title: S. japonicum vitelline laser microdissection microarray replicate 1 of 2

description: S. japonicum vitelline

source_name: S. japonicum vitelline

tag: S. japonicum vitelline


title: S. japonicum gut laser microdissection microarray replicate 2 of 2

status: Public on Sep 12 2008

type: RNA

city: Herston

first: Dr Geoffrey

middle: N

last: Gobert

state: QLD

address: 300 Herston road

department: Infectious Diseases / Molecular Parasitology

country: Australia

institute: Queensland Institute of Medical Research

description: S. japonicum gut

hyb_protocol: One-color Microarray-Based gene expression version 5.5 February 2007

scan_protocol: Microarrays were scanned using the Aglient DNA microarray scanner

data_processing: Agilent Feature Extraction software version 9.5.3.1

molecule: total RNA

organism: Schistosoma japonicum

source_name: S. japonicum gut

label_protocol: Agilent Low RNA Input linear amplification kit

extract_protocol: Trizol / QIAGEN RNeasy isolated total RNA

tag: S. japonicum gut


title: S. japonicum sporocysts life cycle replicate 3 of 3

description: S. japonicum sporocysts

source_name: S. japonicum sporocysts

tag: S. japonicum sporocysts


title: S. japonicum Miracidia life cycle replicate 2 of 3

description: S. japonicum Miracidia

source_name: S. japonicum Miracidia

tag: S. japonicum Miracidia


title: S. japonicum ovary laser microdissection microarray replicate 1 of 2

description: S. japonicum ovary

source_name: S. japonicum ovary

tag: S. japonicum ovary


title: S. japonicum control laser microdissection microarray replicate 1 of 2

description: S. japonicum control

source_name: S. japonicum control

tag: S. japonicum control


title: S. japonicum schistosomula life cycle replicate 3 of 3

description: S. japonicum schistosomula

source_name: S. japonicum schistosomula

tag: S. japonicum schistosomula


title: RKPG9(Rex-1+/-)-#1(251147218916)

status: Public on Sep 13 2008

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Mus musculus

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: TRIZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used.1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using pipette tips. The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4 degree. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 4 degree. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 4 degree. 6. REDISSOLVING THE RNA At the end of the procedure, briefly drying the RNApellet.

tag: embryonic stem cell

tag: Individual Identifier

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: S. japonicum schistosomula life cycle replicate 1 of 3

description: S. japonicum schistosomula


title: S. japonicum sporocysts life cycle replicate 2 of 3

description: S. japonicum sporocysts


title: S. japonicum vitelline laser microdissection microarray replicate 2 of 2

description: S. japonicum vitelline


title: S. japonicum schistosomula life cycle replicate 2 of 3

description: S. japonicum schistosomula


title: S. japonicum Miracidia life cycle replicate 3 of 3

description: S. japonicum Miracidia


title: S. japonicum Eggs life cycle replicate 3 of 3

description: S. japonicum Eggs

source_name: S. japonicum Eggs

tag: S. japonicum Eggs


title: S. japonicum Eggs life cycle replicate 2 of 3

description: S. japonicum Eggs


title: S. japonicum Cercariae life cycle replicate 1 of 3

description: S. japonicum Cercariae

source_name: S. japonicum Cercariae

tag: S. japonicum Cercariae


title: S. japonicum Miracidia life cycle replicate 1 of 3

description: S. japonicum Miracidia


title: S. japonicum Cercariae life cycle replicate 2 of 3

description: S. japonicum Cercariae


title: Adult male S. japonicum week 7 life cycle replicate 2 of 3

description: Adult male S. japonicum week 7

source_name: Adult male S. japonicum week 7

tag: Adult male S. japonicum week 7


title: S. japonicum Cercariae life cycle replicate 3 of 3

description: S. japonicum Cercariae


title: S. japonicum Eggs life cycle replicate 1 of 3

description: S. japonicum Eggs


title: Adult male S. japonicum week 6.5 life cycle replicate 3 of 3

description: Adult male S. japonicum week 6.5

source_name: Adult male S. japonicum week 6.5

tag: Adult male S. japonicum week 6.5


title: Adult male S. japonicum week 7 life cycle replicate 3 of 3

description: Adult male S. japonicum week 7


title: Adult male S. japonicum week 7 life cycle replicate 1 of 3

description: Adult male S. japonicum week 7


title: Adult male S. japonicum week 6.5 life cycle replicate 1 of 3

description: Adult male S. japonicum week 6.5


title: Adult male S. japonicum week 6.5 life cycle replicate 2 of 3

description: Adult male S. japonicum week 6.5


title: Adult male S. japonicum week 6 life cycle replicate 3 of 3

description: Adult male S. japonicum week 6

source_name: Adult male S. japonicum week 6

tag: Adult male S. japonicum week 6


title: Adult male S. japonicum week 4 life cycle replicate 3 of 3

description: Adult male S. japonicum week 4

source_name: Adult male S. japonicum week 4

tag: Adult male S. japonicum week 4


title: Adult male S. japonicum week 4 life cycle replicate 1 of 3

description: Adult male S. japonicum week 4


title: Adult male S. japonicum week 4 life cycle replicate 2 of 3

description: Adult male S. japonicum week 4


title: Adult male S. japonicum week 6 life cycle replicate 1 of 3

description: Adult male S. japonicum week 6


title: Adult male S. japonicum biological replicate life cycle replicate 5 of 6


title: Adult male S. japonicum biological replicate life cycle replicate 4 of 6


title: Adult male S. japonicum biological replicate life cycle replicate 3 of 6


title: Adult female S. japonicum week 7 life cycle replicate 3 of 3

description: S. japonicum female week 7

source_name: S. japonicum

tag: Adult female S. japonicum week 7


title: Adult female S. japonicum week 7 life cycle replicate 1 of 3

description: S. japonicum female week 7

source_name: S. japonicum female week 7

tag: S. japonicum female week 7


title: Adult male S. japonicum biological replicate life cycle replicate 6 of 6


title: Adult male S. japonicum biological replicate life cycle replicate 1 of 6


title: Adult male S. japonicum biological replicate life cycle replicate 2 of 6


title: HUES 8 p 30 sample 3

city: NYC

first: Tim

middle: D

last: Ahfeldt

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from human embryonic stem cell line HUES 8 p 30, taken from a confluent plate.

hyb_protocol: Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).

data_processing: Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.

label: Biotin

organism: Homo sapiens

source_name: human embryonic stem cells HUES 8 p 30

label_protocol: Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA.  Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual.  Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).

extract_protocol: Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.

tag: human embryonic stem cells HUES 8 p 30


title: HUES 8 p 30 sample 2


title: Adult male S. japonicum week 6 life cycle replicate 2 of 3

description: Adult male S. japonicum week 6


title: Adult female S. japonicum week 6.5 life cycle replicate 3 of 3

description: S. japonicum female week 6.5

source_name: S. japonicum female week 6.5

tag: S. japonicum female week 6.5


title: 400 ng NR from  ST-2

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

description: Each feature contains a 90-mer, 70-mer of which is a specific probe for one of the functional genes of interest, and 20-mer of which is a standard reference.

hyb_protocol: hybridization at 55 or 65 oC using Contech hybridization solution

scan_protocol: Affymetrix 418 scanner with GMS Scanner Software Version 1.51.0.42

data_processing: ImaGene 5.6.1 software and excel data filtering

molecule: genomic DNA

organism: uncultured organism

source_name: particulate material from ~4 L of surface seawater

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: DNA was extracted using the Gentra PureGene cell culture protocol (Qigen); RNA was extracted using the RNAqueous kit (Ambion)

treatment_protocol: Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC  until extraction

tag: 400 ng of NR PCR target prepared from DNA extracted from sample ST-2

tag: phytoplankton

tag: Sample collected January 2004

molecule: other

organism: unidentified

source_name: 20-mer standard reference

tag: internal oligo reference


title: 222 ng NR from ST-30A

tag: 222 ng of NR PCR target prepared from cDNA made from RNA extracted from sample ST-30A

tag: Sample collected April 2004


title: Adult female S. japonicum week 6.5 life cycle replicate 2 of 3

description: S. japonicum female week 6.5


title: 400 ng NR from ST-82

tag: 400 ng of NR PCR target prepared from DNA extracted from sample ST-82

tag: Sample collected July 2004


title: BJ hIPS #12p6 afp 4 #12 p 7 sample 3

description: Gene expression data from human induced pluripotent stem cells (secondary), #12 p 6, 4 passages as differentiated cells, reinduction and generation of secondary human induced pluripotent stem cells # 12 passage nr 7 confluent plate Donor BJ

source_name: human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ


title: HUES 8 p 30 sample 1


title: 200 ng NR from ST-82

tag: 200 ng of NR PCR target prepared from DNA extracted from sample ST-82


title: BJ sample 3

description: Gene expression data from human BJ (Donor line) using a confluent plate.

