title: Minimal invasive carcinoma 3

city: Frankfurt

first: Nora

last: Hinsch

address: Theodor-Stern-Kai 7

country: Germany

institute: University hospital Frankfurt/Main

description: Biological replicate 3 of 4.

hyb_protocol: 10µg of DIG-labeled cRNA were hybridized to the Applied Biosystems Human Genome Survey Microarray V.2.0  using the Applied Biosystems Chemiluminescence Detection Kit according manufacturer's instructions (Part Number 4346875D).

scan_protocol: The chemiluminescent signal detection, image acquisition and image preprocessing of the microarrays were performed on the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer using the provided Applied Biosystems Expression Array System Software v 1.1.

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems Expression Array System Software v 1.1. Further statistical analysis was performed with the statistical computing environment R. Additional software packages (ab1700, rma, multtest) were taken from the Bioconductor project. Probe level normalization was conducted using the quantile normalization method. Probeset summarization was calculated using the robust median polish method on the normalized data. For each probeset an additive robust additive model on the logarithmic scale (base 2) was fitted across the arrays, considering the different affinities of the probes via the probe effect. A global filter was used: the signal intensity of a probe set had to be above 100 in at least 25 percent of the samples, if the group size is equal. Also a variance filter was used: the interquartile range of log2 intensities had to be at least 0.5. p-Values were calculated applying the two sample t-test (assuming equal variances in both groups) to identify differentially expressed genes between the two groups. False Discovery Rate (FDR) was used to account for multiple testing. Also Fold Changes (FC) between the two groups were calculated for each gene. Differentially expressed genes were determined with p-value, FDR and FC criteria.

label: Digoxigenin

source_name: minimal invasive follicular thyroid carcinoma

label_protocol: 1 microgram of total RNA was reverse transcribed, amplified and digoxigenin (DIG)-labeled using the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit V.2.0 according to manufacturer's instructions (Part Number 4363142 Rev.A).

extract_protocol: Total RNA was extracted from 5-10 10µm slices of snap frozen material using the Qiagen RNeasy Mini kit according to manufacturer's instructions.

tag: tumor

value: microinvasive follicular thyroid carcinoma

value: Female


title: Minimal invasive carcinoma 4

status: Public on Feb 28 2009

type: RNA

department: Pathology

description: Biological replicate 4 of 4.

molecule: total RNA

organism: Homo sapiens

tag: age

tag: gender

value: Male


title: Gnotobiotic_proximal_colon_E_rectale_B_thetaiotaomicron_#2

status: Public on Mar 01 2009

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

country: USA

institute: Washington University

description: Here we compare patterns of gene expression in the proximal colons of mice that were either germ-free, monoassociated with E.rectale or B. thetaiotaomicron, or  co-colonized with both organisms

hyb_protocol: Following fragmentation of 20 ug of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array. The array was hybridized 16 hours at 45 degrees C with rotation at 60 rpm, then washed with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data was normalized using PLIER

label: biotin

organism: Mus musculus

source_name: proximal colon of mouse colonized with Eubacterium rectale and Bacteroides thetaiotaomicron

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled cRNA(ENZO labeling kit).

extract_protocol: Proximal colon was homgenized in RLT buffer. RNA was extracted using RNeasy mini kit (Qiagen)

tag: NMRI mice, males, 10-14 weeks old


title: Minimal invasive carcinoma 1

description: Biological replicate 1 of 4.


title: Carcinoma 3

description: Biological replicate 3 of 4.

source_name: invasive follicular thyroid carcinoma

value: follicular thyroid carcinoma


title: Carcinoma 2

description: Biological replicate 2 of 4.


title: Carcinoma 4

description: Biological replicate 4 of 4.


title: Minimal invasive carcinoma 2

description: Biological replicate 2 of 4.


title: Carcinoma 1

description: Biological replicate 1 of 4.


title: Adenoma 4

description: Biological replicate 4 of 4.

source_name: follicular thyroid adenoma

value: follicular thyroid adenoma


title: Adenoma 3

description: Biological replicate 3 of 4.


title: young adult_24hr DEHP exposure_rep1

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description: Gene expression data from Caenorhabditis elegans young adults

hyb_protocol: Following fragmentation, 10-15 ug of labeled cRNA was fragmented from 35 to 200 bp by fragmentation buffer (Affymetrix). Fragmented cRNA was hybridized to the C. elegans Genome Arrays (Affymetrix) at 45°C for 16 h according to the Affymetrix standard protocol. After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex.

scan_protocol: Intensities were determined with a GeneChip scanner 3000 (Affymetrix), controlled by GCOS Affymetrix software.

data_processing: Expression profiles were analyzed using GeneChip Operating Software (Affymetrix, CA) and Other programs. We used the Affymetrix software to identify changes in expression levels between fragments of the same tumor specimen using standard protocols recommended by Affymetrix.

organism: Caenorhabditis elegans

source_name: mRNA isolated from wildtype young adult

label_protocol: 5 ug of total RNA from fibroblast cultures was used for labeling.

growth_protocol: C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli and young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce agesynchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.

extract_protocol: The total RNA prepared from the exposed and control worms according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentrations of BPA, DEHP and NP were prepared in k-media (0.032 M KCl and 0.051M NaCl; 28). For toxicity tests, worms were incubated at 20 °C for 24 hr without a food source and then subjected to each type of analysis.

tag: strain

value: wildtype

value: hemaphrodite

value: young adult


title: Anidulans_phk_xylose_rep2

status: Public on Feb 27 2009

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

description: Part of a study of polyketide production in Aspergillus nidulans.

hyb_protocol: Approximately 15 μg of fragmented cRNA was hybridized following the Affymetrix GeneChip Expression Analysis protocol.

scan_protocol: The array was scanned on an Agilent GeneArray Scanner 3000

data_processing: The scanned probe array images (.DAT files) were converted into CEL data files using the GeneChip Operating Software from Affymetrix, and subsequently preprocessed using the statistical language and environment R (www.R-project.org) version 2.5. The probe intensities were normalised for background noise with the robust multiarray average (RMA) method using only perfect match (PM) probes. Normalisation was performed subsequently using the quantiles algorithm. Gene expression values were calculated from the PM probes with the medianpolish summary method.

organism: Aspergillus nidulans

source_name: Mycelium from the exponential phase of a batch cultivation on a xylose medium. Replicate 2.

label_protocol: Affymetrix standard expression labeling according to the Affymetrix GeneChip Expression Analysis Technical Manual

extract_protocol: The cultures were harvested at the late exponential phase at a biomass dry-weight concentration of 6-7 g/L. Mycelium was harvested by filtration through sterile Mira-Cloth (CalBioChem). The mycelium was quickly dried by squeezing, and subsequently frozen in liquid nitrogen. Samples were stored at -80 oC until they were used for RNA extraction. Total RNA was isolated using the Qiagen RNeasy Mini Kit, according to the protocol for isolation of total RNA from plant and fungi.

tag: Strain

value: A. nidulans with a phk K/O. Carbon Source:Xylose. Replicate:2nd.


title: Adenoma 2

description: Biological replicate 2 of 4.


title: young adult_24hr BPA exposure_rep1


title: young adult_24hr NP exposure_rep1


title: Adenoma 1

description: Biological replicate 1 of 4.


title: young adult_24hr AgNPs exposure_rep1

treatment_protocol: From stock solutions, experimental concentration(0.1mg/L) of silver nanoparticle was prepared in k-media (0.032 M KCl and 0.051M NaCl; 28). For toxicity tests, worms were incubated at 20 °C for 24 hr without a food source and then subjected to each type of analysis.


title: Anidulans_phk_xylose_rep1

source_name: Mycelium from the exponential phase of a batch cultivation on a xylose medium. Replicate 1.

value: A. nidulans with a phk K/O. Carbon Source:Xylose. Replicate:1st.


title: Anidulans_phk_xylose_rep3

source_name: Mycelium from the exponential phase of a batch cultivation on a xylose medium. Replicate 3.

value: A. nidulans with a phk K/O. Carbon Source:Xylose. Replicate:3rd.


title: Anidulans_phk_glucose_rep2

source_name: Mycelium from the exponential phase of a batch cultivation on a glucose medium. Replicate 2.

value: A. nidulans with a phk K/O. Carbon Source:Glucose. Replicate:2nd.


title: Anidulans_phk_glucose_rep3

source_name: Mycelium from the exponential phase of a batch cultivation on a glucose medium. Replicate 3.

value: A. nidulans with a phk K/O. Carbon Source:Glucose. Replicate:3rd.


title: young adult_not exposured_rep1

treatment_protocol: Untreated.


title: Anidulans_phk6msa_glucose_rep3

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Glucose. Replicate:3rd.


title: Anidulans_phk6msa_xylose_rep1

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Xylose. Replicate:1st.


title: B.theta-E.rectale-High polysaccharide diet_#3

description: B. thetaiotaomicron and Eubacterium rectale, grown in vivo in the cecum of NMRI inbred mouse fed a plant polysaccharide diet.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Expression analyses were performed using the MAS5 algorithm implemented in BioConductor’s ‘Affy package’, following masking of GeneChip  imperfections with Harshlight - in both cases using the default parameters.

label: Biotin

organism:
Bacteroides thetaiotaomicron
Agathobacter rectalis

source_name: B.theta and E.rectale growing in the cecum of mice fed a high polysaccharide diet

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen RNAeasy column and Ambion DNAfree DNAseI treatment

value: NMRI

value: male

value: 14 weeks

tag: diet

value: high polysaccharide


title: Anidulans_phk6msa_xylose_rep3

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Xylose. Replicate:3rd.


title: Anidulans_phk6msa_glucose_rep2

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Glucose. Replicate:2nd.


title: Anidulans_phk6msa_glucose_rep1

source_name: Mycelium from the exponential phase of a batch cultivation on a glucose medium. Replicate 1.

