title: 24h p65 Control Liver, biological rep1

source_name: Liver collected from wild-type control mice 24h after intratracheal innoculation of S. pneumoniae

value: Liver

value: intratracheal S. pneumoniae for 24h


title: 24h p65 Mutant Liver, biological rep2

status: Public on Feb 16 2012

type: RNA

city: Boston

first: Lee

last: Quinton

state: MA

address: 72 E Concord St

country: USA

institute: Boston University School of Medicine

description: Gene expression data from adult mouse livers

hyb_protocol: 5 ug of labeled sense strand DNA were hybridized for 17h at 45 degrees C on a Genechip Mouse Gene Array 1.0 ST Array.  GeneChips were washed and stainied in the Affymetrix Fluiidix Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7GPlus.

data_processing: CEL files were summarized using the Affymetrix Expression Console (version 1.1). The RMA (Robust Multi-Array Analysis) algorithm was used to generate gene-level data.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver collected from mutant mice lacking RelA in hepatocytes 24h after intratracheal innoculation with S. pneumoniae

label_protocol: Fragmented, biotinlyated sense strand DNA were prepared from 200 ng total RNA using the WT Target labeling kit according to the manufacturer's protocol (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies).  RNA was further purified using the the Qiagen RNEasy kit with the optional DNAse treatment.

tag: tissue

tag: infection

tag: genotype

value: CRE+ liver RelA mutant

tag: genetic background


title: human fimbria, biological rep1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: normal human fimbria, biological rep1

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

label: biotin

organism: Homo sapiens

source_name: fimbria

label_protocol: According to Illumina protocol.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: disease state

value: human fimbria


title: Pinus resinosa_xylem_rep2

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution. Microarray scanner and image analysis software used are described in the Samples section

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

label: Alexa 555

organism: Pinus resinosa

source_name: Pinus resinosa, xylem

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of Picea glauca, Picea mariana, Picea abies, Picea Sitchensis, Pinus strobus, Pinus resinosa and Larix laricina, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type five biological samples were prepared by pooling 6 independent trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types.

value: xylem

tag: time of collection

value: am

tag: replicate

tag: slide batch

tag: microarray scanner

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)

tag: image analysis program

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: Picea glauca_xylem_rep4

organism: Picea glauca

source_name: Picea glauca, xylem


title: Picea mariana_phelloderm_rep2

organism: Picea mariana

source_name: Picea mariana, phelloderm

value: phelloderm


title: 24h Control Liver, biological rep3

source_name: Liver collected from wild-type control mice 24h after intratracheal innoculation of Streptococcus pneumoniae

value: 24h intratracheal Streptococcus pneumoniae

value: CRE- wild-type littermate control


title: Picea glauca_phelloderm_rep3

source_name: Picea glauca, phelloderm


title: Picea glauca_phelloderm_rep4

value: pm


title: 24h Mutant Liver, biological rep2

source_name: Liver collected from mutant mice lacking STAT3 and RelA in hepatocytes 24h after intratracheal innoculation with Streptococcus pneumoniae

value: CRE+ liver STAT3/RelA mutant


title: 24h Mutant Liver, biological rep1


title: 3-methylcholanthrene (5 µM) rep 3

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

description: 3MC 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software

source_name: neonatal mouse ovaries_3-methylcholanthrene (5 µM)_96hr

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: Swiss neonates were sacrificed by CO2 inhalation followed by decapitation. Ovaries were excised, trimmed of excess tissue and placed on culture plate inserts in 6-well tissue culture plate wells floating atop 1.5ml DMEM/F12 medium containing 5% (v/v) fetal calf serum, 1mg/ml bovine serum albumin, 50µg/ml ascorbic acid, 27.5μg/ml insulin–transferrin–selenium, 2.5 mM glutamine and 5U/ml penicillin/streptomycin. Media were supplemented with 40 ng/ml basic fibroblast growth factor, 50 ng/ml leukemia inhibitory factor, and 25 ng/ml stem cell factor. Using fine forceps a drop of medium was placed over the top of each ovary to prevent drying. Ovaries were cultured for 4 days at 37°C and 5% CO2 in air, with media changes every two days.

extract_protocol: Total RNA was isolated from ovaries using two rounds of a modified acid guanidinium thiocyanate–phenol–chloroform protocol: washed cells resuspended in lysis buffer (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarkosyl, 0.72% β-mercaptoethanol). RNA was isolated by phenol/chloroform extraction and isopropanol precipitated.

treatment_protocol: Ovaries were treated with vehicle control medium (0.01% DMSO) or 3MC (5 µM). 3MC culture concentration was determined by pilot studies performed in our laboratory with the intention of inducing overt toxicity.

tag: strain

value: Swiss

tag: age

value: Post natal day 3-4

value: ovary


title: 3-methylcholanthrene (5 µM) rep 2

description: 3MC 2


title: 3-methylcholanthrene (5 µM) rep 1

description: 3MC 1


title: WholeBody_for_tooth_rep1

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: embryonic tissue

hyb_protocol: 16 hr incubation according to Affymetrix protocol

scan_protocol: Double amplified with phycoerythin-tagged Streptavidin, Excitation 488 nm, emission 570 nm

data_processing: Raw data are preprocessed using the robust multiarray average (RMA) rma function in the bioconductor package affy version 0.7

source_name: Whole embryo

label_protocol: cRNA biotin labelled via in vitro transcription

growth_protocol: Timed embryos, plug day recorded as E0.5

extract_protocol: Qiagen Rneasy Mini Kit Extraction Protocol

treatment_protocol: Wild type lens or whole embryonic tissue dissected in 1XPBS from mouse ICR strain, treated with RNAlater (Qiagen) and stored at -80C until RNA isolation

value: Whole embryo

tag: Stage


title: 24h Mutant Liver, biological rep3

value: Liver


title: Tooth_E13.5_rep3

description: embryonic tissue

source_name: Tooth germ

value: Tooth germ


title: WholeBody_for_tooth_rep2

description: embryonic tissue


title: 24h Control Liver, biological rep2


title: WholeBody_for_tooth_rep3

description: embryonic tissue


title: Larix laricina_xylem_rep2

organism: Larix laricina

source_name: Larix laricina, xylem


title: Pinus resinosa_phelloderm_rep2

source_name: Pinus resinosa, phelloderm


title: Control (0.01% DMSO) rep 3

description: Control 3

source_name: neonatal mouse ovaries_DMSO (0.01%)_96hr


title: Picea glauca_xylem_rep3


title: 24h Control Liver, biological rep1


title: 0h Mutant Liver, biological rep3

source_name: Liver collected from uninfected mutant mice lacking STAT3 and RelA in hepatocytes


title: Control (0.01% DMSO) rep 2

description: Control 2


title: Tooth_E13.5_rep1

description: embryonic tissue


title: Tooth_E13.5_rep2

description: embryonic tissue


title: Control (0.01% DMSO) rep 1

description: Control 1


title: 0h Mutant Liver, biological rep2


title: WholeBody_for_lens_rep4

description: embryonic tissue


title: Sort-purified rescued  transgenic CD8 T cells from lymphopenic tolerogenic mouse replicate #4

city: Seattle

first: Andrea

last: Schietinger

state: WA

address: 1959 NE Pacific Street

department: Immunology

institute: University of Washington

description: rescued T cells are defined in this study as tolerant T cells undergoing homeostaic proliferation in lymphopenic, tolerogenic Alb:GAG mice.

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader

data_processing: The data was quantile normalized using the Bioconductor package, “lumi,” and transformed to log2 scale

source_name: mouse splenocytes

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: After FACS-sorting , T-cells were washed twice with cold PBS and cell pellets were frozen and stored at -80C until all samples were collected. RNA was isolated using Qiagen RNeasy Plus Mini Kit per the manufacturer’s instructions and the yield was determined on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). Samples that had an appropriate yield (typically 100ng total RNA) were subsequently analyzed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: cd8 t cells

value: TCR GAGxAlb:GAG transgenic CD8

tag: cd8 t cell subsets

value: Tolerant T cells undergoing homeostatic proliferation in lymphopenic, tolerogenic mouse, 20-22 days post adoptive transfer


title: Picea abies_xylem_rep3

organism: Picea abies

source_name: Picea abies, xylem

value: xylem


title: Sort-purified re-tolerized  transgenic CD8 T cells from lymphorepleted, non-tolerogenic mouse replicate #1

description: re-tolerized T cells are defined in this study as previsouly rescued T cells which become dysfunctional again in lymphorepleted wild-type B6 mice.

value: Tolerant T cells post homeostatic proliferation in lymphoreplete, non-tolerogenic mouse, more than 90 days post transfer


title: Pinus strobus_xylem_rep1

organism: Pinus strobus

source_name: Pinus strobus, xylem

value: am

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)


title: 0h Mutant Liver, biological rep1


title: 0h Control Liver, biological rep1

source_name: Liver collected from uninfected wild-type control mice


title: 0h Control Liver, biological rep2


title: Larix laricina_xylem_rep1

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: Sort-purified rescued  transgenic CD8 T cells from lymphopenic tolerogenic mouse replicate #3


title: Lens_E12.5_rep3

description: embryonic tissue

source_name: Lens

value: Lens


title: Sort-purified rescued  transgenic CD8 T cells from lymphopenic tolerogenic mouse replicate #1


title: Picea mariana_xylem_rep4

source_name: Picea mariana, xylem


title: Pinus resinosa_xylem_rep1

source_name: Pinus resinosa, xylem


title: Sort-purified re-tolerized  transgenic CD8 T cells from lymphorepleted, non-tolerogenic mouse replicate #2


title: Pinus resinosa_phelloderm_rep1

value: phelloderm


title: WholeBody_for_lens_rep3

description: embryonic tissue


title: WholeBody_for_lens_rep1

description: embryonic tissue


title: Lens_E12.5_rep2

description: embryonic tissue


title: 0h Control Liver, biological rep3

value: CRE- wild-type littermate control


title: Sort-purified (CD44hi) tolerant  transgenic CD8 T cells replicate #3

description: Tolerant  T cells were isolated from spleens of transgenic tolerant TCR GAG xAlb:GAG mice and FACS sorted

value: Tolerant


title: ADPKD-46

city: Seoul

first: Yu Mi

last: Woo

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2(i)-ga), Yongsan-gu

country: South Korea

institute: Sookmyung Women's University

description: gene expression data of ADPKD-46

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix)

scan_protocol: The chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: The detection (Present/Absent) call were generated by the Affymetrix microarray suite 5(MAS5) algorithm. The scanned raw files were imported into the statistical programming environment R (Version2.3) for further analysis with tools available from the Bioconductor Project (http://www.bioconductor.org)(M1).   Expression data were normalized and log2 transformed using the robust multichip average (RMA) method implemented in the Bioconductor package RMA (M2, M3). To reduce noise for the significance analysis, probe sets that did not show detection call rate at least 50% of the samples in the comparison were filtered out.

