title: dkfz_CNS-PNET_15-0089

description:
DNA Methylation data from a brain tumor sample
6929718001_R05C01


title: dkfz_CNS-PNET_15-0119

status: Public on Feb 25 2016

type: genomic

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

description:
DNA Methylation data from a brain tumor sample
6229017022_R02C02

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: CNS-PNET

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany). Automated DNA purification from formalin-fixed, paraffin-embedded (FFPE) tissue was performed using the Maxwell Rapid Sample Concentrator (Promega, Madison, USA). DNA from FFPE tissue was restored using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, USA).

tag: institutional tumor diagnosis

value: CNS-PNET

tag: molecular subgroup

value: AT/RT

tag: gender

value: M

tag: age (years)

tag: tumor location

value: temporal lobe


title: dkfz_CNS-PNET_15-0091

description:
DNA Methylation data from a brain tumor sample
6229009095_R05C01


title: dkfz_CNS-PNET_15-0090

description:
DNA Methylation data from a brain tumor sample
9007225086_R05C01

value: F

value: supratentorial (NOS)


title: dkfz_CNS-PNET_15-0088

description:
DNA Methylation data from a brain tumor sample
9878820122_R04C02


title: dkfz_CNS-PNET_15-0087

description:
DNA Methylation data from a brain tumor sample
9283265033_R05C01

value: unclassifiable

value: protuberans/bulb


title: dkfz_CNS-PNET_15-0085

description:
DNA Methylation data from a brain tumor sample
6229017022_R06C02

value: cerebellar


title: dkfz_CNS-PNET_15-0086

description:
DNA Methylation data from a brain tumor sample
6229017057_R03C01


title: dkfz_CNS-PNET_15-0082

description:
DNA Methylation data from a brain tumor sample
6229009095_R02C02

value: ETMR

value: frontal/parietal lobe, right


title: dkfz_CNS-PNET_15-0083

description:
DNA Methylation data from a brain tumor sample
6229009095_R01C02

value: temporal lobe, right


title: dkfz_CNS-PNET_15-0080

description:
DNA Methylation data from a brain tumor sample
8622007061_R02C01


title: dkfz_CNS-PNET_15-0079

description:
DNA Methylation data from a brain tumor sample
3998909025_R02C01

value: frontal/temporal lobe and basal ganglia


title: dkfz_CNS-PNET_15-0098

description:
DNA Methylation data from a brain tumor sample
6229017057_R05C02

value: pineal region


title: dkfz_CNS-PNET_15-0075

description:
DNA Methylation data from a brain tumor sample
9007217108_R02C02


title: dkfz_CNS-PNET_15-0078

description:
DNA Methylation data from a brain tumor sample
7497398017_R06C02


title: dkfz_CNS-PNET_15-0073

description:
DNA Methylation data from a brain tumor sample
7990895159_R06C02


title: dkfz_CNS-PNET_15-0077

description:
DNA Methylation data from a brain tumor sample
6229017057_R05C01


title: dkfz_CNS-PNET_15-0076

description:
DNA Methylation data from a brain tumor sample
9741950039_R04C01

value: parietal lobe


title: dkfz_CNS-PNET_15-0072

description:
DNA Methylation data from a brain tumor sample
9741950056_R03C01


title: dkfz_CNS-PNET_15-0069

description:
DNA Methylation data from a brain tumor sample
6929718001_R01C02

value: temporal/parietal lobe


title: dkfz_CNS-PNET_15-0068

description:
DNA Methylation data from a brain tumor sample
9283265033_R01C02

value: parietal/occipital lobe


title: dkfz_CNS-PNET_15-0071

description:
DNA Methylation data from a brain tumor sample
6229017057_R03C02

value: CNS-PNET


title: dkfz_CNS-PNET_15-0067

description:
DNA Methylation data from a brain tumor sample
8622007065_R06C01

value: precentral


title: dkfz_CNS-PNET_15-0066

description:
DNA Methylation data from a brain tumor sample
8622007149_R01C01


title: dkfz_CNS-PNET_15-0065

description:
DNA Methylation data from a brain tumor sample
8622007097_R01C02

value: M


title: dkfz_CNS-PNET_15-0063

description:
DNA Methylation data from a brain tumor sample
6247004023_R02C02

value: optic chiasm


title: dkfz_CNS-PNET_15-0062

description:
DNA Methylation data from a brain tumor sample
6229009095_R04C02

value: F


title: dkfz_CNS-PNET_15-0061

description:
DNA Methylation data from a brain tumor sample
3998909026_R02C01

value: frontal lobe, bilateral


title: dkfz_CNS-PNET_15-0084

description:
DNA Methylation data from a brain tumor sample
6229017057_R06C01

value: unclassifiable


title: dkfz_CNS-PNET_15-0059

description:
DNA Methylation data from a brain tumor sample
9007225026_R01C02


title: dkfz_CNS-PNET_15-0058

description:
DNA Methylation data from a brain tumor sample
8622007097_R03C01

value: CTRL

value: parieto-central


title: dkfz_CNS-PNET_15-0057

description:
DNA Methylation data from a brain tumor sample
9283265033_R06C01

value: parietal lobe, left


title: dkfz_CNS-PNET_15-0056

description:
DNA Methylation data from a brain tumor sample
9741950056_R05C02


title: dkfz_CNS-PNET_15-0055

description:
DNA Methylation data from a brain tumor sample
9969477108_R05C02

value: thalamic, right


title: dkfz_CNS-PNET_15-0054

description:
DNA Methylation data from a brain tumor sample
9968646164_R02C02


title: dkfz_CNS-PNET_15-0074

description:
DNA Methylation data from a brain tumor sample
6229017023_R01C01


title: dkfz_CNS-PNET_15-0053

description:
DNA Methylation data from a brain tumor sample
7497398016_R01C01


title: dkfz_CNS-PNET_15-0081

description:
DNA Methylation data from a brain tumor sample
3998523019_R05C01

value: EWS

value: temporal lobe, right


title: dkfz_CNS-PNET_15-0048

description:
DNA Methylation data from a brain tumor sample
8622007061_R02C02

value: parietal lobe, right


title: dkfz_CNS-PNET_15-0047

description:
DNA Methylation data from a brain tumor sample
6929718027_R04C02

value: AT/RT


title: dkfz_CNS-PNET_15-0045

description:
DNA Methylation data from a brain tumor sample
8622007061_R03C02


title: dkfz_CNS-PNET_15-0070

description:
DNA Methylation data from a brain tumor sample
8622007065_R02C02

value: frontal lobe, right


title: dkfz_CNS-PNET_15-0052

description:
DNA Methylation data from a brain tumor sample
8622007066_R04C01

value: frontal lobe, left


title: dkfz_CNS-PNET_15-0051

description:
DNA Methylation data from a brain tumor sample
7990908004_R05C02

value: CNS-PNET

value: fronto-dorsal, left


title: dkfz_CNS-PNET_15-0044

description:
DNA Methylation data from a brain tumor sample
9721366138_R06C01

value: frontal lobe


title: dkfz_CNS-PNET_15-0040

description:
DNA Methylation data from a brain tumor sample
6969568009_R02C01

value: spinal (NOS)


title: dkfz_CNS-PNET_15-0042

description:
DNA Methylation data from a brain tumor sample
9283265033_R02C02

value: F

value: spinal (L3-S2)


title: dkfz_CNS-PNET_15-0041

description:
DNA Methylation data from a brain tumor sample
9534104007_R06C01

value: M

value: central region, right


title: dkfz_CNS-PNET_15-0064

description:
DNA Methylation data from a brain tumor sample
9407210157_R02C02


title: dkfz_CNS-PNET_15-0038

description:
DNA Methylation data from a brain tumor sample
3998523076_R02C02

value: hemispheric, right (NOS)


title: dkfz_CNS-PNET_15-0043

description:
DNA Methylation data from a brain tumor sample
10005771024_R01C02

value: pons


title: dkfz_CNS-PNET_15-0046

description:
DNA Methylation data from a brain tumor sample
9007225003_R04C02


title: dkfz_CNS-PNET_15-0037

description:
DNA Methylation data from a brain tumor sample
3998523076_R06C01


title: dkfz_CNS-PNET_15-0036

description:
DNA Methylation data from a brain tumor sample
9741950107_R02C01

value: unclassifiable

value: parietal lobe


title: dkfz_CNS-PNET_15-0035

description:
DNA Methylation data from a brain tumor sample
7497398022_R05C02


title: dkfz_CNS-PNET_15-0060

description:
DNA Methylation data from a brain tumor sample
6929718020_R04C02

value: CPC

value: temporal/parietal/occipital lobe


title: dkfz_CNS-PNET_15-0034

description:
DNA Methylation data from a brain tumor sample
3998909014_R02C02


title: dkfz_CNS-PNET_15-0033

description:
DNA Methylation data from a brain tumor sample
9741950159_R02C01


title: dkfz_CNS-PNET_15-0032

description:
DNA Methylation data from a brain tumor sample
9407210157_R03C01

value: frontal/parietal lobe


title: dkfz_CNS-PNET_15-0031

description:
DNA Methylation data from a brain tumor sample
6229017022_R06C01

value: temporal lobe


title: dkfz_CNS-PNET_15-0049

description:
DNA Methylation data from a brain tumor sample
8622007061_R06C01

value: ETMR

value: parietal lobe, right


title: dkfz_CNS-PNET_15-0027

description:
DNA Methylation data from a brain tumor sample
9741950039_R02C02

value: CNS-PNET


title: dkfz_CNS-PNET_15-0026

description:
DNA Methylation data from a brain tumor sample
6229017022_R04C02

value: frontal lobe


title: dkfz_CNS-PNET_15-0028

description:
DNA Methylation data from a brain tumor sample
9741950056_R02C01


title: dkfz_CNS-PNET_15-0050

description:
DNA Methylation data from a brain tumor sample
6229017023_R01C02


title: dkfz_CNS-PNET_15-0024

description:
DNA Methylation data from a brain tumor sample
9741950158_R05C02

value: cerebral (NOS)


title: dkfz_CNS-PNET_15-0025

description:
DNA Methylation data from a brain tumor sample
6229009095_R06C02

value: F

value: supratentorial (NOS)


title: dkfz_CNS-PNET_15-0039

description:
DNA Methylation data from a brain tumor sample
3999078079_R02C01

value: M

value: hemispheric (NOS)