source_name: human BJ (Donor line)

tag: human BJ (Donor line)


title: BJ hIPS #12p6 afp 4 #12 p 7 sample 1

tag: human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ


title: 400 ng NR from ST-30A

tag: 400 ng of NR PCR target prepared from cDNA made from RNA extracted from sample ST-30A


title: BJ hIPS #12p5 sample 2

description: Gene expression data from human induced pluripotent stem cells, #12 passage 5 using a confluent plate. Donor line human BJ

source_name: human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ


title: Adult female S. japonicum week 6 life cycle replicate 2 of 3

description: S. japonicum female week 6

source_name: S. japonicum female week 6

tag: S. japonicum female week 6


title: BJ hIPS #12p6 afp 4 #12 p 7 sample 2


title: Adult female S. japonicum week 7 life cycle replicate 2 of 3

description: S. japonicum female week 7

tag: Adult female S. japonicum week 7


title: BJ hIPS #8p10 sample 3

description: Gene expression data from human induced pluripotent stem cells, #8 passage 10, using a confluent plate. Donor line human BJ

source_name: human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ


title: Adult female S. japonicum week 4 life cycle replicate 3 of 3

description: Adult female S. japonicum week 4

source_name: S. japonicum female week 4

tag: S. japonicum female week 4


title: Adult female S. japonicum week 6 life cycle replicate 3 of 3

description: S. japonicum female week 6


title: BJ sample 1


title: BJ sample 2


title: 100 ng rbcL from ST-109

tag: 100 ng of rbcL PCR  target prepared from DNA extacted from sample ST-109

tag: Sample collected August 2004


title: Adult female S. japonicum week 6 life cycle replicate 1 of 3

description: Adult female S. japonicum week 4


title: Adult female S. japonicum week 6.5 life cycle replicate 1 of 3

description: S. japonicum female week 6.5

tag: S. japonicum female week 6.5


title: BJ hIPS #12p5 sample 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA.  Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual.  Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).

tag: human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ


title: BJ hIPS #6p9 sample 3

description: Gene expression data from human induced pluripotent stem cells, #6 passage 9, using a confluent plate. Donor line human BJ

source_name: human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ


title: BJ hIPS #8p10 sample 1

tag: human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ


title: BJ hIPS #8p10 sample 2


title: BJ hIPS #12p5 sample 1


title: 100 ng rbcL from ST-108

tag: 100 ng of rbcL PCR  target prepared from DNA extacted from sample ST-108

tag: phytoplankton

tag: internal oligo reference


title: 215 ng NR from ST-79

tag: 215 ng of NR PCR target prepared from cDNA made from RNA extracted from sample ST-79 plus 265 ng of rbcL PCR target prepared from cDNA made from RNA extracted from sample ST-79


title: 200 ng NR from ST-79

tag: 200 ng of NR PCR target prepared from cDNA made from RNA extracted from sample ST-79 plus 1 ng of rbcL PCR target prepared from Navicula sp. culture

tag: Sample collected July 2004


title: 200 ng rbcL from ST-30B plus 1 ng NR

tag: 200 ng of rbcL PCR target prepared from DNA extracted from sample ST-30B plus 1 ng of NR PCR target prepared from Phaeodactylum tricornutum culture

tag: Sample collected April 2004


title: 100 ng rbcL from ST-82

tag: 100 ng of rbcL PCR product prepared from DNA extracted from sample ST-82


title: 144 ng rbcL from ST-82 (3)

tag: 144 ng of rbcL PCR product prepared from DNA extracted from sample ST-82


title: 144 ng rbcL from ST-82 (2)


title: 2000 ng of target from  RNA from ST-30B

tag: 2000 ng of target produced by Klenow random priming of total cDNA made from RNA extracted from sample ST30B


title: 100 ng rbcL from ST-30B

tag: 100 ng of rbcL PCR product prepared from DNA extracted from sample ST-30B,


title: 144 ng rbcL from ST-82


title: 10 ng rbcL from ST-1

tag: 10 ng of rbcL PCR product prepared from DNA extracted from sample ST-1

tag: Sample collected January 2004


title: 730 ng from total DNA from ST-30A

tag: 730 ng target produced by Klenow random priming of total DNA extracted from sample ST30A


title: 400 ng rbcL from ST-30A

tag: 400 ng of rbcL PCR product prepared from cDNA extracted from sample ST-30A


title: BJ hIPS #6p9 sample 1

tag: human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ


title: BJ hIPS #5p9 sample 3

description: Gene expression data from human induced pluripotent stem cells, #5 passage 9, using a confluent plate. Donor line human BJ

source_name: human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ


title: BJ hIPS #5p9 sample 2

tag: human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ


title: 13-month-old wild type B6 mouse vs 13-month-old HBx transfected mouse Replicate 3

status: Public on Sep 11 2008

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University

description: Biological replicate 3 of 3. 13-month-old wildtype b6 mice vs 13-month-old HBx transfected mice

hyb_protocol: After two labeled cDNAs were mixed, the mixture was denaturized 95 ℃ for 2 min and then incubated in 45 ℃ water chamber for 20 min. The cDNA mixture was then placed on Agilent Mouse whole genome 44K (G4122A, Agilent tech) and covered by a hybridization chamber. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: Hybridized slides were scanned with the Axon Instruments GenePix 4000B scanner and the scanned images were analyzed with the software program GenePix Pro 5.1 (Axon, CA) and GeneSpring 7.2 (Sillicongenetics, CA). In order to allow algorithm to eliminate all bad spots, no data points were eliminated by visual inspection from the initial GenePix image. For signal normalization, housekeeping genes (β-actin) and positive control genes (A. thaliana genes) were spotted onto each slide. The signals of these spots were used for normalization. To determine the background signal intensity, we spotted the spotting solution on each slide. To filter out the unreliable data, spots with signal-to-noise (signal – background - background SD) below 100 were not included in the data.

data_processing: Data were normalized by Global, lowess, print-tip and scaled normalization for data reliability. Data were clustered groups of genes that behave similarly across a time course experiments using GeneSpring 7.2(Sillicongenetics). We used the Pearson correlation to separate the gene of similar patterns.

source_name: 13-month-old wild type B6 mouse

label_protocol: Fluorescence labeled cDNA probes were prepared form 30 ㎍ of total RNA by oligo (dT)18-primed polymerization using SuperScript Ⅱ reverse transcriptase (Invitrogen, NY) in a total reaction volume of 30 ㎕. The reverse transcription mixture included 400 U Superscript RNase H-reverse transcriptase (Invitrogen, NY), 15 mM dATP, dTTP and dGTP, 0.6 mM dCTP and 3 mM Cy3 or Cy5 labeled dCTP (NEN Life Science Product Inc.). After reverse transcription, the sample RNA was degraded by adding 5 ㎕ of stop solution (0.5M NaOH/50m EDTA) and incubating 65 ℃ for 10 min. The labeled cDNA mixture was then concentrated using ethanol precipitation method. The concentrated Cy3 and Cy5 labeled cDNAs were resuspended in 10 ㎕ of hybridization solution (GenoCheck, Korea).

growth_protocol: We used HBx Tg mice (C57BL/6J-HBx/HBx transgenic mice). All animals have been maintained in SPF barrier area of the Department of Laboratory Animal Facility, College of Veterinary Medicine, Seoul National University. The temperature (22±2℃), humidity (50±5%) and light (12D/12N) of animal rooms were controlled constantly. All animals were sacrificed under anesthesia.

extract_protocol: Total RNA was extracted from liver of the HBx Tg mice and B6 wild type mice using the TRI REAGENT (MRC, OH) according to the manufacturer’s instructions.

treatment_protocol: Liver was removed, weighted and stored at -70℃ until used. These procedures were reviewed according to the Research Policies and Procedure Guidelines at Institutional Animal Care and Use Committees.

tag: wild type B6 mouse

tag: age

value: 13 month

tag: liver

source_name: 13-month-old HBx transfected mouse

tag: HBx transfected mouse


title: 9-month-old wild type B6 mouse vs 9-month-old HBx transfected mouse Replicate 3

description: Biological replicate 3 of 3. 9-month-old wildtype b6 mice vs 9-month-old HBx transfected mice

source_name: 9-month-old wild type B6 mouse

value: 9 month

source_name: 9-month-old HBx transfected mouse


title: BJ hIPS #5p9 sample 1

description: Gene expression data from human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ


title: 3-month-old wild type B6 mouse vs 3-month-old HBx transfected mouse Replicate 3

description: Biological replicate 3 of 3. 3-month-old wildtype b6 mice vs 3-month-old HBx transfected mice

source_name: 3-month-old wild type B6 mouse

value: 3 month

source_name: 3-month-old HBx transfected mouse


title: Adult female S. japonicum week 4 life cycle replicate 1 of 3

description: Adult female S. japonicum week 4

source_name: Adult female S. japonicum week 4

tag: Adult female S. japonicum week 4


title: 13-month-old wild type B6 mouse vs 13-month-old HBx transfected mouse Replicate 2

description: Biological replicate 2 of 3. 13-month-old wildtype b6 mice vs 13-month-old HBx transfected mice


title: 13-month-old wild type B6 mouse vs 13-month-old HBx transfected mouse Replicate 1

description: Biological replicate 1 of 3. 13-month-old wildtype b6 mice vs 13-month-old HBx transfected mice


title: 3-month-old wild type B6 mouse vs 3-month-old HBx transfected mouse Replicate 2

description: Biological replicate 2 of 3. 3-month-old wildtype b6 mice vs 3-month-old HBx transfected mice


title: 9-month-old wild type B6 mouse vs 9-month-old HBx transfected mouse Replicate 1

description: Biological replicate 1 of 3. 9-month-old wildtype b6 mice vs 9-month-old HBx transfected mice


title: 9-month-old wild type B6 mouse vs 9-month-old HBx transfected mouse Replicate 2

description: Biological replicate 2 of 3. 9-month-old wildtype b6 mice vs 9-month-old HBx transfected mice


title: 3-month-old wild type B6 mouse vs 3-month-old HBx transfected mouse Replicate 1

description: Biological replicate 1 of 3. 3-month-old wildtype b6 mice vs 3-month-old HBx transfected mice


title: Adult female S. japonicum week 4 life cycle replicate 2 of 3

description: Adult female S. japonicum week 4

tag: Adult S. japonicum week 4


title: BJ hIPS #6p9 sample 2


title: Conceptus Morphology_Day 14 Filamentous_Rep1

status: Public on Sep 10 2008

city: Ames

first: Jason

middle: W

last: Ross

state: IA

address: 2356E Kildee Hall

department: Animal Science

institute: Iowa State University

description: Day 14 Filamentous conceptuses collected on day 14 of gestation.

