title: PTZ-LEV_10-2

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. : 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-LEV_10-4(Dyeswap)

status: Public on May 03 2008

type: RNA

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: The data in the file is ratio normalized.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, males, unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle, and flies from identical cultures were first allowed to lay eggs in bottles containing NF. Flies were transferred to fresh bottle every 12 hr. After discarding first 4 batches of bottles, only those flies that emerged in subsequent bottles were used.Flies were collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

tag: Strain

value: Oregon R

tag: Sex

value: Male

tag: Tissue

value: Head

source_name: Drosophila melanogaster, males, unmated, treated

extract_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Levetiracetam (LEV)(mixed in normal fly food at a concentration of 8 and 5 mg/ml, respectively) , in the order: PTZ-7days+ LEV-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: DS-4-3

status: Public on May 01 2008

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description: dog stromal cell line 4, cultured, biological replicate 3

hyb_protocol: standard Affymetrix protocol and reagents

scan_protocol: standard Affymetrix protocol and instruments

data_processing: Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all simples, was also applied.

label: biotin

organism: Canis lupus familiaris

source_name: cultured stromal cell line 4

label_protocol: cRNA was prepared from 8-10 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

growth_protocol: Cloned cell lines were cultured in 10 cm plates for 2-3 days to 80% confluency in RPMI1640 medium supplemented with 10% FBS/2mM glutamine at 37ºC in 5% CO2 . Cells were trypsinized, centrifuged and lysed or lysed directly in the plate with Qiagen RLT buffer.

extract_protocol: Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.

tag: stromal cell line


title: DS-4-1

description: dog stromal cell line 4, cultured, biological replicate 1


title: woodchuck 6337 HCC, rat array

city: Cleveland

first: Fangjing

last: Wang

state: OH

address: Bishop building, Room s731, UH

department: Biomedical Engineering

institute: case Western Reserve University

description: cross-specieis hybridization using Affymetrix rat 230-2  GeneChips® on woodchucks

hyb_protocol: After purification and fragmentation, 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail containing spiked transcript controls. 200 ul of cocktail was loaded onto Affymetrix rat microarrays (Santa Clara, CA) and hybridized for 16 hr at 45 C with agitation.

scan_protocol: Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 450. Arrays were scanned using the high resolution Gene Array scanner 3000.

data_processing: the hybridization results for each transduced/untransduced sample pair were first analyzed using GCOS 1.2 from Affymetrix (Santa Clara, CA). The genes that were differentially expressed in all the sample pairs were considered, and were further analyzed by SAM (developed by the Stanford University). A fold change of 1.5 and delta value above 1.0 was used as the criteria for SAM analysis.

organism: Marmota monax

source_name: woodchuck liver HCC tumor confirmed with ultrasound, rat array

label_protocol: 3 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA. After second strand synthesis, double stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

growth_protocol: In a saparate room at ARC facilty, with dialy water and food change, monitor dialy.

extract_protocol: Qiagen RNeasy Midi Kit according to the protocols provided by the supplier with respect to tissues

treatment_protocol: woodchuck were infected with WHC virus at birth, 1-2 years old, 2.3-5kg, were euthanized using FatalPlus (Vortech Pharmaceuticals, Ltd., Dearborn, MI). All experiments were approved in accordance with the guidelines and recommendations of the Institutional Animal Care and Use Committees of Case Western Reserve University (Cleveland, OH) and Cornell University (Ithaca, NY). HCCs and surrounding liver tissuesLiver tissues were immediately removed from the animals. A pathaologist separated non-cancerous liver and HCC. Tissues were , snap- frozen in liquid nitrogen and stored at -80 C.


title: woodchuck 6337 normal tissue surrounding the liver HCC, rat array

source_name: woodchuck liver tissue with no HCC, but surrouding the HCCs, rat array


title: PTZ-ETH_10-2

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Ethosuximide (ETH)(mixed in normal fly food at a concentration of 8 and 3.48 mg/ml, respectively) in the order: PTZ-7days+ ETH-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

label_protocol: Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: DS-3-3

description: dog stromal cell line 3, cultured, biological replicate 3

source_name: cultured stromal cell line 3


title: DS-2-2

description: dog stromal cell line 2, cultured, biological replicate 2

source_name: cultured stromal cell line 2


title: woodchuck 5904 HCC, rat array

tag: woodchuck liver HCC tumor confirmed with ultrasound


title: DS-3-1

description: dog stromal cell line 3, cultured, biological replicate 1


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 24 h, replicate 3

city: Vancouver

first: Justin

middle: Christian

last: LeBlanc

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 24 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

scan_protocol: Microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments) and spot intensities were quantified using Imagene 6.0 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using GeneSpring version 7.2 (Silicon Genetics) by the intensity-dependent Lowess method, with 20% of the data used for smoothing.  Replicate spots of the same type were combined to yield a single normalized ratio, which is output for the first ID_REF number representing that spot type.

organism: Rhodococcus jostii RHA1

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 24 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 24 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.

growth_protocol: Grown at 30°C and 200 rpm in W minimal medium amended with 20 mM sodium benzoate.

extract_protocol: Cell pellets were vortexed with glass beads, hot phenol, and SDS at final concentrations of 14.3% and 0.9% (vol/vol) respectively.  Debris was precipitated with acetate followed by the addition of 4.0 mL phenol-chloroform (1:1, vol/vol).  Nucleic acids were precipitated with acetate plus isopropanol, treated with DNase, and purified with an RNeasy mini column (Qiagen).

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 at time zero (just after filtration onto nitrocellulose membrane)


title: DS-3-2

description: dog stromal cell line 3, cultured, biological replicate 2


title: DS-2-1

description: dog stromal cell line 2, cultured, biological replicate 1


title: DS-2-3

description: dog stromal cell line 2, cultured, biological replicate 3


title: DS-4-2

description: dog stromal cell line 4, cultured, biological replicate 2


title: DS-1-3

description: dog stromal cell line 1, cultured, biological replicate 3

source_name: cultured stromal cell line 1


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 48 h, replicate 2

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 48 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 48 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 48 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 at time zero (just after filtration onto nitrocellulose membrane)


title: DS-1-1

description: dog stromal cell line 1, cultured, biological replicate 1


title: woodchuck 6361 normal tissue surrounding the liver HCC, rat array

tag: woodchuck liver tissue with no HCC, but surrouding the HCCs


title: ES 129.3 Passage12  LIF+,RA

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description:
This arrays was previously submitted as GSM137386 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.