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Glucose. Replicate:1st.


title: Anidulans_phk6msa_xylose_rep2

value: A. nidulans with a phk K/O and inserted 6msa. Carbon Source:Xylose. Replicate:2nd.


title: Anidulans_A4_xylose_rep3

value: A. nidulans A4. Carbon Source:Xylose. Replicate:3rd


title: Anidulans_A4_xylose_rep2

value: A. nidulans A4. Carbon Source:Xylose. Replicate:2nd


title: Anidulans_A4_xylose_rep1

value: A. nidulans A4. Carbon Source:Xylose. Replicate:1st


title: Anidulans_A4_glucose_rep1

value: A. nidulans A4. Carbon Source:Glucose. Replicate:1st


title: Anidulans_6msa_xylose_rep2

value: A. nidulans AR1 with 6msa inserted. Carbon source:Xylose. Replicate:2nd


title: Anidulans_A4_glucose_rep3

value: A. nidulans A4. Carbon Source:Glucose. Replicate:3rd


title: Anidulans_A4_glucose_rep2

value: A. nidulans A4. Carbon Source:Glucose. Replicate:2nd


title: Anidulans_6msa_xylose_rep1

value: A. nidulans AR1 with 6msa inserted. Carbon source:Xylose. Replicate:1st


title: N2 DPY-27 HD-IP2

type: genomic

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html)

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html)

data_processing: performed at Nimblegen using their standard protocol producing gff files with log2 ratios of experimental/input (http://www.nimblegen.com/products/chip/index.html).

molecule: genomic DNA

source_name: N2 embryo input

label_protocol: Sample labeling protocol provided and performed by Nimblegen using standard NimbleGen protocol

growth_protocol: Wild type, N2, Caenorhabditis elegans were grown on NG pates suplimented with 100 µg/ml carbinicillin and 1 µg/ml IPTG seeded with E. coli HT115 (DE3)

extract_protocol: see PDF linked to GSE14640

treatment_protocol: Embryos used for microarray analysis were obtained from bleached gravid adults.

tag: N2 XX embryo

tag: nonselected input

source_name: N2 embryo DPY-27 IP

tag: DPY-27 IP


title: Anidulans_6msa_xylose_rep3

value: A. nidulans AR1 with 6msa inserted. Carbon Source:Xylose. Replicate:3rd


title: Anidulans_6msa_glucose_rep2

value: A. nidulans AR1 with 6msa inserted. Carbon Source:Glucose. Replicate:2nd.


title: Planktonic Replicate 1

city: Iowa City

first: Megan

middle: L.

last: Falsetta

state: IA

address: 51 Newton Road

department: Microbiology

institute: University of Iowa

description: Neisseria gonorrhoeae 1291 wildtype planktonic cells collected from the runoff of biofilm replicate 1, which was grown in glass flow cells under 150 µl/min continuous flow for 48 hours.  First of two replicate planktonic samples for this study.

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

data_processing: ArrayAssist 5.5.1 software (Stratagene, an Agilent Technologies Company, La Jolla, CA) was used to process array data, which was normalized using the RMA algorithm.  These values were log-transformed for differential expression analysis.

organism: Neisseria gonorrhoeae

source_name: Planktonic cells collected from the runoff of biofilms grown in glass flow cells under 150 µl/min continuous flow for 48 hours

label_protocol: Standard Affymetrix Procedures

growth_protocol: Overnight plate cultures were used to create cell suspensions of N. gonorrhoeae 1291 wildtype for inoculation of biofilm flow chambers.  N. gonorrhoeae was grown in continuous flow chambers in 1:10 GC broth diluted in PBS with 1% IsoVitaleX, and 100 μM sodium nitrite.  Cell suspensions (in biofilm media) of 2 x 108 CFU/ml were used to inoculate 37 x 5 x 5 mm (approximately 1 ml volume) flow cell chamber wells.  These chambers were designed to reduce fluid sheer on biofilm (versus typical 1 mm depth wells).  Flow chambers were incubated under static conditions at 37ºC for 1 hour post inoculation.  Chambers were then incubated for another 48 hours under 150 μl/min flow.  For the first 24 hours of biofilm growth, the effluent was passed through a sterile glass wool filter for the removal of detached biofilm flocs, and collected in a sterile waste flask and cultured to assess culture purity.  At this time, the waste flask was replaced with a second sterile flask containing 10 ml of RNAlater® (Qiagen Corporation, Valencia, CA) and 100 µl of 10% sodium azide.  For the final 24 hours of biofilm growth, the filtered planktonic effluent was collected in this solution to preserve the RNA and prevent transcriptional changes from occurring.  Planktonic RNA was extracted from the collected effluent.  Two flow chambers were filtered into a single planktonic collection flask.

extract_protocol: One RNA sample was extracted from collected effluent of biofilm flow cells.  Planktonic cells were harvested via centrifugation and resuspended in 20 ml PBS for RNA extraction RNA was extracted using a hot acid phenol extraction as follows.  Samples were treated with one volume acid phenol (prepared by adding an equal volume 2M citric acid pH 4.3 to crystalline phenol, equilibrating at room temperature for 24 h) with 0.1% RNase-free SDS, shaken vigorously, and incubated in a water bath at 80°C for 10 minutes, shaking periodically.  The samples were then cooled in an icewater bath until cold, and spun at 7000 rpm for 20 min at 4°C.  The supernatant was removed and extracted with one volume 5:1 phenol:chloroform (Ambion/Applied Biosystems, Austin, TX) and centrifuged for 15 min.  The supernatant was then treated with one volume chloroform and centrifuged for another 15 min.  The supernatant was precipitated with one volume isopropanol with 0.3M sodium acetate overnight at -20°C.  The RNA was pelleted and washed with 80% ethanol and the pellet was dried at room temperature.  The RNA was then DNaseI (New England Biolabs, Boston, MA) digested for 2 h at 37°C and purified using a Qiagen RNeasy MinElute kit.  RNA purity was assessed on an Agilent 2100 Bioanalyzer (Quantum Analytics, Foster City, CA prior to hybridization.

value: Neisseria gonorrhoeae 1291 wildtype,

tag: culture type

value: planktonic cells collected from the runoff of biofilms grown in glass flow cells under 150 µl/min continuous flow for 48 hours,

tag: media

value: 1:10 GC broth diluted in phosphate buffer saline (PBS), supplemented with 100 µM sodium nitrite and 1% Isovitalex,

tag: sample collection

value: collected planktonic cells from biofilm runoff for final 24 hours of biofilm in 100 µl 10% sodium azide and 10 ml RNAlater (Ambion/Applied Biosystem, Austin, TX).  Planktonic runoff from two biofilm flow cells was collected in a single flask and cells were harvested via centrifugation and resuspended in PBS for RNA extraction.


title: 48 hour Biofilm Replicate 2

description: Neisseria gonorrhoeae 1291 wildtype biofilm grown in glass flow cells under 150 µl/min continuous flow for 48 hours.  Second of two replicate biofilm samples for this study.

source_name: Neisseria gonorrheae biofilm grown for 48 hours under continuous flow conditions

growth_protocol: Overnight plate cultures were used to create cell suspensions of N. gonorrhoeae 1291 wildtype for inoculation of biofilm flow chambers.  N. gonorrhoeae was grown in continuous flow chambers in 1:10 GC broth diluted in PBS with 1% IsoVitaleX, and 100 μM sodium nitrite.  Cell suspensions (in biofilm media) of 2 x 108 CFU/ml were used to inoculate 37 x 5 x 5 mm (approximately 1 ml volume) flow cell chamber wells.  These chambers were designed to reduce fluid sheer on biofilm (versus typical 1 mm depth wells).  Flow chambers were incubated under static conditions at 37ºC for 1 hour post inoculation.  Chambers were then incubated for another 48 hours under 150 μl/min flow.

extract_protocol: One RNA sample was extracted from the biofilms present in two flow chambers.  RNA was extracted using a hot acid phenol extraction as follows.  Samples were treated with one volume acid phenol (prepared by adding an equal volume 2M citric acid pH 4.3 to crystalline phenol, equilibrating at room temperature for 24 h) with 0.1% RNase-free SDS, shaken vigorously, and incubated in a water bath at 80°C for 10 minutes, shaking periodically.  The samples were then cooled in an icewater bath until cold, and spun at 7000 rpm for 20 min at 4°C.  The supernatant was removed and extracted with one volume 5:1 phenol:chloroform (Ambion/Applied Biosystems, Austin, TX) and centrifuged for 15 min.  The supernatant was then treated with one volume chloroform and centrifuged for another 15 min.  The supernatant was precipitated with one volume isopropanol with 0.3M sodium acetate overnight at -20°C.  The RNA was pelleted and washed with 80% ethanol and the pellet was dried at room temperature.  The RNA was then DNaseI (New England Biolabs, Boston, MA) digested for 2 h at 37°C and purified using a Qiagen RNeasy MinElute kit.  RNA purity was assessed on an Agilent 2100 Bioanalyzer (Quantum Analytics, Foster City, CA prior to hybridization.

value: biofilm grown in glass flow cells under 150 µl/min continuous flow for 48 hours,

value: collected biofilm cells for RNA extraction directly from flow by sequential PBS washes


title: L1 larvae fed for 12 hr after hatching and then starved for 3 hr

city: Durham

first: L.

middle: Ryan

last: Baugh

state: NC

address: 4314 French Family Science Center

department: Biology

institute: Duke University

description: Gene expression data from larvae hatched in the presence or absence of food.

hyb_protocol: 12.5 micrograms of biotin-labeled cRNA was fragmented and hybridized according to the Affymetrix protocol.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 scanner.

data_processing: Data were processed using Rosetta Resolver version 7.1 (Rosetta Biosoftware); the Affymetrix-Rosetta – Intensity Profile and Experiment Builder pipelines were used.  Data processing resulted in average expression values and associated errors as well as a statistic reporting whether the target transcript was detected above background.  The processing pipelines used include a global error model for the Affymetrix platform that specifies the typical error associated with an expression measurement of a given magnitude.  For each average expression value, the larger of the model-based error and empirical error was reported.

source_name: C. elegans L1 fed 12 rh then starved 3 hr

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for MessageAmp II-Biotin Enhanced kit (Ambion) starting with 100 ng total RNA.

growth_protocol: C. elegans strain N2 was grown in S-complete at a density of 1 worm/microliter with or without 25 mg/ml E. coli HB101 at 20C. Cultures were 10 ml volume (10,000 larvae).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions except 50 micrograms of linear polyacrylamide was added as a carrier (Sigma).  After TRIzol extraction, the RNA pellet was dissolved in Rnase-free water and further purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol and eluted in 14 μl RNAse-free water.

treatment_protocol: Worms were briefly pelleted in a clinical centrifuge, fed samples were washed three times in S-complete.  All but 100 microliters of buffer was removed, and the pelleted worms were frozen in liquid nitrogen.

tag: wild-type; fed then starved

tag: 15 hr after hatching


title: Planktonic Replicate 2

description: Neisseria gonorrhoeae 1291 wildtype planktonic cells collected from the runoff of biofilm replicate 2, which was grown in glass flow cells under 150 µl/min continuous flow for 48 hours.  Second of two replicate planktonic samples for this study.


title: N2 IGG mock HD-IP1

source_name: N2 embryo mock IP

tag: mock IP


title: N2 SDC-3 HD-IP2

source_name: N2 embryo SDC-3 IP

tag: SDC-3 IP


title: N2 SDC-3 HD-IP1


title: Anidulans_6msa_glucose_rep1

value: A. nidulans AR1 with 6msa inserted. Carbon Source:Glucose. Replicate:1st.


title: 48 hour Biofilm Replicate 1

description: Neisseria gonorrhoeae 1291 wildtype biofilm grown in glass flow cells under 150 µl/min continuous flow for 48 hours.  First of two replicate biofilm samples for this study.


