city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep3

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Following the hybridisation for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: All Affymetrix Bovine Genome Array microarrays were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix® GeneChip® Bovine Genome Array data were analysed using Bioconductor [http://www.bioconductor.org] contained within the R statistical package (http://www.r-project.org). Normalisation of raw data was performed using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm. In total, 89 arrays were used for normalisation, including 20 arrays from Mycobacterium avium subspecies paratuberculosis (MAP) stimulated MDM across the same time course and 20 arrays from M. bovis (BCG) stimulated MDM across the same time course. The FARMS algorithm uses only perfect match probes and a quantile normalization procedure, which provides the signal intensities.

source_name: Bovine monocyte-derived macrophages cultured with M. bovis for 24 hr

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

growth_protocol: For monocyte isolation, 300 ml of whole blood was collected in acid citrate dextrose buffer (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) in sterile bottles. Blood was layered onto Accuspin™ tubes containing Histopaque® 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and following density gradient centrifugation, peripheral blood mononuclear cells (PBMC) were collected. Contaminating red blood cells (RBC) were removed following resuspension and subsequent incubation of the PBMC in RBC lysis buffer (10mM KHCO3, 150mM NH4Cl, 0.1mM EDTA pH 8.0) for 5 minutes at room temperature. After incubation, PBMC were washed twice with phosphate-buffered saline (PBS) before resuspending cells in phosphate-buffered saline (PBS) containing 1% bovine serum albumin (BSA, Sigma-Aldrich Ireland Ltd., Dublin, Ireland). Monocytes were then isolated using the MACS protocol and a human anti-CD14 antibody (Miltenyi Biotec Ltd., Surrey, UK), which has been shown to be cross-reactive with bovine monocytes. All procedures were carried out according to the manufacturers’ instructions. The identity and purity of monocytes was confirmed by flow cytometry using an anti-CD14 FITC labelled antibody (data not shown). This method has been previously shown by us to yield a purity of CD14+ cells >= 99%. Purified monocytes were seeded at 1+E6/ml in 24-well tissue culture plates in RPMI 1640 medium (Invitrogen Ltd., Paisley, UK) containing 15% heat inactivated foetal calf serum (FCS; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), 1% non-essential amino acids (NEAA; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), gentamicin (5 µg/ml; Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and incubated at 37°C, 5% CO2. Following 24 hours incubation (day one) the media was replaced with 1ml fresh antibiotic-containing media to remove any non-adhered cells. On day three, media was replaced with 1 ml antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). To ensure that the same number of MDM were subjected to different treatments between experiments, cells were dissociated on day five using a non-enzymatic cell dissociation solution (Sigma-Aldrich Ireland Ltd., Dublin, Ireland), counted and then re-seeded at 2+E5 cells/well in 24-well tissue culture plates (Sarstedt, County Wexford, Ireland) using antibiotic-free culture media. By day eight, 80-100% confluent monolayers of MDM were generated that displayed the characteristic macrophage morphology as confirmed by Giemsa staining. Day eight MDM were used for the in vitro challenge experiments with M. bovis.

extract_protocol: All RNA extractions were performed in the CL3 laboratory using an RNeasy kit incorporating an on-column DNase treatment step (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 8.5. cDNA labelling, hybridisation and scanning for the microarray experiments were performed using a one-cycle amplification/labelling protocol on the Affymetrix GeneChip Bovine Genome Array (http://www.affymetrix.com). This array represents over 23,000 transcripts and includes approximately 19,000 UniGene clusters.

treatment_protocol: All challenge experiments including the preparation of non-challenge control samples were performed in the CL3 laboratory. Prior to the M. bovis challenge experiments, MDMs from two adjacent culture plate wells were lysed using RLT buffer from the RNeasy Mini kit (Qiagen Ltd., Crawley, UK) supplemented with 1% Beta-mercaptoethanol (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and pooled. These samples constituted the 0 hour control MDM samples. MDM samples (seeded at 2E+5 cells per well) were challenged with M. bovis (4E+5 cells/well; based on bacterial cell counts performed using a Petroff Hausser chamber (Fisher-Scientific, Dublin, Ireland) [multiplicity of infection 2:1] and incubated at 37°C, 5% CO2 for 2 hours, 6 hours and 24 hours. For the non-challenged control samples at each time-point, antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only) was added to each well. After 2 hours post-challenge, the media from all 6 hour and 24 hour challenge experiments was replaced with 0.5 ml fresh antibiotic-free culture media per well and re-incubated at 37°C, 5% CO2 until MDM were required for harvesting. Challenged and non-challenged control MDMs were lysed and harvested using RLT/1% Beta-mercaptoethanol buffer (Qiagen Ltd., Crawley, UK) at the designated time points. For each treatment, MDM lysates from two culture plate wells were pooled and stored at 80°C until required for RNA extraction.

value: monocyte-derived macrophage

tag: cattle breed

value: Holstein-Friesian

tag: Sex

value: 3 years

tag: infection

value: Mycobacterium bovis

value: 24 hr


status: Public on Dec 31 2011

type: RNA

description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep2

label: biotin

molecule: total RNA

organism: Bos taurus

tag: tissue

value: Female

tag: age

tag: time point


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep5


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep2

source_name: Bovine monocyte-derived macrophages cultured with M. bovis for 6 hr

value: 6 hr


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep1


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep6


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep3


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep7


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep1


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep6


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep7

source_name: Bovine monocyte-derived macrophages cultured with M. bovis for 2 hr

value: 2 hr


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep4


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep5


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep6


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep4


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep5


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T6 rep4


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep7

source_name: Bovine monocyte-derived macrophages cultured for 24 hr


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep2


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep4


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep3


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep2


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T2 rep3


description: gene expression data from bovine monocyte-derived macrophage challenged with Mycobacterium bovis at T24 rep7


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep5


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep6

source_name: Bovine monocyte-derived macrophages cultured for 6 hr


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep6


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T24 rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep7


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep6

source_name: Bovine monocyte-derived macrophages cultured for 2 hr


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep4

source_name: Bovine monocyte-derived macrophages cultured for 0 hr

value: 0 hr


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep5


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep2


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep4


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep5


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep5


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep3


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep3


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep2


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep4


title: Epididymal Fat GFP- Rep3

city: Boston

first: Rana

middle: K

last: Gupta

state: MA

address: 44 Binney Street CLSB 11119

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

description:
Epididymal Fat stromal vascular cultures from 6-8 week old male mouse
GFP- fibroblasts from epidiymal fat stromal vascular cultures of Zfp423-GFP mice

hyb_protocol: The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45°C.  The chip was then transferred to a fluidics instrument for washes to remove unbound cRNA. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were added using biotinylated anti-streptavidin antibody and SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values

organism: Mus musculus

source_name: proliferating Epididymal Fat GFP- fibroblasts

label_protocol: cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

growth_protocol: all cells were propagated in DMEM/F12 (1:1 ratio) containing 10% fetal bovine serum

extract_protocol: Trizol (Invitrogen) extraction, followed by purification using Qiagen RNeasy column

treatment_protocol: cells used in experiment were grown in DMEM/F12 (1:1 ratio) containing 10% fetal bovine serum and harvested prior to growth arrest

tag: cell type

tag: gender

value: male

tag: genotype

value: Zfp423-GFP transgenic

tag: genetic background

value: FVB and C57BL/6


title: Epididymal Fat GFP- Rep2

value: proliferating Epididymal Fat GFP- fibroblasts


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T2 rep7


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep2


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep7


title: Epididymal Fat GFP- Rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep1


title: Inguinal Fat GFP- Rep3

description:
Inguinal Fat stromal vascular cultures from 6-8 week old male mouse
GFP- fibroblasts from inguinal fat stromal vascular cultures of Zfp423-GFP mice

source_name: proliferating Inguinal FAT GFP- fibroblasts


title: Epididymal Fat GFP+ Rep2

description:
Epididymal Fat stromal vascular cultures from 6-8 week old male mouse
GFP+ fibroblasts from epidiymal fat stromal vascular cultures of Zfp423-GFP mice

source_name: proliferating Epididymal Fat GFP+ fibroblasts

value: proliferating Epididymal Fat Zfp423-GFP+ fibroblasts


title: Epididymal Fat GFP+ Rep3


title: Inguinal Fat GFP- Rep2

value: proliferating Inguinal FAT GFP- fibroblasts


title: Inguinal Fat GFP- Rep1


title: Epididymal Fat GFP+ Rep1


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T0 rep6


title: Inguinal Fat GFP+ Rep3

description:
Inguinal Fat stromal vascular cultures from 6-8 week old male mouse
GFP+ fibroblasts from inguinal fat stromal vascular cultures of Zfp423-GFP mice

source_name: proliferating Inguinal FAT GFP+ fibroblasts

value: proliferating Inguinal FAT Zfp423-GFP+ fibroblasts


title: Inguinal Fat GFP+ Rep2


title: PBMCs_IS_16 [IS]

city: Lisbon

first: Sofia

middle: A

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: group C of hybridized samples

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 – 7G.

data_processing: Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were performed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, performs quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin) in CORRECTED column.

