title: macrophages, patient 67, responder

status: Public on Jul 29 2010

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

description:
20H G_67

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.

hyb_protocol: 750ng of biotinylated cRNA was hybridized onto the HumanRef-8 Expression BeadChips according to the manufacturer's specifications.

scan_protocol: According to the manufacturer, performed by ServiceXS (http://www.servicexs.com).

data_processing: Gene expression analysis was performed by using Illumina's Beadstudio v3 software, followed by a quantile inter-array normalization (R, Bioconductor).

source_name: monocyte-derived macrophages, responder

label_protocol: Default in vitro transcription to produced Biotinylated antisense aRNA by using the Illumina Totalprep RNA amplification kit (#IL1791, Ambion).

growth_protocol: See online data supplement: Pubmed ID 18420941.

extract_protocol: mRNA was extracted from 10 and 10 patients from the extreme ends of the spectrum (very high vs. very low CFI), by using Trizol (Invitrogen) with an RNEasy Micro column cleanup (Qiagen), who were matched for age, sex, medication and other factors that influence collateral artery growth.

treatment_protocol: Subsequently, monocytes were negatively isolated using immunomagnetic beads for stimulation with 10ng/ml LPS for 20h.

tag: race

value: Caucasian

value: blood

tag: cell type

value: CD14+ monocyte-derived macrophages

tag: disease

value: chronic coronary occlusion

tag: collateral flow response

value: sufficient


title: Spleen-control

status: Public on Jul 30 2010

type: RNA

city: New Haven

first: Pramod

middle: K

last: Mistry

state: CT

address: 333 Cedar Street

department: Pediatrics

country: USA

institute: Yale University

description: normal spleen tissue

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomic Suite software v7.3. GC-RMA normalization was applied to normalize gene level intensity.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Spleen-control

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Livers and spleens were remove from euthanized mice and acutely frozen on dry ice and subsequently stored in -80C freever.

extract_protocol: Qiagen lipid mini tissue kit was used for the Total RNA extraction

tag: strain

value: mixed 129svj and C57 BL/6 background

tag: tissue

value: spleen

tag: disease status

value: control


title: macrophages, patient 95, responder

description:
20H G_95

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.

label: Biotin

organism: Homo sapiens


title: H9_feeder_d0-A [miRNA]

city: San Diego

first: Andrew

last: Hinton

state: CA

address: 3525 John Hopkins Ct.

institute: UC, San Diego

description: miRNA expression data from hESCs differentiated 4 days

hyb_protocol: Hybridization, washing, staining, imaging and signal extraction were performed according to Affymetrix-recommended procedures, excet that the 20X GeneChip Eikaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Affymetrix GeneChip® 3000 7G scanner

data_processing: The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization methods described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.  For statistical hypothesis testing, a two-sample t-Test, with assumption of equal variance, was applied.  One-way ANOVA was used for experimental designs with more than two experimental groupings or levels of the same factor.  These tests define which probes are considered to be significantly differentially expressed, or significant, based on a default p-value of 0.001 and log2 difference > 1.

source_name: H9 cells, day 4 of differentiation  (DE)

label_protocol: The 3' ends of the RNA molecules were tailed and biotin-labeled using the mirVana miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit's dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

growth_protocol: H9 were plated on feeder layer of mouse embryonic fibroblasts (MEFs) and grown in DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 10ng/mL activin A

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits

treatment_protocol: For differentiation, growth medium was replaced with RPMI with 0% serum, 100ng/mL activin A and 25 ng/mL Wnt3A for 1 day, followed by RPMI with 0.2% serum and 100ng/mL Activin A for 2 days, followed by RPMI with 2% serum and 100ng/mL Activin A for 1 days.

tag: cell line

value: H9 human embryonic stem cell line

tag: growth protocol

value: feeder layer

tag: time

value: 4 days


title: macrophages, patient 84, responder

description:
20H G_84

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 80, responder

description:
20H G_80

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 83, responder

description:
20H G_83

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 91, responder

description:
20H G_91

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 90, nonresponder

description:
20H B_90

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.

value: insufficient


title: macrophages, patient 72, responder

description:
20H G_72

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 89, nonresponder

description:
20H B_89

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 88, responder

description:
20H G_88

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 73, nonresponder

description:
20H B_73

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 81, responder

description:
20H G_81

CD14+ monocyte-derived macrophages from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 87, nonresponder

description:
20H B_87

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 82, nonresponder

description:
20H B_82

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 91, responder

description:
CD14 G_91

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.

source_name: unstimulated monocytes, responder

treatment_protocol: Subsequently, monocytes were negatively isolated using immunomagnetic beads.

value: CD14+ monocytes


title: CD14+ monocytes, patient 95, responder

description:
CD14 G_95

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 71, nonresponder

description:
20H B_71

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 55, nonresponder

description:
20H B_55

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 69, nonresponder

description:
20H B_69

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 81, responder

description:
CD14 G_81

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: macrophages, patient 85, nonresponder

description:
20H B_85

CD14+ monocyte-derived macrophages from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 88, responder

description:
CD14 G_88

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 77, responder

description:
CD14 G_77

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 80, responder

description:
CD14 G_80

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: Cyt49_feeder-free_d4-B [miRNA]

description: miRNA expression data from hESCs differentiated 4 days

source_name: Cyt49 cells, day 4 of differentiation  (DE)

growth_protocol: Cyt49 were plated on BD matrigel and cultured MEF conditioned medium, containing DMEM/F12 supplemented with 20% knockout serum replacement, 4 ng/mL basic FGF, and 10ng/mL activin A

value: Cyt49 human embryonic stem cell line

value: feeder-free conditions


title: CD14+ monocytes, patient 83, responder

description:
CD14 G_83

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 84, responder

description:
CD14 G_84

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 89, nonresponder

description:
CD14 B_89

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.

source_name: unstimulated monocytes, nonresponder


title: CD14+ monocytes, patient 67, responder

description:
CD14 G_67

CD14+ monocytes derived from a responder patient, with a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 72, responder

description:
CD14 G_72

CD14+ monocytes derived from a responder patient, a collateral flow index (CFI) >0.37. Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 85, nonresponder

description:
CD14 B_85

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 92, nonresponder

description:
CD14 B_92

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 82, nonresponder

description:
CD14 B_82

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 71, nonresponder

description:
CD14 B_71

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 90, nonresponder

description:
CD14 B_90

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 69, nonresponder

description:
CD14 B_69

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 73, nonresponder

description:
CD14 B_73

CD14+ monocytes derived from a nonresponder patient, a collateral flow index (CFI≤0.37). Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: CD14+ monocytes, patient 55, nonresponder

description:
CD14 B_55

Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group). Mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation.


title: Diaphragm_female_High feeding level_animal6

city: Madrid

first: Ana

middle: I

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

description:
Diaphragm 21
Diaphragm sample at 211 days, female, high.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GCOS.

data_processing: Bioconductor, GCRMA.

organism: Sus scrofa

source_name: Diaphragm, 211 days, female, high

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

growth_protocol: Pigs were fed twice daily with the same pelleted diet until feeding restriction treatment.

extract_protocol: RiboPure RNA isolation kit.

treatment_protocol: Diaphragm and Psoas major muscles were maintained at -80ºC.

tag: breed

value: Iberian

tag: gender

value: female

tag: age

value: 211 days

value: diaphragm

tag: diet

value: high level


title: PS_3rd_Quarter_3

city: Kobe

first: Guojun

last: Sheng

state: Hyogo

address: 2-2-3, Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
Pooled samples collected at every 4 hours over 1 day
C3