title: dkfz_CNS-PNET_15-0020

description:
DNA Methylation data from a brain tumor sample
9611519030_R06C01

value: PINEAL

value: third ventricle


title: dkfz_CNS-PNET_15-0015

description:
DNA Methylation data from a brain tumor sample
6929689154_R06C01

value: CTRL

value: frontal lobe, left


title: dkfz_CNS-PNET_15-0017

description:
DNA Methylation data from a brain tumor sample
6229017023_R04C01

value: unclassifiable


title: dkfz_CNS-PNET_15-0019

description:
DNA Methylation data from a brain tumor sample
9741950159_R05C02


title: dkfz_CNS-PNET_15-0023

description:
DNA Methylation data from a brain tumor sample
6229017022_R01C02

value: thalamic


title: dkfz_CNS-PNET_15-0012

description:
DNA Methylation data from a brain tumor sample
8622007067_R01C01

value: parietal/occipital lobe, left


title: dkfz_CNS-PNET_15-0022

description:
DNA Methylation data from a brain tumor sample
8622007065_R04C01

value: occipital/parietal lobe, right


title: dkfz_CNS-PNET_15-0021

description:
DNA Methylation data from a brain tumor sample
3998919098_R01C01

value: postcentral


title: dkfz_CNS-PNET_15-0011

description:
DNA Methylation data from a brain tumor sample
3998952004_R01C01

value: fronto-central


title: dkfz_CNS-PNET_15-0013

description:
DNA Methylation data from a brain tumor sample
10005771024_R06C02

value: CNS-PNET

value: ETMR

value: parietal lobe, right


title: dkfz_CNS-PNET_15-0008

description:
DNA Methylation data from a brain tumor sample
9007225003_R05C02

value: occipital lobe


title: dkfz_CNS-PNET_15-0009

description:
DNA Methylation data from a brain tumor sample
9741950173_R05C02

value: frontal lobe


title: dkfz_CNS-PNET_15-0029

description:
DNA Methylation data from a brain tumor sample
9003865025_R02C02

value: F

value: parietal lobe, left


title: dkfz_CNS-PNET_15-0014

description:
DNA Methylation data from a brain tumor sample
6229017023_R02C02


title: dkfz_CNS-PNET_15-0016

description:
DNA Methylation data from a brain tumor sample
9969477058_R05C01

value: M

value: supratentorial (NOS)


title: dkfz_CNS-PNET_15-0007

description:
DNA Methylation data from a brain tumor sample
6229017057_R04C01


title: dkfz_CNS-PNET_15-0010

description:
DNA Methylation data from a brain tumor sample
9741950086_R06C01


title: dkfz_CNS-PNET_15-0004

description:
DNA Methylation data from a brain tumor sample
9968646163_R04C02

value: temporal lobe


title: dkfz_CNS-PNET_15-0006

description:
DNA Methylation data from a brain tumor sample
9741950159_R06C02


title: dkfz_CNS-PNET_15-0003

description:
DNA Methylation data from a brain tumor sample
8622007070_R02C02

value: CTRL


title: dkfz_CNS-PNET_15-0002

description:
DNA Methylation data from a brain tumor sample
7497398016_R06C01

value: unclassifiable


title: dkfz_CNS-PNET_15-0001

description:
DNA Methylation data from a brain tumor sample
9297949146_R06C02

value: brainstem


title: dkfz_CNS-PNET_15-0018

description:
DNA Methylation data from a brain tumor sample
6229017057_R01C01


title: dkfz_CNS-PNET_15-0005

description:
DNA Methylation data from a brain tumor sample
3998523019_R04C01

value: frontal lobe, left


title: 20 μM PhenDC3 in DMSO, replicate 2

status: Public on Jan 31 2016

type: SRA

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Base-calling and filtering were performed with Illumina RTA and CASAVA software to generate fastq files
[Cuffdiff files]  Fastq files were aligned to the hg19 human transcriptome using TopHat v2.0.11 with settings -p 3 -a 5 --no-coverage-search to generate BAM files
BAM files were used to calculate transcript abundance and differential gene expression using the Cufflinks v2.2.1 cuffdiff analysis tool
[DESeq2 file]  Reads were aligned to the human reference genome hg19 using STAR v2.7 [Dobin A et al. 2013] with the ENCODE processing pipeline standard settings for RNA-seq data (--outFilterType BySJout, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- alignIntronMin 20, --alignIntronMax 1000000 and --alignMatesGapMax 1000000). Reads mapping uniquely to GENCODE-annotated genes were summarised using featureCounts [Liao Y et al. 2014]. The raw gene count matrix was imported into the R environment [R Core Team 2018] for further processing and analysis. Genes with low read counts (less than ~10 reads in more than 3 samples) were filtered out, leaving a set of 20,000 genes to test for differential expression between control (DMSO) and treated (+PhenDC3) conditions. Differential expression analysis was carried out using the R package DESeq2 version 1.18.1 [Love MI et al. 2014]. Unless otherwise stated, differentially expressed genes were identified based on false discovery rate (FDR, using Benjamini-Hochberg adjusted p-values), with the threshold FDR < 1%. A fold-change cutoff was used to create the sets of genes used for G4 enrichment analysis: only ?2-fold (?1-log 2 fold) differentially expressed genes (2xDEGs) were retained.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff results file (.diff): tab-separated text files with results calculated by Cuffdiff based on gene-centered analysis, isoform-specific analysis, or differential splicing analysis

molecule: polyA RNA

source_name: HT-1080 fibrosarcoma cell line

growth_protocol: Cells were cultured in DMEM with 10% FBS, penicillin and streptomycin

extract_protocol:
Total RNA was extracted with TRIzol (Life Technologies)
Libraries were constructed using an Illumina Stranded mRNA Sample preparation kit

tag: cell line

value: HT-1080 fibrosarcoma

tag: treatment

value: 1% DMSO + 20 μM PhenDC3, 48hr


title: DMSO only, replicate 1

value: 1% DMSO Only, 48 hr


title: 20 μM PhenDC3 in DMSO, replicate 1


title: DMSO only, replicate 2


title: DMSO only, replicate 3


title: wdr82sh_scrambled_polII_total_LPS_45min

status: Public on Nov 09 2015

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against polII total

library_source: genomic

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

organism: Mus musculus

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: At day zero bone marrow cells were isolated from FVB/hsd mice and 3 × 10^6 cells/well in a 6-well plate were seeded in BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cells were infected two times pr day for two days consecutive days after plating, using supernatants from transfected Phoenix-ECO packaging cells. After the last infection, cells where transferred to 10 cm culture plates, and puromycin selection (3.5 μg/ml) was started.

extract_protocol:
Roughly 10-20 x 10^6 (for histone modifications) or 100-150 x 10^6 (for Pol II) fixed (1% formaldehyde for 10 min) macrophages were lysed with RIPA buffer and, after chromatin shearing by sonication.  Antibodies were pre-bound overnight to 100 ul of protein G-coupled paramagnetic beads (Dynabeads) in PBS/BSA 0.5%. Beads were then added to lysates and immunoprecipitation was let to proceed overnight. For Ser2-phospho RNA Pol II the ChIP lysates were incubated overnight with the primary antibody and then combined with 100 μl of beads that had previously been coupled overnight with 5 μg of rabbit anti-rat IgG (Jackson ImmunoResearch, #312-005-003). Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

treatment_protocol: BMDMs were either untreated or treated for 4 hrs with lipopolysaccharide (LPS, 10 ng/ml).

tag: strain

value: FVB/Hsd

tag: cell type

value: BMDM cells (7th day of differentiation)

tag: antibody

value: anti-Pol II (Santa Cruz, sc-899)

tag: retroviral infection

value: scrambled

value: LPS (10 ng/ml)


title: 20 μM PhenDC3 in DMSO, replicate 3


title: SCC2_siTAZ_rep1

status: Public on May 26 2015

type: RNA

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from SCC2 cells treated with an siRNA targeting TAZ.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and the Brainarray hugene20sthsentrezgcdf R package (version 16.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.download/HuGene20st_Hs_ENTREZG_16.0.0.zip).

label: biotin

molecule: total RNA

source_name: SCC2 cell line

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: SCC2 cells were cultured using DMEM media supplemented with 10% FBS.

extract_protocol: Total RNA was isolated and purified by RNeasy Mini Kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: RNA interference was performed by transfecting the indicated siRNA using Dharmafect 1 (Thermo Scientific) according to manufacturer's protocol.

value: SCC2 oral cancer cells

value: siTAZ


title: SCC2_siYAP-TAZ_rep1

description: Gene expression data from SCC2 cells treated with siRNAs targeting both TAZ and YAP.

value: siYAP-TAZ


title: SCC2_siYAP_rep1

description: Gene expression data from SCC2 cells treated with an siRNA targeting YAP.

value: siYAP


title: SCC2_siYAP_rep2


title: MIV, biological replicate 3

status: Public on Feb 02 2016

description: Gene expression profile of cell line representing metastatic carcinoma.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce probeset-level expression values using the MicroArray Suite 5.0 (MAS5) algorithm and the default Affymetrix probeset mapping.

source_name: MCF-10A1a cell line

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

growth_protocol: Cells were cultured in DMEM/F12 1:1 mixture medium supplemented with 5% horse serum, 1% penicillin/streptomycin solution, 10 µg/ml insulin, 0.1 µg/ml cholera toxin, 20 ng/ml epidermal growth factor and 0.5 µg/ml hydroxycortisone.

extract_protocol: Trizol extraction of total RNA was performed.

tag: disease state

value: carcinoma, metastatic


title: SCC2_siYAP-TAZ_rep2


title: MIV, biological replicate 1


title: SCC2_siTAZ_rep3


title: MIII, biological replicate 3

description: Gene expression profile of cell line representing carcinoma.

source_name: MCF-10A1h cell line

value: carcinoma


title: SCC2_siTAZ_rep2


title: MIV, biological replicate 2


title: MII, biological replicate 3

description: Gene expression profile of cell line representing carcinoma in situ.

source_name: MCF-10AT1Kcl2 cell line

value: carcinoma in situ


title: SCC2_siYAP_rep3


title: MIII, biological replicate 2


title: MII, biological replicate 1


title: lacZ knockdown

status: Public on Aug 31 2015

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting lacZ.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Rat Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 14.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.

organism: Rattus norvegicus

source_name: NRVM

growth_protocol: NRVMs were recovered in DMEM with 10% FBS + pen/strep/L-glut. After a 24 hour recovery period, NRVMs were switched to a low serum DMEM with 0.5x Nutridoma + pen/strep/L-glut.

extract_protocol: Total RNA from myotubes was preparted by TRIzol© isolation (Invitrogen). Samples were pooled in sets, for a total of 3 biological replicates per condition.

treatment_protocol: One day after cells were switched to recovery media, cells were transduced with a single adenovirus containing an shRNA targeting MEF2D, or the negative control lacZ shRNA.

value: Neonatal rat ventricular myocytes

tag: age

value: 1 to 2 day old rat pups

tag: target

value: lacZ


title: SCC2_siCTL_rep3

description: Gene expression data from SCC2 cells treated with a control siRNA.

value: siCTL


title: SCC2_siYAP-TAZ_rep3


title: MII, biological replicate 2


title: SCC2_siCTL_rep1


title: Mef2d knockdown

description: Gene expression data from neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting Mef2d.


title: SCC2_siCTL_rep2


title: subject 13-005, senescent

status: Public on Mar 10 2015

description:
Sample name: 13-005_S5
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), R (version 2.15.1), and the Brainarray hugene10sthsentrezg R package (version 16.0.0)

source_name: subcutaneous adipocytes

growth_protocol: Preadipocytes were grown in aMEM containing 10% FBS. In senescent cultures, medium was changed twice a week.

