title: Transformants of AK102323 vs Col-0, rep2

city: Yokohama

first: Minami

last: Matsui

address: Suyehirocho 1-7-22 , Tsurumiku

department: Plant Science Center

country: Japan

institute: RIKEN

description: Comparison of gene expression between re-transformants of AK069096 and wild-type plants (Col-0).

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol.

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 5µm resolution, 50% PMT.

data_processing: Spot intensities on the DNA microarray were quantified by Feature Extraction Software ver.7.1.1 (Agilent Technologies) with default parameters.

source_name: re-transformants of AK102323

label_protocol: One micro-gram of total RNA was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: Plants were grown at 22°C in a cultivation container system (ARACON) in long-day conditions (16 hr light and 8 hr dark) under white fluorescent tubes (FL40SW, Sanyo, Osaka, Japan).

extract_protocol: RNAqueous Kit (Ambion, Inc, USA)

tag: Aerial parts of re-transformants of AK102323 in T2 generation

tag: Aerial parts of Col-0


title: Transformants of AK073210 vs Col-0, rep2

status: Public on Dec 01 2008

type: RNA

molecule: total RNA

organism: Arabidopsis thaliana

source_name: re-transformants of AK073210

tag: Aerial parts of re-transformants of AK073210 in T2 generation


title: Transformants of AK102323 vs Col-0, rep1


title: Transformants of AK073675 vs Col-0, rep1

source_name: re-transformants of AK073675

tag: Aerial parts of re-transformants of AK073675 in T2 generation


title: Transformants of AK065297 vs Col-0, rep2

source_name: re-transformants of AK065297

tag: Aerial parts of re-transformants of AK065297 in T2 generation


title: Transformants of AK073112 vs Col-0, rep1

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 5µm resolution, 50% PMT

source_name: re-transformants of AK073112

tag: Aerial parts of re-transformants of AK073112 in T2 generation


title: RESUS-3

city: Houston

first: Karen

last: Uray

state: TX

department: Pediatric Surgery

country: USA

institute: University of Texas Medical School at Houston

description: 384 RESUS

hyb_protocol: 1.5 µg of purified cRNA was fragmented to uniform size and applied to Rat Whole Genome 4x44k arrays (Agilent Technologies) in hybridization buffer.  Arrays were hybridized at 37° C for 18 hrs. in a rotating incubator

scan_protocol: scanned with a G2565 Microarray Scanner (Agilent Technologies)

data_processing:
Arrays were processed and background corrected with default settings of the Agilent Feature Extraction software (Agilent Technologies). Raw data was analyzed with GeneSpring GX v7.3 software (Agilent Technologies).
To compare individual expression values across arrays, raw intensity data from each gene was normalized to the median intensity of each array.

organism: Rattus norvegicus

source_name: intestinal smooth muscle

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample

extract_protocol: distal 1/3 of intestine collected immediately after sacrifice, longitudinal muscle stripped away and forzen in liquid nitrogen

tag: RESUS only

tag: male Sprague Dawley


title: Transformants of AK073210 vs Col-0, rep1


title: RESUS-2

description: 383 RESUS


title: VH-4

description: 386 VH

tag: VH only


title: Transformants of AK065297 vs Col-0, rep1


title: RESUS+VH-4

description: 378 EDEMA

tag: RESUS+VH


title: Transformants of AK073675 vs Col-0, rep2


title: Transformants of AK073112 vs Col-0, rep2


title: RESUS-1

description: 382 RESUS


title: RESUS-4

description: 387 RESUS


title: Transformants of AK069096 vs Col-0, rep1

source_name: re-transformants of AK069096

tag: Aerial parts of re-transformants of AK069096 in T2 generation


title: Transformants of AK069096 vs Col-0, rep2


title: VH-2

description: 380 VH


title: VH-3

description: 385 VH


title: RESUS+VH-3

description: 377 EDEMA


title: CONTROL-3

description: 371 CONTROL

tag: CONTROL


title: CONTROL-4

description: 376 CONTROL


title: Anther-1.0mm Rep4

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description: Discrete stages of anther development were compared.

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.

organism: Zea mays

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy5 or Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

tag: W23 cultivar


title: Mature pollen Rep3

source_name: Mature pollen_I1


title: Binucleate microspore Rep4

source_name: Binucleate microspore_Z4


title: VH-1

description: 379 VH


title: Mature pollen Rep4

source_name: Mature pollen_I2


title: CONTROL-1

description: 369 CONTROL


title: Uninucleate microspore Rep3

source_name: Uninucleate microspore_Y1


title: CONTROL-2

description: 370 CONTROL


title: Quartet Rep4


title: Anther-1.5mm Rep3


title: Anther-1.0mm Rep3


title: Anther-1.5mm Rep4


title: RESUS+VH-1

description: 372 EDEMA


title: Binucleate microspore Rep3

source_name: Binucleate microspore_Z2


title: Quartet Rep3


title: Anther-2.0mm Rep3


title: Uninucleate microspore Rep4

source_name: Uninucleate microspore_Y3


title: Uninucleate microspore Rep1

source_name: Uninucleate microspore_Y4


title: Anther-2.0mm Rep4


title: RESUS+VH-2

description: 373 EDEMA


title: Quartet Rep2


title: Binucleate microspore Rep1

source_name: Binucleate microspore_Z3


title: Anther-1.0mm Rep2


title: Mature pollen Rep2

source_name: Mature pollen_I4


title: Uninucleate microspore Rep2

source_name: Uninucleate microspore_Y2


title: Mature pollen Rep1

source_name: Mature pollen_I3


title: Binucleate microspore Rep2

source_name: Binucleate microspore_Z1


title: Quartet Rep1


title: Anther-2.0mm Rep1


title: Anther-1.5mm Rep1


title: Anther-1.5mm Rep2


title: Anther-1.0mm Rep1


title: RNA_Newman (sarZ) 5hr_sample 2

city: Omaha

first: Paul

middle: M

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw, unscaled signal data

label: biotin

organism: Staphylococcus aureus

source_name: S. aureus strain Newman (sarZ) grown to early stationary phase (5hr)

label_protocol: Affymetrix Antisense labeling of prokaryotic RNA

growth_protocol: S. aureus strain Newman (sarZ) was grown to early stationary phase growth (5hr) in Brain Heart Infusion medium and RNA isolated.

extract_protocol: Mechanical Disruption followed by Qiagen RNeasy with on the column DNase treatment


title: beta 4 expressing MDA-MB-435 (5B3G643)

city: Galveston

first: Kathleen

middle: L

last: O' Connor

address: 301 University Blvd

department: Surgery

institute: University of Texas Medical Branch

description: MDA-MB-435 cell stably tranfected with integrin beta-4 subunit

hyb_protocol: Follow fragmentation, 10ug of cRNA were hybridized for 16 hrs at 45C on HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Gene Array Scanner (Hewlett Packard) 3000

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling

organism: Homo sapiens

source_name: MDA-MB-435 Breast Carcinoma cells from clone 5B3G643

label_protocol: Biotinylated cRNA were prepared accordiing to the standard Affymetrix protocol from 8.4 ug of total RNA

growth_protocol: Cells grown in normal growth medium (10% FCS in DMEM) harvested at 70% confluence in which cells are given fresh growth medium the day before harvest

extract_protocol: RNA was extracted from cells using RNAqueous kit from Ambion


title: mock transfected MDA-MB-435 (6D7G643)

description: MDA-MB-435 cell stably tranfected with vector only

source_name: MDA-MB-435 Breast Carcinoma cells from clone 6D7G643


title: mock transfected MDA-MB-435 (6D2)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 6D2

tag: MDA-MB-435 cell stably tranfected with vector only


title: RNA_Newman (sarZ) 2hr_sample 2

source_name: S. aureus strain Newman (sarZ) grown to exponential phase (2hr)

growth_protocol: S. aureus strain Newman (sarZ) was grown to exponential phase growth (2hr) in Brain Heart Infusion medium and RNA isolated.


title: IL10_Colon_EF.CIF_Rep1_(Pool19)

city: Palmerston North

first: Matthew

last: Barnett

address: Grasslands Research Centre, Tennent Drive

country: New Zealand

institute: AgResearch

hyb_protocol: Microarray hybridization was performed according to a reference design without dye swap. The in situ hybridization kit-plus (Agilent Technologies Inc., Palo Alto, California, USA) was used to hybridize cRNA samples to Agilent Technologies Mouse G4121A - 44k 60mer oligonucleotide arrays. Cy3-labelled cRNA (sample, 0.75 µg) and Cy5-labelled cRNA (reference, 0.75 µg) were hybridised onto the microarray according to the manufacturer’s protocol. Following hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix 4200A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at a photomultiplier tube (PMT) setting of 450 V. Spot identification and quantification were performed using GenePix 6.0 software (Molecular Devices Corporation, Sunnyvale, CA, USA). Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

data_processing:
Statistical analysis was performed using linear models for microarray analysis (limma) within the Bioconductor framework. Before analysis, poor quality spots were manually flagged and filtered out. Quality of the microarray data was assessed on diagnostic plots (boxplots and density plots) and spatial images generated from the raw (non-processed) data. All twenty arrays passed these strict criteria and were included in the analyses. Intensity ratio values for all microarray spots were normalized using a within-slide global Locally Weighted Scatterplot Smoothing (Loess) procedure to remove the effect of systematic variation in the microarrays; no background correction was necessary due to homogeneous hybridization. The normalized data from the arrays of each treatment group were averaged. For each comparison, differentially expressed genes were identified using false discovery rate (FDR) control with a threshold of q < 0.05. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.
The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0.05) were considered to be differentially expressed between treatment.