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm.

organism: Gallus gallus

source_name: Third Quarter of Primitive Streak

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

growth_protocol: Fertilized hens’ eggs were purchased from Shiroyama farm (Kanagawa, Japan) and fresh eggs were incubated without storage at 38.5°C for about 18 hours to reach stage HH4.

extract_protocol: Total RNAs were isolated using Qiagen RNAeasy kit. RNA concentrations were measured and equalized, and RNA quality was checked on gel. 5 ug of total RNA were used for each array.

treatment_protocol: Embryos were collected in Pannett-Compton solution. Only embryos of HH4- and HH4 stages were used for streak dissection. The entire streak was cut out first, and was further cut into four equal pieces along its A/P length. Collected pieces were frozen in liquid nitrogen after pooling about 10 pieces, and about 90 pieces were combined later on to be used for RNA isolation as one sample. The numbering of samples corresponds to the original embryo/streak pool (e.g., A1, B1, C1 and D1 were derived from the same 85 streaks).

tag: sample

value: Primitive Streak Tissue

tag: tissue region

value: Third Quarter

tag: developmental stage

value: Embryonic Stage HH4


title: PS_4th_Quarter_1

description:
Pooled samples collected at every 4 hours over 1 day
D1

source_name: Fourth Quarter of Primitive Streak (most posterior)

value: Fourth Quarter


title: PS_3rd_Quarter_2

description:
Pooled samples collected at every 4 hours over 1 day
C2


title: PS_4th_Quarter_2

description:
Pooled samples collected at every 4 hours over 1 day
D2


title: PS_4th_Quarter_3

description:
Pooled samples collected at every 4 hours over 1 day
D3


title: PS_3rd_Quarter_1

description:
Pooled samples collected at every 4 hours over 1 day
C1


title: PS_1st_Quarter_2

description:
Pooled samples collected at every 4 hours over 1 day
A2

source_name: First Quarter of Primitive Streak (most anterior)

value: First Quarter


title: PS_1st_Quarter_1

description:
Pooled samples collected at every 4 hours over 1 day
A1


title: PS_1st_Quarter_3

description:
Pooled samples collected at every 4 hours over 1 day
A3


title: PS_2nd_Quarter_3

description:
Pooled samples collected at every 4 hours over 1 day
B3

source_name: Second Quarter of Primitive Streak

value: Second Quarter


title: PS_2nd_Quarter_2

description:
Pooled samples collected at every 4 hours over 1 day
B2


title: aERKO V vs BPA 2hr

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
US22502532_251486813435_S02_H.tif
US22502532_251486813435__S02_L.tif
gene expression in aERKO ovariectomized oil vehicle vs BPA 2h treated uterus

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.1), using defaults for all parameters. The default setting for the protocol we used is polynomial data fit.

source_name: aERKO uterus sesame oil V

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA  and Cy5 labeled cRNA were produced according to manufacturer’s protocol.

extract_protocol: pools of 3 frozen uteri were pulverized and homogenized in Trizol (Invitrogen 5- 100 mg tissue/ml Trizol, minimum 800 ul) . Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

treatment_protocol: ovariectomized mice were allowed to rest for 10-14 days, then injected with saline or 250ng estradiol, 100 ul sesame oil or 750 ug BPA or HPTE in 100 ul oil ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

tag: esr1 genotype

value: aERKO (Esr1 null)

value: adult (10+ weeks)

value: ovariectomized female

source_name: aERKO uterus sesame oil BPA 2h


title: aERKO BPA 24hr vs V

description:
US22502532_251486813438_S01_H.tif
US22502532_251486813438__S01_L.tif
gene expression in aERKO ovariectomized oil vehicle vs BPA 24h treated uterus

source_name: aERKO uterus sesame oil BPA 24h


title: PS_2nd_Quarter_1

description:
Pooled samples collected at every 4 hours over 1 day
B1


title: aERKO HPTE 24hr vs V

description:
US22502532_251486813439_S01_H.tif
US22502532_251486813439__S01_L.tif
gene expression in aERKO ovariectomized oil vehicle vs HPTE 24h treated uterus

source_name: aERKO uterus sesame oil HPTE 24h


title: aERKO HPTE 2hr vs V

description:
US22502532_251486813439_S01_H.tif
US22502532_251486813439__S01_L.tif
gene expression in aERKO ovariectomized oil vehicle vs HPTE 2h treated uterus

source_name: aERKO uterus sesame oil HPTE 2h


title: aERKO V vs BPA 24hr

description:
US22502532_251486813435_S02_H.tif
US22502532_251486813435__S02_L.tif
gene expression in aERKO ovariectomized oil vehicle vs BPA 24h treated uterus


title: KIKO HPTE 2hr vs V

description:
US22502532_251486814898_S01_H.tif
US22502532_251486814898__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs HPTE 2h treated uterus

source_name: KIKO uterus sesame oil HPTE 2h

value: KIKO (DNA binding deficient)

source_name: KIKO uterus sesame oil V


title: KIKO BPA 24hr vs V

description:
US22502532_251486814898_S01_H.tif
US22502532_251486814898__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs BPA 24h treated uterus

source_name: KIKO uterus sesame oil BPA 24h


title: KIKO V vs HPTE 24hr

description:
US22502532_251486814897_S01_H.tif
US22502532_251486814897__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs HPTE 24h treated uterus

source_name: KIKO uterus sesame oil HPTE 24h


title: KIKO BPA 2hr vs V

description:
US22502532_251486814898_S01_H.tif
US22502532_251486814898__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs BPA 2h treated uterus

source_name: KIKO uterus sesame oil BPA 2h


title: KIKO V vs BPA 24hr

description:
US22502532_251486814897_S01_H.tif
US22502532_251486814897__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs BPA 24h treated uterus


title: KIKO HPTE 24hr vs V

description:
US22502532_251486814898_S01_H.tif
US22502532_251486814898__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs HPTE 24h treated uterus


title: aERKO BPA 2hr vs V

description:
US22502532_251486813438_S01_H.tif
US22502532_251486813438__S01_L.tif
gene expression in aERKO ovariectomized oil vehicle vs BPA 2h treated uterus


title: KIKO V vs HPTE 2hr

description:
US22502532_251486814897_S01_H.tif
US22502532_251486814897__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs HPTE 2h treated uterus


title: KIKO V vs BPA 2hr

description:
US22502532_251486814897_S01_H.tif
US22502532_251486814897__S01_L.tif
gene expression in KIKO ovariectomized oil vehicle vs BPA 2h treated uterus


title: aERKO V vs HPTE 2hr

description:
US22502532_251486813435_S02_H.tif
US22502532_251486813435__S02_L.tif
gene expression in aERKO ovariectomized oil vehicle vs HPTE 2h treated uterus


title: WT BPA 2hr vs V

description:
US22502532_251486813436_S02_H.tif
US22502532_251486813436__S02_L.tif
gene expression in WT ovariectomized oil vehicle vs BPA 2h treated uterus

source_name: WT uterus sesame oil BPA 2h

value: WT

source_name: WT uterus sesame oil V


title: WT BPA 24hr vs V

description:
US22502532_251486813436_S02_H.tif
US22502532_251486813436__S02_L.tif
gene expression in WT ovariectomized oil vehicle vs BPA 24h treated uterus

source_name: WT uterus sesame oil BPA 24h


title: WT V vs BPA 24hr

description:
US22502532_251486813434_S01_H.tif
US22502532_251486813434__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs BPA 24h treated uterus


title: WT HPTE 2hr vs V

description:
US22502532_251486813438_S01_H.tif
US22502532_251486813438__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs HPTE 2h treated uterus

source_name: WT uterus sesame oil HPTE 2h


title: Tumor 1826

type: genomic

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

description: DNA (bisulfite modified)

