodium selenite (ITS media supplement; Sigma, St Louis, MO), 100 IU/mL penicillin, 100 µg/mL streptomycin, 0.125 µg/mL fungizone (Gibco BRL, Life Technologies), and 0.2 mg/mL gentamycin (Gibco BRL, Life Technologies). Contaminating nonleukemic cells were removed by immunomagnetic beads. as described by Kaspers et al (1994). All resulting samples contained 90% leukemic cells, as determined morphologically by May-Grünwald-Giemsa-stained cytospins (Merck, Darmstadt, Germany). Viably frozen T-ALL cells were used for DNA and RNA extraction, and a minimum of 5 million leukemic cells were lysed in Trizol reagent (Invitrogen, Life Technologies, Breda, The Netherlands) and stored at -80°C.

tag: cell type

value: pediatric T-ALL


title: UPN_016_Relapse


title: UPN_032_Relapse


title: UPN_026_Relapse


title: T-ALL patient #253

description: reanalysis of GSM657750


title: LT122336LU_COPD

tag: age

tag: gold stage

tag: smoker?


title: UPN_017_Relapse


title: T-ALL patient #249

description: reanalysis of GSM657751


title: T-ALL patient #248

description: reanalysis of GSM657819


title: T-ALL patient #251

description: reanalysis of GSM657768


title: T-ALL patient #255


title: LT126327LU_COPD

tag: %predicted fev1 (pre-bd)

tag: %predicted fvc (pre-bd)

tag: %predicted fev1 (post-bd)


title: LT118801RL_ILD

tag: %predicted fvc (post-bd)

tag: %predicted dlco

value: 9-Hypersensitive Pneumonitis (HP)


title: LT130861RU_ILD


title: T-ALL patient #252

description: reanalysis of GSM657725


title: T-ALL patient #256


title: T-ALL patient #247

description: reanalysis of GSM657748


title: T-ALL patient #246

description: reanalysis of GSM657726


title: T-ALL patient #254


title: LT118064RL_COPD

tag: pneumocystis colonization

tag: %emphysema (f-950)


title: UPN_013_Relapse


title: T-ALL patient #245


title: T-ALL patient #244

description: reanalysis of GSM657794


title: T-ALL patient #250

description: reanalysis of GSM657721


title: T-ALL patient #243

description: reanalysis of GSM657752


title: UPN_015_Relapse


title: T-ALL patient #242

description: reanalysis of GSM657745


title: LT112597RU_COPD


title: UPN_014_Relapse


title: UPN_012_Relapse


title: T-ALL patient #239

description: reanalysis of GSM657801


title: UPN_011_Relapse


title: LT113005RU_COPD


title: UPN_010_Relapse


title: T-ALL patient #241


title: LT111643RU_COPD


title: UPN_009_Relapse


title: LT112563LL_COPD


title: UPN_005_Relapse


title: UPN_007_Relapse


title: T-ALL patient #236

description: reanalysis of GSM657815


title: T-ALL patient #240


title: LT109231RU_COPD


title: T-ALL patient #235

description: reanalysis of GSM657727


title: T-ALL patient #238

description: reanalysis of GSM657807


title: LT115251RU_COPD


title: T-ALL patient #237


title: T-ALL patient #234

description: reanalysis of GSM657816


title: UPN_008_Relapse


title: T-ALL patient #232

value: adult T-ALL


title: T-ALL patient #233


title: LT103266RU_ILD


title: T-ALL patient #231

description: reanalysis of GSM657742


title: UPN_004_Relapse

value: relapsed AML


title: T-ALL patient #230

description: reanalysis of GSM657827


title: T-ALL patient #229

description: reanalysis of GSM657728


title: LT098394RL_ILD


title: LT100707RL_ILD


title: LT094532RL_ILD


title: T-ALL patient #228

description: reanalysis of GSM657830


title: T-ALL patient #227

description: reanalysis of GSM657738


title: T-ALL patient #225


title: T-ALL patient #224

description: reanalysis of GSM657808


title: T-ALL patient #226

description: reanalysis of GSM657817


title: T-ALL patient #223


title: UPN_053_Remission

value: complete morphologic remission


title: LT089723LL_COPD

value: Chronic Obstructive Lung Disease


title: UPN_001_Relapse

value: male


title: UPN_002_Relapse

value: female


title: UPN_006_Relapse


title: LT094217RM_ILD


title: LT087663RL_ILD


title: UPN_052_Remission


title: T-ALL patient #221

description: reanalysis of GSM657761


title: T-ALL patient #220

description: reanalysis of GSM657746


title: T-ALL patient #218


title: LT084808LU_COPD


title: UPN_003_Relapse


title: T-ALL patient #222

description: reanalysis of GSM657769


title: T-ALL patient #216

description: reanalysis of GSM657740


title: UPN_051_Remission


title: T-ALL patient #217


title: T-ALL patient #212

description: reanalysis of GSM657770


title: LT084406RU_COPD


title: T-ALL patient #214

description: reanalysis of GSM657762


title: T-ALL patient #219

description: reanalysis of GSM657722


title: T-ALL patient #215

description: reanalysis of GSM657753


title: LT083706RL_COPD


title: T-ALL patient #211

description: reanalysis of GSM657763


title: LT082092RU_ILD


title: T-ALL patient #213


title: T-ALL patient #210

description: reanalysis of GSM657831


title: LT080176RU_COPD


title: T-ALL patient #209

description: reanalysis of GSM657771


title: T-ALL patient #206

description: reanalysis of GSM657732


title: T-ALL patient #207


title: LT080836RL_ILD


title: T-ALL patient #208

description: reanalysis of GSM657832


title: T-ALL patient #205

description: reanalysis of GSM657743


title: LT083759RL_COPD


title: T-ALL patient #204

description: reanalysis of GSM657754


title: UPN_046_Remission


title: LT078696LU_ILD

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: UPN_049_Remission


title: T-ALL patient #203

description: reanalysis of GSM657820


title: UPN_048_Remission


title: LT078404RM_ILD


title: LT077317LI_ILD

value: 1-Mild COPD


title: T-ALL patient #200

description: reanalysis of GSM657818


title: T-ALL patient #201

description: reanalysis of GSM657802


title: LT077082RU_ILD


title: T-ALL patient #202

description: reanalysis of GSM657765


title: T-ALL patient #198

description: reanalysis of GSM657773


title: LT076617LL_COPD

value: Negative


title: T-ALL patient #199

description: reanalysis of GSM657772


title: T-ALL patient #197

description: reanalysis of GSM657825


title: UPN_042_Remission


title: T-ALL patient #195

description: reanalysis of GSM657755


title: T-ALL patient #194

description: reanalysis of GSM657775


title: UPN_045_Remission


title: UPN_043_Remission


title: UPN_040_Remission


title: UPN_047_Remission


title: T-ALL patient #191

description: reanalysis of GSM657777


title: LT072808RL_COPD


title: T-ALL patient #192

description: reanalysis of GSM657776


title: UPN_044_Remission


title: UPN_039_Remission


title: T-ALL patient #193

description: reanalysis of GSM657828


title: UPN_036_Remission


title: T-ALL patient #189

description: reanalysis of GSM657821


title: LT076181LI_COPD


title: T-ALL patient #188

description: reanalysis of GSM657806


title: LT070403LL_COPD

value: Positive


title: T-ALL patient #187

description: reanalysis of GSM657724


title: T-ALL patient #186

description: reanalysis of GSM657756


title: T-ALL patient #190

description: reanalysis of GSM657810


title: LT075462RU_COPD

value: 3-Severe COPD


title: UPN_033_Remission


title: T-ALL patient #184

description: reanalysis of GSM657739


title: T-ALL patient #183


title: T-ALL patient #196

description: reanalysis of GSM657774


title: LT067836RL_ILD

value: Interstitial lung disease


title: UPN_031_Remission


title: LT062141RL_ILD


title: LT072387LU_COPD

value: 4-Very Severe COPD


title: UPN_035_Remission


title: UPN_050_Remission


title: LT061106RL_ILD


title: T-ALL patient #185


title: T-ALL patient #181


title: T-ALL patient #182

description: reanalysis of GSM657757


title: UPN_034_Remission


title: T-ALL patient #180

description: reanalysis of GSM657749


title: UPN_030_Remission


title: UPN_037_Remission


title: UPN_032_Remission


title: UPN_029_Remission


title: T-ALL patient #177


title: T-ALL patient #178


title: T-ALL patient #179

description: reanalysis of GSM657767


title: UPN_028_Remission


title: LT059975LU_COPD


title: T-ALL patient #173

description: reanalysis of GSM657778


title: LT059736LU_ILD


title: T-ALL patient #174


title: LT057972LU_COPD

value: 2-Moderate COPD


title: LT058691LU_COPD


title: T-ALL patient #170

description: reanalysis of GSM657779


title: LT057312LU_ILD


title: UPN_027_Remission


title: UPN_041_Remission


title: UPN_024_Remission


title: T-ALL patient #172

description: reanalysis of GSM657822


title: T-ALL patient #169

description: reanalysis of GSM657780


title: UPN_026_Remission


title: T-ALL patient #171

description: reanalysis of GSM657804


title: LT043798LU_COPD


title: LT043343LU_COPD


title: T-ALL patient #176

description: reanalysis of GSM657833


title: UPN_025_Remission


title: T-ALL patient #166

description: reanalysis of GSM657811


title: T-ALL patient #167

description: reanalysis of GSM657730


title: UPN_023_Remission


title: LT042151RL_ILD

value: 0-At Risk


title: T-ALL patient #163

description: reanalysis of GSM657781

value: pediatric T-ALL


title: T-ALL patient #164

description: reanalysis of GSM657812


title: UPN_038_Remission


title: T-ALL patient #161


title: T-ALL patient #162

description: reanalysis of GSM657782


title: T-ALL patient #165

description: reanalysis of GSM657809


title: T-ALL patient #160

description: reanalysis of GSM657783


title: T-ALL patient #159


title: T-ALL patient #168

description: reanalysis of GSM657834


title: LT039091RL_ILD


title: LT041723RL_ILD


title: T-ALL patient #157

description: reanalysis of GSM657784


title: UPN_022_Remission


title: T-ALL patient #158

description: reanalysis of GSM657823


title: LT035239LU_ILD

value: 9-Hypersensitive Pneumonitis (HP)