source_name: isolated total RNA from kidney of ADPKD-46

label_protocol: Per RNAsample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

extract_protocol: Total RNAs were isolated from kidney of human normal (49 years old/ male) and ADPKD patients (62 years old/ male, 67 years old/ male) using NucleoSpin® RNA Kit (MACHEREY-NAGEL) according to the manufacturer’s instructions.

value: kidney

value: Autosomal dominant polycystic kidney disease

tag: gender

value: male


title: ADPKD-67

description: gene expression data of ADPKD-67

source_name: isolated total RNA from kidney of ADPKD-67


title: Sort-purified (CD44hi) tolerant  transgenic CD8 T cells replicate #2


title: Lens_E11.5_rep3

description: embryonic tissue


title: Sort-purified rescued  transgenic CD8 T cells from lymphopenic tolerogenic mouse replicate #2


title: Lens_E12.5_rep1

description: embryonic tissue


title: Normal-3

description: gene expression data of Normal-3

source_name: isolated total RNA from kidney of Normal-3

value: normal


title: Lens_E11.5_rep2

description: embryonic tissue


title: WholeBody_for_lens_rep2

description: embryonic tissue

value: Whole embryo


title: Lens_E11.5_rep1

description: embryonic tissue


title: Sort-purified (CD44hi/CD62Lhi) memory  transgenic CD8 T cells replicate #1

description: Memory T cells were generated by transfer of 1x10^6 naïve, transgenic TCR GAG CD8 T cells into B6 mice, followed by i.p. infection one day later with 3x10^7 cfu GAG-expressing Listeria monocytogenes . Splenic CD44hi, CD62Lhi memory TCRGAG T cells were sorted at least two months post infection.

value: TCR GAG transgenic CD8

value: Memory


title: Sort-purified (CD44hi/CD62Lhi) memory  transgenic CD8 T cells replicate #3


title: Lens_E10.5_rep2

description: embryonic tissue


title: Picea glauca_xylem_rep1

source_name: Picea glauca, xylem

value: pm


title: Picea abies_xylem_rep2

value: xylem


title: Picea glauca_phelloderm_rep2

source_name: Picea glauca, phelloderm


title: Sort-purified (CD44hi/CD62Lhi) memory transgenic  CD8 T cells replicate #2


title: Pinus strobus_phelloderm_rep2

source_name: Pinus strobus, phelloderm


title: Picea mariana_xylem_rep3


title: Picea mariana_xylem_rep2


title: Lens_E10.5_rep3

description: embryonic tissue


title: Picea glauca_xylem_rep2


title: Sort-purified (CD44hi) tolerant  transgenic CD8 T cells replicate #1

value: TCR GAGxAlb:GAG transgenic CD8


title: Sort-purified (CD8/CD44low) naïve transgenic CD8 T cells replicate#1

description: Naïve T cells were isolated from spleens of transgenic (naïve) TCR GAG mice and FACS sorted

value: Naïve


title: Picea mariana_xylem_rep1

value: am

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)


title: Sort-purified (CD8/CD44low) naïve transgenic CD8 T cells replicate#2


title: Lens_E10.5_rep1

description: embryonic tissue

value: Lens


title: shSca-1-treated Wnt1-YL cells, biological rep 2

description: knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.

source_name: knockdown of Sca-1 by shRNA

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

growth_protocol: Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.

tag: cell line

value: derived from primary MMTV-Wnt1 mammary tumors


title: Larix laricina_phelloderm_rep2

source_name: Larix laricina, phelloderm

tag: tissue

value: phelloderm

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: Picea abies_phelloderm_rep1

source_name: Picea abies, phelloderm


title: Dynasore+BMP-2 rep2

city: Berlin

first: Raghu

last: Bhushan

state: Berlin

address: Thielallee 63

department: Institut für Chemie und Biochemie

country: Germany

institute: Freie Universität

description: replicate 2

data_processing: Rank invariant normalization was performed using the algorithm from BeadStudio 3.0 software (Illumina)

source_name: C2C12 cells

label_protocol: Biotin-labelled cRNA was generated, employing a linear amplification kit (Ambion).

growth_protocol: C2C12 cells were cultured according to standard protocols.

extract_protocol: Total RNA was isolated using NucleoSpin RNA II Isolation Kit (Machery-Nagel) followed by quality assessment using both spectrophotometer (NanoDrop Technologies) and agarose gel electrophoresis.

treatment_protocol: C2C12 cells were serum-starved for 4 h, after 2 h 40 µM dynasore or 0.05 % DMSO was added to the medium. Cells were stimulated for 6 h with 30 nM BMP-2 including dynasore or DMSO.

tag: cell type

value: myoblast

value: C2C12 cells

tag: treatment


title: Pinus strobus_phelloderm_rep3


title: shSca-1-treated Wnt1-YL cells, biological rep 1

description: knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 1


title: Pinus strobus_phelloderm_rep1


title: shSca-1-treated Wnt1-YL cells, biological rep 3

description: knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 3


title: shLuc-treated Wnt1-YL cells, biological rep 3

description: shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 3

source_name: shLuc shRNA control treatment


title: 24 hrs post-TPA

city: Stony Brook

first: Laurie

last: Krug

state: NY

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description: Custom tiled microarray

hyb_protocol: 825 ng linearly amplified cRNA  and hybridization buffer were added, and samples were applied to microarrays at 65 degrees C for 17 hrs.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and Agilent default normalization. Spike-in controls were used to calculate scale factor.

source_name: Infected A20 B cells

label_protocol: 2.5 µg of total RNA were labeled using Aglient “Quick Amp Labeling Kit Two-color” following manufacturer's instructions. Spike-in controls were labeled using Agilent “Two-color Spike-in Kit" following manufacturer's instructions.

growth_protocol: For experimental Cy3 samples: A20 HE2 cells were maintained in RPMI supplemented with 10% serum and 300 microgram per ml hygromycin. For reference Cy5-labeled RNA: NIH 3T3 fibroblasts were cultured in DMEM supplemented in 10% serum.

extract_protocol: Total RNA was prepared using Qiagen midi RNA kit following manufacturer's instructions.

treatment_protocol: For experimental Cy3 samples: A20 HE2 cells were treated with 20 nanograms per ml of 12-O-Tetradecanoylphorbol-13-acetate. For reference Cy5-labeled RNA: Cells were infected in MHV68 WUMS strain at multiplicity of infection of 10 plaque forming units per ml.

tag: infection

value: recombinant murid herpesvirus 4 (MHV68 BAC derived virus harboring hygromycin-enhanced green fluorescent protein)

tag: timepoint

value: 24 hrs

source_name: Infected NIH 3T3 fibroblasts

value: murid herpesvirus 4 (MHV68 WUMS strain)

value: 8 hrs reference


title: Sort-purified (CD8/CD44low) naïve transgenic  CD8 T cells replicate#3

source_name: mouse splenocytes

value: TCR GAG transgenic CD8


title: shLuc-treated Wnt1-YL cells, biological rep 1

description: shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 1


title: 12 hrs post-TPA

description: Custom tiled microarray

value: 12 hrs


title: shLuc-treated Wnt1-YL cells, biological rep 2

description: shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 2


title: 6 hrs post-TPA

description: Custom tiled microarray

value: 6 hrs


title: Control no treatment

description: Custom tiled microarray

value: 0 hrs


title: Picea glauca_phelloderm_rep1

tag: time of collection

value: pm


title: Dynasore rep2

description: replicate 2

value: Dynasore


title: Picea mariana_phelloderm_rep1

source_name: Picea mariana, phelloderm

value: am

tag: replicate

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)


title: SVEU P147_G5_4424+Pol_PreChal_Day0_rep2

status: Public on Feb 15 2012

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

description: US23502338_251542110232_S01_GE1-v5_95_Feb07_1_4.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing._rep