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

data_processing: Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.

molecule: genomic DNA

source_name: DNA

label_protocol: sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)

value: fresh frozen breast tumor


title: WT HPTE 24hr vs V

description:
US22502532_251486813438_S01_H.tif
US22502532_251486813438__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs HPTE 24h treated uterus

source_name: WT uterus sesame oil HPTE 24h


title: WT V vs BPA 2hr

description:
US22502532_251486813434_S01_H.tif
US22502532_251486813434__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs BPA 2h treated uterus


title: WT V vs HPTE 24hr

description:
US22502532_251486813434_S01_H.tif
US22502532_251486813434__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs HPTE 24h treated uterus


title: WT V vs HPTE 2hr

description:
US22502532_251486813434_S01_H.tif
US22502532_251486813434__S01_L.tif
gene expression in WT ovariectomized oil vehicle vs HPTE 2h treated uterus


title: Tumor 1815

description: DNA (bisulfite modified)

scan_protocol: Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.


title: Tumor 1807

description: DNA (bisulfite modified)


title: Tumor 1806

description: DNA (bisulfite modified)


title: Tumor 1775

description: DNA (bisulfite modified)


title: Tumor 1742

description: DNA (bisulfite modified)


title: Tumor 1772

description: DNA (bisulfite modified)


title: Tumor 1758

description: DNA (bisulfite modified)


title: Tumor 1681

description: DNA (bisulfite modified)


title: Tumor 1701

description: DNA (bisulfite modified)


title: Tumor 1678

description: DNA (bisulfite modified)


title: Tumor 1663

description: DNA (bisulfite modified)


title: Tumor 1694

description: DNA (bisulfite modified)


title: Tumor 1659

description: DNA (bisulfite modified)


title: Tumor 1647

description: DNA (bisulfite modified)


title: Lung_PAHmodel_2

city: Tokyo

first: kayoko

last: shimodaira

address: 6-11-1 Omorinishi, Ota-ku

institute: Toho University School of Medicine

description:
Gene expression data of the murine lung after repeated intratracheal injection of Stachybotrys chartarum.
05_E2_No_1071_(Mouse430_2)

hyb_protocol: Following fragmentation, 12.5 μg of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix). The array was incubated for 16 hr at 45°C, then automatically washed and stained with GeneChip(R) Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix GeneChip® Command Console AGCC Software and performed log base 2 transformation.

source_name: Lung tissue specimens from PAH model mouse

growth_protocol: spores of Stachybotrys chartarum and RPMI-1640 medium

extract_protocol: RNA targets preparation were performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix).

value: ddY

value: male

value: Six-weeks-old

value: Lung

tag: agent

value: Stachybotrys chartarum spores

tag: disease state

value: PAH model


title: Lung_control_3

description:
Gene expression data of the murine lung after repeated intratracheal injection of RPMI-1636 medium only, as control mouse.
03_C3_No_1071_(Mouse430_2)

source_name: Lung tissue specimens from normal control mouse

growth_protocol: RPMI-1640 medium

value: control


title: Lung_PAHmodel_1

description:
Gene expression data of the murine lung after repeated intratracheal injection of Stachybotrys chartarum.
04_E1_No_1071_(Mouse430_2)


title: Lung_control_2

description:
Gene expression data of the murine lung after repeated intratracheal injection of RPMI-1636 medium only, as control mouse.
02_C2_No_1071_(Mouse430_2)


title: Lung_PAHmodel_3

description:
Gene expression data of the murine lung after repeated intratracheal injection of Stachybotrys chartarum.
06_E3_No_1071_(Mouse430_2)


title: Lung_control_1

description:
Gene expression data of the murine lung after repeated intratracheal injection of RPMI-1636 medium only, as control mouse.
01_C1_No_1071_(Mouse430_2)


title: Tumor 1567

description: DNA (bisulfite modified)


title: Tumor 1579

description: DNA (bisulfite modified)


title: Tumor 1562

description: DNA (bisulfite modified)


title: Tumor 1553

description: DNA (bisulfite modified)


title: Tumor 1593

description: DNA (bisulfite modified)


title: Tumor 1482

description: DNA (bisulfite modified)


title: Tumor 1536

description: DNA (bisulfite modified)


title: Tumor 1487

description: DNA (bisulfite modified)


title: Tumor 1522

description: DNA (bisulfite modified)


title: Tumor 1474

description: DNA (bisulfite modified)


title: Tumor 1467

description: DNA (bisulfite modified)


title: Tumor 1531

description: DNA (bisulfite modified)


title: Tumor 1458

description: DNA (bisulfite modified)


title: Tumor 1493

description: DNA (bisulfite modified)


title: Tumor 1466

description: DNA (bisulfite modified)


title: Tumor 1456

description: DNA (bisulfite modified)


title: Tumor 1434

description: DNA (bisulfite modified)


title: Tumor 1413

description: DNA (bisulfite modified)


title: Tumor 1319

description: DNA (bisulfite modified)


title: Tumor 1297

description: DNA (bisulfite modified)


title: Tumor 1323

description: DNA (bisulfite modified)


title: Tumor 1258

description: DNA (bisulfite modified)


title: Tumor 1249

description: DNA (bisulfite modified)


title: Tumor 1149

description: DNA (bisulfite modified)


title: Tumor 1156

description: DNA (bisulfite modified)


title: Tumor 1228

description: DNA (bisulfite modified)


title: Tumor 1421

description: DNA (bisulfite modified)


title: Tumor 1422

description: DNA (bisulfite modified)


title: Tumor 1135

description: DNA (bisulfite modified)


title: Tumor 1134

description: DNA (bisulfite modified)


title: Tumor 1404

description: DNA (bisulfite modified)


title: Tumor 991

description: DNA (bisulfite modified)


title: Tumor 966

description: DNA (bisulfite modified)


title: Tumor 1097

description: DNA (bisulfite modified)


title: Tumor 1088

description: DNA (bisulfite modified)


title: Tumor 1142

description: DNA (bisulfite modified)


title: Tumor 940

description: DNA (bisulfite modified)


title: Tumor 934

description: DNA (bisulfite modified)


title: Tumor 956

description: DNA (bisulfite modified)


title: Tumor 965

description: DNA (bisulfite modified)


title: Tumor 997

description: DNA (bisulfite modified)


title: Tumor 1060

description: DNA (bisulfite modified)


title: Tumor 1055

description: DNA (bisulfite modified)


title: Tumor 1042

description: DNA (bisulfite modified)


title: Tumor 1052

description: DNA (bisulfite modified)


title: Tumor 1076

description: DNA (bisulfite modified)


title: Tumor 890

description: DNA (bisulfite modified)


title: Tumor 924

description: DNA (bisulfite modified)


title: Tumor 898

description: DNA (bisulfite modified)


title: Tumor 888

description: DNA (bisulfite modified)


title: Tumor 1033

description: DNA (bisulfite modified)


title: Tumor 1041

description: DNA (bisulfite modified)


title: Tumor 885

description: DNA (bisulfite modified)


title: Tumor 946

description: DNA (bisulfite modified)


title: Tumor 870

description: DNA (bisulfite modified)