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

treatment_protocol: Preadipocytes were irradiated to induce senescence. Sham irradiated cells from the same subject were used as a control. RNA was isolated 20 days after induction of senecence.

tag: subject

value: abdominal subcutaneous preadipocyte

tag: cell state

value: senescent


title: subject 12-024, proliferating

description:
Sample name: 12-024_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.

value: proliferating


title: subject 11-017, senescent

description:
Sample name: 11-017_S7
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 13-009, senescent

description:
Sample name: 13-009_S5
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 13-007, senescent

description:
Sample name: 13-007_S7
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 13-003, senescent

description:
Sample name: 13-003_S6
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 11-012, senescent

description:
Sample name: 11-012_S6
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 11-020, senescent

description:
Sample name: 11-020_S7
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: subject 13-005, proliferating

description:
Sample name: 13-005_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: subject 13-003, proliferating

description:
Sample name: 13-003_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: MIII, biological replicate 1


title: subject 11-020, proliferating

description:
Sample name: 11-020_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: subject 13-007, proliferating

description:
Sample name: 13-007_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: subject 13-009, proliferating

description:
Sample name: 13-009_SQCTR
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: subject 11-017, proliferating

description:
Sample name: 11-017_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: subject 12-024, senescent

description:
Sample name: 12-024_S6
Gene expression data from subcutaneous adipocytes in gamma-irradiation-induced senescence.


title: Chronic Western diet 3

status: Public on Jan 06 2015

description: Gene expression data from mouse aortic tissue, collected 9 weeks after start of a Western (high-fat diet).

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).

extract_protocol: Total RNA was isolated using TriZol extraction reagent (Invitrogen) using TissueLyser II in pre-cooled blocks (Qiagen). RNA was further purified using the RNAeasy kit (Qiagen, Valencia, CA).

tag: tissue type

value: aortic tissue

tag: timepoint

value: chronic

value: Western diet


title: Chronic Pg 2

description: Gene expression data from mouse aortic tissue, collected 9 weeks after the end of P. gingivalis administration.

value: P. gingivalis


title: Chronic Western diet 1

source_name: mouse aortic tissue, collected 9 weeks after start of a Western (high-fat diet).


title: Chronic Pg 3

source_name: mouse aortic tissue, collected 9 weeks after the end of P. gingivalis administration.


title: Chronic control 1

description: Gene expression data from aortic tissue of a control mouse, collected 12 weeks after the start of the experiment.

value: control


title: Chronic Pg 1


title: Chronic Cp 2

description: Gene expression data from mouse aortic tissue, collected 9 weeks after the end of C. pneumoniae administration.

value: C. pneumoniae


title: Chronic Western diet 2


title: Chronic control 3

source_name: aortic tissue of a control mouse, collected 12 weeks after the start of the experiment.


title: Chronic Cp 3

source_name: mouse aortic tissue, collected 9 weeks after the end of C. pneumoniae administration.


title: Chronic Cp 1


title: Acute Cp 2

description: Gene expression data from mouse aortic tissue, collected after 3 weeks of intranasal administration of C. pneumoniae.

value: acute

value: intranasal C. pneumoniae


title: Acute Cp 1

source_name: mouse aortic tissue, collected after 3 weeks of intranasal administration of C. pneumoniae.


title: Acute control 1

description: Gene expression data from aortic tissue of a control mouse, collected 3 weeks after the start of the experiment.


title: Acute Pg 2

description: Gene expression data from mouse aortic tissue, collected after 3 weeks of oral administration of P. gingivalis.

value: oral P. gingivalis


title: Acute Cp 3


title: Acute Pg 1

source_name: mouse aortic tissue, collected after 3 weeks of oral administration of P. gingivalis.


title: Acute control 3

source_name: aortic tissue of a control mouse, collected 3 weeks after the start of the experiment.


title: subject 11-012, proliferating

description:
Sample name: 11-012_SQ
Gene expression data from subcutaneous adipocytes proliferating in culture.


title: Mef2c knockdown, replicate 2

status: Public on Dec 03 2014

description: Gene expression data from C2C12 cells treated with shRNA targeting Mef2c.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 16.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.

source_name: C2C12 cells

growth_protocol: C2C12 myoblasts were maintained in DMEM with 10% FBS + pen/strep/L-glut. Differentiation was induced by switching to a low serum DMEM containing 2% horse serum + pen/strep/L-glut.

treatment_protocol: One day prior to induction of differentiation (transition to low serum media), cells are transduced with a single, or a combination of adenoviruses containing an shRNA targeting a single MEF2 factor, or the negative control lacz shRNA.

tag: RNAi target


title: Acute control 2


title: Mef2d knockdown, replicate 3

description: Gene expression data from C2C12 cells treated with shRNA targeting Mef2d.


title: Mef2d knockdown, replicate 2


title: Mef2c knockdown, replicate 3


title: Mef2d knockdown, replicate 1


title: Mef2b knockdown, replicate 1

description: Gene expression data from C2C12 cells treated with shRNA targeting Mef2b.


title: Mef2b knockdown, replicate 2


title: Mef2a knockdown, replicate 1

description: Gene expression data from C2C12 cells treated with shRNA targeting Mef2a.


title: Mef2b knockdown, replicate 3


title: Mef2a knockdown, replicate 3


title: Mef2a knockdown, replicate 2


title: Acute Pg 3


title: lacZ knockdown, replicate 2

description: Gene expression data from C2C12 cells treated with shRNA targeting lacZ.


title: lacZ knockdown, replicate 3


title: lacZ knockdown, replicate 1


title: superior frontal gyrus_male_94_AD_44

status: Public on Apr 21 2014

city: Irvine

first: Nicole

middle: Claudia

last: Berchtold

state: CA

address: 1226 Gillespie Neuroscience Facility

department: Institute for Memory Impairments and Neurological Disorders

institute: UC Irvine

description: post-mortem tissue

hyb_protocol: Following fragmentation, 30 mg biotin-labeled cRNA were hybridized for 16 hr and rotated at 13 rpm at 50° C on Affymetrix Human HgU133 plus 2.0 microarrays

scan_protocol: Affymetrix Genekeep GCS3000, software version 3.2.2.1515

data_processing: GC-RMA, using Genespring 7.3. data transformation: measurements <0.01 set to 0.01; per chip: normalized to the 50th percentile; per gene: normalize to median

source_name: superior frontal gyrus_male_AD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using robotics system (Biomek FX MicroArray Plex SA System; Beckman Coulter) to optimize consistency in processing

extract_protocol: Trizol extraction of total RNA, followed by purification using Qiagen quick-spin columns

tag: gender

value: male

tag: age (yrs)

tag: brain region

value: superior frontal gyrus

tag: braak stage

value: IV

tag: apoe genotype

tag: mmse


title: superior frontal gyrus_male_86_AD_92

description: post-mortem tissue


title: superior frontal gyrus_male_94_AD_90

description: post-mortem tissue

value: no info


title: superior frontal gyrus_male_94_AD_5

description: post-mortem tissue

value: VI


title: superior frontal gyrus_male_85_AD_74

description: post-mortem tissue

value: II


title: superior frontal gyrus_male_85_AD_51

description: post-mortem tissue

value: III


title: Mef2c knockdown, replicate 1

tag: cell line


title: superior frontal gyrus_female_95_AD_64

description: post-mortem tissue

source_name: superior frontal gyrus_female_AD

value: female


title: superior frontal gyrus_male_76_AD_33

description: post-mortem tissue

value: V


title: superior frontal gyrus_female_94_AD_70

description: post-mortem tissue

value: I


title: superior frontal gyrus_female_90_AD_75

description: post-mortem tissue


title: superior frontal gyrus_female_85_AD_24

description: post-mortem tissue


title: superior frontal gyrus_female_74_AD_37

description: post-mortem tissue


title: superior frontal gyrus_female_91_AD_11

description: post-mortem tissue

value: V-VI


title: superior frontal gyrus_female_76_AD_48

description: post-mortem tissue


title: superior frontal gyrus_female_88_AD_91

description: post-mortem tissue


title: superior frontal gyrus_female_90_AD_23

description: post-mortem tissue


title: superior frontal gyrus_female_85_AD_57

description: post-mortem tissue


title: superior frontal gyrus_female_82_AD_9

description: post-mortem tissue


title: superior frontal gyrus_female_90_AD_36

description: post-mortem tissue


title: superior frontal gyrus_female_86_AD_15

description: post-mortem tissue


title: post-central gyrus_male_94_AD_5

description: post-mortem tissue

source_name: post-central gyrus_male_AD

value: post-central gyrus


title: post-central gyrus_male_94_AD_44

description: post-mortem tissue


title: superior frontal gyrus_female_90_AD_6

description: post-mortem tissue


title: post-central gyrus_male_87_AD_19

description: post-mortem tissue


title: Chronic control 2

value: aortic tissue

value: chronic

tag: treatment

value: control


title: post-central gyrus_male_86_AD_92

description: post-mortem tissue


title: post-central gyrus_male_94_AD_90

description: post-mortem tissue


title: post-central gyrus_male_85_AD_74

description: post-mortem tissue


title: dkfz_CNS-PNET_15-0030

description:
DNA Methylation data from a brain tumor sample
3998909025_R04C01

source_name: CNS-PNET

tag: institutional tumor diagnosis

value: CNS-PNET

tag: molecular subgroup

value: F

tag: age (years)