title: U937 cells_LPS_2hrs

city: Berlin

first: Agnes

last: Baek

address: Ihnestrasse 63-73

department: Dept. of Vetebrate Genomics

institute: Max Planck Institute for Molecular Genetics

description: Replicates averaged

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was acquired as signal intensity of each spot on the array, and signal values of technical and biological replicates were averaged. Normalization was done by variance stabilization method (Weber et al. 2002). Differentially expressed genes were determined based on a comparison of normalized signal intensity ratio between experimental (differentiated and/or stimulated U937 cells) and control (undifferentiated U937 cells) samples

source_name: U937 cells

label_protocol: cRNA synthesis and biotin-labeling was performed using Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted using QIAGEN RNeasy Plus Mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: U937 cells

tag: developmental stage

value: Activated macropahges


title: L1 larvae 3 hr after hatching in the absence of food in the alternative starvation buffer M9

source_name: C. elegans 3 hr L1 arrest in M9

tag: wild-type; starved

tag: 3 hr after hatching


title: U937 cells_PMA_32hrs

description: Replicates averaged

value: Maturing macropahges


title: U937 cells_PMA_24hrs

description: Replicates averaged


title: N2 mock HD-IP2


title: L1 larvae starved for 12 hr after hatching and then fed for 3 hr

source_name: C. elegans L1 arrest 12 hr then fed 3 hr

tag: wild-type; starved then fed


title: U937 cells_PMA_12hrs

description: Replicates averaged


title: L1 larvae 12 hr after hatching in the presence of food

source_name: C. elegans L1 12 hr after hatching

tag: wild-type; fed

tag: 12 hr after hatching


title: L2 larvae 24 hr after hatching in the presence of food

source_name: C. elegans L1 24 hr after hatching

tag: 24 hr after hatching


title: L1 larvae 3 hr after hatching in the presence of food

source_name: C. elegans L1 3 hr after hatching


title: L1 larvae 1 hr after hatching in the presence of food

source_name: C. elegans L1 1 hr after hatching

tag: 1 hr after hatching


title: L1 larvae 24 hr after hatching in the absence of food

source_name: C. elegans 24 hr L1 arrest


title: N2_DPY-27_HD-IP1

hyb_protocol: performed at Nimblegen using their standard protocol (http://www.nimblegen.com/products/chip/index.html).

tag: N2 XX embryo

tag: nonselected input

tag: DPY27 IP


title: L1 larvae 6 hr after hatching in the presence of food

source_name: C. elegans L1 6 hr after hatching

tag: 6hr after hatching


title: Anidulans_phk_glucose_rep1

source_name: Mycelium from the exponential phase of a batch cultivation on a glucose medium. Replicate 1.

tag: Strain

value: A. nidulans with a phk K/O. Carbon Source:Glucose. Replicate:1st.


title: U937 cells_undifferentiated

description: Replicates averaged


title: L1-L2 larvae 15 hr after hatching in the presence of food

source_name: C. elegans L1 15 hr after hatching

tag: 15 hr after hatching


title: N2 SDC-2 HD-IP1

hyb_protocol: Hybridization protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

scan_protocol: Sample scan protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

source_name: N2 embryo input

label_protocol: Sample labeling protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

source_name: N2 embryo SDC-2 IP

tag: SDC-2 IP


title: Input of Hep3BLAP, IP 3 of Hep3BLAP

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description:
ch1: Biological replicate 3 of 3. total genomic DNA from Hep3B cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression(control)
ch2: Biological replicate 3 of 3. genomic DNA from Hep3 cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression and immunoprecipitated with anti-C/EBPbeta

hyb_protocol: The promoter arrays were purchased from Agilent technology. The hybridizations on the human promoter microarray were performed as described in mammalian ChIP on chip V10.0” protocol. This microarray is a set of two slides containing each 244k of 60 mer oligonucleotide characterising 17,000 of the best defined human transcripts sourced from UCSChg17/NCBI. The hybridized microarrays were washed as described in mammalian ChIP on chip V10.0” protocol.

scan_protocol: The hybridized microarrays were scanned with an Agilent B scanner

data_processing: Raw data were extracted using Agilent feature extraction V9.5.1. The data are analyzed using Agilent ChIP analyptic V.1.3 using following parameters: blank substraction normalization, inter array median normalization and intra array median normalization. Bound regions (Picks detection) were detected using a whitehead error model and probabilities of the false discovery rate (PX-bar<10-3) computed from the joint posterior distribution of neighbouring probes (two probes are neighbouring if they are localized to a maximal distance of 1000pb).

source_name: Input of Hep3BLAP

label_protocol:
Amplifications of immunoprecipitated and Input DNA were performed with Ligated Mediate PCR (LM-PCR) procedure : Oberley MJ, Farnham PJ. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol 2003;371:577-96. The reactions were purified using Qiagen Qiaquick PCR purification kit according to the manufacturer’s instruction. The quality of the DNA amplificated and his quantification were performed using the nanodrop microarrays software (ND-100) analysis
Four microgrammes of amplicons for ChIP with anti-C/EBPbeta and input DNA were labelled using the “mammalian ChIP on chip V10.0” protocol. Input DNAs were labelled with Cy3 and immuprecipitated DNA with Cy5. The reactions were equally purified using Qiagen Qiaquick PCR purification kit.

extract_protocol: For genomic DNA extraction and Chromatin ImunoPrecipitation (ChIP) were performed using a ChIP-it express kit (Active motif) according to the manufacturer’s instructions. This kit permited us to cross-link protein to DNA with formaldehyde, lyse cells, sonicate and purify DNA, make ChIP reaction and control enrichment by PCR. Briefly, the genomic DNA of Hep3B Cell line expressing LAP was sonicated with a vibracell 75015 (Bioblock). ChIPs were performed with 10µg of anti-C/EBPß (sc-150X) from Santa cruz

value: Hep3B human hepatoma

tag: agent

value: Hep3B tTA4-pTRE-LAP-flag cultured without doxycycline during 10 days

source_name: genomic DNA immunoprecupitated with anti-C/EBPbeta


title: U937 cells_PMA_6hrs

description: Replicates averaged

tag: cell line


title: 24hr_RO_Normalized

city: Pullman

first: Timothy

last: Doyle

state: WA

address: 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression data from vitamin a deficient testis treated with retinol for 24hrs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RGU34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip® scanner 3000.

data_processing: The data were analyzed with GCOS (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 125.	Data was then normalized in Genespring 7.3 using default paramaters. The normalized signal value is the mean of the replicates for each sample.

organism: Rattus norvegicus

source_name: Vitamin A deficient testis treated with retinol for 24hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using Ambion RNaqueous RNA extraction kit using the manufactorers protocol

tag: tissue

value: Total testis


title: 4hr_RO_Normalized

description: Gene expression data from vitamin a deficient testis treated with retinol for 4hrs

source_name: Vitamin A deficient testis treated with retinol for 4hrs


title: N2 SDC-2 HD-IP2


title: 8hr_RO_Normalized

description: Gene expression data from vitamin a deficient testis treated with retinol for 8hrs

source_name: Vitamin A deficient testis treated with retinol for 8hrs


title: L1 larvae 15 hr after hatching in the absence of food

source_name: C. elegans 15 hr L1 arrest

tag: wild-type; starved


title: Wilms tumour T57 vs foetal kidney

city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

country: United Kingdom

institute: University of Bristol

hyb_protocol: The labeled experimental IP and control DNAs were co-hybridized to the array for 16 - 20 hours (Nimblegen Inc)

scan_protocol: Nimblegen Inc

data_processing: Nimblegen Inc

source_name: MeDIP DNA from Wilms' tumour

label_protocol: 4 micrograms of MeDIP DNA was labelled using Klenow fragment-catalyzed primer extension using Cy dye coupled 9mer primers (Nimblegen Inc).

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. MeDIP (Nat Genet. 2005 Aug;37(8):853-62) and LM-PCR was carried out as described (Genome Res. 2006 Jul;.16(7):890-900)

value: Wilms' tumour

tag: antibody

source_name: MeDIP DNA from normal foetal kidney

value: foetal kidney


title: L1 larvae 0 hr after hatching in the presence of food

source_name: C. elegans L1 0 hr after hatching

tag: 0 hr after hatching


title: Wilms tumour T771 vs foetal kidney


title: L1 larvae 6 hr after hatching in the absence of food

source_name: C. elegans 6 hr L1 arrest


title: L1 larvae 1 hr after hatching in the absence of food

source_name: C. elegans 1 hr L1 arrest


title: L1 larvae 3 hr after hatching in the absence of food

source_name: C. elegans 3 hr L1 arrest

tag: 3 hr after hatching


title: hASC-iPSC-2

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

description: Microarray study was performed in duplicates (hASCs, iPS cells derived from hASCs, and hESCs). Reference control was pooled RNA taken from H9 hESCs, embryoid bodies, and some differentiated cell types such as endothelial cells.

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was hybridized to Agilent 4x44K whole human genome microarrays (G4112F) and processed according to the manufacturer’s instructions.

scan_protocol: The array was scanned using an Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

source_name: iPS cells derived from hASCs

label_protocol: Using Agilent Low RNA Input Fluorescent Linear Amplification Kits, cDNA was reverse transcribed from each RNA sample, as well as from a pooled reference control, and cRNA then transcribed and fluorescently labeled with Cy5/Cy3. cRNA was purified using an RNeasy kit (Qiagen,).

extract_protocol: Total RNA samples were isolated in Trizol (Invitrogen) followed by purification over a Qiagen RNeasy column (Qiagen, Valencia, CA, USA).

tag: iPS cells derived from human adipose stem cells using 4 Yamanaka reprogramming factors

source_name: human embryonic stem cells and embryoid bodies

tag: pooled RNA from H9 hESCs and embryoid bodies


title: Input of Hep3BLAP, IP 1 of Hep3BLAP

description:
ch1: Biological replicate 1 of 3. total genomic DNA from Hep3B cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression(control)
ch2: Biological replicate 1 of 3. genomic DNA from Hep3 cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression and immunoprecipitated with anti-C/EBPbeta


title: hASC-2

source_name: human adipose stem cells

tag: patient-derived adipose stem cells; primary cell line


title: Wilms tumour T581 vs foetal kidney


title: hASC-iPSC-1

source_name: iPS cell derived from hASCs

tag: pooled RNA from H9 hESCs and EBs


title: VAD_Normalized

description: Gene expression data from vitamin a deficient testis

data_processing: The data were analyzed with GCOS (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 125. Data was then normalized in Genespring 7.3 using default parameters. The normalized signal value is the mean of the replicates for each sample.

