title: Control, Array 08394

description: Control vs. control

source_name: Halobacterium NRC-1, Control Culture

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]


title: Germ free  Corpus 1

status: Public on Jun 24 2004

type: RNA

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

description:
Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later  and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum.
Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology

molecule: total RNA

organism: Mus musculus

source_name: Corpus


title: Conventional  Rectum 1

source_name: Rectum


title: Germ free  Descending colon 2

source_name: Descending colon


title: Conventional  Jejenum 1

source_name: Jejenum


title: Conventional  Corpus 2


title: Conventional  Jejenum 2


title: Conventional  Corpus 1


title: Conventional  Descending colon 3


title: Conventional  Descending colon 2


title: 1BJZ02051714_Testi_SeminiferousTubule

status: Public on Mar 19 2004

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

scan_protocol: standard Affymetrix procedures

label: biotin

organism: Homo sapiens

label_protocol: Five micrograms of total RNA was used to synthesize cDNA that was then used as a template to generate biotinylated cRNA using Enzo kits.

extract_protocol: Human tissue samples were obtained from several sources: Clinomics Biosciences (Pittsfield, MA), Clontech, AllCells (Berkeley, CA), Clonetics/BioWhittaker (Walk-ersville, MD), AMS Biotechnology (Abingdon, Oxfordshire, U.K.), and the University of California at San Diego. When samples from four or more subjects were available, equal numbers of male and female subjects were used to make two independent pools; when fewer than four samples were available, RNA samples were pooled, and duplicate amplifications were performed for each pool (detailed annotation for human samples is on our web site, http:\\symatlas.gnf.org)  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).


title: Conventional  Jejenum 3


title: Conventional  Descending colon 1


title: Conventional  Corpus 3


title: Myc-IP-vs-WCE-rep1

status: Public on May 16 2007

type: mixed

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: Genome-wide levels of histone H3. Cells were arrested with alpha factor, chromatin sheared by sonication, and Myc-H3 was IPed and compared to to sonicated input (WCE)

hyb_protocol: was hybridized according to Agilent protocol

scan_protocol: was scanned according to Agilent protocol

molecule: other

organism: Saccharomyces cerevisiae

source_name: Myc-H3 IP rep1

label_protocol: 3 μg of aRNA produced from the linear amplification were used to label probe

extract_protocol: Chromatin sheared by sonication. IPed using anti-Myc Ab (Sigma; monoclonal). Amplified with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification

treatment_protocol: Cells arrest with alpha factor. No Galactose induction

tag: Strain

value: MDY510, Myc-tagged H3

molecule: genomic DNA

source_name: WCE rep1

extract_protocol: Chromatin sheared by sonication.


title: Breast, NOS (excludes Skin of breast C44.5), Infiltrating duct and lobular carcinoma (C50._) (12280334)

status: Public on May 08 2007

type: genomic

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

description: "Breast, NOS (excludes Skin of breast C44.5)"; Infiltrating duct and lobular carcinoma (C50._); University of Pennsylvania; 3/29/2002

hyb_protocol: DNA was resuspended and hybridized to the array for 72h at 37oC on a rotating platform. Additional details are found in: Greshock, J, Naylor, TL, Margolin, A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-87

scan_protocol: Images were scanned with an Axon 4500 microarray scanner (Axon, Union City, CA) and analyzed with GenePix 3.0 software (Axon).

data_processing: All spots were subjected to a pin-tip normalization.

label_protocol: One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA).  Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.

extract_protocol: Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.

tag: Tissue

source_name: pooled male

tag: pooled male


title: RA_x

status: Public on Nov 04 2004

city: Berlin

first: Ute

last: Ungethuem

department: Core Center for Functional Genome Research

country: Germany

institute: Charité University Hospital

description: individual sample, rheumatoid arthritis x, synovial tissue

hyb_protocol: Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to human expression Affymetrix HG U95Av2 GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Affymetrix Microarray Suite MAS 5.0

label: biotin labeled

source_name: rheumatoid arthritis

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (Operon Biotechnology, Huntsville, AL, USA) five micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the bioarray high yield RNA transcription kit (Enzo Diagnostics, Farmindale, N.Y., USA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mM Tris-acetate (pH 8.2), 100 mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes.

growth_protocol: synovectomy

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen).

treatment_protocol: disease modifying antirheumatic drugs (DMARD)

tag: age

tag: gender

value: female