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).  _rep

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags.
Agilent Feature extractor software: 9.5.3.1
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

organism: Macaca mulatta

source_name: PBMC, SIV Pol-stimulated 24hr

growth_protocol: Male rhesus macaques were divided into three vaccine treatment groups (control - no vaccination, vaccination alone, vaccination with RANTES adjuvant). At eight months following the last vaccination, animals were infected intrarectally with SIVmac251. PBMCs were taken from animals at 8 months post-vaccination (pre-SIV challenge) and 10 days post-SIVmac251 challenge. Global gene expression was measured by microarray in PBMC samples following 24hr stimulation with a pool of SIV pol peptides or mock (R10). _rep

extract_protocol: RNA was isolated using RNeasy micro kit w/ QIAshredder (Qiagen)._rep

treatment_protocol: Blood was drawn from animals into Cell Preparation Tubes and immediately spun to isolate the top layer of PBMCs above the polyester gel layer. PBMCs were resuspended in the plasma and stored at 4 degree C overnight. 2x10^6 cells from each animal were either SIV pol peptide or mock stimulated for 24hr. Following stimulation, washed PBMCs were collected into RLT buffer and frozen at -80 degrees C until RNA isolation. _rep

tag: vaccine treatment

value: SIV DNA vaccine with RANTES Adjuvant

tag: technical replicate

value: male

tag: animal id

tag: sample collection time

value: PBMC


title: SVEU P147_G5_4424+R10_PreChal_Day0_rep1

description: US23502338_251542110243_S01_GE1-v5_95_Feb07_1_2.txt

source_name: PBMC, mock (R10) stimulated 24hr

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing._rep

value: 8 months post-vaccination (pre-SIV challenge)


title: DMSO rep2

description: replicate 2

value: myoblast

value: C2C12 cells

value: DMSO


title: DMSO rep 1

description: replicate 1


title: Dynasore+BMP-2 rep1

description: replicate 1


title: Larix laricina_phelloderm_rep1

value: phelloderm

tag: slide batch

tag: microarray scanner

tag: image analysis program

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: DMSO+BMP-2 rep1

description: replicate 1


title: Dynasore rep1

description: replicate 1


title: SVEU P147_G5_4424+Pol_PreChal_Day0_rep1

description: US23502338_251542110237_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4420_R10_Day10_rep2

description: US23502338_251542110700_S01_GE1-v5_95_Feb07_1_4.txt

value: 10 days post-SIV challenge


title: SVEU P147_G5_4420_POL_Day10_rep1

description: US23502338_251542110694_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4417_R10_Day10_rep1

description: US23502338_251542110707_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4424+R10_PreChal_Day0_rep2

description: US23502338_251542110244_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4420_R10_Day10_rep1

description: US23502338_251542110703_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4420_POL_Day10_rep2

description: US23502338_251542110696_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4417_R10_Day10_rep2

description: US23502338_251542110705_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4417_POL_Day10_rep2

description: US23502338_251542110702_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4417_POL_Day10_rep1

description: US23502338_251542110698_S01_GE1-v5_95_Feb07_1_1.txt


title: Picea abies_xylem_rep1

source_name: Picea abies, xylem

value: xylem


title: SVEU P147_G5_4417+R10_PreChal_Day0_rep2

description: US23502338_251542110248_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4417+R10_PreChal_Day0_rep1

description: US23502338_251542110246_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4415_R10_Day10_rep2

description: US23502338_251542110707_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4417+Pol_PreChal_Day0_rep1

description: US23502338_251542110243_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4417+Pol_PreChal_Day0_rep2

description: US23502338_251542110242_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4415_POL_Day10_rep2

description: US23502338_251542110699_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4415_POL_Day10_rep1

description: US23502338_251542110700_S01_GE1-v5_95_Feb07_1_2.txt


title: DMSO+BMP-2 rep2

description: replicate 2


title: SVEU P147_G5_4415+R10_PreChal_Day0_rep2

description: US23502338_251542110238_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4415_R10_Day10_rep1

description: US23502338_251542110708_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4410_R10_Day10_rep1

description: US23502338_251542110705_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4410_POL_Day10_rep1

description: US23502338_251542110702_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4415+Pol_PreChal_Day0_rep2

description: US23502338_251542110231_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4410+Pol_PreChal_Day0_rep1

description: US23502338_251542110249_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4410_POL_Day10_rep2

description: US23502338_251542110698_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4410+R10_PreChal_Day0_rep2

description: US23502338_251542110239_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4410+R10_PreChal_Day0_rep1

description: US23502338_251542110243_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4410_R10_Day10_rep2

description: US23502338_251542110708_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4415+Pol_PreChal_Day0_rep1

description: US23502338_251542110233_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4415+R10_PreChal_Day0_rep1

description: US23502338_251542110242_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4408_R10_Day10_rep1

description: US23502338_251542110714_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4410+Pol_PreChal_Day0_rep2

description: US23502338_251542110247_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G5_4408_POL_Day10_rep2

description: US23502338_251542110712_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4408_R10_Day10_rep2

description: US23502338_251542110711_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G5_4408+Pol_PreChal_Day0_rep2

description: US23502338_251542110233_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4408+R10_PreChal_Day0_rep2

description: US23502338_251542110239_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4408+R10_PreChal_Day0_rep1

description: US23502338_251542110240_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G5_4408_POL_Day10_rep1

description: US23502338_251542110713_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4406_R10_Day10_rep1

description: US23502338_251542110703_S01_GE1-v5_95_Feb07_1_2.txt

value: no vaccine (control)


title: SVEU P147_G4_4406_POL_Day10_rep2

description: US23502338_251542110697_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4406_R10_Day10_rep2

description: US23502338_251542110701_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G5_4408+Pol_PreChal_Day0_rep1

description: US23502338_251542110231_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4406_POL_Day10_rep1

description: US23502338_251542110695_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4406+Pol_PreChal_Day0_rep2

description: US23502338_251542110240_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4406+Pol_PreChal_Day0_rep1

description: US23502338_251542110244_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4406+R10_PreChal_Day0_rep2

description: US23502338_251542110249_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4403_R10_Day10_rep1

description: US23502338_251542110708_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4406+R10_PreChal_Day0_rep1

description: US23502338_251542110255_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4403_POL_Day10_rep2

description: US23502338_251542110703_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4403+Pol_PreChal_Day0_rep2

description: US23502338_251542110244_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4403_R10_Day10_rep2

description: US23502338_251542110706_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4403+Pol_PreChal_Day0_rep1

description: US23502338_251542110239_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4399_R10_Day10_rep1

description: US23502338_251542110711_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4403_POL_Day10_rep1

description: US23502338_251542110699_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4403+R10_PreChal_Day0_rep1

description: US23502338_251542110245_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4399_POL_Day10_rep2

description: US23502338_251542110704_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4403+R10_PreChal_Day0_rep2

description: US23502338_251542110238_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4399+R10_PreChal_Day0_rep2

description: US23502338_251542110251_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4399+Pol_PreChal_Day0_rep2

description: US23502338_251542110246_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4399_POL_Day10_rep1

description: US23502338_251542110706_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4399_R10_Day10_rep2

description: US23502338_251542110710_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4396_POL_Day10_rep2

description: US23502338_251542110705_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4396+R10_PreChal_Day0_rep2

description: US23502338_251542110234_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4396_R10_Day10_rep1

description: US23502338_251542110695_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4396_R10_Day10_rep2

description: US23502338_251542110696_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4396+Pol_PreChal_Day0_rep2

description: US23502338_251542110245_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4396+Pol_PreChal_Day0_rep1

description: US23502338_251542110239_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4392_R10_Day10_rep1

description: US23502338_251542110714_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4392_POL_Day10_rep2

description: US23502338_251542110701_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4399+R10_PreChal_Day0_rep1

description: US23502338_251542110250_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4396_POL_Day10_rep1

description: US23502338_251542110709_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4392_R10_Day10_rep2

description: US23502338_251542110713_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4399+Pol_PreChal_Day0_rep1

description: US23502338_251542110248_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4392_POL_Day10_rep1

description: US23502338_251542110699_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G4_4396+R10_PreChal_Day0_rep1

description: US23502338_251542110236_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4392+R10_PreChal_Day0_rep2

description: US23502338_251542110250_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4392+R10_PreChal_Day0_rep1

description: US23502338_251542110255_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4388+R10_PreChal_Day0_rep2

description: US23502338_251542110234_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4425+R10_PreChal_Day0_rep2

description: US23502338_251542110247_S01_GE1-v5_95_Feb07_1_2.txt

value: SIV DNA vaccine


title: SVEU P147_G4_4388+Pol_PreChal_Day0_rep2

description: US23502338_251542110236_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4425+R10_PreChal_Day0_rep1

description: US23502338_251542110246_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G4_4388+Pol_PreChal_Day0_rep1

description: US23502338_251542110235_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4421_POL_Day10_rep2

description: US23502338_251542110697_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4425+Pol_PreChal_Day0_rep1

description: US23502338_251542110230_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G4_4392+Pol_PreChal_Day0_rep1

description: US23502338_251542110241_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4425_R10_Day10_rep1

description: US23502338_251542110257_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4425_R10_Day10_rep2

description: US23502338_251542110710_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4388+R10_PreChal_Day0_rep1

description: US23502338_251542110235_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G4_4392+Pol_PreChal_Day0_rep2

description: US23502338_251542110244_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4425+Pol_PreChal_Day0_rep2

description: US23502338_251542110231_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4421_R10_Day10_rep2

description: US23502338_251542110694_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4425_POL_Day10_rep2

description: US23502338_251542110707_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4421+Pol_PreChal_Day0_rep2

description: US23502338_251542110251_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4425_POL_Day10_rep1

description: US23502338_251542110704_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4421_R10_Day10_rep1

description: US23502338_251542110695_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4421_POL_Day10_rep1

description: US23502338_251542110694_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4421+R10_PreChal_Day0_rep2

description: US23502338_251542110233_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4416_POL_Day10_rep2

description: US23502338_251542110702_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4416_R10_Day10_rep1

description: US23502338_251542110715_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4416_R10_Day10_rep2

description: US23502338_251542110710_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4416+R10_PreChal_Day0_rep2

description: US23502338_251542110251_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4416_POL_Day10_rep1

description: US23502338_251542110698_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4421+R10_PreChal_Day0_rep1

description: US23502338_251542110230_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4421+Pol_PreChal_Day0_rep1

description: US23502338_251542110247_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4416+R10_PreChal_Day0_rep1

description: US23502338_251542110247_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4416+Pol_PreChal_Day0_rep1