organism: Mus musculus

source_name: Colon Tissue, EF.CIF inoculated mouse

label_protocol: The Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, California, USA) was used to synthesize cDNA and fluorescent cRNA. Labelled cRNA was made on the same day for all sample pools, including the reference sample. cDNA was synthesized from 500 ng of purified total RNA from each pool using T7 promotor primer and Moloney Murine Leukemia Virus Reverse Transcriptase according to the manufacturer’s protocol. Cy3 (PerkinElmer, Waltham, Massachusetts 02451, USA) was used to label sample groups, while the reference RNA was labeled with Cy5 (PerkinElmer, Waltham, Massachusetts 02451, USA).

growth_protocol: Mice were weighed three times a week throughout the experiment to determine body weight changes. To minimize variation in the time interval between the last food intake and tissue sampling, mice were fasted overnight on the night before sampling. On the morning of sampling, food was returned for two hours, followed by a further two hour fast immediately prior to tissue sampling. Blood was collected from euthanised mice by cardiac puncture. Plasma was separated from red blood cells by centrifugation (2000 g, 10 min, 4 ºC), frozen in liquid nitrogen and stored at - 80 ºC. The intestine was removed, cut open lengthwise and flushed with 0.9 % NaCl to remove digesta residues. The proximal half of the colon was cut in two pieces, one for histological evaluation and other for gene expression studies. Samples of the colon tissue for gene expression analysis were frozen in liquid nitrogen and stored at - 80 ºC. Samples for histological analysis were stored in formalin solution (10 % neutral buffered) at room temperature.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol:
Animals. Twenty five male IL-10-/- (C57BL/6J background, formal designation B6.129P2-IL-10<tm1Cgn>/J) mice and twenty five male C57BL/6J (C57) control mice were received from The Jackson Laboratory (Bar Harbor, Maine, USA) at approximately five weeks of age. Mice were housed either in pairs or groups of three (5 mice per treatment) in shoebox-style cages containing untreated wood shavings and a plastic tube for environmental enrichment. The animal room was maintained at a temperature of ~22°C and humidity of ~50% with a 12 hour light/dark cycle. All mice had ad libitum access to water, which was refreshed twice a week. An AIN-76A powdered diet was supplied twice a week, with sufficient provided to meet the daily intake of IL-10-/- mice, as determined in a previous feeding trial (data not shown). The diet for all groups was sterilized by gamma irradiation (Schering-Plough, Wellington, New Zealand) to a level required for SPF conditions, to minimize the possibility of bacterial introduction to the SPF group of animals. All mice were weighed twice weekly and carefully monitored for disease symptoms (weight loss, soft faeces and inactivity).
Experimental design. Both IL-10-/- and C57 mice were randomly divided into five treatment groups with five animals per group.
1. SPF. Housed in Specific Pathogen Free (SPF) conditions (isolator cages supplied with HEPA filtered air (Tecniplast SpA, Buguggiate, Italy)).
2. C. Maintained under conventional conditions.
3. EF. Maintained under conventional conditions and orally inoculated (200 microlitres) with a solutions containing 12 pure strains of Enterococcus (1.2 x 108 colony forming units (CFU)).
4. CIF. Maintained under conventional conditions and orally inoculated with conventional intestinal flora (CIF) derived from healthy age-matched C57BL/6 mice which had been raised under conventional conditions. The CIF inoculation protocol was included to better mimic the complete microbiota associated with the mouse gastrointestinal tract.
5. EF.CIF. Maintained under conventional conditions and orally inoculated with a combination of the EF and CIF inoculation solutions (6.0 x 107 CFU from the EF inoculum).
Preparation of EF bacterial solutions for oral inoculation. Seventy two hours prior to inoculation, colonies of the E. faecalis and E. faecium strains were sub-cultured from slope tubes onto fresh Slanetz & Bartley medium (Oxoid, Hampshire, UK), and incubated at 42°C for 48 h. A single colony from each culture was subsequently transferred to 5 mL of Todd Hewitt Broth (Oxoid, Hampshire, UK), and incubated at 37°C for 24 h. Each Enterococcus culture was centrifuged to pellet the bacterial cells (3,000 g, 10 min, 4°C), which were then re-suspended in 5 mL sterile PBS (pH 7.4) and pooled (EF inoculum).
Preparation of CIF bacterial solutions for oral inoculation. The healthy, age-matched C57BL/6 mice from which flora were being collected were humanely euthanized by CO2 asphyxiation and cervical dislocation and the gastrointestinal tract (from stomach to just below the caecum) removed. Digesta were collected from the intestine and caecum by gently washing with sterile PBS, pH 7.4, then suspended in a total of 30 mL PBS. After mixing by gentle inversion and a settling period of approximately 5 min, the suspension was collected (CIF inoculum). Inoculation solutions EF and CIF were mixed in a 1:1 (v/v) solution to obtain the EF.CIF inoculum.

tag: Strain

tag: Gender

value: male

tag: Age

value: 5 weeks of age at the start of the experiment, 12 weeks of age when tissue samples taken

tag: Tissue

value: colon tissue

source_name: Reference Pooled Sample of colon RNA

label_protocol: As per Channel 1

growth_protocol: As per Channel 1

extract_protocol: As per Channel 1

treatment_protocol: As per Channel 1

value: IL10-/- and C57BL/6J

value: 12 weeks

tag: Reference sample consisted of RNA extracted from colon tissue of all mice in this experiment (both IL10-/- and C57BL/6J) pooled in equimolar amounts.


title: Anther-2.0mm Rep2


title: C57BL/6J_Colon_EF.CIF_Rep1_(Pool17)

value: C57BL/6J mice


title: beta 4 expressing MDA-MB-435 (3A7)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 3A7

tag: MDA-MB-435 cell stably tranfected with integrin beta-4 subunit


title: C57BL/6J_Colon_EF.CIF_Rep2_(Pool18)


title: RNA_Newman 5hr_sample 1

source_name: S. aureus strain Newman grown to early stationary phase (5hr)

growth_protocol: S. aureus strain Newman was grown to early stationary phase growth (5hr) in Brain Heart Infusion medium and RNA isolated.


title: RNA_Newman 2hr_sample 3

source_name: S. aureus strain Newman grown to exponential phase (2hr)

growth_protocol: S. aureus strain Newman was grown to exponential phase growth (2hr) in Brain Heart Infusion medium and RNA isolated.


title: RNA_Newman 5hr_sample 2

tag: S. aureus strain Newman grown to early stationary phase (5hr)


title: mock transfected MDA-MB-435 (6D2G643)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 6D2G643


title: IL10_Colon_EF.CIF_Rep2_(Pool20)


title: RNA_Newman 2hr_sample 1

tag: S. aureus strain Newman grown to exponential phase (2hr)


title: RNA_Newman (sarZ) 2hr_sample 1

tag: S. aureus strain Newman (sarZ) grown to exponential phase (2hr)


title: RNA_Newman 5hr_sample 3


title: RNA_Newman (sarZ) 5hr_sample 1

tag: S. aureus strain Newman (sarZ) grown to early stationary phase (5hr)


title: RNA_Newman (sarZ) 5hr_sample 3


title: mock transfected MDA-MB-435 (6D7)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 6D7


title: beta 4 expressing MDA-MB-435 (3A7G643)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 3A7G643


title: beta 4 expressing MDA-MB-435 (5B3)

source_name: MDA-MB-435 Breast Carcinoma cells from clone 5B3


title: MEF_HtrA2 KO_con_rep3

city: London

first: Kristina

last: Klupsch

address: 44 Lincoln's Inn Fields

department: London Research Institute

country: United Kingdom

institute: Cancer Research UK

description: Gene expression data from HtrA2 KO MEFs treated for 4hrs with vehicle

hyb_protocol: The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.

data_processing: Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.

source_name: HtrA2 KO control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf

growth_protocol: Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).

treatment_protocol: MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.

tag: Genotype

value: HtrA2 knockout, Treatment vehicle 4hrs


title: RNA_Newman 2hr_sample 2


title: DB7 #1

status: Public on Nov 30 2008

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

description: gene expression from tumor

hyb_protocol: Hybridization was performed following Affymetrix standard protocols .GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using an Agilent GeneArray Scanner

data_processing: The data was processed using Affymetrix Microarray Suite version 5.0.0.032.  RMA normalization was performed using BRB Array Tools version 3.7.0

source_name: DB7 transplant tumor

label_protocol: Labeling was performed following the standard Affymetrix protocol

extract_protocol: RNA was extracted by Trizol following the manufacturers suggested protocol.

treatment_protocol: animals were euthanized by cervical dislocation under Avertin anesthesia.  Tumor samples were snap frozen in LN2 prior to RNA isolation

tag: low metastatic


title: MEF_HtrA2 KO_rot_rep3

description: Gene expression data from HtrA2 KO MEFs treated for 4hrs with 1uM rotenone

source_name: HtrA2 KO rotenone

value: HtrA2 knockout, Treatment:1uM rotenone 4hrs


title: MEF_WT_con_rep3

description: Gene expression data from WT MEFs treated for 4hrs with vehicle

source_name: WT MEF control

value: HtrA2 wild type, Treatment vehicle 4hrs


title: Met1#3

description: gene expression from tumor

source_name: Met1 transplant tumor

tag: highly metastatic


title: MEF_WT_con_rep2


title: Met1 #1

description: gene expression from tumor


title: MEF_HtrA2 KO_rot_rep2


title: DB7 #4

description: gene expression from tumor


title: DB7 #3

description: gene expression from tumor


title: MEF_HtrA2 KO_con_rep1


title: MEF_WT_rot_rep1

description: Gene expression data from WT MEFs treated for 4hrs with 1uM rotenone

source_name: WT MEF rotenone


title: MEF_HtrA2 KO_rot_rep1


title: DB7 #2

description: gene expression from tumor


title: MEF_WT_con_rep1


title: MEF_WT_rot_rep3


title: Met1 #2

description: gene expression from tumor


title: MEF_HtrA2 KO_con_rep2


title: Pat 8_skin_baseline

city: Hershey

first: Diane

last: Thiboutot

state: PA

address: 500 University Drive

department: Department of Dermatology; Jake Gittlen Res. Fnd.