title: Tumor 867

description: DNA (bisulfite modified)


title: Tumor 935

description: DNA (bisulfite modified)


title: Tumor 835

description: DNA (bisulfite modified)


title: Tumor 849

description: DNA (bisulfite modified)


title: Tumor 825

description: DNA (bisulfite modified)


title: Tumor 787

description: DNA (bisulfite modified)


title: Tumor 801

description: DNA (bisulfite modified)


title: Tumor 757

description: DNA (bisulfite modified)


title: Tumor 762

description: DNA (bisulfite modified)


title: Tumor 721

description: DNA (bisulfite modified)


title: Tumor 751

description: DNA (bisulfite modified)


title: Tumor 780

description: DNA (bisulfite modified)


title: aERKO V vs HPTE 24hr

description:
US22502532_251486813435_S02_H.tif
US22502532_251486813435__S02_L.tif
gene expression in aERKO ovariectomized oil vehicle vs HPTE 24h treated uterus

source_name: aERKO uterus sesame oil V


title: Tumor 784

description: DNA (bisulfite modified)


title: Tumor 688

description: DNA (bisulfite modified)


title: Tumor 755

description: DNA (bisulfite modified)


title: Tumor 782

description: DNA (bisulfite modified)


title: Tumor 802

description: DNA (bisulfite modified)


title: Tumor 637

description: DNA (bisulfite modified)


title: Tumor 636

description: DNA (bisulfite modified)


title: Tumor 634

description: DNA (bisulfite modified)


title: Tumor 753

description: DNA (bisulfite modified)


title: Tumor 625

description: DNA (bisulfite modified)


title: Tumor 620

description: DNA (bisulfite modified)


title: Tumor 627

description: DNA (bisulfite modified)


title: Tumor 626

description: DNA (bisulfite modified)


title: Tumor 666

description: DNA (bisulfite modified)


title: Tumor 618

description: DNA (bisulfite modified)


title: Tumor 566

description: DNA (bisulfite modified)


title: Tumor 567

description: DNA (bisulfite modified)


title: Tumor 584

description: DNA (bisulfite modified)


title: Tumor 612

description: DNA (bisulfite modified)


title: Tumor 614

description: DNA (bisulfite modified)


title: Tumor 583

description: DNA (bisulfite modified)


title: Tumor 609

description: DNA (bisulfite modified)


title: Tumor 553

description: DNA (bisulfite modified)


title: Tumor 540

description: DNA (bisulfite modified)


title: Tumor 516

description: DNA (bisulfite modified)


title: Tumor 633

description: DNA (bisulfite modified)


title: Tumor 510

description: DNA (bisulfite modified)


title: Tumor 498

description: DNA (bisulfite modified)


title: Tumor 556

description: DNA (bisulfite modified)


title: Tumor 1526

description: DNA (bisulfite modified)


title: mCG-PR+/-RARA+/- ,biological rep5

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were then hybridized to Mouse Exon 1.0ST arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Gene chips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: spleen

label_protocol: Amplified cDNA was biotin labeled using the EncoreTM Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer’s instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA).Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

value: mCG-PR+/- x RARA+/-


title: mCG-PR+/-RARA+/+ ,biological rep1

value: mCG-PR+/- x RARA+/+


title: mCG-PR+/-RARA+/+ ,biological rep2


title: mCG-PR+/-RARA+/- ,biological rep3


title: mCG-PR+/-RARA+/- ,biological rep4


title: mCG-PR+/-RARA+/+ ,biological rep4


title: mCG-PR+/-RARA+/- ,biological rep1


title: mCG-PR+/-RARA+/+ ,biological rep3


title: Tumor 1566

description: DNA (bisulfite modified)


title: mCG-PR+/-RARA+/+ ,biological rep5


title: Tumor 493

description: DNA (bisulfite modified)


title: Tumor 487

description: DNA (bisulfite modified)


title: CD133-  CNC1_rep2

city: shanghai

first: Jian-Ming

last: Feng

address: zuzhongzhi Road

country: China

institute: Shanghai institute of Materia Medica

description: The clonal cells were propagated as SW620 cells

scan_protocol: Standard Affymetrix protocol.

data_processing:
affymetrix-algorithm-name = rma
program-name = Expression Console

label_protocol: Standard Affymetrix protocol.

growth_protocol: The cells were incubated in Leibovitz's L-15 medium supplemented with 10% fatal bovine serum , 100 µg/ml penicillin and 100 µg/ml streptomycin at 37℃ under 100% air.

extract_protocol: The total RNA of the purified  cells was extracted by using the miRNeasy kit (Qiagen, Valencia, CA) according to manufacturer's instructions.

treatment_protocol: Human colon cancer SW620 cell line from American Type Culture Collection (ATCC,CCL_227) were sorted by using the Miltenyi Biotech CD133 Cell Isolation Kit in accordance with manufacturer’s instructions.The single cells were plated and selected as clone cells. The expanded clone cells were further purified by the Miltenyi Biotech CD133 Cell Isolation Kit before microarray assays.

value: colon cancer SW620 cell line

tag: cd133 status


title: Tumor 495

description: DNA (bisulfite modified)


title: CD133-  CNC1_rep1

source_name: Human colon cancer SW620 cell line from American Type Culture Collection (ATCC,CCL_227)


title: CD133+ CPC1_rep2


title: Tumor 491

description: DNA (bisulfite modified)


title: Tumor 470

description: DNA (bisulfite modified)


title: mCG-PR+/-RARA+/- ,biological rep2

tag: strain


title: Tumor 442

description: DNA (bisulfite modified)

tag: tissue


title: Tumor 475

description: DNA (bisulfite modified)


title: Tumor 432

description: DNA (bisulfite modified)


title: Tumor 425

description: DNA (bisulfite modified)


title: Tumor 419

description: DNA (bisulfite modified)


title: Tumor 387

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 5_24 hours_rep 4

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

hyb_protocol: Aliquots of the purified Cy3 and Cy5-labelled samples to be hybridized to the same array were combined such that the final concentration of each dye in the labelled target in the hybridization buffer would be 0.8 pmol/µl. A 4µl volume of ‘Porcine Hybloc’ (Applied Genetic Laboratories) (1 µg/µl) or 10 µl of Human cot-1 DNA (Invitrogen) (1 µg/µl), 1µl of poly dA (8 µg/µl) and 1 µl of yeast tRNA (4 µg/µl) were then added to block non-specific binding of repetitive sequences in the target to the probe sequences on the microarray during hybridization. Next, the sample volume was adjusted to 100 µl using nuclease-free water, and 10µl of 3 M sodium acetate (pH 4.8) and 250 µl of 100% ethanol were added. The mixture was mixed by inversion and the DNA was precipitated by incubation at -80 ºC for 30 minutes followed by centrifugation at 13,000 x G for 20 minutes at 4 ºC. The supernatant was discarded and 500 µl of 70 % ethanol was added. The pellet was washed by vortex then centrifuged at 13,000 G for 5 minutes. The pellet was air-dried for 5 minutes then re-suspended in 50 µl of ‘OpArray Hyb Buffer’. Re-suspension was aided by heating at 65 ºC for 5 minutes, followed by vortex mixing and brief centrifugation.  The ‘target’ DNA was denatured by incubation at 65 ºC for 5 minutes. A 25 x 60 mm ‘Lifterslip’ (Thomas Scientific) was placed over the microarray portion of the slide. The denatured DNA was then applied slowly to the bottom edge of the Lifterslip, from where it was drawn over the array surface by capillary action. The microarray was placed in a Hybridization cassette (Telechem) containing 15 µl of ‘Milli Q’ water in each of its wells. The cassette was sealed and placed on a horizontal surface in a waterbath. The target DNA was hybridized to the microarray at 42 ºC for 15 hours in the dark. After hybridization, each microarray was removed from the hybridization cassette and washed in a slide tray containing Operon Wash Buffer 2 solution at 42 ºC for 10 minutes. They were then transferred to a slide tray containing Operon Wash Buffer 3 and washed for 10 minutes at room temperature. Finally, they were washed twice in Operon Wash Buffer 4 for 5 minutes and dried by centrifugation in at 200xg for 5 minutes. They microarrays were stored in light tight boxes and scanned on the same day.