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

source_name: ES

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: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.

tag: embryonic stem cell

tag: Gender

value: male

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: woodchuck 6361 HCC, rat array


title: MG1.19  Passage 5  LIF+,RA

description:
This arrays was previously submitted as GSM137371 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.


title: ES 129.3 Passage12  LIF-

description:
This arrays was previously submitted as GSM137385 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.


title: woodchuck 5904 normal tissue surrounding the liver HCC, rat array


title: MG1.19  Passage 5  LIF+

description:
This arrays was previously submitted as GSM137369 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.


title: ES 129.3 Passage12  LIF+

description:
This arrays was previously submitted as GSM137384 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 48 h, replicate 3

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 48 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 48 h


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 48 h, replicate 1


title: MG1.19  Passage 5  LIF-

description:
This arrays was previously submitted as GSM137370 and
was normalized with arrays in GSE5914. Since we are
reusing it in this experiment we re-submit it as
a new sample as the normalized values are different
from the previous submitted values.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 24 h, replicate 1

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 24 h


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 24 h, replicate 2

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 24 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 12 h, replicate 2

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 12 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 12 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 12 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 12 h, replicate 1

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 12 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 12 h


title: DS-1-2

description: dog stromal cell line 1, cultured, biological replicate 2


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 6 h, replicate 1

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 6 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 6 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 6 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 6 h, replicate 2

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 6 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 6 h


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 12 h, replicate 3


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 1 h, replicate 2

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 1 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 1 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 1 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 6 h, replicate 3


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 1 h, replicate 1

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 1 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 1 h


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 1 h, replicate 3


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 3 h, replicate 3

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 3 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 3 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 3 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 3 h, replicate 2

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 3 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 3 h


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 30 min, replicate 2

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 30 min and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions:  2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C.  Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 30 min

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 30 min treatment was labelled with Cy5 rather than Cy3) to control for dye bias.


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 30 min, replicate 3

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 30 min treatment was labelled with Cy3 rather than Cy5) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 desiccated (20% RH) for 30 min


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 3 h, replicate 1


title: Rhodococcus jostii RHA1 desiccated at 20% relative humidity for 30 min, replicate 1

growth_protocol: Grown at 30°C and 200 rpm in basal salts medium amended with 20 mM sodium benzoate.


title: NA15510/ABC13_GPL6292

type: genomic

city: Santa Clara

first: Nick

last: Sampas

state: CA

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

description: Female, Yoruba

hyb_protocol: See manufacturer website: <http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=52010>

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing: Agilent Feature Extraction v9.1, default CGH parameters

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Agilent DNA labeling kit

extract_protocol: Performed by the Coriell Cell Repository

tag: Coriell Reference sample

tag: Coriell sample


title: ABC10/NA15510_GPL6292

description: Female, Yoruba


title: NA15510/NA15510 Replicate 3_GPL6292

description: Female, reference


title: ABC9/NA15510_GPL6292

description: Female, Japan


title: NA15510/ABC10_GPL6292

description: Female, Yoruba


title: NA15510/NA15510 Replicate 2_GPL6292

description: Female, reference


title: ABC8/NA15510_GPL6292

description: Male, Yoruba


title: NA15511/ABC11_GPL6292

description: Female, China


title: NA15510/ABC8_GPL6292

description: Male, Yoruba


title: NA15510/NA15510 Replicate 3_GPL5884

description: Female, reference


title: ABC10/NA15510_GPL5884

description: Female, Yoruba


title: ABC7/NA15510_GPL6292

description: Female, Yoruba


title: ABC13/NA15510_GPL6292

description: Female, Yoruba


title: NA15510/ABC7_GPL6292

description: Female, Yoruba


title: NA15510/ABC10_GPL5884

description: Female, Yoruba


title: NA15510/NA15510_GPL6292

description: Female, reference


title: NA15510/ABC12_GPL6292

description: Female, CEPH


title: NA15510/ABC13_GPL5884

description: Female, Yoruba


title: ABC12/NA15510_GPL6292

description: Female, CEPH


title: ABC13/NA15510_GPL5884

description: Female, Yoruba


title: NA15511/ABC9_GPL6292

description: Female, Japan


title: ABC11/NA15510_GPL6292

description: Female, China


title: NA15510/ABC9_GPL5884

description: Female, Japan


title: NA15510/ABC14_GPL6292

description: Female, CEPH


title: ABC14/NA15510_GPL6292

description: Female, CEPH


title: se replicateA

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: see Laubinger et al., 2008, for details

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: Data were quantile normalized and repetitive probes were deleted (see Laubinger et al., 2008, for details)

label: Biotin

organism: Arabidopsis thaliana

source_name: se mutants

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: For synthesis of targets tiling arrays, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

tag: se mutants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: cbp20 replicateA

description: see Laubinger et al., 2008, for details

source_name: cbp20 mutants

tag: cbp20 mutants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: Wild type replicateA

description: see Laubinger et al., 2008, for details

source_name: wild type

tag: wild type plants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: HeLa_NegativeIP_Rep2

city: Durham

first: Adam

middle: R

last: Morris

state: NC

address: Box 3020 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke Uniersity Medical Center

description: Arrays were printed at the Duke Microarray Facility using the Genomics Solutions OmniGrid 300 Arrayer. The arrays contain the Human Operon v3.0.2 arrays (Oligo Source) that possess 34,602 unique optimized 70-mers. RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies). RNA from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, HeLa derived RNA samples were labeled with Cy5 and reference samples were labeled with Cy3. NaOH was used to destroy residual RNA. Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies and scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

scan_protocol: The array was scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

data_processing: All arrays were subject to background subtraction followed by loess normalization within each array and scale normalization across all arrays using the arrayMagic package in R (Buness A., Huber W., Steiner K., Sueltmann H., Poustka A. arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics 2005 21, 554–556). KNN impute package in GenePattern (Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500) was used to impute missing data if a probe had intensity values for at least half the samples. Otherwise the probes were excluded from analysis. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates.

source_name: Negative (preimmune goat serum) IP from HeLa cells

label_protocol: Total RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies). RNA from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, HeLa derived RNA samples were labeled with Cy5 and reference samples were labeled with Cy3.

extract_protocol: total RNA was prepared using TRIzol reagent as instructed and 10µg of total RNA or RNA extracted from an IP using 10µg of antibody was used per reaction

tag: HeLa S3 cell line


title: HeLa_Total_RNA_Rep3

hyb_protocol: In all cases, HeLa derived RNA samples were labeled with Cy5 and reference samples were labeled with Cy3. NaOH was used to destroy residual RNA. Sample and reference cDNA were then pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies and scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

source_name: Total RNA from HeLa cells

source_name: Universal Human Reference RNA, Stratagene


title: HeLa_NegativeIP_Rep3

tag: Universal Human Reference RNA, Stratagene


title: HeLa_Total_RNA_Rep1

tag: HeLa S3 cells


title: cbp20 replicateB

description: see Laubinger et al., 2008, for details


title: abh1 replicateC

description: see Laubinger et al., 2008, for details

source_name: abh1 mutants

tag: abh1 mutants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: abh1 replicateB

description: see Laubinger et al., 2008, for details

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol wash protocol FS450_0001.


title: Wild type replicateB

description: see Laubinger et al., 2008, for details

source_name: Wild type

tag: Wild type plants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: HeLa_NegativeIP_Rep1


title: se replicateB

description: see Laubinger et al., 2008, for details


title: se replicateC

description: see Laubinger et al., 2008, for details


title: NA15510/NA15510 Replicate 2_GPL5884

description: Female, reference


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 48 h, replicate 3

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 48 h

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 at time zero (just after filtration onto nitrocellulose membrane)


title: HeLa_Pum1IP_Rep2

source_name: Pum1 IP from HeLa cells


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 48 h, replicate 2

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 48 h treatment was labelled with Cy5 rather than Cy3) to control for dye bias.