institute: The Pennsylvannia State University College of Medicine

description: Subjects included males and females ages 14 to 40 years who were scheduled by their dermatologist to receive treatment with 13-cis RA (isotretinoin, brand not noted) for severe acne.  All aspects of the patients’ treatment with 13-cis RA apart from the skin biopsies were standard of care and were not part of this research.  Exclusion criteria included patients with underlying medical conditions requiring treatment with systemic medications that might interfere with the gene array analysis.

hyb_protocol: Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the RMA method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003).  To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the medianpolish method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).

source_name: skin, no treatment

extract_protocol: Biopsies were sectioned using a cryostat to facilitate tissue homogenization. Total RNA was isolated and DNase I treated using the Rneasy Fibrous Tissue Kit (Qiagen, Valencia, CA). RNA was ethanol precipitated and quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

treatment_protocol: Human skin biopsies were obtained from patients before isotretinoin and after 8 weeks isotretinoin treatment. Biospies were flash frozen and stored at -80C until RNA isolation

tag: male, 15, Caucasian


title: AKR_2240

description: gene expression from tumor

source_name: (AKR/J x PyMT)F1 female


title: AKR_2242A

description: gene expression from tumor


title: Pat 7_skin_treated

source_name: skin, 8 week isotretinoin treatment

label_protocol: Biotinylated cRNA, produced through in vitro transcription

tag: male, 14, Caucasian


title: DBA_4972

description: gene expression from tumor

source_name: (DBA/2J x PyMT)F1 female


title: Pat 6_skin_treated

tag: female, 24, Hispanic


title: Pat 8_skin_treated


title: Pat 7_skin_baseline


title: AKR_2095A

description: gene expression from tumor


title: Pat 5_skin_treated

tag: male, 18, Caucasian


title: Pat 5_skin_baseline


title: Pat 2_skin_baseline

tag: male, 17, Caucasian


title: Pat 2_skin_treated


title: DBA_4970A

description: gene expression from tumor


title: Pat 4_skin_treated


title: Pat 3_skin_treated

tag: female, 32, Hispanic


title: MEF_WT_rot_rep2


title: Pat 3_skin_baseline


title: Pat 6_skin_baseline


title: Oviduct_from_mated_sample3

status: Public on Nov 24 2008

city: Rehovot

first: Yael

last: Heifetz

address: POB 12

country: Israel

institute: The Hebrew university of Jerusalem

description: Three-day-old mated and unmated females were dissected to remove the oviduct. Mated females were dissected at 3 hrs following the termination of mating. Tracts of 400-500 females of unmated and mated were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Department of Biological Services, Weizmann Institute. Arrays from mated females were compared to unmated females.

hyb_protocol: According to Affymetrix protocols.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 6G System

data_processing: RMA (Irizarry 2003), probe-based linear model (Chu et al 2002)

label: Biotin

organism: Drosophila melanogaster

source_name: Oviduct from 3-day-old mated female

label_protocol: Enzo RNA transcript Labeling Kit, According to Affymetrix protocols.

growth_protocol: All flies were kept in a 12hr light/dark cycle at 23±2 Celsius degrees.

extract_protocol: TRIzol - chloroform

treatment_protocol: Females were all same age (3-day-old) and either mated or not. Mated females were dissected at 3 hrs postmating. Unmated (control) females were dissected at parallel times.

tag: Oviduct from 3-day-old mated female, dissected 3 hrs after mating


title: Oviduct_from_mated_sample2

source_name: oviduct from 3-day-old mated female

tag: oviduct from 3-day-old mated female, dissected 3 hrs after mating


title: Pat 1_skin_treated

tag: female, 22, Black or African American


title: Oviduct_from_mated_sample1


title: DBA_4971A

description: gene expression from tumor


title: Oviduct_from_Unmated_sample3

source_name: oviduct from 3-day-old unmated female

tag: Oviduct from 3-day-old unamted female


title: Pat 1_skin_baseline


title: Pat 4_skin_baseline


title: HCC1954BL_SIDES_H07

status: Public on Nov 14 2008

type: genomic

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Copy numbers were estimated by the pre-processing module

molecule: genomic DNA

source_name: human peripheral blood

label_protocol: Affymetrix standard procedure

growth_protocol: Cell lines were propagated in growth media recommended by the American Type Tissue Collection

extract_protocol: Genomic DNA was extracted with the DNeasy blood and tissue kit (Qiagen) according to manufacturer's instructions

tag: EBV-transformed lymphoblastoid cell line


title: HCC1954BL_WHELK_E04


title: HCC1954BL_VOLTS_C04


title: HCC1954BL_SOARS_C05


title: NCI-H2347

source_name: human lung

tag: lung adenocarcinoma


title: HCC1954BL_UNZIP_H03


title: HCC1954BL_SOPOR_B08


title: HCC1954BL_SHOER_B10


title: HCC1954BL_DRAWS_C04


title: HCC1954BL_PRAWN_A09


title: HCC1954BL_PAVIN_G04

description: PAVIN_p_STY33_Mapping250K_Sty_G04_128860


title: HCC1954BL_HAREM_H03

description: HAREM_p_STY35_Redo_Mapping250K_Sty_H03_151008


title: HCC1954BL_HEWED_H05

description: HEWED_p_250KSty_Plate_20060123_GOOD_H05_46322


title: HCC1954BL_DECAY_D08

description: DECAY_p_STY34_Mapping250K_Sty_D08_131162


title: HCC1954BL_DEBUG_H12

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H12_88348


title: HCC1954BL_LINED_C05

description: LINED_p_STY36_Mapping250K_Sty_C05_147750


title: HCC1954BL_WINZE_D02

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_D02_82026


title: HCC1954BL_HOCUS_B07


title: HCC1954BL_KNACK_E02

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_E02_104588


title: HCC1954BL_LORDS_H12

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H12_88732


title: HCC1954BL_VINOS_B06


title: HCC1954BL_DOLCE_G08


title: HCC1954BL_WHOOP_C07

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_C07_110550


title: HCC1954BL_UNLET_H07


title: HCC1954BL_SPICA_E03

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_E03_121544


title: HCC1954BL_GUSTO_H11


title: HCC1954BL_COMET_E06


title: HCC1954BL_KOALA_E07


title: HCC1954BL_CHAMS_H01

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H01_112330


title: HCC1954BL_CLONE_C05

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_C05_104440


title: Oviduct_from_Unmated_Sample2

hyb_protocol: GeneChips were scanned using the GeneChip Scanner 3000 6G System

scan_protocol: According to Affymetrix protocols.