scan_protocol: The hybridization signal on each microarray was detected by laser induced fluorescence of the Cy3 and Cy5 labelled ‘target’ molecules bound to the individual probe oligonucleotides. The microarrays were scanned using a ‘GenePix 4100A’ scanner (Axon instruments) containing a 532 nm laser and a 635 nm laser, the wavelengths that correspond to the excitation wavelengths of Cy3 and Cy5 respectively. Scan settings were adjusted and scans performed using ‘GenePix Pro version 4.1’ software.    First, each microarray was scanned at a resolution of 40 µm in both the Cy3 and Cy5 channels to determine quickly whether the hybridizations were successful and to identify the area corresponding to the central 8 subgrids on the microarray. This area was then scanned in both the Cy3 and Cy5 channels at a resolution of 5 µm. The photo multiplier tube (PMT) gain settings were adjusted during the scan to ensure that:     • The complete dynamic range of the scanner was being utilized to capture as broad a range of signal intensities as possible.   • The total amount of signal acquired in each channel was approximately the same.    The adjusted gain settings for each channel were then used to scan the entire microarray area at a resolution of 5 µm. False colour images for each channel were saved as TIFF files.

data_processing: Hybridization signal was quantified using ‘Bluefuse’ v3.0 software (BlueGnome). The Cy3 and Cy5 TIFF images for each array, together with a ‘GenePix Array List’ (GAL) file describing the spot layout of the microarray, were loaded into the software. Grid layouts were then placed automatically by the software for each microarray, and checked by eye to ensure they were positioned correctly. The Cy3 and Cy5 signal, and the ratio of expression in the 2 channels, was then quantified. Features with irregularities affecting signal intensity were removed by manual flagging in Bluefuse v3.0. Mean signal intensities for duplicate spots were then calculated, and the data were imported into the ‘R’ based statistical analysis package ‘limma’ (linear models for microarray analysis). The data were normalized using a global Loess algorithm and the data for duplicate spots.

source_name: Lung tissue_Pool of Uninfected control animals

label_protocol: Labelled cDNA targets were prepared using a two step process. First, the target population was amplified by RT-PCR using the SMART template switching system (BD Biosciences). Second, the PCR product was labelled with Cy3 or Cy5-dCTP (GE Healthcare) using a Bioprime DNA Labelling System (Invitrogen). A 500 ng amount of total RNA was mixed with 10 pmol of 3′ SMART CDS primer IIA (5′-AAG CAG TGG TAT CAA CGC AGA GTA C-T30VN-3′) and 10 pmol template switching primer [5′-d(AAG CAG TGG TAT CAA CGC AGA GTA CGC)r(GGG)- 3′].Reverse  transcription was carried out using Powerscript (BD Biosciences). PCR was performed using the first strand cDNA as template with the following PCR primer (5′ AAG AGT GGT ATC AAC GCA GAG T-3′) and HotStar Taq (Qiagen). The conditions were: 95 ºC for 15 minutes, then 18 cycles of 94 ºC for 30 seconds, 65 ºC for 30 seconds and 68 ºC for 6 minutes. PCR products were then purified using a MinElute PCR purification kit (Qiagen).   Purified PCR product in a random primer mix was denatured at 95 ºC for 5 minutes. A low-dCTP mix (5mM dATP, dGTP, and dTTP; 2mM dCTP), Cy3 or Cy5-dCTP (1mM) (GE Healthcare) and 40 units of Klenow polymerase (Invitrogen) were added and the reactions incubated at 37 ºC for 2 hours. Labelled products were purified using Autoseq G-50 columns (GE Healthcare).

growth_protocol: A total of 200 piglets born on a commercial farm in Spain were used for a bacterial challenge experiment. The experimental infection protocol was carried out in 10 separate batches each containing 20 animals over a period of about a year. Each batch of animals contained offspring from 2 different sires; in total 6 sires were used over the 10 batches. The sires (all Landrace-Duroc cross animals) were mated with a Landrace-Large White cross dam line. At birth, piglets were collected from the mother’s birth canal without touching the floor. Their skin was then disinfected using a 2 % iodine solution and they were immediately transferred to a previously cleaned and disinfected barrier isolation unit. For the first 2 days the new-born pigs were fed bovine colostrum ad libitum every 2 hours. Over the next 13 days the piglets were fed a mixture of porridge containing protein and water. The intervals between feeds were increased and the percentage of water in the porridge mix reduced gradually over this period until by day 15 the animals were eating dry food. All piglets were treated with the antibiotic gentamicin for the first 2 days to prevent Escherichia coli (E. coli) infection. Any animals that did succumb to diarrhoea were treated further with gentamicin for 3 days (although treatment was stopped for all animals 8 days prior to challenge), and the animal and surroundings were disinfected to prevent bacteria from spreading. At day 7 nasal swabs were taken from each of the pigs and tested for H. parasuis by PCR. All the pigs were negative for presence of the bacteria at this time. The animals were 21 days old at the start of the challenge experiment.

extract_protocol: Total RNA was extracted using TriReagent (Sigma) according to the manufacturer's instructions. The RNA was then further purified using RNeasy columns (Qiagen) according to the manufacturers instructions. An on column DNase I digest was also performed. RNA quality was determined by chip electrophoresis using a Bioanalyzer in conjunction with the RNA Nano 6000 kit (Agilent). Only samples with a 28:18S rRNA ratio of >1:1 and little visible degradation were taken forward for microarray experiments.