title: T-ALL patient #175

description: reanalysis of GSM657729


title: T-ALL patient #155

description: reanalysis of GSM657786


title: T-ALL patient #154

description: reanalysis of GSM657829


title: T-ALL patient #156

description: reanalysis of GSM657785


title: T-ALL patient #152

description: reanalysis of GSM657787


title: T-ALL patient #153

description: reanalysis of GSM657824


title: UPN_018_Remission


title: T-ALL patient #151


title: LT035774RL_ILD


title: LT034070LU_COPD


title: LT042552RL_ILD


title: LT033422RL_ILD


title: LT034821RU_COPD


title: T-ALL patient #148

description: reanalysis of GSM657790


title: LT030151RU_COPD


title: UPN_017_Remission


title: T-ALL patient #149

description: reanalysis of GSM657789


title: UPN_020_Remission


title: T-ALL patient #147

description: reanalysis of GSM657791


title: T-ALL patient #145

description: reanalysis of GSM657826


title: T-ALL patient #146

description: reanalysis of GSM657792


title: T-ALL patient #144

description: reanalysis of GSM657793


title: LT028427LU_COPD


title: T-ALL patient #150

description: reanalysis of GSM657788


title: T-ALL patient #143

description: reanalysis of GSM657799


title: UPN_014_Remission


title: LT028044RU_COPD


title: T-ALL patient #141

description: reanalysis of GSM657795


title: T-ALL patient #142

description: reanalysis of GSM657813


title: T-ALL patient #140

description: reanalysis of GSM657814


title: LT025997RU_COPD


title: LT024460RU_COPD


title: T-ALL patient #139


title: UPN_015_Remission


title: UPN_019_Remission


title: LT024106RU_COPD


title: T-ALL patient #136

description: reanalysis of GSM657800


title: T-ALL patient #137

description: reanalysis of GSM657796


title: UPN_011_Remission


title: T-ALL patient #138


title: T-ALL patient #135

description: reanalysis of GSM657803


title: UPN_016_Remission


title: UPN_013_Remission


title: UPN_012_Remission


title: UPN_021_Remission


title: T-ALL patient #134

description: reanalysis of GSM657797


title: LT020426LU_COPD


title: LT017275LL_COPD


title: T-ALL patient #133

description: reanalysis of GSM657805


title: LT020259LL_ILD


title: UPN_010_Remission


title: LT008331RL_ILD


title: T-ALL patient #132

description: reanalysis of GSM657798


title: T-ALL patient #128

description: reanalysis of GSM657835


title: T-ALL patient #130

description: reanalysis of GSM657764


title: LT007259RU_ILD


title: T-ALL patient #126


title: T-ALL patient #127

description: reanalysis of GSM657741


title: T-ALL patient #124

value: adult T-ALL


title: LT002902RU_ILD


title: T-ALL patient #131


title: UPN_008_Remission


title: T-ALL patient #129

description: reanalysis of GSM657731


title: UPN_007_Remission


title: UPN_005_Remission


title: LT002501RL_COPD


title: UPN_006_Remission


title: UPN_009_Remission


title: UPN_003_Remission


title: LT295133LL_ILD


title: T-ALL patient #125


title: T-ALL patient #122


title: T-ALL patient #121


title: T-ALL patient #123


title: T-ALL patient #120


title: LT286300LU_CTRL

value: Control


title: UPN_002_Remission

value: complete morphologic remission


title: UPN_004_Remission


title: T-ALL patient #118


title: T-ALL patient #119


title: LT280646RU_CTRL


title: LT280560LU_CTRL


title: T-ALL patient #116


title: T-ALL patient #114


title: T-ALL patient #117


title: T-ALL patient #113


title: UPN_001_Remission


title: T-ALL patient #115


title: T-ALL patient #112


title: LT231373LU_ILD


title: T-ALL patient #111


title: LT198741LU_CTRL


title: LT194990RU_COPD

value: Chronic Obstructive Lung Disease


title: LT231101RL_ILD

value: 4-Desquamative interstitial pneumonia (DIP)


title: T-ALL patient #103


title: UPN_050_Diagnosis

value: female

value: primary AML


title: T-ALL patient #107


title: T-ALL patient #106


title: UPN_053_Diagnosis


title: T-ALL patient #110


title: T-ALL patient #104


title: UPN_051_Diagnosis


title: LT188161LL_ILD


title: T-ALL patient #101


title: T-ALL patient #100


title: LT178307RU_CTRL


title: T-ALL patient #102


title: LT177521RU_CTRL


title: T-ALL patient #105


title: T-ALL patient #96


title: UPN_049_Diagnosis


title: T-ALL patient #98


title: LT163513RL_CTRL


title: LT168204LL_COPD


title: T-ALL patient #97


title: UPN_048_Diagnosis


title: T-ALL patient #95


title: UPN_045_Diagnosis

value: male


title: T-ALL patient #99


title: UPN_047_Diagnosis


title: T-ALL patient #94


title: UPN_052_Diagnosis


title: UPN_046_Diagnosis


title: UPN_044_Diagnosis


title: LDDDD_CT0.5_day3

city: Berlin

first: Christian

middle: Johannes

last: Beck

state: Berlin

address: Invalidenstrasse 43

department: Institute for Theoretical Biology

institute: Humboldt-University Berlin

description: subjective day

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.5 µg of labeled RNA.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays.

data_processing: Raw data were processed using GNU R and MATLAB. Signal intensity was probe-wise LOS normalized, using a oscillation threshold of 0.7.

organism: Synechocystis sp. PCC 6803

source_name: whole cell

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The glucose-tolerant and motile wild-type strain of Synechocystis sp. PCC 6803 originally obtained from S. Shestakov (Moscow State University, Russia) was routinely grown photoautotrophically in BG11-medium at 30°C under continuous illumination with white light of 80 µmol of photons/m^2s  and a continuous stream of air.

extract_protocol: 15 ml of cyanobacterial culture were filtered rapidly through Supor 0.45 µm membrane filters (PALL), immediately stowed with TRIzol reagent (Invitrogen) and frozen in liquid nitrogen. Total RNA samples stored at -20°C were transferred directly to a 65°C water bath for 5 min, mixed with 0.2 ml chloroform per ml of TRIzol and incubated for further 15 min. The dissolving of the membrane and lyses of the cells were supported by vortexing. Centrifugation at maximum speed for 10 min at 4°C separated the phases. The RNA in the supernatant was precipitated by adding 1 volume of isopropanol. Finally isolated total RNA was treated with RNase-free Turbo™DNase (Ambion) by following the manufacturer's instructions, resulting in 40 µl purified RNA solution.

treatment_protocol: Cell concentrations were measured by determining the optical densities of the culture at 750 nm (OD750). Cultures were synchronized with three cycles of light/dark 12h:12h prior sampling.

tag: light regime

value: LDDDD

tag: sample time point


title: LDDDD_CT1.5_day3

description: subjective day


title: LT158011LL_ILD

tag: ild subtype


title: LT159988RL_COPD

value: Negative


title: T-ALL patient #92


title: LDDDD_CT23.5_day2

description: night


title: UPN_041_Diagnosis

tag: gender

tag: disease status


title: LT148286LL_CTRL

tag: disease state

tag: Sex


title: T-ALL patient #93

tag: cell type


title: T-ALL patient #91


title: UPN_043_Diagnosis


title: LDDDD_CT21.5_day2

description: night


title: UPN_039_Diagnosis


title: LDDDD_CT19.5_day2

description: night


title: T-ALL patient #90


title: LT141870LU_CTRL

tag: age

tag: gold stage


title: UPN_042_Diagnosis


title: T-ALL patient #89


title: LDDDD_CT3.5_day3

description: subjective day


title: LT132314LI_CTRL

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: LDDDD_CT15.5_day2

description: night


title: LT141224LL_CTRL

tag: %predicted fvc (pre-bd)

tag: %predicted fev1 (post-bd)


title: LDDDD_CT17.5_day2

description: night


title: LT155982RU_COPD

tag: %predicted fvc (post-bd)

tag: %predicted dlco


title: UPN_038_Diagnosis


title: T-ALL patient #88


title: LDDDD_CT13.5_day2

description: night


title: LT120371LL_CTRL

tag: %emphysema (f-950)