tag: Oviduct from 3-day-old unmated female


title: HCC1954BL_BRISK_F04

description: BRISK_p_STY37_Mapping250K_Sty_F04_147548


title: HCC1954BL_SITED_F04

description: SITED_p_Cancer_Affy_Redo_1_Mapping250K_Sty_F04_110178


title: HCC1954BL_ABORT_C05


title: HCC1143BL_WINZE_A01

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_A01_82004

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 2


title: HCC1954BL_AIRNS_E07


title: HCC1954BL_BOTEL_F04

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_F04_48742


title: HCC1954BL_BARRE_C11


title: HCC1143BL_WHOOP_F01

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_F01_110606


title: HCC1143BL_WINZE_F05

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_F05_82078


title: HCC1143BL_UNZIP_A04


title: HCC1954BL_ACTOR_H07


title: HCC1143BL_VOLTS_A02


title: HCC1143BL_VINOS_A02


title: HCC1143BL_VOLTS_F03


title: HCC1143BL_UNLET_H11


title: HCC1143BL_UNZIP_A02


title: HCC1143BL_SPICA_C11

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_C11_121668


title: HCC1143BL_WHOOP_A01

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_A01_107402


title: HCC1143BL_UNLET_H09


title: HCC1143BL_SOARS_A07


title: HCC1143BL_SOARS_A01


title: HCC1143BL_SHOER_A02


title: HCC1143BL_SITED_C04

description: SITED_p_Cancer_Affy_Redo_1_Mapping250K_Sty_C04_110172


title: HCC1143BL_SPICA_A01

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_A01_121504


title: HCC1143BL_SIDES_H09


title: HCC1143BL_PRAWN_F04


title: HCC1143BL_VINOS_B10


title: HCC1143BL_SIDES_H11


title: HCC1143BL_WHELK_A01


title: HCC1143BL_SOPOR_A01


title: HCC1143BL_SHOER_A06


title: HCC1143BL_WHELK_C10


title: HCC1143BL_SOPOR_E09


title: HCC1143BL_PAVIN_A02

description: PAVIN_p_STY33_Mapping250K_Sty_A02_128816


title: HCC1143BL_PRAWN_A01


title: HCC1143BL_LINED_A01

description: LINED_p_STY36_Mapping250K_Sty_A01_147682


title: HCC1143BL_PAVIN_D08

description: PAVIN_p_STY33_Mapping250K_Sty_D08_128918


title: HCC1143BL_LINED_H01

description: LINED_p_STY36_Mapping250K_Sty_H01_147696


title: HCC1143BL_LORDS_Sty_H10

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H10_88700


title: HCC1143BL_LORDS_Sty_H08

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H08_88668


title: HCC1143BL_GUSTO_C06


title: HCC1143BL_KOALA_B07


title: HCC1143BL_KNACK_C10

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_C10_104712


title: HCC1143BL_GUSTO_A01


title: HCC1143BL_KOALA_A02


title: HCC1143BL_COMET_A01


title: HCC1143BL_DOLCE_A02


title: HCC1143BL_DOLCE_H10


title: HCC1143BL_HAREM_A02

description: HAREM_p_STY35_Redo_Mapping250K_Sty_A02_150978


title: HCC1143BL_DRAWS_H04


title: HCC1143BL_DEBUG_Sty_H10

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H10_88316


title: HCC1143BL_HEWED_A02

description: HEWED_p_250KSty_Plate_20060123_GOOD_A02_46260


title: HCC1143BL_CHAMS_Sty_A01

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_A01_112316


title: HCC1143BL_BRISK_B05

description: BRISK_p_STY37_Mapping250K_Sty_B05_147556


title: HCC1143BL_BRISK_A01

description: BRISK_p_STY37_Mapping250K_Sty_A01_147490


title: HCC1143BL_DRAWS_A02


title: HCC1143BL_DECAY_H03

description: DECAY_p_STY34_Mapping250K_Sty_H03_131090


title: HCC1143BL_CHAMS_Sty_D04

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_D04_112370


title: HCC1143BL_DECAY_A01

description: DECAY_p_STY34_Mapping250K_Sty_A01_131044


title: HCC1143BL_CLONE_Sty_A01

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A01_104372


title: HCC1143BL_COMET_A09


title: HCC1143BL_BARRE_A02


title: HCC1143BL_DEBUG_Sty_H08

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H08_88284


title: HCC1143BL_BOTEL_G04

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_G04_48744


title: HCC1143BL_KNACK_A01

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_A01_104564


title: HCC1143BL_CLONE_Sty_F07

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_F07_104478


title: HCC1143BL_HAREM_F05

description: HAREM_p_STY35_Redo_Mapping250K_Sty_F05_151036


title: HCC1143BL_BARRE_E11


title: HCC1143BL_ACTOR_H11


title: HCC1143BL_BOTEL_E04

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_E04_48740


title: HCC1143BL_HOCUS_A02


title: HCC1143_WINZE_F06

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_F06_82094

source_name: human breast

tag: breast ductal adenocarcinoma


title: HCC1143BL_AIRNS_A02


title: HCC1143BL_AIRNS_C08


title: HCC1143BL_ABORT_C11


title: HCC1143_WHOOP_F02

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_F02_110608


title: HCC1954_WINZE_D03

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_D03_82042


title: HCC1143_VINOS_B09


title: HCC1143BL_ABORT_A01


title: HCC1954_WHELK_E05


title: HCC1143_UNZIP_A01


title: HCC1143_WHELK_C11


title: HCC1143_WHELK_A02


title: HCC1954_UNLET_H08


title: HCC1143BL_ACTOR_H09


title: HCC1143_UNZIP_A03


title: HCC1954_WHOOP_C08

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_C08_110552


title: HCC1143_UNLET_H12


title: HCC1143_VOLTS_F02


title: HCC1143_VOLTS_A01


title: HCC1954_UNZIP_H02


title: HCC1143_VINOS_A01


title: HCC1143_WHOOP_A02

description: WHOOP_p_STY30_(CO-108057)_Mapping250K_Sty_A02_110116


title: HCC1143_STAND_G11

description: STAND_p_Affy_plate_8_Mapping250K_Sty_G11_49432


title: HCC1143_SPICA_A02

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_A02_121520


title: HCC1954_SPICA_E04

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_E04_121560


title: HCC1143_SPICA_C12

description: SPICA_p_Sty32_(CO-166838)_Mapping250K_Sty_C12_121684


title: HCC1954_VOLTS_C03


title: HCC1954_SOPOR_B09


title: HCC1143_STAND_F11

description: STAND_p_Affy_plate_8_Mapping250K_Sty_F11_49430


title: HCC1143_UNLET_H10


title: HCC1954_VINOS_B05


title: HCC1143_SOPOR_E10


title: HCC1143_SOPOR_A02


title: HCC1954_STAND_H11

description: STAND_p_Affy_plate_8_Mapping250K_Sty_H11_49434


title: HCC1143_SIDES_H10


title: HCC1143_SITED_1

description: SITED_p_Cancer_Affy_Redo_1_Mapping250K_Sty_G07_110228


title: HCC1143_SIDES_H12


title: HCC1143_SOARS_A08


title: HCC1954_SIDES_H08


title: HCC1143_SHOER_A01


title: HCC1143_PRAWN_F05


title: HCC1954_REMEX_H11

description: REMEX_p_CO-21477_Mapping250K_Sty_H11_49050


title: HCC1954_PRAWN_A10


title: HCC1143_REMEX_G11

description: REMEX_p_CO-21477_Mapping250K_Sty_G11_49048


title: HCC1143_LORDS_Sty_H09

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H09_88684


title: HCC1143_PRAWN_A02


title: HCC1143_MYNAH_Sty_G11

description: MYNAH_p_Affy_plate_9_Mapping250K_Sty_G11_49240


title: HCC1143_SHOER_A05


title: HCC1954_OKAYS_H11

description: OKAYS_p_CO-21478_Mapping250K_Sty_H11_47782


title: HCC1954_PAVIN_G03

description: PAVIN_p_STY33_Mapping250K_Sty_G03_128844


title: HCC1143_OKAYS_G11

description: OKAYS_p_CO-21478_Mapping250K_Sty_G11_47780


title: HCC1954_SHOER_B09


title: HCC1954_SOARS_C06


title: HCC1143_PAVIN_A01

description: PAVIN_p_STY33_Mapping250K_Sty_A01_128800


title: HCC1143_SOARS_A02


title: HCC1954_OSTIA_H11

description: OSTIA_p_CO-21481_Mapping250K_Sty_H11_47974


title: HCC1954_LORDS_Sty_H11

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H11_88716


title: HCC1954_KOALA_E06


title: HCC1954_MYNAH_Sty_H11

description: MYNAH_p_Affy_plate_9_Mapping250K_Sty_H11_49242


title: HCC1143_OSTIA_G11

description: OSTIA_p_CO-21481_Mapping250K_Sty_G11_47972


title: HCC1143_LINED_H02

description: LINED_p_STY36_Mapping250K_Sty_H02_147712


title: HCC1143_KOALA_B06


title: HCC1143_KOALA_A01


title: HCC1143_LORDS_Sty_H07

description: LORDS_p_Japan_SNP_(CO-59748)_Mapping250K_Sty_H07_88652


title: HCC1143_MYNAH_Sty_F11

description: MYNAH_p_Affy_plate_9_Mapping250K_Sty_F11_49238


title: HCC1954_HOCUS_B06


title: HCC1143_HOCUS_A01


title: HCC1143_KNACK_Sty_C11

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_C11_104728


title: HCC1954_KNACK_Sty_E03

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_E03_104604


title: HCC1143_KNACK_Sty_A02

description: KNACK_p_STY28_(CO-106345)_Mapping250K_Sty_A02_104580


title: pcp2_dr166_cb_ip1: Purkinje Neuron, Cerebellum, TRAP RNA 1

city: New York

first: Nathaniel

last: Heintz

state: NY

address: 1230 York Ave, Box 260

institute: HHMI/Rockefeller University

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

data_processing: GCRMA normalization within biological replicate groups.  Performed with R / Bioconductor.

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 1

label_protocol: Affymetrix two cycle amplification kit, starting with 15 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol extraction, DNAse treatment, and RNeasy-Minelute Cleanup