treatment_protocol: Pigs were randomly allocated to either a control group or an infection group and kept in separate rooms. The pigs in the infection group were inoculated intra-tracheally with a 3 ml suspension of the pathogenic H. parasuis serovar 5, strain 29755, in phosphate buffered saline (PBS) containing 5 x 10^8 colony forming units (cfu) per ml. Control pigs were inoculated in the same manner with PBS alone. Of the 200 animals that started the experiment, 80.5 % of the animals were still alive at the time of challenge. This meant that 133 animals were inoculated with H. parasuis while 29 animals were designated ‘Uninfected control’ animals. The time-course of the experiment was 72 hours, containing 3 time-points at 24, 48 and 72 hours. At each time-point, 1 control animal and 4-5 challenged animals were euthanized. Pigs were monitored daily for clinical signs of disease and approximately equal numbers of pigs were euthanized at 24, 48, and 72 hours post-infection and scored semi-quantitatively for the presence and severity of lesions associated with Glasser's disease and the presence of H. parasuis by culture and PCR. The four clinical signs measured were: 1) demeanour. 2) dysponea. 3) lameness. 4) tremor. The 9 lesions assessed were: 1) pleuritis. 2) hydrothorax. 3) pericarditis. 4) hydropericardium. 5) pleuritis. 6) ascites. 7) meningitis. 8) arthritis. 9) penumonia. The six sites tested by culture and PCR were: 1) pleura. 2) pericardium. 3) peritoneum. 4) carpal joint. 5) foot joint. 6) meninges. The following tissue samples were also taken for each animal and stored in RNA Later (Ambion): lung, pericardium, carpal joint, foot joint, and meninges. The animals were classified into 4 susceptibility groups based on the extent of disease: 1) Fully Resistant. 2) Less Resistant. 3) Less Susceptible. 4) Fully Susceptible. The aim of the microarray experiment was to compare the extremes of susceptibility at early (24 hours) and late (72 hours) infection time-points. It was decided to use lung tissue to study the infection due to the intra-tracheal nature of the challenge. Consequently, 6 'Fully Resistant' animals were chosen for the experiment, and were matched by sire and time-point to 'Susceptible' animals (4 Fully Susceptible animals and 2 Less Susceptible animals). The Fully Resistant animals were negative for the presence of bacteria by culture and PCR at each of the 6 sites tested, and by RT-PCR in lung. They had clinical signs or lesion scores of no more than 1 in no more than 2 sign/lesion categories or a total clinical sign or lesion score of no more than 3. The Less susceptible animals were positive for H parasuis at 4 or fewer sites tested by culture or PCR and had a total score for clinical signs and lesions of  5 or less. The Fully Susceptible animals were positive for bacteria at 5 or more sites by culture or PCR and had total clinical sign and lesion scores of 3 or more. The scoring system is described in detail in the following paper: Blanco, I., Canals, A., Evans, G., Mellencamp, M. A., Cia, C., Deeb, N., Wang, L. and Galina-Pantoja, L., Differences in susceptibility to Haemophilus parasuis infection in pigs. Can J Vet Res 2008. 72: 228-235.

tag: sire

value: unknown

value: lung

source_name: Lung tissue_Susceptible animal 5


title: Lung tissue_Susceptible animal 6_24 hours_rep 4

source_name: Lung tissue_Susceptible animal 6


title: Lung tissue_Susceptible animal 5_24 hours_rep 3


title: Lung tissue_Susceptible animal 6_24 hours_rep 3


title: Tumor 363

description: DNA (bisulfite modified)


title: Tumor 428

description: DNA (bisulfite modified)


title: Tumor 386

description: DNA (bisulfite modified)


title: Tumor 365

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 6_24 hours_rep 2


title: CD133+ CPC1_rep1

tag: cell line


title: Lung tissue_Susceptible animal 6_24 hours_rep 1


title: Lung tissue_Susceptible animal 5_24 hours_rep 1


title: Tumor 348

description: DNA (bisulfite modified)


title: Tumor 339

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 4_72 hours_rep 2

source_name: Lung tissue_Susceptible animal 4


title: Lung tissue_Susceptible animal 5_24 hours_rep 2


title: Lung tissue_Susceptible animal 4_72 hours_rep 4


title: Tumor 336

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 4_72 hours_rep 3


title: Tumor 474

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 3_72 hours_rep 4

source_name: Lung tissue_Susceptible animal 3


title: Lung tissue_Susceptible animal 3_72 hours_rep 2


title: Lung tissue_Susceptible animal 3_72 hours_rep 1


title: Lung tissue_Susceptible animal 4_72 hours_rep 1


title: Lung tissue_Susceptible animal 2_72 hours_rep 3

source_name: Lung tissue_Susceptible animal 2


title: Lung tissue_Susceptible animal 2_72 hours_rep 4


title: Lung tissue_Susceptible animal 2_72 hours_rep 2


title: Lung tissue_Susceptible animal 3_72 hours_rep 3


title: Tumor 279

description: DNA (bisulfite modified)


title: Tumor 306

description: DNA (bisulfite modified)


title: Tumor 320

description: DNA (bisulfite modified)


title: Tumor 271

description: DNA (bisulfite modified)


title: Tumor 266

description: DNA (bisulfite modified)


title: Tumor 260

description: DNA (bisulfite modified)


title: Tumor 257

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 2_72 hours_rep 1


title: Lung tissue_Susceptible animal 1_72 hours_rep 3

source_name: Lung tissue_Susceptible animal 1


title: Lung tissue_Susceptible animal 1_72 hours_rep 2


title: Lung tissue_Susceptible animal 1_72 hours_rep 4


title: Tumor 221

description: DNA (bisulfite modified)


title: Tumor 229

description: DNA (bisulfite modified)


title: Tumor 235

description: DNA (bisulfite modified)


title: Tumor 191

description: DNA (bisulfite modified)


title: Tumor 240

description: DNA (bisulfite modified)


title: Lung tissue_Susceptible animal 1_72 hours_rep 1


title: ITS+2d_rep2

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

description: ITS treated Arabidopsis +2 days of recovery RNA chip 2

hyb_protocol: Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm

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

data_processing:
Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94
Probe-level data were pre-processed using the RMA algorithm (Irizarry et al., 2003), which involves three steps: (i) background correction – where an error component of the intensities is estimated and eliminated; (ii) quantile normalization – where every slide is normalized to have the same cumulative frequency distribution; and (iii) summarization, using the median polish algorithm – where the median values per probe set, adjusted for slide differences, are calculated. RMA ignores the MM probes. On the basis of an empirical Bayes moderated t-statistic for the contrasts (Smyth, 2004), as implemented in the Bioconductor package limma, P values were calculated and then transformed into false-discovery rates, or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue. We compared the results obtained with RMA and those obtained with a mixed-effect anova model (Wolfinger et al., 2001) as a summarization step, after background adjustment (convolution) and quantile normalization had been performed as described for RMA.
R_processed_results_file.txt is available as a supplementary file on the Series record. This file contains the expression values of wt compared to mutants (log2) and their corresponding p-value resulting from the data processing in R

organism: Arabidopsis thaliana

source_name: whole seedlings RNA

label_protocol: RNA (5-μg aliquots) was reverse transcribed using T7 oligodT (Ambion) and Superscript II (Invitrogen) and the second strand synthesised using DNA polymerase I. cDNA was then amplified using IVT (Affymetrix). The resulting cRNA was cleaned up with the GeneChip Sample Cleanup Module (Affymetrix). cRNA (7-μg aliquots) was then reverse transcribed and made double-stranded in the presence of dUTP. Following cleanup (Qiagen kit), the cDNA was fragmented and labelled using the Affymetrix kit 900812 GeneChip® WT Double Stranded DNA Terminal Labeling Kit.

growth_protocol: Plants were grown under standard growth condition with 16 hours of light (long day)

extract_protocol: RNA was extracted using the Ambion miRVANA RNA isolation kit

treatment_protocol: Seeds were surface sterilized in 0.4% sodium-hypochlorite/80% ethanol for 10 min, washed 3 times with 100% ethanol and dried under a laminar-flow hood. Seeds were then plated on Murashige and Skoog (½ MS) medium (Duchefa) containing 0.6% agar and stratified at 6°C for 2 days. Plates were incubated in growth chambers at 21°C with 12 h light/ 12h dark. For cold treatment, plates were incubated at 4°C for the indicated times with the same photoperiod. For the ITS treatment, plates were incubated in a growth chamber at 37°C for 15 h (12 h light/3 h dark).