tag: tumor location

value: frontal/parietal lobe


title: post-central gyrus_female_90_AD_75

description: post-mortem tissue

source_name: post-central gyrus_female_AD


title: post-central gyrus_male_85_AD_51

description: post-mortem tissue

value: male


title: post-central gyrus_female_95_AD_64

description: post-mortem tissue


title: hippocampus_male_94_AD_90

description: post-mortem tissue

value: hippocampus

value: IV


title: post-central gyrus_female_86_AD_15

description: post-mortem tissue

value: VI


title: post-central gyrus_female_85_AD_24

description: post-mortem tissue


title: post-central gyrus_male_76_AD_69

description: post-mortem tissue

value: no info


title: post-central gyrus_female_60_AD_20

description: post-mortem tissue


title: post-central gyrus_female_94_AD_70

description: post-mortem tissue


title: post-central gyrus_male_79_AD_7

description: post-mortem tissue


title: post-central gyrus_male_76_AD_33

description: post-mortem tissue


title: post-central gyrus_female_82_AD_9

description: post-mortem tissue


title: post-central gyrus_female_90_AD_23

description: post-mortem tissue


title: post-central gyrus_female_74_AD_37

description: post-mortem tissue


title: post-central gyrus_female_85_AD_57

description: post-mortem tissue


title: post-central gyrus_female_90_AD_36

description: post-mortem tissue


title: post-central gyrus_female_90_AD_6

description: post-mortem tissue


title: post-central gyrus_female_91_AD_11

description: post-mortem tissue


title: hippocampus_male_94_AD_5

description: post-mortem tissue


title: hippocampus_male_85_AD_51

description: post-mortem tissue

value: III


title: hippocampus_male_87_AD_19

description: post-mortem tissue


title: hippocampus_male_80_AD_43

description: post-mortem tissue


title: hippocampus_male_79_AD_7

description: post-mortem tissue


title: post-central gyrus_female_76_AD_48

description: post-mortem tissue

value: female


title: hippocampus_male_76_AD_69

description: post-mortem tissue


title: post-central gyrus_female_82_AD_13

description: post-mortem tissue


title: hippocampus_female_91_AD_11

description: post-mortem tissue


title: hippocampus_female_85_AD_24

description: post-mortem tissue


title: hippocampus_male_76_AD_33

description: post-mortem tissue

value: V


title: hippocampus_female_90_AD_75

description: post-mortem tissue


title: hippocampus_female_79_AD_16

description: post-mortem tissue


title: hippocampus_female_90_AD_36

description: post-mortem tissue


title: entorhinal cortex_male_76_AD_69

description: post-mortem tissue

source_name: entorhinal cortex_male_AD

value: entorhinal cortex


title: hippocampus_male_86_AD_92

description: post-mortem tissue


title: hippocampus_female_76_AD_48

description: post-mortem tissue


title: hippocampus_female_86_AD_15

description: post-mortem tissue


title: entorhinal cortex_male_94_AD_5

description: post-mortem tissue


title: entorhinal cortex_male_85_AD_74

description: post-mortem tissue

value: II


title: entorhinal cortex_male_94_AD_90

description: post-mortem tissue


title: entorhinal cortex_female_90_AD_75

description: post-mortem tissue

source_name: entorhinal cortex_female_AD


title: entorhinal cortex_female_85_AD_24

description: post-mortem tissue


title: hippocampus_female_60_AD_20

description: post-mortem tissue


title: entorhinal cortex_male_87_AD_19

description: post-mortem tissue


title: hippocampus_female_74_AD_37

description: post-mortem tissue


title: entorhinal cortex_male_86_AD_92

description: post-mortem tissue


title: hippocampus_female_90_AD_23

description: post-mortem tissue


title: entorhinal cortex_female_86_AD_15

description: post-mortem tissue


title: entorhinal cortex_female_90_AD_6

description: post-mortem tissue


title: entorhinal cortex_female_82_AD_9

description: post-mortem tissue


title: entorhinal cortex_female_90_AD_36

description: post-mortem tissue


title: entorhinal cortex_male_85_AD_51

description: post-mortem tissue


title: entorhinal cortex_female_91_AD_11

description: post-mortem tissue

value: V-VI


title: entorhinal cortex_female_76_AD_48

description: post-mortem tissue


title: siRNA TAZ/YAP - 2

status: Public on Apr 02 2014

description: Gene expression data from LM2-4 treated with anti-TAZ/YAP siRNA plus TGF-beta.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.7) and the Brainarray hugene10stv1hsentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/HuGene10stv1_Hs_ENTREZG_14.0.0.zip).

source_name: MDA-MB-231-LM2-4 cell line

growth_protocol: MDA-MB-231-LM2-4 cells were cultured using RPMI media supplemented with 10% FBS.

extract_protocol: Total RNA was isolated and purified by Quick-RNA MiniPrep (Zymogen Research) according to manufacturer’s protocol.

treatment_protocol: RNA interference was performed by transfecting the indicated siRNA using Dharmafect 1 (Thermo Scientific) according to manufacturer’s protocol.

value: MDA-MB-231-LM2-4 breast cancer cells

value: siRNA targetting TAZ/YAP plus TGF-beta


title: SB-431542 - 2

description: Gene expression data from LM2-4 treated with SB-431542 plus TGF-beta.

value: SB-431542 (an inhibitor of the TBRI recpeptor) plus TGF-beta


title: siRNA TEAD1/2/3/4 - 2

description: Gene expression data from LM2-4 treated with anti-TEAD1/2/3/4 siRNA plus TGF-beta.

value: siRNA targetting TEAD1/2/3/4 plus TGF-beta


title: SB-431542 - 3


title: siRNA TAZ/YAP - 3


title: siRNA TEAD1/2/3/4 - 3


title: siRNA TEAD1/2/3/4 - 1


title: siRNA TAZ/YAP - 1


title: siRNA control - 2

description: Gene expression data from LM2-4 treated with control siRNA plus TGF-beta.

value: Control siRNA plus TGF-beta


title: siRNA control - 3


title: siRNA control - 1


title: 93 years oldFemale

status: Public on Mar 16 2014

first: Tun-Hsiang

last: Yang

address: 77 Avenue Louis Pasteur

department: Genetics

institute: HMS

description: 93 years oldFemale

hyb_protocol: Hybridizations were performed in the Genechip hybridization over 640 (60vrpm) for 16 hrs at 45ºC. The probe arrays were then washed, stained in the GeneChip Fluidics Station 400 operated by GeneChip software following the appropriate fluidics protocols.

scan_protocol: Affymetrix Microarray Suite 5.0 was utilized to generate Affymetrix present/absent calls. Probe-level Liner Model (PLM) was used to normalize the arrays at probe level and compute model-based expression values using the PM only model. The dChip software www.dchip.org, [3] was used for clustering visualization.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: 93 years oldFemale

label_protocol: Dissected cortical grey mater was cut into small pieces in the frozen states and ~70 mg was homogenized immediately in Trizol (Gibco) and RNA was isolated. RNA that was intact by electrophoresis and had an A260/A280 ratio ≥ 1.9 was used for cDNA synthesis. cDNA synthesis, cRNA synthesis and fragmentation, and preparation of the hybridization cocktail were carried out according to the Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)

growth_protocol: The postmortem brain tissue samples were neuropathologically normal for age, and were derived from non-demented individuals. Tissue was procured in accordance with institutional guidelines. Human cortical grey matter samples were dissected from the frontal pole (Brodmann area 9, 10), and were snap frozen in liquid nitrogen and stored at -85ºC. Human brain samples with a tissue pH > 6.5 were used to exclude prolonged terminal hypoxia

tag: age

value: 93 years old

tag: Sex

value: Female


title: 105  years old Female

description: 105  years old Female

source_name: 105  years old Female

value: 105  years old


title: 89 years old Male

description: 89 years old Male

source_name: 89 years old Male

value: 89 years old

value: Male


title: 92 years old Male

description: 92 years old Male

source_name: 92 years old Male

value: 92 years old


title: 104  years old Male

description: 104  years old Male

source_name: 104  years old Male

value: 104  years old


title: 77 years old Male

description: 77 years old Male

source_name: 77 years old Male

value: 77 years old


title: 80.6 years old Female

description: 80.6 years old Female

source_name: 80.6 years old Female

value: 80.6 years old


title: 90 years old Male

description: 90 years old Male

source_name: 90 years old Male

value: 90 years old


title: 87 years old Female

description: 87 years old Female

source_name: 87 years old Female

value: 87 years old


title: 82 years old Male

description: 82 years old Male

source_name: 82 years old Male

value: 82 years old


title: 103  years old Female

description: 103  years old Female

source_name: 103  years old Female

value: 103  years old


title: 91 years old Male

description: 91 years old Male

source_name: 91 years old Male

value: 91 years old


title: 84 years old Male

description: 84 years old Male

source_name: 84 years old Male

value: 84 years old


title: 94 years old Female

description: 94 years old Female

source_name: 94 years old Female

value: 94 years old


title: 106  years old Female

description: 106  years old Female

source_name: 106  years old Female

value: 106  years old


title: 86 years old Male

description: 86 years old Male

source_name: 86 years old Male

value: 86 years old


title: 91 years old Female

description: 91 years old Female

source_name: 91 years old Female

value: Female


title: 86 years old Female

description: 86 years old Female

source_name: 86 years old Female


title: 61 years old Female

description: 61 years old Female

source_name: 61 years old Female

value: 61 years old


title: 66 years old Male

description: 66 years old Male

source_name: 66 years old Male

value: 66 years old


title: 48 years old Female

description: 48 years old Female

source_name: 48 years old Female

value: 48 years old


title: 45 years old Male

description: 45 years old Male

source_name: 45 years old Male

value: 45 years old

value: Male


title: 70 years old Male

description: 70 years old Male

source_name: 70 years old Male

value: 70 years old


title: 71 years old Female

description: 71 years old Female

source_name: 71 years old Female

value: 71 years old


title: 51 years old Male

description: 51 years old Male

source_name: 51 years old Male

value: 51 years old


title: 52 years old Male

description: 52 years old Male

source_name: 52 years old Male

value: 52 years old


title: 44 years old Female

description: 44 years old Female

source_name: 44 years old Female

value: 44 years old


title: 40 years old Male

description: 40 years old Male

source_name: 40 years old Male

value: 40 years old


title: 44 years old Female_2

description: 44 years old Female_2

source_name: 44 years old Female_2


title: 36 years old Female

description: 36 years old Female

source_name: 36 years old Female

value: 36 years old


title: 25 years old Female_2

description: 25 years old Female_2

source_name: 25 years old Female_2

value: 25 years old


title: 25 years old Female

description: 25 years old Female

source_name: 25 years old Female


title: 34 years old Female

description: 34 years old Female

source_name: 34 years old Female

value: 34 years old


title: 29 years old Male

description: 29 years old Male

source_name: 29 years old Male

value: 29 years old


title: 37 years old Male

description: 37 years old Male

source_name: 37 years old Male

value: 37 years old


title: 33 years old Female

description: 33 years old Female

source_name: 33 years old Female

value: 33 years old

value: Female


title: 24 years old Male

description: 24 years old Male

source_name: 24 years old Male

value: 24 years old


title: 27 years old Female

description: 27 years old Female

source_name: 27 years old Female

value: 27 years old


title: 26 years old Male

description: 26 years old Male

source_name: 26 years old Male

value: 26 years old


title: 29 years old Female

description: 29 years old Female

source_name: 29 years old Female


title: Whole lung of Rbpjk -/- mouse at embryonic day 18.5, replicate 1

status: Public on Mar 13 2014

description: Gene expression data from whole lung of Rbpjk -/- mouse at embryonic day 18.5