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.

tag: affected status (disease state)

value: IS patient

tag: age-at-examination

tag: age-at-onset

tag: geographical origin

value: Mirandela

tag: clinical characteristics

value: Diabetes, hypercholesterolemia

tag: lifestyle characteristics

value: ever drinker


title: PBMCs_IS_14 [IS]

description: group C of hybridized samples


title: PBMCs_IS_19 [IS]

description: group B of hybridized samples

value: ever smoker, ever drinker


title: PBMCs_IS_11 [IS]

description: group B of hybridized samples


title: PBMCs_IS_8 [IS]

description: group F of hybridized samples

value: female

value: Vila-Real

value: Hypercholesterolemia


title: PBMCs_IS_7 [IS]

description: group A of hybridized samples


title: PBMCs_IS_18 [IS]

description: group B of hybridized samples

value: Hypertension


title: PBMCs_IS_12 [IS]

description: group C of hybridized samples


title: PBMCs_IS_20 [IS]

description: group A of hybridized samples


title: PBMCs_Control_20 [IS]

description: group F of hybridized samples

value: control

value: Lisboa


title: PBMCs_Control_17 [IS]

description: group E of hybridized samples

value: male

value: Hypertension, hypercholesterolemia


title: PBMCs_IS_9 [IS]

description: group A of hybridized samples


title: PBMCs_IS_4 [IS]

description: group B of hybridized samples


title: Inguinal Fat GFP+ Rep1

value: Zfp423-GFP transgenic

value: FVB and C57BL/6


title: PBMCs_IS_15 [IS]

description: group C of hybridized samples

value: Porto


title: PBMCs_IS_6 [IS]

description: group B of hybridized samples


title: PBMCs_IS_5 [IS]

description: group F of hybridized samples


title: PBMCs_IS_10 [IS]

description: group F of hybridized samples


title: PBMCs_IS_1 [IS]

description: group F of hybridized samples


title: PBMCs_IS_17 [IS]

description: group C of hybridized samples


title: PBMCs_IS_2 [IS]

description: group F of hybridized samples


title: PBMCs_Control_19 [IS]

description: group F of hybridized samples

value: ever smoker


title: PBMCs_Control_15 [IS]

description: group F of hybridized samples


title: PBMCs_IS_3 [IS]

description: group B of hybridized samples

value: IS patient


title: PBMCs_Control_18 [IS]

description: group E of hybridized samples


title: PBMCs_Control_10 [IS]

description: group F of hybridized samples


title: PBMCs_Control_14 [IS]

description: group F of hybridized samples


title: PBMCs_Control_16 [IS]

description: group F of hybridized samples


title: PBMCs_Control_11 [IS]

description: group C of hybridized samples


title: PBMCs_Control_6 [IS]

description: group A of hybridized samples

value: Mirandela


title: PBMCs_IS_13 [IS]

description: group C of hybridized samples


title: PBMCs_Control_13 [IS]

description: group F of hybridized samples


title: PBMCs_Control_9 [IS]

description: group D of hybridized samples


title: PBMCs_Control_4 [IS]

description: group C of hybridized samples


title: wt_liver_8779

status: Public on Dec 29 2011

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

country: Germany

institute: University of Ulm

hyb_protocol: 1.65 µg of Cy3-labeled cRNA (specific activity >8.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 55 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarrays (G4846A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the Agilent Scan Control Version A.8.4.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The data was preprocessed according to Agilent's GeneSpring software standard workflow. Gene expression levels were background corrected and signals for duplicated probes were summarized by geometric mean of non-compromised probes. After log2 transformation, a percentile shift normalization at the 75% level and a baseline shift to the median baseline of all probes was performed.

source_name: Trp53 wt liver (not treated)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer.

growth_protocol: Mice were kept in a pathogen-free environment.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice (group: DEN-induced liver tumors) were treated at day 15 with DEN (i.p.; 10µg/g bodyweight).

value: liver

tag: background strain

value: Trp53 wt

tag: treatment


title: wt_liver_7664


title: PBMCs_Control_7 [IS]

description: group A of hybridized samples

value: ever drinker


title: PBMCs_Control_12 [IS]

description: group C of hybridized samples


title: PBMCs_Control_3 [IS]

description: group B of hybridized samples

value: female


title: wt_liver_8778


title: wt_liver_7666


title: PBMCs_Control_2 [IS]

description: group A of hybridized samples


title: PBMCs_Control_5 [IS]

description: group C of hybridized samples


title: PBMCs_Control_8 [IS]

description: group A of hybridized samples


title: PBMCs_Control_1 [IS]

description: group A of hybridized samples


title: p53_ko_9849T3

source_name: Trp53 ko liver tumor (HCC/CCC; not treated)

value: hepatocellular carcinoma (HCC)/cholangiocellular carcinoma (CCC)

value: Trp53 ko


description: gene expression data from bovine monocyte-derived macrophage non-challenged at T6 rep3

value: monocyte-derived macrophage

tag: cattle breed

value: Holstein-Friesian

tag: Sex

value: Female

value: 3 years

value: 6 hr


title: p53_ko_987T2

tag: tissue


title: p53_ko_liver_1776

source_name: Trp53 ko liver (not treated)


title: p53_ko_987T9


title: p53_ko_9485T1


title: p53_ko_297T1


title: p53_ko_liver_1775


title: p53_ko_2130T3


title: p53_ko_liver_1773


title: DEN_442T1

source_name: DEN-induced liver tumor (HCC), Trp53 wt

value: hepatocellular carcinoma (HCC)

value: N-nitrosodiethylamine (DEN)


title: p53_ko_liver_1774


title: DEN_551T1


title: DEN_462T31


title: DEN_537T1


title: DEN_537T2


title: ENCCs_8_rep 15_batch2

status: Public on Dec 07 2011

city: Groningen

first: Duco

last: Schriemer

address: Hanzeplein 1

department: Genetics

country: Netherlands

institute: University Medical Center Groningen

description: ENCCs express YFP flouresence protein, hence they are green.

hyb_protocol: 7.5 to 10 µg of fragmented cRNA were hybridized washed and stained according to The GeneChip Hybridization, Wash and Stain kit (#900720) on a Affymetrix GeneChip Mouse Genome 430-2.0 Array.

scan_protocol: The software program Affymetrix ‘GeneChip Command Console (v1.1)’ was used to operate the staining, washing and scanning of the GeneChips.

data_processing: Values were initially RMA preprocessed, after which each sample was Quantile Normalized to a normal distribution.

source_name: ENCCs isolated from mouse embryonic day 14.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: ENCCs were kept in DMEM-F12 medium supplemented with 1% N2 and 2% B27 and 20ng/ml of medium FGF and EGF, 1% Penicillin-Streptomycin in fibronectin coated of 24-wells plate

extract_protocol: RNA isolation was performed using the RNeasy Mini Kit according to the manufacture’s instruction

treatment_protocol: ENCCs were isolated by dissected of mouse embryonic gut E14.5 and to get pure ENCCs we FACS sorted the cells suspension. From one gut the YFP-ENCCs were collected in two wells of 24-wells plate. One well was treated with 50 ng/ml of GDNF and one as control was not treated with GDNF. Half of medium was changed every two days and EGF/FGF was add freshly and also GDNF to the well that need to be treated

value: enteric neural crest cells

tag: age

tag: genotype/variation

value: Transgenic mice carrying Wnt1-Cre-recombinase and a LoxP/R26-YFP

tag: gdnf-stimulated

value: yes


title: DEN_431T2


title: ENCCs_8_rep 14_batch2

tag: cell type

value: no


title: ENCCs_3_rep 5_batch2


title: ENCCs_3_rep 4_batch2


title: DEN_551T2

tag: genotype


title: ENCCs_2_rep 3_batch2


title: ENCCs_9_rep 17_batch2


title: ENCCs_9_rep 16_batch2


title: Gut_8_rep25_batch2

description: Gut were dissected from Duodenum to Anus

source_name: Mouse embryonic gut, embryonic day 14.5

value: enteric neural crest cells from embryonic gut

value: wild type


title: Gut_4_rep21_batch2


title: ENCCs_2_rep 26_batch2


title: Gut_7_rep24_batch2


title: Gut_6_rep23_batch2


title: Gut_1_rep18_batch2


title: Gut_5_rep22_batch2


title: Gut_3_rep20_batch2


title: ENCCs_8_rep 15_batch1


title: ENCCs_9_rep 16_batch1


title: ENCCs_8_rep 14_batch1


title: ENCCs_6_rep 10_batch1


title: ENCCs_5_rep 8_batch1


title: ENCCs_7_rep 13_batch1


title: ENCCs_7_rep 12_batch1


title: ENCCs_4_rep 7_batch1


title: ENCCs_4_rep 6_batch1


title: ENCCs_6_rep 11_batch1


title: ENCCs_3_rep 4_batch1


title: ENCCs_2_rep 3_batch1


title: ENCCs_5_rep 9_batch1


title: Healthy-10 +IFN-γ

status: Public on Nov 30 2011

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Healthy-10 +IFN-γ

extract_protocol: Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: disease state

value: healthy

tag: group

value: IFN-γ


title: ENCCs_1_rep 1_batch1


title: Gut_2_rep19_batch2


title: Healthy-10 +placebo

source_name: Healthy-10 +placebo

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

value: placebo


title: T-cell ALL prä MLL_00225

status: Public on Nov 25 2011

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

label: Biotin

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

value: T-cell acute lymphoblastic leukemia

tag: gene fusion

value: no fusion

tag: lineage

value: prä

value: mononuclear cells


title: ENCCs_9_rep 17_batch1


title: Normal breast tissue Replicate 5

status: Public on Nov 11 2011

type: genomic

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Biological replicate 5 of 10,normal breast tissue,non-breast cancer patient

hyb_protocol: According to the instructions of Agilent Oligo aCGH  Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization. Following global mean normalization, probes with an intensity <400 were discarded from further analysis.