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 48 h

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 at time zero (just after filtration onto nitrocellulose membrane)


title: HeLa_Total_RNA_Rep2


title: HeLa_Pum1IP_Rep3


title: ABC9/NA15510_GPL5884

description: Female, Japan


title: HeLa_Pum1IP_Rep1


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 48 h, replicate 1


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 24 h, replicate 1

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 24 h

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For one of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 24 h treatment was labelled with Cy3 rather than Cy5) to control for dye bias.


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 12 h, replicate 3

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 12 h


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 12 h, replicate 1

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 12 h


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 24 h, replicate 3

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 24 h


title: ABC8/NA15510_GPL5884

description: Male, Yoruba


title: NA15510/ABC8_GPL5884

description: Male, Yoruba


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 12 h, replicate 2


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 6 h, replicate 2

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 6 h


title: Wild type replicateC

description: see Laubinger et al., 2008, for details


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 24 h, replicate 2


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 6 h, replicate 1

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 6 h


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 6 h, replicate 3


title: NA15510/NA15510_GPL5884

description: Female, reference


title: ABC11/NA15510_GPL5884

description: Female, China


title: ABC7/NA15510_GPL5884

description: Female, Yoruba


title: NA15510/ABC14_GPL5884

description: Female, CEPH


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 3 h, replicate 3

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 3 h


title: EcR DamID, replicate 2, slide 13378 Treatment

city: New Haven

first: Zareen

last: Gauhar

state: CT

address: 333 Cedar St, 386 NSB

department: Genetics

institute: Yale

description: Embryonic Drosophila cells, Kc167 cells

hyb_protocol: Samples were hybridized to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed as described the arrays were washed on an orbital platform in non-stringent buffer (6x SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45°C. This was followed by a 30 second wash in ice cold stringent buffer. The arrays were dried in an eppindorf centrifuge.

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Axon 4000B laser scanner) at 5 µm resolution and intensity data were extracted with NimbleScan software (NimbleGen Systems).

data_processing: unprocessed raw signal

source_name: Embryonic Drosophila cells, Kc167 cells, expressing EcR-Dam

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

extract_protocol: Sample extraction was performed as previously described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: EcR-Dam (EXPERIMENTAL)


title: NA15510/ABC12_GPL5884

description: Female, CEPH


title: NA15510/ABC11_GPL5884

description: Female, China


title: NA15510/ABC7_GPL5884

description: Female, Yoruba


title: ABC12/NA15510_GPL5884

description: Female, CEPH


title: EcR DamID, replicate 3, slide 14458 Treatment

description: Embryonic Drosophila cells, Kc167 cells


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 1 h, replicate 1

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 1 h


title: EcR DamID, replicate 3, slide 14458 Reference

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam (REFERENCE)


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 1 h, replicate 3

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 1 h


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 3 h, replicate 1

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 3 h


title: ABC14/NA15510_GPL5884

description: Female, CEPH

tag: Coriell sample

tag: Coriell Reference sample


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 30 min, replicate 2

source_name: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 30 min

label_protocol: Cy-labelled cDNA was prepared by indirect labelling.  For two of the three hybridizations, the Cy3/Cy5 dyes were reversed (i.e., cDNA from the T = 30 min treatment was labelled with Cy5 rather than Cy3) to control for dye bias.


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 30 min, replicate 3

tag: mid-exponential phase, benzoate-grown Rhodococcus jostii RHA1 incubated at 100% relative humidity (30°C) for 30 min


title: EcR DamID, replicate 2, slide 13378 Reference

description: Embryonic Drosophila cells, Kc167 cells


title: C_080306_02_PDS283_W E

status: Public on Apr 30 2008

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: Control genomic dna (untreated)

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software; linearly scaled to intesity of 500, 2-sided upper quantile normalization.

source_name: PBLC;UWStam:PBLC;Lymphocyte;normal;blood;unknown/unknown;RPMI;PBLC;Control genomic dna (untreated)

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K

tag: PBLC; ATCC


title: C_080306_03_PDS283_W E

description: Control genomic dna (untreated)


title: E_080225_02_DS8486_W G

description: DnaseI enriched

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: SKNS; ATCC


title: E_080115_01_DS8476_W G

description: DnaseI enriched


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 1 h, replicate 2


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 3 h, replicate 2


title: E_080102_08_DS8482_W G

description: DnaseI enriched


title: E_080102_07_DS8470_W G

description: DnaseI enriched


title: E_080102_05_DS8464_W G

description: DnaseI enriched


title: E_080102_06_DS8468_W G

description: DnaseI enriched


title: E_080115_02_DS8479_W G

description: DnaseI enriched


title: E_080102_04_DS8429_W G

description: DnaseI enriched


title: E_080225_01_DS8427_W G

description: DnaseI enriched


title: EcR DamID, replicate 1, slide 13366 Treatment

description: Embryonic Drosophila cells, Kc167 cells


title: USP DamID, replicate 1, slide 13371 Treatment

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing USP-Dam

tag: USP-Dam (EXPERIMENTAL)


title: USP DamID, replicate 3, slide 14455 Treatment

description: Embryonic Drosophila cells, Kc167 cells


title: E_080102_03_DS8425_W G

description: DnaseI enriched


title: Rhodococcus jostii RHA1 incubated at 100% relative humidity for 30 min, replicate 1


title: USP DamID, replicate 2, slide 13369 Treatment

description: Embryonic Drosophila cells, Kc167 cells


title: USP DamID, replicate 3, slide 14455 Reference

description: Embryonic Drosophila cells, Kc167 cells


title: cbp20 replicateC

description: see Laubinger et al., 2008, for details

source_name: cbp20 mutants

tag: cbp20 mutants (Col-0 background) were grown for 14 days under LL conditions at 23°C. Whole plants were harvested and frozen in liquid nitrogen.


title: E_071203_03_DS8385_W A

description: DnaseI enriched

tag: HL60; ATCC


title: E_071203_02_DS8382_W A

description: DnaseI enriched


title: E_071203_01_DS8376_W A

description: DnaseI enriched


title: USP DamID, replicate 2, slide 13369 Reference

description: Embryonic Drosophila cells, Kc167 cells


title: C_080225_07_PDS283_W A

description: Control genomic dna (untreated)


title: C_080225_06_PDS283_W A

description: Control genomic dna (untreated)


title: E_080102_01_DS8419_W G

description: DnaseI enriched


title: C_080115_07_DS8546_W A

description: Control genomic dna (untreated)

source_name: OVCAR-3;ATCC:HTB-161;ovary;adenocarcinoma;epithelial;adult/female;RPMI;OVCAR;Control genomic dna (untreated)

tag: OVCAR; ATCC


title: C_080225_05_PDS283_W A

description: Control genomic dna (untreated)


title: C_080115_06_DS8546_W A

description: Control genomic dna (untreated)


title: E_080102_02_DS8422_W G

description: DnaseI enriched


title: EcR DamID, replicate 1, slide 13366 Reference

description: Embryonic Drosophila cells, Kc167 cells


title: C_080306_01_PDS283_W E

description: Control genomic dna (untreated)