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.7), using R version 2.12.0 and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).

source_name: Whole lung of RbpjkCNULL (Shhcre/+; RbpjkFlox/Flox) mouse at embryonic day 18.5

label_protocol: Total RNA (5 ng) was reverse transcribed using Ovation Pico WTA System V2 (Nugen, San Carlos, California). The obtained SPIA-amplified cDNA was purified using Agencourt RNA clean XP Purification Beads and fragmented (5 ng) and labeled with biotin using the Encore Biotin Module (NuGEN, San Carlos, California). SPIA-amplified cDNA and fragmented cDNA quality controls were carried out by running an mRNA Pico assay in the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA from lungs of various stages and genotypes was isolated using TRIzol (Invitrogen).

tag: strain

tag: developmental stage

tag: genotype

value: Rbpjk -/-


title: Whole lung of Rbpjk -/- mouse at embryonic day 18.5, replicate 3


title: Whole lung of Rbpjk -/- mouse at embryonic day 18.5, replicate 2


title: Whole lung of wildtype mouse at embryonic day 18.5, replicate 2

description: Gene expression data from whole lung of wildtype mouse at embryonic day 18.5

source_name: Whole lung of Control (Shh cre/+) mouse at embryonic day 18.5

value: Wildtype


title: Whole lung of wildtype mouse at embryonic day 18.5, replicate 1


title: 26 years old Male_2

description: 26 years old Male_2

source_name: 26 years old Male_2

value: Male


title: Whole lung of wildtype mouse at embryonic day 18.5, replicate 3


title: FRT_dex_IgG

status: Public on Nov 05 2013

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: isogenic HEK293 control FRT cells were created by using the Flp-In System (Invitrogen)

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim the raw  reads to 40 bp and sequence duplicates were collapsed
the reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9. with the command line: -e 70 -l 50 -n 1 -k 1 -m1 \ -t -p 12 -q -S --best
peaks were called using MACS program version 1.4.2. with the following setting: bandwidth (100 for GR; 200 for SUMO_2_3), mfold (10,30 for GR; 10,15 for SUMO_2_3), p-value cut-off (0.0001), Input as control for GR and IgG for SUMO_2_3
statistically significant peaks had tags (> 50), fold enrichment (> 8), false discovery rate (< 0.1) and peak had to be present in two biological replicates
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks from each immunoprecipitated sample: chr, start, end, length, summit, tags, -log10(p-value), fold enrichment, FDR(%)

source_name: Isogenic HEK293 Cells

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator

extract_protocol:
Lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, as utilized at the Gene Core in EMBL, Heidelberg, Germany

treatment_protocol: Isogenic HEK293 cells were seeded at 70 % confluence in 175 cm2 bottles and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated with 100 nM of dexamethasone for 1 h prior ChIP

value: Human Embryonal Kidney Cells

tag: chip antibody

value: IgG (Santa Cruz, sc-2027, lot # A2412)

tag: stably expressing

value: dexamethasone

tag: concentration

tag: time

value: 1 h


title: RNA-Seq analysis of cDNA_Lib 2 derived from human hippocampus middle cells; cDNA_Lib 2

status: Public on Jun 22 2013

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15433
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 2.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Brain Hippocampus Middle, Donor 149 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16656
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 103,897,010
PERCENT_READS_MAPPING_TO_UCSC_GENES: 69.68
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.58

**********************************************************************

ANALYSIS FILE NAME: GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 2.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Brain Hippocampus Middle, Donor 149 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16665
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BHM mRNA 49
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle mRNA-Seq Donor 149 Library cDNA_Lib 2 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 103,897,010
PERCENT_READS_MAPPING_TO_UCSC_GENES: 69.68
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.58

**********************************************************************

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; cDNA_Lib 2

extract_protocol: Library construction protocol: Strand specific cDNA libraries were constructed for Illumina sequencing using the dUTP method essentially as described in S. Zhong et al, Cold Spring Harbor Protoc 8, 940 - 949 (2011).

tag: sample common name

value: Brain, Hippocampus Middle

tag: sra sample accession

value: Post-Mortem

value: no AD evident at demise

tag: disease

value: Hippocampus Middle

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 1.8X SPRI cleanup (no size selection)

value: Dynabeads mRNA purification kit (Invitrogen)

value: 95C  2mins, 10 cycles of: 98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C

value: NNNNNN

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: PFU Ultra II

value: CAAGCAGAAGACGGCATACGAGAT

value: 98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min.

value: mRNA-Seq

value: We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h.


title: Airway smooth muscle, control animal 1

description: Gene expression data from microdissected airway smooth muscle from control animal

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.10.0) and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).

source_name: Microdissected airway smooth muscle

growth_protocol: SMA-GFP mice were crossed with NG2-DsRed mice.  Double fluorescent mice were used.  In these mice, bronchial smooth muscle is singly GFP+, while vascular smooth muscle is GFP+;DsRed+/

extract_protocol: Total RNA was isolated using QIAGEN’s RNeasy kit (Qiagen, Valencia, CA) and sample integrity was verified using RNA 6000 Pico Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were sensitized by two IP injections of 50 ug OVA at day 0 and day 7 followed by 5 days of OVA nebulization between day 14-day 18.  Mice were sacrificed on day 19 followed by cell isolation.

tag: group

value: Control


title: Airway smooth muscle, asthma animal 1

description: Gene expression data from microdissected airway smooth muscle from animal with experimentally-induced asthma

value: Asthma


title: SB-431542 - 1

source_name: MDA-MB-231-LM2-4 cell line

tag: cell line

value: MDA-MB-231-LM2-4 breast cancer cells

tag: treatment

value: SB-431542 (an inhibitor of the TBRI recpeptor) plus TGF-beta


title: Airway smooth muscle, control animal 2


title: Cavin-1 knockout 4

status: Public on Jun 07 2013

description: Alveolar macrophages from Cavin-1 knockout 4

source_name: Alveolar macrophages, C57BL/6 Cavin-1 -/-

growth_protocol: Cavin1 knock-out mice on a C57Bl/6 background were generated and studies were performed on 2 month old female mice.

value: Cavin-1 -/-

tag: genetic background

tag: cell type

value: alveolar macrophage


title: Cavin-1 knockout 2

description: Alveolar macrophages from Cavin-1 knockout 2


title: Cavin-1 knockout 3

description: Alveolar macrophages from Cavin-1 knockout 3


title: Airway smooth muscle, asthma animal 2


title: Airway smooth muscle, control animal 3


title: Airway smooth muscle, asthma animal 3


title: Cavin-1 knockout 1

description: Alveolar macrophages from Cavin-1 knockout 1


title: Wild-type 3

description: Alveolar macrophages from wild-type 3

source_name: Alveolar macrophages, C57BL/6 wild-type mouse

value: wild-type


title: Wild-type 2

description: Alveolar macrophages from wild-type 2


title: TCDD 3

status: Public on Dec 05 2012

hyb_protocol: Purified cRNA was fragmented and hybridized (15 ug) to the GeneChip Zebrafish Genome Array (Affymetrix, Santa Clara, CA) for 16 hours in GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinilated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Sataining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Gene expression levels were generated using the MicroArray Suite 5.0 (MAS5) algorithm in Affymetrix Gene Expression Console, scaling to a global mean intensity of 500.

organism: Danio rerio

source_name: 1nM TCDD

label_protocol: Total RNA (1 ug) was reverse transcribed using One Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA) and  the obtained double-stranded cDNA was purified with GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). The obtained cDNA was used as a template for in vitro transcription using GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA). The obtained Biotin-labeled cRNA was purified using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA)

growth_protocol: Adult wild-type zebrafish (Danio rerio) from a commercial supplier (EkkWill, Gibsonton, FL) were maintained in 30 gallon aquaria at 28.5 degrees Celsius in a 14:10 hour light: dark cycle.  Embryos were collected by natural spawning, washed and incubated, 100 to 120 embryos/plate in 150mL petri plates in 50mL egg water (Westerfield 2000) at 28.5 degrees Celsius in a 14:10 hour light: dark cycle.

extract_protocol: ~30 larvae/sample were collected at 96 hpf in 1.5ml microfuge tubes, quick-frozen on dry ice, and stored at -70 degrees C for RNA extraction.  Pooled frozen embryos were homogenized in Tri Reagent (Sigma), according to the manufacturer’s protocol to extract total RNA.  RNA was resuspended in Diethylpyrocarbonate (DEPC) -treated water and treated with DNaseI (Roche, Indianapolis, IN).  Quantity and quality were confirmed by UV spectrophotometry and gel electrophoresis. RNA was re-purified using the RNeasy kit according to manufacturer’s instructions (Qiagen, Valencia, CA)

treatment_protocol: Treatment chemicals were dissolved in dimethylsulfoxide (DMSO) and added to embryo media between 72 and 96 hpf

tag: tissue

value: whole larvae

value: 96hpf (hours post-fertilization)


title: E2 2

source_name: 0.1 microM E2


title: Wild-type 1

description: Alveolar macrophages from wild-type 1


title: E2+TCDD 3

source_name: 0.1microM E2+1nM TCDD


title: E2+TCDD 2


title: TCDD 2


title: TCDD 1


title: E2 3


title: DMSO 3

source_name: 0.1% DMSO


title: E2 1


title: E2+TCDD 1


title: DMSO 1


title: Severe 867

status: Public on Aug 01 2011

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: Severe AD; correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with Expression Console version 1.1 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: laser capture CA1 tissue gray matter from formalin fixed, paraffin embedded specimens

label_protocol: 50 ng of extracted purified nucleic acid underwent RNA amplification using WT-Ovation FFPE System (NuGen) followed by FL-Ovation cDNA Biotin Module V2 (NuGen) for labeling and microarray (Affymetrix HGU133 v2) hybridization.