description: US23502338_251542110243_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4413_R10_Day10_rep2

description: US23502338_251542110711_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4413+Pol_PreChal_Day0_rep1

description: US23502338_251542110248_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4413_R10_Day10_rep1

description: US23502338_251542110714_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4411_R10_Day10_rep2

description: US23502338_251542110694_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4413+Pol_PreChal_Day0_rep2

description: US23502338_251542110255_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4411_R10_Day10_rep1

description: US23502338_251542110695_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4413_POL_Day10_rep1

description: US23502338_251542110701_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4411+R10_PreChal_Day0_rep1

description: US23502338_251542110237_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4411+R10_PreChal_Day0_rep2

description: US23502338_251542110230_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4413_POL_Day10_rep2

description: US23502338_251542110698_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4416+Pol_PreChal_Day0_rep2

description: US23502338_251542110240_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4413+R10_PreChal_Day0_rep2

description: US23502338_251542110232_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4411+Pol_PreChal_Day0_rep2

description: US23502338_251542110232_S01_GE1-v5_95_Feb07_1_3.txt


title: SVEU P147_G1_4411_POL_Day10_rep2

description: US23502338_251542110706_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4411_POL_Day10_rep1

description: US23502338_251542110705_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4387_R10_Day10_rep2

description: US23502338_251542110697_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4411+Pol_PreChal_Day0_rep1

description: US23502338_251542110230_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4413+R10_PreChal_Day0_rep1

description: US23502338_251542110235_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4387_POL_Day10_rep1

description: US23502338_251542110704_S01_GE1-v5_95_Feb07_1_2.txt


title: SVEU P147_G1_4387_R10_Day10_rep1

description: US23502338_251542110696_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4387_POL_Day10_rep2

description: US23502338_251542110709_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4387+R10_PreChal_Day0_rep2

description: US23502338_251542110249_S01_GE1-v5_95_Feb07_1_1.txt


title: SVEU P147_G1_4387+Pol_PreChal_Day0_rep2

description: US23502338_251542110237_S01_GE1-v5_95_Feb07_1_4.txt


title: SVEU P147_G1_4387+Pol_PreChal_Day0_rep1

description: US23502338_251542110236_S01_GE1-v5_95_Feb07_1_3.txt


title: BA02_bone_hibernating_N04-047

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

country: China

institute: Shanghai institute for biology science

description: bone tissue from hibernating black bear

hyb_protocol: The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Ursus americanus

source_name: bone, hibernating

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

tag: tissue type

value: bone


title: BA02_bone_active_N03-111

description: bone tissue from active black bear

source_name: bone, active

tag: gender


title: BA02_bone_active_N04-104

description: bone tissue from active black bear


title: rad53.MMS.30.2vsrad53.UT.30.2

city: La Jolla

first: Dwight

last: Kuo

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: Raw data file: US22502657_251507211207_S01_H_flip_1-4.avg.gpr

hyb_protocol: Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77

scan_protocol: GenePix 4000A Scanner, Quantitation w/ GenePix 6.0

data_processing: lowess normalized, quantile normalized, LIMMA model

organism: Saccharomyces cerevisiae

growth_protocol: Mating pheromone arrest synchrony experiments were carried out as described in de Bruin RA, Kalashnikova TI, Chahwan C, McDonald WH, Wohlschlegel J, Yates J, 3rd, Russell P, Wittenberg C (2006) Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell 23:483-496

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen).

treatment_protocol: Conditions are untreated (UT), methyl methane sulfonate (MMS-0.033%), camptothecin (CPT-50uM), and hydroxyurea (HU-0.2M)

tag: strain

tag: genotype/variation

tag: agent

value: UT

tag: time (min.)

value: MMS


title: BA02_bone_active_N05-132

description: bone tissue from active black bear


title: rad53.UT.30.2vsrad53.HU.30.2

description: Raw data file: US22502657_251507211207_S01_H_flip_3-4.avg.gpr

label_protocol: Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77

value: HU


title: BA02_bone_active_N05-131

description: bone tissue from active black bear


title: BA02_bone_hibernating_N03-056

description: bone tissue from hibernating black bear


title: rad53.HU.75.2vsrad53.MMS.75.2

description: Raw data file: US22502657_251507210791_S01_H_flip_2-4.avg.gpr


title: BA02_bone_hibernating_N05-034

description: bone tissue from hibernating black bear


title: BA02_bone_active_N04-113

description: bone tissue from active black bear


title: BA02_bone_active_N03-152

description: bone tissue from active black bear


title: rad53.HU.30.2vsrad53.MMS.30.2

description: Raw data file: US22502657_251507210791_S01_H_flip_3-4.avg.gpr


title: BA02_bone_hibernating_N06-030

description: bone tissue from hibernating black bear


title: rad53.UT.0.1vsrad53.HU.75.1

description: Raw data file: US22502657_251507211207_S01_H_flip_4-4.avg.gpr


title: BA02_bone_hibernating_N05-035

description: bone tissue from hibernating black bear


title: rad53.HU.75.1vsrad53.HU.30.1

description: Raw data file: US22502657_251507211206_S01_H_flip_1-4.avg.gpr


title: BA02_bone_hibernating_N08-025

description: bone tissue from hibernating black bear


title: rad53.HU.30.1vsrad53.UT.0.1

description: Raw data file: US22502657_251507211206_S01_H_flip_2-4.avg.gpr


title: rad53.MMS.75.1vsrad53.MMS.30.1

description: Raw data file: US22502657_251507211206_S01_H_flip_4-4.avg.gpr


title: rad53.MMS.75.2vsrad53.UT.75.2

description: Raw data file: US22502657_251507210791_S01_H_flip_4-4.avg.gpr


title: rad53.UT.0.1vsrad53.MMS.75.1

description: Raw data file: US22502657_251507211206_S01_H_flip_3-4.avg.gpr


title: rad53.UT.75.2vsrad53.HU.75.2

description: Raw data file: US22502657_251507211207_S01_H_flip_2-4.avg.gpr


title: rad53.UT.0.1vsrad53.UT.75.1

description: Raw data file: US22502657_251507211205_S01_H_flip_2-4.avg.gpr


title: rad53.MMS.30.1vsrad53.ut.0.1

description: Raw data file: US22502657_251507211205_S01_H_flip_1-4.avg.gpr


title: rad53.UT.75.1vsrad53.UT.30.1

description: Raw data file: US22502657_251507211205_S01_H_flip_3-4.avg.gpr


title: H1

city: Poitiers

first: ulrich

last: cortes

address: 350 av. Jacques Coeur

country: France

institute: CHU Poitiers

description: Human ES cell line

data_processing:
Ct value of 40 was affected in case of non amplification (undetermined data)
Normalisation were performed using GAPDH as housekeeping gene
Target gene signals normalized to GAPDH; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_GAPDH)]. Fold-change was determined as Log10RQ GSCs1-11/H1 (RQ: Relative Quantity)

label: TaqMan

source_name: Human embryonic

label_protocol: High Capacity RNA-tocDNA kit (Applied Biosystems)

growth_protocol: Neurobasal medium (w/o serum)