title: UPN_040_Diagnosis


title: UPN_037_Diagnosis


title: LT115840LL_CTRL


title: LDDDD_CT11.5_day2

description: subjective day

tag: light regime


title: UPN_035_Diagnosis


title: LT109097LL_ILD

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD


title: T-ALL patient #87


title: T-ALL patient #84


title: LDDDD_CT9.5_day2

description: subjective day

tag: sample time point


title: UPN_036_Diagnosis


title: LT089451RU_CTRL


title: T-ALL patient #83


title: LDDDD_CT7.5_day2

description: subjective day


title: T-ALL patient #85


title: UPN_034_Diagnosis


title: T-ALL patient #86


title: LDDDD_CT5.5_day2

description: subjective day


title: LT077800RU_CTRL


title: T-ALL patient #82


title: LT075094LU_CTRL


title: UPN_032_Diagnosis


title: LT058156LU_CTRL


title: LDDDD_CT1.5_day2

description: subjective day


title: UPN_033_Diagnosis


title: T-ALL patient #80


title: T-ALL patient #81


title: UPN_030_Diagnosis


title: LDDDD_CT0.5_day2

description: subjective day


title: LT055745RU_CTRL


title: UPN_031_Diagnosis


title: T-ALL patient #78


title: LT044225RL_CTRL


title: T-ALL patient #79


title: LDDDD_CT23.5_day1

description: night


title: LDDDD_CT17.5_day1

description: night


title: UPN_029_Diagnosis


title: LDDDD_CT3.5_day2

description: subjective day


title: UPN_027_Diagnosis


title: UPN_028_Diagnosis


title: T-ALL patient #76


title: LT030041RU_COPD

value: 1-Mild COPD


title: LT023631RU_CTRL


title: LT012861RU_COPD

tag: pneumocystis colonization

value: 4-Very Severe COPD


title: LDDDD_CT5.5_day1

description: day


title: UPN_026_Diagnosis

tag: gender


title: T-ALL patient #75


title: LDDDD_CT11.5_day1

description: day


title: LDLLL_CT3.5_day3

description: day

value: LDLLL


title: LT046027RL_CTRL

value: 0-At Risk


title: UPN_025_Diagnosis

tag: disease status


title: T-ALL patient #77


title: T-ALL patient #74


title: LDLLL_CT1.5_day3

description: day


title: LT010012LU_CTRL

tag: disease state


title: T-ALL patient #73


title: LDLLL_CT0.5_day3

description: day


title: LT003990RU_CTRL

tag: Sex


title: LT264690LU_ILD

value: Interstitial lung disease

tag: ild subtype


title: LT258372RL_ILD

tag: age


title: T-ALL patient #70

tag: cell type

value: pediatric T-ALL


title: LDLLL_CT21.5_day2

description: subjective night


title: T-ALL patient #64


title: UPN_023_Diagnosis


title: LT205601LL_ILD

tag: smoker?


title: UPN_021_Diagnosis


title: UPN_024_Diagnosis


title: LDLLL_CT23.5_day2

description: subjective night


title: T-ALL patient #66

value: adult T-ALL


title: LDLLL_CT17.5_day2

description: subjective night


title: T-ALL patient #61


title: UPN_019_Diagnosis


title: UPN_020_Diagnosis


title: LDLLL_CT13.5_day2

description: subjective night


title: UPN_016_Diagnosis


title: LDLLL_CT15.5_day2

description: subjective night


title: LDLLL_CT19.5_day2

description: subjective night


title: UPN_022_Diagnosis


title: T-ALL patient #63


title: LT181242RM_CTRL

value: Control

tag: gold stage

tag: %predicted fev1 (pre-bd)


title: LDLLL_CT11.5_day2

description: day


title: T-ALL patient #60


title: UPN_017_Diagnosis


title: LT174005RL_CTRL

tag: %predicted fvc (pre-bd)

tag: %predicted fev1 (post-bd)


title: LT188012RL_CTRL

tag: %predicted fvc (post-bd)

tag: %predicted dlco


title: T-ALL patient #57


title: LT172184LU_CTRL


title: KO_treatedAOMDSS_rep3

city: Scottsdale

first: Tze Wei

last: Poh

state: AZ

address: 13400 E Shea Boulevard

institute: Mayo Clinic

description:
KO AOM+DSS 3
Gene expression in colonic mucosa of treated KO chimeras.

hyb_protocol: Labeled cRNA (1.65mg) was fragmented at 60°C for 30 minutes in a reaction volume of 55ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Microarray 4x44K (G4122F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash buffer 2, then dried immediately.

scan_protocol: 4x44 whole mouse genome slides were scanned immediately after washing and feature extracted on an Agilent scanner as per manufacturer's instructions.

data_processing:
Set the threshold at 1, set the 75th percentile signal value to normalize and then perform baseline transformation to median of all samples.
Microarray data were loaded onto GeneSpring 11.5 for analysis. During analysis, the gene list data were filtered to remove compromised signals. Unpaired t test was performed between samples from control and AOM+DSS treated mice within each group of chimeras to determine the genes that were significantly altered (p<0.05) upon treatment between WT→WT and KO→WT mice. Genes that were altered less than 2 fold upon treatment with AOM+DSS were subsequently excluded from the gene list. In order to determine which genes were involved in the development of larger tumors observed in KO→WT mice, Venn diagram analysis was used to analyse only genes that were differentially regulated 2 fold or more in KO→WT mice only or both KO→WT and WT→WT mice. Genes that were differentially regulated in WT→WT mice only were not included in the analysis.

organism: Mus musculus

source_name: Colon mucosa, Muc1 KO donor, mouse treated with AOM and DSS

label_protocol: Cy3 labeled cRNA was generated from 1 ug RNA per sample, using the Quick Amp Labeling kit (Agilent), followed by RNeasy column purification (QIAGEN, Valencia, CA). Quantification and dye incorporation of the labeled cRNA were performed using the Nanodrop (Thermo Scientific, Waltham, MA).

extract_protocol: Colons were opened longitudinally, washed in PBS and the mucosa from each colon was scraped and individually snap frozen in liquid nitrogen. RNA from colonic mucosa was isolated using the RNeasy MiniKit (Qiagen, Valencia, CA).

treatment_protocol: Two groups of WT→WT (C57BL/6 WT recipient with C57BL/6 WT donor bone marrow) and KO→WT (C57BL/6 WT recipient with C57BL/6 Muc1 KO donor bone marrow) mice were injected intraperitoneally with 12.5mg/kg of azoxymethane (AOM). Five days later, colitis was induced in the mice by administration of 2% DSS in the drinking water for 4 days, followed by another 14 days of regular water. This cycle was repeated again, followed by a final administration of 2.5% DSS in drinking water for 5 days. Mice were sacrificed 1 day after the last DSS drinking cycle for dissection of colons and extraction of colonic mucosa.

tag: strain/background

tag: chimera type

value: Muc1 KO donor, WT recipient

tag: treatment

value: azoxymethane (AOM) + dextran sodium sulfate (DSS)

tag: tissue

value: colon mucosa


title: UPN_013_Diagnosis

tag: gender

value: female

tag: disease status


title: UPN_015_Diagnosis

value: primary AML


title: LDLLL_CT5.5_day2

description: day

tag: light regime

tag: sample time point


title: KO_treatedAOMDSS_rep2

description:
KO AOM+DSS 2
Gene expression in colonic mucosa of treated KO chimeras.


title: UPN_018_Diagnosis

value: male


title: LDLLL_CT0.5_day2

description: day


title: LT171169LU_CTRL

source_name: Flash frozen whole lung

tag: disease state

tag: Sex

tag: age


title: T-ALL patient #53

tag: cell type


title: KO_treatedAOMDSS_rep1

description:
KO AOM+DSS 1
Gene expression in colonic mucosa of treated KO chimeras.


title: LT167208LL_CTRL

tag: gold stage

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: UPN_014_Diagnosis


title: T-ALL patient #51


title: T-ALL patient #52


title: LT187987LL_ILD

tag: %emphysema (f-950)

tag: %predicted fvc (pre-bd)

tag: ild subtype


title: LT160423LL_CTRL

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)

tag: %predicted dlco


title: WT_treatedAOMDSS_rep3

description:
WT AOM+DSS 3
Gene expression in colonic mucosa of treated WT chimeras.

source_name: Colon mucosa, WT donor, mouse treated with AOM and DSS

tag: strain/background

tag: chimera type

value: WT donor, WT recipient

tag: treatment

tag: tissue


title: LDLLL_CT5.5_day1

description: day

tag: light regime

tag: sample time point


title: UPN_009_Diagnosis

tag: gender

tag: disease status


title: LT137431RL_ILD

tag: disease state

tag: Sex

tag: age


title: LT157253RL_ILD

tag: %emphysema (f-950)

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: WT_treatedAOMDSS_rep2

description:
WT AOM+DSS 2
Gene expression in colonic mucosa of treated WT chimeras.


title: LDLLL_CT23.5_day1

description: night


title: WT_treatedAOMDSS_rep1

description:
WT AOM+DSS 1
Gene expression in colonic mucosa of treated WT chimeras.


title: LT136731LU_CTRL

tag: gold stage

tag: %predicted fvc (pre-bd)


title: KO_untreated_control_rep3

description:
KO control 3
Gene expression in colonic mucosa of untreated KO chimeras.