molecule: genomic DNA

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 5

label_protocol: The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.

extract_protocol: DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.

value: normal breast

tag: patient

value: 51 years

tag: sample type

value: methylated

source_name: input, normal breast tissue,non-breast cancer patient 5

value: Input


title: Breast cancer tissue Replicate 8

description: Biological replicate 8 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 8

value: breast cancer

value: 43 years

source_name: input,breast cancer tissue,breast cancer patient 8


title: Normal breast tissue Replicate 10

description: Biological replicate 10 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 10

value: 33 years

source_name: input, normal breast tissue,non-breast cancer patient 10


title: Normal breast tissue Replicate 7

description: Biological replicate 7 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 7

value: 35 years

source_name: input, normal breast tissue,non-breast cancer patient 7


title: Normal breast tissue Replicate 6

description: Biological replicate 6 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 6

value: 39 years

source_name: input, normal breast tissue,non-breast cancer patient 6


title: Breast cancer tissue Replicate 9

description: Biological replicate 9 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient9

value: 44 years

source_name: input,breast cancer tissue,breast cancer patient9


title: Breast cancer tissue Replicate 10

description: Biological replicate 10 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 10

value: 49 years

source_name: input,breast cancer tissue,breast cancer patient 10


title: Breast cancer tissue Replicate 7

description: Biological replicate 7 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient7

source_name: input,breast cancer tissue,breast cancer patient7


title: suspension cells grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, and antibiotics rep2

status: Public on Nov 04 2011

city: San Francisco

first: Kevin

last: Wilhelmsen

state: CA

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

description:
test
THP1_#2

data_processing:
For the normalization it uses the average of two housekeeping genes: HPRT1 , 18s
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold-change values were caluculated using 2^-deltadeltaCt, where deltadeltaCt=(average deltaCt_test - average deltaCt control) and reports test/control (i.e. THP1/THP1 and HUVEC/THP1) ratios [available as a Series Supplementary file].

label: FAM Taqman

label_protocol: PCR assays were performed using the TaqMan® Human Toll-Like Receptors Pathway Arrays (4418838) (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 2000 ng total RNA using the  High Capacity RNA-to-cDNA Kit from Applied Biosystems). 2.5 ng cDNA used per well. Quantitative real-time PCR were performed (ABI Prism 7000 Sequence Detection System; Applied Biosystems) at 95°C for 20 sec was followed by 40 cycles of 1 sec at 95C and 20 sec at 60C.

growth_protocol: HUVEC: EGM-2 media (2% FBS) (Clonetics Corp; Walkersville, MD); THP1: RPMI 1640 supplemented with 10% FBS, L-glutamine, and antibiotics

extract_protocol: Total RNA was extracted with High Capacity RNA-to-cDNA Kit from AB (4387406)

tag: cell line

value: monocytic cell


title: Breast cancer tissue Replicate 6

description: Biological replicate 6 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 6

source_name: input,breast cancer tissue,breast cancer patient 6


title: Normal breast tissue Replicate 8

description: Biological replicate 8 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 8

value: 30 years

source_name: input, normal breast tissue,non-breast cancer patient 8


title: Breast cancer tissue Replicate 3

description: Biological replicate 3 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 3

source_name: input,breast cancer tissue,breast cancer patient 3


title: Normal breast tissue Replicate 2

description: Biological replicate 2 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 2

value: 37 years

source_name: input, normal breast tissue,non-breast cancer patient 2


title: ZR-75-1/NDRG1 E_dye flip

city: Oslo

first: Elisabet

last: Gjernes

address: Department of Medical Genetics | University of Oslo P.O. Box 1036 Blindern,

department: Department of Medical Genetics

country: Norway

institute: University of Oslo/Oslo University Hospital

hyb_protocol: 2 µg of labelled cRNA (Cy3 and Cy5) was hybridized to Human 1A (V2) Oligo Microarrays (Agilent G4110B) according to the manufacturers instructions.

scan_protocol: Scanned on a Genepix 4000B skanner, adjusting the PMT so the count ration was close to 1, and the intensity of the spots didn't exceed 65000.

data_processing: Images was processed using GenePix Pro 6, and spots were manually flagged. Normalization was by Lowess. For dye flip experiments (df), values in the gpr file is not inverted. For matrix data sheet all values are sample/ref [normalized log2 ratio representing test/reference data is available as a Series Supplementary file].

source_name: ZR-75-1 cells pSiRPG C overexpr.

label_protocol: 2.5 µg of total RNA were labelled using  a modified Low RNA Input Fluorescent Linear Amplification Protocol (Agilent Technologies, Hu et al, Biotechniques 2005).

growth_protocol: ME16C2 and SUM102 cells was grown in TCF-EGM, ZR-75-1 cells was grown in RPMI1640  with 10% FCS.

extract_protocol: Total RNA was extracted using Rneasy (Qiagen) following the manufacturers instructions.

treatment_protocol: Stably transduced cell populations was selected with 2 µg/ml puromycin.

value: empty vector control (pSiRPG)

source_name: ZR-75-1 cells NDRG1 E overexpr.

value: transduced with NDRG1 overexpression construct


title: Breast cancer tissue Replicate 5

description: Biological replicate 5 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 5

value: 55 years

source_name: input,breast cancer tissue,breast cancer patient 5


title: Breast cancer tissue Replicate 4

description: Biological replicate 4 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 4

value: 57 years

source_name: input,breast cancer tissue,breast cancer patient 4


title: ZR-75-1/NDRG1 F

source_name: ZR-75-1 cells NDRG1 F overexpr.


title: Breast cancer tissue Replicate 1

description: Biological replicate 1 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 1

value: 40 years

source_name: input,breast cancer tissue,breast cancer patient 1


title: ZR-75-1/NDRG1 C_dye flip

source_name: ZR-75-1 cells pSiRPG C

source_name: ZR-75-1 cells NDRG1 C overexpr.


title: Breast cancer tissue Replicate 2

description: Biological replicate 2 of 10,cancer tissue,breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched,breast cancer tissue,breast cancer patient 2

value: methylated

source_name: input,breast cancer tissue,breast cancer patient 2


title: Normal breast tissue Replicate 1

description: Biological replicate 1 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 1

value: normal breast

value: 29 years

source_name: input, normal breast tissue,non-breast cancer patient 1

value: Input


title: Normal breast tissue Replicate 4

description: Biological replicate 4 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 4

value: 27 years

source_name: input, normal breast tissue,non-breast cancer patient 4


title: ZR-75-1/NDRG1 B_dye flip

source_name: ZR-75-1 cells pSiRPG B

source_name: ZR-75-1 cells NDRG1 B overexpr.


title: ZR-75-1/NDRG1 A_dye flip

source_name: ZR-75-1 cells

value: parental control

source_name: ZR-75-1 cells NDRG1 A overexpr.


title: SUM102 NDRG1 siRNA 7B_dye flip

source_name: SUM102 cells pSiRPG B

source_name: SUM102 cells siRNA 7B

value: transduced with siRNA against NDRG1


title: Normal breast tissue Replicate 3

description: Biological replicate 3 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 3

value: 33 years

source_name: input, normal breast tissue,non-breast cancer patient 3


title: ZR-75-1/NDRG1 A


title: ZR-75-1/NDRG1 D

source_name: ZR-75-1 cells NDRG1 D overexpr.

source_name: ZR-75-1 cells pSiRPG C overexpr.


title: ZR-75-1/NDRG1 B


title: ZR-75-1/NDRG1 C

source_name: ZR-75-1 cells NDRG1 C overexpr.