value: 9 days

value: seedlings

tag: treatment group

value: ITS treated +2 days of recovery


title: ITS_rep2

description: ITS treated Arabidopsis RNA chip 2

value: 7 days

value: ITS treated


title: CTS+2d_rep1

description: CTS treated Arabidopsis +2 days of recovery RNA chip 1

value: CTS treated +2 days of recovery


title: ITS_rep3

description: ITS treated Arabidopsis RNA chip 3


title: Tumor 179

description: DNA (bisulfite modified)

value: fresh frozen breast tumor


title: ITS+2d_rep3

description: ITS treated Arabidopsis +2 days of recovery RNA chip 3


title: CTS_rep3

description: CTS treated Arabidopsis RNA chip 3

value: CTS treated


title: Tumor 167

description: DNA (bisulfite modified)


title: CTS+2d_rep3

description: CTS treated Arabidopsis +2 days of recovery RNA chip 3


title: CTS+2d_rep2

description: CTS treated Arabidopsis +2 days of recovery RNA chip 2


title: Lung tissue_Fully Resistant animal 6_24 hours_rep 1

source_name: Lung tissue_Fully Resistant animal 6


title: Lung tissue_Fully Resistant animal 6_24 hours_rep 4


title: Lung tissue_Fully Resistant animal 6_24 hours_rep 3


title: Lung tissue_Fully Resistant animal 5_24 hours_rep 2

source_name: Lung tissue_Fully Resistant animal 5


title: CTS_rep2

description: CTS treated Arabidopsis RNA chip 2


title: CTS_rep1

description: CTS treated Arabidopsis RNA chip 1


title: pH7 control vrs. DPD treated

city: Jerusalem

first: reuven

last: aharoni

address: 28 mara

department: oral biology

country: Israel

institute: hebrew university

description: replicate 4 of 4

hyb_protocol: The samples were resuspended in hybridization buffer containing 50 % formamide, 5x SSC, 0.1 % SDS and 20 µg yeast tRNA, and heated at 95 °C for 5 min. Following a quick centrifugation, the Cy dye-coupled probes were applied to microarray slides and incubated overnight at 42 °C. Hybridization was carried out in Corning hybridization chambers submerged in a water bath.

scan_protocol: Slides were scanned using a Genepix 4000B scanner (Axon, Silicon Valley, CA, USA).

data_processing:
Fluorescence intensities were quantitatively analyzed using GenePix Pro 4.1 software (Axon). The result files (gpr) produced by GenePix were analyzed utilizing the LIMMA [26] software package, available from the CRAN site http://www.r-project.org. Spots flagged not found or absent in GenePix were removed by filtering.
A P value < 0.05 confidence level was used to pinpoint significantly differentiated genes. Genes had to have an A-value (A = log2 [Cy3 × Cy5]/2), the average expression level for the gene across all arrays and channels, of more than 8.5

organism: Streptococcus mutans UA159

label_protocol: cDNA was generated with random hexamers (6 µg) from 2 µg total RNA using the superscript III reverse transcriptase (Invitrogen). The reverse transcription reaction was carried out at 42 °C overnight with aminoallyl (aa) labelled dUTP. Removal of unincorporated aa-dUTP and free amines was carried out using Microcon YM-30 (Millipore) filters according to the manufacturer's recommendations. Coupling of aminoallyl labelled cDNA to Cy-dye esters was performed in 0.1 M sodium carbonate buffer (pH 8.6) for 1 h at room temperature. Removal of free dyes was accomplished with Qiagen QIAquick PCR purification columns. The labelling level was quantified using a spectrophotometer (ND-100, Nanodrop Technologies). Each Cy3-labelled sample was mixed with an equal amount of Cy5-labelled sample, and the mixtures were allowed to dry in a speed vacuum for about 1 h.

extract_protocol: Cell  pellets were re-suspended with RLT lysis buffer (Qiagen), transferred into a 2-ml microcentrifuge tube containing 100 mg of 1-mm-diameter glass beads (Sigma-Aldrich, St. Louis, MO, USA) and were  disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA). DNA-free RNA was extracted from the resulted supernatant using the RNeasy minikit according to the manufacturer's protocol (Qiagen). The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The quality and integrity of the total RNA was determined by running all samples in an Agilent Technologies 2100 bioanalyzer (Agilent Technologies, Waldbronn, Germany);

tag: growth ph

tag: treatment

source_name: Ph7 DPD

value: DPD


title: Cultivars Bale and Bacho without Phosphorus rep 1

city: Hannover

first: Frank

last: Stahl

state: Niedersachsen

address: Callinstr. 5

department: Technische Chemie

country: Germany

institute: Leibniz Universität Hannover

description: The purpose of the present study is to determine the effect of Phosphorus deficiency on gene expression level using microarray analysis to identify genes responsible for root hair development. Phosphorus deficiency induced the formation of root hairs to explore a greater soil volume but molecular mechanisms were unknown. Therefore, microarray experiments were performed using root tips of Brassica carinata cultivars Bale and Bacho, respectively differing in root hair length during Phosphorus deficiency. Experimental design was carried out in nutrient solution in a climate chamber with controlled environmental conditions (20°C, 16h day/8h night cycle, 70% relative humidity) in a randomized design. 25 root tips from 10 day old seedlings grown without Phosphorus of 1cm length were harvested and immediately frozen in liquid nitrogen. Gene expression analyses were performed

hyb_protocol: During reverse transcription 100µg of purified total RNA was converted into Cy3 and Cy5 labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation Cy3 and Cy5 labeled cDNAs were detected fluorimetrically.

scan_protocol: The hybridized chips were scanned six times with an Axon 400B™ scanner at different settings, both changing the PMT and the laser power settings.

data_processing: Primary image analysis was performed using the software tool Gene Pix Pro 6.0™. The within this process generated primary data were utilized for further analysis. In the secondary analysis data from different scans were first normalized by using the median of all background intensities, which were therefore checked for outliers.

organism: Brassica carinata

source_name: roots from cultivar Bale

label_protocol: During reverse transcription 100µg of purified total RNA was converted into Cy5 labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation Cy5 labeled cDNAs were detected fluorimetrically

growth_protocol: Seeds of Brassica carinata cv. Bale were vernalized in the dark for three days at 4°C and then germinated for 5 days in the growth chamber with 16h light (20°C)/8h dark (15°C) photoperiod, a photosynthetically active radiation of 200µmol photons m-2s-1 and a relative humidity of 70%. Uniform seedlings were transferred to a continuously aerated nutrient solution containing 1mM Pi as KH2PO4 or free of Pi. The other nutrient composition in the solution was in mM: 2.25 Ca(NO3)2; 2.5 K2SO4; 1 MgSO4; 0.25 KCl; and in µM 25 H3BO3; 1.5 MnSO4; 1.5 ZnSO4; 0.5 CuSO4; 0.025 (NH4)6Mo7O24 and 35.8 Fe (FeIII- EDTA) at pH 5.5.

extract_protocol: 100µg total RNA was isolated from roots using the TRIzol® reagent (Invitrogen; USA).

treatment_protocol: The samples originate from roots of cultivars Bale grown in Phosphorus deficient conditions

tag: cultivar

value: Bale

source_name: roots from cultivar Bacho

label_protocol: During reverse transcription 100µg of purified total RNA was converted into Cy3 labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation Cy3 labeled cDNAs were detected fluorimetrically

growth_protocol: Seeds of Brassica carinata cv. Bacho were vernalized in the dark for three days at 4°C and then germinated for 5 days in the growth chamber with 16h light (20°C)/8h dark (15°C) photoperiod, a photosynthetically active radiation of 200µmol photons m-2s-1 and a relative humidity of 70%. Uniform seedlings were transferred to a continuously aerated nutrient solution containing 1mM Pi as KH2PO4 or free of Pi. The other nutrient composition in the solution was in mM: 2.25 Ca(NO3)2; 2.5 K2SO4; 1 MgSO4; 0.25 KCl; and in µM 25 H3BO3; 1.5 MnSO4; 1.5 ZnSO4; 0.5 CuSO4; 0.025 (NH4)6Mo7O24 and 35.8 Fe (FeIII- EDTA) at pH 5.5.