title: E_071203_07_DS8401_W G

description: DnaseI enriched


title: E_080225_04_DS8689_W C

description: DnaseI enriched

tag: NHBE; ATCC


title: E_071203_06_DS8396_W G

description: DnaseI enriched


title: E_071015_05_DS7712_W C

description: DnaseI enriched

tag: BJ; ATCC


title: E_071107_03_DS7754_W C

description: DnaseI enriched


title: E_071203_05_DS8393_W G

description: DnaseI enriched


title: E_071203_08_DS8405_W G

description: DnaseI enriched


title: E_070904_04_DS7864_W C

description: DnaseI enriched


title: E_070904_05_DS7866_W C

description: DnaseI enriched


title: E_071023_04_DS8017_W G

description: DnaseI enriched

tag: SKMC; ATCC


title: C_080205_03_PDS283_W C

description: Control genomic dna (untreated)


title: C_080205_02_PDS283_W C

description: Control genomic dna (untreated)


title: E_071023_03_DS7911_W G

description: DnaseI enriched


title: C_070904_03_DS8185_W C

description: Control genomic dna (untreated)

source_name: BJ;ATCC:CRL-2522;skin;foreskin;normal;fibroblast;newborn/male;MEM;BJ-tert;Control genomic dna (untreated)


title: E_071023_02_DS7909_W G

description: DnaseI enriched


title: E_070918_12_DS8023_W G

description: DnaseI enriched


title: abh1 replicateA

description: see Laubinger et al., 2008, for details

source_name: abh1 mutants

tag: abh1 mutants (generated in Col-0 background) were grown for 14 days in LL conditions at 23°C. Whole plants were frozen in liquid nitrogen and total RNA was isolated using using the RNeasy Plant Mini Kit (Qiagen).


title: C_080115_05_DS8546_W A

description: Control genomic dna (untreated)


title: C_070904_02_DS8185_W C

description: Control genomic dna (untreated)


title: E_070918_11_DS8027_W G

description: DnaseI enriched


title: E_070918_10_DS8020_W G

description: DnaseI enriched


title: E_070918_09_DS8018_W G

description: DnaseI enriched


title: E_080109_02_DS8529_W F

description: DnaseI enriched

tag: PBER; UWStam


title: C_070904_01_DS8185_W C

description: Control genomic dna (untreated)


title: E_071002_06_DS8072_W F

description: DnaseI enriched


title: E_070918_08_DS7914_W G

description: DnaseI enriched


title: E_071002_05_DS8071_W F

description: DnaseI enriched


title: E_071107_04_DS7982_W B

description: DnaseI enriched

tag: HELA; ATCC


title: C_080205_01_PDS283_W C

description: Control genomic dna (untreated)


title: E_080225_03_DS8683_W B

description: DnaseI enriched

tag: HMEC; ATCC


title: E_070918_04_DS8200_W B

description: DnaseI enriched


title: E_070918_02_DS8139_W B

description: DnaseI enriched


title: E_070918_03_DS8196_W B

description: DnaseI enriched


title: E_080109_03_DS8531_W F

description: DnaseI enriched

tag: FLER; UWStam


title: E_070918_06_DS7910_W G

description: DnaseI enriched


title: E_070918_07_DS7913_W G

description: DnaseI enriched


title: E_070918_05_DS7908_W G

description: DnaseI enriched


title: E_071002_08_DS8076_W F

description: DnaseI enriched


title: E_070904_12_DS8125_W B

description: DnaseI enriched


title: E_070918_01_DS8134_W B

description: DnaseI enriched


title: C_071106_05_PDS279_W G

description: Control genomic dna (untreated)

source_name: SK-N-SH;ATCC:HTB-11;brain;neuroblastoma;neuronal;adolescent/female;MEM;SKNS;SKNSH;Control genomic dna (untreated)


title: C_071106_04_PDS279_W G

description: Control genomic dna (untreated)


title: E_070904_11_DS7976_W B

description: DnaseI enriched


title: BT474-Alk5TD Cell Replicate 3

city: Nashville

first: Shizhen Emily

state: TN

address: 2220 Pierce AVE, PRB-771

department: Cancer Biology

institute: Vanderbilt University

description: Biological replicate 3 of 3. The differential gene expression in BT474-Alk5TD cells (Cy5-labeled) was determined by comparing to BT474-pBMN cells (Cy3-labeled).

hyb_protocol: Dried-down targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target. The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station (BioMicro Systems, Inc., 4 chamber model).  Immediately prior to hybridization, the microarrays were first vigorously dunked in a 0.2% SDS solution at room temp followed by  prehybridization in a solution of 5x SSC, 1% SDS, and 1% BSA at 55° C for 60 minutes.  Following prehybridization, the arrays were vigorously washed in 9 exchanges of ddH2O to remove all traces of the prehybridization solution, rinsed in isopropanol, and dried at room temperature.  The target samples were denatured at 95°C for three minutes and placed on the prehybridized arrays, covered with specialized hybridization chambers from BioMicro Inc (Salt Lake City, UT).  Arrays were hybridized using the MAUI hybridization system (BioMicro) for 16 hours at 42° C using the manufacturer’s mixing protocol “B”.  After hybridization, the arrays were washed in 2X SSC/0.1% SDS at 55° C with agitation for 5 minutes then washed with two successive 5 minute washes with 1x SSC and 0.1xSSC at RT.  The washed arrays were dried by centrifugation at 50xg for 5 minutes and immediately scanned using a GenePix 4000B microarray scanner [Axon Instruments, Union City, CA].

scan_protocol: Microarrays were scanned using a GenePix 4000B microarray scanner and GenePix Pro version 6 [Axon Instruments, Union City, CA].

data_processing: Raw data was loaded into GeneSpring (v.7) [Agilent Technologies, Inc.] using GenePix-format defaults. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. After normalization, all data was filtered to eliminate all data points that may not be reliable. This included flagged spots, lowly expressed spots (signal less than 200), and spots with negative signal values. After filtering, the genes were chosen for further analysis on the basis of fold change of treated samples vs. controls (2 and higher up- or down-regulation) in 2 or 3 experiments with P value of <0.05. Finally, Excel file was created for genes representing proteins with specific molecular functions (e.g., transcriptional factors) or  known to be involved in different cellular processes (e.g., apoptosis).

source_name: BT474 cells expressing Alk5TD

label_protocol: Microarray services were performed by the Vanderbilt Microarray Shared Resource (http://www.vmsr.net). The integrity of RNA preparations was controlled using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). By combining specific fluorescent assays with standard spectrophotometry, the amount of RNA, DNA and protein present was specifically quantitated for a more rigorous quality control of each sample. Those samples meeting minimum QC/QA requirements were used to generate cDNA targets for hybridization to spotted arrays according to VMSR standard protocol (http://www.vmsr.net/microarray/protocols.vmsr). Briefly, 5-10 ug of total RNA from each sample were reverse transcribed using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA).  Generated cDNA targets were purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA). The purified cDNA targets were dried to completion and then differentially coupled to ester-linked Cy3 (BT474-pBMN) or Cy5 (BT474-Alk5TD) dye (Amersham, Piscataway, NJ). After quenching of unbound dye with 4M Hydroxylamine, Cy3- and Cy5-labeled cDNA target pairs were combined and cleaned up over QIAquick columns (Qiagen, Valencia, CA). Ambion ArrayControl™ RNA Spikes (Ambion, cat#1780) were added at concentrations ranging from 0 – 200pg per spike per Reverse Transcriptase reaction.  These 8 control spike-ins hybridize to the Ambion ArrayControl™ Sense Oligo Spots spotted on VMSR arrays.