extract_protocol: Total RNA

tag: cell type

value: Human embryonic

tag: Stage


title: GSC-10

description: Glioma Stem-like Cell line-10

source_name: Glioblastoma

value: Glioblastoma

value: grade IV


title: GSC-11

description: Glioma Stem-like Cell line-11


title: gsp.40.2vsgsp.nrm1.40.1

description: Raw data file: US22502657_251507210789_S01_H_flip_1-4.avg.gpr

value: galsicΔP, nrm1Δ


title: gsp.nrm1.40.2vsgsp.nrm1.100.2

description: Raw data file: US22502657_251507210789_S01_H_flip_4-4.avg.gpr


title: gsp.nrm1.100.2vsgsp.0.1

description: Raw data file: US22502657_251507210789_S01_H_flip_3-4.avg.gpr

value: galsicΔP


title: gsp.nrm1.40.1vsgsp.100.2

description: Raw data file: US22502657_251507210790_S01_H_flip_3-4.avg.gpr


title: gsp.nrm1.100.1vsgsp.40.2

description: Raw data file: US22502657_251507210790_S01_H_flip_4-4.avg.gpr


title: GSC-9

description: Glioma Stem-like Cell line-9


title: ut.75vscpt.75

description: Raw data file: US22502657_251507210786_S01_H_flip_2-4.avg.gpr

value: wildtype

value: CPT


title: gsp.40.1vsgsp.100.1

description: Raw data file: US22502657_251507210788_S01_H_flip_3-4.avg.gpr


title: gsp.100.1vsgsp.0.2

description: Raw data file: US22502657_251507210788_S01_H_flip_2-4.avg.gpr


title: GSC-8

description: Glioma Stem-like Cell line-8


title: cpt.75vsmms.75

description: Raw data file: US22502657_251507210786_S01_H_flip_1-4.avg.gpr


title: GSC-7

description: Glioma Stem-like Cell line-7


title: rad53.UT.30.1vsrad53.UT.0.1

description: Raw data file: US22502657_251507211205_S01_H_flip_4-4.avg.gpr


title: hu.75vsut.75

description: Raw data file: US22502657_251507210786_S01_H_flip_3-4.avg.gpr


title: gsp.0.1vsgsp.40.1

description: Raw data file: US22502657_251507210788_S01_H_flip_4-4.avg.gpr


title: mms.75vshu.75

description: Raw data file: US22502657_251507210786_S01_H_flip_4-4.avg.gpr


title: ut.45vscpt.45

description: Raw data file: US22502657_251507210784_S01_H_flip_2-4.avg.gpr


title: GSC-6

description: Glioma Stem-like Cell line-6


title: mms.45vshu.45

description: Raw data file: US22502657_251507210784_S01_H_flip_4-4.avg.gpr


title: hu.45vsut.45

description: Raw data file: US22502657_251507210784_S01_H_flip_3-4.avg.gpr


title: gsp.100.2vsgsp.nrm1.100.1

description: Raw data file: US22502657_251507210789_S01_H_flip_2-4.avg.gpr


title: cpt.30vsmms.30

description: Raw data file: US22502657_251507210691_S01_H_flip_1-4.avg.gpr


title: GSC-3

description: Glioma Stem-like Cell line-3


title: GSC-4

description: Glioma Stem-like Cell line-4


title: GSC-1

description: Glioma Stem-like Cell line-1


title: hu.30vsut.30

description: Raw data file: US22502657_251507210691_S01_H_flip_3-4.avg.gpr


title: GSC-2

description: Glioma Stem-like Cell line-2


title: ut.30vscpt.30

description: Raw data file: US22502657_251507210691_S01_H_flip_2-4.avg.gpr


title: hu.60vsut.60

description: Raw data file: US22502657_251507210690_S01_H_flip_4-4.avg.gpr


title: ut.60vscpt.60

description: Raw data file: US22502657_251507210690_S01_H_flip_3-4.avg.gpr


title: ut.0vsut.75

description: Raw data file: US22502657_251507210796_S01_H_flip_3-4.avg.gpr


title: cpt.60vsmms.60

description: Raw data file: US22502657_251507210690_S01_H_flip_2-4.avg.gpr


title: GSC-5

description: Glioma Stem-like Cell line-5


title: ut.75vsut.60

description: Raw data file: US22502657_251507210796_S01_H_flip_2-4.avg.gpr


title: hu.75vshu.60

description: Raw data file: US22502657_251507210689_S01_H_flip_3-4.avg.gpr


title: mms.0vshu.75

description: Raw data file: US22502657_251507210689_S01_H_flip_4-4.avg.gpr


title: hu.45vshu.30

description: Raw data file: US22502657_251507210689_S01_H_flip_1-4.avg.gpr


title: hu.30vsut.0

description: Raw data file: US22502657_251507210796_S01_H_flip_4-4.avg.gpr


title: mms.30vshu.30

description: Raw data file: US22502657_251507210691_S01_H_flip_4-4.avg.gpr


title: ut.60vsut.45

description: Raw data file: US22502657_251507210796_S01_H_flip_1-4.avg.gpr


title: mms.60vshu.60

description: Raw data file: US22502657_251507210690_S01_H_flip_1-4.avg.gpr


title: hu.60vshu.45

description: Raw data file: US22502657_251507210689_S01_H_flip_2-4.avg.gpr


title: ESC_R1_MeDIP_2

type: genomic

city: Tokyo

first: Takayuki

last: Isagawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

country: Japan

institute: The University of Tokyo

description: Methylated DNA immunoprecipitation-on-chip analysis of R1 ES cell

hyb_protocol: The mixture containing 2 ug of the labeled DNA was directly used for hybridization.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: MAT (Johnson et al., 2006) was used to process the CEL files. Duplicate sample and control CEL files were used to calculate MAT score. BAR files were generated by using Mm_PromPR_v02-1_NCBIv36.bpmap.

molecule: genomic DNA

label_protocol: The digested cDNA was labeled using 50 U of terminal transferase (Roche, Penzberg, Germany) and 71.4 uM of Biotin-11-ddATP (PerkinElmer, Boston, MA, USA) at 37degrees Celsius for 2 h

extract_protocol: Genomic DNA was isolated with an QIAamp DNA Micro Kit  (Qiagen).

value: male

value: ES cell


title: gsp.0.2vsgsp.nrm1.40.2

description: Raw data file: US22502657_251507210788_S01_H_flip_1-4.avg.gpr


title: cpt.75vscpt.60

description: Raw data file: US22502657_251507210795_S01_H_flip_1-4.avg.gpr


title: mms.60vsmms.45

description: Raw data file: US22502657_251507210277_S01_H_flip_3-4.avg.gpr


title: cpt.45vsmms.45

description: Raw data file: US22502657_251507210784_S01_H_flip_1-4.avg.gpr


title: mms.45vsmms.30

description: Raw data file: US22502657_251507210277_S01_H_flip_2-4.avg.gpr


title: ut.0vscpt.75

description: Raw data file: US22502657_251507210795_S01_H_flip_2-4.avg.gpr


title: cpt.45vscpt.30

description: Raw data file: US22502657_251507210278_S01_H_flip_3-4.avg.gpr


title: mms.30vsmms.0

description: Raw data file: US22502657_251507210277_S01_H_flip_1-4.avg.gpr


title: cpt.30vsut.0

description: Raw data file: US22502657_251507210278_S01_H_flip_2-4.avg.gpr


title: ut.0vsmms.75

description: Raw data file: US22502657_251507210278_S01_H_flip_1-4.avg.gpr


title: mms.75vsmms.60

description: Raw data file: US22502657_251507210277_S01_H_flip_4-4.avg.gpr


title: ut.45vsut.30

description: Raw data file: US22502657_251507210795_S01_H_flip_4-4.avg.gpr


title: ut.30vsut.0

description: Raw data file: US22502657_251507210795_S01_H_flip_3-4.avg.gpr


title: cpt.60vscpt.45

description: Raw data file: US22502657_251507210278_S01_H_flip_4-4.avg.gpr


title: ESC_R1_MeDIP_1


title: ESC_R1_INPUT_1

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of R1 ES cell


title: Sperm_ICR_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Sperm

value: ICR

value: Sperm


title: ESC_R1_INPUT_2


title: Sperm_ICR_MeDIP_1


title: Sperm_ICR_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Sperm


title: Sperm_ICR_INPUT_1


title: Sk_muscle_ICR_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Skletal muscle

value: Sleletal muscle


title: Sk_muscle_ICR_MeDIP_1


title: Sk_muscle_ICR_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Skletal muscle


title: Sk_muscle_ICR_INPUT_1


title: Liver_ICR_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Liver

value: Liver


title: Liver_ICR_MeDIP_1


title: Liver_ICR_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Liver


title: Brain_ICR_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Brain

value: Brain


title: Liver_ICR_INPUT_1


title: SVEU P147_G1_4387+R10_PreChal_Day0_rep1

description: US23502338_251542110250_S01_GE1-v5_95_Feb07_1_2.txt

value: SIV DNA vaccine

value: 8 months post-vaccination (pre-SIV challenge)

value: PBMC


title: IFNa rep3

city: Los Angeles

first: Su-Yang

last: Liu

address: 615 Charles E. Young Dr. South Rm 246

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

hyb_protocol: Hybridization was performed according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

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

source_name: Bone marrow macrophages treated with IFNa (62U/mL) for 2.5hrs

label_protocol: Cy3 cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow was harvested from the femur of mice and plated in 10cm dishes in Dulbecco's MEM (Gibco), 10%FBS, 1% Penicillin/Streptomycin and ~10ng/mL of M-CSF for 7 days. The media was refreshed on day 4.

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

treatment_protocol: IFNa and IFNg was resuspended in DMEM and added to day 7 BMM in growth media to a final concentration 62U/mL and 1U/mL, respectively.  After 2.5 hours, the media was removed and the cells were collected in 1mL of TRIzol (Invitrogen) and further processed for RNA purification.

tag: Sex

value: female

tag: age

value: 6 weeks

tag: tissue

value: bone marrow-derived macrophages

tag: treatment

value: interferon-alpha


title: Monreal stylar canal cells, biological rep2

city: Catania

first: Marco

last: Caruso

email: mcaruso@unict.it, slamalfa@unict.it

address: Via Valdisavoia 5

department: Dipartimento di Scienze delle Produzioni Agrarie e Alimentari

country: Italy

institute: University of Catania

description: Gene expression data from the cells surrounding the stylar canals, collected from the upper style

hyb_protocol: Following fragmentation, 10 ug aRNA were hybridized at Centro National de Biotecnologia, Madrid, Spain. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were normalized by Robust Multi-Array Analysis (RMA) method using R/Bioconductor.

organism: Citrus x clementina

source_name: Laser microdissected stylar canal cells

label_protocol: RNA samples were subjected to a two-round amplification TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre Biotechnologies, Madison, WI, USA) following the manufacturer’s instructions

extract_protocol: RNA isolation was performed from ~ 10000 cells using the RNeasy Micro Kit (Qiagen) following the manufacturer's instructions.

tag: genotype

value: Monreal


title: Comune stylar canal cells, biological rep1

value: Comune


title: Monreal stylar canal cells, biological rep3


title: Comune stylar canal cells, biological rep3


title: Brain_ICR_MeDIP_1


title: Monreal stylar canal cells, biological rep1


title: IFNg rep3

source_name: Bone marrow macrophages treated with IFNg (1U/mL) for 2.5hrs

value: interferon-gamma


title: Media rep3

source_name: Bone marrow macrophages, untreated (media only)


title: Comune stylar canal cells, biological rep2


title: IFNa rep2


title: IFNa rep1


title: Brain_ICR_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Brain

value: male


title: Paraxial_mesoderm_SK7_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Paraxial mesoderm derived from SK7

value: Paraxial Mesoderm


title: Brain_ICR_INPUT_1

value: ICR


title: Media rep2


title: pup.liver.lung.rep.5

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: Agilent's In situ Hybridization kit

scan_protocol: Agilent DNA microarray scanner

data_processing: Rosetta Resolver Feature Extraction Version 8.5.1.1

label_protocol: Agilent's Low input RNA Linear Amp kit

growth_protocol: See manuscript

extract_protocol: GE2-SSPE_95_Feb07 with FE version 9.5

treatment_protocol: See manuscript

value: pup

value: liver/lung

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740100

value: Universal Mouse Reference RNA:Stratagene Catalog #740100


title: adult.liver.lung.rep.3

value: adult


title: adult.liver.lung.rep.2


title: Media rep1


title: adult.liver.lung.rep.4


title: Paraxial_mesoderm_SK7_INPUT_1

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Paraxial mesoderm derived from SK7


title: pup.liver.lung.rep.4


title: Endoderm_SK7_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of Endoderm derived from SK7

value: Endoderm


title: adult.liver.lung.rep.1


title: IFNg rep1


title: Endoderm_SK7_MeDIP_1


title: CD44v8-10(-) 4T1-2

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University School of Medicine

description: Gene expression data from 4T1 cells depending on the CD44v8-10 expression, respectively

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 on GeneChipMouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix® GeneChip® Operating Software (GCOS) Version 1.04 using Affymetrix default analysis settings and global scaling as normalization method.