source_name: Vitamin A deficient testis


title: L1 larvae 0 hr after hatching in the absence of food

source_name: C. elegans 0 hr L1 arrest


title: L1 larvae 12 hr after hatching in the absence of food

source_name: C. elegans 12 hr L1 arrest

tag: 12 hr after hatching


title: embryo 2 hr before hatching

source_name: C. elegans 3-fold embryo

tag: wild-type

tag: 3-fold embryo, 2 hr before hatching


title: 46h mosquito embryo RNA, biological replicate 1

status: Public on Feb 26 2009

first: Yury

last: Goltsev

address: 585 LSA, UC Berkeley

institute: UC Berkeley

description: for further information please refer to (Goltsev et al, Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo. 2009, Developmental Biology)

hyb_protocol: Regular, following the guidelines from Affymetrix.

scan_protocol: Arrays were hybridized and scanned with a GeneArray Scanner (Hewlett-Packard/Affymetrix).

data_processing: RMA-express software was used for processing of raw expression data and estimation of log base 2 expression values.

organism: Anopheles gambiae

source_name: 46h mosquito embryo

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

growth_protocol: Mosquito eggs were aged in water at 25C.

extract_protocol: Total RNA extraction were performed by Trizol, followed by purification on RNAeasy (Qiagen) column.

treatment_protocol: Staged mosquito eggs were collected into meshed basket, treated in 25% household bleach for 1min.16 seconds, washed thoroughly with streaming water and subjected to RNA prep.

tag: strain

value: Kisumu


title: 43h mosquito embryo RNA, biological replicate 3

source_name: 43h mosquito embryo


title: 46h mosquito embryo RNA, biological replicate 3


title: Input of Hep3BLAP, IP 2 of Hep3BLAP

description:
ch1: Biological replicate 2 of 3. total genomic DNA from Hep3B cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression(control)
ch2: Biological replicate 2 of 3. genomic DNA from Hep3 cells transfected by the Tet-OFF system which provides a doxycyclin controlled LAP over-expression and immunoprecipitated with anti-C/EBPbeta

source_name: Input of Hep3BLAP

source_name: genomic DNA immunoprecupitated with anti-C/EBPbeta


title: 43h mosquito embryo RNA, biological replicate 1


title: 43h mosquito embryo RNA, biological replicate 2


title: 49h mosquito embryo RNA, biological replicate 1

source_name: 49h mosquito embryo


title: 52h mosquito embryo RNA, biological replicate 1

source_name: 52h mosquito embryo


title: Wilms tumour T783 vs foetal kidney

source_name: MeDIP DNA from Wilms' tumour

source_name: MeDIP DNA from normal foetal kidney


title: U937 cells_VitD3_24hrs

description: Replicates averaged

source_name: U937 cells

tag: developmental stage

value: Monocytes


title: Liver_PPAR_D200_Replicate 10

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

description: The Type column in the raw file indicates whether the spot corresponds to background (50% DMSO alone), to a mouse transcript (mouse cDNA fragment in 50% DMSO) or to a yeast spiked-in mRNA (yeast cDNA fragment in 50% DMSO)

hyb_protocol: The arrays were prehybridized for 6h at 65°C in a rotating oven (Qbiogen) in 60 ml individual polypropylene tubes (Nalge Nunc) containing 4 ml of hybridization solution (5X SSC, 5X Denhardt’s solution, 0.5% SDS, 100 μg salmon sperm DNA). 33P-labeled cDNAs were added to the hybridization solution (5ml final volume). Arrays were hybridized for 24h at 65°C. Arrays were washed twice for 30 min and once for 1h at 65°C in 10 ml 0.1X SSC, 0.1% SDS.

scan_protocol: The arrays were exposed for 72 h to a phosphor screen (Molecular Dynamics) and scanned on a STORM 860 phosphorimager (Amersham Biosciences). Images were quantified using Image Master Array v.2.0 (Amersham Biosciences).

data_processing: All data were log2 transformed. For each array, outlier background spots (50% DMSO alone) were detected and filtered out using boxplots. The normality of the background was evaluated using a Shapiro-Wilk test. Each spot on each array was declared present only when its signal exceeded the mean background + 2 standard deviations. The 265 spots declared present on at least 20% of the arrays were kept for further analysis. Data were normalized using the mean log signal of the yeast spiked-in mRNAs. All analyses were done under R (www.r-project.org) using the functions available at http://www.inra.fr/internet/Centres/toulouse/pharmacologie/pharmaco-moleculaire/technologie/fonctions.R.

source_name: Liver of medium dose DEHP-treated mouse

label_protocol: Five µg of total RNA and a mix of 13 selected yeast spiked-in mRNAs were reverse-transcribed with SuperScript II reverse transcriptase (Invitrogen) using 2µg oligo-dT primers (Invitrogen) and 1.5µg random hexamers in the presence of 40 µCi of [33P]dCTP (Perkin). The RNA matrix was degraded by alkaline lysis (SDS 0.2%, EDTA 50 mM, and NaOH 300 mM final, 68°C, 45 min). Following neutralization (Tris-HCl, pH 7.5, 500 mM final), unincorporated nucleotides were removed on Sephadex G50 columns (Amersham Biosciences). 33P-labeled cDNAs were denatured for 5 min at 95°C and incubated in 1 ml of hybridization solution (5X SSC, 5X Denhardt’s solution, 0.5% SDS, 100μg salmon sperm DNA) in the presence of 6µg of dA60.

growth_protocol: Male PPARalpha-null mice on a C57BL/6J genetic background, and aged-matched wild-type counterparts (Charles River, Les Oncins, France; 4 weeks acclimatization) were housed in polycarbonate cages at 22+2°C on a 12 hour light/dark cycle and allowed free access to water and food. In vivo studies were conducted under European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, liver was removed, weighted, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 18-22 week-old mice were randomly divided into 6 groups (vehicle-treated, or DEHP-treated at doses 20 or 200 mg/kg/day for wild type and PPARalpha-deficient mice, n=10 per group). Di-(2-ethylhexyl)-phthalate (DEHP, 20 or 200 mg/kg/day) in solution into corn oil (low or medium dose DEHP-treated groups respectively) or corn oil (vehicle-treated group) were administered for 21 days by daily gavage.

tag: genotype

value: PPARalpha-deficient

tag: gender

value: Male

tag: age

value: 23-25 weeks

tag: dose

value: 200 mg DEHP/kg/day

tag: treatment length

value: 21 days

tag: administration

value: daily gavage

value: liver


title: 40h mosquito embryo RNA, biological replicate 3

source_name: 40h mosquito embryo


title: Liver_PPAR_D200_Replicate 9

tag: tissue


title: 40h mosquito embryo RNA, biological replicate 2


title: Liver_PPAR_D200_Replicate 8


title: Liver_PPAR_D200_Replicate 4


title: Liver_PPAR_D200_Replicate 6


title: Liver_PPAR_D200_Replicate 7


title: Liver_PPAR_D200_Replicate 5


title: Liver_PPAR_D200_Replicate 3


title: Wilms tumour T62L vs foetal kidney

tag: antibody


title: 40h mosquito embryo RNA, biological replicate 1


title: 37h mosquito embryo RNA, biological replicate 3

source_name: 37h mosquito embryo


title: 14h mitotic selection

city: Hanover

first: Michael

last: Whitfield

state: NH

address: 7400 Remsen

department: Genetics

institute: Dartmouth Medical School

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16453.gif
Measurement: time(relative) 14 h
Replicate: shake 1

hyb_protocol: For microarray hybridization, refer to Whitfield ML. et al., Mol Biol Cell, 2002. 13(6): p. 1977-2000.

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Hela Reference 3, total RNA amplified by Whitfield's modified protocol

label_protocol: not provided

extract_protocol: Reference RNA was extracted from asynchronously growing HeLa cells using TRIzol.

source_name: 14h mitotic selection

extract_protocol: Total RNA was prepared using ULTRASPEC RNA isolation system.

tag: 14h mitotic selection


title: Liver_PPAR_D200_Replicate 2


title: 37h mosquito embryo RNA, biological replicate 2


title: 31h mosquito embryo RNA, biological replicate 3

source_name: 31h mosquito embryo


title: 34h mosquito embryo RNA, biological replicate 2

source_name: 34h mosquito embryo


title: Liver_PPAR_D200_Replicate 1


title: 34h mosquito embryo RNA, biological replicate 1


title: 6h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16447.gif
Measurement: time(relative) 6 h
Replicate: shake 1

tag: Hela Reference 3, total RNA amplified by Whitfield's modified protocol

source_name: 6h mitotic selection

tag: 6h mitotic selection


title: 2h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16435.gif
Measurement: time(relative) 2 h
Replicate: shake 1

source_name: 2h mitotic selection

tag: 2h mitotic selection


title: hASC-1

source_name: human adipose stem cell

tag: patient-derived adipose stem cell; primary cell line.

source_name: human embryonic stem cells and embryoid bodies

tag: pooled RNA from H9 hESCs and embryoid bodies


title: 34h mosquito embryo RNA, biological replicate 3


title: 12h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16452.gif
Measurement: time(relative) 12 h
Replicate: shake 1

source_name: 12h mitotic selection

tag: 12h mitotic selection


title: 10h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16451.gif
Measurement: time(relative) 10 h
Replicate: shake 1

source_name: 10h mitotic selection

tag: 10h mitotic selection


title: 8h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16450.gif
Measurement: time(relative) 8 h
Replicate: shake 1

source_name: 8h mitotic selection

tag: 8h mitotic selection


title: Liver_PPAR_D20_Replicate 9

source_name: Liver of low dose DEHP-treated mouse

tag: strain

tag: genotype

value: 20 mg DEHP/kg/day


title: Liver_PPAR_D20_Replicate 10

tag: gender

tag: age


title: Liver_PPAR_D20_Replicate 7

tag: dose

tag: treatment length


title: Liver_PPAR_D20_Replicate 8

tag: administration

tag: tissue


title: 28.5h mosquito embryo RNA, biological replicate 3

source_name: 28.5h mosquito embryo


title: Liver_PPAR_D20_Replicate 5


title: Liver_PPAR_D20_Replicate 6


title: 31h mosquito embryo RNA, biological replicate 1


title: 4h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16444.gif
Measurement: time(relative) 4 h
Replicate: shake 1

source_name: 4h mitotic selection

tag: 4h mitotic selection


title: Liver_PPAR_D20_Replicate 4


title: Liver_PPAR_D20_Replicate 3


title: 28.5h mosquito embryo RNA, biological replicate 2


title: 0h mitotic selection

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16425.gif
Measurement: time(relative) 0 h
Replicate: shake 1

tag: Hela Reference 3, total RNA amplified by Whitfield's modified protocol

source_name: 0h mitotic selection

tag: 0h mitotic selection


title: Liver_PPAR_D20_Replicate 2


title: 46h mosquito embryo RNA, biological replicate 2

source_name: 46h mosquito embryo


title: 31h mosquito embryo RNA, biological replicate 2


title: 25h mosquito embryo RNA, biological replicate 3

source_name: 25h mosquito embryo


title: 22h mosquito embryo RNA, biological replicate 3

source_name: 22h mosquito embryo


title: 28.5h mosquito embryo RNA, biological replicate 1


title: 25h mosquito embryo RNA, biological replicate 2


title: Liver_PPAR_D20_Replicate 1


title: 25h mosquito embryo RNA, biological replicate 1


title: Liver_PPAR_Control_Replicate 10

source_name: Liver of vehicle-treated mouse

value: 0 mg DEHP/kg/day


title: Liver_PPAR_Control_Replicate 9


title: Liver_PPAR_Control_Replicate 8


title: Liver_PPAR_Control_Replicate 6


title: 22h mosquito embryo RNA, biological replicate 2


title: Liver_PPAR_Control_Replicate 7


title: 19h mosquito embryo RNA, biological replicate 2

source_name: 19h mosquito embryo


title: 22h mosquito embryo RNA, biological replicate 1


title: Histone H3 ChIP in ARPE cells

city: Los Angeles

first: Wei

last: Xie

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

institute: UCLA

description: Histone H3 IP vs. input

hyb_protocol: Hybridization was done according to manufacturer's protocol.