growth_protocol: BT474-pBMN and BT474-Alk5TD cells were grown in IMEM with 10% FBS

extract_protocol: Total RNA was isolated from one 100 mm cell culture dish of each cell lines using Trizol Reagent (Invitrogen) followed by RNeasy Mini Kit (Qiagen, Valencia, CA) and RNase-Free DNase Set (Qiagen, Valencia, CA) according to the manufacturer’s instructions. To elute RNA from columns at final elution, 30-40 ul water were used to get about 30-50 ug total RNA.

treatment_protocol: No treatment. Both cell types were harvested when they reached 70-80% confluency in 100 mm dishes

tag: BT474 human breast cancer cells (Organ

value: mammary gland; breast, Tissue:duct, Disease:ductal carcinoma, Age:60 years adult, Gender:female)

source_name: BT474 cells expressing pBMN vector


title: C_071106_03_PDS279_W G

description: Control genomic dna (untreated)


title: E_080109_04_DS8533_W F

description: DnaseI enriched

source_name: ESER;UWStam:ES-Ery;Embryonic Stem Cell;normal;erythroid;embryo/unknown;primary;ESER;DnaseI enriched

tag: ESER; UWStam


title: E_070904_10_DS7980_W B

description: DnaseI enriched


title: E_071002_03_DS8029_W F

description: DnaseI enriched


title: E_070904_09_DS7986_W B

description: DnaseI enriched


title: BT474-Alk5TD Cell Replicate 2

description: Biological replicate 2 of 3. The differential gene expression in BT474-Alk5TD cells (Cy5-labeled) was determined by comparing to BT474-pBMN cells (Cy3-labeled).


title: E_070904_08_DS7982_W B

description: DnaseI enriched


title: E_071203_04_DS8416_W F

description: DnaseI enriched

tag: CACO; ATCC


title: C_080204_08_PDS283_W B

description: Control genomic dna (untreated)

tag: PBLC; ATCC


title: E_071029_03_DS8307_W F

description: DnaseI enriched


title: E_071029_04_DS8310_W F

description: DnaseI enriched


title: E_070904_07_DS7933_W B

description: DnaseI enriched


title: E_071022_04_DS8237_W F

description: DnaseI enriched


title: C_080204_07_PDS283_W B

description: Control genomic dna (untreated)


title: C_080226_03_PDS283_W F

description: Control genomic dna (untreated)


title: C_080204_06_PDS283_W B

description: Control genomic dna (untreated)


title: E_070904_06_DS7928_W B

description: DnaseI enriched


title: E_071002_07_DS8075_W F

description: DnaseI enriched


title: E_071015_04_DS7759_W D

description: DnaseI enriched

tag: HEPG; ATCC


title: E_071022_03_DS8235_W F

description: DnaseI enriched


title: E_071024_06_DS8304_W F

description: DnaseI enriched


title: E_071015_02_DS8212_W D

description: DnaseI enriched


title: C_080226_01_PDS283_W F

description: Control genomic dna (untreated)


title: E_071002_04_DS8030_W F

description: DnaseI enriched


title: C_080213_03_PDS283_W D

description: Control genomic dna (untreated)


title: C_080213_02_PDS283_W D

description: Control genomic dna (untreated)


title: C_071024_03_PDS273_W F

description: Control genomic dna (untreated)

source_name: CACO2;ATCC:HTB-37;colon;colorectal adenocarcinoma;adult/male;MEM;CACO;Control genomic dna (untreated)


title: C_080213_01_PDS283_W D

description: Control genomic dna (untreated)


title: E_071024_05_DS8244_W F

description: DnaseI enriched


title: C_071023_01_PDS273_W F

description: Control genomic dna (untreated)


title: E_071015_03_DS8214_W D

description: DnaseI enriched


title: C_080226_02_PDS283_W F

description: Control genomic dna (untreated)


title: C_071024_04_PDS273_W F

description: Control genomic dna (untreated)


title: USP DamID, replicate 1, slide 13371 Reference

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam (REFERENCE)


title: WAT_WT_HFD+Rosi

status: Public on Apr 29 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Arrays were hybridized according to the standard protocols of Affymetrix (16 hours at 42 degrees centigrade)

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G, according to the standard protocols of Affymetrix

data_processing: Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470]

source_name: white adipose tissue

label_protocol: The RNA (5µg) was labled using the Affymetrix One-cycle Target Labeling Assay kit, according to the manufacteror's instructions.

extract_protocol: Epididymal adipose tissue was excised, homogenized in TRIzol reagent. RNA isolated was further purified using Qiagen RNEasy columns.

tag: 129S1/SvImJ, Male


title: Mxi1 +/+ control (1Y)

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

description: Mxi1 +/+ control (1Y)

hyb_protocol: Biotin-labeled cRNA was hybridized to the array overnight in a shaking incubator at 37°C and excess target sequence was washed away using a series of SSC washes.

scan_protocol: The array was stained by treatment with streptavidin-Alexaflour 647 (Molecular Probes), the excess was washed away, and the array was scanned at an excitation wavelength of 632 nm using an Axon Instruments GenePix scanner.

data_processing: CodeLink Expression Analysis Software

source_name: Kidney

label_protocol: Ten micrograms of total RNA was amplified and labeled cRNA was produced using the kit available from Amersham and designed for use with the CodeLink® arrays.

extract_protocol: Total RNA was extracted by using an RNeasy Tissue Mini kit (QIAGEN, No. 74104) according to the instructions of the manufacturer and treated DNase at 37℃ for 40min in order to protect against genomic DNA contamination.

tag: Mxi1 +/+ control (1Y)


title: WAT_WT_HFD


title: Mxi1 -/- experiment (1Y)

description: Mxi1 -/- experiment (1Y)

tag: Mxi1 -/- experiment (1Y)


title: Pilocytic Astrocytoma, Case no. 51 (1Mb Resolution)

status: Public on Apr 28 2008

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: Log2 tumour/reference intensity ratios for analysis of copy number variations

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45µg of Cot1 DNA and ethanol precipitated. The precipitated DNA was dissolved in 30µl of hybridisation buffer, incubated at 37˚C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humidified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37˚C for 48 hours under a coverslip. The arrays were then washed successively in 1x PBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42˚C for 30 min once, 1x PBS/0.05% Tween20 at room temperature for 15min and 1x PBS for 5min twice.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of the 5Mb-clones in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.

source_name: Primary tumour sample

label_protocol: 400ng of genomic DNA was labelled with a Bioprime labelling kit (Invitrogen)

extract_protocol: Proteinase K digestion followed by phenol:chloroform extraction

tag: Male

tag: Age

tag: Location

value: Cerebellum

source_name: Mixed normal blood from 20 individuals (reference)

label_protocol: 400ng of tumour and reference genomic DNA were labelled with Cy5-dCTP and Cy3-dCTP (GE Healthcare), respectively, using BioPrime kit (Invitrogen) according to the manufacturer’s instruction, except that custom-prepared dNTP (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM) was used. After overnight incubation at 37°C, the labelled DNA were purified using a G-50 spin column (GE Healthcare).

tag: Female


title: Pilocytic Astrocytoma, Case no. 50 (1Mb Resolution)

value: Child

value: 4th ventricle


title: Pilocytic Astrocytoma, Case no. 67 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 60 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 49 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 57 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 68 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 48 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 65 (1Mb Resolution)

value: Brain stem


title: Pilocytic Astrocytoma, Case no. 52 (1Mb Resolution)


title: BT474-Alk5TD Cell Replicate 1

description: Biological replicate 1 of 3. The differential gene expression in BT474-Alk5TD cells (Cy5-labeled) was determined by comparing to BT474-pBMN cells (Cy3-labeled).