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

growth_protocol: All types of 4T1 cells were cultured with RPMI 1640 medium with 10% bovine serum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.And RNA was prepared using the RNAeasy mini(QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each cell population was maintained in the normoxia conditions. All the cells were manually selected under the dissecting scope. All the cancer cells were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: cell line

value: breast cancer cells

tag: cd44v8-10 expression


title: IFNg rep2


title: CD44v8-10(+) 4T1-1


title: CD44v8-10(+) 4T1-2


title: Paraxial_mesoderm_SK7_MeDIP_1


title: CD44v8-10(-) 4T1-1


title: pup.liver.lung.rep.2


title: Paraxial_mesoderm_SK7_INPUT_2


title: pup.liver.lung.rep.1


title: pup.liver.lung.rep.3


title: Endoderm_SK7_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Endoderm derived from SK7


title: Endoderm_SK7_INPUT_1


title: embryo.liver.lung.rep2

value: embryo


title: embryo.liver.lung.rep3


title: embryo.liver.lung.rep4


title: embryo.liver.lung.rep5


title: embryo.liver.lung.rep1


title: Liver_ICR

description: Liver from ICR strain mouse

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45 degree Celsius, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual.  Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

data_processing: Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.

source_name: Liver from ICR strain mouse

label_protocol: Total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix).  Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit (Qiagen).

value: Liver


title: LiverCLRefMixB1 (19CL) vs. SNU475 LivCL

city: LA

first: Richard

middle: S

last: Finn

address: 10833 Le Conte, 11-934 Factor Building

department: Medicine-Hem/Onc

institute: UCLA

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization;: (1) no background subtraction, (2) special detrend Off, (3) adjust background globally Off, (4) red autoestimate Off, and (5) green autoestimate Off. Rosetta Resolver (v.7.2.2.0) was used for subsequent analysis of the array data

source_name: LivCLMixRefC1 (reference)

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

growth_protocol: All cell lines were characterized using mtDNA sequence prior to use

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol. The reference mix (LiverCLRefMixB1) contained equal amounts of each liver cell line with the exception of JHH1.

tag: sample type

value: reference mix containing equal amounts of 19 liver cell lines

value: liver cells

value: hepatocellular carcinoma cells


title: LiverCLRefMixB1 (19CL) vs. SNU449 LivCL


title: Brain_ICR

description: Brain from ICR strain mouse

source_name: Brain from ICR strain mouse

value: Brain


title: LiverCLRefMixB1 (19CL) vs. SNU423 LivCL


title: Ectoderm_SK7_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of Ectoderm derived from SK7

value: Ectoderm


title: Ectoderm_SK7_MeDIP_1

description: Methylated DNA immunoprecipitation-on-chip analysis of Ectoderm derived from SK7


title: Sk_muscle_ICR

description: Skeletal muscle from ICR strain mouse

source_name: Skeletal muscle from ICR strain mouse

value: Sleletal muscle


title: adult.brain.rep.5

value: brain


title: Paraxial_mesoderm_SK7

description: Paraxial mesoderm derived from SK7

source_name: Paraxial mesoderm derived from SK7

value: male

value: Paraxial Mesoderm


title: Ectoderm_SK7_MeDIP_2

value: ICR


title: Ectoderm_SK7_INPUT_1


title: LiverCLRefMixB1 (19CL) vs. SNU398 LivCL


title: LiverCLRefMixB1 (19CL) vs. SNU387 LivCL


title: adult.brain.rep.3


title: adult.brain.rep.1


title: ESC_SK7_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of SK7 ES cell

value: ES cell


title: Ectoderm_SK7

description: Ectoderm derived from SK7

source_name: Ectoderm derived from SK7


title: LiverCLRefMixB1 (19CL) vs. SNU182 LivCL


title: ESC_SK7_MeDIP_1


title: ESC_SK7_INPUT_2

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of SK7 ES cell


title: adult.brain.rep.4

value: Universal Mouse Reference RNA:Stratagene Catalog #740100


title: LiverCLRefMixB1 (19CL) vs. SKHep1 LivCL


title: Endoderm_SK7

description: Endoderm derived from SK7

source_name: Endoderm derived from SK7


title: LiverCLRefMixB1 (19CL) vs. PLC/PRF5 LivCL


title: ESC_SK7_INPUT_1


title: adult.brain.rep.2

value: adult


title: pup.brain.rep.4

value: pup


title: LiverCLRefMixB1 (19CL) vs. JHH7 LivCL


title: Oct4GipES_Luc_esiRNA_72h_rep3

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

description: Gene expression data from Oct4-Gip ES cells 72h after Luc-esiRNA (negative control) treatment.

hyb_protocol: After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.

scan_protocol: Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.

data_processing: The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.

source_name: Oct4-Gip ES cells, Luc RNAi, 72h post transfection

label_protocol: Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).

growth_protocol: ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.

extract_protocol: Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene).  Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.

treatment_protocol: Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).

value: Oct4-Gip ES

tag: RNAi

value: Luciferase

tag: treatment time


title: LiverCLRefMixB1 (19CL) vs. JHH6 LivCl


title: Oct4GipES_Panct1_esiRNA_72h_rep3

description: Gene expression data from Oct4-Gip ES cells 72h after Panct1-esiRNA treatment.

source_name: Oct4-Gip ES cells, Panct1 RNAi, 72h post transfection


title: ESC_SK7

description: ES cell line SK7

source_name: ES cell line SK7

tag: gender


title: Oct4GipES_Luc_esiRNA_72h_rep1


title: LiverCLRefMixB1 (19CL) vs. JHH5 LivCL


title: pup.brain.rep.5

tag: strain


title: BA01_bone_active_N03-111

description: bone tissue from active black bear

source_name: bone, active

tag: tissue type

value: bone


title: pup.brain.rep.2


title: BA01_bone_active_N05-132

description: bone tissue from active black bear


title: pup.brain.rep.3


title: pup.brain.rep.1


title: embryo.brain.rep4

value: embryo


title: LiverCLRefMixB1 (19CL) vs. JHH4 LivCL

value: reference mix containing equal amounts of 19 liver cell lines

value: liver cells


title: Oct4GipES_Luc_esiRNA_72h_rep2


title: LiverCLRefMixB1 (19CL) vs. JHH2 LivCl

value: hepatocellular carcinoma cells


title: Oct4GipES_Panct1_esiRNA_72h_rep2


title: embryo.brain.rep5


title: Oct4GipES_Panct1_esiRNA_72h_rep1


title: LiverCLRefMixB1 (19CL) vs. JHH1 LivCL


title: BA01_bone_active_N05-131

description: bone tissue from active black bear


title: oviductal epithelial cell cultured with red blood cells, rep 2

city: Sheffield

first: Ahmed

last: Aldarmahi

address: Tree Root Walk

department: Reproducitve Medicine

country: United Kingdom

institute: The University of Sheffield

description: Gene expression data from oviductal epithelial cell cultured with red blood cell

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridised for 16 hours at 45°C on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 30007G Scanner

data_processing: The data were analysed using the Microarray Suite software version 5.1 (MAS 5.1 Affymetrix). Genespring software (Version 10.0, Agilent) was used for all statistical analysis (P ≤ 0.05). Metacore software was used for the bioinformatic and pathways analysis.

organism: Sus scrofa

source_name: OPEC and sow red blood cell

label_protocol: The 3’IVT expression kit (Affymetrix, Santa Clara, CA, USA) was used to prepare cDNA from which biotin labelled antisense RNA was synthesised as described in the manual. The provided artificial Poly-A RNA control created from bacterial mRNA were spiked in at known concentrations as exogenous positive control to monitor the target labelling process.

growth_protocol: OPEC were cultured in 6-wel plate until confluence stage at 37°C, 5% CO2 and 95% humidity for 24 hours in HAM-12 media.

extract_protocol: Total RNA extraction was carried out using TRI reagent standard protocol according to the manufacturer instruction (Sigma).

treatment_protocol: OPEC co-incubated with (i) bacteria (1 X 10 ˄ 8 bacteria), (ii) sperm (1 X 10 ˄ 6 spermatozoa/ml) or (iii) red blood cell (5 x 10 ˄ 6 red blood cell/ml at 37°C, 5% CO2 and 95% humidity for 24 hours in HAM-12 media.