tag: TRAP RNA

tag: Driver

value: pcp2, Line:DR166, Region:Cerebellum


title: HCC1143_HEWED_A01

description: HEWED_p_250KSty_Plate_20060123_GOOD_A01_46244


title: pcp2_dr166_cb_ip2: Purkinje Neuron, Cerebellum, TRAP RNA 2

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 2


title: pcp2_dr166_cb_ip3: Purkinje Neuron, Cerebellum, TRAP RNA 3

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 3


title: chat_bs_ip3: Motor Neurons, Brainstem, TRAP RNA 3

source_name: Motor Neurons, Brainstem, TRAP RNA 3

value: chat, Line:DW167, Region:Brainstem


title: HCC1954_HEWED_H04

description: HEWED_p_250KSty_Plate_20060123_GOOD_H04_46306


title: HCC1954_DRAWS_C03


title: HCC1143_DOLCE_A01


title: HCC1143_DOLCE_H09


title: d2_str_ip3: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 3

value: drd2, Line:CP101, Region:Striatum


title: HCC1143_DRAWS_A01


title: chat_bs_ip1: Motor Neurons, Brainstem, TRAP RNA 1

source_name: Motor Neurons, Brainstem, TRAP RNA 1


title: HCC1143_GUSTO_A02


title: chat_bs_ip2: Motor Neurons, Brainstem, TRAP RNA 2

source_name: Motor Neurons, Brainstem, TRAP RNA 2


title: d2_str_ip2: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 2


title: HCC1954_GUSTO_H12


title: HCC1954_DOLCE_G07


title: d2_str_ip1: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 1


title: HCC1143_DECAY_A02

description: DECAY_p_STY34_Mapping250K_Sty_A02_131060


title: HCC1143_DRAWS_H03


title: d1_str_ip3: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 3

value: drd1, Line:CP73, Region:Striatum


title: HCC1954_DECAY_D07

description: DECAY_p_STY34_Mapping250K_Sty_D07_131146


title: d1_str_ip2: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 2


title: pcp2_cb_ub3: Purkinje Neuron, Cerebellum, Unbound RNA 3

tag: cytoplasmic polysomal RNA, unbound


title: HCC1954_DEBUG_H11

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H11_88332


title: pcp2_cb_ub2: Purkinje Neuron, Cerebellum, Unbound RNA 2


title: pcp2_cb_ub1: Purkinje Neuron, Cerebellum, Unbound RNA 1


title: d1_str_ip1: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 1


title: HCC1143_GUSTO_C07


title: HCC1954_LINED_C06

description: LINED_p_STY36_Mapping250K_Sty_C06_147766


title: HCC1143_LINED_A02

description: LINED_p_STY36_Mapping250K_Sty_A02_147698


title: HCC1143_WINZE_A02

description: WINZE_p_Sty19_CORRECTED_Mapping250K_Sty_A02_82020


title: HCC1954_COMET_E07


title: HCC1143_DECAY_H04

description: DECAY_p_STY34_Mapping250K_Sty_H04_131106


title: HCC1143_COMET_A02


title: HCC1954_CLONE_C06

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_C06_104456


title: HCC1143_COMET_A10


title: d1_str_ub1: Drd1+ Medium Spiny Neurons, Striatum, Unbound RNA 1


title: chat_bs_ub1: Motor Neurons, Brainstem, Unbound RNA 1

source_name: Motor Neurons, Brainstem, Unbound RNA 1


title: HCC1143_CLONE_F08

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_F08_104494


title: d2_str_ub1: Drd2+ Medium Spiny Neurons, Striatum, Unbound RNA 1


title: chat_bs_ub2: Motor Neurons, Brainstem, Unbound RNA 2

source_name: Motor Neurons, Brainstem, Unbound RNA 2


title: HCC1143_BIELD_G11

description: BIELD_p_CO-21480_Mapping250K_Sty_G11_48368


title: HCC1143_DEBUG_H09

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H09_88300


title: HCC1954_BLEAK_H11

description: BLEAK_p_CO-21475_Mapping250K_Sty_H11_47398


title: HCC1143_DEBUG_H07

description: DEBUG_p_Japan_SNP_(CO-58875)_Mapping250K_Sty_H07_88268


title: HCC1143_BLEAK_G11

description: BLEAK_p_CO-21475_Mapping250K_Sty_G11_47396


title: HCC1143_BARRE_E10


title: d2_str_ub2: Drd2+ Medium Spiny Neurons, Striatum, Unbound RNA 2


title: d1_str_ub2: Drd1+ Medium Spiny Neurons, Striatum, Unbound RNA 2


title: HCC1143_BRISK_A02

description: BRISK_p_STY37_Mapping250K_Sty_A02_147506


title: HCC1143_BRISK_B06

description: BRISK_p_STY37_Mapping250K_Sty_B06_147572


title: HCC1954_BRISK_F03

description: BRISK_p_STY37_Mapping250K_Sty_F03_147532


title: HCC1954_BIELD_H11

description: BIELD_p_CO-21480_Mapping250K_Sty_H11_48370


title: HCC1143_BOTEL_G03

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_G03_48728


title: HCC1954_BOTEL_F03

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_F03_48726


title: HCC1143_BARRE_A01


title: HCC1143_BOTEL_E03

description: BOTEL_p_CO-22577_(STY6)_Mapping250K_Sty_E03_48724


title: HCC1954_BARRE_C10


title: HCC1143_CLONE_A02

description: CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A02_104388


title: HCC1954_AIRNS_E08


title: HCC1954_CHAMS_H02

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H02_112346


title: HCC1143_CHAMS_D05

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_D05_112386


title: chat_bs_ub3: Motor Neurons, Brainstem, Unbound RNA 3

source_name: Motor Neurons, Brainstem, Unbound RNA 3


title: HCC1954_ATLAS_H11

description: ATLAS_p_CO-21476_Mapping250K_Sty_H11_47590


title: HCC1143_ATLAS_G11

description: ATLAS_p_CO-21476_Mapping250K_Sty_G11_47588


title: HCC1143_AIRNS_C09


title: HCC1143_CHAMS_A02

description: CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_A02_112332


title: HCC1143_ABORT_C12


title: HCC1954_ABORT_C06


title: HCC1143_ACTOR_H10


title: HCC1143_ACTOR_H12


title: D1_IP1: Drd1a Medium spiny neurons, dissected mouse striatum.

data_processing:
In Genespring GX 7.3.1, GCRMA normalization was performed within the two biological replicate groups (IP and WB), and expression values on each chip were further normalized to the expression values of several positive control genes and to a constant value of 0.01.
Using the Limma package from Bioconductor project, data were converted to log2 scale.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (IP, see accompanying manuscript) or total homogenized tissue (WB), followed by Trizol-LS extraction, DNAse treatment, and RNeasy-Minelute Cleanup.

value: Drd1a, Line:CP73, Region:striatum


title: HCC1143_ABORT_A02


title: D2_IP2: Drd2 Medium spiny neurons, dissected mouse striatum.

value: Drd2, Line:CP101, Region:striatum


title: D1_IP2: Drd1a Medium spiny neurons, dissected mouse striatum.


title: D2_IP3: Drd2 Medium spiny neurons, dissected mouse striatum

data_processing:
In Genespring GX 7.3.1, data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.
Using the Limma package from Bioconductor project, data were converted to log2 scale.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol-LS extraction, DNAse treatment, and RNeasy-Minelute Cleanup.


title: D2_IP1: Drd2 Medium spiny neurons, dissected mouse striatum.


title: D1_IP3: Drd1a Medium spiny neurons, dissected mouse striatum.


title: D2_IP3: Drd2 Medium spiny neurons, dissected mouse striatum.


title: D1_IP3: Drd1a Medium spiny neurons, dissected mouse striatum


title: HCC1143_AIRNS_A01


title: D2_IP2: Drd2 Medium spiny neurons, dissected mouse striatum


title: D2_IP1: Drd2 Medium spiny neurons, dissected mouse striatum


title: HCC1954_ACTOR_H08


title: D1_IP2: Drd1a Medium spiny neurons, dissected mouse striatum


title: D1_IP1: Drd1a Medium spiny neurons, dissected mouse striatum


title: NCI-H2347

description: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_H06_350870

data_processing: Copy numbers were estimated by a copy number pipeline according to The Cancer Genome Atlas Research Network (2008) Nature