extract_protocol: RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Ambion)

tag: Sex

value: Female

tag: age

value: 94 years old

tag: disease status

value: Severe


title: DMSO 2

tag: developmental stage


title: Severe 872

value: 79 years old


title: Severe 1036

value: 93 years old


title: Severe 819


title: Severe 701

value: Male

value: 85 years old


title: Moderate 1031

description: Moderate AD; correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores

value: 86 years old

value: Moderate


title: Moderate 832

value: 89 years old


title: Moderate 826


title: Moderate 965

value: 82 years old


title: Moderate 856

value: 83 years old


title: Moderate 1037


title: Severe 807


title: Moderate 1025

value: 81 years old


title: Severe 723

value: 65 years old


title: Control 1040

description: Control; correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores

value: 87 years old

value: Control


title: Incipient 720

description: Incipient AD; correlation of the expression of each gene was tested with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores

value: 95 years old

value: Incipient


title: Incipient 715

value: Female

value: 101 years old


title: Control 1008

value: 92 years old


title: Moderate 1020

value: 79 years old


title: Incipient 994


title: Incipient 1043

value: 97 years old


title: Incipient 1034

value: Male

value: 88 years old


title: Incipient 1019


title: Incipient 1029

value: 91 years old


title: Control 1018


title: Control 1012

value: 80 years old


title: Control 1030


title: Control 1015

value: 75 years old


title: mRNA parietal lobe Control number 15

status: Public on Jan 31 2010

city: Los Angeles

first: Juan

last: Nunez-Iglesias

address: 1050 Childs Way, RRI-201

department: Computational Biology

institute: University of Southern California

hyb_protocol: Affymetrix EukGE-WS2v5_450

scan_protocol: Affymetrix type M10 scanner, Affymetrix GeneChip Operating Software

data_processing: R/Bioconductor, RMA normalization

label: biotin (Affymetrix IVT Labeling Kit)

source_name: Parietal lobe, Control

label_protocol: Affymetrix IVT Labeling Kit

extract_protocol: TriReagent (Sigma-Aldrich) followed by purification with Rneasy mini columns (Qiagen)

tag: gender

value: female

tag: pmi

tag: diagnosis

value: normal

tag: b&b score

value: III

value: Parietal lobe


title: mRNA parietal lobe Control number 18


title: mRNA parietal lobe Control number 10

value: male

value: O


title: mRNA parietal lobe Alzheimer's disease number 2

source_name: Parietal lobe, Alzheimer's disease

value: AD

value: V-VI


title: mRNA parietal lobe Alzheimer's disease number 3

value: VI


title: Control 1003

value: Control


title: mRNA parietal lobe Alzheimer's disease number 16


title: mRNA parietal lobe Control number 6

value: II


title: WKY_Nicotine_Rep2_Normalized

status: Public on Sep 16 2009

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

hyb_protocol: Labeled cRNA targets were fragmented at 94ºC for 20 minutes prior hybridization with arrays at 37ºC during 18 hours. After the hybridization, the bioarrays were washed and bound targets were detected following incubation with Cy5-Streptavidin (GE Healthcare, UK). The bioarrays were washed, dried and protected from light. All samples processed in parallel and the arrays were incubated simultaneously using the same working solution to limit technical variation across the experiments.

scan_protocol: Following the hybridization, bioarrays were scanned immediately in a GenePix 4000B scanner (Molecular Dynamics, USA).

data_processing:
CodeLink Expression Analysis software (GE Healthcare) was used to extract background-subtracted spot intensities from microarray images.
To make experiments comparable, intensity data from different hybridizations were normalized by the quantile method.

label: biotin-NTP

label_protocol: Target labeling and hybridization was performed strictly as recommended by the array manufacturer (GE Healthcare, UK). In brief, the purified and high-quality total RNA was used in reverse transcription reactions to convert messenger RNA (mRNA) in double-stranded cDNA prior to biotin labeling. cRNA was synthesized by in vitro transcription of cDNA and simultaneously labeled with biotin-NTP mix. The samples were filtered to recover biotinilated cRNA. Assessment of cRNA concentration, purity and quality was done using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). All the samples presented high quality and purity (260/280 ratio of 2.0).

extract_protocol: Cells from three dishes were pooled and total RNA was extracted according to the manufacturer instructions using the RNAspin Mini Kit (GE Healthcare, UK). The RNA was purified and treated with DNAse before the assessment of its concentration and quality by UV spectrophotometry and agarose gel electrophoresis, respectively.

treatment_protocol: Cultured cells (n=3 from each strain) were treated with 10μM of nicotine (Sigma), diluted in fresh culture medium, over 24 hours. Cell cultures kept for the same period of time in fresh medium without nicotine were used as a control. The experiment was repeated three times using different pools of animals. At the end of the treatment, cells from SHR or WKY animals, treated or untreated with nicotine, were lysed for RNA extraction.

tag: Pons and medulla oblongata of one-day old SHR and WKY rats (n=20) were dissected out and dissociated in cold isotonic salt solution, pH 7.4. Cells were suspended in Neurobasal A media (Invitrogen) supplemented with L-glutamine (250umol/L, Sigma), glutamax (250umol/L, Gibco), B27 (2%, Gibco) e gentamicin (40mg/L, Gibco). Viable cells were counted and plated on poly-D-lysine-coated culture dishes (35mm, Nunclon, USA) at the concentration of 1800 cells/mm2. The experiment was repeated three times for each strain using different pools of animal tissue. Cultures were kept in a humidified incubator with 5%CO2 and 95% air, at 37ºC, for 9 days prior to mRNA extraction.


title: Control 976

value: 85 years old


title: SHR_Nicotine_Rep1_Normalized


title: WKY_Rep2_Normalized

status: Public on Dec 31 2008

source_name: WKY


title: WKY_Nicotine_Rep3_Normalized


title: WKY_Nicotine_Rep1_Normalized


title: SHR_Nicotine_Rep3_Normalized


title: WKY_Rep3_Normalized


title: SHR_Nicotine_Rep2_Normalized


title: mRNA parietal lobe Alzheimer's disease number 12

value: V


title: SHR_Rep1_Normalized

source_name: SHR


title: SuperiorFrontalGyrus_male_66yrs_indiv63

status: Public on Oct 09 2008

description: Postmortem brain tissue from cognitively intact individual.

hyb_protocol: Using a robotics system (Biomek FX MicroArray Plex SA System; Beckman Coultier) to optimize consistency in processing and minimize handling variability, each fragmented, biotin-labeled cRNA sample (30 mg) was individually hybridized to an Affymetrix Hg-U133 plus 2.0 chip for 16 hours and rotated at 13 rpm at 50C.

scan_protocol: The chips were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: GC-RMA expression values were obtained from CEL files using GeneSpring 7.3.1 software.  PLIER expression values were obtained using Expression Console software using default settings.  PLIER and GC-RMA data were processed using GeneSpring 7.0 software, with default normalizations (Data transformation:set values<0.01 to 0.01; per chip: normalize to 50th percentile; per gene: normalize to median).

source_name: brain, superior frontal gyrus, male, 66 years

label_protocol: Total RNA (10 ug) from each sample was used to generate first strand cDNA using a T7-linked-(dT)24 primer, followed by in vitro transcription using the ENZO BioArray High-Yield RNA transcript labeling kit (ENZO Farmingdale, NY) to generate biotin-labeled cRNA target.

extract_protocol: Total RNA was extracted from 10-200 mg of frozen, unfixed tissue using Trizol reagent (Invitrogen, Carlsbad CA), and purified using quick spin columns (Qiagen, Valencia CA).  RNA quality was assessed using the Agilent BioAnalyzer (Agilent Technologies, Palo Alto, CA) and UV spectrophotometer for the presence of sharp peaks and 28S/18S RNA.

tag: individual

tag: brain region

value: superior frontal gyrus

tag: age (yrs)


title: SuperiorFrontalGyrus_male_80yrs_indiv15

status: Public on May 01 2009

description: Brain from cognitively intact individual.