source_name: Colon mucosa, Muc1 KO donor, untreated control

value: untreated


title: T-ALL patient #50

description: reanalysis of GSM657766

tag: cell type


title: UPN_010_Diagnosis


title: LDLDL_CT1.5_day3

description: day

value: LDLDL


title: LDLDL_CT3.5_day3

description: day


title: KO_untreated_control_rep2

description:
KO control 2
Gene expression in colonic mucosa of untreated KO chimeras.

tag: strain/background


title: UPN_011_Diagnosis


title: UPN_012_Diagnosis


title: T-ALL patient #46

description: reanalysis of GSM657733


title: LT122757RU_CTRL

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: LT132955RU_CTRL

tag: %predicted dlco


title: LDLDL_CT0.5_day3

description: day

tag: light regime


title: LDLLL_CT11.5_day1

description: day

tag: sample time point


title: T-ALL patient #45


title: T-ALL patient #56


title: T-ALL patient #43


title: T-ALL patient #49

description: reanalysis of GSM657723


title: LDLDL_CT23.5_day2

description: night


title: WT_untreated_control_rep3

description:
WT control 3
Gene expression in colonic mucosa of untreated WT chimeras.

source_name: Colon mucosa, WT donor, untreated control

tag: chimera type

tag: treatment

tag: tissue


title: LT121655RL_CTRL

tag: disease state

tag: Sex


title: LDLDL_CT21.5_day2

description: night


title: LT117785RL_CTRL

tag: age


title: UPN_003_Diagnosis

tag: gender

tag: disease status


title: UPN_004_Diagnosis


title: T-ALL patient #38


title: UPN_005_Diagnosis


title: HPC-Differentiated-VD3

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 2123 Adelbert Road, RT400-L

department: Biochemistry

institute: Case Western Reserve University

description: total RNA extracted from differentated HPC treated with vitamin D3

hyb_protocol: Total 1 microgram RNA at 100 nanogram per microliter for each sample were sent for a single-channel gene expression microarray studies using HumanRef-8 chip (V3_0_R3_11282963) on Illumina BeadStation platform.

scan_protocol: The raw data were collected by scanning the chip on Illumina BeadStation.

data_processing: Background subtracted raw data were exported and the following analysis was done in R/Bioconductor environment. The data was preprocessed by R (2.15.0), lumi package (2.8.0). The raw data was vst transformed and rsn normalized.

source_name: HPC, differentiated, vitamine D3 reated

label_protocol: The RNA were converted to aRNA and appropriately labelled using MessageAmp Biotin aRNA Amplification Kit (Ambion) following the manufacturer's instructions.

extract_protocol: The total RNAs of these cells were isolated using USB prepEase RNA spin kit following the manufacturer's instructions.

value: HPC

value: in vitro differentiate with 100 nM vitamin D3 (VD3)


title: T-ALL patient #47

description: reanalysis of GSM657836


title: LT122283RM_CTRL

tag: gold stage

tag: smoker?

tag: %predicted fev1 (pre-bd)


title: T-ALL patient #36

tag: cell type


title: KO_untreated_control_rep1

description:
KO control 1
Gene expression in colonic mucosa of untreated KO chimeras.

tag: strain/background


title: LT113211RL_CTRL

tag: %predicted fvc (pre-bd)


title: UPN_002_Diagnosis


title: WT_untreated_control_rep1

description:
WT control 1
Gene expression in colonic mucosa of untreated WT chimeras.


title: WT_untreated_control_rep2

description:
WT control 2
Gene expression in colonic mucosa of untreated WT chimeras.


title: T-ALL patient #39

description: reanalysis of GSM657837


title: UPN_006_Diagnosis


title: T-ALL patient #35

description: reanalysis of GSM657734


title: LDLDL_CT15.5_day2

description: night


title: HPC-Differentiated-Dex-rep2

description: total RNA extracted from differentated HPC treated with dexdexamethasone

source_name: HPC, differentiated, dexdexamethasone treated

value: in vitro differentiate with 100 nM dexamethasone (Dex)


title: T-ALL patient #40

description: reanalysis of GSM657758


title: LT115873LU_CTRL

tag: %emphysema (f-950)

value: 0-At Risk

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)

tag: %predicted dlco


title: LDLDL_CT17.5_day2

description: night

tag: light regime

tag: sample time point


title: LT104535RL_CTRL

tag: disease state


title: LDLLL_CT17.5_day1

description: night

value: LDLLL


title: LDLDL_CT11.5_day2

description: day


title: HPC-Differentiated-Dex-rep1

tag: treatment


title: UPN_008_Diagnosis


title: UPN_001_Diagnosis


title: LT097622RU_CTRL

tag: Sex

tag: age


title: LT095376RL_CTRL


title: HPC-Differentiated-Vehicle-rep1

description: total RNA extracted from differentated HPC treated with vehicle control

source_name: HPC, differentiated, Vehicle treated

value: in vitro differentiate with vehicle


title: LDLDL_CT9.5_day2

description: day


title: LT092669LU_ILD

value: Interstitial lung disease

tag: ild subtype


title: LDLDL_CT5.5_day2

description: day


title: LDLDL_CT19.5_day2

description: night


title: T-ALL patient #31

value: pediatric T-ALL


title: HPC-Undifferentiated-Vehicle

description: total RNA extracted from undifferentated HPC treated with vehicle control

source_name: HPC, undifferentiated, Vehicle treated

value: undifferentiated with vehicle


title: T-ALL patient #32

description: reanalysis of GSM657735


title: T-ALL patient #29

description: reanalysis of GSM657737


title: T-ALL patient #27

description: reanalysis of GSM657747


title: LDLDL_CT7.5_day2

description: day


title: LDLDL_CT3.5_day2

description: day


title: T-ALL patient #30

description: reanalysis of GSM657736


title: TRIKI 3/ DMSO 6, biol. Repl.3, tech. Repl.1

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

hyb_protocol: Samples were combined and hybridized to a custom oligoarray with 4 x 44k elements manufactured by Agilent Technologies (GPL8606). Hybridization and washing steps were performed according to Agilent instructions.

scan_protocol: The washed slides were scanned using GenePix4000B (Molecular Devices) scanner.

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the background subtracted intensities (gProcessedSignal and rProcessedSignal) were LOWESS normalized.  Log2 ratio (Treated/Control) intensities was calculated.

organism: Schistosoma mansoni

source_name: Control female sample 6

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: Adult worms were obtained by portal perfusion of 42-days infected hamsters

extract_protocol: RNA from all samples was extracted using Trizol reagent (Invitrogen) followed by DNase treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions.

treatment_protocol: Adult worms were kept in culture for 48 h with Herbimycin A (4.5 µM ) or TGF beta receptor type I kinase inhibitor (TRIKI, 300 nM) or a combined treatment with both inhibitors (Herbimycin A 4.5µM and TRIKI 300nM) or the vehicle solution (DMSO)

tag: developmental stage

value: adult

source_name: TRIKI treated females sample 3


title: LDLDL_CT0.5_day2

description: day


title: LT063974LL_ILD

tag: smoker?


title: LT073345RU_CTRL

value: Control

tag: gold stage

tag: %predicted fev1 (pre-bd)


title: HPC-Differentiated-Vehicle-rep2

tag: cell type


title: TRIKI 2/ DMSO 5, biol. Repl.2, tech. Repl.2

source_name: TRIKI treated females sample 2

value: female

source_name: Control female sample 5


title: LDLDL_CT1.5_day2

description: day


title: TRIKI 2/ DMSO 5, biol. Repl.2, tech. Repl.1


title: T-ALL patient #25

value: adult T-ALL


title: LT077355RU_CTRL

tag: %predicted fvc (pre-bd)


title: LDLDL_CT21.5_day1

description: night


title: LDLDL_CT23.5_day1

description: night


title: LT071706RL_ILD

tag: %emphysema (f-950)


title: T-ALL patient #23


title: Herbimycin A + TRIKI 2/ DMSO 8, biol. Repl.2, tech Repl.2

source_name: Control female sample 8

source_name: Herbimycin A + TRIKI treated females sample 2


title: TRIKI 3/ DMSO 6, biol. Repl.3, tech. Repl.2


title: Herbimycin A + TRIKI 2/ DMSO 8, biol. Repl.2, tech Repl.1


title: T-ALL patient #24

source_name: leukemia


title: T-ALL patient #22

description: reanalysis of GSM657760


title: LDLDL_CT19.5_day1

description: night

source_name: whole cell


title: LT056464LL_ILD


title: LT058983RL_CTRL


title: LT061842RL_CTRL


title: Herbimycin A + TRIKI 1/ DMSO 7, biol. Repl.1, tech Repl.1

source_name: Control female sample 7

source_name: Herbymicin A + TRIKI treated females sample 1


title: T-ALL patient #19


title: T-ALL patient #21

description: reanalysis of GSM657744


title: TRIKI 1/ DMSO 4, biol. Repl.1, tech. Repl.1

source_name: TRIKI treated females sample 1

source_name: Control female sample 4


title: LT052751LL_CTRL

source_name: Flash frozen whole lung


title: T-ALL patient #14


title: LDLDL_CT13.5_day2

description: night


title: LT047679RL_CTRL


title: LT045714LU_CTRL


title: Herbimycin A + TRIKI 1/ DMSO 7, biol. Repl.1, tech Repl.2

source_name: Herbimycin A + TRIKI treated females sample 1


title: LDLDL_CT15.5_day1

description: night


title: LT058471RU_CTRL

tag: %predicted fev1 (post-bd)