source_name: ZR-75-1 cells pSiRPG C


title: SUM102 NDRG1 siRNA 4B_dye flip

source_name: SUM102 cells siRNA 4B


title: SUM102 NDRG1 siRNA 7B


title: SUM102 NDRG1 siRNA 7A

source_name: SUM102 cells siRNA 7A

source_name: SUM102 cells pSiRPG A


title: SUM102 NDRG1 siRNA 4A_dye flip

source_name: SUM102 cells siRNA 4A


title: SUM102 NDRG1 siRNA 7A_dye flip


title: SUM102 NDRG1 siRNA 4B


title: ME16C2 NDRG1 siRNA 4B_dye flip

source_name: ME16C2 cells pSiRPG B

source_name: ME16C2 cells siRNA 4B


title: ME16C2 NDRG1 siRNA7A

source_name: ME16C2 cells siRNA 7A

source_name: ME16C2 cells pSiRPG A


title: SUM102 NDRG1 siRNA 4A


title: ME16C2 NDRG1 siRNA 7B

source_name: ME16C2 cells siRNA 7B


title: ME16C2 NDRG1 siRNA 7B_dye flip


title: ME16C2 NDRG1 siRNA 7A_dye flip


title: ME16C2 NDRG1 siRNA 4B


title: ZR-75-1_48h_1_dye flip

description: Replicate 1 of 3, df

hyb_protocol: 2 µg of labelled cRNA (Cy3 and Cy5) was hybridized to Human Whole Genome Oligo Microarrays (G4112A, Agilent) according to the manufacturers instructions.

scan_protocol: Arrays were scanned on a Genepix 4000B scanner, adjusting the PMT so the count ration was close to 1, and the intensity of the spots didn't exceed 65000.

growth_protocol: MCF-7 and ZR-75-1 cells was grown in RPMI1640  with 10% FCS.

extract_protocol: Total RNA was extracted using Rneasy (Qiagen) following the manufacturers instructions. For cells kept at 1% O2, lysis buffer was added while the cells were in the hypoxic chamber.

treatment_protocol: Control cells and cells for hypoxia were plated at equal density and same timepoint. Cells were kept in a hypoxic chamber (MIC101, Billups-Rothenberg) at 1% O2 for 24 and 48 hours. Control cells were kept in a cell incubator with 21% O2.

source_name: ZR-75-1 48h hypoxia


title: ZR-75-1_48h_2

description: Replicate 2 of 3


title: MCF-7_48h_3_dye flip

description: Replicate 3 of 3, df

source_name: MCF-7 48h hypoxia


title: ME16C2 NDRG1 siRNA 4A_dye flip

source_name: ME16C2 cells siRNA 4A


title: MCF-7_48h_2_dye flip

description: Replicate 2 of 3, df


title: ME16C2 NDRG1 siRNA 4A


title: ZR-75-1_24h_2

description: Replicate 2 of 2

source_name: ZR-75-1 24h hypoxia


title: ZR-75-1_24h_1

description: Replicate 1 of 2


title: MCF-7_48h_1

description: Replicate 1 of 3


title: MCF-7_24h_2

description: Replicate 2 of 2

source_name: MCF-7 24h hypoxia


title: MCF-7_24h_1

description: Replicate 1 of 2


title: ZR-75-1_48h_3

description: Replicate 3 of 3


title: Brahmins Uttar Pradesh India D238

status: Public on Dec 12 2011

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3_A   Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Brahmins

tag: region

value: Uttar Pradesh India

value: blood


title: normal-5

status: Public on Sep 01 2011

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

country: Japan

institute: Kyushu university

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies), which used the  LOWESS (locally weighted linear regression curve fit) normalization method. Further analyses were performed using GeneSpring version 7.3.

source_name: normal epithelium

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual (Agilent Technologies).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy minElute Spin Column (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection

value: microdissected colorectal normal cells

value: normal

tag: sample identifier

value: M

tag: tumor-nodes-metastasis (tnm) classification - t

value: ND

tag: tumor-nodes-metastasis (tnm) classification - n

tag: tumor-nodes-metastasis (tnm) classification - m

tag: fstage

tag: tnm (stage)

tag: dukes

tag: his type

tag: depth


title: normal-3

tag: cell type

tag: age


title: CRC-129

source_name: colorectal cancer

value: microdissected colorectal cancer cells

value: tumor

value: C

value: wel

value: pSS


title: CRC-132

value: A

value: mod

value: pMP


title: CRC-128

value: F

value: B


title: normal-2


title: normal-4


title: CRC-130


title: CRC-122

value: D

value: pAI


title: CRC-125


title: CRC-126


title: CRC-124


title: CRC-117

value: pSM


title: CRC-120


title: normal-1

value: microdissected colorectal normal cells


title: CRC-131


title: CRC-121

value: pSE


title: CRC-116


title: CRC-118

value: M

value: pA


title: CRC-119

value: microdissected colorectal cancer cells


title: CRC-123

value: tumor


title: ENCCs_3_rep 5_batch1

description: ENCCs express YFP flouresence protein, hence they are green.

source_name: ENCCs isolated from mouse embryonic day 14.5

value: enteric neural crest cells

tag: genotype/variation

value: Transgenic mice carrying Wnt1-Cre-recombinase and a LoxP/R26-YFP

tag: background strain

tag: gdnf-stimulated

value: yes


title: ENCCs_1_rep 2_batch1


title: CRC-115

tag: sample type

tag: gender

value: C

value: pSS


title: CRC-114

value: mod


title: CRC-111


title: Normal breast tissue Replicate 9

description: Biological replicate 9 of 10,normal breast tissue,non-breast cancer patient

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 9

tag: tissue

value: normal breast

tag: patient

value: 26 years

value: methylated

source_name: input, normal breast tissue,non-breast cancer patient 9

value: Input


title: CRC-113

tag: sample identifier

value: F

tag: tumor-nodes-metastasis (tnm) classification - t

value: wel


title: CRC-112

tag: tumor-nodes-metastasis (tnm) classification - n

tag: tumor-nodes-metastasis (tnm) classification - m

value: B


title: CRC-108

value: M

tag: fstage

tag: tnm (stage)

value: pSE


title: CRC-109

value: microdissected colorectal cancer cells

tag: dukes

tag: his type


title: CRC-99

tag: cell type

value: tumor

tag: depth


title: CRC-96

tag: age


title: CRC-103

value: D


title: CRC-105


title: CRC-107


title: CRC-98

value: pSI


title: CRC-95

value: A

value: pSM


title: CRC-106


title: CRC-92


title: CRC-93

value: C


title: CRC-110


title: CRC-104

value: mod

value: pMP


title: CRC-94

value: pSS


title: CRC-90


title: CRC-89

value: por


title: CRC-100


title: CRC-97


title: CRC-91


title: CRC-88


title: CRC-87


title: CRC-86


title: CRC-82


title: CRC-84


title: CRC-83


title: CRC-80


title: CRC-85


title: CRC-79


title: CRC-81


title: CRC-78


title: CRC-75


title: CRC-21


title: CRC-13


title: CRC-77


title: CRC-20


title: CRC-2


title: human lung cancer sample MDA114

city: Dallas

first: Xilong

last: Li

address: 5323 Harry Hines Blvd

department: Clinical Science

institute: UT Southwestern Medical  Center

description:
We randomly selected 100 NSCLC FFPE samples with annotated clinical information from the UT-Lung SPORE Tissue Bank from 2001-2005.
death_event: 1 = death, 0 = alive

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Microarray data analysis and quality control were based on the percentage of present calls calculated by the MAS5 package.

source_name: Non-Small-Cell Lung Cancer

label_protocol: Total RNA was processed for analysis on the Affymetrix U133 plus 2.0 arrays according to Affymetrix protocols for first- and second-strand synthesis, biotin labeling and fragmentation.

extract_protocol: FFPE tumor specimens were cut into serial sections with a thickness of 10 μm. For the pathological diagnosis, one slide was stained with H&E and evaluated by a pathologist. Other sections were stained with nuclear fast red (NFR, American MasterTech Scientific Inc., Lodi, CA) to enable visualization of histology.  Tumor tissue was isolated using manual macro-dissection when the tumor area was > 0.5 x 0.5 mm or laser capture microdissection (P.A.L.M. Microlaser Technologies AG, Munich, Germany) in cases of smaller tumor areas.  At least 50 mm2 of tumor tissue was collected from each FFPE block. The extraction of RNA from tissue samples was done by a proprietary procedure of Response Genetics, Inc. (United States Patent Application 20090092979) designed to optimize the yield of higher molecular weight RNA fragments from FFPE specimens.