tag: agent

value: sow red blood cell

value: OPEC


title: oviductal epithelial cell cultured with red blood cells, rep 3


title: embryo.brain.rep3

value: brain


title: BA01_bone_active_N04-113

description: bone tissue from active black bear

value: male


title: oviductal epithelial cell cultured with red blood cells, rep 1


title: embryo.brain.rep2


title: BA01_bone_active_N03-152

description: bone tissue from active black bear


title: LiverCLRefMixB1 (19CL) vs. HUH1 LivCL


title: LiverCLRefMixB1 (19CL) vs. HLF LivCL

source_name: HLF

value: HLF


title: BA01_bone_active_N04-104

description: bone tissue from active black bear


title: LiverCLRefMixB1 (19CL) vs. HLE LivCL

source_name: HLE

value: HLE


title: BA01_bone_hibernating_N06-030

description: bone tissue from hibernating black bear

source_name: bone, hibernating


title: LiverCLRefMixB1 (19CL) vs. HUH7 LivCL


title: embryo.brain.rep1


title: LiverCLRefMixB1 (19CL) vs. HepG2 LivCL


title: oviductal epithelial cell cultured with sperm, rep 3

description: Gene expression data from oviductal epithelial cell cultured with sperm

source_name: OPEC and  fresh boar spermatozoa

value: fresh boar spermatozoa


title: oviductal epithelial cell cultured with sperm, rep 1


title: UTI89_Y_2E_2

city: Stanford

first: JI YOUN

last: Lim

address: 380 Roth way, KECK 359

department: Chemistry

institute: Stanford University

description: Bacteria were grown at 26°C for 24 hours

hyb_protocol: Biotinylated cDNA in 130 microliter hybridization cocktail was injected to each array and hybridized at 45C for 16 hours with rotation of 60 rpm in GeneChoip Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChips were scanned with GeneChip 7G Plus Scanner (Affymetrix)

data_processing: Microarray Suite version 5.0 (MAS 5.0) were used data analysis with Affymetrix default analysis settings.

organism: Escherichia coli UTI89

source_name: E. coli UTI89 in YESCA broth containing 2% EtOH

label_protocol: Fragmented cDNA was used for terminal labeling to generate Biotin-labeled cRNA in the presence of Terminal Deoxynucloetidyl Transferase (Promega) using GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: Bacteria were grown in YESCA broth at 26°C for 24 hours

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

treatment_protocol: After 24 hours incubation at 26C, 12 ml of bacteria cell culture was mixed with 24 ml of RNAprotect Bacteria Reagent (Qiagen) to stabilize RNA.

tag: protocol

value: YESCA broth containing 2% EtOH


title: BA01_bone_hibernating_N08-025

description: bone tissue from hibernating black bear


title: LiverCLRefMixB1 (19CL) vs. Hep3B LivCL

tag: cell type


title: BA01_bone_hibernating_N05-034

description: bone tissue from hibernating black bear


title: UTI89_Y_2

source_name: E. coli UTI89 in YESCA broth

value: YESCA broth


title: oviductal epithelial cell cultured with bacteria, rep 1

description: Gene expression data from oviductal epithelial cell cultured with bacteria

source_name: OPEC and Escherichia coli K12 strain MG1655

value: Escherichia coli K12 strain MG1655


title: oviductal epithelial cell cultured with sperm, rep 2


title: BA01_bone_hibernating_N03-056

description: bone tissue from hibernating black bear


title: BA01_bone_hibernating_N04-047

description: bone tissue from hibernating black bear


title: UTI89_Y_4D

source_name: E. coli UTI89 in YESCA broth containing 4% DMSO

value: YESCA broth containing 4% DMSO


title: BA01_bone_hibernating_N05-035

description: bone tissue from hibernating black bear


title: UTI89_Y_1


title: oviductal epithelial cell cultured with bacteria, rep 2


title: oviductal epithelial cell cultured with bacteria, rep 3


title: oviductal epithelial cell, rep 1

description: Gene expression data from oviductal epithelial cell

source_name: Porcine oviductal epithelial cell line (OPEC)


title: oviductal epithelial cell, rep 3


title: Retina_110

status: Public on Feb 14 2012

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description: R_IA319-00 Mac_AMD

hyb_protocol: Probe fragmentation and hybridization was carried out using the Agilent Gene Expression Hybridization Kit (Part #: 5188-5242) according to the methods of the manufacturer (Quick Amp Labeling Protocol, Version 5.7). Arrays were hybridized for 17 hr at 65°C. Arrays were washed for 1 min using Agilent Gene Expression Wash Buffer 1 (Part #: 5188-5325) + 0.005% Triton X-102 at room temperature and for 1 min at 37°C with Agilent Gene Expression Wash Buffer 2 (Part #: 5188-5326) + 0.005% Triton X-102. The washed arrays were then rinsed with acetonitrile for 10 sec and coated with Agilent Stabilization and Drying solution for 30 sec.

scan_protocol: Scanner: Bio-Rad VersArray™ ChipReader 3mm System.  Raw Data Quantification: VersArray™ Analyzer 4.5 [Median raw spot intensity within thresholds (5-65,535), Global Median Background Subtraction (Global background from negative control cells, zero order polynomial approximation), Local Regression Cross-channel Normalization (span = 10%, sub-sampling = 5, single pass)].

data_processing:
The data were processed and normalized using a universal reference design. The Lowess normalized raw data were further background corrected by subtraction of the minimum value of the Agilent negative controls (3xSLv1) to obtain the net intensity. Any values less than one standard deviation of the negative control probes were set to a value equal to the standard deviation of the negative controls for that sample. The individual probe net intensity values for both the experimental and reference samples were then divided by the sum of all array probes for that sample and experimental:reference probe ratios were calculated. Each experimental:reference probe ratio was then multiplied by the geometric mean of the corresponding reference probe expressed as percent total of all reference array probes. Values less than the equivalent of the standard deviation of all experimental array negative control spots were set to that equivalent and all values were then multiplied by an arbitrary constant (100,000) so that all expression values were greater than 1. For the two samples with replicates, the average expression values were calculated.

The supplementary files include the raw data (GSMxxx_*_raw.txt) and the data after Lowess normalization and background correction (GSMxxx_*.txt).

source_name: Macular Retina, AMD

label_protocol: All probe labeling was carried out using the Agilent Low Input Quick Amp Labeling Kit (Part #: 5190-2306, Version 5.7) according to the methods of the manufacturer using 250 ng of total RNA with the exception that spike-in controls were not used.

growth_protocol: RPE-choroid and retinal samples were isolated from human eye cups obtained from direct sources at the University of Iowa (G.S.H.), the Lion's Eye Bank of Oregon, or direct sources at the University of California, Santa Barbara. The Iowa eyes were selected from a well-characterized repository of 3,903 donors. Medical and ophthalmic histories, a family questionnaire, blood, and sera, were obtained from the majority of donors. All Iowa eyes were read and classified by retinal specialists using gross pathologic features, and when available, the corresponding fundus photographs and angiograms. Iowa eyes were subsequently graded for AMD subtypes using a modified scheme based on the Rotterdam Grading Scale (Normal: no signs of ocular abnormalities; MD1: hard  macular drusen only; MD2: soft distinct drusen only; Dry AMD: soft indistinct or reticular drusen only, soft distinct drusen with pigmentary abnormalities, or soft indistinct or reticular drusen with pigmentary abnormalities; CNV: sub-retinal choroidal neovascularization; GA: sharply demarcated area of apparent absence of the RPE (>175 mm)  involving central macular region; GA/CNV: geographic atrophy with choroidal neovascularization). Eight mm macular trephine punches and 6 mm temporally adjacent extramacular trephine punches of the RPE-choroid and retina were collected from Iowa eyes within 4 hr postmortem, flash frozen in liquid N2, and stored at -80 oC. The Oregon and Santa Barbara eyes only received a general classification of AMD based on patient histories supported by ophthalmological records. Detailed sample preparation for these eyes is published in Radeke et al. Exp. Eye Res. 85, 366-380 (2007).

extract_protocol: Total RNA was purified from the RPE-choroid and retina samples obtained from the University of Iowa ocular tissue repository using a Qiagen RNeasy Miniprep kit and on-column DNAse 1 digestion according to the methods of the manufacturer. Total RNA was purified from samples obtained from the Lion's Eye Bank of Oregon and the University of California, Santa Barbara using a Qiagen RNeasy Miniprep kit according to the methods of the manufacturer. Contaminating DNA was digested off-column with DNase I and the DNA-depleted RNA was repurified using the Qiagen RNeasy Miniprep.

value: macular Retina

tag: age (years)

tag: ocular disease

value: AMD

tag: amd classification

tag: patient identifier

tag: rna integrity number (rin)