scan_protocol: Scanning was done according to manufacturer's protocol.

data_processing:
Data was processed first using Agilent Feature Extraction, and then using Agilent ChIP-Analytics software v1.3, which produced one file that combined the hybridization data from Agilent Human Promoter ChIP-on-Chip Set 244K Microarrays 1 and 2. Data was not used directly from Feature Extraction.
The IP and Input channels were normalized after both inter- and intra- array normalization according to manufacturer's instructions.

source_name: Histone H3 IP, ARPE cells

label_protocol: Labeling was performed according to manufacturer's protocol.

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3. DNA was then extracted using standard protocols.

tag: cell line

value: cultured somatic cell line ARPE

source_name: Histone H3 Input

extract_protocol: Genomic DNA was isolated using standard procedures without immunoprecipitations.


title: Liver_PPAR_Control_Replicate 4


title: 16h mosquito embryo RNA, biological replicate 3

source_name: 16h mosquito embryo


title: 16h mosquito embryo RNA, biological replicate 2


title: Liver_PPAR_Control_Replicate 5


title: 19h mosquito embryo RNA, biological replicate 3


title: 16h mosquito embryo RNA, biological replicate 1


title: 19h mosquito embryo RNA, biological replicate 1


title: Liver_WT_D200_Replicate 9

source_name: Liver of medium dose DEHP-treated mouse

value: Wild Type

value: 21 weeks


title: Liver_WT_D200_Replicate 10


title: 10h mosquito embryo RNA, biological replicate 3

source_name: 10h mosquito embryo


title: Liver_WT_D200_Replicate 8


title: 13h mosquito embryo RNA, biological replicate 1

source_name: 13h mosquito embryo


title: 13h mosquito embryo RNA, biological replicate 2


title: 10h mosquito embryo RNA, biological replicate 2


title: 13h mosquito embryo RNA, biological replicate 3


title: Liver_PPAR_Control_Replicate 2


title: Liver_WT_D200_Replicate 7


title: 10h mosquito embryo RNA, biological replicate 1


title: Liver_WT_D200_Replicate 6


title: Liver_WT_D200_Replicate 4


title: Liver_WT_D200_Replicate 5


title: Liver_WT_D200_Replicate 3


title: 8h mosquito embryo RNA, biological replicate 1

source_name: 8h mosquito embryo


title: 7h mosquito embryo RNA, biological replicate 3

source_name: 7h mosquito embryo


title: Liver_PPAR_Control_Replicate 3


title: 7h mosquito embryo RNA, biological replicate 2


title: Liver_WT_D20_Replicate 10

source_name: Liver of low dose DEHP-treated mouse


title: Liver_WT_D200_Replicate 1


title: 7h mosquito embryo RNA, biological replicate 1


title: Liver_WT_D200_Replicate 2


title: Liver_WT_D20_Replicate 9


title: 6h mosquito embryo RNA, biological replicate 1

source_name: 6h mosquito embryo


title: 6h mosquito embryo RNA, biological replicate 2


title: 6h mosquito embryo RNA, biological replicate 3


title: 8h mosquito embryo RNA, biological replicate 2


title: Liver_WT_D20_Replicate 8


title: 37h mosquito embryo RNA, biological replicate 1

source_name: 37h mosquito embryo


title: 4h mosquito embryo RNA, biological replicate 3

source_name: 4h mosquito embryo


title: Liver_WT_D20_Replicate 7


title: Liver_WT_D20_Replicate 6


title: 4h mosquito embryo RNA, biological replicate 2


title: Liver_WT_D20_Replicate 5


title: Liver_WT_D20_Replicate 4


title: Liver_WT_D20_Replicate 2


title: Liver_WT_Control_Replicate 9


title: 2h mosquito embryo RNA, biological replicate 2

source_name: 2h mosquito embryo


title: Liver_WT_D20_Replicate 3


title: Liver_PPAR_Control_Replicate 1


title: 2h mosquito embryo RNA, biological replicate 1


title: Liver_WT_Control_Replicate 10


title: Liver_WT_D20_Replicate 1


title: 2h mosquito embryo RNA, biological replicate 3


title: 10.5h mosquito embryo RNA, biological replicate 3

description: Formaldehyde-fixed embryo.

hyb_protocol: regular, as described by Affymetrix manual

data_processing: RMAexpress

source_name: 10.5h mosquito embryo

label_protocol: Affymetrix protocol and kit for two step amplification was used

extract_protocol: RNA from fixed material was extracted by RecoverALL (Ambion)

treatment_protocol: see (Goltsev, Rezende et al 2008). Hand-dissected fixed 10.5h mosquito embryos were used as source


title: 4h mosquito embryo RNA, biological replicate 1


title: Liver_WT_Control_Replicate 6


title: 10.5h mosquito embryonic serosa RNA, biological replicate 2

description: Formaldehyde-fixed embryonic serosa.

scan_protocol: regular, as described by Affymetrix manual

source_name: 10.5h mosquito embryonic serosa

treatment_protocol: see (Goltsev, Rezende et al 2008). Hand-dissected fixed 10.5h mosquito embryonic serosa was used as source


title: Liver_WT_Control_Replicate 8

source_name: Liver of vehicle-treated mouse


title: 10.5h mosquito embryo RNA, biological replicate 2

description: Formaldehyde-fixed embryo.


title: 10.5h mosquito embryonic serosa RNA, biological replicate 3

description: Formaldehyde-fixed embryonic serosa.


title: 10.5h mosquito embryonic serosa RNA, biological replicate 1

description: Formaldehyde-fixed embryonic serosa.


title: Histone H3 ChIP in HSF6 cells

description: Histone H3 IP vs. input

source_name: Histone H3 IP, HSF6 cells

value: cultured human embryonic stem cell line HSF6


title: 10.5h mosquito embryo RNA, biological replicate 1

description: Formaldehyde-fixed embryo.


title: Liver_WT_Control_Replicate 7


title: Liver_WT_Control_Replicate 5


title: Liver_WT_Control_Replicate 3


title: Liver_WT_Control_Replicate 2


title: Liver_WT_Control_Replicate 1


title: Liver_WT_Control_Replicate 4


title: 120 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36097.gif
Measurement: time(relative) 2 h
Replicate: shake 2

source_name: Amplified RNA from each time point from Shake2 was pooled and used as a reference.

source_name: 120 min Mitotic Shake-off

tag: 120 min Mitotic Shake-off


title: Tel_Fad_Treated1

city: Ottawa

first: Martin

last: Paquette

state: Ontario

address: 30 Marie Curie

department: Department of Biology

country: Canada

institute: University of Ottawa

description: Treated 1

hyb_protocol: Labeled complementary RNA was hybridized to the Affymetrix microarrays according to the specifications of the manufacturer (Affymetrix) at the Affymetrix gene expression facility at the Ottawa Hospital Research Institute (Ottawa).

scan_protocol: Scanning was done according to the specifications of the manufacturer (Affymetrix) at the Affymetrix gene expression facility at the Ottawa Hospital Research Institute (Ottawa).

data_processing: Analysis was done with Genespring GX (Agilent).  Data was normalized by: (1) setting expression measurements < 0.01 to 0.01, (2) per chip normalization to the 50th percentile, and (3) per gene normalization to specific samples.

organism: Danio rerio

source_name: Danio rerio - Telencephalon - 10 days exposure to 200ug/L of Fadrozole (slide 2511)

label_protocol: Ten micrograms of each RNA sample was labeled using the Super Script II (Invitrogen) and the Enzo BioArray HighYield RNA transcript labeling kit (Affymetrix).

extract_protocol: RNeasy Mini (qiagen)

value: Telencephalon

tag: developmental stage

value: Sexually mature males


title: Tel_Fad_Control2

description: Control 2

source_name: Danio rerio - Telencephalon - control - (slide 2571)


title: genotype: 11542  - pathogen isolates: K1 - time: 32 - rep2

status: Public on Feb 25 2009

city: Ames

first: PLEXdb Curator

middle: Sudhansu

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: bcd1 mutant, pathogen isolate K1, time 32, rep-2

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 32)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  GH grown and inoculated in 18oC chamber

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

tag: organism part

tag: seedling growth

tag: development stage

value: first leaf unfolded GRO:0007060

value: 7 days after sowing

tag: growth media

value: peat/perlite/soil

value: bcd1 mutant, pathogen isolate K1

tag: time


title: Tel_Fad_Treated2

description: Treated 2

source_name: Danio rerio - Telencephalon - 10 days exposure to 200ug/L of Fadrozole (slide 2572)


title: Tel_Fad_Control3

description: Control 3

source_name: Danio rerio - Telencephalon - control (slide 2510)


title: Tel_Fad_Control1

description: Control 1

source_name: Danio rerio - Telencephalon - control (slide 2509)


title: genotype: 11542  - pathogen isolates: K1 - time: 24 - rep3

description: bcd1 mutant, pathogen isolate K1, time 24, rep-3

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 24)

tag: age

tag: genotype


title: genotype: 11542  - pathogen isolates: K1 - time: 24 - rep2

description: bcd1 mutant, pathogen isolate K1, time 24, rep-2


title: genotype: 11542  - pathogen isolates: K1 - time: 20 - rep2

description: bcd1 mutant, pathogen isolate K1, time 20, rep-2

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 20)


title: genotype: 11542  - pathogen isolates: K1 - time: 20 - rep3

description: bcd1 mutant, pathogen isolate K1, time 20, rep-3


title: genotype: 11542  - pathogen isolates: K1 - time: 24 - rep1

description: bcd1 mutant, pathogen isolate K1, time 24, rep-1


title: genotype: 11542  - pathogen isolates: K1 - time: 32 - rep1

description: bcd1 mutant, pathogen isolate K1, time 32, rep-1


title: 8h mosquito embryo RNA, biological replicate 3

description: for further information please refer to (Goltsev et al, Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo. 2009, Developmental Biology)

source_name: 8h mosquito embryo

tag: strain

value: Kisumu


title: Tel_Fad_Treated3

description: Treated 3

source_name: Danio rerio - Telencephalon - 10 days exposure to 200ug/L of Fadrozole (slide 2512)


title: genotype: 11542  - pathogen isolates: K1 - time: 20 - rep1

description: bcd1 mutant, pathogen isolate K1, time 20, rep-1


title: genotype: 11542  - pathogen isolates: K1 - time: 32 - rep3

description: bcd1 mutant, pathogen isolate K1, time 32, rep-3


title: 90 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36095.gif
Measurement: time(relative) 1.5 h
Replicate: shake 2

tag: Amplified RNA from each time point from Shake2 was pooled and used as a reference.