title: Pilocytic Astrocytoma, Case no. 47 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 45 (1Mb Resolution)


title: H3K4me2 ChIP in   U-EML replicate 2 array 1 of 2

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: H3K4me2 ChIP in   U-EML replicate 2

hyb_protocol: Agilent hybridization protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B. Images were quantified using Agilent Feature Extraction Software

data_processing: log intensity ratios calculated from of median Cy5/Cy3 signal signal.

source_name: H3K4me2 ChIP in   U-EML replicate 2, labeled with Cyanine-5 (red).

label_protocol: Agilent labeling protocol

growth_protocol: EML cells were plated in 45mls of normal growth medium plus 10U/ml of human erythropoietin (Epo; Ortho) at 75,000 cells/ml in a T75 culture flask and cultured for two days.

extract_protocol:
FACS sorting for ChIP assays: Approximately 3x108 undifferentiated or differentiated EML cells were labeled with either anti-Sca-1-PE (undifferentiated) or anti-c-Kit-FITC (differentiated) for 25 minutes, washed in cold PBS/2% FBS, filtered through 0.30um mesh and FACS sorted. The top 80% of Sca+ undifferentiated cells and the c-Kit- erythroid cells (based on an unstained control) were sorted. The cells maintained at 4C pre-sort and post-sort. Due to the loss of certain histone modifications during the sorting procedure, we placed these cells back in culture in the appropriate growth conditions for 2 hours prior to processing for ChIP assays.
Genomic DNA was extracted following ChIP assays using the SDS/Proteinase K method per the ChIP protocol. During subsequent amplification and labeling steps, DNA was purified using Qiagen MinElute columns.

tag: cells

source_name: H3K4me2 input in   U-EML replicate 2, labeled with Cyanine-3 (green).

extract_protocol: see channel 1


title: WAT_WT_LFD


title: H3K4me3 ChIP in E-EML replicate 1 array 2 of 2

description: H3K4me3 ChIP in E-EML replicate 1

source_name: H3K4me3 ChIP in E-EML replicate 1, labeled with Cyanine-5 (red).

source_name: H3K4me3 input in E-EML replicate 1, labeled with Cyanine-3 (green).


title: H3K4me3 ChIP in   U-EML replicate 2 array 2 of 2

description: H3K4me3 ChIP in   U-EML replicate 2

source_name: H3K4me3 ChIP in   U-EML replicate 2, labeled with Cyanine-5 (red).

source_name: H3K4me3 input in   U-EML replicate 2, labeled with Cyanine-3 (green).


title: H3K4me2 ChIP in   U-EML replicate 2 array 2 of 2

description: H3K4me2 ChIP in   U-EML replicate 2


title: H3K4me2 ChIP in U-EML replicate 1 array 2 of 2

description: H3K4me2 ChIP in U-EML replicate 1

source_name: H3K4me2 ChIP in U-EML replicate 1, labeled with Cyanine-5 (red).

source_name: H3K4me2 input in U-EML replicate 1, labeled with Cyanine-3 (green).


title: Pilocytic Astrocytoma, Case no. 42 (1Mb Resolution)

value: Left frontal lobe


title: Pilocytic Astrocytoma, Case no. 43 (1Mb Resolution)

value: Optic nerve


title: Pilocytic Astrocytoma, Case no. 44 (1Mb Resolution)


title: H3K4me3 ChIP in U-EML replicate 1 array 1 of 2

description: H3K4me3 ChIP in U-EML replicate 1

source_name: H3K4me3 ChIP in U-EML replicate 1, labeled with Cyanine-5 (red).

source_name: H3K4me3 input in U-EML replicate 1, labeled with Cyanine-3 (green).


title: Pilocytic Astrocytoma, Case no. 41 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 35 (1Mb Resolution)

value: Adult


title: Pilocytic Astrocytoma, Case no. 32 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 30 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 40 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 27 (1Mb Resolution)


title: H3K4me2 ChIP in U-EML replicate 1 array 1 of 2

description: H3K4me2 ChIP in U-EML replicate 1


title: Pilocytic Astrocytoma, Case no. 37 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 39 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 29 (1Mb Resolution)


title: H3K4me2 ChIP in E-EML replicate 1 array 2 of 2

description: H3K4me2 ChIP in E-EML replicate 1

source_name: H3K4me2 ChIP in E-EML replicate 1, labeled with Cyanine-5 (red).

source_name: H3K4me2 input in E-EML replicate 1, labeled with Cyanine-3 (green).


title: Pilocytic Astrocytoma, Case no. 28 (1Mb Resolution)

value: Right temporal lobe


title: Pilocytic Astrocytoma, Case no. 33 (1Mb Resolution)

value: 3rd ventricle


title: H3K4me3 ChIP in   U-EML replicate 2 array 1 of 2

description: H3K4me3 ChIP in   U-EML replicate 2


title: Pilocytic Astrocytoma, Case no. 25 (1Mb Resolution)


title: H3K4me3 ChIP in E-EML replicate 1 array 1 of 2

description: H3K4me3 ChIP in E-EML replicate 1


title: H3K4me3 ChIP in U-EML replicate 1 array 2 of 2

description: H3K4me3 ChIP in U-EML replicate 1


title: H3K4me2 ChIP in E-EML replicate 1 array 1 of 2

description: H3K4me2 ChIP in E-EML replicate 1


title: Pilocytic Astrocytoma, Case no. 20 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 19 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 23 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 24 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 18 (1Mb Resolution)

value: Pineal region


title: Pilocytic Astrocytoma, Case no. 14 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 9 (1Mb Resolution)

value: Hypothalamus


title: Pilocytic Astrocytoma, Case no. 10 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 8 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 7 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 15 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 5 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 2 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 16 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 3 (1Mb Resolution)


title: Pilocytic Astrocytoma, Case no. 1 (1Mb Resolution)


title: ECOR26_glucose_rep1

status: Public on Apr 25 2008

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

description: Transcriptome profiling of E. coli MG1655, E. coli EDL933, E. coli ECOR26, and E. coli Nissle 1917 grown on mouse cecal mucus as carbon source

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2-450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000.