value: lung

tag: histology

value: Squamous

value: IIIB

tag: progression

tag: Stage

tag: race

value: African American

tag: smoking

value: No


title: CRC-15

tag: sample type

tag: gender

value: F

value: wel


title: CRC-14

value: microdissected colorectal cancer cells

value: tumor

tag: sample identifier

tag: tumor-nodes-metastasis (tnm) classification - t


title: human lung cancer sample MDA90

tag: tissue

value: M

value: Caucasian


title: CRC-6

tag: tumor-nodes-metastasis (tnm) classification - n

tag: tumor-nodes-metastasis (tnm) classification - m

tag: fstage

value: B

value: pA


title: CRC-10

tag: tnm (stage)

tag: dukes

tag: his type


title: human lung cancer sample MDA117

value: Adenocarcinoma

value: IB


title: CRC-16

tag: cell type

tag: age

value: A

tag: depth

value: pMP


title: CRC-1

value: C

value: mod

value: pSE


title: CRC-76


title: CRC-4

value: pSM


title: human lung cancer sample MDA120

value: lung

tag: histology

value: IA

tag: progression

tag: Stage

value: No


title: human lung cancer sample MDA91

value: Squamous

value: IIB

value: F

tag: race

tag: smoking


title: Kol Uttar Pradesh India evo_32

tag: gender

value: Female

tag: population

value: Kol

tag: region

value: Uttar Pradesh India

value: blood


title: human lung cancer sample MDA81

tag: tissue

value: IB

value: M

value: Caucasian


title: human lung cancer sample MDA85

value: Adenocarcinoma


title: human lung cancer sample MDA84


title: human lung cancer sample MDA76


title: human lung cancer sample MDA79


title: human lung cancer sample MDA66


title: human lung cancer sample MDA67

value: IIIB


title: human lung cancer sample MDA75

value: IIA


title: human lung cancer sample MDA63


title: human lung cancer sample MDA87


title: human lung cancer sample MDA72


title: human lung cancer sample MDA70


title: human lung cancer sample MDA74

value: IIIA


title: human lung cancer sample MDA78

value: lung


title: human lung cancer sample MDA61


title: human lung cancer sample MDA62


title: human lung cancer sample MDA59

value: Yes


title: human lung cancer sample MDA58


title: human lung cancer sample MDA53

value: IA


title: human lung cancer sample MDA52

value: Squamous


title: human lung cancer sample MDA60


title: human lung cancer sample MDA48


title: human lung cancer sample MDA50

value: IIB


title: human lung cancer sample MDA49

value: F


title: human lung cancer sample MDA47


title: human lung cancer sample MDA44


title: human lung cancer sample MDA42


title: human lung cancer sample MDA37


title: human lung cancer sample MDA41


title: human lung cancer sample MDA46


title: human lung cancer sample MDA35


title: human lung cancer sample MDA26


title: human lung cancer sample MDA27


title: human lung cancer sample MDA28


title: human lung cancer sample MDA39


title: human lung cancer sample MDA24


title: human lung cancer sample MDA33


title: human lung cancer sample MDA25


title: human lung cancer sample MDA18


title: human lung cancer sample MDA21


title: human lung cancer sample MDA30

value: African American


title: human lung cancer sample MDA45


title: human lung cancer sample MDA32


title: human lung cancer sample MDA23


title: human lung cancer sample MDA51


title: human lung cancer sample MDA20


title: human lung cancer sample MDA9


title: human lung cancer sample MDA10


title: human lung cancer sample MDA5


title: human lung cancer sample MDA14


title: NBL 14 cell line

status: Public on Jul 07 2011

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

institute: Erasmus MC

description: Gene expression data of neuroblastoma cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU 133 Plus2.0 arrays. GeneChips were washed and stained according to Affymetrix protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT value 500) as normalization method.

source_name: NBL cell line 14

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions

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

value: neuroblastoma cell line

value: male

tag: mycn status

value: MYCN amplified

tag: alk mutation status

value: wild type


title: 20050421_11_NCCIT_1_04-15-05

status: Public on Jul 09 2011

city: Seattle

first: Alvin

middle: Y

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

institute: University of Washington

description: EC stem-like cells

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: Embryonal carcinoma cell line NCCIT

label_protocol: GeneChip® Two-Cycle Target Labeling Kit

growth_protocol: Cells were isolated after overnight tissue digestion with collagenase in serum-free RPMI1640 media.

extract_protocol: Sorted cell populations were lysed in RLT buffer for RNA isolation.

treatment_protocol: Cells were labeled with dye conjugated-antiCD monoclonal antibodies and sorted by MACS

tag: tissue/origin

value: germ cell tumor line

value: Embryonal carcinoma cell line NCCIT


title: 20100726_01_H1_culture

description: ES cells

source_name: Human embryonic stem cells

label_protocol: GeneChip® One-Cycle Target Labeling Kit

value: human stem cell XY

value: Human embryonic stem cells


title: NBL 10 cell line

source_name: Derivative NBL16

value: derivative of neuroblastoma cell line NBL16

value: female

value: no MYCN amplification

value: mutated


title: NBL 17 cell line

source_name: NBL cell line 17

value: amplified


title: NBL 8 cell line

source_name: NBL cell line 8


title: NBL 12 cell line

source_name: NBL cell line 12


title: NBL 11 cell line


title: NBL 13 cell line

source_name: NBL cell line 13


title: NBL 7 cell line

source_name: NBL cell line 7


title: NBL 3 cell line

source_name: NBL cell line 3


title: GFP-negative cells from TinD-GFP embryos, replicate 1

status: Public on Jun 06 2011

city: Bethesda

first: Shaad

middle: M.

last: Ahmad

state: MD

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

institute: National Heart Lung and Blood Institute

description: FACS-sorted GFP negative cells from single cell suspensions of embryos with TinD-GFP insertions targeting GFP to Tinman-expressing cardiac mesodermal cells staged to late stage 11/early stage 12

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductors' affy package in conjunction with Choe et al.'s goldenspike package (Choe et al. Genome Biol. 2005).

organism: Drosophila melanogaster

source_name: FACS-sorted Drosophila cells

label_protocol: Approximately 2-5 ug of total RNA was processed to produce biotinylated cRNA targets

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

tag: genotype/variation

value: TinD-GFP

tag: developmental stage

value: late stage 11/early stage 12


title: NBL 5 cell line

source_name: NBL cell line 5

tag: cell type


title: NBL 9 cell line

source_name: NBL cell line 9


title: GFP-positive cells from TinD-GFP embryos, replicate 1

description: FACS-sorted GFP positive cells from single cell suspensions of embryos with TinD-GFP insertions targeting GFP to Tinman-expressing cardiac mesodermal cells staged to late stage 11/early stage 12


title: GFP-negative cells from TinD-GFP embryos, replicate 2

value: FACS-sorted GFP negative cells from single cell suspensions of embryos


title: MS BPao 1 rep2

status: Public on Jun 01 2011

city: Aurora

first: Michael

middle: J

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

data_processing:
Microarray data were generated using Affymetrix protocols as previously described (Frisk et al., 2004, Lizewski et al., 2004, Morici et al., 2007). Absolute expression transcript levels were normalized for each chip by globally scaling all probe sets to a target signal intensity of 500. Three statistical algorithms (detection, change call, and signal log ratio) were then used to identify differential gene expression in experimental and control samples. The detection metric (presence, absence, or marginal) for a particular gene was determined using default parameters in MAS software (version 5.0; Affymetrix). Batch analysis was performed in MAS to make pairwise comparisons between individual experimental and control GeneChips in order to generate change calls and a signal log ratio for each transcript. These data were imported into Data Mining Tools (version 3.0; Affymetrix). Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. We defined a positive change call as one in which greater than 50% of the transcripts had a call of increased (I) or marginally increased (MI) for up-regulated genes and decreased (D) or marginally decreased (MD) for down-regulated genes. Finally, the mean value of the signal log ratios from each comparison file was calculated.  Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than of equal to 1 for down-regulated transcripts were kept in the final list of genes. Signal log ratio values were converted from log2 and expressed as fold changes.

Frisk, A., J. R. Schurr, G. Wang, D. C. Bertucci, L. Marrero, S. H. Hwang, D. J. Hassett & M. J. Schurr, (2004) Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells. Infect. Immun. 72: 5433-5438.
Lizewski, S. E., J. R. Schurr, D. W. Jackson, A. Frisk, A. J. Carterson & M. J. Schurr, (2004) Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J. Bacteriol. 186: 5672-5684.
Morici, L. A., A. J. Carterson, V. E. Wagner, A. Frisk, J. R. Schurr, K. H. zu Bentrup, D. J. Hassett, B. H. Iglewski, K. Sauer & M. J. Schurr, (2007) Pseudomonas aeruginosa AlgR represses the Rhl quorum-sensing system in a biofilm-specific manner. J. Bacteriol. 189: 7752-7764.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa grown in a flow-through bioflm

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol. End labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix).

growth_protocol: P. aeruginosa and P. aeruginosa delta PA4101 (bfmR) were grown in a flow-through bioflm on minimal medium with 10 mM glutamate for 6 days.

extract_protocol: Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

treatment_protocol: None.

tag: growth condition

value: biofilm


title: GFP-negative cells from TinD-GFP embryos, replicate 3


title: MS BPao 1 rep3

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: NBL 1 cell line

source_name: NBL cell line 1

value: neuroblastoma cell line


title: GFP-positive cells from TinD-GFP embryos, replicate 2

value: FACS-sorted GFP positive cells from single cell suspensions of embryos


title: MS Pao 1 rep1

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: db/db mouse sample 410

status: Public on Feb 18 2011

city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

description: Gene expression data from 24 week db/db mouse sciatic nerve

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute.  The samples were Robust Multi-array Average (RMA).