source_name: 90 min Mitotic Shake-off

tag: 90 min Mitotic Shake-off


title: 105 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36096.gif
Measurement: time(relative) 1.75 h
Replicate: shake 2

source_name: 105 min Mitotic Shake-off

tag: 105 min Mitotic Shake-off


title: 60 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36093.gif
Measurement: time(relative) 1 h
Replicate: shake 2

source_name: 60 min Mitotic Shake-off

tag: 60 min Mitotic Shake-off


title: 75 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36094.gif
Measurement: time(relative) 1.25 h
Replicate: shake 2

source_name: 75 min Mitotic Shake-off

tag: 75 min Mitotic Shake-off


title: 30 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36091.gif
Measurement: time(relative) 0.5 h
Replicate: shake 2

source_name: 30 min Mitotic Shake-off

tag: 30 min Mitotic Shake-off


title: 45 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36092.gif
Measurement: time(relative) 0.75 h
Replicate: shake 2

source_name: Amplified RNA from each time point from Shake2 was pooled and used as a reference.

source_name: 45 min Mitotic Shake-off

tag: 45 min Mitotic Shake-off


title: genotype: 11542  - pathogen isolates: K1 - time: 16 - rep3

description: bcd1 mutant, pathogen isolate K1, time 16, rep-3

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 16)


title: genotype: 11542  - pathogen isolates: K1 - time: 16 - rep1

description: bcd1 mutant, pathogen isolate K1, time 16, rep-1


title: 0 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36089.gif
Measurement: time(relative) 0 h
Replicate: shake 2

source_name: 0 min Mitotic Shake-off

tag: 0 min Mitotic Shake-off


title: genotype: 11542  - pathogen isolates: K1 - time: 8 - rep3

description: bcd1 mutant, pathogen isolate K1, time 8, rep-3

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 8)

tag: germplasm name


title: genotype: 11542  - pathogen isolates: K1 - time: 8 - rep2

description: bcd1 mutant, pathogen isolate K1, time 8, rep-2

tag: organism part


title: genotype: 11542  - pathogen isolates: K1 - time: 8 - rep1

description: bcd1 mutant, pathogen isolate K1, time 8, rep-1

tag: seedling growth


title: 15 min Mitotic Shake-off

description:
Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36090.gif
Measurement: time(relative) 0.25 h
Replicate: shake 2

source_name: 15 min Mitotic Shake-off

tag: 15 min Mitotic Shake-off


title: genotype: 11542  - pathogen isolates: 5874 - time: 32 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 32, rep-2

tag: development stage

tag: growth media

value: bcd1 mutant, pathogen isolate 5874


title: genotype: 11542  - pathogen isolates: 5874 - time: 24 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 24, rep-1

tag: age

tag: time


title: genotype: 11542  - pathogen isolates: K1 - time: 0 - rep1

description: bcd1 mutant, pathogen isolate K1, time 0, rep-1

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: K1 - time: 0)

tag: genotype


title: genotype: 11542  - pathogen isolates: K1 - time: 0 - rep3

description: bcd1 mutant, pathogen isolate K1, time 0, rep-3


title: genotype: 11542  - pathogen isolates: 5874 - time: 16 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 16, rep-3


title: genotype: 11542  - pathogen isolates: K1 - time: 0 - rep2

description: bcd1 mutant, pathogen isolate K1, time 0, rep-2


title: genotype: 11542  - pathogen isolates: 5874 - time: 20 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 20, rep-2


title: genotype: 11542  - pathogen isolates: 5874 - time: 20 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 20, rep-1


title: genotype: 11542  - pathogen isolates: 5874 - time: 24 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 24, rep-2


title: genotype: 11542  - pathogen isolates: 5874 - time: 20 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 20, rep-3


title: genotype: 11542  - pathogen isolates: 5874 - time: 16 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 16, rep-1


title: genotype: 11542  - pathogen isolates: 5874 - time: 16 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 16, rep-2


title: genotype: 11542  - pathogen isolates: 5874 - time: 32 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 32, rep-3


title: genotype: 11542  - pathogen isolates: 5874 - time: 32 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 32, rep-1


title: genotype: 11542  - pathogen isolates: 5874 - time: 0 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 0, rep-3

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: 5874 - time: 0)


title: genotype: 11542  - pathogen isolates: 5874 - time: 24 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 24, rep-3


title: genotype: 11542  - pathogen isolates: 5874 - time: 8 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 8, rep-1

source_name: ##;PO:0009011## (genotype: 11542  - pathogen isolates: 5874 - time: 8)


title: genotype: 11542  - pathogen isolates: 5874 - time: 8 - rep3

description: bcd1 mutant, pathogen isolate 5874, time 8, rep-3


title: genotype: 11542  - pathogen isolates: 5874 - time: 0 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 0, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 32 - rep1

description: Widtype, pathogen isolate K1, time 32, rep-1

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 32)

value: Widtype, pathogen isolate K1


title: genotype: Mla6 - pathogen isolates: K1 - time: 32 - rep2

description: Widtype, pathogen isolate K1, time 32, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 32 - rep3

description: Widtype, pathogen isolate K1, time 32, rep-3


title: genotype: Mla6 - pathogen isolates: K1 - time: 24 - rep3

description: Widtype, pathogen isolate K1, time 24, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 24)


title: genotype: Mla6 - pathogen isolates: K1 - time: 24 - rep2

description: Widtype, pathogen isolate K1, time 24, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 24 - rep1

description: Widtype, pathogen isolate K1, time 24, rep-1


title: genotype: 11542  - pathogen isolates: 5874 - time: 0 - rep1

description: bcd1 mutant, pathogen isolate 5874, time 0, rep-1


title: genotype: Mla6 - pathogen isolates: K1 - time: 20 - rep3

description: Widtype, pathogen isolate K1, time 20, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 20)


title: genotype: Mla6 - pathogen isolates: K1 - time: 20 - rep1

description: Widtype, pathogen isolate K1, time 20, rep-1


title: genotype: 11542  - pathogen isolates: K1 - time: 16 - rep2

description: bcd1 mutant, pathogen isolate K1, time 16, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 16 - rep3

description: Widtype, pathogen isolate K1, time 16, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 16)


title: genotype: 11542  - pathogen isolates: 5874 - time: 8 - rep2

description: bcd1 mutant, pathogen isolate 5874, time 8, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 16 - rep2

description: Widtype, pathogen isolate K1, time 16, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 20 - rep2

description: Widtype, pathogen isolate K1, time 20, rep-2


title: genotype: Mla6 - pathogen isolates: K1 - time: 0 - rep2

description: Widtype, pathogen isolate K1, time 0, rep-2

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 0)


title: genotype: Mla6 - pathogen isolates: 5874 - time: 32 - rep3

description: Widtype, pathogen isolate 5874, time 32, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 32)

value: Widtype, pathogen isolate 5874


title: genotype: Mla6 - pathogen isolates: K1 - time: 0 - rep1

description: Widtype, pathogen isolate K1, time 0, rep-1


title: genotype: Mla6 - pathogen isolates: K1 - time: 8 - rep1

description: Widtype, pathogen isolate K1, time 8, rep-1

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: K1 - time: 8)


title: genotype: Mla6 - pathogen isolates: K1 - time: 8 - rep3

description: Widtype, pathogen isolate K1, time 8, rep-3


title: genotype: Mla6 - pathogen isolates: K1 - time: 16 - rep1

description: Widtype, pathogen isolate K1, time 16, rep-1


title: cns PSA against uncoated

city: Hannover

first: Cornelia

last: Repenning

address: Callinstr 5

institute: Institut fuer Technische Chemie

description:
Isolated RNA 4 days after growing on different surfaces
Gene expression of cells grown on coated and uncoated surfaces were analysed.

hyb_protocol: The differently labelled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Processed Data: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

source_name: PSA

label_protocol:
The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSA labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy5 signals of microarray detection.
5 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Fluorescein-dCTP.

extract_protocol: The isolation of RNA was accomplished by using the Invitrogen TRIzol Reagent®(Invitrogen, Carlsbad, Germany) according to the manufacturers´ protocol.

tag: surface

value: PSA

tag: cell type

value: Schwann cells

source_name: uncoated

label_protocol:
The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSA labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3 signals of microarray detection.
5 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Fluorescein-dCTP.

value: uncoated


title: genotype: Mla6 - pathogen isolates: K1 - time: 8 - rep2

description: Widtype, pathogen isolate K1, time 8, rep-2


title: genotype: Mla6 - pathogen isolates: 5874 - time: 32 - rep2

description: Widtype, pathogen isolate 5874, time 32, rep-2


title: genotype: Mla6 - pathogen isolates: 5874 - time: 20 - rep3

description: Widtype, pathogen isolate 5874, time 20, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 20)


title: cns laminin against PSA

source_name: laminin

value: laminin


title: genotype: Mla6 - pathogen isolates: K1 - time: 0 - rep3

description: Widtype, pathogen isolate K1, time 0, rep-3


title: genotype: Mla6 - pathogen isolates: 5874 - time: 20 - rep2

description: Widtype, pathogen isolate 5874, time 20, rep-2


title: genotype: Mla6 - pathogen isolates: 5874 - time: 24 - rep1

description: Widtype, pathogen isolate 5874, time 24, rep-1

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 24)


title: genotype: Mla6 - pathogen isolates: 5874 - time: 20 - rep1

description: Widtype, pathogen isolate 5874, time 20, rep-1


title: genotype: Mla6 - pathogen isolates: 5874 - time: 32 - rep1

description: Widtype, pathogen isolate 5874, time 32, rep-1


title: genotype: Mla6 - pathogen isolates: 5874 - time: 24 - rep3

description: Widtype, pathogen isolate 5874, time 24, rep-3


title: genotype: Mla6 - pathogen isolates: 5874 - time: 16 - rep2

description: Widtype, pathogen isolate 5874, time 16, rep-2

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 16)


title: genotype: Mla6 - pathogen isolates: 5874 - time: 16 - rep1

description: Widtype, pathogen isolate 5874, time 16, rep-1


title: genotype: Mla6 - pathogen isolates: 5874 - time: 24 - rep2

description: Widtype, pathogen isolate 5874, time 24, rep-2


title: genotype: Mla6 - pathogen isolates: 5874 - time: 8 - rep3

description: Widtype, pathogen isolate 5874, time 8, rep-3

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 8)


title: genotype: Mla6 - pathogen isolates: 5874 - time: 16 - rep3

description: Widtype, pathogen isolate 5874, time 16, rep-3


title: cns uncoated against laminin


title: Luteal before run

city: Tübingen

first: Stephan

last: Symons

address: Sand 14

department: Department for Information and Cognitive Sciences

institute: Center for Bioinformatics Tuebingen

description: Female (luteal phase) before run vs. reference.