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003.

organism: Escherichia coli

source_name: ECOR26, glucose minimal medium, control

label_protocol: RNA was converted to cDNA by first strand synthesis using Superscript II (Invitrogen) and random hexamers.  The cDNA was fragmented and biotinylated (Enzo Kit, Roche Diagnostics), according to the Affymetrix prokaryotic labeling protocol.

growth_protocol: For DNA array experiments, cells were grown in triplicate at 37oC without shaking in 18 mm test tubes containing 5 ml of the MOPS-based culture medium designed by Neidhardt.  Mouse cecal mucus was prepared from streptomycin-treated CD-1 mice (not colonized with E. coli).  Cultures were grown in triplicate to A600 = 0.4 in MOPS medium containing 10 mg/ml of lyophilized mucus or glucose (0.2%).

extract_protocol: Cultures were diluted into DNA-RNA Protect (Sierra Diagnostics) to inhibit RNA degradation and the RNA was purified using RNeasy minkits with the optional DNase treatment  (Qiagen).

tag: Escherichia coli ECOR26

tag: wild-type


title: NISSLE_glucose_rep1

source_name: NISSLE, glucose minimal medium, control

tag: Escherichia coli Nissle 1917


title: EDL933_mucus_rep2

source_name: EDL933, mucus (10 mg/ml), test

tag: Escherichia coli EDL936


title: NISSLE_mucus_rep1

source_name: NISSLE, mucus (10 mg/ml), test


title: ECOR26_glucose_rep2


title: NISSLE_glucose_rep2


title: EDL933_mucus_rep1

tag: Escherichia coli EDL935


title: NISSLE_mucus_rep2


title: ECOR26_mucus_rep1

source_name: ECOR26, mucus (10 mg/ml), test


title: MG1655_mucus_rep2

source_name: MG1655, mucus (10 mg/ml), test

tag: Escherichia coli MG1655


title: EDL933_glucose_rep1

source_name: EDL933, glucose minimal medium, control

tag: Escherichia coli EDL933


title: MG1655_glucose_rep1

source_name: MG1655, glucose minimal medium, control


title: Pilocytic Astrocytoma, Case no. 12 (1Mb Resolution)

source_name: Primary tumour sample

source_name: Mixed normal blood from 20 individuals (reference)


title: EDL933_glucose_rep2

tag: Escherichia coli EDL934


title: MG1655_glucose_rep2


title: MG1655_mucus_rep1


title: ECOR26_mucus_rep2


title: NA01416_Nsp_CN2_rep3

status: Public on Apr 24 2008

first: Fan

last: Shen

address: 3420 Central Expressway

institute: Affymetrix, Inc

description: Sample NA01416 was hybridized to Nsp CN arrays in triplicates

hyb_protocol: The DNA samples are hybridized to the arrays at 49oC in a buffer that contains MES (58 mM), Denhardt's solution (2.5X), EDTA (6 mM), Herring Sperm DNA (0.12 mg/ml), Human Cot-1 DNA (0.01 mg/ml), Tween-20 (0.01%), DMSO (5 %), and TMACl (2.7M). The arrays are then washed using Wash A (6X SSPE, 0.01% Tween 20) at 25oC followed by washing with Wash B (0.6X SSPE, 0.01% Tween 20)at 45oC. The arrays are then stained with streptavidin conjugated to phycoerythrin (SAPE) for 10 minutes at 25oC, followed by staining with a biotinylated goat Anti-streptavidin antibody for 10 minutes at 25oC, followed by another stain with SAPE at 25oC. There is then a final wash with Wash A at 30oC.

scan_protocol: The arrays are scanned on a GCS3000 scanner (Affymetrix).

data_processing: Intensity data are extracted using Affymetrix Power Tool software package (http://www.affymetrix.com/support/developer/powertools/index.affx)

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository

label_protocol: Standard Affymetrix protocol.

extract_protocol: DNA from cell lines was purchased from the Coriell Institute for Medical Research (Camden, NJ).

tag: HapMap sample


title: NA06061_Nsp_CN2_rep2

description: Sample NA06061 was hybridized to Nsp CN arrays in triplicates


title: NA04626_Nsp_CN2_rep3

description: Sample NA04626 was hybridized to Nsp CN arrays in triplicates


title: NA10851_Nsp_CN1_rep3

description: Sample NA10851 was hybridized to Nsp CN arrays in triplicates


title: NA04626_Nsp_CN2_rep2


title: NA01416_Nsp_CN2_rep2


title: NA15510_Nsp_CN2_rep3

description: Sample NA15510 was hybridized to Nsp CN arrays in triplicates


title: NA06061_Nsp_CN2_rep1


title: NA01416_Nsp_CN1_rep2


title: NA06061_Nsp_CN1_rep3


title: NA06061_Nsp_CN2_rep3


title: NA10851_Nsp_CN2_rep3


title: NA04626_Nsp_CN1_rep1


title: NA04626_Nsp_CN1_rep2


title: NA01416_Nsp_CN1_rep3


title: NA10851_Nsp_CN2_rep2


title: NA15510_Nsp_CN1_rep2


title: NA12156_CN1

description: Hapmap sample NA12156 was hybridized to Nsp CN arrays


title: NA06061_Nsp_CN1_rep2


title: NA04626_Nsp_CN1_rep3


title: NA12155_CN1

description: Hapmap sample NA12155 was hybridized to Nsp CN arrays


title: NA01416_Nsp_CN1_rep1


title: NA15510_Nsp_CN1_rep3


title: NA10851_Nsp_CN1_rep1


title: HA1ER M2 rep1

city: Salt Lake City

first: Donald

last: Ayer

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah, Huntsman Cancer Institute

description: HA1ER M2 rep1

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution.  Images were quantified using Agilent Feature Extraction software version 9.5

data_processing: LOWESS normalized data obtained from log2 of red processed signal/processed green signal

source_name: Glucose starved, MondoA knockdown HA1ER cells

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: Cells were maintained in alpha-MEM with 10% Bovine Growth Serum and 0.5% Pen/Strep

extract_protocol: Total RNA was produced by RNAeasy with DNase treatment.

treatment_protocol: Cell were plated on 60mm dishes at 80% confluence, glucose was removed overnight followed by a 3 hour add-back of 2-deoxyglucose

tag: Glucose starved

source_name: 2-deoxyglucose induced, MondoA knockdown HA1ER cells

tag: 2-deoxyglucose induced


title: NA15510_Nsp_CN1_rep1


title: HA1ER M2 rep3

description: HA1ER M2 rep3


title: HA1ER M2 rep2

description: HA1ER M2 rep2


title: HA1ER M2 rep4

description: HA1ER M2 rep4


title: NA10851_Nsp_CN1_rep2


title: NA04626_Nsp_CN2_rep1


title: HA1ER NS rep2

description: HA1ER NS rep2

source_name: Glucose starved, Control HA1ER cells

source_name: 2-deoxyglucose induced, Control HA1ER cells


title: NA06061_Nsp_CN1_rep1


title: NA15510_Nsp_CN2_rep2


title: HA1ER NS rep4

description: HA1ER NS rep4


title: ES 129.3 Passage12  LIF+,RA(251279910101)

description: ES

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)

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See NIA Array Analysis website for details.

source_name: ES 129.3 Passage12  LIF+,RA

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).