title: NCI-H2347BL

description: DITSY_p_CLLGasHpc_SNP6_GenomeWideSNP_6_H05_350868


title: HCC1954BL_COTES_B08

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_B08_292934

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 40


title: HCC1954BL_STAIR_C05

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_C05_238410

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 39


title: HCC1954BL_PUNAS_F10

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_F10_238300

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 38


title: HCC1954BL_TRIBE_G11

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_G11_155888

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 35


title: HCC1954BL_TRIBE_B01

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_B01_155718

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 34


title: HCC1954_COTES_B07

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_B07_292932


title: HCC1954BL_TRIGS_G11

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G11_223258

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 37


title: HCC1954_STAIR_C06

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_C06_238412


title: HCC1954BL_GHATS_G10

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G10_160242

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 36


title: HCC1954BL_GLEYS_H02

description: GLEYS_p_6.0_Test_GenomeWideEx_6_H02_140756

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 33


title: HCC1954_FALLS_G08

description: FALLS_p_TCGAaffxB4_1_GenomeWideSNP_6_G08_190676


title: HCC1954BL_GLEYS_C04

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C04_140778

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 31


title: HCC1954BL_GLEYS_B01

description: GLEYS_p_6.0_Test_GenomeWideEx_6_B01_140728

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 30


title: HCC1954_GHATS_G09

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_G09_160226


title: HCC1954_TRIBE_B02

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_B02_155734


title: HCC1954_GLEYS_B02

description: GLEYS_p_6.0_Test_GenomeWideEx_6_B02_140744


title: HCC1143BL_COTES_A02

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_A02_292898

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 27


title: HCC1954_TRIBE_G12

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_G12_155904


title: HCC1954_GLEYS_C05

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C05_140794


title: HCC1143BL_COTES_F06

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_F06_293026

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 28


title: HCC1954_TRIGS_G10

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G10_223242


title: HCC1954_PUNAS_F11

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_F11_238302


title: HCC1954BL_GLEYS_D02

description: GLEYS_p_6.0_Test_GenomeWideEx_6_D02_140748

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 32


title: HCC1954_GLEYS_D03

description: GLEYS_p_6.0_Test_GenomeWideEx_6_D03_140764

tag: breast ductal adenocarcinoma


title: HCC1954_GLEYS_H03

description: GLEYS_p_6.0_Test_GenomeWideEx_6_H03_140772


title: HCC1954_GLEYS_H01

description: GLEYS_p_6.0_Test_GenomeWideEx_6_H01_140740


title: HCC1143BL_SHUNT_A02

description: SHUNT_p_TCGA_sigwga_Affx_Sty_GenomeWideSNP_6_A02_228706

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 22


title: HCC1143BL_STAIR_G10

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_G10_238516

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 26


title: HCC1143BL_PUNAS_A01

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_A01_238162

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 24


title: HCC1143BL_FALLS_A03

description: FALLS_p_TCGAaffxB4_1_GenomeWideSNP_6_A03_190522

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 19


title: HCC1143BL_TRIGS_G09

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G09_223226

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 21


title: HCC1143BL_TRIGS_G07

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G07_223194

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 20


title: HCC1143BL_GHATS_H10

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H10_160244

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 10


title: HCC1143BL_STAIR_A02

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_A02_238356

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 25


title: HCC1143BL_GHATS_H09

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H09_160228

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 11


title: HCC1143BL_GHATS_H04

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H04_160148

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 9


title: HCC1143BL_GHATS_A02

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_A02_160102

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 12


title: HCC1143BL_PUNAS_D05

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_D05_238242

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 23


title: HCC1143BL_GLEYS_C11

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C11_140890

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 4


title: HCC1143BL_GLEYS_G08

description: GLEYS_p_6.0_Test_GenomeWideEx_6_G08_140850

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 5


title: HCC1143BL_TRIBE_D02

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_D02_155738

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 6


title: HCC1143BL_GLEYS_A01

description: GLEYS_p_6.0_Test_GenomeWideEx_6_A01_140726

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 2


title: HCC1143BL_GHATS_H03

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_H03_160132

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 15


title: HCC1143BL_TRIBE_E06

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_E06_155804

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 7


title: HCC1143_PUNAS_A02

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_A02_238164

tag: breast ductal adenocarcinoma


title: HCC1143BL_GLEYS_C09

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C09_140858

tag: EBV-transformed lymphoblastoid cell line with gain of chromosome 3


title: HCC1143_STAIR_G09

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_G09_238514


title: HCC1143_COTES_A01

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_A01_292896


title: HCC1143_STAIR_A01

description: STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_A01_238354


title: HCC1143_COTES_F05

description: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_F05_293024


title: HCC1143_SHUNT_A01

description: SHUNT_p_TCGA_sigwga_Affx_Sty_GenomeWideSNP_6_A01_228690


title: HCC1143_PUNAS_D06

description: PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_D06_238244


title: HCC1143_TRIGS_G08

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G08_223210


title: HCC1143_TRIGS_G06

description: TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_G06_223178


title: differentiated C2C12 cells mono nucleosomal chromatin fragments chip on chip replicate 2

status: Public on Nov 06 2008

first: Brian

last: Dynlacht

department: Cancer Institute

institute: NYU Medical Center

description: genome-wide nucleosome density profiles in differentiated C2C12 cells by chip on chip

hyb_protocol: Hybridization onto the mouse tiling array, which includes 244K features, washing and scanning were carried out according to the manufacturers instructions.

scan_protocol: According to Agilent Scanning Software

data_processing: Log ratios were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

source_name: Input for mouse mono nucleosomal chromatin fragments

label_protocol: input samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy3 using Invitrogen CHG kit (18095-011). Labelling reaction were cleauned up by invitrogen bind and elute CGH columns (18095-011).

growth_protocol: C2C12 cells were grown in DMEM supplemented with 10% fetal bovine serum. Differentiated cells were obtained by culturing confluent C2C12 cells in DMEM supplemented with 2% horse serum. Differentiated cells were separated from undifferentiated cells using diluted trypsin.

extract_protocol: Differentiated C2C12 cells were cross-linked by addition of formaldehyde (to 1% final concentration) to separated differentiated myotubes. Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m). Cells were washed with PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 1 mm benzamidine, 50 μg/ml TLCK, 50 μg/ml TPCK, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in sonication buffer (1 mm EDTA, 0.5 mm EGTA, 10 mm Tris at pH 8, and protease inhibitors), and sonicated on ice to an average length of 350 bp

tag: The C2C12 murine myoblast cell line (obtained from ATCC)

source_name: mono nucleosomal chromatin fragments

label_protocol: IP samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy5 using Invitrogen CHG kit (18095-011). Labelling reaction were cleauned up by invitrogen bind and elute CGH columns (18095-011).

extract_protocol: Differentiated C2C12 cells were cross-linked by addition of formaldehyde (to 1% final concentration) to separated differentiated myotubes. Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m).Cells were washed with PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 1 mm benzamidine, 50 μg/ml TLCK, 50 μg/ml TPCK, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in MNase buffer (10 mM Tris at pH 7.4, 60 mM KCl, 15 mM NaCl, 2 mM CaCl2), briefly washed, and treated with ~150U MNase (Worthington) at room temperature for 30 min. The reaction was quenched with 10 mM EDTA and sonicated.


title: differentiated C2C12 cells H3 lysine 4 tri methylation chip on chip tiling array replicate 2

description: Histone H3 lysine 4 tri methylation genome-wide binding profiles in differentiated C2C12 cells by chip on chip

source_name: Input for mouse histone H3 lysine 4 tri methylation chromatin immunoprecipitation

source_name: IP for mouse histone H3 lysine 4 tri methylation chromatin immunoprecipitation


title: differentiated C2C12 cells mono nucleosomal chromatin fragments chip on chip replicate 1

extract_protocol: Differentiated C2C12 cells were cross-linked by addition of formaldehyde (to 1% final concentration) to separated differentiated myotubes. Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m).Cells were washed with PBS and scraped into PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 1 mm benzamidine, 50 μg/ml TLCK, 50 μg/ml TPCK, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in MNase buffer (10 mM Tris at pH 7.4, 60 mM KCl, 15 mM NaCl, 2 mM CaCl2), briefly washed, and treated with ~150U MNase (Worthington) at room temperature for 30 min. The reaction was quenched with 10 mM EDTA and sonicated.


title: cycling C2C12 cells mono nucleosomal chromatin fragments chip on chip replicate 2

description: genome-wide nucleosome density profiles in cycling C2C12 cells by chip on chip

growth_protocol: C2C12 cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Cycling C2C12 cells were grown on 15-cm2 dishes and cross-linked by addition of formaldehyde (to 1% final concentration) to attached cells. Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m).Cells were washed with PBS and scraped into PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 1 mm benzamidine, 50 μg/ml TLCK, 50 μg/ml TPCK, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in MNase buffer (10 mM Tris at pH 7.4, 60 mM KCl, 15 mM NaCl, 2 mM CaCl2), briefly washed, and treated with ~150U MNase (Worthington) at room temperature for 30 min. The reaction was quenched with 10 mM EDTA and sonicated.


title: differentiated C2C12 cells H3 pan acetylation chip on chip tiling array replicate 1

description: Histone H3 pan acetylation genome-wide binding profiles in differentiated C2C12 cells by chip on chip

source_name: Input for mouse histone H3 pan acetylation chromatin immunoprecipitation

source_name: IP for mouse histone H3 pan acetylation chromatin immunoprecipitation


title: cycling C2C12 cells mono nucleosomal chromatin fragments chip on chip replicate 1


title: HCC1143_TRIBE_E05

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_E05_155788


title: cycling C2C12 cells histone H3 pan-acetylation chip on chip replicate 2

description: Histone H3 pan acetylation genome-wide binding profiles in cycling C2C12 cells by chip on chip

source_name: Input for mouse histone H3 pan acetylation immunoprecipitation


title: differentiated C2C12 cells H3 pan acetylation chip on chip tiling array replicate 2


title: differentiated C2C12 cells Sin3B binding chip on chip tiling array replicate 4

description: Sin3B genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse Sin3B chromatin immunoprecipitation

source_name: IP for mouse Sin3B chromatin immunoprecipitation


title: cycling C2C12 cells histone H3 lysine 4 tri methylation chip on chip replicate 1

description: Histone H3 lysine 4 tri methylation genome-wide binding profiles in cycling C2C12 cells by chip on chip

source_name: IP for mouse histone H3 pan acetylation immunoprecipitation


title: cycling C2C12 cells histone H3 pan-acetylation chip on chip replicate 1


title: differentiated C2C12 cells H3 lysine 4 tri methylation chip on chip tiling array replicate 1


title: HCC1143_FALLS_A01

description: FALLS_p_TCGAaffxB4_1_GenomeWideSNP_6_A01_190518

source_name: human breast


title: cycling C2C12 cells mono nucleosomal chromatin fragments chip on chip replicate 3


title: HCC1143_GHATS_C07

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_C07_160186


title: HCC1143_TRIBE_H11

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_H11_155890


title: HCC1143_GLEYS_C06

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C06_140810


title: differentiated C2C12 cells Sin3B binding chip on chip tiling array replicate 3


title: HCC1143_GHATS_A01

description: GHATS_p_TCGAaffx_B3_GBM_GenomeWideSNP_6_A01_160086


title: HCC1143_GLEYS_G09

description: GLEYS_p_6.0_Test_GenomeWideEx_6_G09_140866


title: HCC1143_GLEYS_C10

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C10_140874


title: differentiated C2C12 cells Sin3A binding chip on chip tiling array replicate 3

description: Sin3A genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse Sin3a chromatin immunoprecipitation

source_name: IP for mouse Sin3A chromatin immunoprecipitation


title: HCC1143_GLEYS_A02

description: GLEYS_p_6.0_Test_GenomeWideEx_6_A02_140742


title: differentiated C2C12 cells Sin3B binding chip on chip tiling array replicate 1


title: cycling C2C12 cells histone H3 lysine 4 tri methylation chip on chip replicate 2

source_name: Input for mouse histone H3 lysine 4 tri methylation immunoprecipitation

source_name: IP for mouse histone H3 lysine 4 tri methylation immunoprecipitation


title: HCC1143_FALLS_A02

description: FALLS_p_TCGAaffxB4_1_GenomeWideSNP_6_A02_190520


title: differentiated C2C12 cells RBP2 binding chip on chip tiling array replicate 3

description: RBP2 genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse RBP2 chromatin immunoprecipitation

source_name: IP for mouse RBP2 chromatin immunoprecipitation


title: differentiated C2C12 cells Sin3A binding chip on chip tiling array replicate 2


title: Tor1Mutant_Rep_1

status: Public on Nov 01 2008

city: Los Angeles

first: Huanying

last: Ge

address: 1050 Childs Way, RRI building 408D

department: Biology

institute: Computational biology and bioinformatics

description: Microarray Experiment is done in UCLA DNA array Core Facility

hyb_protocol: Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/, The biotin-labeled cRNA was hybridized to Affymetrix GeneChip® Yeast2.0 Array.