hyb_protocol: Hybridization was performed for 14h at 48°C.

scan_protocol: Scanned using scanner from Affymetrix  (Santa Clara, California, USA). The photomultiplier tube voltage was set to 100% for both green and red channels. The resulting green and red images were overlaid using ImaGene 5.0 (Biodiscovery Inc. El Segundo, California, USA) as well as for raw data collection.

data_processing: Background correction: normexp (default parameters), intra-array normalization:printtip loess (default parameters), inter-array normalization: quantile normalization (default parameters), using limma package for R.

source_name: peripheral blood, luteal, rested

label_protocol: Amplification of sample RNA was performed using Ambion´s Amino Allyl Message Amp II aRNA Amplification Kit (Ambion Inc., Austin, Texas, USA) together with Amersham CyDye Post-labeling Reactive Pack (GE Healthcare, Buckinghamshire, UK) following the manufacturer`s protocols, and assessing dye incorporation using a Nano Drop ND-1000 spectrophotometer  (NanoDrop Technologies, Wilmington, Delaware, USA).

extract_protocol: EDTA anti-coagulated venous blood samples were drawn one hour before and immediately after the running exercise. Peripheral blood mononuclear cells (PBMC) were isolated using the Ficoll-hypaque density gradient technique. After gathering the cells in RLT-buffer, total RNA was extracted using an RNeasy minikit (Qiagen, Hilden Germany) in accordance with the manufacturer’s protocol. The RNA was pooled using equal amounts of RNA. The integrity of extracted RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California, USA).

treatment_protocol: Probands were on no medication and exercised regularly. Female probands did not use oral contraceptives.

tag: sample

value: pooled rna

tag: gender

value: female

tag: cyclus phase

value: luteal

value: 1h before run

tag: mean age

tag: mean body mass index

tag: mean training sessions per week

tag: mean training distance per week

tag: mean viat

source_name: Control

tag: reference

value: UniRNA

tag: provider

value: Stratagene, La Jolla, California, USA


title: Luteal after run

description: Female (luteal phase) after run vs. reference.

source_name: peripheral blood, luteal, exercised

value: 1h after run


title: Follicular before run

description: Female (follicular phase) before run vs. reference.

source_name: peripheral blood, follicular, rested

value: follicular

tag: mean  viat


title: Follicular after run

description: Female (follicular phase) after run vs. reference.

source_name: peripheral blood, follicular, exercised


title: genotype: Mla6 - pathogen isolates: 5874 - time: 0 - rep3

description: Widtype, pathogen isolate 5874, time 0, rep-3.

source_name: ##;PO:0009011## (genotype: Mla6 - pathogen isolates: 5874 - time: 0)

tag: germplasm name

tag: organism part

tag: seedling growth

tag: development stage

value: first leaf unfolded GRO:0007060

value: 7 days after sowing

tag: growth media

value: peat/perlite/soil


title: Male after run

description: Male after run vs. reference.

source_name: peripheral blood, male, exercised

value: male

tag: time


title: genotype: Mla6 - pathogen isolates: 5874 - time: 0 - rep2

description: Widtype, pathogen isolate 5874, time 0, rep-2.

tag: age

tag: genotype

value: Widtype, pathogen isolate 5874


title: genotype: Mla6 - pathogen isolates: 5874 - time: 0 - rep1

description: Widtype, pathogen isolate 5874, time 0, rep-1.


title: Male before run

description: Male before run vs. reference.

source_name: peripheral blood, male, rested

tag: sample

tag: gender


title: Cortex 54ko

city: madrid

first: Ana

last: Dopazo

address: Melchor Fdez Almagro

department: Genomics Unit

country: Spain

institute: CNIC

description: Cux2 knock-out

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.

source_name: cerebral cortex, knock-out

label_protocol: For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

extract_protocol: Cerebral cortex were dissected and total RNA was obtained using Qiagen RNAeasy kit.

tag: tissue

value: brain


title: Cortex 15WT

description: WT

source_name: cerebral cortex, wild-type


title: U373MG_p53_12h

status: Public on Feb 24 2009

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: among 36864 spots, 23504 spots were analyzed in this assay

hyb_protocol: Labeled cDNAs were mixed with microarray hybridization solution version 2 (Amersham) and formamide (Sigma) to a final concentration of 50%. After hybridization for 14-16 hours at 42 oC in Automated Slide Processor, the slides were washed in 2xSSC and 1% SDS for 10min at 55 oC, washed in 0.2xSSC and 0.1% SDS for 10min at 55 oC, and washed in 0.1xSSC for 1 min at room temperature in Automated Slide Processor.

scan_protocol: Microarray slides were scanned using the Array Scanner Generation III (Amersham) after hybridization.

data_processing: Images were gridded and the fluorescent intensity of each spot (Cy3/Cy5) was evaluated photometrically by the ArrayVision computer program (Imaging Research, Inc., St. Catharines, Ontario, Canada) . The fluorescent intensities of Cy3 (p53) and Cy5 (LacZ) for each target spot were adjusted so that the mean Cy3/Cy5 ratio of the 52 housekeeping genes was equal to one. Because data derived from low signal intensities are less reliable, we determined a cut-off value on each slide and excluded genes from further analysis when both Cy3 and Cy5 dyes yielded signal intensities lower than the cut-off value. For other genes, we calculated the Cy3/Cy5 ratio using the raw data of each sample.

source_name: Ad-p53 infected U373MG cells 12h

label_protocol: 2.5 ug aliquots of mRNA from Ad-p53 infected U373 cells or Ad-LacZ infected cells were annealed with random primer for 10 min at 70oC. They were labeled in a 50ul volume by reverse transcription reaction for 2 hours at 37oC using Superscript II reverse transcriptase (Invitrogen) with 1mM Cy3-dCTP for Ad-p53 infected cells or Cy5-dCTP for Ad-LacZ infected cells (Amersham) and 25mM each dATP, dGTP, and dTTP. The labeling reaction was stopped by adding 6ul 2.5 N NaOH and incubation for 30 min at 65oC and neutralized by 20ul 1M Tris-HCl (pH7.4) and 7ul 2.5N HCl. The labeled cDNAs were purified by QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: 2,000,000 of U373MG cells were plated on 10 cm dishes prior to the adenoviral infection.  Cells were grown in EMEM containing 10% FBS

extract_protocol: Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, mRNAs were purified using mRNA purification kit  (GE healthcare).

treatment_protocol: U373MG cells were infected with Ad-p53 or Ad-LacZ at 8 MOI for 1 hour. Then cells were harvested at indicated time point.

tag: cell line

source_name: Ad-LacZ infected U373MG cells


title: genotype: Mla6 - pathogen isolates: 5874 - time: 8 - rep1

description: Widtype, pathogen isolate 5874, time 8, rep-1


title: genotype: Mla6 - pathogen isolates: 5874 - time: 8 - rep2

description: Widtype, pathogen isolate 5874, time 8, rep-2


title: Cortex 53ko

description: Cux2 knock-out


title: U373MG_p53_48h

source_name: Ad-p53 infected U373MG cells 48h


title: Cortex 16WT

description: WT


title: Cortex 48ko

description: Cux2 knock-out


title: dexrazoxane control 1

city: Mainz

first: Shiwei

last: Deng

address: Obere Zahlbacher Str. 67

institute: Uni Mainz

description:
>99.5% TOP2A expression can be silenced in HTETOP cells by the addition of tetracycline
pooled RNA from three cell passages was used for hybridization

hyb_protocol: Following fragmentation, cRNA were hybridized to Human Genome U133 Plus 2.0 GeneChips from Affymetrix.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000.

data_processing: The images were processed by GeneChip Operating Software 1.3 and the raw data were normalized by Robust Multiarray Analysis (RMA).

source_name: control HTETOP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using peqGOLD Total RNA Kit according to the manufacturer’s instructions.

treatment_protocol: HTETOP cells were treated with 100 µM dexrazoxane or vehicle for 24 hours.

value: HTETOP


title: U373MG_p53_24h

source_name: Ad-p53 infected U373MG cells 24h


title: Cortex 62WT

description: WT


title: U373MG_p53_6h

source_name: Ad-p53 infected U373MG cells 6h


title: U373MG_p53_0h

source_name: Ad-p53 infected U373MG cells 0h


title: HepG2-plate-exp2-plate2-rep2

city: Setagaya

first: Seiichi

last: Ishida

address: 1-18-1, Kamiyoga

department: Pharmacology

institute: National Institute of Health Sciences

description: Data from 2nd plate culture (five days). plate; 2, GeneChip measurement; 2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: HepG2 cells cultured in tissue culture plate, five days

label_protocol: Standard Affymetrix protocol with 10.0 ug of total RNA

growth_protocol: Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum was used as medium. Cells were cultured in the radial flow bioreactor cell culture system (ABLE Corporation, Tokyo) of 5ml capacity or in the tissue culture plate  (60 mm diameter; BD Falcon, Franklin Lakes, NJ).  Hydroxyapatite with a dimmer of 0.6 - 1.0 mm was used as the scaffold of cells in the radial flow bioreactor cell culture system.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: Cells were washed twice with phosphate buffered saline (PBS ; SIGMA, St. Louis, MO)

tag: HepG2 human hepatocellular carcinoma cell line

tag: human liver cancer


title: HepG2-plate-exp2-plate3-rep1

description: Data from 2nd plate culture (five days). plate; 3, GeneChip measurement; 1


title: HepG2-plate-exp2-plate3-rep2

description: Data from 2nd plate culture (five days). plate; 3, GeneChip measurement; 2


title: HepG2-plate-exp2-plate1-rep2

description: Data from 2nd plate culture (five days). plate; 1, GeneChip measurement; 2


title: HepG2-plate-exp1-plate2-rep1

description: Data from 1st plate culture (five days). plate; 2, GeneChip measurement; 1