source_name: brain, superior frontal gyrus, male, 80 years


title: SHR_Rep2_Normalized


title: WKY_Rep1_Normalized


title: SuperiorFrontalGyrus_female_82yrs_indiv98

source_name: brain, superior frontal gyrus, female, 82 years


title: SHR_Rep3_Normalized


title: EntorhinalCortex_female_82yrs_indiv98

source_name: brain, entorhinal cortex, female, 82 years

value: entorhinal cortex


title: Hippocampus_female_82yrs_indiv98

source_name: brain, hippocampus, female, 82 years

value: hippocampus


title: PostcentralGyrus_female_82yrs_indiv98

source_name: brain, postcentral gyrus, female, 82 years

value: postcentral gyrus


title: SuperiorFrontalGyrus_male_75yrs_indiv96

source_name: brain, superior frontal gyrus, male, 75 years


title: EntorhinalCortex_male_75yrs_indiv96

source_name: brain, entorhinal cortex, male, 75 years


title: SuperiorFrontalGyrus_female_91yrs_indiv94

source_name: brain, superior frontal gyrus, female, 91 years

value: female


title: PostcentralGyrus_female_91yrs_indiv94

source_name: brain, postcentral gyrus, female, 91 years


title: SuperiorFrontalGyrus_female_47yrs_indiv88

source_name: brain, superior frontal gyrus, female, 47 years


title: PostcentralGyrus_male_69yrs_indiv93

source_name: brain, postcentral gyrus, male, 69 years


title: Hippocampus_male_75yrs_indiv96

source_name: brain, hippocampus, male, 75 years


title: EntorhinalCortex_male_69yrs_indiv93

source_name: brain, entorhinal cortex, male, 69 years


title: SuperiorFrontalGyrus_male_69yrs_indiv93

source_name: brain, superior frontal gyrus, male, 69 years


title: PostcentralGyrus_female_47yrs_indiv88

source_name: brain, postcentral gyrus, female, 47 years


title: EntorhinalCortex_female_47yrs_indiv88

source_name: brain, entorhinal cortex, female, 47 years


title: Hippocampus_male_69yrs_indiv93

source_name: brain, hippocampus, male, 69 years


title: PostcentralGyrus_male_45yrs_indiv87

source_name: brain, postcentral gyrus, male, 45 years


title: Hippocampus_female_91yrs_indiv94

source_name: brain, hippocampus, female, 91 years


title: Hippocampus_female_47yrs_indiv88

source_name: brain, hippocampus, female, 47 years


title: EntorhinalCortex_male_45yrs_indiv87

source_name: brain, entorhinal cortex, male, 45 years


title: Hippocampus_male_45yrs_indiv87

source_name: brain, hippocampus, male, 45 years


title: SuperiorFrontalGyrus_male_42yrs_indiv86

source_name: brain, superior frontal gyrus, male, 42 years


title: EntorhinalCortex_female_91yrs_indiv94

source_name: brain, entorhinal cortex, female, 91 years


title: PostcentralGyrus_male_42yrs_indiv86

source_name: brain, postcentral gyrus, male, 42 years


title: SuperiorFrontalGyrus_male_45yrs_indiv87

source_name: brain, superior frontal gyrus, male, 45 years


title: EntorhinalCortex_male_42yrs_indiv86

source_name: brain, entorhinal cortex, male, 42 years


title: EntorhinalCortex_male_22yrs_indiv85

source_name: brain, entorhinal cortex, male, 22 years


title: PostcentralGyrus_male_22yrs_indiv85

source_name: brain, postcentral gyrus, male, 22 years


title: SuperiorFrontalGyrus_male_33yrs_indiv84

source_name: brain, superior frontal gyrus, male, 33 years


title: SuperiorFrontalGyrus_male_22yrs_indiv85

source_name: brain, superior frontal gyrus, male, 22 years


title: PostcentralGyrus_male_33yrs_indiv84

source_name: brain, postcentral gyrus, male, 33 years


title: PostcentralGyrus_female_48yrs_indiv81

source_name: brain, postcentral gyrus, female, 48 years


title: Hippocampus_male_20yrs_indiv83

source_name: brain, hippocampus, male, 20 years


title: SuperiorFrontalGyrus_female_48yrs_indiv81

source_name: brain, superior frontal gyrus, female, 48 years


title: SuperiorFrontalGyrus_female_30yrs_indiv82

source_name: brain, superior frontal gyrus, female, 30 years


title: EntorhinalCortex_male_33yrs_indiv84

source_name: brain, entorhinal cortex, male, 33 years


title: EntorhinalCortex_female_44yrs_indiv80

source_name: brain, entorhinal cortex, female, 44 years


title: PostcentralGyrus_male_20yrs_indiv83

source_name: brain, postcentral gyrus, male, 20 years


title: Hippocampus_female_44yrs_indiv80

source_name: brain, hippocampus, female, 44 years


title: Hippocampus_female_48yrs_indiv81

source_name: brain, hippocampus, female, 48 years


title: EntorhinalCortex_male_20yrs_indiv83

source_name: brain, entorhinal cortex, male, 20 years


title: PostcentralGyrus_female_44yrs_indiv80

source_name: brain, postcentral gyrus, female, 44 years


title: EntorhinalCortex_male_69yrs_indiv8

source_name: brain, entorhinal cortex, male, 69 years


title: Hippocampus_female_30yrs_indiv82

source_name: brain, hippocampus, female, 30 years


title: EntorhinalCortex_female_30yrs_indiv82

source_name: brain, entorhinal cortex, female, 30 years


title: Hippocampus_male_20yrs_indiv78


title: SuperiorFrontalGyrus_female_44yrs_indiv80

source_name: brain, superior frontal gyrus, female, 44 years


title: EntorhinalCortex_female_48yrs_indiv81

source_name: brain, entorhinal cortex, female, 48 years


title: Hippocampus_male_69yrs_indiv8

source_name: brain, hippocampus, male, 69 years


title: SuperiorFrontalGyrus_male_20yrs_indiv83

source_name: brain, superior frontal gyrus, male, 20 years


title: SuperiorFrontalGyrus_male_20yrs_indiv78


title: PostcentralGyrus_male_69yrs_indiv8

source_name: brain, postcentral gyrus, male, 69 years


title: PostcentralGyrus_female_36yrs_indiv79

source_name: brain, postcentral gyrus, female, 36 years


title: SuperiorFrontalGyrus_male_69yrs_indiv8

source_name: brain, superior frontal gyrus, male, 69 years


title: SuperiorFrontalGyrus_male_20yrs_indiv77


title: SuperiorFrontalGyrus_female_36yrs_indiv79

source_name: brain, superior frontal gyrus, female, 36 years


title: EntorhinalCortex_male_20yrs_indiv78


title: PostcentralGyrus_male_20yrs_indiv78


title: Hippocampus_male_20yrs_indiv77

source_name: brain, hippocampus, male, 20 years


title: SuperiorFrontalGyrus_female_26yrs_indiv76

source_name: brain, superior frontal gyrus, female, 26 years


title: PostcentralGyrus_male_20yrs_indiv77

source_name: brain, postcentral gyrus, male, 20 years


title: EntorhinalCortex_female_26yrs_indiv76

source_name: brain, entorhinal cortex, female, 26 years


title: Hippocampus_male_86yrs_indiv73

source_name: brain, hippocampus, male, 86 years


title: SuperiorFrontalGyrus_male_40yrs_indiv68

source_name: brain, superior frontal gyrus, male, 40 years


title: SuperiorFrontalGyrus_male_86yrs_indiv73

source_name: brain, superior frontal gyrus, male, 86 years


title: PostcentralGyrus_male_40yrs_indiv68

source_name: brain, postcentral gyrus, male, 40 years


title: PostcentralGyrus_female_26yrs_indiv76

source_name: brain, postcentral gyrus, female, 26 years


title: EntorhinalCortex_male_52yrs_indiv71

source_name: brain, entorhinal cortex, male, 52 years


title: PostcentralGyrus_male_52yrs_indiv71

source_name: brain, postcentral gyrus, male, 52 years


title: EntorhinalCortex_male_40yrs_indiv68

source_name: brain, entorhinal cortex, male, 40 years


title: PostcentralGyrus_male_86yrs_indiv73

source_name: brain, postcentral gyrus, male, 86 years


title: PostcentralGyrus_male_75yrs_indiv72

source_name: brain, postcentral gyrus, male, 75 years


title: EntorhinalCortex_male_86yrs_indiv73

source_name: brain, entorhinal cortex, male, 86 years


title: SuperiorFrontalGyrus_male_52yrs_indiv71

source_name: brain, superior frontal gyrus, male, 52 years


title: Hippocampus_male_52yrs_indiv71

source_name: brain, hippocampus, male, 52 years


title: PostcentralGyrus_male_69yrs_indiv67

source_name: brain, postcentral gyrus, male, 69 years


title: Hippocampus_male_69yrs_indiv67

source_name: brain, hippocampus, male, 69 years


title: SuperiorFrontalGyrus_male_75yrs_indiv72

source_name: brain, superior frontal gyrus, male, 75 years


title: SuperiorFrontalGyrus_male_21yrs_indiv66

source_name: brain, superior frontal gyrus, male, 21 years


title: EntorhinalCortex_male_21yrs_indiv66

source_name: brain, entorhinal cortex, male, 21 years


title: PostcentralGyrus_male_21yrs_indiv66

source_name: brain, postcentral gyrus, male, 21 years


title: EntorhinalCortex_male_20yrs_indiv77

source_name: brain, entorhinal cortex, male, 20 years


title: PostcentralGyrus_female_85yrs_indiv54

source_name: brain, postcentral gyrus, female, 85 years


title: SuperiorFrontalGyrus_female_91yrs_indiv59

source_name: brain, superior frontal gyrus, female, 91 years


title: EntorhinalCortex_female_85yrs_indiv54

source_name: brain, entorhinal cortex, female, 85 years


title: SuperiorFrontalGyrus_male_70yrs_indiv53

source_name: brain, superior frontal gyrus, male, 70 years


title: PostcentralGyrus_male_70yrs_indiv53

source_name: brain, postcentral gyrus, male, 70 years


title: SuperiorFrontalGyrus_female_85yrs_indiv54

source_name: brain, superior frontal gyrus, female, 85 years


title: PostcentralGyrus_female_64yrs_indiv52

source_name: brain, postcentral gyrus, female, 64 years


title: EntorhinalCortex_female_64yrs_indiv52

source_name: brain, entorhinal cortex, female, 64 years


title: SuperiorFrontalGyrus_female_70yrs_indiv47

source_name: brain, superior frontal gyrus, female, 70 years


title: PostcentralGyrus_female_70yrs_indiv47

source_name: brain, postcentral gyrus, female, 70 years


title: SuperiorFrontalGyrus_female_74yrs_indiv38

source_name: brain, superior frontal gyrus, female, 74 years


title: SuperiorFrontalGyrus_female_64yrs_indiv52

source_name: brain, superior frontal gyrus, female, 64 years


title: Hippocampus_female_70yrs_indiv47

source_name: brain, hippocampus, female, 70 years


title: SuperiorFrontalGyrus_male_85yrs_indiv46

source_name: brain, superior frontal gyrus, male, 85 years


title: Hippocampus_male_85yrs_indiv46

source_name: brain, hippocampus, male, 85 years


title: PostcentralGyrus_female_90yrs_indiv40

source_name: brain, postcentral gyrus, female, 90 years


title: SuperiorFrontalGyrus_male_97yrs_indiv34

source_name: brain, superior frontal gyrus, male, 97 years


title: Hippocampus_female_64yrs_indiv52

source_name: brain, hippocampus, female, 64 years


title: SuperiorFrontalGyrus_female_44yrs_indiv42

source_name: brain, superior frontal gyrus, female, 44 years


title: PostcentralGyrus_male_85yrs_indiv46

source_name: brain, postcentral gyrus, male, 85 years


title: PostcentralGyrus_female_37yrs_indiv45

source_name: brain, postcentral gyrus, female, 37 years


title: Hippocampus_female_74yrs_indiv38

source_name: brain, hippocampus, female, 74 years


title: EntorhinalCortex_female_74yrs_indiv38

source_name: brain, entorhinal cortex, female, 74 years


title: SuperiorFrontalGyrus_female_37yrs_indiv45

source_name: brain, superior frontal gyrus, female, 37 years


title: EntorhinalCortex_female_34yrs_indiv35