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

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

data_processing: 1st.  dChip’s method of invariant set normalization in which the chip with the median intensity value was used as the baseline against which the brightnesses of the remaining chips were adjusted in order to be of a comparable level.  2nd. Standardization was conducted by calculating model-based expression indices (MBEI) using dChip’s Perfect-Match (PM)-only model.  This additional modeling reduces the variance of expression level estimates by accounting for probe differences.  3rd. Data were log transformed to improve statistical performance by approximating a normal distribution within each gene.  The log base2 scale is favorable because each unit difference represents a 2-fold difference.

label: GeneChip DNA Labeling Reagent

organism: Sus scrofa

source_name: Day 14 filamentous

label_protocol: cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gilts were group housed.  Estrus detection was conducted twice daily.  Gilts were mated naturally with an intact boar at the onset of their second estrus following a normal estrous cycle and again 24 hours later.

extract_protocol: We utilized RNAwiz (Ambion).  According to the manufacturers recommendations.

treatment_protocol: Conceptuses were collected by flushing the uteri with 20 mL of physiological saline.  Morphological data of the embryos were recorded and the conceptuses were placed into a cryogenic vial, snap-frozen in liquid nitrogen and then placed in the -80C until utilized.

tag: Crossbred, cyclic gilts were approximately 8-10 months of age.  Day 14 Filamentous  conceptuses were collected on day 14 of gestation.


title: Conceptus Morphology_Day 14 Filamentous_Rep3


title: Conceptus Morphology_Day 14 Filamentous_Rep2


title: Conceptus Morphology_Day 12 Filamentous_Rep2

description: Day 12 Filamentous conceptuses collected on day 12 of gestation.

source_name: Day 12 filamentous

tag: Crossbred, cyclic gilts were approximately 8-10 months of age.  Day 12 Filamentous  conceptuses were collected on day 12 of gestation.


title: Conceptus Morphology_Day 12 Filamentous_Rep3


title: Conceptus Morphology_Day 12 Filamentous_Rep1


title: Conceptus Morphology_Day 12 Filamentous_Rep4


title: Conceptus Morphology_Tubular (20-80mm)_Rep4

description: Tubular embryos (20-80 mm) collected on day 11-12 of gestation.

source_name: Tubular embryos

tag: Crossbred, cyclic gilts were approximately 8-10 months of age.  Tubular (20-80 mm) embryos were collected on approximately day 11-12 of gestation.


title: Conceptus Morphology_Tubular (20-80mm)_Rep3


title: Conceptus Morphology_Day 14 Filamentous_Rep4


title: Conceptus Morphology_Tubular (20-80mm)_Rep2


title: Conceptus Morphology_Spherical (8-10mm)_Rep3

description: Spherical embryos (8-10 mm) collected on day 11 of gestation.

source_name: Spherical embryos

tag: Crossbred, cyclic gilts were approximately 8-10 months of age.  Spherical embryos were collected on approximately day 11 of gestation and were 8-10 mm in diameter.


title: Conceptus Morphology_Spherical (8-10mm)_Rep4


title: Populus deltoides Root Sample17

city: Gainesville

first: Matias

last: Kirst

state: FL

institute: University of Florida

description: All procedures were carried out at Nimblegen facilities (Madison, Wisconsin).

hyb_protocol: Cy3-labeled samples (1-4 ug) were resuspended in hybridization buffer and hybridization component A (NimbleGen, Madison, WI), denatured at 95C for 5 minutes, loaded in the microarray chamber and allowed to hybridize at 42°C overnight (16-20h). Slides were then washed twice in Wash I (15 sec and 2 minutes), once in each of Wash II (1 min)and Wash III (15 sec) and dried.

scan_protocol: Slides were scanned with a GenePix 4000B Scanner. Initial pre-scannign was performed at PMT Gain = 500 and Power (%) = 100. After the pre-scan, the PMT was adjusted to avoid saturated spots.

data_processing:
Microarray data was normalized using the quantile normalization procedure described by Bolstad and colleagues (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bioinformatics. 2003 Jan 22;19(2):185-93.).

organism: Populus deltoides

source_name: Populus deltoides whole-root at six weeks

label_protocol: RNA was converted to double-stranded cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturer’s protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37°C, prior to denaturation and hybridization to a microarray.

growth_protocol: Plants were received as as hardwood cuttings. After rooting, bud break and shoot elongation, fresh softwood terminal cuttings were harvested and placed in rooting media pellets (Jiffy Forestry Products, Lorain, OH) for two weeks. Rooted cuttings were planted in two gallon pots and grown for six weeks in ebb-and-flow benches in a greenhouse under long day conditions (16h light:8hr dark) and standard nutrient regime (Hocking’s Modified Complete Fertilizer) supplemented with 25mM nitrogen (NH4NO3).

extract_protocol: At harvest, the main plant organs (stems, roots, leaves and sylleptic branches) were collected separately. Stems were further dissected into secondary xylem tissue and phloem/bark/immature xylem. Leaf, secondary xylem, and root tissue from two biological replicates of each genotype were selected for gene expression analysis. All tissue was flash-frozen in liquid nitrogen immediately after harvest and stored at -80° Celsius (C) prior to lyophilization and subsequent RNA isolation. RNA was extracted following the procedure described by Chang and colleagues (Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 117–121). After extraction, RNA samples were treated with RQ1 DNase (Promega USA, Madison, WI), purified in RNAeasy Plant Mini Kit columns (Qiagen USA, Valencia, CA), and integrity evaluated on 1% w/v agarose gels.

tag: Whole roots harvested from a Populus deltoides genotype D124 after six weeks of growth in a greenhouse.


title: Conceptus Morphology_Tubular (20-80mm)_Rep1


title: Populus deltoides Leaf Sample17

source_name: Populus deltoides mid-leaf at six weeks

tag: Mid-leaf harvested from a Populus deltoides genotype D124 after six weeks of growth in a greenhouse.


title: Conceptus Morphology_Spherical (8-10mm)_Rep2


title: effects of MN1 expression in the presence of ATRA_6

status: Public on Sep 09 2008

city: Rotterdam

first: Magda

last: Meester

address: Dr. Molewaterplein 40

department: Pathology

country: Netherlands

institute: Erasmus Medical Center

description: Dye swap and/or biological duplicate of I5, I3, J9

hyb_protocol: labeled aRNA was fragmented (Ambion RNA Fragmentation Reagents) and mixed with blocking solution containing Poly d(A), Cot-1 DNA and yeast t-RNA. Hybridization was overnight at 42C on a Tecan HS4800 hybridization station. Protocol: M016 (http://erasmusmc.nl/biomics). It includes a 15 min prehybridization with a solution containing 4% (w/v) BSA.

scan_protocol: Perkin Elmer ScanArray Express HT instrument Imagene software version 6.0

data_processing: Imagene data was uploaded into the CMF database (NKI, The Netherlands) and normalized using lowess subarray method. No background correction.

source_name: number 46, exp A

label_protocol: 3 ug of RNA was used for linear amplification using the Superscript III RNA amplification kit (Invitrogen). 1 ug of amplified RNA was labeled using the ULS-Cy3/5 aRNA fluorescent labeling kit (Kreatech)

growth_protocol: cell were cultured in RPMI 1640 with 10% FCS, pen/strep, 0.5 ug/ml puromycin, 100 ug/ml hygromycin and 1ug/ml tetracyclin.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified using RNeasy columns

treatment_protocol: tetracyclin-controlled gene expression was induced by resuspending the cells in fresh medium without tetracyclin. If desired, ATRA was added to a final concentration of 1 uM.

tag: see experimental_design.jpg

tag: MN1 is a derivative of U937 and MN1 is under control of TET system

source_name: number 34, exp A


title: effects of MN1 expression in the presence of ATRA_7

description: Dye swap and/or biological duplicate of I4, I2, J6

source_name: number 33, exp B

source_name: number 45. exp B


title: effects of TET release in control cell line_12

description: Dye swap and/or biological duplicate of A2, A5, J4

source_name: number 4, exp B

tag: UHD is a derivative of U937 and serves as control cell line

source_name: number 16, exp B


title: effects of MN1 expression in the presence of ATRA_8

description: Dye swap and/or biological duplicate of I5, I3, J7

source_name: number 34, exp B

source_name: number 46, exp B


title: cell line differences_20

description: Dye swap and/or biological duplicate of H2, H5, I8

source_name: number 29, exp B

source_name: number 54, exp B

tag: MN1-TEL is a derivative of U937 and MN1-TEL is under control of TET system


title: cell line differences_16

description: Dye swap and/or biological duplicate of H1, H4, J0

source_name: number 53, exp A

source_name: number 28, exp A


title: Populus deltoides Leaf Sample12


title: difference between MN1 and MN1-TEL effects_12

description: Dye swap and/or biological duplicate of I1, I0, J2

source_name: number 41, exp B

source_name: number 66, exp B


title: effects of TET release in control cell line_11

description: Dye swap and/or biological duplicate of A2, A5, J5

source_name: number 16, exp A

source_name: number 4, exp A


title: effects of MN1 expression in the presence of ATRA_5

description: Dye swap and/or biological duplicate of I4, I2, J8

source_name: number 45, exp A

source_name: number 33, exp A


title: cell line differences_18

description: Dye swap and/or biological duplicate of H0, H3, I6

source_name: number 27, exp B

source_name: number 52, exp B


title: cell line differences_15

description: Dye swap and/or biological duplicate of H0, H3, I9

source_name: number 52, exp A

source_name: number 27, exp A


title: Populus deltoides Xylem Sample12

source_name: Populus deltoides differentiating xylem at six weeks

tag: Differentiating xylem harvested from a Populus deltoides genotype D124 after six weeks of growth in a greenhouse.