title: HepG2-plate-exp2-plate1-rep1

description: Data from 2nd plate culture (five days). plate; 1, GeneChip measurement; 1


title: HepG2-plate-exp1-plate3-rep2

description: Data from 1st plate culture (five days). plate; 3, GeneChip measurement; 2


title: HepG2-plate-exp1-plate2-rep2

description: Data from 1st plate culture (five days). plate; 2, GeneChip measurement; 2


title: HepG2-RFB-exp2-part3-rep2

description: Data from 2nd RFB culture (six days). portion of the reactor; 3, GeneChip measurement; 2

source_name: HepG2 cells cultured in RFB, six days


title: HepG2-plate-exp1-plate3-rep1

description: Data from 1st plate culture (five days). plate; 3, GeneChip measurement; 1


title: HepG2-plate-exp2-plate2-rep1

description: Data from 2nd plate culture (five days). plate; 2, GeneChip measurement; 1


title: HepG2-RFB-exp2-part3-rep1

description: Data from 2nd RFB culture (six days). portion of the reactor; 3, GeneChip measurement; 1


title: HepG2-RFB-exp2-part2-rep1

description: Data from 2nd RFB culture (six days). portion of the reactor; 2, GeneChip measurement; 1


title: HepG2-RFB-exp1-part3-rep2

description: Data from 1st RFB culture (six days). portion of the reactor; 3, GeneChip measurement; 2


title: HepG2-RFB-exp2-part1-rep1

description: Data from 2nd RFB culture (six days). portion of the reactor; 1, GeneChip measurement; 1


title: HepG2-plate-exp1-plate1-rep2

description: Data from 1st plate culture (five days). plate; 1, GeneChip measurement; 2


title: HepG2-RFB-exp1-part3-rep1

description: Data from 1st RFB culture (six days). portion of the reactor; 3, GeneChip measurement; 1


title: HepG2-RFB-exp1-part1-rep1

description: Data from 1st RFB culture (six days). portion of the reactor; 1, GeneChip measurement; 1


title: HepG2-RFB-exp2-part1-rep2

description: Data from 2nd RFB culture (six days). portion of the reactor; 1, GeneChip measurement; 2


title: PBMC_PPD_029

city: London

first: Helen

middle: Alison

last: Fletcher

address: Keppel Street

department: IID

institute: London School of Hygiene & Tropical Medicine

description: healthy HIV negative infant vaccinated with BCG within 48hrs of birth

hyb_protocol: Amplified RNA (1000ng per array) was hybridized to the Illumina HumanRefSeq-8 BeadChip according to the manufacturer's instructions (Illumina, San Diego, CA, USA).

scan_protocol: Arrays were scanned with an Illumina bead array reader confocal scanner, according to the manufacturer's instructions.  Hardware BeadStation systeIllumina Inc. Software BeadStudio version 1.5.1.3

data_processing: Data was background subtracted using the BeadStudio version 1.5.1.3 software by subtracting the AVG-Signal-negative value for each array from each transcript value. The data was normalized using the VSN2 software: Variance stabilization and calibration for microarray data, which is available as part of the BioConductor project.

source_name: PBMC, PPD stimulated 12 hours

label_protocol: A median 124ng (range 63-174ng) extracted RNA was amplified using the Illumina RNA Amplification Kit (Ambion, Austin, TX, USA), based on the Eberwine protocol [13]. A Biotin-16-UTP label was incorporated into amplified RNA during the in vitro transcription process (Perkin Elmer Life and Analytical Sciences, Woodbridge, Ontario, Canada).

growth_protocol: PBMC were thawed, washed in RPMI 1640 (Biowhittaker, Walkersville, MD, USA), and “rested” for 6 hours at 1 X 106 cells in 1ml 10% pooled human AB serum in RPMI 1640 supplemented with L-glutamine at 2mM (Biowhittaker), at 37°C and in 5% CO2.

extract_protocol: PBMC were harvested and processed with the QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany), according to the manufacturers instructions. to isolate RNA.  RNA was DNAse treated using the on-column DNAse digestion kit (Qiagen, Hilden, Germany).

treatment_protocol: PPD (20µg/ml) or BCG, reconstituted from the vaccine vial as previously described [12], at an MOI of 0.18, was then added to the cells.  PBMC incubated with medium alone served as negative (unstimulated) control. Incubation was continued for 12 hours at 37°C and in 5% CO2.

tag: 10 week old infant


title: HepG2-RFB-exp1-part1-rep2

description: Data from 1st RFB culture (six days). portion of the reactor; 1, GeneChip measurement; 2


title: HepG2-RFB-exp2-part2-rep2

description: Data from 2nd RFB culture (six days). portion of the reactor; 2, GeneChip measurement; 2


title: PBMC_BCG_028

source_name: PBMC, BCG stimulated 12 hours


title: HepG2-RFB-exp1-part2-rep1

description: Data from 1st RFB culture (six days). portion of the reactor; 2, GeneChip measurement; 1


title: PBMC_BCG_029


title: PBMC_PPD_028


title: HepG2-RFB-exp1-part2-rep2

description: Data from 1st RFB culture (six days). portion of the reactor; 2, GeneChip measurement; 2


title: PBMC_UNS_029

source_name: PBMC, unstimulated 12 hours


title: PBMC_UNS_028


title: PBMC_PPD_011


title: PBMC_UNS_027


title: PBMC_BCG_011


title: PBMC_PPD_027


title: PBMC_UNS_009


status: Public on Feb 23 2009

type: other

city: La Jolla

first: Gregg

last: Silverman

address: 9500 Gilman Dr

department: Medicine

institute: UC San Diego School of Medicine

description: No Antibody (Negative Control)

hyb_protocol: On each slide were two nitrocellulose pads, with most antigens printed at 200 mg/ml on each pad in six replicates at known positions that alternated with printing of buffer alone to eliminate carry-over. Slides were then blocked (Whatman blocking buffer) and incubated for 2 h with 400 ml of serum diluted at 1 : 200 in phosphate-buffered saline (PBS), pH 7·4.

scan_protocol: Slides were washed with PBS, water-rinsed and then scanned (Genepix 4000B; Molecular Devices, Sunnyvale, CA, USA) using Genepix Pro version 6·0 software at 532 and 635 nm to detect IgG and IgM reactivity, respectively, with images saved as tiff files.

data_processing: Genepix Pro version 6·0 software was used to analyse the intensity of each spot with foreground and background fluorescence intensities determined for each spot on the slide, with output as a gpr file. Data were extracted from the gpr files with r software (http://www.r-project.org). Background correction used a Matlab script, and the mean values for replicate spots determined with jmp version 7·0 software (http://www.jmp.com). Comparisons of array data for subjects and controls were performed and visual depictions generated with Cluster version 3·0 (Stanford University)  and Java TreeView (http://rana.lbl.gov/EisenSoftware.htm). Background levels were therefore determined based on replicate slides developed without antibodies, and with sera from healthy adult controls (not shown). In these studies, a level of 600 digital fluorescence intensity units was set as a threshold for significant reactivity, which was greater than the mean background plus 2 standard deviations (s.d.).

molecule: other

organism: unidentified

label_protocol: After washing with Tris-buffered saline/0·1% Tween 20, the slides were reacted with Cy-5 labelled anti-human IgG and Cy-3- labelled anti-human IgM (Jackson Immunoresearch, West Grove, PA, USA) for 1 h incubation, then washed with PBS/0·05% Tween20.

growth_protocol: The mice were from a 14-week old C57BL/6 strain. The monoclonal antibodies were derived from hybridoma supernatant

extract_protocol: At the end of the injection courses, the mice were bled for their serum. Monoclonal antibodies were purified using standard protocols for IgM purifications.

treatment_protocol: The mouse serum was either naive, injected with saline (PBS) or injected with 25 million apoptotic thymocytes at three weekly timepoints.

tag: strain

tag: concentration


title: Apoptotic B

type: protein

description: Serum from a second mouse immunized with apoptotic cells

molecule: protein

value: 1:200 Dilution

value: Serum


title: E17.5 vs. E12 Dlk+ cells

first: Chen

last: Yenrong

address: yayoi 1-1-1, bunkyo_ku

institute: the university of Tokyo

description: Isolate hepatoblast by ant-Dlk antibody though MACS

hyb_protocol: Probe solutions are thoroughly resuspended by incubating at 65°C for 5 min. with mixing. The probe is applied to the array and covered with a 22 mm2 glass cover-slip, and placed in a sealed chamber to prevent evaporation. After hybridization at 60°C for 6.5 hours, the slide is washed in three consecutive washes of decreasing ionic strength.

scan_protocol: The microarray is scanned in both Cy3 and Cy5 channels with Axon GenePix  scanners (Foster City, CA) with a 10 mm resolution. The signal is converted into 16-bits per-pixel resolution, yielding a 65,536 count dynamic range.

data_processing:
Incyte GEMtool software (Incyte Pharmaceuticals, Inc., Palo Alto, CA) was used for image analysis. The element are determined by a gridding and region detection algorithm. The area surrounding each element image is used to calculate a local background and is subtracted from the total element signal. Background subtracted element signals are used to calculate Cy3:Cy5 ratios.
The average of the resulting total Cy3 and Cy5 signal gives a ratio that is used to balance or normalize the signals.

source_name: E17.5 Dlk+ hepatocye

label_protocol: Isolated mRNA is reverse transcribed with 5’ Cy3 or Cy5 labeled random 9-mers (Operon Technologies, Inc., Alameda, CA). Reactions are incubated for 2 hrs. at 37°C with 200 ng polyA RNA, 200 Units M-MLV reverse transcriptase (Life Technologies, Gaithersburg, MD), 4 mM DTT, 1 unit RNase Inhibitor (Ambion, Austin, TX), 0.5 mM dNTPs, and 2 mg labeled 9-mers in 25 mL volume with enzyme buffer supplied by the manufacturer. The reactions is terminated by incubation at 85°C for 5 min. The paired reactions are combined and purified with a TE-30 column (Clontech, Palo Alto, CA), brought to 90 mL with dH2O, and precipitated with 2 mL 1mg/mL glycogen, 60 mL 5M NH4OAc, and 300 mL EtOH. After centrifugation the supernatant is decanted and the pellet is resuspended in 24 mL of hybridization buffer: 5XSSC, 0.2% SDS, 1 mM DTT.

growth_protocol: mice growth in 25°C

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

treatment_protocol: fetal liver cells were dissected in the liver perfusion medium (Invitrogen), and a single cell suspension was obtained by collagenase digestion. Using anti-Dlk antibody to isolate Dlk postive cells (hepatoblast) and collect the cells by MACS Separator.

tag: Dlk+ Cells from E17 fetal liver

source_name: E12 day Hepatoblast

tag: Dlk+ Cells from E12 fetal liver