source_name: brain, entorhinal cortex, female, 34 years


title: EntorhinalCortex_female_70yrs_indiv47

source_name: brain, entorhinal cortex, female, 70 years


title: EntorhinalCortex_male_85yrs_indiv46

source_name: brain, entorhinal cortex, male, 85 years


title: PostcentralGyrus_female_74yrs_indiv38

source_name: brain, postcentral gyrus, female, 74 years


title: EntorhinalCortex_female_37yrs_indiv45

source_name: brain, entorhinal cortex, female, 37 years


title: Hippocampus_female_91yrs_indiv40-04

source_name: brain, hippocampus, female, 91 years


title: PostcentralGyrus_male_97yrs_indiv34

source_name: brain, postcentral gyrus, male, 97 years


title: SuperiorFrontalGyrus_female_34yrs_indiv35

source_name: brain, superior frontal gyrus, female, 34 years


title: Hippocampus_male_97yrs_indiv34

source_name: brain, hippocampus, male, 97 years


title: PostcentralGyrus_female_74yrs_indiv30


title: EntorhinalCortex_male_97yrs_indiv34

source_name: brain, entorhinal cortex, male, 97 years


title: SuperiorFrontalGyrus_male_28yrs_indiv29

source_name: brain, superior frontal gyrus, male, 28 years


title: EntorhinalCortex_male_28yrs_indiv29

source_name: brain, entorhinal cortex, male, 28 years


title: SuperiorFrontalGyrus_male_83yrs_indiv28

source_name: brain, superior frontal gyrus, male, 83 years


title: SuperiorFrontalGyrus_female_74yrs_indiv30

source_name: brain, superior frontal gyrus, female, 74 years


title: PostcentralGyrus_male_83yrs_indiv28

source_name: brain, postcentral gyrus, male, 83 years


title: PostcentralGyrus_male_28yrs_indiv29

source_name: brain, postcentral gyrus, male, 28 years


title: EntorhinalCortex_female_44yrs_indiv42

source_name: brain, entorhinal cortex, female, 44 years


title: SuperiorFrontalGyrus_female_74yrs_indiv18


title: PostcentralGyrus_female_74yrs_indiv21


title: EntorhinalCortex_male_83yrs_indiv28

source_name: brain, entorhinal cortex, male, 83 years


title: Hippocampus_female_74yrs_indiv21

source_name: brain, hippocampus, female, 74 years


title: PostcentralGyrus_female_92yrs_indiv26

source_name: brain, postcentral gyrus, female, 92 years


title: SuperiorFrontalGyrus_female_45yrs_indiv17

source_name: brain, superior frontal gyrus, female, 45 years


title: Hippocampus_male_83yrs_indiv28

source_name: brain, hippocampus, male, 83 years


title: SuperiorFrontalGyrus_female_92yrs_indiv26

source_name: brain, superior frontal gyrus, female, 92 years


title: Hippocampus_female_74yrs_indiv18


title: Hippocampus_female_45yrs_indiv17

source_name: brain, hippocampus, female, 45 years


title: EntorhinalCortex_female_45yrs_indiv17

source_name: brain, entorhinal cortex, female, 45 years


title: SuperiorFrontalGyrus_female_74yrs_indiv21


title: EntorhinalCortex_female_99yrs_indiv2

source_name: brain, entorhinal cortex, female, 99 years


title: SuperiorFrontalGyrus_female_99yrs_indiv2

source_name: brain, superior frontal gyrus, female, 99 years


title: PostcentralGyrus_female_99yrs_indiv2

source_name: brain, postcentral gyrus, female, 99 years


title: Hippocampus_female_99yrs_indiv2

source_name: brain, hippocampus, female, 99 years


title: SuperiorFrontalGyrus_female_91yrs_indiv27

source_name: brain, superior frontal gyrus, female, 91 years


title: EntorhinalCortex_female_74yrs_indiv18

source_name: brain, entorhinal cortex, female, 74 years


title: PostcentralGyrus_female_91yrs_indiv27

source_name: brain, postcentral gyrus, female, 91 years


title: EntorhinalCortex_female_74yrs_indiv21


title: Hippocampus_male_91yrs_indiv16-07

source_name: brain, hippocampus, male, 91 years


title: PostcentralGyrus_male_80yrs_indiv15

source_name: brain, postcentral gyrus, male, 80 years


title: PostcentralGyrus_male_95yrs_indiv14

source_name: brain, postcentral gyrus, male, 95 years


title: Hippocampus_male_80yrs_indiv15

source_name: brain, hippocampus, male, 80 years


title: SuperiorFrontalGyrus_male_45yrs_indiv12

source_name: brain, superior frontal gyrus, male, 45 years


title: SuperiorFrontalGyrus_male_95yrs_indiv14

source_name: brain, superior frontal gyrus, male, 95 years


title: EntorhinalCortex_male_95yrs_indiv14

source_name: brain, entorhinal cortex, male, 95 years


title: EntorhinalCortex_male_80yrs_indiv15

source_name: brain, entorhinal cortex, male, 80 years


title: Hippocampus_male_95yrs_indiv14

source_name: brain, hippocampus, male, 95 years


title: PostcentralGyrus_male_45yrs_indiv12

source_name: brain, postcentral gyrus, male, 45 years


title: Hippocampus_female_82yrs_indiv111

source_name: brain, hippocampus, female, 82 years


title: EntorhinalCortex_male_45yrs_indiv12

source_name: brain, entorhinal cortex, male, 45 years


title: Hippocampus_female_96yrs_indiv105

source_name: brain, hippocampus, female, 96 years


title: Hippocampus_male_84yrs_indiv108

source_name: brain, hippocampus, male, 84 years


title: Hippocampus_male_82yrs_indiv106

source_name: brain, hippocampus, male, 82 years


title: Hippocampus_female_87yrs_indiv109

source_name: brain, hippocampus, female, 87 years


title: SuperiorFrontalGyrus_female_91yrs_indiv10

source_name: brain, superior frontal gyrus, female, 91 years


title: PostcentralGyrus_female_91yrs_indiv10

source_name: brain, postcentral gyrus, female, 91 years


title: non-demented individual with intermediate Alzheimer's pathologies - primary visual cortex 5

status: Public on Dec 05 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Affymetrix Human Genome U133 Plus 2.0 array

hyb_protocol: Affymetrix manufacturer's protocol

scan_protocol: Affymetrix manufacturer's protocol

data_processing: MAS 5.0; target intensity scaling to 150

source_name: primary visual cortex 5

label_protocol: Affymetrix double round amplification protocol

extract_protocol: Arcturus PicoPure RNA isolation kit

tag: primary visual cortex

value: layer III non-tangle bearing neurons


title: PostcentralGyrus_female_34yrs_indiv35

source_name: brain, postcentral gyrus, female, 34 years


title: non-demented individual with intermediate Alzheimer's pathologies - primary visual cortex 4

source_name: primary visual cortex 4


title: non-demented individual with intermediate Alzheimer's pathologies - primary visual cortex 2

source_name: primary visual cortex 2


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 4

source_name: superior frontal gyrus 4

tag: superior frontal gyrus


title: non-demented individual with intermediate Alzheimer's pathologies - primary visual cortex 1

source_name: primary visual cortex 1


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 2

source_name: superior frontal gyrus 2


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 5

source_name: middle temporal gyrus 5

tag: middle temporal gyrus


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 4

source_name: middle temporal gyrus 4


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 5

source_name: superior frontal gyrus 5


title: non-demented individual with intermediate Alzheimer's pathologies - posterior cingulate cortex 5

source_name: posterior cingulate cortex 5

tag: posterior cingulate cortex


title: non-demented individual with intermediate Alzheimer's pathologies - posterior cingulate cortex 3

source_name: posterior cingulate cortex 3


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 1

source_name: superior frontal gyrus 1


title: non-demented individual with intermediate Alzheimer's pathologies - posterior cingulate cortex 2

source_name: posterior cingulate cortex 2


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 6

source_name: middle temporal gyrus 6


title: non-demented individual with intermediate Alzheimer's pathologies - posterior cingulate cortex 4

source_name: posterior cingulate cortex 4

value: layer III non-tangle bearing neurons from the posterior cingulate cortex of mild cognitive impaired post-mortem brains


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 3

source_name: superior frontal gyrus 3


title: non-demented individual with intermediate Alzheimer's pathologies - primary visual cortex 3

source_name: primary visual cortex 3


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 1

source_name: middle temporal gyrus 1


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 2

source_name: middle temporal gyrus 2


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 6

source_name: hippocampus 6

tag: hippocampus (ca1)


title: non-demented individual with intermediate Alzheimer's pathologies - superior frontal gyrus 6

source_name: superior frontal gyrus 6


title: non-demented individual with intermediate Alzheimer's pathologies - middle temporal gyrus 3

source_name: middle temporal gyrus 3


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 3

source_name: hippocampus 3


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 2

source_name: hippocampus 2


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 5

source_name: hippocampus 5


title: non-demented individual with intermediate Alzheimer's pathologies - entorhinal cortex 2

source_name: entorhinal cortex 2

tag: entorhinal cortex

value: layer II stellate non-tangle bearing neurons


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 4

source_name: hippocampus 4


title: non-demented individual with intermediate Alzheimer's pathologies - hippocampus 1

source_name: hippocampus 1


title: non-demented individual with intermediate Alzheimer's pathologies - entorhinal cortex 1

source_name: entorhinal cortex 1


title: non-demented individual with intermediate Alzheimer's pathologies - entorhinal cortex 6

source_name: entorhinal cortex 6


title: non-demented individual with intermediate Alzheimer's pathologies - entorhinal cortex 4

source_name: entorhinal cortex 4


title: non-demented individual with intermediate Alzheimer's pathologies - posterior cingulate cortex 1

source_name: posterior cingulate cortex 1


title: VCX_affected_8

status: Public on Oct 23 2007

description:
arrayconsortium.tgen.org::biosample.459602
cortical layer III neurons

hyb_protocol: Affymetrix's manufacturer's protocol: hybridization onto Affymetrix Human Genome U133 Plus 2.0 array

scan_protocol: Affymetrix GCOS

data_processing: MAS5.0; target scaling to 150

source_name: brain, Primary visual cortex

label_protocol: Affymetrix double-round expression profiling

extract_protocol: Arcturus PicoPure

tag: Sample Amount

value: 10 ng

tag: Bio-Source Name

tag: Organism

value: Human

tag: Organ/Tissue Type

value: brain

tag: Organ Region

value: Primary Visual Cortex

tag: Cell Type

value: pyramidal neuron

tag: Ethnicity

value: unknown

tag: Developmental Stage

value: Adult

tag: Disease State

value: Alzheimer's Disease

tag: Sex

value: male

tag: Genetic Variation

tag: Age

value: 68 years