title: Populus deltoides X Populus trichocarpa Root Sample1

organism: Populus trichocarpa x Populus deltoides

source_name: Populus hybrid (Populus deltoides X Populus trichocarpa) whole-root at six weeks

tag: Whole roots harvested from a Populus hybrid (Populus deltoides X Populus trichocarpa) genotype 52-225 after six weeks of growth in a greenhouse.


title: cell line differences_19

description: Dye swap and/or biological duplicate of H1, H4, I7

source_name: number 28, exp B

source_name: number 53, exp B


title: cell line differences_17

description: Dye swap and/or biological duplicate of H2, H5, J1

source_name: number 54. exp A

source_name: number 29, exp A


title: Populus deltoides X Populus trichocarpa Xylem Sample6

source_name: Populus hybrid (Populus deltoides X Populus trichocarpa) differentiating xylem at six weeks

tag: Differentiating xylem harvested from a Populus hybrid (Populus deltoides X Populus trichocarpa) genotype 52-225 after six weeks of growth in a greenhouse.


title: Populus deltoides X Populus trichocarpa Root Sample5


title: Populus deltoides X Populus trichocarpa Leaf Sample5

source_name: Populus hybrid (Populus deltoides X Populus trichocarpa) mid-leaf at six weeks

tag: Mid-leaf harvested from a Populus hybrid (Populus deltoides X Populus trichocarpa) genotype 52-225 after six weeks of growth in a greenhouse.


title: Populus deltoides Xylem Sample17


title: Populus deltoides Root Sample12

source_name: Populus deltoides whole-root at six weeks


title: Populus deltoides X Populus trichocarpa Leaf Sample1


title: effects of MN1 expression in the presence of ATRA_2

description: Dye swap and/or biological duplicate of I5, J7, J9

source_name: number 34, exp A

source_name: number 46, exp A


title: effects of MN1 expression in the presence of ATRA_3

description: Dye swap and/or biological duplicate of I2, J6, J8

source_name: number 45. exp B

source_name: number 33, exp B


title: effects of MN1 expression_11

description: Dye swap and/or biological duplicate of H7, A8, B1

source_name: number 41, exp A


title: cell line differences_13

description: Dye swap and/or biological duplicate of H1, I7, J0


title: cell line differences_12

description: Dye swap and/or biological duplicate of H0, I6, I9

source_name: number 52, exp B

source_name: number 27, exp B


title: effects of MN1 expression in the presence of ATRA_1

description: Dye swap and/or biological duplicate of I4, J6, J8

source_name: number 33, exp A

source_name: number 45, exp A


title: Conceptus Morphology_Spherical (8-10mm)_Rep1

description: Spherical embryos (8-10 mm) collected on day 11 of gestation.

source_name: Spherical embryos

label_protocol: cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)


title: effects of ATRA, MN1-TEL is present (ON)_8

description: Dye swap and/or biological duplicate of E9, E7, G7

source_name: number 65, exp B

source_name: number 71, exp B


title: effects of MN1-TEL expression_11

description: Dye swap and/or biological duplicate of H9, B4, B7

source_name: number 66, exp A

source_name: number 54, exp A


title: difference between MN1 and MN1-TEL effects_9

description: Dye swap and/or biological duplicate of I1, J2, J3


title: difference between MN1 and MN1-TEL effects_10

description: Dye swap and/or biological duplicate of I0, J2, J3

source_name: number 66, exp B

source_name: number 41, exp B


title: effects of MN1 expression in the presence of ATRA_4

description: Dye swap and/or biological duplicate of I3, J7, J9

source_name: number 46, exp B

source_name: number 34, exp B


title: cell line differences_11

description: Dye swap and/or biological duplicate of H5, I8, J1

source_name: number 29, exp A

source_name: number 54. exp A


title: cell line differences_9

description: Dye swap and/or biological duplicate of H3, I6, I9

source_name: number 27, exp A

source_name: number 52, exp A


title: Populus deltoides X Populus trichocarpa Xylem Sample1

description: All procedures were carried out at Nimblegen facilities (Madison, Wisconsin).

source_name: Populus hybrid (Populus deltoides X Populus trichocarpa) differentiating xylem at six weeks


title: effects of MN1-TEL expression_12

description: Dye swap and/or biological duplicate of H8, B4, B7

source_name: number 54, exp B


title: effects of ATRA, MN1-TEL is present (ON)_7

description: Dye swap and/or biological duplicate of E8, E6, G6

source_name: number 64, exp B

source_name: number 70, exp B


title: cell line differences_10

description: Dye swap and/or biological duplicate of H4, I7, J0

source_name: number 28, exp A

source_name: number 53, exp A


title: ChIP_H3K9me2_crosslinked_rep1

type: genomic

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: no additional information

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

data_processing: Each probe was assigned a log of the ratio between H3K9me2 (Cy5) and H3 (Cy3) signal. Z-scores were calculated for each probe by subtracting the mean log ratio from individual log ratios and dividing by the standard deviation for the entire array.

organism: Arabidopsis thaliana

source_name: ChIP crosslinked H3K9me2

growth_protocol: Plants were grown under continuous light for three weeks.

extract_protocol:
ChIP was performed as described:
Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002)
Dependence of heterochromatic histone H3 methylation patterns on the
Arabidopsis gene DDM1. Science 297: 1871–1873.
Mouse monoclonal antibody anti-H3K9me2 (Abcam #ab1220; http://www.abcam.com) was used for immunoprecipitation.

treatment_protocol: Aerial part of the plants were crosslinked in 1% formaldehyde for 15 minutes. Crosslinking was stopped with addition of glycine to 0.125 M final concentration and plants were frozen in the liquid nitrogen.

tag: Col-0, 3 week old, aerial part of the plant

source_name: ChIP crosslinked H3

extract_protocol:
ChIP was performed as described:
Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002)
Dependence of heterochromatic histone H3 methylation patterns on the
Arabidopsis gene DDM1. Science 297: 1871–1873.
Rabbit polyclonal antibody anti-H3 (Abcam #ab1791; http://www.abcam.com) was used for immunoprecipitation.


title: effects of ATRA, MN1-TEL is present (ON)_6

description: Dye swap and/or biological duplicate of E9, E7, G9

source_name: number 71, exp A

source_name: number 65, exp A


title: effects of ATRA, MN1-TEL is present (ON)_5

description: Dye swap and/or biological duplicate of E8, E6, G8

source_name: number 70, exp A

source_name: number 64, exp A


title: ChIP_H3K9me2_native_rep3

description: no additional information

scan_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: Chip native H3K9me2

extract_protocol:
Native chromatin immunoprecipitation: Plant tissue was resuspended
in 10 ml of HBM buffer (25 mM Tris-Cl pH7.6, 440 mM sucrose, 10 mM MgCl2 and 0.1% Triton-X, 10 mM
β-mercaptoethanol, 2mM spermine, 1 mM PMSF, 1 ug/ml pepstatin and EDTA-free protease inhibitor
cocktail (Roche), homogenized and filtered through Miracloth (Calbiochem). After spinning at 3000 rpm
for 5 min (SS-34, Sorvall), the pellet was resuspended in 5 ml of NIB buffer (20 mM Tris-Cl pH7.6, 250
mM sucrose, 5 mM MgCl2, 5 mM KCl, 0.1% Triton-X, 10 mM β-mercaptoethanol), applied to a 15/50%
Percoll (GE Healthcare) gradient in NIB and spun 2000 rpm for 20 min (SS-34, Sorvall). Isolated nuclei
were washed two times in NIB buffer and flash frozen in liquid nitrogen in HBC buffer (25 mM Tris-Cl
pH7.6, 25 mM Tris-Cl pH7.6, 440 mM sucrose, 10 mM MgCl2 and 0.1% Triton-X, 10 mM β-
mercaptoethanol, 20% glycerol). Nuclei from 1/5 of each preparation were treated with four ul of RNAse
A, 10 ug/ul, (Qiagen) and used for Micrococcal Nuclease (Takara) digestion for 6 minutes (final
concentration 0.2 U/ul) in digestion buffer (16 mM Tris-Cl, pH 7.6, 50 mM NaCl, 2.5 mM CaCl2, 0.01 mM
PMSF and EDTA-free protease inhibitor cocktail (Roche) and stopped with 10 mM EDTA.
Mononucleosomes were released by treating nuclei with 0.1% Triton-X for 1-2 hours in the cold, and then
pelleting the debris by centrifuging at 3500 rpm for 3 min (Eppendorf, 5415R). 500 ul of
supernatant was applied to 50 ul of Dynabeads Protein A (Invitrogen) that was preincubated with 2.5 ug
of the appropriate antibody in buffer (20 mM Tris-Cl, pH 7.6, 50 mM NaCl, 5 mM EDTA and 0.1% Triton) and
incubated overnight. Beads were washed (10 min incubation in the cold) with 500 ul of the
following buffers: 50 mM Tris-Cl pH 7.6, 10 mM EDTA, 0.1 mM PMSF, protease inhibitor cocktail (Roche)
with changing concentration of NaCl – 50 mM, 100 mM and 150 mM. Final wash was done in TE buffer,
without incubation and immunocomplexes were eluted with 500 ul of 0.1% SDS and 0.1 M NaHCO3 at
65 C for 10 min. DNA was then purified using conventional phenol-chlorophorm extraction and
ethanol/salt precipitation. DNA amplification was performed using the GenomePlex® Whole Genome
Amplification Kit (Sigma).
Mouse monoclonal antibody anti-H3K9me2 (Abcam #ab1220; http://www.abcam.com) for immunoprecipitation.