treatment_protocol: The samples originate from roots of cultivars Bacho grown in Phosphorus deficient conditions

value: Bacho


title: Cultivars Bale and Bacho without Phosphorus rep 2

value: grown in Phosphorus deficient conditions


title: Lung tissue_Fully Resistant animal 5_24 hours_rep 3


title: pH6 control vrs. DPD treated

description: replicate 4 of 4

source_name: Ph6 DPD


title: ITS_rep1

description: ITS treated Arabidopsis RNA chip 1

tag: age


title: Lung tissue_Fully Resistant animal 5_24 hours_rep 4


title: Tumor 161

description: DNA (bisulfite modified)

source_name: DNA


title: ITS+2d_rep1

description: ITS treated Arabidopsis +2 days of recovery RNA chip 1


title: pH5 DPD treated  vrs. control

description: replicate 2 of 2

source_name: Ph5 DPD


title: Lung tissue_Fully Resistant animal 6_24 hours_rep 2


title: Cultivars Bale and Bacho without Phosphorus rep 2 dye swap


title: Cultivars Bale and Bacho without Phosphorus rep 1 dye swap


title: pH5 control vrs. DPD treated

description: replicate 1 of 2

source_name: pH5 DPD


title: Tumor 116

description: DNA (bisulfite modified)


title: Tumor 112

description: DNA (bisulfite modified)


title: pH6 control vrs. pH7 control

description: replicate 3 of 3


title: Lung tissue_Fully Resistant animal 5_24 hours_rep 1

source_name: Lung tissue_Pool of Uninfected control animals


title: Tumor 82

description: DNA (bisulfite modified)


title: Tumor 103

description: DNA (bisulfite modified)


title: Tumor 79

description: DNA (bisulfite modified)


title: pH6 control vrs. pH5 control

description: replicate 3 of 3


title: pH7 control vrs pH5 control rep2

description: replicate 3 of 3


title: Tumor 52

description: DNA (bisulfite modified)


title: Tumor 151

description: DNA (bisulfite modified)


title: pH5 control vrs.pH6 control

description: replicate 2 of 3


title: pH6 DPD treated vrs control rep2

description: replicate 3 of 4

source_name: pH6 DPD


title: pH7 control vrs pH6 control

description: replicate 2 of 3


title: pH5 control vrs pH7 control

description: replicate 2 of 3


title: Tumor 29

description: DNA (bisulfite modified)


title: Tumor 28

description: DNA (bisulfite modified)


title: pH6 control vrs DPD treated

description: replicate 2 of 4

source_name: pH 6


title: Lung tissue_Fully Resistant animal 3_72 hours_rep 4

source_name: Lung tissue_Fully Resistant animal 3


title: pH7 DPD treated vrs control

description: replicate 3 of 4


title: Lung tissue_Fully Resistant animal 4_72 hours_rep 2

source_name: Lung tissue_Fully Resistant animal 4


title: Lung tissue_Fully Resistant animal 4_72 hours_rep 4


title: Tumor 11

description: DNA (bisulfite modified)


title: Lung tissue_Fully Resistant animal 4_72 hours_rep 1


title: Lung tissue_Fully Resistant animal 2_72 hours_rep 4

source_name: Lung tissue_Fully Resistant animal 2


title: Lung tissue_Fully Resistant animal 3_72 hours_rep 2


title: Lung tissue_Fully Resistant animal 3_72 hours_rep 3


title: Tumor 9

description: DNA (bisulfite modified)


title: Tumor 7

description: DNA (bisulfite modified)


title: Lung tissue_Fully Resistant animal 2_72 hours_rep 3


title: Tumor 6

description: DNA (bisulfite modified)


title: Lung tissue_Fully Resistant animal 4_72 hours_rep 3


title: pH6 DPD treated vrs control rep1

description: replicate 1 of 4


title: Tumor 1

description: DNA (bisulfite modified)


title: Tumor 4

description: DNA (bisulfite modified)


title: pH7 control vrs DPD treated rep2

description: replicate 2 of 4


title: Lung tissue_Fully Resistant animal 2_72 hours_rep 1


title: pH6 control vrs pH7 control

description: replicate 1 of 3


title: Lung tissue_Fully Resistant animal 3_72 hours_rep 1


title: Lung tissue_Fully Resistant animal 1_72 hours_rep 4

source_name: Lung tissue_Fully Resistant animal 1


title: pH5 control vrs pH6 control

description: replicate 1 of 3


title: Lung tissue_Fully Resistant animal 1_72 hours_rep 2


title: pH7 control vrs DPD treated rep1

description: Replicate 1 of 4


title: Lung tissue_Fully Resistant animal 1_72 hours_rep 3


title: Lung tissue_Fully Resistant animal 2_72 hours_rep 2


title: pH7 control vrs pH5 control rep1

description: Replicate 1 of 3


title: Lung tissue_Fully Resistant animal 1_72 hours_rep 1


title: Nasal epithelial cells EB_6_5d_295_HCHO_THI08031_Rat230_2_THI 08031

status: Public on Jul 28 2010

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description:
time point: 5d
dose: 6
EB_6_5d_295_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0, RMA normalization

organism: Rattus norvegicus

source_name: Nasal epithelial cells

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen Micro RNA kit

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hours per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: dilution

tag: bioanalyzer results

value: good

tag: sample preservation

value: Cells suspended in RNAlater at 4 degrees Centigrade for 24 hours and then frozen at -20 degrees Centigrade until processed for RNA.

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Deep pentobarbital anesthesia followed by exsanguination

tag: sex

value: Male

tag: units of age

value: weeks

value: Nasal epithelial cells (level II region)

tag: tissue harvest methods

value: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium.

tag: units of harvest time point

value: days

tag: time point

value: formaldehyde

tag: dose


title: Nasal epithelial cells EB_6_13w_319_HCHO_THI08031_Rat230_2_THI 08031

description:
time point: 13w
dose: 6
EB_6_13w_319_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 6, Units of Treatment Time: hours per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: array type

tag: ratio

tag: rna integrity number

tag: age

tag: tissue

tag: agent


title: Nasal epithelial cells EB_6_4w_310_HCHO_THI08031_Rat230_2_THI 08031

description:
time point: 4w
dose: 6
EB_6_4w_310_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

tag: amount to core

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: Nasal epithelial cells EB_6_4w_309_HCHO_THI08031_Rat230_2_THI 08031

description:
time point: 4w
dose: 6
EB_6_4w_309_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: sex

tag: units of age


title: Nasal epithelial cells EB_6_5d_298_HCHO_THI08031_Rat230_2_THI 08031

description:
time point: 5d
dose: 6
EB_6_5d_298_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

tag: array type

tag: ratio

tag: tissue harvest methods

tag: units of harvest time point

tag: time point

tag: dose


title: Nasal epithelial cells EB_6_4w_303_HCHO_THI08031_Rat230_2_THI 08031

description:
time point: 4w
dose: 6
EB_6_4w_303_HCHO_THI08031_Rat230_2_THI 08031: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: age

tag: tissue

tag: agent