title: UPN_007_Diagnosis

source_name: bone marrow

tag: gender

tag: disease status

value: primary AML


title: T-ALL patient #12


title: TRIKI 1/ DMSO 4, biol. Repl.1, tech. Repl.2


title: LDLDL_CT11.5_day1

description: day

tag: light regime


title: LDLDL_CT9.5_day1

description: day

tag: sample time point


title: Herbimycin A + TRIKI 3/ DMSO 9, biol. Repl.3, tech Repl.1

source_name: Control female sample 9

source_name: Herbimycin A + TRIKI treated females sample 3


title: T-ALL patient #11


title: LT037781RU_CTRL

tag: disease state

tag: %predicted fvc (post-bd)

tag: %predicted dlco


title: Herbimycin A + TRIKI 3/ DMSO 9, biol. Repl.3, tech Repl.2

tag: Sex


title: T-ALL patient #13


title: LDLDL_CT13.5_day1

description: night


title: LT028264RL_CTRL

tag: age


title: LDLDL_CT7.5_day1

description: day


title: T-ALL patient #9


title: Herbimycin A 3/ DMSO 3, biol. Repl.3, tech. Repl.2

source_name: Control females sample 3

tag: developmental stage

source_name: Herbimycin A treated females biol. Rep.3


title: T-ALL patient #10


title: Herbimycin A 2/ DMSO 2, biol. Repl.2, tech. Repl.2

source_name: Herbimycin A treated females sample 2

source_name: Control females sample 2


title: LDLDL_CT5.5_day1

description: day


title: LT022835RL_CTRL


title: T-ALL patient #34

description: reanalysis of GSM657759


title: Herbimycin A 2/ DMSO 2, biol. Repl.2, tech. Repl.1


title: Herbimycin A 3/ DMSO 3, biol. Repl.3, tech. Repl.1

source_name: Herbimycin A treated females sample 3

source_name: DMSO (control) treated females biol. Rep.3


title: T-ALL patient #7

source_name: leukemia


title: LT001796RU_CTRL

tag: smoker?


title: Striatum_GHD-1 (reps 1 and 2)

city: Tainan

first: Shang-Hsun

last: Yang

department: Department of Physiology, College of Medicine; Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng-Kung University

description:
This mice showed weak motor functions of HD.
G1_1
G1_2

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: GHD striatum

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Mice were matained at National Cheng Kung University, Tainan, Taiwan(ROC) with approvement of the Institutional Animal Care and Use Committees. Under constant environment (22°C; 12-h light/dark cycle), the mice were fed with tap water and standard laboratory chow ad libitum.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: The HD transgenic mouse line carried GFP gene fused with exon 1 of the human HTT gene with 84 CAG trinucleotide repeats, and transgene was driven by a human ubiquitin promoter. The HD transgenic mouse line overexpressing miR-196a were obtained by breeding HD transgenic mice with miR-196a mice, which carry percusior miR-196a driven by  a human ubiquitin promoter.

tag: tissue

value: Striatum

value: 12 months

value: Male

tag: strain

value: FVB

tag: genotype/variation

value: HD transgenic


title: Striatum_D-Tg-3 (reps 1 and 2)

description:
This mice showed improved motor functions of HD.
D3_1
D3_2

source_name: D-Tg striatum

value: HD transgenic mice overexpressing miR-196a


title: Herbimycin A 1/ DMSO 1, biol. Repl.1, tech. Repl.1

source_name: Herbimycin A treated females sample 1

source_name: DMSO (control) treated females biol. Rep.1


title: Striatum_GHD-2 (reps 1 and 2)

description:
This mice showed weak motor functions of HD.
G2_1
G2_2


title: LT001600RL_ILD

tag: %predicted fev1 (pre-bd)

tag: %predicted fvc (pre-bd)

tag: ild subtype


title: T-ALL patient #6

tag: cell type


title: Striatum_D-Tg-2 (reps 1 and 2)

description:
This mice showed improved motor functions of HD.
D2_1
D2_2

tag: gender


title: LT000842RU_CTRL

tag: gold stage

value: 0-At Risk


title: LT004173LL_ILD


title: Zebrafish, adult, xanthophores

city: Suita

first: hiroki

last: hamada

state: Osaka

address: 1-3 Yamadaoka

department: Frontier Biosciences

country: Japan

institute: Osaka University

hyb_protocol: standard Affymetrix labeling, hybridization, scanning, and MAS 5.0 data processing were performed by outsourcing service in RIKEN CDB, Japan.

organism: Danio rerio

source_name: Melanophores from adult zebrafish fins

growth_protocol: Zebrafish were obtained from pet shop.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions.

treatment_protocol: Caudal and anal fins were collected from 1,000 adult zebrafish and were incubated in a trypsin solution containing 2.5 mg/ml trypsin, 1.2 mg/ml bovine serum albumin, and 1 mM EDTA for 1 overnight at 4℃. The fins were then washed with 1×PBS for 5mins at 1,000rpm five times at 28℃. After collagenase treatment melanophores and xanthophores were isolated as described in Inaba et al 2012.

value: caudal and anal fins

tag: genotype

value: wild type

value: adult (over 2 months old)

value: Melanophore


title: T-ALL patient #1


title: Zebrafish, adult, melanophores

scan_protocol: standard Affymetrix labeling, hybridization, scanning, and MAS 5.0 data processing were performed by outsourcing service in RIKEN CDB, Japan.

source_name: Xanthophores from adult zebrafish fins

value: Xanthophore


title: Herbimycin A 1/ DMSO 1, biol. Repl.1, tech. Repl.2

source_name: Control females sample 1

value: adult

source_name: Herbimycin A treated females biol. Rep.1


title: Striatum_D-Tg-1 (reps 1 and 2)

description:
This mice showed improved motor functions of HD.
D1_1
D1_2


title: T-ALL patient #5


title: RIL88_T_10j_U3

status: Public on May 29 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: A quantitative resistance of sunflower to downy mildew (Plasmopara halstedii) has been mapped on LG10 (Vear et al., 2008). Is this quantitative resistance involving novel biological mechanisms?

hyb_protocol: labelled extract quantity: 5.5ug

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), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Helianthus annuus

source_name: control, water inoculation, 3hour

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: aerial - Containment culture chamber Media: compost Hygrometry: 70% humidity Temperature: 20°C Light: 16h day/8h night

treatment_protocol: Inoculation of germinated seeds (aged of 2 or 3 days) with downy mildew or water for control, during 3 hours. Seeds are then sow and plants are harvested 6 or 10 days after inoculation. Mouzeyar et al. 1993

value: 10 day

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

value: early stage of first 2 leafs


title: XRQ_334_6j_U1

source_name: pathogen infection, downy mildew race 334, 3hour

value: 6 day

value: early stage of cotyledons


title: XRQ_710_10j_U1

source_name: pathogen infection, downy mildew race 710, 3hour


title: RIL43_710_6j_U3


title: PSC8_710_10j_U2


title: LDLDL_CT17.5_day1

description: night

source_name: whole cell

tag: light regime

value: LDLDL

tag: sample time point


title: RIL43_710_6j_U1


title: RIL43_710_10j_U3


title: XRQ_710_10j_U2


title: T-ALL patient #8

value: adult T-ALL


title: PSC8_T_10j_U3


title: RIL43_710_6j_U2


title: RIL43_710_10j_U1


title: PSC8_710_10j_U1


title: PSC8_T_10j_U2


title: PSC8_T_6j_U1


title: XRQ_T_6j_U3


title: XRQ_710_10j_U3


title: RIL43_T_10j_U2


title: PSC8_710_10j_U3


title: RIL88_710_6j_U3


title: XRQ_710_6j_U2


title: PSC8_334_6j_U2


title: MC-MT Rep 2_Pectorlais

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.