source_name: Chip native H3

extract_protocol:
Native chromatin immunoprecipitation: Plant tissue was resuspended
in 10 ml of HBM buffer (25 mM Tris-Cl pH7.6, 440 mM sucrose, 10 mM MgCl2 and 0.1% Triton-X, 10 mM
β-mercaptoethanol, 2mM spermine, 1 mM PMSF, 1 ug/ml pepstatin and EDTA-free protease inhibitor
cocktail (Roche), homogenized and filtered through Miracloth (Calbiochem). After spinning at 3000 rpm
for 5 min (SS-34, Sorvall), the pellet was resuspended in 5 ml of NIB buffer (20 mM Tris-Cl pH7.6, 250
mM sucrose, 5 mM MgCl2, 5 mM KCl, 0.1% Triton-X, 10 mM β-mercaptoethanol), applied to a 15/50%
Percoll (GE Healthcare) gradient in NIB and spun 2000 rpm for 20 min (SS-34, Sorvall). Isolated nuclei
were washed two times in NIB buffer and flash frozen in liquid nitrogen in HBC buffer (25 mM Tris-Cl
pH7.6, 25 mM Tris-Cl pH7.6, 440 mM sucrose, 10 mM MgCl2 and 0.1% Triton-X, 10 mM β-
mercaptoethanol, 20% glycerol). Nuclei from 1/5 of each preparation were treated with four ul of RNAse
A, 10 ug/ul, (Qiagen) and used for Micrococcal Nuclease (Takara) digestion for 6 minutes (final
concentration 0.2 U/ul) in digestion buffer (16 mM Tris-Cl, pH 7.6, 50 mM NaCl, 2.5 mM CaCl2, 0.01 mM
PMSF and EDTA-free protease inhibitor cocktail (Roche) and stopped with 10 mM EDTA.
Mononucleosomes were released by treating nuclei with 0.1% Triton-X for 1-2 hours in the cold, and then
pelleting the debris by centrifuging at 3500 rpm for 3 min (Eppendorf, 5415R). 500 ul of
supernatant was applied to 50 ul of Dynabeads Protein A (Invitrogen) that was preincubated with 2.5 ug
of the appropriate antibody in buffer (20 mM Tris-Cl, pH 7.6, 50 mM NaCl, 5 mM EDTA and 0.1% Triton) and
incubated overnight. Beads were washed (10 min incubation in the cold) with 500 ul of the
following buffers: 50 mM Tris-Cl pH 7.6, 10 mM EDTA, 0.1 mM PMSF, protease inhibitor cocktail (Roche)
with changing concentration of NaCl – 50 mM, 100 mM and 150 mM. Final wash was done in TE buffer,
without incubation and immunocomplexes were eluted with 500 ul of 0.1% SDS and 0.1 M NaHCO3 at
65 C for 10 min. DNA was then purified using conventional phenol-chlorophorm extraction and
ethanol/salt precipitation. DNA amplification was performed using the GenomePlex® Whole Genome
Amplification Kit (Sigma).
Rabbit polyclonal antibody anti-H3 (Abcam #ab1791; http://www.abcam.com) was used for immunoprecipitation.

treatment_protocol: Plants were frozen in the liquid nitrogen.


title: ChIP_H3K9me2_native_rep2

description: no additional information

source_name: ChIP native H3K9me2

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

treatment_protocol: Plants were frozen in the liquid nitrogen

source_name: ChIP native H3


title: cell line differences_8

description: Dye swap and/or biological duplicate of F1, F3, F5

source_name: number 2, exp B

source_name: number 52, exp B


title: cell line differences_7

description: Dye swap and/or biological duplicate of F0, F2, F4

source_name: number 27, exp B


title: ChIP_H3K9me2_native_rep1

description: no additional information


title: cell line differences_14

description: Dye swap and/or biological duplicate of H2, I8, J1

source_name: number 54, exp B

source_name: number 29, exp B


title: effects of ATRA, MN1 switched OFF_8

description: Dye swap and/or biological duplicate of E5, E3, G1

source_name: number 28, exp B

source_name: number 34, exp B


title: cell line differences_6

description: Dye swap and/or biological duplicate of F1, F3, G5

source_name: number 52, exp A

source_name: number 2, exp A


title: effects of ATRA, MN1 switched OFF_6

description: Dye swap and/or biological duplicate of E5, E3, G3

source_name: number 34, exp A

source_name: number 28, exp A


title: effects of ATRA, MN1-TEL is present (ON)_3

description: Dye swap and/or biological duplicate of E6, G6, G8

source_name: number 70, exp B

source_name: number 64, exp B


title: cell line differences_4

description: Dye swap and/or biological duplicate of F1, F5, G5


title: cell line differences_5

description: Dye swap and/or biological duplicate of F0, F2, G4

source_name: number 27, exp A


title: effects of ATRA, MN1 switched OFF_7

description: Dye swap and/or biological duplicate of E4, E2, G0

source_name: number 33, exp B


title: effects of ATRA, MN1 switched OFF_5

description: Dye swap and/or biological duplicate of E4, E2, G2

source_name: number 33, exp A


title: effects of ATRA, MN1-TEL is present (ON)_4

description: Dye swap and/or biological duplicate of E7, G7, G9

source_name: number 71, exp B

source_name: number 65, exp B


title: cell line differences_2

description: Dye swap and/or biological duplicate of F3, F5, G5


title: cell line differences_3

description: Dye swap and/or biological duplicate of F0, F4, G4

source_name: number 2, exp B


title: effects of ATRA, MN1 switched OFF_4

description: Dye swap and/or biological duplicate of E3, G1, G3


title: effects of ATRA, MN1-TEL is present (ON)_2

description: Dye swap and/or biological duplicate of E9, G7, G9

source_name: number 65, exp A

source_name: number 71, exp A


title: effects of ATRA, MN1 is present (ON)_5

description: Dye swap and/or biological duplicate of E0, D8, F8

source_name: number 45, exp A

source_name: number 39, exp A


title: XY rrp2 S3

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

hyb_protocol: Prior to hybridization, slides were pre-hybridized in a solution of 5xSSC (1×SSC = 0.15 M sodium chloride/0.015 M sodium citrate, pH 7), 0.1% SDS, and 0.1% (w/v) bovine serum albumin (BSA) for 30 min at 55  oC.  Following pre-hybridization, slides were washed 5 times in distilled water, dipped in isopropanol, dried by centrifugation, and immediately used in the hybridization.  After purification of labeled DNA using the Qiaquick PCR purification kit (Qiagen, Valencia, CA), equal amounts of labeled 297 and B31 DNA were combined and applied to arrays.  Slides were covered with lifter coverslips (Erie Scientific Company, Portsmouth, NH), placed into a humidified hybridization chamber (Ambion, Austin, TX), and the chamber was placed into a hybridization oven set at 50 oC.  After hybridization overnight, slides were washed twice with 2×SSC/0.1% SDS for 15 min at 42 oC, twice with 0.1×SSC/0.1% SDS for 15 min at room temperature, and twice with 0.1×SSC for 1 min at room temperature. Washed slides were then dried by centrifugation and scanned immediately.

scan_protocol: Hybridized slides were scanned on an Axon 4000B microarray scanner using GenePix Pro 6.1 (Molecular Devices, Sunnyvale, CA).

data_processing: The image was analyzed using the GenePix program and data then were analyzed with Acuity 4.0 microarray informatics software according to the manufacturer’s instruction (Molecular Devices), using ratio-based normalization method and a cutoff value of a 2-fold change.  Statistical analyses were performed using the one and two-sample significance test (p<0.05) in the Acuity program, which is a two-sample t-test between two groups of arrays. Differentially expressed genes were identified by both fold change and statistical significance.

organism: Borreliella burgdorferi

label_protocol: cDNA was synthesized from extracted RNA and labeled with Cy3 or Cy5 using the Amersham post-labeling kit according to the manufacturer’s instructions (Amersham Biosciences), with minor modifications. Briefly, 10 g of total RNA were converted to cDNA using CyScript reverse transcriptase, in the presence of 1 μl of random nanomers (Amersham Biosciences) and 4.5 μg of random hexamers (Invitrogen).  The resulting cDNA was labeled with Cy3 or Cy5.  Cy3- or Cy5-labeled cDNA from RNA extracted from parental 297 were then combined with their corresponding Cy5- or Cy3-labeled cDNA generated from RNA derived from the mutants; e.g. Cy5-labeled 297 cDNA and Cy3-labeled mutant cDNA or Cy3-labeled 297 cDNA and Cy5-labeled mutant cDNA.  Labeled probes were purified using the Qiaquick PCR purification kit (Qiagen) and then used in subsequent microarray experiments.