value: not determined

source_name: Reference RNA

value: RPE-choroid and retina

tag: disease state

value: normal and AMD

value: pool


title: Retina_115

description: R_IA058-98 Mac_AMD

tag: tissue

value: female

value: dry AMD


title: Retina_104

description: R_IA077-96 Mac_AMD

value: GA


title: Retina_118

description: R_IA107-97 Mid_AMD

source_name: Extramacular Retina, AMD

value: extramacular Retina


title: Retina_103

description: R_IA113-00 Mid_AMD

value: male

value: CNV


title: Retina_112

description: R_IA100-97 Mid_AMD

value: GA/CNV


title: Retina_108

description: R_IA068-00 Mac_AMD


title: Retina_116

description: R_IA058-98 Mid_AMD


title: Retina_105

description: R_IA077-96 Mid_AMD


title: Retina_101

description: R_IA256-00 Mid_AMD


title: Retina_102

description: R_IA113-00 Mac_AMD


title: Retina_117

description: R_IA107-97 Mac_AMD


title: Retina_96

description: R_IA173-00 Mid_AMD


title: Retina_97

description: R_IA213-99 Mid_AMD


title: Retina_98

description: R_IA222-99 Mac_AMD


title: Retina_100

description: R_IA256-00 Mac_AMD


title: oviductal epithelial cell, rep 2

tag: cell line

value: OPEC


title: Retina_113

description: R_IA103-00 Mac_AMD

tag: sample type


title: Retina_107

description: R_IA100-98 Mid_AMD


title: Retina_106

description: R_IA100-98 Mac_AMD


title: Retina_99

description: R_IA222-99 Mid_AMD


title: Retina_114

description: R_IA103-00 Mid_AMD


title: Retina_95

description: R_IA173-00 Mac_AMD


title: Retina_89

description: R_IA316-99 Mac_AMD


title: Retina_88

description: R_IA285-99 Mid_AMD


title: Retina_90

description: R_IA316-99 Mid_AMD


title: Retina_87

description: R_IA285-99 Mac_AMD


title: Retina_83

description: R_IA405-99 Mac_AMD


title: Retina_81

description: R_IA163-00 Mac_AMD


title: Retina_84

description: R_IA405-99 Mid_AMD


title: Retina_93

description: R_IA124-00 Mac_AMD


title: Retina_92

description: R_IA294-00 Mid_AMD


title: Retina_85

description: R_IA239-00 Mac_AMD


title: Retina_94

description: R_IA124-00 Mid_AMD


title: Retina_77

description: R_IA356-99 Mac_AMD


title: Retina_82

description: R_IA163-00 Mid_AMD


title: Retina_91

description: R_IA294-00 Mac_AMD


title: Retina_78

description: R_IA356-99 Mid_AMD


title: Retina_79

description: R_IA117-00 Mac_AMD


title: Retina_86

description: R_IA239-00 Mid_AMD


title: Retina_76

description: R_IA186-98 Mid_AMD


title: Retina_75

description: R_IA186-98 Mac_AMD


title: Retina_80

description: R_IA117-00 Mid_AMD


title: Retina_73

description: R_IA306-99 Mac_AMD


title: Retina_72

description: R_IA199-00 Mid_AMD


title: Retina_65

description: R_IA407-99 Mac_AMD


title: Retina_69

description: R_IA090-98 Mac_AMD


title: Retina_64

description: R_IA139-98 Mid_AMD


title: Retina_66

description: R_IA407-99 Mid_AMD


title: Retina_71

description: R_IA199-00 Mac_AMD


title: Retina_68

description: R_IA035-98 Mid_AMD


title: Retina_62

description: R_IA191-97 Mid_AMD


title: Retina_63

description: R_IA139-98 Mac_AMD


title: Retina_70

description: R_IA090-98 Mid_AMD


title: Retina_60

description: R_IA262-00 Mac_AMD


title: Retina_61

description: R_IA191-97 Mac_AMD


title: Retina_57

description: R_IA202-99 Mid_AMD


title: Retina_109

description: R_IA068-00 Mid_AMD


title: Retina_58

description: R_IA005-98 Mac_AMD


title: Retina_59

description: R_IA005-98 Mid_AMD


title: Retina_67

description: R_IA035-98 Mac_AMD


title: Retina_74

description: R_IA306-99 Mid_AMD


title: Retina_56

description: R_IA202-99 Mac_AMD


title: Retina_54

description: R_IA177-00 Mac

source_name: Macular Retina, normal

value: normal


title: Retina_52

description: R_IA448-99 Mac


title: Retina_51

description: R_IA205-98 Mid

source_name: Extramacular Retina, normal


title: Retina_45

description: R_IA059-00 Mid


title: Retina_55

description: R_IA177-00 Mid


title: Retina_44

description: R_IA059-00 Mac


title: Retina_46

description: R_IA195-00 Mac


title: PARP-1 Replicate 3

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard Nimblegen hybridization and washing.

scan_protocol: Standard Nimblegen scanning.

data_processing: For each factor of interest, the log2 ratio data from each replicate was grouped based on probe length (50- to 75-mer) and subjected to lowess normalization within each group.  The normalized data was then scaled based on the sum of squares of each replicate.  The average values of the normalized and scaled log2 ratio data from all replicates were used to generate a composite file.  The composite data were processed using a 1 kb moving window with 250 bp steps.  The mean probe log2 ratio and p-value from Wilcoxon signed-rank test were calculated for each window. Significant peaks were defined as the center of three consecutive windows with positive means, the center window with a mean greater than either adjacent window, and all windows having p-values less than 0.016.  See supplemental materials in Krishnakumar, R., Gamble, M. J., Frizzell, K. M., Berrocal, J. G., Kininis, M., and Kraus, W. L. (2008) Science 319, 819-821 for more details.

source_name: PARP-1 - ChIP'd DNA

label_protocol: The immunoprecipitated genomic DNA was blunted, amplified by ligation-mediated PCR (LM-PCR), and used to probe a promoter DNA microarray from Nimblegen.  Input DNA was labeled with Cy5 and IP'd DNA was labeled with Cy3 using a random primer approach.

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C.  The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length.  The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A- or G-agarose beads.  The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against FLAG or PARP-1, or without antibodies as a control.  Protein A-agarose beads were used for PARP-1 ChIP and protein G-agarose beads were used for FLAG ChIP.  The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and  RNase H, respectively.  The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

tag: genotype/variation

value: parental

tag: chip antibody

source_name: PARP-1 - ChIP input DNA

value: none (input)


title: PARP-1 Replicate 2


title: Retina_50

description: R_IA205-98 Mac

value: macular Retina

tag: gender


title: Retina_48

description: R_IA436-99 Mac


title: Retina_53

description: R_IA448-99 Mid


title: Retina_49

description: R_IA436-99 Mid


title: Retina_111

description: R_IA100-97 Mac_AMD

value: AMD


title: Retina_47

description: R_IA195-00 Mid

value: not determined


title: Retina_39

description: R_IA172-97 Mid

value: RPE-choroid and retina


title: Retina_43

description: R_IA200-00 Mid

value: normal and AMD


title: Retina_38

description: R_IA172-97 Mac

value: pool


title: Retina_37

description: R_IA020-98 Mid

value: female


title: Retina_36

description: R_IA020-98 Mac


title: Retina_35

description: R_IA266-99 Mac


title: Retina_42

description: R_IA200-00 Mac


title: FLAG-NMNAT-1 Replicate B

source_name: FLAG-NMNAT-1 - ChIP'd DNA

value: ectopically expressig FLAG-NMNAT-1

value: anti-FLAG

source_name: FLAG-NMNAT-1 - ChIP input DNA


title: PARP-1 Replicate 1


title: Retina_34

description: R_IA377-99 Mid

value: extramacular Retina


title: Retina_41

description: R_IA420-99 Mid


title: Retina_33

description: R_IA377-99 Mac

value: male


title: Retina_40

description: R_IA420-99 Mac


title: Retina_31

description: R_IA106-00 Mac


title: Retina_30

description: R_IA092-00 Mac


title: Retina_24

description: R_IA073-98 Mid


title: FLAG-NMNAT-1 Replicate A


title: Retina_27

description: R_IA041-99 Mid


title: Retina_32

description: R_IA106-00 Mid


title: Retina_28

description: R_IA039-98 Mac


title: Retina_21

description: R_IA358-99 Mac


title: Retina_25

description: R_IA070-99 Mid


title: Retina_23

description: R_IA073-98 Mac


title: Retina_20

description: R_IA359-99 Mid


title: Retina_26

description: R_IA041-99 Mac


title: Retina_22

description: R_IA358-99 Mid


title: Retina_29

description: R_IA039-98 Mid


title: Retina_19

description: R_IA359-99 Mac


title: Retina_12

description: R_IA341-99 Mid


title: Retina_17

description: R_IA156-98 Mac


title: Retina_18

description: R_IA156-98 Mid


title: Retina_16

description: R_IA115-98 Mid


title: Retina_11

description: R_IA341-99 Mac


title: Retina_14

description: R_IA194-00 Mid


title: Retina_15

description: R_IA115-98 Mac


title: Retina_10

description: R_IA100-99 Mid


title: Retina_13

description: R_IA194-00 Mac


title: Retina_6

description: R_IA132-98 Mid


title: Retina_8

description: R_IA387-99 Mid


title: Retina_5

description: R_IA132-98 Mac


title: Retina_4

description: R_IA151-98 Mid


title: Retina_1

description: R_IA177-96 Mac


title: Retina_3

description: R_IA151-98 Mac


title: Retina_9

description: R_IA100-99 Mac


title: RPEChoroid_175

description: RC_IA058-98 Mac_AMD

source_name: Macular RPE-choroid, AMD

value: macular RPE-choroid

value: dry AMD


title: Retina_7

description: R_IA387-99 Mac


title: RPEChoroid_174

description: RC_IA103-00 Mid_AMD

source_name: Extramacular RPE-choroid, AMD

value: extramacular RPE-choroid


title: RPEChoroid_176

description: RC_IA058-98 Mid_AMD


title: RPEChoroid_173

description: RC_IA103-00 Mac_AMD


title: RPEChoroid_172

description: RC_OR017-99 Mid_AMD

value: clinical AMD diagnosis


title: Retina_2

description: R_IA177-96 Mid

value: normal


title: RPEChoroid_171

description: RC_OR017-99 Mac_AMD


title: RPEChoroid_177

description: RC_IA107-97 Mac_AMD


title: RPEChoroid_169

description: RC_IA100-97 Mac_AMD

value: GA/CNV


title: RPEChoroid_168

description: RC_IA319-00 Mid_AMD


title: RPEChoroid_170

description: RC_IA100-97 Mid_AMD


title: RPEChoroid_167

description: RC_IA319-00 Mac_AMD


title: RPEChoroid_153

description: RC_IA222-99 Mid_AMD


title: RPEChoroid_159

description: RC_OR008-99 Mac_AMD


title: RPEChoroid_162

description: RC_IA077-96 Mid_AMD

value: GA


title: RPEChoroid_152

description: RC_IA222-99 Mac_AMD

value: AMD


title: RPEChoroid_160

description: RC_OR008-99 Mid_AMD


title: RPEChoroid_161

description: RC_IA077-96 Mac_AMD


title: RPEChoroid_163

description: RC_IA100-98 Mac_AMD


title: RPEChoroid_166

description: RC_IA068-00 Mid_AMD

value: not determined


title: RPEChoroid_148

description: RC_IA173-00 Mac_AMD

value: RPE-choroid and retina


title: RPEChoroid_147

description: RC_IA124-00 Mid_AMD

value: normal and AMD