organism: Junco hyemalis

source_name: male treated with testosterone [MT]

label_protocol: ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

extract_protocol:
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

tag: Sex

value: male

value: pectoralis muscle

tag: biological replicate

source_name: control male [MC]


title: PSC8_T_6j_U2

tag: age


title: XRQ_T_6j_U2


title: PSC8_334_10j_U1


title: XRQ_T_10j_U2


title: XRQ_710_6j_U3


title: RIL43_T_10j_U1


title: FT-MC Rep 2_Pectorlais

source_name: female treated with testosterone [FT]

value: female


title: RIL88_T_6j_U1


title: FT-FC Rep 2_Pectorlais

source_name: control female [FC]


title: XRQ_334_6j_U2


title: FC-MT Rep 2_Pectorlais


title: PSC8_T_6j_U3


title: MC-FC Rep 2_Pectorlais


title: FT-MT Rep 1_Pectorlais


title: RIL88_T_6j_U2


title: RIL43_T_10j_U3


title: PSC8_334_10j_U2


title: MC-FT Rep 1_Pectorlais


title: FC-MC Rep 1_Pectorlais


title: RIL88_710_10j_U1


title: PSC8_710_6j_U2


title: RIL88_710_6j_U1


title: MT-FC Rep 1_Pectorlais


title: LT026501RL_CTRL

source_name: Flash frozen whole lung

tag: disease state

value: Control

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: MC-MT Rep 2_Liver

tag: tissue

value: liver


title: XRQ_334_6j_U3


title: MT-MC Rep 1_Pectorlais


title: RIL43_710_10j_U2


title: PSC8_710_6j_U3


title: FC-FT Rep 1_Pectorlais


title: MT-FT Rep 1_Pectorlais


title: FT-MC Rep 2_Liver


title: FC-MT Rep 2_Liver


title: FT-MT Rep 1_Liver


title: FC-FT Rep 1_Liver


title: FT-FC Rep 2_Liver


title: RIL43_T_6j_U1


title: MT-FT Rep 1_Liver


title: RIL88_710_6j_U2


title: MC-FC Rep 2_Liver


title: MT-FC Rep 1_Liver


title: RIL88_T_10j_U1


title: MC-FT Rep 1_Liver


title: XRQ_710_6j_U1


title: XRQ_T_6j_U1


title: MT-MC Rep 1_Liver


title: B. subtilis remA+ vs remA- Replicate 3

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

description: Biological replicate 3 of 3.  B. sutilis strain 3610 remA+,epsH-, sinR-  vs remA-, epsH-, sinR- cells harvested in MSgg medium at and optical denisty (600nm) between 1.0-1.3

hyb_protocol: Hybridizations were incubated at 65˚C for 17 hours.  After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.

scan_protocol: Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology

data_processing: Standard lowess normalization using Bioconductor (and run in R) was performed on the processed signal given by the Agilent Feature Extraction Software (v 8.5.1.1) (used for background subtraction and lowess)  and the geometric mean of the probes was used to give the final value for each gene and nc-RNA.

organism: Bacillus subtilis

source_name: epsH-, sinR- cells

label_protocol: 6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP .  Cy3 and Cy5 were purchased from GE Healthcare

growth_protocol: Cells were grown in MSgg Medium to an Optical Density (600nm) of between 1.0-1.1

extract_protocol: RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit

treatment_protocol: After reaching the desired optical densitiy cells an equal volume of -20C methanol was added to the culture.  Cells were pelleted, supernatant was removed, and cell pellets were stored at -80C.

tag: strain

value: epsH-, sinR-

source_name: epsH-, sinR-, remA- cells

value: epsH-, sinR-, remA-


title: FC-MC Rep 1_Liver


title: XRQ_T_10j_U1


title: RIL88_T_10j_U2


title: RIL88_710_10j_U2


title: PSC8_T_10j_U1


title: SAHA HIP pool mouse 5+6

city: Boston

first: Frederick

middle: Albert

last: Schroeder

address: 185 Cambridge Street

institute: Harvard/MGH

description:
COL_5871833029_F
SAHA HIP 5+6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with GeneSpring (v 11.5.1)
All microarray analysis and gene set analysis (GSA) was performed using GeneSpring software (v.11.5.1) with raw signals adjusted using quantile normalization and baseline transformation with the median signal in all samples set to zero.  Data were included in subsequent analyses if the normalized signal, thresholded at 0.8, was 'present' for 3 of 3 replicates for like treatment and tissue groups.

source_name: SAHA treated mice, 5and6 of 6, RNA from dissected HIP

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: treatment

value: SAHA 25mg/kg

tag: brain region

value: Hippocampus

tag: array id


title: B. subtilis remA+ vs remA- Replicate 1

description: Biological replicate 1 of 3.  B. sutilis strain 3610 remA+,epsH-, sinR-  vs remA-, epsH-, sinR- cells harvested in MSgg medium at and optical denisty (600nm) between 1.0-1.1


title: CI-994 HIP pool mouse 5+6

description:
COL_5871833029_D
CI-994 HIP 5+6

source_name: CI-994 treated mice, 5and6 of 6, RNA from dissected HIP

tag: gender


title: RIL88_T_6j_U3


title: Vehicle HIP pool mouse 5+6

description:
COL_5871833029_B
Vehicle HIP 5+6

source_name: Vehicle treated mice, 5and6 of 6, RNA from dissected HIP

value: Vehicle


title: SAHA HIP pool mouse 3+4

description:
COL_5871833029_E
SAHA HIP 3+4

source_name: SAHA treated mice, 3and4 of 6, RNA from dissected HIP


title: RIL43_T_6j_U3


title: CI-994 HIP pool mouse 3+4

description:
COL_5871833029_C
CI-994 HIP 3+4

source_name: CI-994 treated mice, 3and4 of 6, RNA from dissected HIP


title: Cpd-60 HIP pool mouse 5+6

description:
COL_5871833029_A
Cpd-60 HIP 5+6

source_name: Cpd-60 treated mice, 5and6 of 6, RNA from dissected HIP

value: Cpd60 45mg/kg


title: RIL88_710_10j_U3

value: 10 day


title: PSC8_710_6j_U1


title: PSC8_334_6j_U3


title: CI-994 HIP pool mouse 1+2

description:
COL_5871833017_E
CI-994 HIP 1+2

source_name: CI-994 treated mice, 1and2 of 6, RNA from dissected HIP


title: SAHA HIP pool mouse 1+2

description:
COL_5871833017_F
SAHA HIP 1+2

source_name: SAHA treated mice, 1and2 of 6, RNA from dissected HIP


title: Vehicle HIP pool mouse 1+2

description:
COL_5871833017_C
Vehicle HIP 1+2

source_name: Vehicle treated mice, 1and2 of 6, RNA from dissected HIP


title: RIL43_T_6j_U2

source_name: control, water inoculation, 3hour


title: XRQ_334_10j_U3

source_name: pathogen infection, downy mildew race 334, 3hour

value: early stage of first 2 leafs


title: XRQ_334_10j_U2


title: Vehicle HIP pool mouse 3+4

description:
COL_5871833017_D
Vehicle HIP 3+4

source_name: Vehicle treated mice, 3and4 of 6, RNA from dissected HIP


title: PSC8_334_10j_U3


title: HT29 resistant cells replicate 2

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

hyb_protocol: miRNA Microarray System protocol v.1.0. See Agilent Technologies website.

scan_protocol: Scanned on a GenePix 4000B (Axon) scanner.

data_processing: Data files from miRNA and mRNA (previously submitted to GEO as GSE11440) microarrays were analyzed with GeneSpring GX11.5 software (Agilent Technologies) to find differentially expressed miRNAs and their cellular target genes in the resistant cell lines compared to their sensitive counterparts. Triplicate samples for each condition, sensitive and resistant, for both miRNA and mRNA, were imported into one single experiment. Average values of the replicate spots of each miRNA were background subtracted, and normalized against the median of the control samples. Gene and miRNA expression was calculated as the ratio of the values obtained in the resistant condition relative to the control, after normalization of the data using Volcano plot filtering. T-test unpaired was used for statistical analyses.

source_name: HT29 methotrexate-resistant cells

label_protocol: miRNA Microarray System protocol v.1.0. See Agilent Technologies website for miRNA labelling protocol.

extract_protocol: Real Total microRNA kit (Real)

tag: cell line

tag: cell type

value: colon cancer

tag: methotrexate sensitivity

value: resistant


title: Cpd-60 HIP pool mouse 1+2

description:
COL_5871833017_A
Cpd-60 HIP 1+2

source_name: Cpd-60 treated mice, 1and2 of 6, RNA from dissected HIP


title: Cpd-60 HIP pool mouse 3+4

description:
COL_5871833017_B
Cpd-60 HIP 1+2

source_name: Cpd-60 treated mice, 3and4 of 6, RNA from dissected HIP


title: XRQ_T_10j_U3

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


title: HT29 sensitive cells replicate 3

source_name: HT29 methotrexate-sensitive cells

value: sensitive


title: HT29 sensitive cells replicate 2

description: miRNA expression profile of HT29 cells sensitive to Methotrexate


title: XRQ_334_10j_U1


title: SAHA NAc pool mouse 5+6

description:
COL_5871833016_F
SAHA NAc 5+6

source_name: SAHA treated mice, 5and6 of 6, RNA from dissected NAc

value: Nucleus Accumbens


title: CI-994 NAc pool mouse 3+4

description:
COL_5871833016_C
CI-994 NAc 3+4

source_name: CI-994 treated mice, 3and4 of 6, RNA from dissected NAc

value: male


title: CI-994 NAc pool mouse 5+6

description:
COL_5871833016_D
CI-994 NAc 5+6

source_name: CI-994 treated mice, 5and6 of 6, RNA from dissected NAc


title: PSC8_334_6j_U1

value: 6 day

value: early stage of cotyledons


title: B. subtilis remA+ vs remA- Replicate 2

description: Biological replicate 2 of 3.  B. sutilis strain 3610 remA+,epsH-, sinR-  vs remA-, epsH-, sinR- cells harvested in MSgg medium at and optical denisty (600nm) between 1.0-1.2