extract_protocol: RNA was extracted from three biological replicates of wild-type parental strain B. burgdorferi 297 and the rpoS, rpoN and rrp2 mutants using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol.  An additional phenol-chloroform extraction was performed, after which the RNA was precipitated using isopropanol.  Digestion of contaminating genomic DNA in the RNA samples was performed using RNase-free DNase I (GenHunter Technology, Nashville, TN) and removal of DNA was confirmed by PCR amplification using primers flaB1 specific for the B. burgdorferi flaB gene (see Table S1).  RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) in the Microarray Core Facility in the UT Southwestern Medical Center.

tag: CDNA

source_name: XY424.3 (rrp2 in 5A18 background)


title: cell line differences_1

description: Dye swap and/or biological duplicate of F2, F4, G4


title: effects of ATRA, MN1 switched OFF_3

description: Dye swap and/or biological duplicate of E2, G0, G2

source_name: number 27, exp B


title: effects of ATRA, MN1-TEL is present (ON)_1

description: Dye swap and/or biological duplicate of E8, G6, G8

source_name: number 64, exp A

source_name: number 70, exp A


title: XY rrp2 S6


title: effects of ATRA, MN1 is present (ON)_8

description: Dye swap and/or biological duplicate of E1, D9, F7

source_name: number 40, exp B

source_name: number 46, exp B


title: XY rrp2 S2


title: XY rrp2 S5


title: effects of ATRA, MN1 is present (ON)_4

description: Dye swap and/or biological duplicate of D9, F7, F9

source_name: number 46 exp B


title: effects of ATRA, MN1 switched OFF_1

description: Dye swap and/or biological duplicate of E4, G0, G2

source_name: number 27, exp A


title: XY rrp2 S1


title: effects of ATRA, MN1 switched OFF_2

description: Dye swap and/or biological duplicate of E5, G1, G3

source_name: number 28, exp A

source_name: number 34, exp A


title: rrp2 S6

source_name: rrp2 (297 background)


title: rrp2 S3


title: rrp2 S1


title: rrp2 S2


title: difference between MN1 and MN1-TEL effects_8

description: Dye swap and/or biological duplicate of B9, C1, D5

source_name: number 65, exp B


title: effects of ATRA, MN1 is present (ON)_2

description: Dye swap and/or biological duplicate of E1, F7, F9

source_name: number 40, exp A

source_name: number 46, exp A


title: rrp2 S5


title: effects of ATRA, MN1 is present (ON)_3

description: Dye swap and/or biological duplicate of D8, F6, F8

source_name: number 45, exp B

source_name: number 39, exp B


title: effects of MN1-TEL expression_9

description: Dye swap and/or biological duplicate of B2, B5, D0

source_name: number 52, exp B

source_name: number 64, exp B


title: difference between MN1 and MN1-TEL effects_6

description: Dye swap and/or biological duplicate of B9, C1, D7

source_name: number 65, exp A


title: rrp2 S4


title: rpoN S5

source_name: rpoN


title: effects of ATRA, MN1 is present (ON)_1

description: Dye swap and/or biological duplicate of E0, F6, F8

source_name: number 39, exp A

source_name: number 45, exp A


title: effects of MN1-TEL expression_10

description: Dye swap and/or biological duplicate of B3, B6, D1

source_name: number 53, exp B


title: effects of ATRA, MN1 is present (ON)_6

description: Dye swap and/or biological duplicate of E1, D9, F9


title: difference between MN1 and MN1-TEL effects_11

description: Dye swap and/or biological duplicate of I1, I0, J3

source_name: number 66, exp A

source_name: number 41, exp A


title: difference between MN1 and MN1-TEL effects_7

description: Dye swap and/or biological duplicate of B8, C0, D4


title: difference between MN1 and MN1-TEL effects_5

description: Dye swap and/or biological duplicate of B8, C0, D6

source_name: number 64, exp A


title: effects of MN1-TEL expression_7

description: Dye swap and/or biological duplicate of B2, B5, D2

source_name: number 52, exp A


title: rpoS S4

source_name: rpoS


title: rpoN S3


title: rpoS S5


title: rpoN S1


title: rpoS S6


title: effects of MN1 expression_10

description: Dye swap and/or biological duplicate of A7, B0, C7

source_name: number 28, exp B

source_name: number 40, exp B


title: effects of MN1-TEL expression_8

description: Dye swap and/or biological duplicate of B3, B6, D3

source_name: number 53, exp A


title: rpoS S2


title: effects of MN1 expression_9

description: Dye swap and/or biological duplicate of A6, A9, C6

source_name: number 27, exp B


title: rpoN S2

data_processing: The image  was analyzed using the GenePix program and data then were analyzed with Acuity 4.0 microarray informatics software according to the manufacturer’s instruction (Molecular Devices), using ratio-based normalization method and a cutoff value of a 2-fold change.  Statistical analyses were performed using the one and two-sample significance test (p<0.05) in the Acuity program, which is a two-sample t-test between two groups of arrays. Differentially expressed genes were identified by both fold change and statistical significance.

tag: cDNA


title: effects of TET release in control cell line_10

description: Dye swap and/or biological duplicate of C3, A1, A4

source_name: number 3, exp B

source_name: number 15, exp B


title: effects of MN1 expression_7

description: Dye swap and/or biological duplicate of A6, A9, C8

source_name: number 27, exp A


title: effects of TET release in control cell line_7

description: Dye swap and/or biological duplicate of C4, A0, A3

source_name: number 14, exp A

source_name: number 2, exp.A


title: rpoS S1


title: difference between MN1 and MN1-TEL effects_2

description: Dye swap and/or biological duplicate of H068C1 and H068D5 and H068D7

source_name: number 40, exp A

source_name: number 65, exp A


title: rpoS S3


title: difference between MN1 and MN1-TEL effects_3

description: Dye swap and/or biological duplicate of H068B8 and H068D4 and H068D6

source_name: number 64, exp B

source_name: number 39, exp B


title: difference between MN1 and MN1-TEL effects_4

description: Dye swap and/or biological duplicate of H068B9 and H068D5 and H068D7

source_name: number 65, exp B


title: rpoN S4

source_name: rpoN


title: FNA15_PRE

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description:
Two replicated (dye-swaped) data were combined for analysis
IDC, invasive ductal carcinoma; ILC, invasive lobular carcinoma; LVI, lymphovascular invasion; EIC, extensive intraductal component; ER, estrogen receptor; PR, progesterone receptor; ERBB2, HER2 status. ER, PR, and HER2 status as reported on standard surgical pathology reports were determined by immunohistochemistry, or by fluorescent in situ hybridization for HER2 according to our institutional standard of practice.

hyb_protocol: The generated cDNA probes were then purified and denatured. The labeled targets were hybridized to UHN h19k cDNA microarrays.

scan_protocol: Scanned at 16 bits using the Genepix Axon Scanner 4000A (Molecular Devices Corp) at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Devices Corp).

data_processing: Each quantified output file in GenePix report (GPR) format was directly transferred into Acuity 4.0 (Molecular Devices Corp.) for analysis. After Lowess slide normalization, any uninformative microarray data were flagged and filtered. The dye-swaped signal log2 ratios were inverted before the data of the replicate were combined, resulting in 16 PRE and 16 POST specimens for analysis finally. Probes with minimal changes in expression level (Log2 ratio >=1 or <=-1 in not more than 2 tumors) were removed, resulting in a list of 4,056 probes in the matrix dataset.

label: Cy5, Cy3

source_name: Pre-operative, palpable invasive breast cancer

label_protocol: The amplified RNA species from FNABs and an amplified Universal Human Reference RNA (Stratagene; La Jolla, CA) were directly labeled using cyanine 5 and cyanine 3 fluorescent dyes from 5 to 10μg of RNA according to the UHN Microarray Centre instructions. Dye-swap technical replicate was carried out for every FNABs.

extract_protocol: Total RNA was extracted using RNAeasy Micro kit (Qiagen) then amplified using the MessageAmp aRNA kit (Ambion) according to the manufacturer's instructions.

tag: Patient No.