source_name: 24 week db/db mouse sciatic nerve

label_protocol: Of the total RNA, 75 ng from each sample was amplified and biotin-labeled using the Ovation™ Biotin-RNA Amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s protocol

extract_protocol: Total RNA was isolated from sciatic nerve using a commercially available silica gel-based isolation protocol (RNeasy Mini Kit, QIAGEN Inc., Valencia, CA) including an on-column DNase digestion following the manufacturer's protocol.  RNA quantity and quality was measured by microfluid electrophoresis using the RNA 6000 Pico LabChip® on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: sciatic nerve

tag: strain

value: BKS

value: db/db

tag: age

value: 24 weeks


title: db/+ mouse sample 105

description: Gene expression data from 24 week db/+ mouse sciatic nerve

source_name: 24 week db/+ mouse sciatic nerve

value: db/+


title: NBL 4 cell line

source_name: NBL cell line 4

value: male

value: MYCN amplified

value: wild type


title: db/db mouse sample 112


title: db/db mouse sample 411


title: NBL 6 cell line

source_name: NBL cell line 6


title: db/db mouse sample 110


title: db/db mouse sample 409


title: db/+ mouse sample 106


title: db/+ mouse sample 104


title: db/db mouse sample 111


title: GFP-positive cells from TinD-GFP embryos, replicate 3


title: db/+ mouse sample 404


title: db/+ mouse sample 407


title: db/+ mouse sample 103


title: db/+ mouse sample 101


title: C57_apoA-I_rep 3

status: Public on Jun 15 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Intra-peritoneally inject 2 ml of 4% Brewer’s thioglycolate to mouse (5.8 mg thioglycolate/150 mg agar/200cc H20) and euthanize mouse 96 h later.  Wash abdominal cavity with 10 ml of ice cold sterile PBS (endotoxin free) twice to remove cells from peritoneum.  Keep cells on ice. 2. Spin down cells 1,000 RPM, 6 min, 4°C. Wash two times with sterile cold PBS-CMF (10-30 mls), decanting.  Resuspend in DMEM+pen/strep+0.1% FBS.  Count cells, and plate 1.5 million cells/well in 1 ml in a 12 well plate (can plate as low as 1.1 million if necessary, but keep consistent between cell types).  Let settle for at least 2 h before changing media to cholesterol-loading media (1ml/well).  Make fresh cholesterol-loading media every time:  DMEM (0.1% FBS)/2mg/ml BSA (low LPS)/10ug/ml cholesterol, adding cholesterol at the end (after the FBS and BSA) while swirling.  Let media swirl on rocker for 5 min. before using to ensure cholesterol is completely in solution.  Incubate overnight.  Next day:  Wash 2x with warm sterile 1x PBS-CMF.  Change media to DMEM/penstrep/2mg/ml BSA (low LPS)/25µg/ml polymyxin B (1ml/well).  Incubate 30 min. before performing treating with ApoA-I (10 ug/ml) for 2 h.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5).  The resulting data were imported into Rosetta Resolver (v7.1) and log10 intensities were exported.

source_name: C57BL/6 mice, apoA-I treated, 2 h

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer's protocol.

tag: Cell type

value: peritoneal macrophages

tag: Strain

tag: Gender

value: female

tag: Age

value: 10 weeks


title: C57_apoA-I_rep 1


title: MyD88ko_control_rep 2

description: Intra-peritoneally inject 2 ml of 4% Brewer’s thioglycolate to mouse (5.8 mg thioglycolate/150 mg agar/200cc H20) and euthanize mouse 96 h later.  Wash abdominal cavity with 10 ml of ice cold sterile PBS (endotoxin free) twice to remove cells from peritoneum.  Keep cells on ice. 2. Spin down cells 1,000 RPM, 6 min, 4°C. Wash two times with sterile cold PBS-CMF (10-30 mls), decanting.  Resuspend in DMEM+pen/strep+0.1% FBS.  Count cells, and plate 1.5 million cells/well in 1 ml in a 12 well plate (can plate as low as 1.1 million if necessary, but keep consistent between cell types).  Let settle for at least 2 h before changing media to cholesterol-loading media (1ml/well).  Make fresh cholesterol-loading media every time:  DMEM (0.1% FBS)/2mg/ml BSA (low LPS)/10ug/ml cholesterol, adding cholesterol at the end (after the FBS and BSA) while swirling.  Let media swirl on rocker for 5 min. before using to ensure cholesterol is completely in solution.  Incubate overnight.  Next day:  Wash 2x with warm sterile 1x PBS-CMF.  Change media to DMEM/penstrep/2mg/ml BSA (low LPS)/25µg/ml polymyxin B (1ml/well).

source_name: MyD88 null mice, control treated, 2 h


title: C57_control_rep 1

source_name: C57BL/6 mice, control treated, 2 h


title: MyD88ko_apoA-I_rep 2

description: Intra-peritoneally inject 2 ml of 4% Brewer’s thioglycolate to mouse (5.8 mg thioglycolate/150 mg agar/200cc H20) and euthanize mouse 96 h later.  Wash abdominal cavity with 10 ml of ice cold sterile PBS (endotoxin free) twice to remove cells from peritoneum.  Keep cells on ice. 2. Spin down cells 1,000 RPM, 6 min, 4°C. Wash two times with sterile cold PBS-CMF (10-30 mls), decanting.  Resuspend in DMEM+pen/strep+0.1% FBS.  Count cells, and plate 1.5 million cells/well in 1 ml in a 12 well plate (can plate as low as 1.1 million if necessary, but keep consistent between cell types).  Let settle for at least 2 h before changing media to cholesterol-loading media (1ml/well).  Make fresh cholesterol-loading media every time:  DMEM (0.1% FBS)/2mg/ml BSA (low LPS)/10ug/ml cholesterol, adding cholesterol at the end (after the FBS and BSA) while swirling.  Let media swirl on rocker for 5 min. before using to ensure cholesterol is completely in solution.  Incubate overnight.  Next day:  Wash 2x with warm sterile 1x PBS-CMF.  Change media to DMEM/penstrep/2mg/ml BSA (low LPS)/25µg/ml polymyxin B (1ml/well). .

source_name: MyD88 null mice, apoA-I treated, 2 h


title: MyD88ko_apoA-I_rep 1


title: MyD88ko_control_rep 1


title: C57_apoA-I_rep 2


title: Xen cells

status: Public on May 17 2010

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: Gene expression of mouse extraembryonic endoderm stem cells.

hyb_protocol: For microarray analysis, 100ng of total RNA was amplified and hybridized to the Mouse Gene 1.0 ST array (Affymetrix). This service was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada

scan_protocol: According to standard Affymetrix protocol. This service was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada

data_processing: Data was processed using Expression Console from Affymetrix using the PLIER algorithm.

source_name: extraembryonic endoderm stem cells

growth_protocol: R1 and E14TG2a (ES cells), A4 and G3 (TS cells) and F3 and F4 (XEN cells) were cultured in the absence of feeder cells according to standard protocols (http://www.sickkids.ca/research/rossant/custom/stemCells.asp). To induce TS cell differentiation, 1 x 10E5 cells were plated on to each well of a 6-well plate in standard TS cell conditions for 24h, rinsed twice with PBS and cultured for six days in unconditioned TS cell media without FGF4 and heparin.

extract_protocol: RNA was processed using the RNeasy Mini Kit (Qiagen) with on-column RNase-free DNase (Qiagen) digestion.

tag: cell line

value: extraembryonic endoderm stem cells

tag: embryo stage

value: pre-implantation primitive endoderm, inner cell mass (ICM)


title: MyD88ko_control_rep 3


title: C57_control_rep 2


title: MyD88ko_apoA-I_rep 3


title: TS cells

description: Gene expression of mouse trophoblast stem cells.

source_name: trophoblast stem cells

label_protocol: According to standard Affymetrix protocol. This service was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada

value: trophoblast stem cells

value: pre-implantation trophoblast


title: C57_control_rep 3


title: 04-TB-155-1C

status: Public on Jan 08 2010

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

description: Location: Left; DukesStage: D; Age_Diag: 81; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

data_processing: Use the simpleaffy package in R/Bioconductor to calculate MAS5.0 calls. These values were subsequently normalized using quantile normalization.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: Location

value: Left; DukesStage:D; Age_Diag:81; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-TB-055-1L

description: Location: Left; DukesStage: D; Age_Diag: 46; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:46; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 04-TB-007-1C

description: Location: Right; DukesStage: D; Age_Diag: 57; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:57; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 03-TB-014-1I

description: Location: Left; DukesStage: D; Age_Diag: 73.4; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:73.4; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 03-TB-083-1A

description: Location: Left; DukesStage: D; Age_Diag: 76; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:76; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-TB-042-1I

description: Location: Left; DukesStage: D; Age_Diag: 79; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:79; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-TB-038-1K

description: Location: Right; DukesStage: D; Age_Diag: 54; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:54; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: R1 ES cells

description: Gene expression of mouse R1 embryonic stem cells.