source_name: epsH-, sinR- cells

tag: genotype

source_name: epsH-, sinR-, remA- cells


title: Vehicle NAc pool mouse 5+6

description:
COL_5871833016_B
Vehicle NAc 5+6

source_name: Vehicle treated mice, 5and6 of 6, RNA from dissected NAc


title: SAHA NAc pool mouse 3+4

description:
COL_5871833016_E
SAHA NAc 3+4

source_name: SAHA treated mice, 3and4 of 6, RNA from dissected NAc


title: Cpd-60 NAc pool mouse 5+6

description:
COL_5871833016_A
Cpd-60 NAc 5+6

source_name: Cpd-60 treated mice, 5and6 of 6, RNA from dissected NAc


title: SAHA NAc pool mouse 1+2

description:
COL_5871833013_F
SAHA NAc 1+2

source_name: SAHA treated mice, 1and2 of 6, RNA from dissected NAc


title: HT29 resistant cells replicate 3


title: Vehicle NAc pool mouse 3+4

description:
COL_5871833013_D
Vehicle NAc 3+4

source_name: Vehicle treated mice, 3and4 of 6, RNA from dissected NAc


title: HT29 sensitive cells replicate 1


title: HT29 resistant cells replicate 1


title: CI-994 NAc pool mouse 1+2

description:
COL_5871833013_E
CI-994 NAc 1+2

source_name: CI-994 treated mice, 1and2 of 6, RNA from dissected NAc


title: Cpd-60 NAc pool mouse 3+4

description:
COL_5871833013_B
Cpd-60 NAc 1+2

source_name: Cpd-60 treated mice, 3and4 of 6, RNA from dissected NAc


title: CI-994 PFC pool mouse 5+6

description:
COL_5871833010_D
CI-994 PFC 5+6

source_name: CI-994 treated mice, 5and6 of 6, RNA from dissected PFC

value: PFC


title: Obese_Thoracic aorta_85

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

hyb_protocol: 130 µl of hybridization solution containing 50 ng/µl of fragmented aRNA was hybridized to the porcine genome array genechip (Affymetrix, Santa Clara, CA) at 45ºC for 20 hrs.  After hybridization, the chips were washed and stained with R-phycoerythrin-streptavidin on Affymetrix fluidics station 450 using fluidics protocol Midi_euk2v3-450.

scan_protocol: The microarrays were then scanned and data acquired using an Affymetrix GeneChip Scanner 3000 driven by GCOS 1.2 software (Affymetrix)

data_processing:
The RAW CEL files were analyzed primarily with the Bioconductor affy package. Probel-level summaries were constructed using the expresso function with the follwing settings:
bgcorrect.method=rma,normalize.method=qspline,pmcorrect.method=pmonly,summary.method=medianpolish. Non-specific filtering was then run using the Bioconductor genefilter package wiht the nsFilter function with following settings: require.entrez=FALSE, require.GOBP=FALSE, require.GOCC=FALSE, require.GOMF=FALSE, require.CytoBand=FALSE,remove.dupEntrez=FALSE, var.filter=FALSE, feature.exclude=c(^AFFX,^RPTR). This essentially filters out only the internal control probes.

organism: Sus scrofa

source_name: Whole artery, Thoracic aorta, Obese pig

label_protocol: Biotin-labeled antisense RNA (aRNA) target was produced from porcine tissue total RNA (0.5µg) using the MessageAmpTM Premier RNA amplification kit (Ambion, Austin, TX) according to manufacturer’s procedures and as described previously.  Briefly, the total RNA was reverse transcribed to first strand cDNA with an oligo(dT) primer bearing a 5’-T7 promoter using ArrayScript reverse transcriptase.  The first strand cDNA then underwent second-strand synthesis to produce double stranded cDNA template for in vitro transcription.  The biotin-labeled aRNA was synthesized using T7 RNA transcriptase with biotin-NTP mix.

extract_protocol: The animals were euthanized by removal of the heart in full compliance with the American Veterinary Medical Association Guidelines on Euthanasia.  The LAD and descending thoracic aorta were dissected clean of perivascular fat and excess adventitia. Both arteries and the perivascular fat adjacent to the LAD were rinsed with ice-cold Krebs saline, and immediately frozen at -80°C or used for functional assessment (see below).  Samples were homogenized with a mortar and pestle.  Isolation of total RNA was performed using the Qiagen’s RNeasy Mini Kit (Qiagen, Valencia, CA) for the arteries and the Qiagen’s RNeasy Lipid Tissue Kit for the perivascular fat.  The product was eluted in a 100 µl volume with a 2 µl aliquot being used for spectrophotometric quantification.  Twenty-five nanograms of each sample were used in an Experion StdSens RNA Analysis to confirm optimal concentration and optimal quality of RNA.

treatment_protocol: In order to utilize the Ossabaw pig as a model of childhood obesity, 5-6 week old Ossabaw pigs (n=11) were randomly divided into two experimental groups and fed either commercially available low fat  (n=6) or high-fat/high fructose corn syrup/high cholesterol (n=5) diets for 16 weeks.  This age in miniature swine is equivalent to adolescent/juvenile humans. All pigs were individually housed in a core animal care facility at the University of Missouri under temperature controlled conditions (20–23°C) with a 12-h:12-h light-dark cycle.  Animals were provided food daily.

value: Whole artery

tag: condition

value: Obese

tag: artery type

value: Thoracic aorta

tag: pigid

tag: chipid

tag: date of sacrifice

tag: date of microarray experiment


title: HSC_NrasG12D/G12D_rep1

city: Guangzhou

first: jinyong

last: wang

state: Guangdong

address: 190 Kaiyuan road

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Accademy of Sciences

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K  using Agilent’s recommended hybridization chamber and oven.

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

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). This software offers – among other features – the possibility to compare two single intensity profiles in a ratio experiment. All samples were labeled with Cy3, here, the ratio experiments are designated as control versus (vs.) sample experiments (automated data output of the Resolver system).

label_protocol: Miltenyi Biotec’s undisclosed protocol

extract_protocol: Qiagen microRNA extraction

tag: tissue

value: Bone marrow


title: SAHA PFC pool mouse 5+6

description:
COL_5871833010_F
SAHA PFC 5+6

source_name: SAHA treated mice, 5and6 of 6, RNA from dissected PFC

tag: strain

value: SAHA 25mg/kg


title: CI-994 PFC pool mouse 1+2

description:
COL_5871833003_E
CI-994 PFC 1+2

source_name: CI-994 treated mice, 1and2 of 6, RNA from dissected PFC

tag: treatment


title: Obese_LAD-PVAT_85

source_name: adipose tissue, LAD-PVAT, Obese pig

value: adipose tissue

tag: adipose type

value: LAD-PVAT


title: HSC_Nras+/+_rep1


title: Lean_Thoracic aorta_86

source_name: Whole artery, Thoracic aorta, Lean pig

value: Lean


title: Cpd-60 PFC pool mouse 5+6

description:
COL_5871833010_A
Cpd-60 PFC 5+6

source_name: Cpd-60 treated mice, 5and6 of 6, RNA from dissected PFC

value: Cpd60 45mg/kg

tag: brain region

tag: array id


title: Vehicle PFC pool mouse 1+2

description:
COL_5871833003_C
Vehicle PFC 1+2

source_name: Vehicle treated mice, 1and2 of 6, RNA from dissected PFC

tag: gender

value: Vehicle


title: SAHA PFC pool mouse 1+2

description:
COL_5871833003_F
SAHA PFC 1+2

source_name: SAHA treated mice, 1and2 of 6, RNA from dissected PFC


title: Cpd-60 NAc pool mouse 1+2

description:
COL_5871833013_A
Cpd-60 NAc 1+2

source_name: Cpd-60 treated mice, 1and2 of 6, RNA from dissected NAc


title: Lean_LAD_86

source_name: Whole artery, LAD, Lean pig

value: LAD


title: SAHA PFC pool mouse 3+4

description:
COL_5871833010_E
SAHA PFC 3+4

source_name: SAHA treated mice, 3and4 of 6, RNA from dissected PFC


title: HSC_Nras+/+_rep2


title: Vehicle PFC pool mouse 3+4

description:
COL_5871833003_D
Vehicle PFC 3+4

source_name: Vehicle treated mice, 3and4 of 6, RNA from dissected PFC


title: HSC_NrasG12D/+_rep1


title: HSC_NrasG12D/G12D_rep3


title: Vehicle PFC pool mouse 5+6

description:
COL_5871833010_B
Vehicle PFC 5+6

source_name: Vehicle treated mice, 5and6 of 6, RNA from dissected PFC


title: HSC_NrasG12D/+_rep3


title: Lean_LAD-PVAT_86

source_name: adipose tissue, LAD-PVAT, Lean pig


title: HSC_NrasG12D/G12D_rep2


title: Vehicle NAc pool mouse 1+2

description:
COL_5871833013_C
Vehicle NAc 1+2

source_name: Vehicle treated mice, 1and2 of 6, RNA from dissected NAc


title: HSC_NrasG12D/+_rep2


title: CI-994 PFC pool mouse 3+4

description:
COL_5871833010_C
CI-994 PFC 3+4

source_name: CI-994 treated mice, 3and4 of 6, RNA from dissected PFC


title: Obese_LAD_85

source_name: Whole artery, LAD, Obese pig


title: Cpd-60 PFC pool mouse 3+4

description:
COL_5871833003_B
Cpd-60 PFC 1+2

source_name: Cpd-60 treated mice, 3and4 of 6, RNA from dissected PFC


title: Cpd-60 PFC pool mouse 1+2

description:
COL_5871833003_A
Cpd-60 PFC 1+2

source_name: Cpd-60 treated mice, 1and2 of 6, RNA from dissected PFC


title: Obese_LAD-PVAT_81


title: Obese_LAD_81


title: Lean_LAD_73


title: Human neurons, biological rep1

city: Omaha,

first: Sowmya

middle: V

last: Yelamanchili

state: NE

address: 985800 Nebraska Medical Center - DRC 1 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical center

description: miRNA expression data from neurons derived from neural progenitor cells

hyb_protocol: Hybridization was performed according to the affymetrix protocol. GeneChips were washed and stained in the Affymetrix Gene chip system.