tag: Tumor Type

value: IDC

tag: Tumor Size(cm)

tag: Tumor Grade

tag: LVI

tag: EIC

tag: ER

tag: PR

tag: palpable invasive breast cancer

label: Cy3, Cy5

source_name: Universal RNA

tag: Stratagene Universal RNA


title: effects of TET release in control cell line_9

description: Dye swap and/or biological duplicate of C2, A0, A3

source_name: number 2, exp B

tag: see experimental_design.jpg

tag: UHD is a derivative of U937 and serves as control cell line

source_name: number 14, exp B


title: difference between MN1 and MN1-TEL effects_1

description: Dye swap and/or biological duplicate of H068C0 and H068D4 and H068D6

source_name: number 39, exp A

tag: MN1 is a derivative of U937 and MN1 is under control of TET system

source_name: number 64, exp A

tag: MN1-TEL is a derivative of U937 and MN1-TEL is under control of TET system


title: effects of MN1-TEL expression_4

description: Dye swap and/or biological duplicate of  H068D0 and  H068D2 and H068B2

source_name: number 52, exp B


title: effects of TET release in control cell line_8

description: Dye swap and/or biological duplicate of C5, A1, A4

source_name: number 15, exp A

source_name: number 3, exp A


title: FNA16_POST

source_name: Post-operative, palpable invasive breast cancer


title: effects of MN1-TEL expression_5

description: Dye swap and/or biological duplicate of  H068D1 and  H068D3 and H068B3

source_name: number 53, exp B


title: FNA14_PRE


title: FNA15_POST


title: FNA13_POST


title: FNA12_PRE


title: FNA14_POST

value: IDC/ILC


title: effects of MN1-TEL expression_6

description: Dye swap and/or biological duplicate of H068B4 and H068H8 and H068H9

source_name: number 66, exp B

source_name: number 54, exp B


title: FNA13_PRE


title: effects of MN1-TEL expression_2

description: Dye swap and/or biological duplicate of  H068D1 and  H068D3 and H068B6

source_name: number 53, exp A

source_name: number 65, exp A


title: FNA12_POST


title: effects of MN1 expression_6

description: Dye swap and/or biological duplicate of H068A8 and H068H6 and H068H7

source_name: number 41, exp B

source_name: number 29, exp B


title: effects of MN1-TEL expression_1

description: Dye swap and/or biological duplicate of  H068D0 and  H068D2 and H068B5

source_name: number 52, exp A


title: FNA11_PRE

source_name: Pre-operative, palpable invasive breast cancer

source_name: Universal RNA


title: FNA11_POST


title: effects of MN1 expression_5

description: Dye swap and/or biological duplicate of  H068C7 and  H068C9 and H068A7

source_name: number 40, exp B

source_name: number 28, exp B


title: effects of MN1-TEL expression_3

description: Dye swap and/or biological duplicate of H068B7 and H068H8 and H068H9

source_name: number 54, exp A

source_name: number 66, exp A


title: FNA16_PRE


title: FNA10_POST


title: FNA09_PRE


title: effects of MN1 expression_4

description: Dye swap and/or biological duplicate of  H068C6 and  H068C8 and H068A6

source_name: number 39, exp B

source_name: number 27, exp B


title: effects of MN1 expression_8

description: Dye swap and/or biological duplicate of A7, B0, C9

source_name: number 40, exp A

source_name: number 28, exp A


title: FNA10_PRE


title: FNA08_POST

description:
Two replicated data were combined for analysis
IDC, invasive ductal carcinoma; ILC, invasive lobular carcinoma; LVI, lymphovascular invasion; EIC, extensive intraductal component; ER, estrogen receptor; PR, progesterone receptor; ERBB2, HER2 status. ER, PR, and HER2 status as reported on standard surgical pathology reports were determined by immunohistochemistry, or by fluorescent in situ hybridization for HER2 according to our institutional standard of practice.

label: Cy5, Cy5

source_name: Post-operative, palpable invasive breast cancer

label: Cy3, Cy3


title: FNA07_POST


title: FNA09_POST


title: FNA07_PRE


title: effects of MN1 expression_2

description: Dye swap and/or biological duplicate of  H068C7 and  H068C9 and H068B0


title: FNA08_PRE


title: FNA06_PRE


title: FNA05_PRE


title: effects of ATRA, MN1 is present (ON)_7

description: Dye swap and/or biological duplicate of E0, D8, F6

source_name: number 45. exp B


title: effects of MN1 expression_3

description: Dye swap and/or biological duplicate of H068B1 and H068H6 and H068H7

source_name: number 29, exp A

source_name: number 41, exp A


title: FNA06_POST

description:
Two replicated (dye-swaped) data were combined for analysis
IDC, invasive ductal carcinoma; ILC, invasive lobular carcinoma; LVI, lymphovascular invasion; EIC, extensive intraductal component; ER, estrogen receptor; PR, progesterone receptor; ERBB2, HER2 status. ER, PR, and HER2 status as reported on standard surgical pathology reports were determined by immunohistochemistry, or by fluorescent in situ hybridization for HER2 according to our institutional standard of practice.


title: effects of MN1 expression_1

description: Dye swap and/or biological duplicate of  H068C6 and  H068C8 and H068A9

source_name: number 27, exp A

source_name: number 39, exp A


title: FNA05_POST


title: effects of TET release in control cell line_5

description: Dye swap and/or biological duplicate of  H068C3 and  H068C5 and H068A1

source_name: number 15, exp B

source_name: number 3, exp B


title: effects of TET release in control cell line_6

description: Dye swap and/or biological duplicate of  H068A2 and  H068J4 and H068J5

source_name: number 16, exp B

source_name: number 4, exp B


title: FNA04_POST

source_name: Universal RNA


title: FNA03_PRE

source_name: Pre-operative, palpable invasive breast cancer


title: FNA02_PRE


title: FNA01_PRE


title: FNA02_POST


title: FNA04_PRE


title: effects of TET release in control cell line_2

description: Dye swap and/or biological duplicate of  H068C3 and  H068C5 and H068A4

source_name: number 3, exp A

source_name: number 15, exp A


title: effects of TET release in control cell line_4

description: Dye swap and/or biological duplicate of  H068C2 and  H068C4 and H068A0

source_name: number 14, exp B

source_name: number 2, exp B


title: FNA03_POST


title: MXC_liver_1

status: Public on Sep 08 2008

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Biological replicate 1 of 4: treated liver

hyb_protocol: All protocols label, hybridization, and scanning are found in can be found One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com

data_processing: Lowess normalization in JMP genomics, smooting factor set at 0.2

organism: Micropterus salmoides

source_name: treated liver; 48 hours

extract_protocol: RNA STAT60 protocol (Tel-test, Friendswood, TX)

treatment_protocol: LMB single i.p. injected methoxchlor for 48 hours

tag: male


title: CTRL_liver_4

description: Biological replicate 4 of 4: control liver

scan_protocol: All protocols label, hybridization, and scanning are found in can be found One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com

source_name: control liver

treatment_protocol: control


title: MXC_liver_3

description: Biological replicate 3 of 4: treated liver

label_protocol: All protocols label, hybridization, and scanning are found in can be found One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com


title: FNA01_POST

source_name: Post-operative, palpable invasive breast cancer


title: effects of TET release in control cell line_3

description: Dye swap and/or biological duplicate of  H068A5 and  H068J4 and H068J5

source_name: number 4, exp A

source_name: number 16, exp A


title: CTRL_liver_2

description: Biological replicate 2 of 4: control liver


title: MXC_liver_2

description: Biological replicate 2 of 4: treated liver


title: MXC_liver_4

description: Biological replicate 4 of 4: treated liver


title: CTRL_liver_3

description: Biological replicate 3 of 4: control liver


title: Colon_treated_rep4

city: Amsterdam

first: Antonie

last: Zwiers

address: Van der Boechorststraat 7

department: MCBI

institute: Vrije Universiteit Medical Center

description: Biological replicate 4 of 4 treated

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner (Agilent Technologies). Spots were quantified by Imagene 5.5.4 software (Biodiscovery Ltd, Marina del Rey, CA, USA), using the default settings.

data_processing: The BioConductor package Limma (Smyth and Speed 2003) version 2.6.0 was used to perform data processing. Background correction according to 'Edwards' was applied with an offset of 30. Intensity-dependent normalization using local estimation (‘Loess’) was performed separately on each sector of the array. In addition, ‘scale’ (or ‘quantile’) normalization was applied, which makes the data more comparable across different arrays. Spots were included in the analysis when in at least 80% of the microarrays a reliable data point was obtained for that element (defined by a minimal signal intensity > 50 for both Cy3 and Cy5). Data are expressed as normalized log2 ratios of fluorescence intensities of the experimental over the reference sample. The use of a common reference sample allows comparison of the relative expression levels across all samples. Therefore, the expression levels were median centered, i.e. each spotted element was expressed relative to the median expression level of that element across all samples. Genes represented more than once on the microarrays were averaged from sequences with the same Unigene cluster ID.

source_name: Colon treated

label_protocol: RNA labeling protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Strain

value: SJL/J

tag: Gender

value: male

tag: Age

value: 6 weeks

tag: Tissue

value: Colon

source_name: Common reference pool from pooled colon derived total RNA of treated and non-treated mice

value: pooled colon


title: Colon_treated_rep1

description: Biological replicate 1 of 4 treated


title: Colon_NonTreated_rep4

description: Biological replicate 4 of 4 Non-treated

source_name: Colon Non-treated


title: CTRL_liver_1

description: Biological replicate 1 of 4: control liver


title: Colon_NonTreated_rep3

description: Biological replicate 3 of 4 Non-treated


title: N2aF1_vs_N2apcl

city: Paris

first: Marc-Henri

last: Stern

address: 26 rue d'Ulm

department: Research Dept

country: France

institute: INSERM/Curie Institute

description: Laser power 100%; resolution 10 microm; PMT Cy5 : 780; PMT Cy3 : 600.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

scan_protocol: After drying by centrifugation, slides were read with GenePix 4000B scanner (Molecular Devices, Sunnyvale, California, USA). Results were analysed with GenePix Pro 5.1 software.

data_processing: MANOR (Neuvial et al, 2006 BMC Bioinformatics 7, 264)

source_name: N2aF1 subline

label_protocol: After DpnII digestion (New England Biolabs, Ipswich, Massassuchets, USA) and purification with PCR Purification Kit (Qiagen, Oslo, Norway), 1 microg of tested DNA was labeled by random priming (BioPrime DNA Labeling System Kit, Invitrogen, Carlsbad, California, USA) with dCTP-Cy5 (GE Healthcare, Piscataway, New-Jersey, USA). The reaction was performed at 37°C for 3 hr and purified on Microcon YM30 (Millipore).