data_processing:
The normalization is carried out in a pairwise fashion. Namely, for each wild type sample (W1, W2, W3), three replicates of a mutant are normalized with respect to each reference. Take sch9Δ (triplicates: S1, S2 and S3) or example, the normalized arrays with respect to W1, W2, W3 are respectively denoted by S1\W1, S2\W1, S3\W1, S1\W2, S2\W2, S3\W2, S1\W3, S2\W3, S3\W3. We group the wild type and normalized mutant arrays by the reference, and then summarize each group. Take sch9Δ for example. We summarize the four arrays (the reference plus three normalized) W1, S1\W1, S2\W1, S3\W1 together. This leads to three estimates of expression fold changes of the mutant versus the wild type. In total, we have nine estimates from three wild type references, and we take their median difference as the final estimate. The details for this pre-processing can be found in [Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, et al. (2007) Significant and Systematic Expression Differentiation in Long-Lived Yeast Strains. PLoS ONE 2(10): e1095. doi:10.1371/journal.pone.0001095]

Signal estimates for individual samples were not generated by the analysis. See the Series record for expression fold change estimates.

organism: Saccharomyces cerevisiae

source_name: Tor1 Mutant

growth_protocol: Each strain was inoculated in 1 mL SDC and grown overnight. Saturated overnight cultures were then diluted into 3 flasks each containing 50 mL of culture. All samples were incubated at 30°C with shaking (2200 rpm) until day 2.5. In the SDC medium, a substantial proportion of yeast cells are still dividing before day 2. At older ages, such as day 3–5, most of the cells become hypometabolic, which is associated with a dramatic drop in transcription. We harvest mRNA at day 2.5 so that we can extract enough mRNA for microarray experiment while avoid the noise introduced by the transcriptional activities of dividing cells.

extract_protocol: Total RNA was isolated from day 2.5 post-diauxic yeast cultures (2.0×108 cells) according to the acid phenol protocol. Briefly, yeast were collected by centrifugation, washed with cold water once, and resuspended in 400 µl of 10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS. After adding 400 µl of warm acid phenol the cell suspension was incubated at 65°C for 20 minutes with vortexing every 5 minutes, centrifuged and the supernatant extracted twice with acid phenol and once with chloroform. Total RNA was recovered by precipitation with ethanol and cleaned up by using the RNAsy kit (Qiagen). RNA (5 µg/sample) was sent to the UCLA DNA array Core Facility.

tag: Strain

value: Tor1 Mutant


title: Tor1Mutant_Rep_3

scan_protocol: Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/


title: differentiated C2C12 cells Sin3A binding chip on chip tiling array replicate 1


title: differentiated C2C12 cells Sin3B binding chip on chip tiling array replicate 2


title: differentiated C2C12 cells Sin3B binding chip on chip replicate 2

hyb_protocol: Hybridization onto the mouse promoter array, which includes 244K features distributed onto two slides (Agilent –G4490), washing and scanning were carried out according to the manufacturers instructions.


title: Meiotic DNA DSB in Saccharomyces cerevisiae

first: Nicolas

last: Robine

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description: S. cerevisiae (SK1)

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix5.1 software

data_processing: Ratio were averaged from 2 replicated experiments and background-normalized using the procedure previously described (Buhler et al., 2007). Genomic location considered as background were defined in (Buhler et al., 2007) as located in the middle (more than 2kb from the 3' and 5' boundaries) of long coding sequences.

source_name: Rfa1 IP

label_protocol: two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml.

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 2.5µl of rabbit polyclonal anti Rfa1 and 30 µl protein G magnetic beads suspension (Dynal).

tag: Rfa1 chromatin IP at 5h in meiosis in dmc1∆ cells (strain ORD7354)

source_name: Whole-cell extract

label_protocol: DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS and lyzed in ChIP lysis buffer.

tag: Rfa1 chromatin input at 5h in meiosis in dmc1∆ cells (strain ORD7354)


title: differentiated C2C12 cells RBP2 binding chip on chip tiling array replicate 2


title: Ras2Mutant_Rep_3

source_name: Ras2 Mutant

label_protocol: Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/

value: Ras2 Mutant


title: differentiated C2C12 cells E2F4 binding chip on chip tiling array replicate 3

description: E2F4 genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse E2F4 chromatin immunoprecipitation

source_name: IP for mouse E2F4 chromatin immunoprecipitation


title: Meiotic DNA DSB in set1∆ cells in Saccharomyces cerevisiae

description: S. cerevisiae (SK1)

tag: Rfa1 chromatin IP at 7h in meiosis in set1∆ dmc1∆ cells (strain ORD9624)

tag: Rfa1 chromatin input at 7h in meiosis in set1∆ dmc1∆ cells (strain ORD9624)


title: Ras2Mutant_Rep_2


title: differentiated C2C12 cells RBP2 binding chip on chip tiling array replicate 1


title: differentiated C2C12 cells E2F4 binding chip on chip tiling array replicate 1


title: Tor1Mutant_Rep_2


title: Ras2Mutant_Rep_1


title: Sch9Mutant_Rep_3

source_name: Sch9 Mutant

value: Sch9 Mutant


title: WildType_Rep_3

source_name: Wild Type

value: Wild Type


title: Sch9Mutant_Rep_2


title: Sch9Mutant_Rep_1


title: HCC1143_TRIBE_D01

description: TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_D01_155722


title: WildType_Rep_2


title: WildType_Rep_1


title: differentiated C2C12 cells E2F4 binding chip on chip tiling array replicate 2


title: HCC1143_GLEYS_C12

description: GLEYS_p_6.0_Test_GenomeWideEx_6_C12_140906


title: differentiated C2C12 cells Sin3B binding chip on chip replicate 1

description: Sin3B genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse Sin3B chromatin immunoprecipitation

source_name: IP for mouse Sin3B chromatin immunoprecipitation


title: PKI_IL1b_donor3

city: Winston-Salem

first: Anna

last: Misior

address: Medical Center Blvd

department: Center for Human Genomics

institute: Wake Forest University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized with GCRMA and differential expression was analyzed with affylmGUI.

source_name: human airway smooth muscle, expressing PKI-GFP, 8h IL-1b

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary human airway smooth muscle cells expressing GFP or PKI-GFP were grown in F12+10% FBS media and at confluence sreum starved for 24h.

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

treatment_protocol: Cells were pretreated with vehicle or 10 nM fluticasone propionate and then stimulated for 8h with 20U/ml IL-1beta, 10 nM EGF or both (E+I).

tag: primary tracheal human airway smooth muscle


title: differentiated C2C12 cells E2F4 binding chip on chip replicate 2

source_name: Elute from a mouse E2F4 chromatin immunoprecipitation


title: PKI_IL1b_donor4


title: PKI_IL1b_donor2


title: PKI_Flu+IL1b_donor3

source_name: human airway smooth muscle, expressing PKI-GFP, 30 min Flu pretx and 8h IL-1b


title: PKI_Flu+IL1b_donor4


title: PKI_Flu+EGF_donor4

source_name: human airway smooth muscle, expressing PKI-GFP, 30 min Flu pretx and 8h EGF


title: PKI_Flu+EGF_donor3


title: PKI_Flu+IL1b_donor2


title: S_uberis_strain_QMP B5-166

status: Public on Sep 13 2009

city: Ithaca

first: Michael

middle: J

last: Stanhope

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

description:
test strain supplementary file names: D2S1H2.gpr (array 4) D2S2H3.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887

hyb_protocol: Standard hybridization conditions for the biotinylated target included preblocking for 30 min at 50°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) containing 0.05% Tween 20, 5x Denhardt's solution, and 100ng/ul salmon sperm DNA followed by hybridization of the biotinylated target in hybridization solution (6x SSPE, 20-50ng/ul labeled DNA and 0.05% SDS) overnight at 50°C. The arrays were then washed once for at least 15 min with SSPE wash 1 (6x SSPE, 0.05% Tween-20) and then for 1 min with each of the following solutions: SSPE wash 2 (3x SSPE, 0.05% Tween-20), SSPE wash 3 (0.5x SSPE, 0.05% Tween-20), and PBST wash (2x PBS, 0.1% Tween-20), followed by a final 2x PBS wash at room temperature. The hybridized array was then blocked with 5X PBS-Casein Blocking Buffer (Cat # P804901, BioFX Laboratories, Owings Mills, MD) for 15 min at room temperature and labeled for 30 min with Cy5-streptavidin (Cat # PA45001, GE Healthcare, Amersham Biosciences, Piscataway, NJ) using the 1 mg/ml stock solution diluted 1:1,000 in 5X PBS-Casein buffer. The arrays were scanned after they were washed twice with each of PBST and PBS solutions.

scan_protocol: Hybridized microarrays covered with the imaging solution and the coverslip were scanned with an Axon GenePix™ 4000B laser scanner (Axon Instruments, Union City, CA) using the following parameters:Wavelengths=635, ScanPower=100, FocusPosition=100, PixelSize=5 .

data_processing: After scanning, the image was saved as a .tiff file from which the data were extracted using GenePix software.  The raw hybridization signal values, displayed in the GenePix Pro analysis Results (GPR) file, were log2-transformed to be used in subsequent analysis. Signal intensities of replicate microarrays of the reference strain 0140J were averaged, and served as denominator to obtain log-ratio values of the intensities between each array of test strain and reference strain. The log-ratio values for each array were normalized by median subtraction so that the median log ratio of each array was equal to 0.  The normalized log2 (test/reference) values of replicate arrays for each test strain were averaged to determine the presence or absence of a gene in each strain.  The cutoff was empirically set at -2.