source_name: embryonic stem cells R1

value: embryonic stem cells R1

value: pre-implantation epiblast, inner cell mass (ICM)


title: 03-TB-012-1I

description: Location: Left; DukesStage: D; Age_Diag: 67; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:67; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 01-TB-035-1E

description: Location: Left; DukesStage: D; Age_Diag: 69; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:69; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-TB-040-1H

description: Location: Right; DukesStage: A; Age_Diag: 47; Gender: F; DFS_Time: 64.5; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:47; Gender:F; DFS_Time:64.5; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: NBL 16 cell line

description: Gene expression data of neuroblastoma cell line

source_name: NBL cell line 16

value: neuroblastoma cell line

tag: gender

value: female

value: no MYCN amplification

value: mutated


title: 02-TB-061-1E

description: Location: Right; DukesStage: A; Age_Diag: 73; Gender: M; DFS_Time: 1.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:A; Age_Diag:73; Gender:M; DFS_Time:1.8; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: 01-TB-006-1A


title: ctrl2, gene level data

status: Public on Sep 13 2009

city: Cambridge

first: Xinshu

last: Xiao

address: 77 Mass Ave. MIT, 68-211

department: Biology

institute: MIT

description: ctrl2, gene level data

hyb_protocol: Hybridization was performed according to manufacturer's protocol by the MIT BioMicrocenter

scan_protocol: Scanning was performed according to manufacturer's protocol by the MIT BioMicrocenter

data_processing: The raw intensity data (CEL files) of exon arrays obtained from Affymetrix GeneArray Scanner were processed using the Affymetrix Power Tools (APT, see http://www.affymetrix.com/support/developer/powertools/index.affx).   RMA background correction and quantile normalization of the probe intensities were performed in the R package affy using custom CDF (version 9) mapping of probes to Ensembl genes.

source_name: control siRNA transfection in 293T cells

label_protocol: Labeling was performed according to manufacturer's protocol by the MIT BioMicrocenter

growth_protocol: 293T cells were cultured with D-MEM medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using trizol / chlorophorm extraction followed by isopropanol precipitation and RNeasy column purification (Qiagen). The quality of the total RNA was verified using the BioAnalyzer (Agilent).

treatment_protocol:
RNAi Protocol 1, used for hkd1 and ctrl1, Day 0: plate cells in 10cm dishes. Day 1: transfect 20nM siRNA with Lipofectamine 2000 (Invitrogen).
RNAi Protocol 2, used for hkd2, hkd3, ctrl2, ctrl3. Day 0: plate cells in 10cm dishes. Day 1: transfect 20nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 2: transfect 50nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 4: harvest cells. Transfections were conducted using protocols suggested by the manufacturer of the transfection reagent.

tag: control


title: NBL 15 cell line

source_name: NBL cell line 15

tag: mycn status

value: MYCN amplified

tag: alk mutation status

value: amplified


title: hkd3, gene level data

description: hkd3, gene level data

source_name: hnRNP H siRNA transfection in 293T cells

tag: H knockdown


title: 03-TB-005-1J

description: Location: Left; DukesStage: A; Age_Diag: 60; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:60; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: hkd1, gene level data

description: hkd1, gene level data


title: 02-TB-062-1D

description: Location: Left; DukesStage: A; Age_Diag: 67; Gender: F; DFS_Time: 14.4; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:A; Age_Diag:67; Gender:F; DFS_Time:14.4; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: ctrl1, gene level data

description: ctrl1, gene level data


title: hkd2, gene level data

description: hkd2, gene level data


title: ctrl3, gene level data

description: ctrl3, gene level data


title: MCC Patient 25

status: Public on Nov 14 2009

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Gene expression

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. Cox regression hazards model was applied to the processed data using the survival package. All analyses were performed using R software.

source_name: Moffitt Cancer Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: ethnicity

value: caucasian

tag: grade

value: 2 - Moderately differentiated (MD)

tag: overall_event (death from any cause)

value: no death

tag: dss_event (disease specific survival; death from cancer)

tag: dfs_event (disease free survival; cancer recurrence)

value: no recurrence

tag: overall survival follow-up time


title: L-07-1

status: Public on Aug 25 2009

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Rat Exon 1.0 ST array (Affymetrix) at 45oC for 16 h. After hybridization, non-specifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and .CEL intensity files were produced using GeneChip Operating Software version 1.4 (Affymetrix).

data_processing: Data were processed using OneChannelGUI in Bioconductor. The core set of probes was used and RMA was used to normlise the data. Limma was used to detect differentially exprressed genes.

organism: Rattus norvegicus

label_protocol: Biotin-labeled targets for the microarray experiment were prepared using 1µg of total RNA. Ribosomal RNA was removed with the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen), and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA, USA).

growth_protocol: All rats were housed individually, given free access to water and standard commercial rat chow (Special Diet Services, Witham, Essex, UK), and maintained under controlled conditions of temperature (21±1°C) and humidity (50±10%), under a 12 hr light/dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified by Dnase treatment and Rneasy Mini kit (Qiagen, UK).

treatment_protocol: Animals (12-14 weeks old) from each strain were randomly divided into three groups (8 rats per group). Animals from groups 1 and 2 were given 100 mg/kg body weight/day I3C by gastric gavage for 7 and 10 days, respectively. Control group 3 was gavaged with carrier (vegetable oil).

tag: Tissue

value: kidney. Age:12 weeks. Gender:male


title: L-07-4


title: L-07-2


title: L-07-3


title: F-07-3


title: F-07-1


title: F-07-4


title: F-07-2


title: LF-07-1


title: FL-07-4


title: LF-07-2


title: LF-07-3


title: LF-07-4


title: FL-07-1


title: L-10-2


title: L-10-4


title: L-10-3


title: ES H3K9me2 biological_replicate 2

status: Public on Jun 21 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Input for ES H3K9me2 Chip-chip replicate 2

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure

scan_protocol: Scanning was performed with NImbleScan.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H3K9me2 ChIP DNA from embryonic stem cells

label_protocol: According to Nimblegen guidelines

growth_protocol: embryonic stem cells were cultured as dercribed previously (Bibel 2007)

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the  Top2β antibody and the material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.

treatment_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the following antibodies: anti-dimethyl-H3K9 (LP Bio, no. AR-0108) and the material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.

tag: genotype

value: wildtype

tag: cell type

value: embryonic stem cells

tag: strain

tag: chip antibody

tag: vendor

value: LP Bio

tag: catalog no

source_name: Input DNA from embryonic stem cells

value: wild type


title: hkd1, exon level data

description: hkd1, exon level data

data_processing: The raw intensity data (CEL files) of exon arrays obtained from Affymetrix GeneArray Scanner were processed using the Affymetrix Power Tools (APT, see http://www.affymetrix.com/support/developer/powertools/index.affx). RMA background correction and quantile normalization of the probe intensities were performed in the R package affy using custom CDF (version 9) mapping of probes to Ensembl exons.

treatment_protocol:
RNAi Protocol 1, used for hkd1 and ctrl1, Day 0: plate cells in 10cm dishes. Day 1: transfect 20nM siRNA with Lipofectamine 2000 (Invitrogen). Day 3: harvest cells.
RNAi Protocol 2, used for hkd2, hkd3, ctrl2, ctrl3. Day 0: plate cells in 10cm dishes. Day 1: transfect 20nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 2: transfect 50nM siRNA using Dharmafect 1 (Dharmacon) as transfection reagent. Day 4: harvest cells. Transfections were conducted using protocols suggested by the manufacturer of the transfection reagent.


title: ctrl2, exon level data

description: ctrl2, exon level data

tag: control


title: FL-07-3


title: F-10-2


title: L-10-1


title: hkd2, exon level data

description: hkd2, exon level data


title: hkd3, exon level data

description: hkd3, exon level data


title: ctrl3, exon level data

description: ctrl3, exon level data


title: F-10-3


title: TN H3K9me2 biological_replicate 1

description: Input for TN H3K9me2 Chip-chip replicate 1

source_name: H3K9me2 ChIP DNA from Terminally differentiated Neurons (TN)

growth_protocol: neurons were derived as dercribed previously (Bibel 2007)

value: Terminally differentiated Neurons (TN)

source_name: Input DNA neuronal cells


title: ES H3K9me2 biological_replicate 1

description: Input for ES H3K9me2 Chip-chip replicate 1


title: FL-10-1


title: FL-10-2


title: FL-10-3


title: LF-10-1


title: FL-10-4


title: ctrl1, exon level data

description: ctrl1, exon level data


title: LF-10-4


title: LF-10-3


title: LF-10-2


title: F-10-4


title: F-10-1


title: L-00-4


title: L-00-3


title: F-00-2


title: F-00-1


title: LF-00-4


title: L-00-2


title: F-00-4


title: L-00-1


title: F-00-3


title: L-07-4


title: TN H3K9me2 biological_replicate 2

description: Input for TN H3K9me2 Chip-chip replicate 2


title: L-07-1


title: L-07-3


title: F-07-3


title: LF-00-3


title: FL-00-2


title: F-07-1


title: LF-00-2


title: L-07-2


title: FL-00-1


title: LF-07-2


title: FL-00-3


title: F-07-2


title: LF-00-1


title: LF-07-3


title: FL-00-4


title: LF-07-1


title: F-07-4


title: LF-07-4


title: FL-07-3


title: FL-07-1


title: F-10-3


title: L-10-4


title: FL-07-4


title: L-10-2


title: L-10-1


title: F-00-3


title: F-10-1


title: LF-10-2


title: L-00-4


title: FL-10-2


title: FL-10-4


title: L-10-3


title: L-00-2


title: FL-07-2


title: F-00-2


title: LF-10-3


title: F-00-1


title: L-00-1


title: F-10-2


title: LF-00-4


title: L-00-3


title: LF-00-3


title: LF-10-1


title: F-00-4


title: FL-10-3


title: LF-00-2


title: bioCnot3

status: Public on Jun 30 2009

city: Boston

first: guang

last: hu

address: NRB 160, 77 Ave. Louis Pasteur

institute: Brigham and Women's Hospital, Harvard Medical School

description:
IP samples:
bioCnot3_1.CEL
bioCnot3_2.CEL
bioCnot3_3.CEL
Control samples:
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

hyb_protocol: According to standard Affymetrix protocols.

