title: Wild-type for Histone H2B^3-37 replicate 1

description: Wild-type yeast strain


title: Wild-type for Histone H2B^3-37 and H2B^30-37 replicate 2

status: Public on Apr 08 2006

type: RNA

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

country: USA

institute: Washington State University

description: Wild-type yeast strain

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast RNA

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown to mid-log phase (OD600=0.5-0.7) in rich media (YPD).  Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: PY014 (wild-type Histone H2B)


title: Non-malignant 39NN

status: Public on Oct 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were carried out as one-color hybridizations on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies. Analyses were done initially with matched malignant and non-malignant sample pairs.

hyb_protocol: Labeled samples were hybridized on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies encoding probes for 470 human and 64 human viral microRNAs from the Sanger database v9.1. Microarrays were washed according to the supplier’s protocol.

scan_protocol: Microarrays were scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.

data_processing: Features were extracted with an image analysis tool version A.9.5.3 using default protocols and settings (Agilent Technologies). Data analysis was carried out on the Rosetta Inpharmics gene expression data management and analysis system Resolver Version 7.0. Intensity experiments were created with the Intensity Experiment Manager from Resolver by combining all hybridizations derived from malignant and non-malignant samples, respectively. ‘In silico’ ratio profiles and ratio experiments were generated by the Ratio Experiment Wizard after selection of either malignant and non-malignant samples derived from individual patients or by combining malignant and non-malignant intensity experiments. A two-sample Students t-test was applied on all intensity profiles, while a one-sample t-test was applied to the ratio experiments comprising individual patients. Principal Component Analysis (PCA) was used for data reduction on either experiment or reporter level. Cluster analysis was done on features or reporter levels with the 2D Matrix Wizard from Resolver with an agglomerative algorithm using average link as heuristic criteria and Manhattan distance as metric similarity measure on both, intensity profiles and ratio experiments. All analysis criteria were combined making the microarray results extremely robust and highly reproducible.

organism: Homo sapiens

source_name: human kidney

label_protocol: An amount of 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase (GE Healthcare, Chalfont St. Giles, United Kingdom), denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate having a single Cy3 label attached to the 3’ phosphate of the nucleotide (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: Immediately after nephrectomy matched malignant and non-malignant specimens from the same kidney were collected in RNAlater Stabilization Reagent (Qiagen, Hilden, Germany), stored at room temperature for 2 h, subsequently overnight at 4°C and at -80°C until RNA isolation. Total RNA including small and micro RNAs were isolated from about 50 mg of tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. This approach combines phenol/guanidine thiocyanate-based tissue lysis and silika membrane-based binding with purification of isolated total RNA including micro and small RNAs. Briefly, samples were homogenized in Qiazol lysis buffer with the TissueLyser (Qiagen) twice for 1 min at 30 Hz. After a centrifugation and phase separation step RNA was immobilized at the silika-membrane of the kit including spin column several times washed, and eluted with water. The RNA was stored at -80°C. The total RNA yield and the ratio of absorbance at 260 nm to 280 nm (A260/A280 ratio) were measured with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Montchanin, DE, USA). The integrity of total RNA was assessed with the 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA). The Agilent 2100 Expert software B.02.05 was used to generate the RNA Integrity Number (RIN) as criterion of the RNA quality. Furthermore, the ratio of miRNA fraction to small RNA in isolated total RNA was monitored by use of the Agilent Small RNA kit.

tag: kidney non-malignant sample

tag: Matched kidney tissue samples were derived from adult patients undergoing radical nephrectomy. Tumor types were clear renal cell carcinoma. Tumor classification and stage were established according to the 2002 TNM System and the 2004 WHO Classification.


title: Non-malignant 33NN


title: Non-malignant 27NN


title: Mutant Histone H2B K->G replicate 2

description: Mutant yeast strain Histone H2B K->G

tag: PY029 (mutant Histone H2B K->G)


title: Wild-type for Histone H2B K->G replicate 1

description: Wild-type yeast strain


title: Mutant Histone H2B^3-32 replicate 3

description: Mutant yeast strain Histone H2B^3-32

tag: PY016 (mutant Histone H2B^3-32)


title: Wild-type for Histone H2B K->G replicate 2

description: Wild-type yeast strain


title: Mutant Histone H2B K->G replicate 1

description: Mutant yeast strain Histone H2B K->G


title: Mutatant Histone H2B^3-32 replicate 2

description: Mutant yeast strain Histone H2B^3-32


title: Wild-type for H2B^3-32, H2B K->G, and  H2B^3-37 replicate 3

description: Wild-type yeast strain


title: Mutant Histone H2B^3-32 replicate 1

description: Mutant yeast strain Histone H2B^3-32


title: Wild-type for H2B^3-32 replicate 2

description: Wild-type yeast strain


title: Wild-type for H2B^3-32 replicate 1

description: Wild-type yeast strain


title: ovary b

status: Public on Oct 18 2000

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
Dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = gonad, female, sex

organism: Drosophila melanogaster

source_name: y w[67c1] ovary


title: 39260

status: Public on Jan 28 2006

city: Beltsville

first: Robert

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: Single channel hybridization of biotin-labeled samples detected by Cy3-streptavidin staining

data_processing: is based on the SAS Mixed Model

organism: Bos taurus

source_name: Parenchyma of an OVX animal treated with corn oil (control)

tag: both the raw and normalized values are log 2 based.