organism: Streptococcus uberis

source_name: buffalo milk, individual

label_protocol: Genomic DNA was digested by sonication to sizes of 200-600bp, as visualized by agarose gel electrophoresis, then purified by using the Qiagen Qiaquick PCR purification kit.  Purified fragments (1 to 2 ug) of test strain as well as reference strain 0140J were labeled with Biotin, using Mirus Label IT® µArray® Biotin Labeling Kit (Cat #MIR 8050, Mirus Corp., Madison, WI) according to the manufacturer’s instructions, followed by removal of unincorporated dyes using Qiaquick (Qiagen) columns and then hybridized to the microarray.

extract_protocol:
using BioRad Aquapure Kit

1. Grow overnight culture of Streptococcus uberis in Todd Hewitt Broth at 37C
2. Pipet 1ml of culture into 1.7ml microfuge tube
3. Pellet cells at 13,000-16,000g for 15 seconds. Discard supernatant
4. Add 300ul of Genomic DNA lysis Solution and pipet up and down to suspend
5. Add 1.5ul of 4,000u/ml lysozyme (up to 10,000u/ml)
6. Incubate at 80C for 5 minutes to lyse cells
7. Add 1.5ul RNase solution (4mg/ml) to lysate
8. Mix by invertin 25 times and incubate at 37C for 45 minutes
9. Allow to cool to room temperature
10. Add 100ul Protein Precipitation Solution
11. Vortex vigorously for 20 seconds
12. Precipitate on ice for 5 minutes
13. Pellet at 13,000-16,000g for 3 minutes
14. Transfer supernatant into clean 1.7ml tube containing 300ul 100% isoproponol
15. Mix sample by inverting 50 times
16. Centrifuge 13,000-16,000g for 1 minute to pellet DNA
17. Discard supernatant
18. Wash pellet with 300ul 70% ethanol by inverting tube several times
19. Centrifuge 13,000-16,000g 1 minute. Carefully pour off ethanol. Pellet may be loose.
20. Invert and drain tube, allow to air dry for 10-15 minutes
21. Add 50ul DNA hydration solution
22. Incubate at 65C for 5 minutes (up to an hour). Additional incubation at room temperature may be required.
23. Mix gently, pulse spin.

tag: reference strain 0140J, Country:UK


title: PKI_Flu+EGF_donor2


title: PKI_Flu+E+I_donor3

source_name: human airway smooth muscle, expressing PKI-GFP, 30 min Flu pretx and 8h EGF+IL-1b


title: PKI_Flu_donor4

source_name: human airway smooth muscle, expressing PKI-GFP, 30 min Flu pretx


title: PKI_Flu_donor3


title: differentiated C2C12 cells Sin3a binding chip on chip replicate 2

description: Sin3a genome-wide binding profiles in Differentiated C2C12 cells by chip on chip

source_name: Input for mouse Sin3a chromatin immunoprecipitation

label_protocol: input samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy3 using Invitrogen CHG kit (18095-011). labeling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).

source_name: Elute from a mouse Sin3a chromatin immunoprecipitation

label_protocol: IP samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy5 using Invitrogen CHG kit (18095-011). labeling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).


title: differentiated C2C12 cells Sin3a binding chip on chip replicate 1

label_protocol: Input samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy3 using Invitrogen CHG kit (18095-011). Labelling reaction were cleauned up by invitrogen bind and elute CGH columns (18095-011).


title: PKI_EGF_donor3

source_name: human airway smooth muscle, expressing PKI-GFP, 8h EGF


title: PKI_Flu+E+I_donor4


title: PKI_E+I_donor4

source_name: human airway smooth muscle, expressing PKI-GFP, 8h EGF+IL-1b


title: PKI_basal_donor2

source_name: human airway smooth muscle, expressing PKI-GFP, basal


title: PKI_basal_donor4


title: PKI_basal_donor1


title: PKI_Flu_donor2


title: PKI_E+I_donor2


title: GFP_IL1b_donor4

source_name: human airway smooth muscle, expressing GFP, 8h IL-1b


title: PKI_Flu+E+I_donor2


title: differentiated C2C12 cells E2F4 binding chip on chip replicate 1

source_name: Input for mouse E2F4 chromatin immunoprecipitation


title: GFP_IL1b_donor3


title: PKI_EGF_donor4


title: GFP_IL1b_donor2


title: PKI_basal_donor3


title: GFP_Flu+IL1b_donor2

source_name: human airway smooth muscle, expressing GFP, 30 min Flu pretx and 8h IL-1b


title: GFP_Flu+IL1b_donor4


title: GFP_Flu+EGF_donor3

source_name: human airway smooth muscle, expressing GFP, 30 min Flu pretx and 8h EGF


title: GFP_Flu+EGF_donor4


title: GFP_Flu+E+I_donor2

source_name: human airway smooth muscle, expressing GFP, 30 min Flu pretx and 8h EGF+IL-1b


title: GFP_Flu+E+I_donor3


title: GFP_Flu_donor4

source_name: human airway smooth muscle, expressing GFP, 30 min Flu pretx


title: GFP_Flu+E+I_donor4


title: GFP_Flu_donor3


title: GFP_EGF_donor3

source_name: human airway smooth muscle, expressing GFP, 8h EGF


title: GFP_Flu+IL1b_donor3


title: GFP_EGF_donor4


title: GFP_Flu+EGF_donor2


title: GFP_EGF_donor1


title: GFP_Flu_donor2


title: GFP_E+I_donor4

source_name: human airway smooth muscle, expressing GFP, 8h EGF+IL-1b


title: GFP_E+I_donor3


title: PKI_EGF_donor2


title: GFP_E+I_donor2


title: GFP_E+I_donor1


title: PKI_E+I_donor1


title: GFP_basal_donor4

source_name: human airway smooth muscle, expressing GFP, basal


title: GFP_basal_donor3


title: GFP_basal_donor2


title: PKI_E+I_donor3


title: GFP_basal_donor1


title: SUM44_p76

city: Washington

first: Rebecca

middle: B.

last: Riggins

state: DC

address: E412 Research Building, 3970 Reservoir Rd. NW

department: Oncology, and Lombardi Comprehensive Cancer Center

institute: Georgetown University

description: comparison of invasive lobular breast carcinoma cell line SUM44 and its TAM-resistant variant, LCCTam

hyb_protocol: standard Affymetrix protocol

scan_protocol: Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: RMA

source_name: SUM44 breast cancer cell line, passage 76

label_protocol: standard one-cycle Affymetrix protocol

growth_protocol: cultured in SFIH (Ham's F12) to 70% confluency

extract_protocol: Trizol (Invitrogen; Carlsbad, CA), 2 ml per T-25 cm^2 flask, followed by Qiagen RNeasy cleanup protocol

tag: ER+/PR+ invasive lobular breast carcinoma cell line.  Original publication


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-468B

status: Public on Oct 31 2008

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

description: No additional information.

hyb_protocol: Sample Hybridization Protocol Qty. of labeled target: 5 ug of total RNA Other: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Scanning Protocol Other: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing:
Data Processing Protocol
Calculation Method: Raw data were normalized and analyzed in GENESPRING software version 6.1.1 (Silicon Genetics, Redwood City, CA). GENESPRING generated an average value of the spot replicates of each miRNA. After data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip on median normalization and a normalization to specific samples used as common reference for miRNA expression.

label: alexa 647

label_protocol:
Labeling Protocol
Other: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol:
Tri-Reagent Protocol
Other: Total RNA isolation was performed using the Tri-Reagent Protocol (Molecular Research Center, Cincinnati)

tag: Gender

value: male

tag: Tissue

value: liver tissue (non-tumorous)

tag: Disease state

tag: Individual

tag: Clinical info

value: Follow up status:dead


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-464B

description: No additional information.


title: SUM44_p74

source_name: SUM44 breast cancer cell line, passage 74


title: SUM44_p75

source_name: SUM44 breast cancer cell line, passage 75


title: Hepatocellular carcinoma (HCC), mestasis free, 03-460B

description: No additional information.

value: Follow up status:alive


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-456B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-455B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, AN B

description: No additional information.

source_name: AN B

value: AN B


title: Hepatocellular carcinoma (HCC), mestasis free, 03-452B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-450B

description: No additional information.

value: Follow up status:


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-443B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-442B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-439B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-457B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-438B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-435B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-441B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-427B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-424B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-416B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-434B

description: No additional information.


title: PKI_EGF_donor1


title: Hepatocellular carcinoma (HCC), mestasis free, 03-418B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-422B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-415B

description: No additional information.

value: female


title: Hepatocellular carcinoma (HCC), mestasis free, 03-425B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-398B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-397B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-405B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-383B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-369B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-384B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-387B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-374B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-366B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-394B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-364B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-381B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-354B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-361B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-375B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-365B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-345B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-360B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-356B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-350B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-339B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-343B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-335B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-336B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-349B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-342B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-334B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-329B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-326B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-316B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-333B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-322B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-314B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-315B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-319B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-317B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-292B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-311B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-301B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-313B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-306B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-321B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-291B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-312B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-309B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-285B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-305B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-268B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-467B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-277B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-284B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-278B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-255B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-269B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-273B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-265B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-281B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-280B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-272B

description: No additional information.


title: Hepatocellular carcinoma (HCC), mestasis free, 03-262B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-295B

description: No additional information.


title: GFP_EGF_donor2


title: Hepatocellular carcinoma (HCC), mestasis free, 03-251B

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous mestasis, 03-270B

description: No additional information.