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/strepromycin and  1 uM RA.                            refully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.

tag: embryonic stem cell

tag: Strain

tag: Gender

source_name: Universal Mouse Reference RNA

growth_protocol: The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

tag: Universale Mouse Reference


title: HA1ER NS rep1

description: HA1ER NS rep1


title: Control_24h-2

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

country: Japan

institute: AIST

description:
Keyword = rice
Keyword = light

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

organism: Oryza sativa

source_name: Pure air and light_Control_Replication1

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in growth chamber in soil for 14 days

extract_protocol: TRIZOL Reagent method

treatment_protocol: Healthy seedlings at 0 h, control

tag: Healthy plants, untreated

source_name: Pure air and light_Treated_Replication1

treatment_protocol: Under continuous light for 24 h

tag: Pure air light control plants


title: Control_24h

description:
Keyword = rice
Keyword = light


title: Control_1h-2

description:
Keyword = rice
Keyword = light

treatment_protocol: Under continuous light for 1 h


title: Control_12h-2

description:
Keyword = rice
Keyword = light

treatment_protocol: Under continuous light for 12 h


title: OZONE_1h

description:
Keyword = rice
Keyword = ozone

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Gene Pix Scanner

data_processing: The GeneSpring Ver. 4 software was used for normalization.

treatment_protocol: Fumigated for 1 h

tag: Fumigated plants


title: HA1ER NS rep3

description: HA1ER NS rep3


title: OZONE_24h

description:
Keyword = rice
Keyword = ozone

treatment_protocol: Fumigated for 24 h


title: NA10831_CN1

description: Hapmap sample NA10831 was hybridized to Nsp CN arrays


title: ES 129.3 Passage12  LIF-(251279910100)

description: ES

source_name: ES 129.3 Passage12  LIF-

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extractedllet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

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


title: ES 129.3 Passage12  LIF+(251279910099)

description: ES

source_name: ES 129.3 Passage12  LIF+

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/strepromycin.at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: OZONE_12h

description:
Keyword = rice
Keyword = ozone

treatment_protocol: Fumigated for 12 h


title: Normal Biological Replicate 5

status: Public on Apr 23 2008

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

description: Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.

hyb_protocol: Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)

data_processing: We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these

source_name: Skeletal muscle tibialis anterior (TA) from Normal wild-type mice

label_protocol: 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493

growth_protocol: male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.

extract_protocol: Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

tag: Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.


title: MG1.19  Passage 5  LIF+(251279910062)

description: ES

source_name: MG1.19  Passage 5  LIF+

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS; LIF (ESGRO) 1000 u/ml; 1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercaptoethanol, and penicillin/strepromycin.


title: MG1.19  Passage 5  LIF-(251279910063)

description: ES

source_name: MG1.19  Passage 5  LIF-

growth_protocol: ES grown without feeders on gelatin coated, 6-well plates, 100000 cells/well (10000 cells/cm2), in complete ES medium: DMEM, 15% FBS;1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate, 0.1 mM beta-mercapto ethanol, and penicillin/streptomycin,Neomycin(200ug/ml). Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extractedature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.


title: MG1.19  Passage 5  LIF+,RA(251279910064)

description: ES

source_name: MG1.19  Passage 5  LIF+,RA


title: Ozone_24h

description:
Keyword = rice
Keyword = ozone


title: Normal Biological Replicate 6


title: Ozone_12h

description:
Keyword = rice
Keyword = ozone


title: Normal Biological Replicate 1


title: Control_12h

description:
Keyword = rice
Keyword = light


title: Normal Biological Replicate 3


title: Normal Biological Replicate 2


title: mdx Biological Replicate 6

source_name: Skeletal muscle tibialis anterior (TA) from mdx line

tag: Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.


title: mdx Biological Replicate 5


title: NA12145_CN1

description: Hapmap sample NA12145 was hybridized to Nsp CN arrays


title: mdx Biological Replicate 4


title: Normal Biological Replicate 4


title: mdx Biological Replicate 1


title: Control_1h

description:
Keyword = rice
Keyword = light


title: mdx Biological Replicate 2


title: mdx Biological Replicate 3


title: Fiona Biological Replicate 4

source_name: Skeletal muscle tibialis anterior (TA) from fiona transgenic line

tag: Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.


title: Fiona Biological Replicate 1

tag: Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction. Biological Replicate 1.


title: Fiona Biological Replicate2


title: Fiona Biological Replicate3


title: Fiona Biological Replicate 5


title: Ozone_1h

description:
Keyword = rice
Keyword = ozone


title: Decidua e19.0, biological rep2 (Series 2)

city: Stanford

first: Kirstin

last: Knox

address: 300 Pasteur Dr.

institute: Stanford Univeristy

description: Gene expression data from maternal decidua at e19.0

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: In order to control for differences in overall strength of hybridization, all arrays were normalized to the same median intensity using the dCHIP invariant set method.  Modeling was performed using the dCHIP Perfect Match (PM) modeling algorithm.

source_name: Mouse decidual tissue at embryonic day 19.0, biological replicate 2

label_protocol: For each sample, labeled cRNA was prepared from 10 ug of starting RNA according to Affymetrix  protocols. Briefly, RNA was reverse transcribed and the resulting double stranded cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  The cDNA was used as a template for a biotin labeling in vitro transcription.  The resulting cRNA was purified using an Rneasy column, quantified, then fragmented using KOAc RNA fragmentation buffer.

growth_protocol: For all dissected samples, a minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage. The one exception is e8.5: for this experiment (Series 2) only one of the placenta_e8.5 sample is used (see extract protocol below).  For the two undissected samples, a single C57BL/6 female was sacrificed at e17.0 and two individual, undissected placentas were collected to generate two replicates.  In all cases, fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.

extract_protocol: Each sample was homogenized in Trizol with a rotor homogenizer.  RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated.  Note: Due to limited tissue availability, two of the full timecourse e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) included in Series 1 were homogenized in Ambion lysis buffer rather than Trizol and were purified with Ambion Rnaqueous rather than Quiagen Rneasy, so are not included in the Series 2 experiment.

treatment_protocol: For dissected samples, placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells.  Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation.  Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging.  For undissected samples, single undissected e17.0 placentas were flash frozen and stored at –80°  C until RNA isolation.

value: Swiss Webster

tag: Tissue

value: decidua (maternal origin)


title: Decidua e19.0, biological rep1 (Series 2)

source_name: Mouse decidual tissue at embryonic day 19.0, biological replicate 1


title: Decidua e17.0, biological rep2 (Series 2)

description: Gene expression data from maternal decidua at e17.0

source_name: Mouse decidual tissue at embryonic day 17.0, biological replicate 2


title: Decidua P0, biological rep1 (Series 2)

description: Gene expression data from maternal decidua at P0

source_name: Mouse decidual tissue at postnatal day 0, biological replicate 1


title: Decidua e15.0, biological rep1 (Series 2)

description: Gene expression data from maternal decidua at e15.0

source_name: Mouse decidual tissue at embryonic day 15.0, biological replicate 1


title: Decidua e17.0, biological rep1 (Series 2)

source_name: Mouse decidual tissue at embryonic day 17.0, biological replicate 1


title: Decidua e12.0, biological rep2 (Series 2)

description: Gene expression data from maternal decidua at e12.0

source_name: Mouse decidual tissue at embryonic day 12.0, biological replicate 2


title: Decidua e9.0, biological rep2 (Series 2)

description: Gene expression data from maternal decidua at e9.0

source_name: Mouse decidual tissue at embryonic day 9.0, biological replicate 2


title: Decidua e15.0, biological rep2 (Series 2)

source_name: Mouse decidual tissue at embryonic day 15.0, biological replicate 2


title: Decidua e9.0, biological rep1 (Series 2)

source_name: Mouse decidual tissue at embryonic day 9.0, biological replicate 1


title: NA10851_Nsp_CN2_rep1

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository


title: Decidua e8.5, biological rep1, technical rep2 (Series 2)

description: Gene expression data from maternal decidua at e8.5

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 1, technical replicate 2


title: Decidua e12.0, biological rep1 (Series 2)

source_name: Mouse decidual tissue at embryonic day 12.0, biological replicate 1