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

data_processing: The data were analyzed using the Partek Genomics Suite and probe sets mapped to genes using the database for annotation

label: FlashTag Biotin HSR labeling was performed according to the Genisphere protocol from 200ng total RNA (Genisphere Technical Support).

source_name: 84 NPC-NEU miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL

growth_protocol: Dissociated fetal tissue is placed in neural progentior media for 1 week to give rise to neurospheres or neural progenitor cells (NPCs).

extract_protocol: NPCs were placed in differentiation media for 2-3weeks to differentiate into neurons.

tag: source tissue

value: Fetal brain source tissue

tag: gestation

value: 84 days in utero

tag: cell type

value: neural progenitor cells differentiating into neurons


title: Lean_LAD_80


title: Human neurons, biological rep2

source_name: 85 NPC-NEU miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL

label_protocol: FlashTag Biotin HSR labeling was performed according to the Genisphere protocol from 200ng total RNA (Genisphere Technical Support).


title: Lung_CD11b_MAC_1

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description: Healthy donor,Mus Musculus,Lung,Dendritic Cell,CD45+, GR1-, SSClow, CD11c+, MHCII+, CD11b+, CD24-,total RNA,biotin, cy3

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised according using the Quantile Normalization method within the LUMI package in R/Bioconductor v2.12.2.

label: biotin, cy3

source_name: Healthy donor

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis

extract_protocol: Total cellular RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion Inc, Austin, TX, USA) and prepared for microarray (Illumina Mouse WG6, Illumina Inc, San Diego, CA, USA) according to manufacturer’s instructions.

value: Lung

value: Dendritic Cell

tag: cell subtype

value: male

tag: genotype/variation

value: Wildtype


title: Human neurons, biological rep3

hyb_protocol: Hybridization was performed according to the affymetrix protocol. GeneChips were washed and stained in the Affymetrix Gene chip system

source_name: 90 NPC-NEU miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL


title: Human neural progenitor cells, biological rep2

description: miRNA expression data from neural progenitor cells

data_processing: The data were analyzed using the Partek Genomics Suite and probe sets mapped to genes using the database for annotation.

source_name: 85 NPC miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL

treatment_protocol: Dissociated fetal tissue is placed in neural progentior media for 1 week to give rise to neurospheres or neural progenitor cells (NPCs).

value: neural progenitor cells


title: Lung_CD11b_DC_2

description: Healthy donor,Mus Musculus,Lung,Dendritic Cell,CD45+, GR1-, SSClow, CD11c+, MHCII+, CD11b+, CD24+,total RNA,biotin, cy3

scan_protocol: According to beadchip array manufacturer's protocol


title: Lean_Thoracic aorta_80

source_name: Whole artery, Thoracic aorta, Lean pig

value: Whole artery

tag: condition

tag: artery type

value: Thoracic aorta


title: Lung_CD11b_DC_3

value: CD45+, GR1-, SSClow, CD11c+, MHCII+, CD11b+, CD24+


title: Lung_CD11b_MAC_3

value: CD45+, GR1-, SSClow, CD11c+, MHCII+, CD11b+, CD24-


title: Obese_Thoracic aorta_57

source_name: Whole artery, Thoracic aorta, Obese pig

value: Obese

tag: pigid

tag: chipid


title: Lean_LAD-PVAT_63

value: adipose tissue

value: Lean

value: LAD-PVAT

tag: date of sacrifice

tag: date of microarray experiment


title: Lean_LAD-PVAT_80

tag: tissue


title: Human neural progenitor cells, biological rep3

source_name: 90 NPC miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL


title: Lean_LAD-PVAT_73


title: Obese_LAD_57

value: LAD


title: Lung_CD11b_MAC_2

tag: strain


title: Lean_Thoracic aorta_73


title: Human neural progenitor cells, biological rep1

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

source_name: 84 NPC miRNA 4-23-10_(miRNA-1_0_2Xgain).CEL

extract_protocol: NPCs were placed in differentiation media for 2-3weeks  to differentiate into neurons.

value: Fetal brain source tissue


title: Obese_LAD-PVAT_57

source_name: adipose tissue, LAD-PVAT, Obese pig

tag: adipose type


title: MWCNT 48 h w/o IL-13 54__72

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

hyb_protocol: The labeled cRNA was fragmented, hybridized to Affymetrix Human Genome U133A 2.0 arrays (Affymetrix, Santa Clara, CA), and stained using phycoerythreinconjugated streptavidin (Molecular Probes, Eugene, OR).

scan_protocol: Affymetrix Standard Protocol

data_processing: Data analysis: Affymetrix Cel files produced from the expression experiment were analyzed using JMP Genomics 4.1 software from SAS Institute. Data normalization was performed using a Standard Normalization implemented by the Data Standardize AP in JMP Genomics.  Expression values were standardized to the mean with a scale equivalent to the standard deviation.

source_name: AT CC16Lu

label_protocol: stranded cDNA was synthesized from RNA using an oligo-dT24-T7. Biotinylated cRNA was synthesized from an aliquot of the cDNA template using the T7 RNA Transcript Labeling Kit (ENZO Diagnostics, Farmingdale NY).

growth_protocol: A separate, frozen stock was used for each experiment. Individual stocks were thawed and expanded by growth in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and antibiotic-antimycotic (Invitrogen, Carlsbad, CA).  Cells were passaged twice in 175 cm2 flasks, liberated with trypsin-EDTA, and seeded in 100 cm2 plates with 0.5-1x105 cells per plate.  Cells were grown to confluence and culture medium replaced with a serum-free defined medium (SFDM) comprised of Ham’s F12, 0.25% BSA, 1 g/L insulin, 0.55 g/L transferrin, 0.67 mg/L sodium selenite and antibiotic-antimycotic 24 h prior to treatment.

extract_protocol: A two-phase purification method was used to isolate mRNA with reduced nanoparticle contamination. RNALater® was removed by centrifugation and washing with DPBS.  RNA was isolated by adding 1 ml RNA STAT-60 reagent (Sigma-Alrich, St. Louis, MO) to microfuge tubes for 5-10 min, extraction with 0.2 ml chloroform, and isolation of the aqueous phase.  The majority of remaining MWCNT and CBNP were effectively trapped in the phenol/chloroform phase or were co-precipitated with denatured proteins.  The clear aqueous phase was isolated and RNA precipitated with isopropanol and washed with 70% ethanol.  The resulting pellet was resuspended in 100 µl RNAse-free water and 350 µl of buffer RLT added prior to transferring to an RNEasy spin column.  Purification then proceeded according to the manufacturer’s instructions for the RNEasy Mini Kit and included an on-column DNAse I digestion (Qiagen, Valencia, CA).  RNA quality verified spectrophotometrically on a Nano Drop 1000 (Nano Drop, Inc., Wilmonton, DE) and by gel electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell line

tag: treatment

value: MWCNT w/o IL-13

tag: time


title: Obese_Thoracic aorta_55


title: MWCNT 48 h with IL-13 53__71

value: MWCNT with IL-13


title: Obese_LAD_55


title: Obese_LAD-PVAT_55


title: Lean_LAD-PVAT_56

source_name: adipose tissue, LAD-PVAT, Lean pig


title: vehicle control 48 h with IL-13 49__67

value: vehicle control with IL-13


title: MWCNT 24 h w/o IL-13 48__66


title: MWCNT 24 h with IL-13 47__65


title: Lean_LAD-PVAT_48


title: Lean_LAD_48

source_name: Whole artery, LAD, Lean pig


title: CBNP 48 h with IL-13 51__69

value: CBNP with IL-13


title: vehicle control 48 h w/o IL-13 50__68

value: vehicle control w/o IL-13


title: Lean_LAD_56


title: Obese_Thoracic aorta_81


title: Lean_Thoracic aorta_56


title: Lean_Thoracic aorta_48


title: vehicle control 24 h with IL-13 43__61


title: Obese_LAD-PVAT_51


title: CBNP 24 h w/o IL-13 46__64

value: CBNP w/o IL-13


title: Obese_Thoracic aorta_51


title: MWCNT 4 h w/o IL-13 42__60

value: 4 h


title: Obese_LAD_51

value: Whole artery


title: CBNP 48 h w/o IL-13 52__70


title: CBNP 24 h with IL-13 45__63


title: Lung_CD11b_DC_1

value: Lung

value: Dendritic Cell

tag: gender

value: male

value: Wildtype


title: MWCNT 4 h with IL-13 41__59


title: vehicle control 24 h w/o IL-13 44__62


title: Lean_LAD_63


title: CBNP 4 h w/o IL-13 40__58


title: vehicle control 4 h w/o IL-13 38__56r


title: vehicle control 48 h with IL-13 31__49