data_processing: MAT (Johnson et al., 2006) was used to process the raw CEL files with the following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10. BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv33.bpmap and genomic coordinates in BED files were converted to new coordinates based on mouse genome assembly mm8.

source_name: bioCnot3 ChIP DNA from ES cells (3 repeats)

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

growth_protocol: Normal J1 ES growth condition

extract_protocol: bioChIP (biotin-mediated ChIP) was performed as described previously (Kim et al., 2008).

tag: J1 ES cells

source_name: Mock biotin ChIP DNA from ES cells expression BirA (4 repeats)

tag: Reference for bioChIP


title: LF-00-1


title: bioTrim28

description:
IP samples:
bioTrim28_1.CEL
bioTrim28_2.CEL
bioTrim28_3.CEL
Control samples:
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

scan_protocol: According to standard Affymetrix protocols.

source_name: bioTrim28 ChIP DNA from ES cells (3 repeats)


title: FL-00-2


title: FL-00-1


title: FL-10-1


title: FL-00-4


title: H3K9ac_in30minPI_H3

status: Public on Jun 01 2009

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description: H3K4ac ChIP in EL4 cells stimulated with PMA and Ionomcyin for 30 minutes, using total histone 3 ChIP as control, 2 biological replicates

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven and washed with Fluidics station 450 protocol FS450_0001

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

data_processing: All analysis was performed with NCBI build 36 of the mouse genome. The model-based analysis of tiling array (MAT) algorithm (Johnson WE et al PNAS 2006) was used to find regions of H3K9Ac with a bandwidth of 250bp and a max gap of 150bp. Either the matching total input DNA or H3 chips (as stated) were used as control samples.

source_name: H3K9ac ChIP DNA from EL4 cells stimulated for 30 min with PMA/IoM

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: EL-4 were cultured in RPMI 1640 medium with 10 mM HEPES, 10% fetal calf serum (FCS; CSL, Australia), 120 microg/ml penicillin, and 16 microg/ml gentamycin.

extract_protocol: ChIP assays were performed as previously described (Chen et al. Mol. Cell. Biol (2005) 25:3209) with some modifications. Briefly, cells were harvested and cross-linked with formaldehyde. Cells were lysed and then sonicated using the Bioruptor (Diagenode) to give fragments between 200bp to 1000bp lengths. Samples were precleared with protein-A agarose/salmon sperm DNA beads (Upstate) then immunoprecipitated with 2.5 microg anti-histone-H3 (Abcam), 4 microg anti-acetyl-H3K9 (Upstate) or mock immunoprecipiatated. Immune complexes were recovered using salmon sperm DNA/protein A-agarose, washed and eluted. Following cross-link reversal and proteinase K treatment immunoprecipitated DNA was purified by phenol–chloroform extraction and ethanol precipitation.10ng ChIP DNA was amplified with the Whole Genome Amplification (WGA) kit from Sigma as per manufacturers instructions but with incorporation of dUTP.

treatment_protocol: EL4 cells were stimulated with PMA (10 ng/ml phorbol myristate acetate) and Ionomcyin (1 microM) for 0h, 0.5h or 4h

tag: Antibody

tag: Cell Line

tag: Treatment

tag: Time

source_name: Pan Histone H3 ChIP DNA from EL4 cells stimulated for 30 min with PMA/IoM

value: Histone H3


title: H3K9ac_in4hPI_H3

description: H3K4ac ChIP in EL4 cells stimulated with PMA and Ionomcyin for 4 hours, using using total histone 3 ChIP as control, 2 biological replicates

source_name: H3K9ac ChIP DNA from EL4 cells stimulated for 4h with PMA/IoM

value: PMA (10 ng/ml phorbol myristate acetate) and Ionomcyin (1 microM)

source_name: Pan Histone H3 ChIP DNA from EL4 cells stimulated for 4h with PMA/IoM


title: H3K9ac_in30minPI_TI

description: H3K4ac ChIP in EL4 cells stimulated with PMA and Ionomcyin for 30 minutes, using Total Input DNA as control, 2 biological replicates

source_name: Total input DNA from EL4 cells stimulated for 30 min with PMA/IoM

tag: total input DNA


title: H3K9ac_inNonStim_H3

description: H3K4ac ChIP in Non-stimulated EL4 cells, using Total Histone 3 ChIP as control, 2 biological replicates (for time course comparison)

source_name: H3K9ac ChIP DNA from EL4 cells

value: Unstimulated

source_name: Pan Histone H3 ChIP DNA from EL4 cells


title: H3K9ac_inNonStim_TI

description: H3K4ac ChIP in Non-stimulated EL4 cells, using Total Input DNA as control, 2 biological replicates (for time course comparison)

source_name: Total input DNA from EL4 cells


title: NoAb_against_TotalInput

description: No Antibody (mock) ChIP in Non-stimulated EL4 cells, using Total Input DNA as control, 3 biological replicates

source_name: no antibody ChIP DNA from EL4 cells


title: H3K9ac_against_TotalInput

description: H3K4ac ChIP in Non-stimulated EL4 cells, using Total Input DNA as control, 3 biological replicates


title: H3K9ac_against_TotalH3

description: H3K4ac ChIP in Non-stimulated EL4 cells, using Total Histone 3 ChIP as control, 3 biological replicates


title: H3K9ac_in4hPI_TI

description: H3K4ac ChIP in EL4 cells stimulated with PMA and Ionomcyin for 4 hours, using Total Input DNA as control, 2 biological replicates

source_name: Total input DNA from EL4 cells stimulated for 4h with PMA/IoM


title: FL-00-3


title: striatum: putamen and caudate nucleus, right, biological rep4

status: Public on May 18 2009

city: New Haven

first: Matthew

middle: Bonser

last: Johnson

state: CT

address: 333 Cedar St., SHM C-316

department: Neurobiology

institute: Yale University School of Medicine

description: exon-level analysis

hyb_protocol: Samples were hybridized according to Affymetrix protocols

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Data were processed using Partek Genomics Suite. Core probesets were imported using RMA defaults with probe GC content correction

label_protocol: Samples were treated with the RNeasy Mini Kit (Qiagen) to exclude smaller RNAs, and fragmented and labeled using the Affymetrix Whole Transcript Sense Target Labeling Assay.

growth_protocol: not applicable

extract_protocol: Samples were dissected from late 2nd trimester human brains obtained from the Albert Einstein College of Medicine Human Fetal Tissue Repository and total RNA isolated using TRIzol.

treatment_protocol: not applicable

tag: Age

value: 23 weeks gestation

tag: Post-Mortem Interval <1hr


title: ventrolateral prefrontal neocortex, left, biological rep4

description: exon-level analysis


title: temporal association cortex, left, biological rep4

description: exon-level analysis

source_name: temporal association cortex, left


title: motor-somatosensory neocortex, right, biological rep4

description: exon-level analysis

source_name: motor-somatosensory neocortex, right


title: LF-10-4

tag: Tissue


title: mediodorsal thalamus, left, biological rep4

description: exon-level analysis

source_name: mediodorsal thalamus, left


title: temporal association cortex, right, biological rep4

description: exon-level analysis

source_name: temporal association cortex, right


title: F-10-4


title: striatum: putamen and caudate nucleus, left, biological rep4

description: exon-level analysis


title: mediodorsal thalamus, right, biological rep4

description: exon-level analysis

source_name: mediodorsal thalamus, right


title: ventrolateral prefrontal neocortex, right, biological rep4

description: exon-level analysis


title: mediodorsal thalamus, right, biological rep3

description: exon-level analysis

value: 21 weeks gestation


title: temporal auditory neocortex, left, biological rep4

description: exon-level analysis

source_name: temporal auditory neocortex, left


title: motor-somatosensory neocortex, left, biological rep4

description: exon-level analysis

source_name: motor-somatosensory neocortex, left


title: occipital visual neocortex, left, biological rep4

description: exon-level analysis

source_name: occipital visual neocortex, left


title: medial prefrontal neocortex, right, biological rep4

description: exon-level analysis

source_name: medial prefrontal neocortex, right


title: parietal association neocortex, left, biological rep4

description: exon-level analysis

source_name: parietal association neocortex, left


title: temporal association cortex, right, biological rep3

description: exon-level analysis