growth_protocol: Cells were maintained in DMEM with glutamax, 1.0 mM sodium pyruvate and 1% L-glutamin penicillin/streptomycin (Invitrogen Life Technologies, Cergy Pontoise, France) supplemented with 10% heat-inactivated fetal calf serum, in an atmosphere of 5% CO2, 95% air.

extract_protocol: DNA was phenol/chloroform extracted and treated with ribonuclease A (Fermentas, Burlington, Ontario, Canada) as recommended by the manufacturer.

tag: N2aF1 subline, resistant to 22L prion strain

label_protocol: After DpnII digestion (New England Biolabs, Ipswich, Massassuchets, USA) and purification with PCR Purification Kit (Qiagen, Oslo, Norway), 1 microg of reference DNA was labeled by random priming (BioPrime DNA Labeling System Kit, Invitrogen, Carlsbad, California, USA) with dCTP-Cy3 (GE Healthcare, Piscataway, New-Jersey, USA). The reaction was performed at 37°C for 3 hr and purified on Microcon YM30 (Millipore).

tag: N2a parental cell line


title: N2aG9_vs_N2apcl

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50 % formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37°C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: N2aG9 subline

tag: N2aG9 subline, susceptible to 22L prion strain


title: N2aF1_vs_A/HeJ

description: laser power 100%; resolution 10 microm; PMT Cy5 : 750; PMT Cy3 : 600.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt’s solution) and put on treated microarray slides. After 24hr hybridization at 37C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: A/HeJ

tag: A/HeJ is the albino mouse strain in which arose the spontaneous neuroblastoma at the origin of the clone N2a.


title: MOCK RIP (Prot.A) N.2A

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78040.gif
Antibody used in IP: no

hyb_protocol: Cy3- and Cy5-labeled aaRNA probes were mixed and applied to arrays in hybridization solution (3x SSC, 20 ug poly(A) RNA [Invitrogen], 20 ug yeast tRNA [Invitrogen], 20 ug Human Cot-1 DNA [Invitrogen], 20 mM HEPES [pH 7.0] and 0.3% SDS) for 18 h at 65°C. The arrays were then washed sequentially in 400 ml of 2x SSC with 0.1% SDS, 1x SSC, and 0.2x SSC. The first wash was performed for 5 min at 65°C, the subsequent washes were performed for 5 min at RT. The arrays were dried by centrifugation and immediately scanned.

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 11:43:57; Parameter PMT Volts = 380; Parameter Scan Date = 2007-12-12; Parameter Pixel Size = 10; Parameter Laser on time = 30914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 11:43:57; Parameter PMT Volts = 400; Parameter Scan Date = 2007-12-12; Parameter Pixel Size = 10; Parameter Laser on time = 30914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

data_processing: The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel. To identify transcripts that were specifically enriched by association with PUM2, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays. VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aaRNA from extract

label_protocol: Poly-adenylated RNAs were amplified in the presence of aminoallyl-UTP with Amino Allyl MessageAmp II aRNA kit (Ambion). For this purpose, 500 ng total RNA from extracts and half (50-100 ng) of the immunopurified RNAs were used for amplification. 8 ug of the amplified RNAs (aaRNA) were fluorescently labeled with NHS-monoester Cy3 and Cy5 dyes (GE HealthSciences), except for mock RNA samples, where an aaRNA amount proportional to the yield obtained from corresponding PUM affinity isolates was used.

extract_protocol: Total RNA was isolated from cell extracts and immunopurified samples with the mirVanaTM PARISTM kit (Ambion). RNA was quantified with a NanoDrop device (Witeg AG).

tag: aaRNA from extract

source_name: aaRNA from MOCK RIP

tag: aaRNA from MOCK RIP


title: PUM2 RIP N.2A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76366.gif
Antibody used in IP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.00; Parameter Scan Time = 11:24:22; Parameter PMT Volts = 360; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28143; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.00; Parameter Scan Time = 11:24:22; Parameter PMT Volts = 380; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28143; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

source_name: aaRNA from PUM2 RIP

tag: aaRNA from PUM2 RIP


title: N2a58_vs_N2apcl

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37°C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: N2a58 subline

tag: Subline N2a58, susceptible to prion


title: N2aR10_vs_N2apcl

description: Laser power 100%; resolution 10 microm; PMT Cy5 : 830; PMT Cy3 : 660.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10 % dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: N2aR10 subline

tag: N2aR10 subline, susceptible to 22L prion strain


title: N2aG9_vs_A/HeJ

description: Laser power 100%; resolution 10 microm; PMT Cy5 : 750; PMT Cy3 : 600.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65C, and for 5 min in 0.5X SSC, 0.03 % SDS at 45°C.


title: MOCK RIP (Prot.A) N.1A

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76365.gif
Antibody used in IP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 11:42:46; Parameter PMT Volts = 330; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28162; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 11:42:46; Parameter PMT Volts = 390; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28162; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: PUM2 RIP N.3A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78041.gif
Antibody used in IP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 12:05:51; Parameter PMT Volts = 390; Parameter Scan Date = 2007-12-12; Parameter Pixel Size = 10; Parameter Laser on time = 30936; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.05; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 12:05:51; Parameter PMT Volts = 390; Parameter Scan Date = 2007-12-12; Parameter Pixel Size = 10; Parameter Laser on time = 30935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: Colon_treated_rep3

description: Biological replicate 3 of 4 treated


title: Colon_NonTreated_rep2

description: Biological replicate 2 of 4 Non-treated


title: MOCK RIP (Prot.A) N.3A

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78968.gif
Antibody used in IP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.50; Parameter Scan Time = 10:10:44; Parameter PMT Volts = 380; Parameter Scan Date = 2008-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 33086; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.50; Parameter Scan Time = 10:10:44; Parameter PMT Volts = 400; Parameter Scan Date = 2008-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 33085; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: PUM2 RIP N.1A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76364.gif
Antibody used in IP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.25; Parameter Scan Time = 12:01:05; Parameter PMT Volts = 330; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28180; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.25; Parameter Scan Time = 12:01:05; Parameter PMT Volts = 390; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 28180; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: N2aD11_vs_N2apcl

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37C in 20 microL of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37°C, slides were washed for 5min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: N2aD11 subline

tag: N2aD11 subline, susceptible to 22L prion strain


title: effects of TET release in control cell line_1

description: Dye swap and/or biological duplicate of  H068C2 and  H068C4 and H068A3

source_name: number 2, exp.A

tag: see experimental_design.jpg

tag: UHD is a derivative of U937 and serves as control cell line

source_name: number 14, exp A


title: Colon_treated_rep2

description: Biological replicate 2 of 4 treated


title: PUM1 RIP N.3B

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76042.gif
Antibody used in RIP: yes

hyb_protocol: Cy3- and Cy5-labeled aaRNA probes were mixed and applied to arrays in hybridization solution (3x SSC, 20 ug poly(A) RNA [Invitrogen], 20 ug yeast tRNA [Invitrogen], 20 ug Human Cot-1 DNA [Invitrogen], 20 mM HEPES [pH 7.0] and 0.3% SDS) for 18 h at 65 degree C. The arrays were then washed sequentially in 400 ml of 2x SSC with 0.1% SDS, 1x SSC, and 0.2x SSC. The first wash was performed for 5 min at 65 degree C, the subsequent washes were performed for 5 min at RT. The arrays were dried by centrifugation and immediately scanned.

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.63; Parameter Scan Time = 10:56:23; Parameter PMT Volts = 350; Parameter Scan Date = 2007-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 26657; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.63; Parameter Scan Time = 10:56:23; Parameter PMT Volts = 380; Parameter Scan Date = 2007-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 26656; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

data_processing:
Arrays were normalized computationally by the Stanford Microarray Database (SMD). The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel.To identify transcripts that were specifically enriched by association with PUM1, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aaRNA from PUM1 RIP

tag: aaRNA from PUM1 RIP


title: N2apcl_vs_A/HeJ

description: Laser power 100%; resolution 10 microm; PMT Cy5 : 740; PMT Cy3 : 600.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microL of hybridization buffer (50 % formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt’s solution) and put on treated microarray slides. After 24hr hybridization at 37°C, slides were washed for 5 min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.


title: N2aR4_vs_N2apcl

description: laser power 100%; resolution 10 microm; PMT Cy5 : 830; PMT Cy3 : 670.

hyb_protocol: After denaturation at 92°C, these DNAs were pre-hybridized with 80 microg of mouse Cot-1 DNA (Roche) for 30 min at 37°C in 20 microl of hybridization buffer (50% formamide, 40 mM NaH2PO4, 0.1% SDS, 10% dextran sulfate, 2X SSC, Denhardt s solution) and put on treated microarray slides. After 24hr hybridization at 37C, slides were washed for 5 min in 0.5X SSC, 0.03% SDS at 65°C, and for 5 min in 0.5X SSC, 0.03% SDS at 45°C.

source_name: N2aR4 subline

tag: N2aR4 subline, resistant to 22L prion strain

growth_protocol: Cells were maintained in DMEM with glutamax, 1.0 mM sodium pyruvate and 1% L-glutamin penicillin/streptomycin (Invitrogen Life Technologies, Cergy Pontoise, France) supplemented with 10% heat-inactivated fetal calf serum, in an atmosphere of 5% CO2, 95% air